PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Age-dependent changes in the transverse carpal ligament and median nerve: a cadaveric histological and biomechanical study
items: The role of gut microbiota in Hirschsprung’s disease: from pathogenic mechanisms to microbiota-targeted therapies
items: Assessing the reliability of baseline maximum voluntary contraction protocols
items: Sex-dependent predictors of binge drinking among males and females in North Dakota
items: Improving drought tolerance in some wheat genotypes with foliar application of silicon nanoparticles in Al-Dawadmi, Saudi Arabia
items: Morphological description and near-complete mitochondrial genome of Haemoproteus (Parahaemoproteus) trarotraro n. sp.: a widely distributed species reported in Brazilian falcons
items: Occurrence and prognosis of metabolic dysfunction-associated steatosis liver disease and gastrointestinal tumors: a systematic review and meta-analysis
items: RNA-Seq analysis reveals regulatory networks driven by EpCAM overexpression in esophageal adenocarcinoma cells
items: Monitoring environmental impacts of a designated aquaculture area in the Karaburun Peninsula using Google Earth Engine
items: Integration of metabolomics and transcriptomics to reveal metabolic characteristics and the role of mTORC1 in β-cell proliferation induced by a short-term high-fat diet
items: Unraveling microbial diversity and physicochemical hazard level in Thai traditional fermented shrimp paste (Kapi)
items: Proteomic landscape of colorectal cancer liver metastasis: molecular signatures and novel therapeutic targets
items: Isometric muscle strength profile of lower limbs for children and adolescents between 7 and 15 years of age
items: Comparative analysis of carotenoid accumulation during the flowering period in three Coreopsis tinctoria cultivars with different petal colors
items: Evaluating multiple stability methods to screen bread wheat genotypes (F7 generation) under drought-stressed environments
items: Metabarcoding and targeted barcoding can enhance Norwegian Continental Shelf macrofauna species inventories
items: Using deep learning to predict tyrosinase inhibitors for treating hyperpigmentation disorders
items: Poly(ADP-ribose) polymerase (PARP) inhibitors in cardiovascular, and cerebrovascular diseases: mechanisms, current trends and challenge for clinical translation
items: Anti-oncogenic and immunological functions of ATP23 in CMS4 colon adenocarcinoma based on a machine learning computational framework
items: A double agent? Unveiling the chemical profile of the pathogenic fungus Pyrrhoderma noxium as an endophyte in true mangroves
items: Assessing the resilience of portable vision tests to an uncontrolled home environment
items: The suitability of structural soil for the development of trees growing in urban areas
items: Variation in zoo diets, offerings of leafy browse, and body condition scores in Matschie’s tree kangaroos (Dendrolagus matschiei) and their associations with gut microbiome composition
items: Serum docosahexaenoic acid as a predictor of hospital readmission in chronic obstructive pulmonary disease exacerbation: a retrospective cohort study
items: Analysis of the long-term solubility and phases of five different root canal sealers in phosphate buffered saline: an in vitro study
items: Hippocampal expression of Wnt7a and β-catenin in depression: evidence from chronic unpredictable mild stress
items: Responses of leaf anatomy, growth, and physiology in backcross 1 progeny from Saccharum spp. hybrids and S. spontaneum under drought stress at early growth phase
items: Heatstroke knowledge and predictors among Hajj health volunteers in Saudi Arabia: a cross-sectional study
items: https://peerj.com/articles/20815
items: Video game use, lifestyle and its association with becoming overweight or obese in Mexican adolescents
items: Altered anterior segment biometrics in cataract patients with retinitis pigmentosa: a propensity-matched analysis suggests patterns of zonular weakness
items: The structure of personality in Parkinson’s disease and the effects of age, years since diagnosis, and impulsivity
items: Quantitative image analysis applied to revise the taxonomy of the Palearctic Earophila badiata species group (Lepidoptera: Geometridae: Larentiinae)
items: Relationship between perceived risk and compliance with infection control measures during the first year of a pandemic
items: Effect of Triton all-in-one irrigant on electronic working length determination using two apex locators: an in vitro study
items: Quality, reliability and popularity assessment of Turkish YouTube videos on human papillomavirus and its vaccine: content analysis
items: Glacier boundary extraction and spatiotemporal variation analysis in Geladandong region
items: Probiotic-infused activated charcoal/ hydroxyapatite microbeads: a novel strategy to disinfection
items: Immune-neural regulatory mechanism of osteoporosis induced by androgen deficiency
items: Association between myosteatosis and survival of patients with esophageal and gastro-esophageal junction cancer: a meta-analysis
items: In vitro bioactivity and phytochemical characterization of a polyherbal extract with antioxidant and anticancer properties
items: Test–retest reliability of kicking performance assessments over a 2-day interval in elite youth soccer players
items: Physiological dynamics of body temperature and heart rate during hibernation periods in male Japanese black bears (Ursus thibetanus japonicus)
items: Behavioral implications of an embedded tyrannosaurid tooth and associated tooth marks on an articulated skull of Edmontosaurus from the Hell Creek Formation, Montana
items: Digesting an ancient ecosystem: coprolites from the Grippia bonebed, Lower Triassic, Svalbard
items: The burden of neural tube defects in Southern Ethiopia: trends, hotspots, and public health implications
items: Comprehensive efficacy of different prostate resection volumes for patients with benign prostatic hyperplasia: a systematic review and meta-analysis
items: https://peerj.com/articles/20801
items: Serum lncRNA H19/miR-675 /PPARα expression before middle gestation and their associations with macrosomia risk in singleton pregnancies without gestational diabetes mellitus: a preliminary study
items: AKT1 but not AKT2 single nucleotide polymorphisms are associated with the risk of microscopic polyangiitis
items: Physical exercise programmes to improve insomnia or poor sleep quality in non-hospitalised elderly people: a systematic review and meta-analysis
items: The soil depth determines soil multifunctionality via shaping the soil properties and microbial diversity
items: Evaluation of phosphorus sources in tomato plants inoculated with plant growth-promoting rhizobacteria
items: Research on the construction of growth models for dominant tree species in the Manas River Basin, Xinjiang
items: Targetome profile of hsa-miR-93-5p is resistant to isoform formation in prostate adenocarcinoma
items: Molecular classification and prognosis study of pancreatic ductal adenocarcinoma through multi-omics integrated clustering analysis
items: BCTI: a Bayesian network-based method for revealing critical transitions in complex biological systems
items: Proteome-wide analysis by liquid chromatography tandem mass spectrometry reveals the role of retinoic acid during adipogenesis in human bone mesenchymal stem cells
items: Characteristics and evolution of pelvic floor structures in female patients aged over 40 years with constipation—a retrospective cohort study
items: Risk prediction models for sepsis-associated encephalopathy: a systematic evaluation and meta-analysis
items: Inclined treadmill walking kinetics of the non-paretic leg in early post-stroke survivors: an observational case-control study
items: Aging-related CD8+ T cell alterations and calcium/calmodulin dependent protein kinase 1D activation in the pathogenesis of diabetic kidney disease
items: Seasonal abundance of six tephritid species and the fruiting phenology of their main hosts in northern Jiangxi, China
items: Knowledge, attitudes, and practices regarding chronic sinusitis and its surgical treatment: a cross-sectional study in China
items: Gene mapping and development of molecular markers for thousand-grain weight in rye based on bulked segregant analysis
items: Pan-cancer multi-omics profiling of OAS3 reveals its immunological and prognostic associations across human cancers
items: In vitro polyploid induction in Allium grayi Regel using colchicine
items: Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community
items: Epigenetic activation of SLC7A11 defines a ferroptosis—immune axis and enables robust DNA methylation-based diagnosis of lung squamous cell carcinoma
items: Interactions between dense seasonal macroalgal mats and oysters on natural and constructed shellfish reefs
items: Multiomics analysis of polyamine metabolism in colorectal cancer, highlighting the key role of extracellular putrescine in impairing CXCR6+CD8+ T cell anti-tumor activity
items: Chinese thyroid imaging reporting and data system with redefined marked hypoechogenicity for thyroid malignancy risk stratification demonstrates improved diagnostic accuracy

Age-dependent changes in the transverse carpal ligament and median nerve: a cadaveric histological and biomechanical study
type: item
type: AcademicArticle
description: Background Age-related alterations in the transverse carpal ligament (TCL) and the median nerve are thought to increase susceptibility to carpal tunnel syndrome in older individuals. This study aimed to investigate the mechanical properties of the TCL and histological changes in both the TCL and the median nerve in cadavers across a wide age range. Methods Fifty formalin-embalmed cadavers (40–93 years old) were studied, yielding 100 TCL specimens. A digital palpation device (MyotonPRO) was used in situ to measure TCL dynamic stiffness, elasticity (logarithmic decrement), mechanical stress relaxation time, and creep at proximal, middle, and distal regions. After testing, each TCL and corresponding median nerve were excised. Masson’s trichrome staining and scanning electron microscopy were performed to assess collagen fiber organization, fibroblast density, and nerve structure. Pearson’s correlation was used to determine associations between TCL properties and age. Results An age-dependent increase in TCL stiffness was observed, alongside decreased elasticity, relaxation time, and creep. Histological analyses revealed reduced fibroblast density, disorganized collagen fibers with large clefts between bundles, and increased fine collagen meshwork in interfascicular matrix in older specimens. Furthermore, thinning of connective tissue layers surrounding the median nerve and diminished myelin sheaths were noted with advancing age. Conclusion This cadaveric study reveals that the TCL stiffens and becomes structurally disorganized with advancing age, paralleled by degenerative changes in the median nerve. Such age-related alterations may predispose elderly individuals to a higher risk of carpal tunnel syndrome, underscoring the need for targeted preventive and therapeutic strategies.
format: application/pdf
format: text/html
creator: Apichaya Niyomchan
creator: Akkradate Siriphorn
creator: Kanet Kathinted
creator: Benjaporn Pamornpol
subject: Anatomy and Physiology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.20878
publisher: PeerJ Inc.
rights: © 2026 Niyomchan et al.
abstract: Background Age-related alterations in the transverse carpal ligament (TCL) and the median nerve are thought to increase susceptibility to carpal tunnel syndrome in older individuals. This study aimed to investigate the mechanical properties of the TCL and histological changes in both the TCL and the median nerve in cadavers across a wide age range. Methods Fifty formalin-embalmed cadavers (40–93 years old) were studied, yielding 100 TCL specimens. A digital palpation device (MyotonPRO) was used in situ to measure TCL dynamic stiffness, elasticity (logarithmic decrement), mechanical stress relaxation time, and creep at proximal, middle, and distal regions. After testing, each TCL and corresponding median nerve were excised. Masson’s trichrome staining and scanning electron microscopy were performed to assess collagen fiber organization, fibroblast density, and nerve structure. Pearson’s correlation was used to determine associations between TCL properties and age. Results An age-dependent increase in TCL stiffness was observed, alongside decreased elasticity, relaxation time, and creep. Histological analyses revealed reduced fibroblast density, disorganized collagen fibers with large clefts between bundles, and increased fine collagen meshwork in interfascicular matrix in older specimens. Furthermore, thinning of connective tissue layers surrounding the median nerve and diminished myelin sheaths were noted with advancing age. Conclusion This cadaveric study reveals that the TCL stiffens and becomes structurally disorganized with advancing age, paralleled by degenerative changes in the median nerve. Such age-related alterations may predispose elderly individuals to a higher risk of carpal tunnel syndrome, underscoring the need for targeted preventive and therapeutic strategies.
bibliographic citation: Niyomchan et al. (2026) Age-dependent changes in the transverse carpal ligament and median nerve: a cadaveric histological and biomechanical study. PeerJ 14:e20878 https://doi.org/10.7717/peerj.20878
date submitted: 2025-11-22
date accepted: 2026-01-12
issued: 2026-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niyomchan
  given name: Apichaya
author list: Agent
  family name: Siriphorn
  given name: Akkradate
author list: Agent
  family name: Kathinted
  given name: Kanet
author list: Agent
  family name: Pamornpol
  given name: Benjaporn
doi: 10.7717/peerj.20878
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-24
copyright: © 2026 Niyomchan et al.
attribution name: Niyomchan et al.

The role of gut microbiota in Hirschsprung’s disease: from pathogenic mechanisms to microbiota-targeted therapies
type: item
type: AcademicArticle
description: Hirschsprung’s disease (HSCR) is a common congenital disorder characterized by abnormal enteric nervous system development. Recent studies have demonstrated that gut microbiota and their metabolites play a significant role in the pathogenesis of HSCR. This review systematically examines the interplay between gut dysbiosis and pathophysiological alterations in HSCR, including disruptions in microbial composition, aberrant metabolite profiles, impaired intestinal barrier function, and dysregulated neuro-immune modulation. Research indicates that HSCR patients exhibit a characteristic gut microbial imbalance, which may influence the development and function of the enteric nervous system by altering the intestinal microenvironment, including metabolic profiles and immune status. Furthermore, this review explores the potential therapeutic value of microbiota-targeted interventions, such as probiotics and fecal microbiota transplantation (FMT), in HSCR treatment, providing a theoretical foundation for novel therapeutic strategies. These findings not only enhance the understanding of HSCR pathogenesis but also offer new perspectives for clinical prevention and treatment.
format: application/pdf
format: text/html
creator: Yuan Zhao
creator: Dehong Chen
creator: Kaiwen Qi
subject: Microbiology
subject: Evidence Based Medicine
subject: Gastroenterology and Hepatology
subject: Global Health
subject: Pediatrics
description: doi:10.7717/peerj.20854
publisher: PeerJ Inc.
rights: © 2026 Zhao et al.
abstract: Hirschsprung’s disease (HSCR) is a common congenital disorder characterized by abnormal enteric nervous system development. Recent studies have demonstrated that gut microbiota and their metabolites play a significant role in the pathogenesis of HSCR. This review systematically examines the interplay between gut dysbiosis and pathophysiological alterations in HSCR, including disruptions in microbial composition, aberrant metabolite profiles, impaired intestinal barrier function, and dysregulated neuro-immune modulation. Research indicates that HSCR patients exhibit a characteristic gut microbial imbalance, which may influence the development and function of the enteric nervous system by altering the intestinal microenvironment, including metabolic profiles and immune status. Furthermore, this review explores the potential therapeutic value of microbiota-targeted interventions, such as probiotics and fecal microbiota transplantation (FMT), in HSCR treatment, providing a theoretical foundation for novel therapeutic strategies. These findings not only enhance the understanding of HSCR pathogenesis but also offer new perspectives for clinical prevention and treatment.
bibliographic citation: Zhao et al. (2026) The role of gut microbiota in Hirschsprung’s disease: from pathogenic mechanisms to microbiota-targeted therapies. PeerJ 14:e20854 https://doi.org/10.7717/peerj.20854
date submitted: 2025-09-11
date accepted: 2026-01-05
issued: 2026-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Dehong
author list: Agent
  family name: Qi
  given name: Kaiwen
doi: 10.7717/peerj.20854
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-24
copyright: ©2026 Zhao et al.
attribution name: Zhao et al.

Assessing the reliability of baseline maximum voluntary contraction protocols
type: item
type: AcademicArticle
description: Background Maximum Voluntary Isometric Contractions (MVICs) are commonly used to normalize contraction intensity as a percentage of maximum; however, there is substantial variation in reported baseline MVIC protocols and no known consensus on their reliability. As such, the purpose of this study was to determine the method of baseline MVIC calculation that maximizes between-session reliability. Methods Eighteen participants performed five knee extension, elbow flexion, and hand grip MVICs during four experimental sessions. Thirty-two methods of calculating baseline MVIC were evaluated using differing numbers of contractions, using the peak or average, and the presence of a familiarisation session and/or practice contraction. The level of significance was set at p ≤ 0.05 for all results presented. Reliability statistics were assessed across the 32 calculation methods, as was the effect of contraction and session number on MVIC strength. Results Within-day Intraclass Correlation Coefficients (ICCs) estimates ranged from 0.94 to 0.98 for all contraction types and sessions, with between-day ICC estimates ranging from 0.85 to 0.99. Reliability marginally increased as more contractions were factored for both average and peak. Familiarisation and practice only improved reliability for elbow flexion. All baseline MVIC methods had acceptable between-day reliability. Multiple approaches to calculating baseline MVIC are reliable, but the most efficient method is to use the peak of one contraction. This approach balances high reliability with reduced participant fatigue and testing time, making it a practical option for both research and clinical applications.
format: application/pdf
format: text/html
creator: Gillian E. Slade
creator: Michael W.B. Watterworth
creator: Nicholas J. La Delfa
subject: Anatomy and Physiology
subject: Kinesiology
subject: Biomechanics
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20848
publisher: PeerJ Inc.
rights: © 2026 Slade et al.
abstract: Background Maximum Voluntary Isometric Contractions (MVICs) are commonly used to normalize contraction intensity as a percentage of maximum; however, there is substantial variation in reported baseline MVIC protocols and no known consensus on their reliability. As such, the purpose of this study was to determine the method of baseline MVIC calculation that maximizes between-session reliability. Methods Eighteen participants performed five knee extension, elbow flexion, and hand grip MVICs during four experimental sessions. Thirty-two methods of calculating baseline MVIC were evaluated using differing numbers of contractions, using the peak or average, and the presence of a familiarisation session and/or practice contraction. The level of significance was set at p ≤ 0.05 for all results presented. Reliability statistics were assessed across the 32 calculation methods, as was the effect of contraction and session number on MVIC strength. Results Within-day Intraclass Correlation Coefficients (ICCs) estimates ranged from 0.94 to 0.98 for all contraction types and sessions, with between-day ICC estimates ranging from 0.85 to 0.99. Reliability marginally increased as more contractions were factored for both average and peak. Familiarisation and practice only improved reliability for elbow flexion. All baseline MVIC methods had acceptable between-day reliability. Multiple approaches to calculating baseline MVIC are reliable, but the most efficient method is to use the peak of one contraction. This approach balances high reliability with reduced participant fatigue and testing time, making it a practical option for both research and clinical applications.
bibliographic citation: Slade et al. (2026) Assessing the reliability of baseline maximum voluntary contraction protocols. PeerJ 14:e20848 https://doi.org/10.7717/peerj.20848
date submitted: 2025-10-13
date accepted: 2026-01-05
issued: 2026-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Slade
  given name: Gillian E.
author list: Agent
  family name: Watterworth
  given name: Michael W.B.
author list: Agent
  family name: La Delfa
  given name: Nicholas J.
doi: 10.7717/peerj.20848
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-24
copyright: ©2026 Slade et al.
attribution name: Slade et al.

Sex-dependent predictors of binge drinking among males and females in North Dakota
type: item
type: AcademicArticle
description: Background North Dakota has one of the highest rates of binge drinking in the United States, but little is known about how the predictors of binge drinking differ between males and females within the state. Therefore, the objective of this study was to identify and compare the sex-dependent predictors of binge drinking in North Dakota. Methods Data were obtained from the North Dakota Behavioral Risk Factor Surveillance System (BRFSS) for the years 2017–2021. The BRFSS is a population based cross-sectional telephone survey administered annually by the North Dakota Department of Health and Human Services (NDDHHS) in coordination with the Centers for Disease Control and Prevention (CDC). The study population included all males and females aged ≥ 18 years in the North Dakota BRFSS database from 2017 to 2021 who responded to the questions “During the past 30 days, how many days per week or per month did you have at least one drink of any alcoholic beverage such as beer, wine, a malt beverage or liquor?” and “Considering all types of alcoholic beverages, how many times during the past 30 days did you have five or more drinks (for men) or four or more drinks (for women) on an occasion?.” Potential predictors of binge drinking were selected using a conceptual model and included: race, age, income, education, urban or rural residence, and frequent physical or mental distress. Separate binary logistic regression models of binge drinking were fitted for males and females. Results The odds of binge drinking declined with increasing age in both sexes. Males who were Black or other races and ethnicities besides American Indian had lower odds of binge drinking than White males. Additionally, males had significantly higher odds of binge drinking if they lived in a rural county, had a household income ≥ $75,000, or had more than a high school education compared to those who lived in an urban county, had a household income < $75,000, or had no more than a high school education. White…
format: application/pdf
format: text/html
creator: Corey A. Day
creator: Howard Onyuth
creator: Grace Njau
creator: Matthew Schmidt
creator: Agricola Odoi
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.20830
publisher: PeerJ Inc.
rights: © 2026 Day et al.
abstract: Background North Dakota has one of the highest rates of binge drinking in the United States, but little is known about how the predictors of binge drinking differ between males and females within the state. Therefore, the objective of this study was to identify and compare the sex-dependent predictors of binge drinking in North Dakota. Methods Data were obtained from the North Dakota Behavioral Risk Factor Surveillance System (BRFSS) for the years 2017–2021. The BRFSS is a population based cross-sectional telephone survey administered annually by the North Dakota Department of Health and Human Services (NDDHHS) in coordination with the Centers for Disease Control and Prevention (CDC). The study population included all males and females aged ≥ 18 years in the North Dakota BRFSS database from 2017 to 2021 who responded to the questions “During the past 30 days, how many days per week or per month did you have at least one drink of any alcoholic beverage such as beer, wine, a malt beverage or liquor?” and “Considering all types of alcoholic beverages, how many times during the past 30 days did you have five or more drinks (for men) or four or more drinks (for women) on an occasion?.” Potential predictors of binge drinking were selected using a conceptual model and included: race, age, income, education, urban or rural residence, and frequent physical or mental distress. Separate binary logistic regression models of binge drinking were fitted for males and females. Results The odds of binge drinking declined with increasing age in both sexes. Males who were Black or other races and ethnicities besides American Indian had lower odds of binge drinking than White males. Additionally, males had significantly higher odds of binge drinking if they lived in a rural county, had a household income ≥ $75,000, or had more than a high school education compared to those who lived in an urban county, had a household income < $75,000, or had no more than a high school education. White…
bibliographic citation: Day et al. (2026) Sex-dependent predictors of binge drinking among males and females in North Dakota. PeerJ 14:e20830 https://doi.org/10.7717/peerj.20830
date submitted: 2025-03-09
date accepted: 2025-12-31
issued: 2026-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Day
  given name: Corey A.
author list: Agent
  family name: Onyuth
  given name: Howard
author list: Agent
  family name: Njau
  given name: Grace
author list: Agent
  family name: Schmidt
  given name: Matthew
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.20830
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-24
copyright: ©2026 Day et al.
attribution name: Day et al.

Improving drought tolerance in some wheat genotypes with foliar application of silicon nanoparticles in Al-Dawadmi, Saudi Arabia
type: item
type: AcademicArticle
description: Water stress, even at light or moderate levels, can negatively affect wheat physiology by altering gas exchange and photosynthetic pigments, thereby restricting growth, while severe stress further amplifies these effects and leads to more pronounced yield reductions. Foliar application of silicon nanoparticles (SiNPs) may help mitigate some of these detrimental effects on wheat’s physiological and agronomic traits, as evaluated over two growing seasons at a single location. To test this hypothesis, two field experiments were conducted during the 2022/2023 and 2023/2024 winter seasons at the Experimental Farm in Al-Dawadmi, Saudi Arabia. The study evaluated the response of eight wheat genotypes to foliar-applied SiNPs under three irrigation regimes representing full, moderate, and severe water stress conditions. Agronomic and physiological characteristics of wheat were negatively affected by moderate and severe water stress. In comparison to the untreated control, the application of 100 and 200 mg L−1 of SiNPs, particularly at the higher concentration, alleviated some of the negative effects of water stress on various physiological and yield traits, with Giza 171, SOKOLL, and Giza 168 showing the most pronounced improvements. In the same context, under severe water stress, SiNP application improved net photosynthesis (up to 57.19%), transpiration rate (up to 36.20%), stomatal conductance (up to 31.34%), intercellular CO2 concentration (up to 34.21%), water use efficiency (up to 15.69%), relative water content (up to 38.16%), chlorophyll content (up to 37.51%), spikes per plant (up to 50.80%), grains per spike (up to 56.52%), and grain yield per hectare (up to 50.33%). These results demonstrate the potential of SiNP application to improve drought tolerance in wheat genotypes under the specific agro-ecological conditions of Al-Dawadmi and highlight genotype-specific responses, particularly in Giza 171 and SOKOLL. While confirming previous findings on the role of silico…
format: application/pdf
format: text/html
creator: Mesfer M. Alqahtani
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20823
publisher: PeerJ Inc.
rights: © 2026 Alqahtani
abstract: Water stress, even at light or moderate levels, can negatively affect wheat physiology by altering gas exchange and photosynthetic pigments, thereby restricting growth, while severe stress further amplifies these effects and leads to more pronounced yield reductions. Foliar application of silicon nanoparticles (SiNPs) may help mitigate some of these detrimental effects on wheat’s physiological and agronomic traits, as evaluated over two growing seasons at a single location. To test this hypothesis, two field experiments were conducted during the 2022/2023 and 2023/2024 winter seasons at the Experimental Farm in Al-Dawadmi, Saudi Arabia. The study evaluated the response of eight wheat genotypes to foliar-applied SiNPs under three irrigation regimes representing full, moderate, and severe water stress conditions. Agronomic and physiological characteristics of wheat were negatively affected by moderate and severe water stress. In comparison to the untreated control, the application of 100 and 200 mg L−1 of SiNPs, particularly at the higher concentration, alleviated some of the negative effects of water stress on various physiological and yield traits, with Giza 171, SOKOLL, and Giza 168 showing the most pronounced improvements. In the same context, under severe water stress, SiNP application improved net photosynthesis (up to 57.19%), transpiration rate (up to 36.20%), stomatal conductance (up to 31.34%), intercellular CO2 concentration (up to 34.21%), water use efficiency (up to 15.69%), relative water content (up to 38.16%), chlorophyll content (up to 37.51%), spikes per plant (up to 50.80%), grains per spike (up to 56.52%), and grain yield per hectare (up to 50.33%). These results demonstrate the potential of SiNP application to improve drought tolerance in wheat genotypes under the specific agro-ecological conditions of Al-Dawadmi and highlight genotype-specific responses, particularly in Giza 171 and SOKOLL. While confirming previous findings on the role of silico…
bibliographic citation: Alqahtani (2026) Improving drought tolerance in some wheat genotypes with foliar application of silicon nanoparticles in Al-Dawadmi, Saudi Arabia. PeerJ 14:e20823 https://doi.org/10.7717/peerj.20823
date submitted: 2025-07-04
date accepted: 2025-12-29
issued: 2026-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alqahtani
  given name: Mesfer M.
doi: 10.7717/peerj.20823
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-24
copyright: ©2026 Alqahtani
attribution name: Alqahtani

Morphological description and near-complete mitochondrial genome of Haemoproteus (Parahaemoproteus) trarotraro n. sp.: a widely distributed species reported in Brazilian falcons
type: item
type: AcademicArticle
description: Haemosporida are vector-borne parasitic protozoa known to be present in birds of most avian orders. However, despite their perceived diversity using DNA barcode approaches, describing and delimiting species is challenging, particularly for those parasites found in non-passerine birds. In this study, we describe Haemoproteus trarotraro n. sp., a species found in two Falconiform hosts, the Crested Caracara (Caracara plancus plancus, type host) and the Yellow-headed Caracara (Daptrius chimachima chimachima), both sampled in Brazil at a wildlife rehabilitation center using microscopy and molecular tools. Haemoproteus trarotraro n. sp. is distinguished from the two other haemoproteid species described in Falconiformes, H. brachiatus and H. tinnunculi , by the absence of gametocytes that fully encircle the host-cell nucleus, and by the presence of numerous small vacuoles scattered throughout the cytoplasm of macrogametocytes. Both the partial cytb gene and the mtDNA genome for this new species are reported. The sequencing of the cytb barcode fragment revealed that H. trarotraro n. sp. reported here corresponds to a Haemoproteus sp. haplotype (GenBank Accession (AF465594) lineage POLPLA01 in Malavi) previously reported from Caracara plancus cheriway in Florida, USA. Although it diverges by only 2% at the cytb level from H. tinnunculi and H. brachiatus, H. trarotraro n. sp. is not a sister lineage to these taxa. Instead, phylogenetic analyses place it within a distinct but closely related, well-supported clade comprising lineages infecting American Kestrels (Falco sparverius). This study contributes, through an integrative taxonomic approach, to the ongoing discussion about species delimitation within the order Haemosporida.
format: application/pdf
format: text/html
creator: Lis Marques de C. Vieira
creator: M Andreina Pacheco
creator: Ananias A. Escalante
creator: Erika M. Braga
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Parasitology
subject: Taxonomy
description: doi:10.7717/peerj.20653
publisher: PeerJ Inc.
rights: © 2026 Vieira et al.
abstract: Haemosporida are vector-borne parasitic protozoa known to be present in birds of most avian orders. However, despite their perceived diversity using DNA barcode approaches, describing and delimiting species is challenging, particularly for those parasites found in non-passerine birds. In this study, we describe Haemoproteus trarotraro n. sp., a species found in two Falconiform hosts, the Crested Caracara (Caracara plancus plancus, type host) and the Yellow-headed Caracara (Daptrius chimachima chimachima), both sampled in Brazil at a wildlife rehabilitation center using microscopy and molecular tools. Haemoproteus trarotraro n. sp. is distinguished from the two other haemoproteid species described in Falconiformes, H. brachiatus and H. tinnunculi , by the absence of gametocytes that fully encircle the host-cell nucleus, and by the presence of numerous small vacuoles scattered throughout the cytoplasm of macrogametocytes. Both the partial cytb gene and the mtDNA genome for this new species are reported. The sequencing of the cytb barcode fragment revealed that H. trarotraro n. sp. reported here corresponds to a Haemoproteus sp. haplotype (GenBank Accession (AF465594) lineage POLPLA01 in Malavi) previously reported from Caracara plancus cheriway in Florida, USA. Although it diverges by only 2% at the cytb level from H. tinnunculi and H. brachiatus, H. trarotraro n. sp. is not a sister lineage to these taxa. Instead, phylogenetic analyses place it within a distinct but closely related, well-supported clade comprising lineages infecting American Kestrels (Falco sparverius). This study contributes, through an integrative taxonomic approach, to the ongoing discussion about species delimitation within the order Haemosporida.
bibliographic citation: Vieira et al. (2026) Morphological description and near-complete mitochondrial genome of Haemoproteus (Parahaemoproteus) trarotraro n. sp.: a widely distributed species reported in Brazilian falcons. PeerJ 14:e20653 https://doi.org/10.7717/peerj.20653
date submitted: 2025-10-16
date accepted: 2025-12-02
issued: 2026-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vieira
  given name: Lis Marques de C.
author list: Agent
  family name: Pacheco
  given name: M Andreina
author list: Agent
  family name: Escalante
  given name: Ananias A.
author list: Agent
  family name: Braga
  given name: Erika M.
doi: 10.7717/peerj.20653
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-24
copyright: ©2026 Vieira et al.
attribution name: Vieira et al.

Occurrence and prognosis of metabolic dysfunction-associated steatosis liver disease and gastrointestinal tumors: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background The metabolic dysfunction-associated steatotic liver disease (MASLD) is one of the most common causes of chronic and abnormal liver function tests globally. The relationship between metabolic MASLD and gastrointestinal tumors (GI) remains controversial. Methodology We conducted a systematic review based on a protocol registered with PROSPERO (CRD42024590389). PubMed, Cochrane Library, Web of Science, and Embase were systematically searched until November 2025, Quality assessment and data extraction were performed by two investigators, and the hazard ratios and their corresponding 95% confidence intervals were combined using Stata for data analysis. Results A total of 29 studies were included, we found that MASLD were related to colorectal polyps (I2 = 62.7, HR = 1.42, 95% CI [1.22–1.66]), colorectal cancer (I2 = 82.8%, HR = 1.22, 95% CI [1.16–1.29]), p < 0.001) and esophagus cancer (I2 =88.4, HR = 1.14, 95% CI [1.05–1.24], p < 0.001), gastric cancer (I2 = 88, HR = 1.18, 95% CI [1.1–1.26]), cholangiocarcinoma (I2 = 73.7, HR = 1.26, 95% CI [1.1 7–1. 36], P < 0.001) and gallbladder cancer (I2 = 56.1, HR = 1.41, 95% CI [1.03–1.92], P < 0.001). Factors like follow-up time, study methods and countries contributed to heterogeneity of studies. Lastly, incidence rates (IR) and prognosis of GI cancer in patients with MASLD were highly correlated. Conclusion We conclude that there is a significant association and prognosis between MASLD and gastrointestinal tumors. Further studies should focus on prospective studies and mechanistic insights.
format: application/pdf
format: text/html
creator: Siyu Duan
creator: Yiyi Wei
creator: Zhuoyu Ding
creator: Chaomin Pan
creator: Li Yang
creator: Yan Gu
creator: Xinke Wang
subject: Gastroenterology and Hepatology
subject: Pathology
description: doi:10.7717/peerj.20616
publisher: PeerJ Inc.
rights: © 2026 Duan et al.
abstract: Background The metabolic dysfunction-associated steatotic liver disease (MASLD) is one of the most common causes of chronic and abnormal liver function tests globally. The relationship between metabolic MASLD and gastrointestinal tumors (GI) remains controversial. Methodology We conducted a systematic review based on a protocol registered with PROSPERO (CRD42024590389). PubMed, Cochrane Library, Web of Science, and Embase were systematically searched until November 2025, Quality assessment and data extraction were performed by two investigators, and the hazard ratios and their corresponding 95% confidence intervals were combined using Stata for data analysis. Results A total of 29 studies were included, we found that MASLD were related to colorectal polyps (I2 = 62.7, HR = 1.42, 95% CI [1.22–1.66]), colorectal cancer (I2 = 82.8%, HR = 1.22, 95% CI [1.16–1.29]), p < 0.001) and esophagus cancer (I2 =88.4, HR = 1.14, 95% CI [1.05–1.24], p < 0.001), gastric cancer (I2 = 88, HR = 1.18, 95% CI [1.1–1.26]), cholangiocarcinoma (I2 = 73.7, HR = 1.26, 95% CI [1.1 7–1. 36], P < 0.001) and gallbladder cancer (I2 = 56.1, HR = 1.41, 95% CI [1.03–1.92], P < 0.001). Factors like follow-up time, study methods and countries contributed to heterogeneity of studies. Lastly, incidence rates (IR) and prognosis of GI cancer in patients with MASLD were highly correlated. Conclusion We conclude that there is a significant association and prognosis between MASLD and gastrointestinal tumors. Further studies should focus on prospective studies and mechanistic insights.
bibliographic citation: Duan et al. (2026) Occurrence and prognosis of metabolic dysfunction-associated steatosis liver disease and gastrointestinal tumors: a systematic review and meta-analysis. PeerJ 14:e20616 https://doi.org/10.7717/peerj.20616
date submitted: 2025-02-21
date accepted: 2025-11-29
issued: 2026-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Duan
  given name: Siyu
author list: Agent
  family name: Wei
  given name: Yiyi
author list: Agent
  family name: Ding
  given name: Zhuoyu
author list: Agent
  family name: Pan
  given name: Chaomin
author list: Agent
  family name: Yang
  given name: Li
author list: Agent
  family name: Gu
  given name: Yan
author list: Agent
  family name: Wang
  given name: Xinke
doi: 10.7717/peerj.20616
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-24
copyright: ©2026 Duan et al.
attribution name: Duan et al.

RNA-Seq analysis reveals regulatory networks driven by EpCAM overexpression in esophageal adenocarcinoma cells
type: item
type: AcademicArticle
description: Esophageal cancer is a formidable malignancy, presenting a significant health challenge due to its widespread prevalence and associated high mortality rates. Epithelial cell adhesion molecule (EpCAM), a pro-oncogenic glycoprotein, has been identified as an upregulated protein in esophageal adenocarcinoma (ESCA) through multi-OMICS platforms. However, its functional role in ESCA remains relatively understudied. Here, we investigated the contribution of EpCAM to ESCA pathogenesis using an EpCAM-null ESCA cell line, FLO-1, as a gain-of-function model. Introduction of a recombinant EpCAM–GFP fusion construct into FLO-1 cells resulted in enhanced cell migration, adhesion, clonogenic survival, and invasive capacity, supporting a pro-tumorigenic role for EpCAM. To define EpCAM-associated regulatory networks, RNA sequencing was performed on EpCAM-overexpressing cells, revealing 797 differentially expressed genes. Functional enrichment analyses indicated significant involvement of pathways related to cell adhesion, cell motility, transmembrane activity, and neuronal-associated processes, with enrichment in plasma membrane, focal adhesion, and neuron projection terminus compartments. Protein–protein interaction network analysis identified key hub genes, including SOX2, COL1A1, LOX, COL3A1, LUM, PXDN, BDNF, NCAM1, TLR2, and CCL5, linking EpCAM signaling to PI3K–Akt, ECM–receptor interaction, and focal adhesion pathways. Importantly, quantitative polymerase chain reaction (qPCR) validation of selected hub genes confirmed significant upregulation of the extracellular matrix components COL1A1 and PXDN in EpCAM-overexpressing FLO-1 cells, supporting the transcriptomic predictions and implicating ECM remodeling as a downstream consequence of EpCAM signaling. Collectively, these findings demonstrate that EpCAM promotes aggressive cellular phenotypes in ESCA and drives transcriptional programs associated with adhesion, invasion, and extracellular matrix regulation, highlighting poten…
format: application/pdf
format: text/html
creator: M. Aiman Mohtar
creator: Siti Nurmi Nasir
creator: Zuraini Abd Razak
creator: Hanif Zulkhairi Mohamad Said
creator: Syazalina Zahari
creator: Saiful Effendi Syafruddin
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.20877
publisher: PeerJ Inc.
rights: © 2026 Mohtar et al.
abstract: Esophageal cancer is a formidable malignancy, presenting a significant health challenge due to its widespread prevalence and associated high mortality rates. Epithelial cell adhesion molecule (EpCAM), a pro-oncogenic glycoprotein, has been identified as an upregulated protein in esophageal adenocarcinoma (ESCA) through multi-OMICS platforms. However, its functional role in ESCA remains relatively understudied. Here, we investigated the contribution of EpCAM to ESCA pathogenesis using an EpCAM-null ESCA cell line, FLO-1, as a gain-of-function model. Introduction of a recombinant EpCAM–GFP fusion construct into FLO-1 cells resulted in enhanced cell migration, adhesion, clonogenic survival, and invasive capacity, supporting a pro-tumorigenic role for EpCAM. To define EpCAM-associated regulatory networks, RNA sequencing was performed on EpCAM-overexpressing cells, revealing 797 differentially expressed genes. Functional enrichment analyses indicated significant involvement of pathways related to cell adhesion, cell motility, transmembrane activity, and neuronal-associated processes, with enrichment in plasma membrane, focal adhesion, and neuron projection terminus compartments. Protein–protein interaction network analysis identified key hub genes, including SOX2, COL1A1, LOX, COL3A1, LUM, PXDN, BDNF, NCAM1, TLR2, and CCL5, linking EpCAM signaling to PI3K–Akt, ECM–receptor interaction, and focal adhesion pathways. Importantly, quantitative polymerase chain reaction (qPCR) validation of selected hub genes confirmed significant upregulation of the extracellular matrix components COL1A1 and PXDN in EpCAM-overexpressing FLO-1 cells, supporting the transcriptomic predictions and implicating ECM remodeling as a downstream consequence of EpCAM signaling. Collectively, these findings demonstrate that EpCAM promotes aggressive cellular phenotypes in ESCA and drives transcriptional programs associated with adhesion, invasion, and extracellular matrix regulation, highlighting poten…
bibliographic citation: Mohtar et al. (2026) RNA-Seq analysis reveals regulatory networks driven by EpCAM overexpression in esophageal adenocarcinoma cells. PeerJ 14:e20877 https://doi.org/10.7717/peerj.20877
date submitted: 2025-07-09
date accepted: 2026-01-12
issued: 2026-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohtar
  given name: M. Aiman
author list: Agent
  family name: Nasir
  given name: Siti Nurmi
author list: Agent
  family name: Abd Razak
  given name: Zuraini
author list: Agent
  family name: Mohamad Said
  given name: Hanif Zulkhairi
author list: Agent
  family name: Zahari
  given name: Syazalina
author list: Agent
  family name: Syafruddin
  given name: Saiful Effendi
doi: 10.7717/peerj.20877
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-23
copyright: © 2026 Mohtar et al.
attribution name: Mohtar et al.

Monitoring environmental impacts of a designated aquaculture area in the Karaburun Peninsula using Google Earth Engine
type: item
type: AcademicArticle
description: Satellite-based monitoring of aquaculture impacts remains constrained by the absence of standardized, reproducible methodologies capable of capturing long-term environmental dynamics. This study introduces a novel framework that integrates Difference-in-Differences (DiD) causal inference with multi-decadal Moderate Resolution Imaging Spectroradiometer (MODIS) satellite data and Google Earth Engine (GEE) cloud computing to evaluate aquaculture-related changes in coastal ecosystems. Using 20 years of satellite observations (2002–2022) from the Karaburun Peninsula, İzmir, Türkiye, we compared three representative sites: an aquaculture zone, a coastal area influenced by human settlements, and an offshore reference site with minimal anthropogenic activity. The human-impacted coastal site consistently exhibited the highest concentrations of surface parameters, reflecting dominant background anthropogenic influences. However, DiD analysis revealed no statistically significant differences in chlorophyll-a (Chl-a), particulate organic carbon (POC), or other parameters between the aquaculture and control sites, indicating that potential aquaculture-related effects remained below the detection threshold of the 1 km MODIS resolution. Despite these null results, the study demonstrates the feasibility and limitations of combining causal inference and cloud-based remote sensing for aquaculture monitoring. This methodological integration provides a scalable, cost-effective, and transferable framework for detecting and interpreting environmental change across large spatial and temporal domains. By defining the sensitivity limits of satellite-based detection, this work lays a foundation for future applications that merge high-resolution sensors, in-situ validation, and process-based modeling in sustainable aquaculture management.
format: application/pdf
format: text/html
creator: Deniz Devrim Tosun
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
subject: Environmental Health
description: doi:10.7717/peerj.20873
publisher: PeerJ Inc.
rights: © 2026 Tosun
abstract: Satellite-based monitoring of aquaculture impacts remains constrained by the absence of standardized, reproducible methodologies capable of capturing long-term environmental dynamics. This study introduces a novel framework that integrates Difference-in-Differences (DiD) causal inference with multi-decadal Moderate Resolution Imaging Spectroradiometer (MODIS) satellite data and Google Earth Engine (GEE) cloud computing to evaluate aquaculture-related changes in coastal ecosystems. Using 20 years of satellite observations (2002–2022) from the Karaburun Peninsula, İzmir, Türkiye, we compared three representative sites: an aquaculture zone, a coastal area influenced by human settlements, and an offshore reference site with minimal anthropogenic activity. The human-impacted coastal site consistently exhibited the highest concentrations of surface parameters, reflecting dominant background anthropogenic influences. However, DiD analysis revealed no statistically significant differences in chlorophyll-a (Chl-a), particulate organic carbon (POC), or other parameters between the aquaculture and control sites, indicating that potential aquaculture-related effects remained below the detection threshold of the 1 km MODIS resolution. Despite these null results, the study demonstrates the feasibility and limitations of combining causal inference and cloud-based remote sensing for aquaculture monitoring. This methodological integration provides a scalable, cost-effective, and transferable framework for detecting and interpreting environmental change across large spatial and temporal domains. By defining the sensitivity limits of satellite-based detection, this work lays a foundation for future applications that merge high-resolution sensors, in-situ validation, and process-based modeling in sustainable aquaculture management.
bibliographic citation: Tosun (2026) Monitoring environmental impacts of a designated aquaculture area in the Karaburun Peninsula using Google Earth Engine. PeerJ 14:e20873 https://doi.org/10.7717/peerj.20873
date submitted: 2025-10-05
date accepted: 2026-01-09
issued: 2026-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tosun
  given name: Deniz Devrim
doi: 10.7717/peerj.20873
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-23
copyright: © 2026 Tosun
attribution name: Tosun

Integration of metabolomics and transcriptomics to reveal metabolic characteristics and the role of mTORC1 in β-cell proliferation induced by a short-term high-fat diet
type: item
type: AcademicArticle
description: Background Pancreatic β-cell proliferation is essential for maintaining the balance of β-cell mass, and an elevated metabolic load can stimulate their proliferation. Numerous studies have shown that a short-term high-fat diet increases metabolic load without affecting insulin sensitivity, thereby promoting the proliferation of pancreatic β-cells. However, the underlying mechanisms of this effect remain to be fully elucidated. Results A model has been constructed in our study to emulate pancreatic β-cell proliferation induced by a short-term high-fat diet, aiming to scrutinize the underlying mechanisms. Integrated transcriptomic and metabolomic analyses suggest that the mTORC1 signaling pathway may be crucial in this induced proliferation. Further analysis revealed that rapamycin, a specific inhibitor of the mTORC1 pathway, can inhibit proliferation induced by the short-term high-fat diet. Conclusion Our study confirms the significant role of the mTORC1 signaling pathway in pancreatic β-cell proliferation induced by a short-term high-fat diet.
format: application/pdf
format: text/html
creator: Jiajia Wang
creator: Jing Li
creator: Yunshan Li
creator: Mengran Liu
creator: Shan Huang
creator: Wenyi Li
subject: Biochemistry
subject: Cell Biology
subject: Genomics
subject: Metabolic Sciences
description: doi:10.7717/peerj.20871
publisher: PeerJ Inc.
rights: © 2026 Wang et al.
abstract: Background Pancreatic β-cell proliferation is essential for maintaining the balance of β-cell mass, and an elevated metabolic load can stimulate their proliferation. Numerous studies have shown that a short-term high-fat diet increases metabolic load without affecting insulin sensitivity, thereby promoting the proliferation of pancreatic β-cells. However, the underlying mechanisms of this effect remain to be fully elucidated. Results A model has been constructed in our study to emulate pancreatic β-cell proliferation induced by a short-term high-fat diet, aiming to scrutinize the underlying mechanisms. Integrated transcriptomic and metabolomic analyses suggest that the mTORC1 signaling pathway may be crucial in this induced proliferation. Further analysis revealed that rapamycin, a specific inhibitor of the mTORC1 pathway, can inhibit proliferation induced by the short-term high-fat diet. Conclusion Our study confirms the significant role of the mTORC1 signaling pathway in pancreatic β-cell proliferation induced by a short-term high-fat diet.
bibliographic citation: Wang et al. (2026) Integration of metabolomics and transcriptomics to reveal metabolic characteristics and the role of mTORC1 in β-cell proliferation induced by a short-term high-fat diet. PeerJ 14:e20871 https://doi.org/10.7717/peerj.20871
date submitted: 2025-05-15
date accepted: 2026-01-09
issued: 2026-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jiajia
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Li
  given name: Yunshan
author list: Agent
  family name: Liu
  given name: Mengran
author list: Agent
  family name: Huang
  given name: Shan
author list: Agent
  family name: Li
  given name: Wenyi
doi: 10.7717/peerj.20871
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-23
copyright: © 2026 Wang et al.
attribution name: Wang et al.

Unraveling microbial diversity and physicochemical hazard level in Thai traditional fermented shrimp paste (Kapi)
type: item
type: AcademicArticle
description: Fermented shrimp paste (Kapi) is a culturally significant condiment valued for its flavor and nutritional value. However, inconsistent production practices may lead to microbial contamination and histamine accumulation, posing health risks. Understanding microbial diversity, salt-tolerant pathogens, and the effectiveness of hygienic controls is essential for improving product safety and quality consistency. This study assessed the microbial and physicochemical characteristics of seven Kapi produced under varying hygienic conditions: a certified commercial export product (M1), a traditionally fermented product using 25% (w/w) salt (M2), wet-market bulk products (M3, M4), and sealed community-enterprise products (M5, M6, M7). Microbiological hazards were characterized using Oxford Nanopore sequencing, and physicochemical analyses, including histamine content, were conducted. M1 exhibited the highest safety and quality, with no detected pathogens. In contrast, M3 and M5 contained high microbial loads, including Staphylococcus aureus, Bacillus cereus, Clostridium perfringens, and fungi. Bacterial diversity varied significantly across samples, with M3 and M4 showing the greatest richness, whereas M6 had the lowest. Dominant species identified were Lentibacillus salinarum, Lentibacillus amyloliquefaciens, and Lentibacillus kimchi in M1, M3, and M4, and Staphylococcus sciuri in M2, M5, and M6, all of which possessed histamine-degrading potential. Alkalibacterium kapii dominated M7, while histamine-producing Jeotgalicoccus halotolerans was found in M5–M7. Physicochemical variations corresponded with production practices. M6 showed the highest histamine level (39.4 mg/kg), while M1 and M4 had the lowest (12.7 and 9.5 mg/kg, respectively), indicating differences in hygiene and salt management. Overall, microbial and physicochemical hazard levels were closely associated with production environments. To enhance the safety and consistency of Kapi, we propose a risk-based framewo…
format: application/pdf
format: text/html
creator: Thitikorn Mahidsanan
creator: Pattama Srinamngoen
creator: Priyada Sittisart
subject: Agricultural Science
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.20864
publisher: PeerJ Inc.
rights: © 2026 Mahidsanan et al.
abstract: Fermented shrimp paste (Kapi) is a culturally significant condiment valued for its flavor and nutritional value. However, inconsistent production practices may lead to microbial contamination and histamine accumulation, posing health risks. Understanding microbial diversity, salt-tolerant pathogens, and the effectiveness of hygienic controls is essential for improving product safety and quality consistency. This study assessed the microbial and physicochemical characteristics of seven Kapi produced under varying hygienic conditions: a certified commercial export product (M1), a traditionally fermented product using 25% (w/w) salt (M2), wet-market bulk products (M3, M4), and sealed community-enterprise products (M5, M6, M7). Microbiological hazards were characterized using Oxford Nanopore sequencing, and physicochemical analyses, including histamine content, were conducted. M1 exhibited the highest safety and quality, with no detected pathogens. In contrast, M3 and M5 contained high microbial loads, including Staphylococcus aureus, Bacillus cereus, Clostridium perfringens, and fungi. Bacterial diversity varied significantly across samples, with M3 and M4 showing the greatest richness, whereas M6 had the lowest. Dominant species identified were Lentibacillus salinarum, Lentibacillus amyloliquefaciens, and Lentibacillus kimchi in M1, M3, and M4, and Staphylococcus sciuri in M2, M5, and M6, all of which possessed histamine-degrading potential. Alkalibacterium kapii dominated M7, while histamine-producing Jeotgalicoccus halotolerans was found in M5–M7. Physicochemical variations corresponded with production practices. M6 showed the highest histamine level (39.4 mg/kg), while M1 and M4 had the lowest (12.7 and 9.5 mg/kg, respectively), indicating differences in hygiene and salt management. Overall, microbial and physicochemical hazard levels were closely associated with production environments. To enhance the safety and consistency of Kapi, we propose a risk-based framewo…
bibliographic citation: Mahidsanan et al. (2026) Unraveling microbial diversity and physicochemical hazard level in Thai traditional fermented shrimp paste (Kapi). PeerJ 14:e20864 https://doi.org/10.7717/peerj.20864
date submitted: 2025-07-11
date accepted: 2026-01-08
issued: 2026-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mahidsanan
  given name: Thitikorn
author list: Agent
  family name: Srinamngoen
  given name: Pattama
author list: Agent
  family name: Sittisart
  given name: Priyada
doi: 10.7717/peerj.20864
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-23
copyright: ©2026 Mahidsanan et al.
attribution name: Mahidsanan et al.

Proteomic landscape of colorectal cancer liver metastasis: molecular signatures and novel therapeutic targets
type: item
type: AcademicArticle
description: Background Liver metastasis accounts for most deaths in colorectal cancer patients, but we still lack a clear understanding of how this devastating process unfolds at the molecular level. Identifying these mechanisms could lead to better ways to predict and treat metastatic disease. Methods We performed proteomic analysis on 38 tissue samples, including benign adenomas, primary colorectal tumors, and liver metastases, to map the molecular changes that drive cancer spread to the liver. Results We found striking differences in protein expression patterns across tissue types. Primary tumors showed massive protein changes compared to normal tissue (nearly 1,900 alterations), but liver metastases were surprisingly selective in their modifications (just 89 unique changes from primary tumors). This specificity indicates that liver colonization depends on precise molecular adjustments rather than random cellular disruption. The proteins involved in metastasis fell into three main categories: tissue restructuring to support tumor growth, mechanisms to avoid immune detection, and blood clotting factors that help cancer cells establish themselves in the liver. We validated three biomarkers with clinical potential: HDHD3 shows promise for detecting existing metastases, while OLFM4 and ZNF34 can help identify primary tumors at high risk for spreading. Conclusions Our work reveals that colorectal cancer liver metastasis involves targeted molecular changes rather than widespread cellular chaos. The biomarkers we identified could improve early detection of metastatic risk and guide more personalized treatment decisions for patients.
format: application/pdf
format: text/html
creator: Hongyuan Shen
creator: Jia Li
creator: Guoqing Wang
creator: Xiangyu Su
creator: Zhigang Zhang
creator: Jinjun Shi
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.20856
publisher: PeerJ Inc.
rights: © 2026 Shen et al.
abstract: Background Liver metastasis accounts for most deaths in colorectal cancer patients, but we still lack a clear understanding of how this devastating process unfolds at the molecular level. Identifying these mechanisms could lead to better ways to predict and treat metastatic disease. Methods We performed proteomic analysis on 38 tissue samples, including benign adenomas, primary colorectal tumors, and liver metastases, to map the molecular changes that drive cancer spread to the liver. Results We found striking differences in protein expression patterns across tissue types. Primary tumors showed massive protein changes compared to normal tissue (nearly 1,900 alterations), but liver metastases were surprisingly selective in their modifications (just 89 unique changes from primary tumors). This specificity indicates that liver colonization depends on precise molecular adjustments rather than random cellular disruption. The proteins involved in metastasis fell into three main categories: tissue restructuring to support tumor growth, mechanisms to avoid immune detection, and blood clotting factors that help cancer cells establish themselves in the liver. We validated three biomarkers with clinical potential: HDHD3 shows promise for detecting existing metastases, while OLFM4 and ZNF34 can help identify primary tumors at high risk for spreading. Conclusions Our work reveals that colorectal cancer liver metastasis involves targeted molecular changes rather than widespread cellular chaos. The biomarkers we identified could improve early detection of metastatic risk and guide more personalized treatment decisions for patients.
bibliographic citation: Shen et al. (2026) Proteomic landscape of colorectal cancer liver metastasis: molecular signatures and novel therapeutic targets. PeerJ 14:e20856 https://doi.org/10.7717/peerj.20856
date submitted: 2025-10-29
date accepted: 2026-01-06
issued: 2026-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Shen
  given name: Hongyuan
author list: Agent
  family name: Li
  given name: Jia
author list: Agent
  family name: Wang
  given name: Guoqing
author list: Agent
  family name: Su
  given name: Xiangyu
author list: Agent
  family name: Zhang
  given name: Zhigang
author list: Agent
  family name: Shi
  given name: Jinjun
doi: 10.7717/peerj.20856
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-23
copyright: ©2026 Shen et al.
attribution name: Shen et al.

Isometric muscle strength profile of lower limbs for children and adolescents between 7 and 15 years of age
type: item
type: AcademicArticle
description: Background Muscle strength is a key determinant of health-related physical fitness and has become a significant biological predictor of overall health and lifespan. This study aimed to characterize the development of isometric strength in the lower limbs of Chilean schoolchildren and adolescents aged 7 to 15 years. Specifically, it sought to: (a) determine when sex-based differences in lower limb strength first appear; (b) identify key developmental stages where significant gains in muscle strength occur in boys and girls; and (c) analyze the contribution of individual muscle groups to total lower limb strength while accounting for sex and age differences. Methodology This cross-sectional study evaluated the maximum isometric strength of seven lower limb muscle groups in a sample of 302 Chilean children, divided into nine age groups at one-year intervals. Hand-held dynamometry was used for isometric strength assessment. Data analysis included a two-factor analysis of variance (ANOVA) for maximum isometric strength and a stepwise multiple linear regression analysis to the entire sample. Results Multiple comparisons showed significant differences between the ages of 9 and 12; and sex. The narrowest age range in the progression of maximum isometric strength were: 9–11 years for knee flexors in females (p = 0.0201) and 9–12 years for males (p = 0.0008). Hip flexors, dorsiflexors, hip extensors and knee extensors explained the highest percentage of variance (R2 = 0.897, p < 0.0001) in the total lower limb strength. Conclusion Our findings show that lower limb isometric strength in Chilean schoolchildren and adolescents increases from age 10, with boys outperforming girls by age 15. Hip flexors mainly explain total strength, offering a useful reference to detect within and between subject strength deficits.
format: application/pdf
format: text/html
creator: Oscar Bustos-Moyano
creator: Eduardo Guzmán-Muñoz
creator: Pablo Valdes-Badilla
creator: Diego Frugone-Zaror
creator: Flor Miño-Cornejo
creator: Felipe Araya-Quintanilla
creator: Guillermo Mendez-Rebolledo
subject: Anatomy and Physiology
subject: Kinesiology
subject: Pediatrics
subject: Rehabilitation
description: doi:10.7717/peerj.20799
publisher: PeerJ Inc.
rights: © 2026 Bustos-Moyano et al.
abstract: Background Muscle strength is a key determinant of health-related physical fitness and has become a significant biological predictor of overall health and lifespan. This study aimed to characterize the development of isometric strength in the lower limbs of Chilean schoolchildren and adolescents aged 7 to 15 years. Specifically, it sought to: (a) determine when sex-based differences in lower limb strength first appear; (b) identify key developmental stages where significant gains in muscle strength occur in boys and girls; and (c) analyze the contribution of individual muscle groups to total lower limb strength while accounting for sex and age differences. Methodology This cross-sectional study evaluated the maximum isometric strength of seven lower limb muscle groups in a sample of 302 Chilean children, divided into nine age groups at one-year intervals. Hand-held dynamometry was used for isometric strength assessment. Data analysis included a two-factor analysis of variance (ANOVA) for maximum isometric strength and a stepwise multiple linear regression analysis to the entire sample. Results Multiple comparisons showed significant differences between the ages of 9 and 12; and sex. The narrowest age range in the progression of maximum isometric strength were: 9–11 years for knee flexors in females (p = 0.0201) and 9–12 years for males (p = 0.0008). Hip flexors, dorsiflexors, hip extensors and knee extensors explained the highest percentage of variance (R2 = 0.897, p < 0.0001) in the total lower limb strength. Conclusion Our findings show that lower limb isometric strength in Chilean schoolchildren and adolescents increases from age 10, with boys outperforming girls by age 15. Hip flexors mainly explain total strength, offering a useful reference to detect within and between subject strength deficits.
bibliographic citation: Bustos-Moyano et al. (2026) Isometric muscle strength profile of lower limbs for children and adolescents between 7 and 15 years of age. PeerJ 14:e20799 https://doi.org/10.7717/peerj.20799
date submitted: 2025-04-17
date accepted: 2025-12-24
issued: 2026-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bustos-Moyano
  given name: Oscar
author list: Agent
  family name: Guzmán-Muñoz
  given name: Eduardo
author list: Agent
  family name: Valdes-Badilla
  given name: Pablo
author list: Agent
  family name: Frugone-Zaror
  given name: Diego
author list: Agent
  family name: Miño-Cornejo
  given name: Flor
author list: Agent
  family name: Araya-Quintanilla
  given name: Felipe
author list: Agent
  family name: Mendez-Rebolledo
  given name: Guillermo
doi: 10.7717/peerj.20799
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-23
copyright: ©2026 Bustos-Moyano et al.
attribution name: Bustos-Moyano et al.

Comparative analysis of carotenoid accumulation during the flowering period in three Coreopsis tinctoria cultivars with different petal colors
type: item
type: AcademicArticle
description: Coreopsis tinctoria Nutt., known for its vibrant flower colors, possesses significant ornamental and medicinal value, making it a highly promising medicinal flower variety. It is widely favored by consumers as a health tea, with flower color being a crucial quality factor. The growth indicators and pigment content during the flow-ering period were determined in three C. tinctoria cultivars exhibiting different petal colors: ‘JS’ (entirely golden yellow), ‘LS’ (golden yellow tops with reddish-brown bases), and ‘MS’ (entirely reddish-brown). Additionally, a comparative metabolomic analysis of carotenoid metabolites was conducted. The results showed that the three C. tinctoria cultivars exhibited distinct differences in flower phenotypes and growth characteristics. For example, plant height and stem diameter significantly differed among ‘JS’, ‘LS’, and ‘MS’ at various flowering stages. The total carotenoid content of ‘JS’, ‘LS’, and ‘MS’ was mainly concentrated in the early flowering stage (S2), full flowering stage (S3) and late flowering stage (S4), with significant differences observed. ‘LS’ and ‘JS’ reached their highest total carotenoid content in stages S3 and S4, respectively. Analysis revealed 58 carotenoid metabolites (seven carotenes and 51 xanthophylls) with abundances that varied significantly by flower color and developmental stage. Of these, 12 metabolites (two carotenes and 10 xanthophylls) were significantly enriched in the carotenoid pathway and exhibited notably high accumulation during the S2 and S3 stages, suggesting their important role in petal coloration variation. This study provides a theoretical basis for understanding the flower color mechanism of C. tinctoria and lays a foundation for the extraction and utilization of its active components.
format: application/pdf
format: text/html
creator: Shuaijie Gao
creator: Hong Jiang
creator: Zhiyuan Li
creator: Yong Qin
subject: Biotechnology
subject: Developmental Biology
subject: Plant Science
subject: Synthetic Biology
description: doi:10.7717/peerj.20721
publisher: PeerJ Inc.
rights: © 2026 Gao et al.
abstract: Coreopsis tinctoria Nutt., known for its vibrant flower colors, possesses significant ornamental and medicinal value, making it a highly promising medicinal flower variety. It is widely favored by consumers as a health tea, with flower color being a crucial quality factor. The growth indicators and pigment content during the flow-ering period were determined in three C. tinctoria cultivars exhibiting different petal colors: ‘JS’ (entirely golden yellow), ‘LS’ (golden yellow tops with reddish-brown bases), and ‘MS’ (entirely reddish-brown). Additionally, a comparative metabolomic analysis of carotenoid metabolites was conducted. The results showed that the three C. tinctoria cultivars exhibited distinct differences in flower phenotypes and growth characteristics. For example, plant height and stem diameter significantly differed among ‘JS’, ‘LS’, and ‘MS’ at various flowering stages. The total carotenoid content of ‘JS’, ‘LS’, and ‘MS’ was mainly concentrated in the early flowering stage (S2), full flowering stage (S3) and late flowering stage (S4), with significant differences observed. ‘LS’ and ‘JS’ reached their highest total carotenoid content in stages S3 and S4, respectively. Analysis revealed 58 carotenoid metabolites (seven carotenes and 51 xanthophylls) with abundances that varied significantly by flower color and developmental stage. Of these, 12 metabolites (two carotenes and 10 xanthophylls) were significantly enriched in the carotenoid pathway and exhibited notably high accumulation during the S2 and S3 stages, suggesting their important role in petal coloration variation. This study provides a theoretical basis for understanding the flower color mechanism of C. tinctoria and lays a foundation for the extraction and utilization of its active components.
bibliographic citation: Gao et al. (2026) Comparative analysis of carotenoid accumulation during the flowering period in three Coreopsis tinctoria cultivars with different petal colors. PeerJ 14:e20721 https://doi.org/10.7717/peerj.20721
date submitted: 2025-08-12
date accepted: 2025-12-11
issued: 2026-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Shuaijie
author list: Agent
  family name: Jiang
  given name: Hong
author list: Agent
  family name: Li
  given name: Zhiyuan
author list: Agent
  family name: Qin
  given name: Yong
doi: 10.7717/peerj.20721
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-23
copyright: ©2026 Gao et al.
attribution name: Gao et al.

Evaluating multiple stability methods to screen bread wheat genotypes (F7 generation) under drought-stressed environments
type: item
type: AcademicArticle
description: Wheat, as a staple food crop, faces productivity challenges under diverse environmental conditions, particularly in semi-arid regions. Enhancing genotype performance and stability across multiple environments is essential for sustainable wheat production and food security. This study aimed to evaluate the grain yield performance and stability of 165 F7 wheat genotypes, along with four check cultivars, across four agro-ecologically distinct environments: Karaj, Zarghan, Kermanshah, and Nishapur, with the latter representing drought-prone conditions. The genetic materials used were derived from both local germplasm and International Maize and Wheat Improvement Center; “Centro Internacional de Mejoramiento de Maíz y Trigo” (CIMMYT) sources, ensuring a wide genetic base and reflecting the benefits of international collaboration in crop improvement. A combination of univariate and multivariate stability analyses, including combined-analysis of variance (ANOVA), the additive main effects and multiplicative interaction (AMMI) and genotype and genotype × environment interaction (GGE) model heatmap-clustering, and correlation plots, was conducted to explore the genotype-by-environment interactions (GEI). An R-based script was developed and introduced to facilitate reproducible and efficient computation of these stability models (Supplementary Materials). The ANOVA revealed significant genotype-by-environment interaction (GEI) effects, highlighting the necessity for robust statistical approaches. AMMI analysis showed that the first two interaction principal components (IPCA1 and IPCA2) accounted for over 83% of the interaction variance, effectively capturing differential genotype responses. Genotypes G48, G46, and G122 were consistently high-yielding and stable across all environments. Local genotypes demonstrated broad adaptability, while CIMMYT-derived lines exhibited superior performance under drought conditions, especially in Nishapur. This study demonstrates the utility …
format: application/pdf
format: text/html
creator: Armin Saed-Moucheshi
creator: Shahryar Sasani
creator: Farshad Bakhtiar
creator: Davod Roodi
creator: Shokoofeh Sarikhani Khorami
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20505
publisher: PeerJ Inc.
rights: © 2026 Saed-Moucheshi et al.
abstract: Wheat, as a staple food crop, faces productivity challenges under diverse environmental conditions, particularly in semi-arid regions. Enhancing genotype performance and stability across multiple environments is essential for sustainable wheat production and food security. This study aimed to evaluate the grain yield performance and stability of 165 F7 wheat genotypes, along with four check cultivars, across four agro-ecologically distinct environments: Karaj, Zarghan, Kermanshah, and Nishapur, with the latter representing drought-prone conditions. The genetic materials used were derived from both local germplasm and International Maize and Wheat Improvement Center; “Centro Internacional de Mejoramiento de Maíz y Trigo” (CIMMYT) sources, ensuring a wide genetic base and reflecting the benefits of international collaboration in crop improvement. A combination of univariate and multivariate stability analyses, including combined-analysis of variance (ANOVA), the additive main effects and multiplicative interaction (AMMI) and genotype and genotype × environment interaction (GGE) model heatmap-clustering, and correlation plots, was conducted to explore the genotype-by-environment interactions (GEI). An R-based script was developed and introduced to facilitate reproducible and efficient computation of these stability models (Supplementary Materials). The ANOVA revealed significant genotype-by-environment interaction (GEI) effects, highlighting the necessity for robust statistical approaches. AMMI analysis showed that the first two interaction principal components (IPCA1 and IPCA2) accounted for over 83% of the interaction variance, effectively capturing differential genotype responses. Genotypes G48, G46, and G122 were consistently high-yielding and stable across all environments. Local genotypes demonstrated broad adaptability, while CIMMYT-derived lines exhibited superior performance under drought conditions, especially in Nishapur. This study demonstrates the utility …
bibliographic citation: Saed-Moucheshi et al. (2026) Evaluating multiple stability methods to screen bread wheat genotypes (F7 generation) under drought-stressed environments. PeerJ 14:e20505 https://doi.org/10.7717/peerj.20505
date submitted: 2025-04-23
date accepted: 2025-11-10
issued: 2026-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saed-Moucheshi
  given name: Armin
author list: Agent
  family name: Sasani
  given name: Shahryar
author list: Agent
  family name: Bakhtiar
  given name: Farshad
author list: Agent
  family name: Roodi
  given name: Davod
author list: Agent
  family name: Sarikhani Khorami
  given name: Shokoofeh
doi: 10.7717/peerj.20505
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-23
copyright: ©2026 Saed-Moucheshi et al.
attribution name: Saed-Moucheshi et al.

Metabarcoding and targeted barcoding can enhance Norwegian Continental Shelf macrofauna species inventories
type: item
type: AcademicArticle
description: Metabarcoding of bulk community samples is a powerful tool to characterize marine softbottom macrofaunal communities, but high-quality taxonomic assignment is dependent on adequate sequence coverage in taxonomic databases. Here, our main aim was to advance metabarcoding as a complement to benthic morphological taxonomy in biodiversity inventories on the Norwegian Continental Shelf (NCS). We used morphological taxonomy, barcoding, and metabarcoding for two objectives, namely to (1) increase macrofauna barcode coverage for a selection of species, and (2) provide an in-depth comparison of morphology and metabarcoding data from mock bulk samples of softbottom macrofauna. We used morphological taxonomy to identify 257 morphotaxa from 32 sieved grab sampling stations at eight areas on the NCS. For the first objective (barcoding), 45 species (95 specimens) were selected from these 32 stations based on incomplete sequence coverage in online repositories, obtaining barcodes for 25 (cytochrome oxidase subunit 1, COI), 35 (18S rDNA), and 24 (28S rDNA) species. Results typically showed an increase in taxonomic assignment of 4–5 ranks in the subsequent metabarcoding data for these particular species. For the second objective (metabarcoding), mock bulk samples with a known taxonomic composition including Annelida, Arthropoda, Mollusca and a single brachiopod, were sequenced using the COI and 18S rDNA V1-V2 partitions from a subset of eight stations from three of the areas. COI Barcode of Life Data System (BOLD) and MIDORI2 assignment with some additional manual sequence curation recovered 100 distinct species-rank taxa compared to 120 species-rank taxa (152 taxa total) from morphology based taxonomic identification. Assignment of 18S rDNA using SILVA recovered 29 unique species including 13 not found in the COI data. Annelida, Arthropoda, and Mollusca were all well-represented in metabarcoding data, and abundance biases were associated with disparate species in a range of clades.…
format: application/pdf
format: text/html
creator: Jon T. Hestetun
creator: Anders Lanzén
creator: Jon Anders Kongsrud
creator: Tom Alvestad
creator: Per-Otto Johansen
creator: Thomas G. Dahlgren
subject: Biodiversity
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.20849
publisher: PeerJ Inc.
rights: © 2026 Hestetun et al.
abstract: Metabarcoding of bulk community samples is a powerful tool to characterize marine softbottom macrofaunal communities, but high-quality taxonomic assignment is dependent on adequate sequence coverage in taxonomic databases. Here, our main aim was to advance metabarcoding as a complement to benthic morphological taxonomy in biodiversity inventories on the Norwegian Continental Shelf (NCS). We used morphological taxonomy, barcoding, and metabarcoding for two objectives, namely to (1) increase macrofauna barcode coverage for a selection of species, and (2) provide an in-depth comparison of morphology and metabarcoding data from mock bulk samples of softbottom macrofauna. We used morphological taxonomy to identify 257 morphotaxa from 32 sieved grab sampling stations at eight areas on the NCS. For the first objective (barcoding), 45 species (95 specimens) were selected from these 32 stations based on incomplete sequence coverage in online repositories, obtaining barcodes for 25 (cytochrome oxidase subunit 1, COI), 35 (18S rDNA), and 24 (28S rDNA) species. Results typically showed an increase in taxonomic assignment of 4–5 ranks in the subsequent metabarcoding data for these particular species. For the second objective (metabarcoding), mock bulk samples with a known taxonomic composition including Annelida, Arthropoda, Mollusca and a single brachiopod, were sequenced using the COI and 18S rDNA V1-V2 partitions from a subset of eight stations from three of the areas. COI Barcode of Life Data System (BOLD) and MIDORI2 assignment with some additional manual sequence curation recovered 100 distinct species-rank taxa compared to 120 species-rank taxa (152 taxa total) from morphology based taxonomic identification. Assignment of 18S rDNA using SILVA recovered 29 unique species including 13 not found in the COI data. Annelida, Arthropoda, and Mollusca were all well-represented in metabarcoding data, and abundance biases were associated with disparate species in a range of clades.…
bibliographic citation: Hestetun et al. (2026) Metabarcoding and targeted barcoding can enhance Norwegian Continental Shelf macrofauna species inventories. PeerJ 14:e20849 https://doi.org/10.7717/peerj.20849
date submitted: 2025-08-15
date accepted: 2026-01-05
issued: 2026-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hestetun
  given name: Jon T.
author list: Agent
  family name: Lanzén
  given name: Anders
author list: Agent
  family name: Kongsrud
  given name: Jon Anders
author list: Agent
  family name: Alvestad
  given name: Tom
author list: Agent
  family name: Johansen
  given name: Per-Otto
author list: Agent
  family name: Dahlgren
  given name: Thomas G.
doi: 10.7717/peerj.20849
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-20
copyright: ©2026 Hestetun et al.
attribution name: Hestetun et al.

Using deep learning to predict tyrosinase inhibitors for treating hyperpigmentation disorders
type: item
type: AcademicArticle
description: Background In recent years, skin health has garnered widespread attention, with hyperpigmentation disorders caused by excessive melanin deposition emerging as a particularly prominent concern. Tyrosinase, as the rate-limiting enzyme in the melanin synthesis process, has long been a major focus in the development of its inhibitors. However, only a limited number of tyrosinase inhibitors are currently available for clinical treatment of such disorders, and they are associated with certain toxicity concerns. Consequently, there is an urgent need to develop novel inhibitors that combine high efficacy with low toxicity. Recent studies have shown that deep learning technology exhibits strong capabilities in uncovering the intrinsic patterns of data and predicting the biological activities of compounds, providing a significant opportunity for the rapid screening of novel tyrosinase inhibitors. Methods Based on a dataset of tyrosinase-related compounds, this study constructed a deep learning model to predict compounds that inhibit tyrosinase activity. Using this model, we conducted activity predictions for 36,585 compound and selected the top 100 molecules with the highest prediction scores for screening and verification. Results Literature comparison revealed that 53 of these molecules had been reported to inhibit tyrosinase activity, providing initial support for the model’s reliability. After further screening based on specific criteria, 10 candidate molecules were ultimately selected for molecular docking studies. The docking results indicated that these molecules had good binding potential with the target protein, indirectly supporting the accuracy of the model’s prediction. The final experimental verification revealed that compounds 5 and 10 significantly inhibited tyrosinase activity and reduced melanin content.
format: application/pdf
format: text/html
creator: RenHui Wu
creator: MengMeng Yang
creator: TianChi Wu
creator: RongZhen Li
creator: Yuhui Wang
creator: XiaoTian Xu
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Dermatology
subject: Pharmacology
description: doi:10.7717/peerj.20845
publisher: PeerJ Inc.
rights: © 2026 Wu et al.
abstract: Background In recent years, skin health has garnered widespread attention, with hyperpigmentation disorders caused by excessive melanin deposition emerging as a particularly prominent concern. Tyrosinase, as the rate-limiting enzyme in the melanin synthesis process, has long been a major focus in the development of its inhibitors. However, only a limited number of tyrosinase inhibitors are currently available for clinical treatment of such disorders, and they are associated with certain toxicity concerns. Consequently, there is an urgent need to develop novel inhibitors that combine high efficacy with low toxicity. Recent studies have shown that deep learning technology exhibits strong capabilities in uncovering the intrinsic patterns of data and predicting the biological activities of compounds, providing a significant opportunity for the rapid screening of novel tyrosinase inhibitors. Methods Based on a dataset of tyrosinase-related compounds, this study constructed a deep learning model to predict compounds that inhibit tyrosinase activity. Using this model, we conducted activity predictions for 36,585 compound and selected the top 100 molecules with the highest prediction scores for screening and verification. Results Literature comparison revealed that 53 of these molecules had been reported to inhibit tyrosinase activity, providing initial support for the model’s reliability. After further screening based on specific criteria, 10 candidate molecules were ultimately selected for molecular docking studies. The docking results indicated that these molecules had good binding potential with the target protein, indirectly supporting the accuracy of the model’s prediction. The final experimental verification revealed that compounds 5 and 10 significantly inhibited tyrosinase activity and reduced melanin content.
bibliographic citation: Wu et al. (2026) Using deep learning to predict tyrosinase inhibitors for treating hyperpigmentation disorders. PeerJ 14:e20845 https://doi.org/10.7717/peerj.20845
date submitted: 2025-09-18
date accepted: 2026-01-05
issued: 2026-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: RenHui
author list: Agent
  family name: Yang
  given name: MengMeng
author list: Agent
  family name: Wu
  given name: TianChi
author list: Agent
  family name: Li
  given name: RongZhen
author list: Agent
  family name: Wang
  given name: Yuhui
author list: Agent
  family name: Xu
  given name: XiaoTian
doi: 10.7717/peerj.20845
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-20
copyright: ©2026 Wu et al.
attribution name: Wu et al.

Poly(ADP-ribose) polymerase (PARP) inhibitors in cardiovascular, and cerebrovascular diseases: mechanisms, current trends and challenge for clinical translation
type: item
type: AcademicArticle
description: Poly(ADP-ribose) polymerase (PARP) inhibitors constitute the inaugural targeted therapy shown to enhance the prognosis of individuals with hereditary tumors, initially utilized in the management of patients with germline BRCA1/2-associated breast cancer. With ongoing research, PARP inhibitors (PARPi) are currently under extensive investigation for their applicability across a spectrum of diseases, encompassing oncology, cardiovascular diseases, and cerebrovascular diseases. This narrative review provides a comprehensive synthesis of the biological rationale, existing evidence, recent advancements, and prospective future directions of PARPi in the treatment of cancers, cardiovascular diseases, and cerebrovascular disorders. We provide a comprehensive overview of the recent advancements, advantages, and limitations associated with both clinically approved and investigational PARPi. Beyond their application in oncology, PARPi demonstrate significant potential in other therapeutic domains, including cardiovascular diseases. As our comprehension of the biological functions of PARP and its molecular mechanisms advances, it is anticipated that the therapeutic applications of these inhibitors will broaden considerably. Future research endeavors should prioritize the identification of predictive biomarkers across various diseases and the development of strategies to circumvent drug resistance. Consequently, the integration of fundamental and clinical research on PARPi across diverse diseases is essential to establish a foundational framework for clinical translation.
format: application/pdf
format: text/html
creator: Jinlin Fan
creator: Yanfangfei Song
subject: Biochemistry
subject: Cardiology
subject: Clinical Trials
subject: Drugs and Devices
subject: Oncology
description: doi:10.7717/peerj.20842
publisher: PeerJ Inc.
rights: © 2026 Fan and Song
abstract: Poly(ADP-ribose) polymerase (PARP) inhibitors constitute the inaugural targeted therapy shown to enhance the prognosis of individuals with hereditary tumors, initially utilized in the management of patients with germline BRCA1/2-associated breast cancer. With ongoing research, PARP inhibitors (PARPi) are currently under extensive investigation for their applicability across a spectrum of diseases, encompassing oncology, cardiovascular diseases, and cerebrovascular diseases. This narrative review provides a comprehensive synthesis of the biological rationale, existing evidence, recent advancements, and prospective future directions of PARPi in the treatment of cancers, cardiovascular diseases, and cerebrovascular disorders. We provide a comprehensive overview of the recent advancements, advantages, and limitations associated with both clinically approved and investigational PARPi. Beyond their application in oncology, PARPi demonstrate significant potential in other therapeutic domains, including cardiovascular diseases. As our comprehension of the biological functions of PARP and its molecular mechanisms advances, it is anticipated that the therapeutic applications of these inhibitors will broaden considerably. Future research endeavors should prioritize the identification of predictive biomarkers across various diseases and the development of strategies to circumvent drug resistance. Consequently, the integration of fundamental and clinical research on PARPi across diverse diseases is essential to establish a foundational framework for clinical translation.
bibliographic citation: Fan et al. (2026) Poly(ADP-ribose) polymerase (PARP) inhibitors in cardiovascular, and cerebrovascular diseases: mechanisms, current trends and challenge for clinical translation. PeerJ 14:e20842 https://doi.org/10.7717/peerj.20842
date submitted: 2025-09-11
date accepted: 2026-01-05
issued: 2026-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Jinlin
author list: Agent
  family name: Song
  given name: Yanfangfei
doi: 10.7717/peerj.20842
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-20
copyright: © 2026 Fan and Song
attribution name: Fan and Song

Anti-oncogenic and immunological functions of ATP23 in CMS4 colon adenocarcinoma based on a machine learning computational framework
type: item
type: AcademicArticle
description: Background Consensus Molecular Subtype (CMS) 4 and BRAF mutations are poor prognostic indicators for colon adenocarcinoma (COAD). Although the prevalence of BRAF-mutated COAD is higher in the CMS1 subtype, we have identified certain cases of CMS4 subtypes in patients with BRAF mutations. However, there is currently a lack of research exploring whether this particular type of COAD exhibits a worse prognosis and unraveling its underlying mechanism. Methods This retrospective study analyzed the transcriptome profiles and clinical parameters of COAD patients from six public datasets. Kaplan–Meier plots and bioinformatics methods predicted the correlation between ATP23 expression and patient survival. We compared enriched pathways, genomic mutations, immune cell infiltration, copy number alterations, cell–cell communication, and TIDE scores between ATP23-high and ATP23-low groups. Furthermore, in vitro experiments verified the potential roles of ATP23 in COAD. Results The expression of ATP23 was significantly lower in tumor tissues, particularly in the CMS4 subtype. No significant correlation was observed between ATP23 expression and clinical characteristics or molecular mutations in COAD. Higher ATP23 levels were associated with improved survival rates in COAD patients. In vitro experiments indicated that ATP23 inhibits the proliferation, migration, and invasion capabilities of COAD cells. Moreover, decreased ATP23 expression may impair oxidative phosphorylation in T cells, contributing to the formation of an immune-evasive microenvironment, and potentially leading to reduced efficacy of both immunotherapy and conventional chemotherapy. Conclusions ATP23 is a potential prognostic marker for COAD patients. Reduced ATP23 expression may inhibit oxidative phosphorylation in T cells and contribute to the formation of an immunosuppressive microenvironment.
format: application/pdf
format: text/html
creator: Yafei Yin
creator: Huimin Zhang
creator: Shuai Li
creator: Ruru Gu
creator: Jian Wang
creator: Zhen Zhang
creator: Juntao Sun
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.20838
publisher: PeerJ Inc.
rights: © 2026 Yin et al.
abstract: Background Consensus Molecular Subtype (CMS) 4 and BRAF mutations are poor prognostic indicators for colon adenocarcinoma (COAD). Although the prevalence of BRAF-mutated COAD is higher in the CMS1 subtype, we have identified certain cases of CMS4 subtypes in patients with BRAF mutations. However, there is currently a lack of research exploring whether this particular type of COAD exhibits a worse prognosis and unraveling its underlying mechanism. Methods This retrospective study analyzed the transcriptome profiles and clinical parameters of COAD patients from six public datasets. Kaplan–Meier plots and bioinformatics methods predicted the correlation between ATP23 expression and patient survival. We compared enriched pathways, genomic mutations, immune cell infiltration, copy number alterations, cell–cell communication, and TIDE scores between ATP23-high and ATP23-low groups. Furthermore, in vitro experiments verified the potential roles of ATP23 in COAD. Results The expression of ATP23 was significantly lower in tumor tissues, particularly in the CMS4 subtype. No significant correlation was observed between ATP23 expression and clinical characteristics or molecular mutations in COAD. Higher ATP23 levels were associated with improved survival rates in COAD patients. In vitro experiments indicated that ATP23 inhibits the proliferation, migration, and invasion capabilities of COAD cells. Moreover, decreased ATP23 expression may impair oxidative phosphorylation in T cells, contributing to the formation of an immune-evasive microenvironment, and potentially leading to reduced efficacy of both immunotherapy and conventional chemotherapy. Conclusions ATP23 is a potential prognostic marker for COAD patients. Reduced ATP23 expression may inhibit oxidative phosphorylation in T cells and contribute to the formation of an immunosuppressive microenvironment.
bibliographic citation: Yin et al. (2026) Anti-oncogenic and immunological functions of ATP23 in CMS4 colon adenocarcinoma based on a machine learning computational framework. PeerJ 14:e20838 https://doi.org/10.7717/peerj.20838
date submitted: 2025-04-21
date accepted: 2026-01-05
issued: 2026-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Yafei
author list: Agent
  family name: Zhang
  given name: Huimin
author list: Agent
  family name: Li
  given name: Shuai
author list: Agent
  family name: Gu
  given name: Ruru
author list: Agent
  family name: Wang
  given name: Jian
author list: Agent
  family name: Zhang
  given name: Zhen
author list: Agent
  family name: Sun
  given name: Juntao
doi: 10.7717/peerj.20838
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-20
copyright: ©2026 Yin et al.
attribution name: Yin et al.

A double agent? Unveiling the chemical profile of the pathogenic fungus Pyrrhoderma noxium as an endophyte in true mangroves
type: item
type: AcademicArticle
description: Pyrrhoderma noxium, commonly referred to as the brown root rot pathogen, has previously been recognized as a pathogenic species. However, it has been largely overlooked for its capability to produce useful bioactive compounds. In this study, we report for the first time that the fungus has been isolated as an endophytic fungus (EF) from the leaves of true mangrove plant species, and chemically profiled the fungal isolates to identify potential bioactive compounds. Three P. noxium isolates (AA2AA, BG3BA and SA2AA) were successfully identified via DNA barcoding and were subjected to methanolic extraction prior to chemical profiling via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Despite proximity of the host plants, our results, comprising morphological characteristics, phylogenetic analysis, and the Jaccard Similarity Index based on the detected compounds showed that AA2AA and SA2AA possess greater similarity compared to any of them with BG3BA. Compounds produced by the P. noxium isolates were classified into six main classes (i.e., amino acids and peptides, aromatics, terpenoids, phenolics, other lipids, and other alkaloids) and these compounds are believed to facilitate the equilibrium in endophyte-host interactions. According to literature, the identified compounds from the P. noxium isolates have previously been reported to possess anticancer, antioxidant, anti-inflammatory, antibacterial, antifungal, and antiviral activities, indicating significant potential for pharmaceutical applications. Besides, the chemical profiles of the P. noxium isolates determined in this study may serve as a reference for subsequent research on the biological control of P. noxium infection.
format: application/pdf
format: text/html
creator: Ming Han Han
creator: Jing Sien Chang
creator: Jen-Kit Tan
creator: Swee Keong Yeap
creator: Wei Lun Ng
creator: Yoong Soon Yong
subject: Biochemistry
subject: Biotechnology
subject: Mycology
description: doi:10.7717/peerj.20826
publisher: PeerJ Inc.
rights: © 2026 Han et al.
abstract: Pyrrhoderma noxium, commonly referred to as the brown root rot pathogen, has previously been recognized as a pathogenic species. However, it has been largely overlooked for its capability to produce useful bioactive compounds. In this study, we report for the first time that the fungus has been isolated as an endophytic fungus (EF) from the leaves of true mangrove plant species, and chemically profiled the fungal isolates to identify potential bioactive compounds. Three P. noxium isolates (AA2AA, BG3BA and SA2AA) were successfully identified via DNA barcoding and were subjected to methanolic extraction prior to chemical profiling via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Despite proximity of the host plants, our results, comprising morphological characteristics, phylogenetic analysis, and the Jaccard Similarity Index based on the detected compounds showed that AA2AA and SA2AA possess greater similarity compared to any of them with BG3BA. Compounds produced by the P. noxium isolates were classified into six main classes (i.e., amino acids and peptides, aromatics, terpenoids, phenolics, other lipids, and other alkaloids) and these compounds are believed to facilitate the equilibrium in endophyte-host interactions. According to literature, the identified compounds from the P. noxium isolates have previously been reported to possess anticancer, antioxidant, anti-inflammatory, antibacterial, antifungal, and antiviral activities, indicating significant potential for pharmaceutical applications. Besides, the chemical profiles of the P. noxium isolates determined in this study may serve as a reference for subsequent research on the biological control of P. noxium infection.
bibliographic citation: Han et al. (2026) A double agent? Unveiling the chemical profile of the pathogenic fungus Pyrrhoderma noxium as an endophyte in true mangroves. PeerJ 14:e20826 https://doi.org/10.7717/peerj.20826
date submitted: 2025-07-18
date accepted: 2025-12-30
issued: 2026-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Ming Han
author list: Agent
  family name: Chang
  given name: Jing Sien
author list: Agent
  family name: Tan
  given name: Jen-Kit
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Ng
  given name: Wei Lun
author list: Agent
  family name: Yong
  given name: Yoong Soon
doi: 10.7717/peerj.20826
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-20
copyright: ©2026 Han et al.
attribution name: Han et al.

Assessing the resilience of portable vision tests to an uncontrolled home environment
type: item
type: AcademicArticle
description: Background In ophthalmology (and medicine more widely) there is increasing interest in telemedicine: having patients perform tests at home for greater efficiency and to meet growing demand. However, despite this increased interest in vision home monitoring, many vision tests are evaluated in standardised clinical settings, not home environments. Here, we investigated the resilience of two portable contrast sensitivity tests to the sorts of potentially confounding factors that may be encountered in a home setting. Methods Normally sighted adults (n = 107) performed two contrast sensitivity tests (one pen-and-paper and one tablet-based). Testing took place in a furnished apartment, where we could control/measure various extraneous factors (including illumination, time of day, seating type, screen cleanliness). Key outcome measures were raw contrast sensitivity scores, test-retest repeatability, and test duration; and how these metrics varied with extraneous factors. Results No effect of time of day, participant motivation, or seating type was observed (all PBonferroni > 0.140). Scores on the pen-and-paper test were not affected by illumination (PBonferroni = 0.348), except when tests were conducted in extreme darkness (≤1 lux; PBonferroni = 0.036). A follow-up study indicated that screen smudging (caused by fingerprints) had no significant effect on the outcome of the tablet-based test (P = 0.573). Conclusion Taken together, the results indicate that, contrary to our expectations, both digital and pen-and-paper contrast sensitivity tests appear relatively resilient to many of the sorts of extraneous factors encountered in a home setting. This speaks to the potential viability of vision home monitoring, though study limitations and necessary future work are discussed.
format: application/pdf
format: text/html
creator: Peter F. Reddingius
creator: Mehal Rathore
creator: David P. Crabb
creator: Pete R. Jones
subject: Ophthalmology
subject: Translational Medicine
description: doi:10.7717/peerj.20657
publisher: PeerJ Inc.
rights: © 2026 Reddingius et al.
abstract: Background In ophthalmology (and medicine more widely) there is increasing interest in telemedicine: having patients perform tests at home for greater efficiency and to meet growing demand. However, despite this increased interest in vision home monitoring, many vision tests are evaluated in standardised clinical settings, not home environments. Here, we investigated the resilience of two portable contrast sensitivity tests to the sorts of potentially confounding factors that may be encountered in a home setting. Methods Normally sighted adults (n = 107) performed two contrast sensitivity tests (one pen-and-paper and one tablet-based). Testing took place in a furnished apartment, where we could control/measure various extraneous factors (including illumination, time of day, seating type, screen cleanliness). Key outcome measures were raw contrast sensitivity scores, test-retest repeatability, and test duration; and how these metrics varied with extraneous factors. Results No effect of time of day, participant motivation, or seating type was observed (all PBonferroni > 0.140). Scores on the pen-and-paper test were not affected by illumination (PBonferroni = 0.348), except when tests were conducted in extreme darkness (≤1 lux; PBonferroni = 0.036). A follow-up study indicated that screen smudging (caused by fingerprints) had no significant effect on the outcome of the tablet-based test (P = 0.573). Conclusion Taken together, the results indicate that, contrary to our expectations, both digital and pen-and-paper contrast sensitivity tests appear relatively resilient to many of the sorts of extraneous factors encountered in a home setting. This speaks to the potential viability of vision home monitoring, though study limitations and necessary future work are discussed.
bibliographic citation: Reddingius et al. (2026) Assessing the resilience of portable vision tests to an uncontrolled home environment. PeerJ 14:e20657 https://doi.org/10.7717/peerj.20657
date submitted: 2025-08-13
date accepted: 2025-12-02
issued: 2026-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reddingius
  given name: Peter F.
author list: Agent
  family name: Rathore
  given name: Mehal
author list: Agent
  family name: Crabb
  given name: David P.
author list: Agent
  family name: Jones
  given name: Pete R.
doi: 10.7717/peerj.20657
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-20
copyright: ©2026 Reddingius et al.
attribution name: Reddingius et al.

The suitability of structural soil for the development of trees growing in urban areas
type: item
type: AcademicArticle
description: Background Tree survival in urbanized areas is increasingly challenged by dense city infrastructure, including underground systems. Engineered planting systems, such as structural substrates, offer more effective solutions for tree planting in urban sites where natural soil is unavailable. This study aims to assess the physiological responses of trees to different substrates in the context of long-term growth in modified urban habitats. Methods Eight Tilia tomentosa Moench trees were planted in four substrate types: structural soil (SS), a mixture of crushed stone and soil; compacted soil (CS), simulating urban soil conditions; a mixture of soil and rubble with impermeable pavement (AS), representing harsh urban conditions; and natural soil (C), serving as the control. In the fifth and sixth years after planting, chlorophyll a fluorescence, relative chlorophyll content (Chl), and epidermal flavanols (Flv) were measured. Results The highest values Fv/Fm were observed in the control and SS samples (average Fv/Fm: 0.78–0.85), indicating good tree health, in contrast to the AS group. Energy dissipation per reaction center (DI0/RC) showed no significant differences between SS and C, except in September 2022. Indicators such as energy transfer into the electron transport chain (ET0/TR0), performance index (PIABS), and chlorophyll content declined slightly in SS compared to C, but remained higher than in AS and similar to CS. Flavanol content was lower in both the control and SS groups, suggesting no evident stress response. Conclusion This study confirms that structural soil provides favorable habitat conditions for urban trees, supporting undisturbed photosynthetic processes over the long term, comparable to natural soil. Structural substrates show strong potential as effective solutions for improving urban tree soil conditions, particularly in areas with soil compaction or limited root space beneath pavements. Future research should explore potential nutrient limitation…
format: application/pdf
format: text/html
creator: Joanna Kosno-Jończy
creator: Marzena Suchocka
creator: Tatiana Swoczyna
creator: Joanna Dudek-Klimiuk
creator: Żaneta Tuchowska
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.20407
publisher: PeerJ Inc.
rights: © 2026 Kosno-Jończy et al.
abstract: Background Tree survival in urbanized areas is increasingly challenged by dense city infrastructure, including underground systems. Engineered planting systems, such as structural substrates, offer more effective solutions for tree planting in urban sites where natural soil is unavailable. This study aims to assess the physiological responses of trees to different substrates in the context of long-term growth in modified urban habitats. Methods Eight Tilia tomentosa Moench trees were planted in four substrate types: structural soil (SS), a mixture of crushed stone and soil; compacted soil (CS), simulating urban soil conditions; a mixture of soil and rubble with impermeable pavement (AS), representing harsh urban conditions; and natural soil (C), serving as the control. In the fifth and sixth years after planting, chlorophyll a fluorescence, relative chlorophyll content (Chl), and epidermal flavanols (Flv) were measured. Results The highest values Fv/Fm were observed in the control and SS samples (average Fv/Fm: 0.78–0.85), indicating good tree health, in contrast to the AS group. Energy dissipation per reaction center (DI0/RC) showed no significant differences between SS and C, except in September 2022. Indicators such as energy transfer into the electron transport chain (ET0/TR0), performance index (PIABS), and chlorophyll content declined slightly in SS compared to C, but remained higher than in AS and similar to CS. Flavanol content was lower in both the control and SS groups, suggesting no evident stress response. Conclusion This study confirms that structural soil provides favorable habitat conditions for urban trees, supporting undisturbed photosynthetic processes over the long term, comparable to natural soil. Structural substrates show strong potential as effective solutions for improving urban tree soil conditions, particularly in areas with soil compaction or limited root space beneath pavements. Future research should explore potential nutrient limitation…
bibliographic citation: Kosno-Jończy et al. (2026) The suitability of structural soil for the development of trees growing in urban areas. PeerJ 14:e20407 https://doi.org/10.7717/peerj.20407
date submitted: 2024-12-10
date accepted: 2025-10-27
issued: 2026-02-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kosno-Jończy
  given name: Joanna
author list: Agent
  family name: Suchocka
  given name: Marzena
author list: Agent
  family name: Swoczyna
  given name: Tatiana
author list: Agent
  family name: Dudek-Klimiuk
  given name: Joanna
author list: Agent
  family name: Tuchowska
  given name: Żaneta
doi: 10.7717/peerj.20407
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-20
copyright: ©2026 Kosno-Jończy et al.
attribution name: Kosno-Jończy et al.

Variation in zoo diets, offerings of leafy browse, and body condition scores in Matschie’s tree kangaroos (Dendrolagus matschiei) and their associations with gut microbiome composition
type: item
type: AcademicArticle
description: Recommended zoo diets for the arboreal folivore, the Matschie’s tree kangaroo (Dendrolagus matschiei; TK) were recently found to be much lower in fiber and higher in starch than wild diet items for this species. In contrast to wild animals, zoo-housed TKs are ~30–40% higher in body mass, known to suffer from infections indicating immune dysfunction, and exhibit various reproductive issues. These problems may have ties to gut microbiome dysbiosis related to differences in diet between captive and wild individuals, but to date, the microbiome of TKs has not been explored. This study aimed to (1) quantify the macronutrient intake of zoo-housed TKs and compare the intake of over-conditioned animals to those at ideal body condition, and (2) examine gut microbial communities for any differences associated with TK macronutrient intake, leafy browse offerings, or body condition. Detailed diet intake information (n = 31 individuals at 16 facilities accredited by the Association of Zoos and Aquariums) was collected for approximately 1 week at two different time points (i.e., July–September and January–March). Body condition scores were recorded by primary caregivers or veterinary staff no more than one month from each diet intake week. Fecal samples (n = 57) were collected concurrently during the diet recording weeks. We used 16S rRNA gene amplicon sequencing to examine TK gut microbiota. We found that animals assigned over-conditioned body scores consumed significantly more kilocalories compared to animals assigned an ideal body condition score. These differences were driven primarily by significantly greater crude protein and starch intake in over-conditioned TKs. TKs offered high and intermediate amounts of leafy browse exhibited substantially different fecal microbial communities compared to animals offered low or no browse. Our results indicate that formulation of diets for zoo-housed TKs, similar to other folivores, should closely resemble the macronutrient and caloric …
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format: text/html
creator: Diana C. Koester
creator: Maura R. Plocek
creator: Ellen S. Dierenfeld
creator: Katherine R. Amato
creator: Noah T. Dunham
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.20875
publisher: PeerJ Inc.
rights: © 2026 Koester et al.
abstract: Recommended zoo diets for the arboreal folivore, the Matschie’s tree kangaroo (Dendrolagus matschiei; TK) were recently found to be much lower in fiber and higher in starch than wild diet items for this species. In contrast to wild animals, zoo-housed TKs are ~30–40% higher in body mass, known to suffer from infections indicating immune dysfunction, and exhibit various reproductive issues. These problems may have ties to gut microbiome dysbiosis related to differences in diet between captive and wild individuals, but to date, the microbiome of TKs has not been explored. This study aimed to (1) quantify the macronutrient intake of zoo-housed TKs and compare the intake of over-conditioned animals to those at ideal body condition, and (2) examine gut microbial communities for any differences associated with TK macronutrient intake, leafy browse offerings, or body condition. Detailed diet intake information (n = 31 individuals at 16 facilities accredited by the Association of Zoos and Aquariums) was collected for approximately 1 week at two different time points (i.e., July–September and January–March). Body condition scores were recorded by primary caregivers or veterinary staff no more than one month from each diet intake week. Fecal samples (n = 57) were collected concurrently during the diet recording weeks. We used 16S rRNA gene amplicon sequencing to examine TK gut microbiota. We found that animals assigned over-conditioned body scores consumed significantly more kilocalories compared to animals assigned an ideal body condition score. These differences were driven primarily by significantly greater crude protein and starch intake in over-conditioned TKs. TKs offered high and intermediate amounts of leafy browse exhibited substantially different fecal microbial communities compared to animals offered low or no browse. Our results indicate that formulation of diets for zoo-housed TKs, similar to other folivores, should closely resemble the macronutrient and caloric …
bibliographic citation: Koester et al. (2026) Variation in zoo diets, offerings of leafy browse, and body condition scores in Matschie’s tree kangaroos (Dendrolagus matschiei) and their associations with gut microbiome composition. PeerJ 14:e20875 https://doi.org/10.7717/peerj.20875
date submitted: 2025-04-22
date accepted: 2026-01-12
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koester
  given name: Diana C.
author list: Agent
  family name: Plocek
  given name: Maura R.
author list: Agent
  family name: Dierenfeld
  given name: Ellen S.
author list: Agent
  family name: Amato
  given name: Katherine R.
author list: Agent
  family name: Dunham
  given name: Noah T.
doi: 10.7717/peerj.20875
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: © 2026 Koester et al.
attribution name: Koester et al.

Serum docosahexaenoic acid as a predictor of hospital readmission in chronic obstructive pulmonary disease exacerbation: a retrospective cohort study
type: item
type: AcademicArticle
description: Background The beneficial effects of omega-3 fatty acids for patients with chronic obstructive pulmonary disease (COPD) had been observed, including attenuating lung function decline and reducing their respiratory symptom burdens. However, the impact of omega-3 fatty acids on COPD exacerbation-related outcomes remains unclear. This study aimed to evaluate whether reduced serum omega-3 fatty acid levels are associated with a higher risk of future hospital readmission due to COPD exacerbation (ECOPD). Methods This retrospective cohort study included 88 patients hospitalized for ECOPD between April 2017 and March 2018. Clinical data were collected, and serum omega-3 fatty acid levels were analyzed using liquid chromatography-mass spectrometry (LC-MS). All patients were followed up for a median period of 53.5 months and categorized into two groups based on whether they experienced ECOPD-related readmission during the follow-up period. The clinical characteristics and serum levels of omega-3 fatty acid levels, including docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), between the two groups were compared. Additionally, patients were categorized into low and high DHA groups based on the median DHA level, and the association between DHA level and ECOPD-related readmission rate was analyzed using a Cox regression model. Result Patients who experienced ECOPD-related readmission during the follow-up period (n = 36) had lower serum levels of DHA than those who did not experience readmission. The serum levels of EPA did not significantly differ between groups. Kaplan–Meier curve showed that patients in the low-DHA group exhibited a significantly higher ECOPD-related readmission rate compared to those in the high-DHA group (log-rank p = 0.023). Multivariable Cox regression analysis identified low DHA level as an independent risk factor for ECOPD-related readmission. A nomogram based on DHA levels demonstrated good predictive performance. Conclusion A low DHA level ser…
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format: text/html
creator: Qiqiang Zhou
creator: Yating Wang
creator: Chun Chang
creator: Xiaoyan Gai
creator: Yahong Chen
creator: Ying Liang
creator: Yongchang Sun
subject: Biochemistry
subject: Internal Medicine
subject: Respiratory Medicine
description: doi:10.7717/peerj.20865
publisher: PeerJ Inc.
rights: © 2026 Zhou et al.
abstract: Background The beneficial effects of omega-3 fatty acids for patients with chronic obstructive pulmonary disease (COPD) had been observed, including attenuating lung function decline and reducing their respiratory symptom burdens. However, the impact of omega-3 fatty acids on COPD exacerbation-related outcomes remains unclear. This study aimed to evaluate whether reduced serum omega-3 fatty acid levels are associated with a higher risk of future hospital readmission due to COPD exacerbation (ECOPD). Methods This retrospective cohort study included 88 patients hospitalized for ECOPD between April 2017 and March 2018. Clinical data were collected, and serum omega-3 fatty acid levels were analyzed using liquid chromatography-mass spectrometry (LC-MS). All patients were followed up for a median period of 53.5 months and categorized into two groups based on whether they experienced ECOPD-related readmission during the follow-up period. The clinical characteristics and serum levels of omega-3 fatty acid levels, including docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), between the two groups were compared. Additionally, patients were categorized into low and high DHA groups based on the median DHA level, and the association between DHA level and ECOPD-related readmission rate was analyzed using a Cox regression model. Result Patients who experienced ECOPD-related readmission during the follow-up period (n = 36) had lower serum levels of DHA than those who did not experience readmission. The serum levels of EPA did not significantly differ between groups. Kaplan–Meier curve showed that patients in the low-DHA group exhibited a significantly higher ECOPD-related readmission rate compared to those in the high-DHA group (log-rank p = 0.023). Multivariable Cox regression analysis identified low DHA level as an independent risk factor for ECOPD-related readmission. A nomogram based on DHA levels demonstrated good predictive performance. Conclusion A low DHA level ser…
bibliographic citation: Zhou et al. (2026) Serum docosahexaenoic acid as a predictor of hospital readmission in chronic obstructive pulmonary disease exacerbation: a retrospective cohort study. PeerJ 14:e20865 https://doi.org/10.7717/peerj.20865
date submitted: 2025-09-24
date accepted: 2026-01-08
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Qiqiang
author list: Agent
  family name: Wang
  given name: Yating
author list: Agent
  family name: Chang
  given name: Chun
author list: Agent
  family name: Gai
  given name: Xiaoyan
author list: Agent
  family name: Chen
  given name: Yahong
author list: Agent
  family name: Liang
  given name: Ying
author list: Agent
  family name: Sun
  given name: Yongchang
doi: 10.7717/peerj.20865
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Zhou et al.
attribution name: Zhou et al.

Analysis of the long-term solubility and phases of five different root canal sealers in phosphate buffered saline: an in vitro study
type: item
type: AcademicArticle
description: Background The long-term success of root canal therapy depends substantially on the physicochemical stability of endodontic sealers, particularly their solubility and the development of stable crystalline phases during setting. Tricalcium silicate-based sealers (TSBSs) have shown promising biological properties, yet their reported solubility profiles remain inconsistent, raising concerns regarding degradation, gap formation, and the potential for periapical irritation. This study evaluated and compared the solubility and crystalline phase evolution of five commercially available root canal sealers immersed in phosphate-buffered saline (PBS) over extended time intervals. Methods Twenty-five disc-shaped specimens (n = 5 per material) were prepared using AH Plus Bioceramic (AHPBC), AH Plus (AHP), Ceraseal (CS), BioRoot RCS (BRCS), and MTA Fillapex (MTAF). Solubility was assessed gravimetrically after immersion in PBS for 24 h, 28 days, and 6 months. Phase analysis was performed at each interval using X-ray diffraction (XRD) to identify changes in crystallinity. Results The solubility values varied markedly among the materials and increased over time for most groups. AHP consistently demonstrated the lowest solubility across all intervals, whereas MTAF and BRCS presented the highest values. XRD analysis revealed distinct crystalline phase patterns for each sealer. AHPBC and CS maintained relatively stable crystalline structures throughout the study period. In contrast, BRCS and MTAF exhibited noticeable fluctuations, and AHP showed high crystallinity initially and after 6 months, indicating greater structural stability. Conclusion AHP displayed the most favourable physicochemical stability, with minimal solubility and sustained crystallinity. AHPBC and CS also demonstrated stable long-term behaviour, whereas BRCS and MTAF showed greater solubility and structural changes. These findings suggest limitations in the long-term durability of these materials. These findings un…
format: application/pdf
format: text/html
creator: Bridhi Jalan
creator: Karthik Shetty
creator: Vasavi Kumblekar
creator: Roma M
creator: Heeresh Shetty
subject: Dentistry
description: doi:10.7717/peerj.20853
publisher: PeerJ Inc.
rights: © 2026 Jalan et al.
abstract: Background The long-term success of root canal therapy depends substantially on the physicochemical stability of endodontic sealers, particularly their solubility and the development of stable crystalline phases during setting. Tricalcium silicate-based sealers (TSBSs) have shown promising biological properties, yet their reported solubility profiles remain inconsistent, raising concerns regarding degradation, gap formation, and the potential for periapical irritation. This study evaluated and compared the solubility and crystalline phase evolution of five commercially available root canal sealers immersed in phosphate-buffered saline (PBS) over extended time intervals. Methods Twenty-five disc-shaped specimens (n = 5 per material) were prepared using AH Plus Bioceramic (AHPBC), AH Plus (AHP), Ceraseal (CS), BioRoot RCS (BRCS), and MTA Fillapex (MTAF). Solubility was assessed gravimetrically after immersion in PBS for 24 h, 28 days, and 6 months. Phase analysis was performed at each interval using X-ray diffraction (XRD) to identify changes in crystallinity. Results The solubility values varied markedly among the materials and increased over time for most groups. AHP consistently demonstrated the lowest solubility across all intervals, whereas MTAF and BRCS presented the highest values. XRD analysis revealed distinct crystalline phase patterns for each sealer. AHPBC and CS maintained relatively stable crystalline structures throughout the study period. In contrast, BRCS and MTAF exhibited noticeable fluctuations, and AHP showed high crystallinity initially and after 6 months, indicating greater structural stability. Conclusion AHP displayed the most favourable physicochemical stability, with minimal solubility and sustained crystallinity. AHPBC and CS also demonstrated stable long-term behaviour, whereas BRCS and MTAF showed greater solubility and structural changes. These findings suggest limitations in the long-term durability of these materials. These findings un…
bibliographic citation: Jalan et al. (2026) Analysis of the long-term solubility and phases of five different root canal sealers in phosphate buffered saline: an in vitro study. PeerJ 14:e20853 https://doi.org/10.7717/peerj.20853
date submitted: 2025-10-27
date accepted: 2026-01-05
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jalan
  given name: Bridhi
author list: Agent
  family name: Shetty
  given name: Karthik
author list: Agent
  family name: Kumblekar
  given name: Vasavi
author list: Agent
  family name: M
  given name: Roma
author list: Agent
  family name: Shetty
  given name: Heeresh
doi: 10.7717/peerj.20853
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Jalan et al.
attribution name: Jalan et al.

Hippocampal expression of Wnt7a and β-catenin in depression: evidence from chronic unpredictable mild stress
type: item
type: AcademicArticle
description: This study sought to examine the impact of Wnt7a/β-catenin signaling on depressive-like behaviors by using a rodent model subjected to chronic unpredictable mild stress (CUMS). Hippocampal Wnt7a and β-catenin expression levels were analyzed to investigate their mechanistic involvement in depression. Therefore, 20 male Sprague-Dawley rats were randomly allocated to the control or the CUMS experimental groups. The CUMS group underwent a 30-day stress protocol involving randomized stimuli. This study was authorized by the Ethics Committee (approval no. YXLL2022006). Following model establishment, depression-related behavioral phenotypes were quantitatively evaluated using standardized behavioral paradigms, the sucrose preference test (SPT), and the open field test (OFT), targeting core symptom domains such as anhedonia and alterations in locomotor activity. The morphology of hippocampal CA2 and DG area neurons was examined using hematoxylin and eosin staining, while immunofluorescence and Western blotting assessed Wnt7a and β-catenin expression. Western blotting also assessed GSK-3β and p-GSK-3β expression. Results indicated that CUMS rats showed markedly lower SPT indices (P < 0.05) and decreased OFT parameters (total distance traveled, central zone activity, speed, and central zone duration) versus controls (P < 0.05). Notably, Wnt7a, β-catenin, GSK-3β, and p-GSK-3β were significantly upregulated in the hippocampal tissues of rats in CUMS group (P < 0.05). Collectively, this study found that CUMS-induced depression is associated with a significant upregulation of hippocampal Wnt7a, β-catenin, and GSK-3β, along with increased GSK-3β phosphorylation. This correlative evidence points to Wnt pathway activation in depression pathogenesis and warrants further mechanistic investigation.
format: application/pdf
format: text/html
creator: Zehao Zhang
creator: Jialong Huang
creator: Hongyue Yu
creator: Zi jun Ji
creator: Zijuan Ding
creator: Yiting Wang
creator: Jinyu Kang
creator: Zhen Li
creator: Zhuxin Sui
subject: Cell Biology
subject: Neurology
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20837
publisher: PeerJ Inc.
rights: © 2026 Zhang et al.
abstract: This study sought to examine the impact of Wnt7a/β-catenin signaling on depressive-like behaviors by using a rodent model subjected to chronic unpredictable mild stress (CUMS). Hippocampal Wnt7a and β-catenin expression levels were analyzed to investigate their mechanistic involvement in depression. Therefore, 20 male Sprague-Dawley rats were randomly allocated to the control or the CUMS experimental groups. The CUMS group underwent a 30-day stress protocol involving randomized stimuli. This study was authorized by the Ethics Committee (approval no. YXLL2022006). Following model establishment, depression-related behavioral phenotypes were quantitatively evaluated using standardized behavioral paradigms, the sucrose preference test (SPT), and the open field test (OFT), targeting core symptom domains such as anhedonia and alterations in locomotor activity. The morphology of hippocampal CA2 and DG area neurons was examined using hematoxylin and eosin staining, while immunofluorescence and Western blotting assessed Wnt7a and β-catenin expression. Western blotting also assessed GSK-3β and p-GSK-3β expression. Results indicated that CUMS rats showed markedly lower SPT indices (P < 0.05) and decreased OFT parameters (total distance traveled, central zone activity, speed, and central zone duration) versus controls (P < 0.05). Notably, Wnt7a, β-catenin, GSK-3β, and p-GSK-3β were significantly upregulated in the hippocampal tissues of rats in CUMS group (P < 0.05). Collectively, this study found that CUMS-induced depression is associated with a significant upregulation of hippocampal Wnt7a, β-catenin, and GSK-3β, along with increased GSK-3β phosphorylation. This correlative evidence points to Wnt pathway activation in depression pathogenesis and warrants further mechanistic investigation.
bibliographic citation: Zhang et al. (2026) Hippocampal expression of Wnt7a and β-catenin in depression: evidence from chronic unpredictable mild stress. PeerJ 14:e20837 https://doi.org/10.7717/peerj.20837
date submitted: 2025-09-24
date accepted: 2026-01-05
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Zehao
author list: Agent
  family name: Huang
  given name: Jialong
author list: Agent
  family name: Yu
  given name: Hongyue
author list: Agent
  family name: Ji
  given name: Zi jun
author list: Agent
  family name: Ding
  given name: Zijuan
author list: Agent
  family name: Wang
  given name: Yiting
author list: Agent
  family name: Kang
  given name: Jinyu
author list: Agent
  family name: Li
  given name: Zhen
author list: Agent
  family name: Sui
  given name: Zhuxin
doi: 10.7717/peerj.20837
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Zhang et al.
attribution name: Zhang et al.

Responses of leaf anatomy, growth, and physiology in backcross 1 progeny from Saccharum spp. hybrids and S. spontaneum under drought stress at early growth phase
type: item
type: AcademicArticle
description: A deeper understanding of the anatomical, physiological, and morphological responses of interspecific hybrid sugarcane to water deficit conditions could enhance the efficiency of developing drought-resistance varieties. This study aimed to investigate the responses of anatomical characteristics of backcross (BC) 1 interspecific hybrids, produced by crossing commercial cane with wild-type sugarcane, under drought and well-watered treatment. A two—factorial pot experiment in a completely randomized design (CRD) with three replications was conducted. Soil volume water contents were 12.34% prior to the start of drought treatment. Two water regimes, field capacity (FC) and drought stress (DS), were tested, with the DS treatment involving water withholding for 51 st to 110 th days after planting (DAP). Fifteen sugarcane genotypes were evaluated, including ten BC1 interspecific hybrids, two commercial varieties (F152 and UT5), the wild type (ThS98-94), the F1 interspecific hybrid male parent (F4-19), and KK3 as a drought resistance check. Anatomical, physiological, and morphological traits were measured at 110 DAP; results indicated that BC1-1-7, BC1-1-44, and BC1-1-50 exhibited superior traits than the other BC1 interspecific hybrids in this study. These genotypes had a high morphological drought resistance index (DRI) for tiller height and tiller number, and the anatomical leaf had low leaf thickness (% reduction from FC by 14.0%, 10.0% and 3.9%, respectively) and vertical length of bulliform cells (% reduction from FC by 26.2%, 23.9% and 4.9%, respectively) but high cuticle thickness (an increase from FC by 10.7%, 18.3% and 19.7%, respectively) and stomatal crypt depth (an increase from FC by 21.0%, 12.9% and 13.4%, respectively), resembling those of the wild type and F1 interspecific hybrid. Additionally, BC1-1-7 demonstrated greater drought resistance, characterized by low stomatal conductance (% reduction from FC by 90.6%), reduced transpiration rates (% reduction fr…
format: application/pdf
format: text/html
creator: Kanlayanee Wiangwiset
creator: Patcharin Songsri
creator: Nakorn Jongrungklang
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20822
publisher: PeerJ Inc.
rights: © 2026 Wiangwiset et al.
abstract: A deeper understanding of the anatomical, physiological, and morphological responses of interspecific hybrid sugarcane to water deficit conditions could enhance the efficiency of developing drought-resistance varieties. This study aimed to investigate the responses of anatomical characteristics of backcross (BC) 1 interspecific hybrids, produced by crossing commercial cane with wild-type sugarcane, under drought and well-watered treatment. A two—factorial pot experiment in a completely randomized design (CRD) with three replications was conducted. Soil volume water contents were 12.34% prior to the start of drought treatment. Two water regimes, field capacity (FC) and drought stress (DS), were tested, with the DS treatment involving water withholding for 51 st to 110 th days after planting (DAP). Fifteen sugarcane genotypes were evaluated, including ten BC1 interspecific hybrids, two commercial varieties (F152 and UT5), the wild type (ThS98-94), the F1 interspecific hybrid male parent (F4-19), and KK3 as a drought resistance check. Anatomical, physiological, and morphological traits were measured at 110 DAP; results indicated that BC1-1-7, BC1-1-44, and BC1-1-50 exhibited superior traits than the other BC1 interspecific hybrids in this study. These genotypes had a high morphological drought resistance index (DRI) for tiller height and tiller number, and the anatomical leaf had low leaf thickness (% reduction from FC by 14.0%, 10.0% and 3.9%, respectively) and vertical length of bulliform cells (% reduction from FC by 26.2%, 23.9% and 4.9%, respectively) but high cuticle thickness (an increase from FC by 10.7%, 18.3% and 19.7%, respectively) and stomatal crypt depth (an increase from FC by 21.0%, 12.9% and 13.4%, respectively), resembling those of the wild type and F1 interspecific hybrid. Additionally, BC1-1-7 demonstrated greater drought resistance, characterized by low stomatal conductance (% reduction from FC by 90.6%), reduced transpiration rates (% reduction fr…
bibliographic citation: Wiangwiset et al. (2026) Responses of leaf anatomy, growth, and physiology in backcross 1 progeny from Saccharum spp. hybrids and S. spontaneum under drought stress at early growth phase. PeerJ 14:e20822 https://doi.org/10.7717/peerj.20822
date submitted: 2024-11-22
date accepted: 2025-12-29
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiangwiset
  given name: Kanlayanee
author list: Agent
  family name: Songsri
  given name: Patcharin
author list: Agent
  family name: Jongrungklang
  given name: Nakorn
doi: 10.7717/peerj.20822
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Wiangwiset et al.
attribution name: Wiangwiset et al.

Heatstroke knowledge and predictors among Hajj health volunteers in Saudi Arabia: a cross-sectional study
type: item
type: AcademicArticle
description: Background Heatstroke is a life-threatening condition resulting from prolonged exposure to high temperatures or intense physical activity, especially during the summer. Pilgrims performing Hajj are particularly vulnerable because of factors such as advanced age, chronic health conditions, and failure to follow safety guidelines. Health volunteers play a key role in prevention and response. Aim This study aimed to assess health volunteers’ knowledge and identify predictors of such knowledge. Methods A cross-sectional study was conducted among 772 health volunteers during Hajj 2024 in Saudi Arabia. A self-designed questionnaire was developed and utilized to assess participants’ knowledge of heatstroke and to identify predictors of such knowledge. Data were collected electronically and analyzed via Jeffrey’s Amazing Statistics Program (JASP). Results Analysis revealed that (n = 576) 74.6% of health volunteers had satisfactory heatstroke knowledge, though critical gaps persisted. While recognition of specific symptoms (e.g., lethal temperatures >39.5 °C; 90.8%) and preventive measures was strong, pathophysiological understanding was poor, with only 5.2% correctly interpreting body temperature thresholds. Logistic regression identified significant predictors: a medical educational background (odds ratio (OR) = 4.51, p < .001), employment (OR = 2.45, p < .001), and previous first aid training (OR = 2.51, p = .003) increased odds of satisfactory knowledge. Significant regional disparities existed, with the Middle Region associated with higher odds (OR = 2.14, p = .019) and the Southwest Region with lower odds (OR = 0.31, p = .004). Conclusion In conclusion, this study found that while a majority of Hajj health volunteers possess satisfactory heatstroke knowledge, significant and systematic disparities exist. The findings robustly demonstrate that knowledge is not uniformly distributed but is significantly predicted by educational background, occupational status, and geogra…
format: application/pdf
format: text/html
creator: Fatmah Alamoudi
creator: Halah Almulla
creator: Magda Yousif
creator: Nouf Alnaimi
creator: Adil Abdalla
creator: Mahmoud Abdel Hameed Shahin
creator: Faizan Kashoo
subject: Emergency and Critical Care
subject: Public Health
subject: Science and Medical Education
subject: Environmental Health
subject: Healthcare Services
description: doi:10.7717/peerj.20816
publisher: PeerJ Inc.
rights: © 2026 Alamoudi et al.
abstract: Background Heatstroke is a life-threatening condition resulting from prolonged exposure to high temperatures or intense physical activity, especially during the summer. Pilgrims performing Hajj are particularly vulnerable because of factors such as advanced age, chronic health conditions, and failure to follow safety guidelines. Health volunteers play a key role in prevention and response. Aim This study aimed to assess health volunteers’ knowledge and identify predictors of such knowledge. Methods A cross-sectional study was conducted among 772 health volunteers during Hajj 2024 in Saudi Arabia. A self-designed questionnaire was developed and utilized to assess participants’ knowledge of heatstroke and to identify predictors of such knowledge. Data were collected electronically and analyzed via Jeffrey’s Amazing Statistics Program (JASP). Results Analysis revealed that (n = 576) 74.6% of health volunteers had satisfactory heatstroke knowledge, though critical gaps persisted. While recognition of specific symptoms (e.g., lethal temperatures >39.5 °C; 90.8%) and preventive measures was strong, pathophysiological understanding was poor, with only 5.2% correctly interpreting body temperature thresholds. Logistic regression identified significant predictors: a medical educational background (odds ratio (OR) = 4.51, p < .001), employment (OR = 2.45, p < .001), and previous first aid training (OR = 2.51, p = .003) increased odds of satisfactory knowledge. Significant regional disparities existed, with the Middle Region associated with higher odds (OR = 2.14, p = .019) and the Southwest Region with lower odds (OR = 0.31, p = .004). Conclusion In conclusion, this study found that while a majority of Hajj health volunteers possess satisfactory heatstroke knowledge, significant and systematic disparities exist. The findings robustly demonstrate that knowledge is not uniformly distributed but is significantly predicted by educational background, occupational status, and geogra…
bibliographic citation: Alamoudi et al. (2026) Heatstroke knowledge and predictors among Hajj health volunteers in Saudi Arabia: a cross-sectional study. PeerJ 14:e20816 https://doi.org/10.7717/peerj.20816
date submitted: 2025-07-12
date accepted: 2025-12-28
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alamoudi
  given name: Fatmah
author list: Agent
  family name: Almulla
  given name: Halah
author list: Agent
  family name: Yousif
  given name: Magda
author list: Agent
  family name: Alnaimi
  given name: Nouf
author list: Agent
  family name: Abdalla
  given name: Adil
author list: Agent
  family name: Shahin
  given name: Mahmoud Abdel Hameed
author list: Agent
  family name: Kashoo
  given name: Faizan
doi: 10.7717/peerj.20816
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Alamoudi et al.
attribution name: Alamoudi et al.

https://peerj.com/articles/20815
type: item
type: AcademicArticle
title: Adjusted effect size, area under the curve, and c-statistic for evaluating the association between uric acid and mortality in US adults using unweighted and survey-weighted regression, propensity, and prognostic score
description: Population-based surveys and databases are useful sources for developing prognostic and diagnostic models requiring receiver operating characteristic (ROC) or precision-recall curve (PRC) analyses. The performance of the models is typically summarized with the area under the ROC (rAUC) or PR curves (pAUC) or c-statistic, depending on the study design and analysis. However, these surveys and databases sometimes involve sampling weights due to complex sampling designs. The sampling weights need to be included in the analysis to produce accurate estimates of effect size as well as performance measures. Different types of adjusted analyses, including survey-weighted adjusted analysis, propensity score weight-adjusted (PropSWA), and prognostic score weight-adjusted (ProgSWA) analyses, are typically performed using logistic or Cox regressions as per the study objectives and outcome. We applied these adjusted analyses and compared the effect sizes with or without incorporating sampling weights in the analyses. We explored the relationship between uric acid levels and all-cause mortality in US adults using the National Health and Nutrition Examination Survey dataset, which employs a complex sampling design requiring weight-adjusted analyses. All the models, including unweighted (hazard ratio (HR): 1.09; 95% confidence interval (CI) [1.05–1.12]), survey-weighted (HR: 1.09; 95% CI [1.06–1.12]), unweighted ProgSWA (HR: 1.11; 95% CI [1.07–1.15]), survey-weighted ProgSWA (HR: 1.12; 95% CI [1.09–1.16]), unweighted PropSWA (HR: 1.18; 95% CI [1.12–1.24]), and weighted PropSWA (HR: 1.16; 95% CI [1.10–1.22]) analyses yielded a consistent and positive association between uric acid levels and risk of mortality. These associations were unchanged in various sensitivity analyses. We found marked differences in effect size and predictive performance measures between weighted and unweighted analyses, especially with four categories of uric acid levels. In simulation studies, a survey-weight…
format: application/pdf
format: text/html
creator: Shakeel Ahmed
creator: Alok Kumar Dwivedi
subject: Cardiology
subject: Epidemiology
subject: Public Health
subject: Science and Medical Education
subject: Statistics
description: doi:10.7717/peerj.20815
publisher: PeerJ Inc.
rights: © 2026 Ahmed and Dwivedi
abstract: Population-based surveys and databases are useful sources for developing prognostic and diagnostic models requiring receiver operating characteristic (ROC) or precision-recall curve (PRC) analyses. The performance of the models is typically summarized with the area under the ROC (rAUC) or PR curves (pAUC) or c-statistic, depending on the study design and analysis. However, these surveys and databases sometimes involve sampling weights due to complex sampling designs. The sampling weights need to be included in the analysis to produce accurate estimates of effect size as well as performance measures. Different types of adjusted analyses, including survey-weighted adjusted analysis, propensity score weight-adjusted (PropSWA), and prognostic score weight-adjusted (ProgSWA) analyses, are typically performed using logistic or Cox regressions as per the study objectives and outcome. We applied these adjusted analyses and compared the effect sizes with or without incorporating sampling weights in the analyses. We explored the relationship between uric acid levels and all-cause mortality in US adults using the National Health and Nutrition Examination Survey dataset, which employs a complex sampling design requiring weight-adjusted analyses. All the models, including unweighted (hazard ratio (HR): 1.09; 95% confidence interval (CI) [1.05–1.12]), survey-weighted (HR: 1.09; 95% CI [1.06–1.12]), unweighted ProgSWA (HR: 1.11; 95% CI [1.07–1.15]), survey-weighted ProgSWA (HR: 1.12; 95% CI [1.09–1.16]), unweighted PropSWA (HR: 1.18; 95% CI [1.12–1.24]), and weighted PropSWA (HR: 1.16; 95% CI [1.10–1.22]) analyses yielded a consistent and positive association between uric acid levels and risk of mortality. These associations were unchanged in various sensitivity analyses. We found marked differences in effect size and predictive performance measures between weighted and unweighted analyses, especially with four categories of uric acid levels. In simulation studies, a survey-weight…
bibliographic citation: Ahmed et al. (2026) Adjusted effect size, area under the curve, and c-statistic for evaluating the association between uric acid and mortality in US adults using unweighted and survey-weighted regression, propensity, and prognostic score. PeerJ 14:e20815 https://doi.org/10.7717/peerj.20815
date submitted: 2025-06-06
date accepted: 2025-12-28
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmed
  given name: Shakeel
author list: Agent
  family name: Dwivedi
  given name: Alok Kumar
doi: 10.7717/peerj.20815
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: © 2026 Ahmed and Dwivedi
attribution name: Ahmed and Dwivedi

Video game use, lifestyle and its association with becoming overweight or obese in Mexican adolescents
type: item
type: AcademicArticle
description: Background Mexico has high levels of adolescent obesity (40.4%), with an increase from 17.6 to 18.1% between 2020 and 2023. Technological advancement and early access to electronic devices and video games after the COVID-19 pandemic, along with morbid lifestyles, contribute to this problem. Objective To determine the association between video game use, lifestyle, and obesity in adolescents. Methods A cross-sectional, analytical study was conducted. Subjects with and without video game use and percentiles >5 and <95 were included. Those with metabolic, hormonal, neurological, and autoimmune diseases were excluded. Questionnaires were administered regarding lifestyle and video game use. A multiple binary logistic regression model including the variables male sex, morbid lifestyle, video game use, and physical inactivity was developed, yielding exponential B coefficients, 95% CI, and p-values. Results Of 272 subjects, males predominated with 51.8%, and obesity of 75.7%. The use of video games and morbid lifestyle showed an OR 10.67 (95% CI [5.33–20.58]) and 3.55 (95% CI [1.99–6.36]), respectively. In the adjusted model, the use of video games and physical inactivity obtained an exponential of B of 6.89 (95% CI [3.17–14.94]) and B of 3.12 (95% CI [1.49–6.50]). Conclusions The importance of family physician intervention on obesogenic factors in adolescents and their families to reduce the risk of harmful behaviours by promoting physical activity and a healthy lifestyle.
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format: text/html
creator: Yuriko Islas Mendoza
creator: Francisco Vargas Hernandez
creator: Diana Alejandra Bermudez Zapata
creator: María G. Saucedo Martínez
creator: Luis R. García Cortes
creator: Everardo Villar Aguirre
creator: Jehú A. Tamayo Calderón
creator: Oscar Jiménez Jalpa
creator: Elizabeth García Cortés
creator: Víctor M. Camarillo Nava
creator: Saul Jimenez Hernandez
creator: Dana A. Pérez Camargo
creator: Víctor M. Enríquez Estrada
creator: Fernando Palacios Torres
subject: Global Health
subject: Pediatrics
subject: Metabolic Sciences
subject: Obesity
description: doi:10.7717/peerj.20779
publisher: PeerJ Inc.
rights: © 2026 Islas Mendoza et al.
abstract: Background Mexico has high levels of adolescent obesity (40.4%), with an increase from 17.6 to 18.1% between 2020 and 2023. Technological advancement and early access to electronic devices and video games after the COVID-19 pandemic, along with morbid lifestyles, contribute to this problem. Objective To determine the association between video game use, lifestyle, and obesity in adolescents. Methods A cross-sectional, analytical study was conducted. Subjects with and without video game use and percentiles >5 and <95 were included. Those with metabolic, hormonal, neurological, and autoimmune diseases were excluded. Questionnaires were administered regarding lifestyle and video game use. A multiple binary logistic regression model including the variables male sex, morbid lifestyle, video game use, and physical inactivity was developed, yielding exponential B coefficients, 95% CI, and p-values. Results Of 272 subjects, males predominated with 51.8%, and obesity of 75.7%. The use of video games and morbid lifestyle showed an OR 10.67 (95% CI [5.33–20.58]) and 3.55 (95% CI [1.99–6.36]), respectively. In the adjusted model, the use of video games and physical inactivity obtained an exponential of B of 6.89 (95% CI [3.17–14.94]) and B of 3.12 (95% CI [1.49–6.50]). Conclusions The importance of family physician intervention on obesogenic factors in adolescents and their families to reduce the risk of harmful behaviours by promoting physical activity and a healthy lifestyle.
bibliographic citation: Islas Mendoza et al. (2026) Video game use, lifestyle and its association with becoming overweight or obese in Mexican adolescents. PeerJ 14:e20779 https://doi.org/10.7717/peerj.20779
date submitted: 2025-07-17
date accepted: 2025-12-19
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Islas Mendoza
  given name: Yuriko
author list: Agent
  family name: Vargas Hernandez
  given name: Francisco
author list: Agent
  family name: Bermudez Zapata
  given name: Diana Alejandra
author list: Agent
  family name: Saucedo Martínez
  given name: María G.
author list: Agent
  family name: García Cortes
  given name: Luis R.
author list: Agent
  family name: Villar Aguirre
  given name: Everardo
author list: Agent
  family name: Tamayo Calderón
  given name: Jehú A.
author list: Agent
  family name: Jiménez Jalpa
  given name: Oscar
author list: Agent
  family name: García Cortés
  given name: Elizabeth
author list: Agent
  family name: Camarillo Nava
  given name: Víctor M.
author list: Agent
  family name: Jimenez Hernandez
  given name: Saul
author list: Agent
  family name: Pérez Camargo
  given name: Dana A.
author list: Agent
  family name: Enríquez Estrada
  given name: Víctor M.
author list: Agent
  family name: Palacios Torres
  given name: Fernando
doi: 10.7717/peerj.20779
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: © 2026 Islas Mendoza et al.
attribution name: Islas Mendoza et al.

Altered anterior segment biometrics in cataract patients with retinitis pigmentosa: a propensity-matched analysis suggests patterns of zonular weakness
type: item
type: AcademicArticle
description: Purpose To explore the spatial structure of the anterior segment biometrics in cataract patients with retinitis pigmentosa (RP). Methods This is a retrospective study. We conducted a propensity score matching analysis (1:3) on anterior segment data of RP patients and normal cataract patients who underwent cataract surgery from August 2023 to February 2025. Baseline variables (age, gender, axial length, and Pentacam Nucleus Staging (PNS) score) were balanced to compare the differences in anterior segment biometric measurements between the two groups. Results We analyzed the anterior segment data of 37 cataract patients with RP and 102 simple cataract patients. The RP group exhibited a thicker lens (p < 0.001), a more anterior lens position (p = 0.003), a shallower anterior chamber depth (p < 0.001), and greater corneal astigmatism (p < 0.001). The shallower anterior chamber depth showed a positive correlation with a more anterior lens position (r = 0.84, p < 0.001) and the relative lens position (r = 0.59, p < 0.001). Discussions RP patients exhibit a thicker lens, a more anteriorly positioned lens, shallower anterior chamber depth, and greater corneal astigmatism. These changes can be explained by zonular weakness. Decision-making surrounding intraocular lens selection in eyes with RP, cataract, and zonular compromise may be enhanced through proper identification of preoperative biometric irregularities in the anterior segment.
format: application/pdf
format: text/html
creator: Yonglin Chen
creator: Zhiheng Lian
creator: Yongguo Xiang
creator: Hong Cheng
creator: Chong Tang
creator: Yanlin Yang
creator: Liang Liang
creator: Juan Kang
creator: Ke Hu
creator: Shijie Zheng
subject: Anatomy and Physiology
subject: Evidence Based Medicine
subject: Internal Medicine
subject: Ophthalmology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.20760
publisher: PeerJ Inc.
rights: © 2026 Chen et al.
abstract: Purpose To explore the spatial structure of the anterior segment biometrics in cataract patients with retinitis pigmentosa (RP). Methods This is a retrospective study. We conducted a propensity score matching analysis (1:3) on anterior segment data of RP patients and normal cataract patients who underwent cataract surgery from August 2023 to February 2025. Baseline variables (age, gender, axial length, and Pentacam Nucleus Staging (PNS) score) were balanced to compare the differences in anterior segment biometric measurements between the two groups. Results We analyzed the anterior segment data of 37 cataract patients with RP and 102 simple cataract patients. The RP group exhibited a thicker lens (p < 0.001), a more anterior lens position (p = 0.003), a shallower anterior chamber depth (p < 0.001), and greater corneal astigmatism (p < 0.001). The shallower anterior chamber depth showed a positive correlation with a more anterior lens position (r = 0.84, p < 0.001) and the relative lens position (r = 0.59, p < 0.001). Discussions RP patients exhibit a thicker lens, a more anteriorly positioned lens, shallower anterior chamber depth, and greater corneal astigmatism. These changes can be explained by zonular weakness. Decision-making surrounding intraocular lens selection in eyes with RP, cataract, and zonular compromise may be enhanced through proper identification of preoperative biometric irregularities in the anterior segment.
bibliographic citation: Chen et al. (2026) Altered anterior segment biometrics in cataract patients with retinitis pigmentosa: a propensity-matched analysis suggests patterns of zonular weakness. PeerJ 14:e20760 https://doi.org/10.7717/peerj.20760
date submitted: 2025-10-05
date accepted: 2025-12-17
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yonglin
author list: Agent
  family name: Lian
  given name: Zhiheng
author list: Agent
  family name: Xiang
  given name: Yongguo
author list: Agent
  family name: Cheng
  given name: Hong
author list: Agent
  family name: Tang
  given name: Chong
author list: Agent
  family name: Yang
  given name: Yanlin
author list: Agent
  family name: Liang
  given name: Liang
author list: Agent
  family name: Kang
  given name: Juan
author list: Agent
  family name: Hu
  given name: Ke
author list: Agent
  family name: Zheng
  given name: Shijie
doi: 10.7717/peerj.20760
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Chen et al.
attribution name: Chen et al.

The structure of personality in Parkinson’s disease and the effects of age, years since diagnosis, and impulsivity
type: item
type: AcademicArticle
description: Background Parkinson’s disease (PD) is a progressive neurodegenerative disorder primarily characterized by motor and cognitive symptoms. However, emerging evidence suggests that personality alterations may also be present, potentially affecting patients’ quality of life and clinical outcomes. Prior studies have identified patterns such as lower openness and extraversion and higher neuroticism in PD patients, although findings have been inconsistent. This study aimed to investigate the structural organization of personality in PD using a network-based approach, and to examine the influence of age, sex, disease duration, and impulsive-compulsive symptoms on personality traits. Methods A total of 237 PD patients (aged 45–86) completed the HEXACO Adjective Scale (HAS), assessing six personality traits: Honesty-Humility (H), Emotionality (E), Extraversion (X), Agreeableness (A), Conscientiousness (C), and Openness (O). Impulsive-compulsive behaviors were assessed using the Questionnaire for Impulsive-Compulsive Disorders in Parkinson’s Disease–Rating Scale (QUIP-RS). Personality structure was analyzed via Exploratory Graph Analysis (EGA), a network model that identifies item clusters based on conditional dependencies. Multivariate multiple linear regression was used to test the effects of demographic and clinical variables on trait expression. Results EGA identified seven item-level communities. Traits E, X, and C formed coherent and distinct clusters, while items from A and H tended to cluster based on item polarity (positive vs. negative wording) rather than theoretical trait boundaries. O items split into two distinct communities, one composed of the items from the Unconventionality facet, and the other encompassing the remaining O items. At the trait level, HEXACO dimensions grouped into two higher-order clusters: a Cooperativity–Integrity community (H, A, C) and an Engagement community (E, X, O). Regression analyses showed that higher ICD symptoms predicted lower le…
format: application/pdf
format: text/html
creator: Stefano Vicentin
creator: Lavinia Chiriatti
creator: Giorgia Cona
subject: Cognitive Disorders
subject: Evidence Based Medicine
subject: Neurology
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20725
publisher: PeerJ Inc.
rights: © 2026 Vicentin et al.
abstract: Background Parkinson’s disease (PD) is a progressive neurodegenerative disorder primarily characterized by motor and cognitive symptoms. However, emerging evidence suggests that personality alterations may also be present, potentially affecting patients’ quality of life and clinical outcomes. Prior studies have identified patterns such as lower openness and extraversion and higher neuroticism in PD patients, although findings have been inconsistent. This study aimed to investigate the structural organization of personality in PD using a network-based approach, and to examine the influence of age, sex, disease duration, and impulsive-compulsive symptoms on personality traits. Methods A total of 237 PD patients (aged 45–86) completed the HEXACO Adjective Scale (HAS), assessing six personality traits: Honesty-Humility (H), Emotionality (E), Extraversion (X), Agreeableness (A), Conscientiousness (C), and Openness (O). Impulsive-compulsive behaviors were assessed using the Questionnaire for Impulsive-Compulsive Disorders in Parkinson’s Disease–Rating Scale (QUIP-RS). Personality structure was analyzed via Exploratory Graph Analysis (EGA), a network model that identifies item clusters based on conditional dependencies. Multivariate multiple linear regression was used to test the effects of demographic and clinical variables on trait expression. Results EGA identified seven item-level communities. Traits E, X, and C formed coherent and distinct clusters, while items from A and H tended to cluster based on item polarity (positive vs. negative wording) rather than theoretical trait boundaries. O items split into two distinct communities, one composed of the items from the Unconventionality facet, and the other encompassing the remaining O items. At the trait level, HEXACO dimensions grouped into two higher-order clusters: a Cooperativity–Integrity community (H, A, C) and an Engagement community (E, X, O). Regression analyses showed that higher ICD symptoms predicted lower le…
bibliographic citation: Vicentin et al. (2026) The structure of personality in Parkinson’s disease and the effects of age, years since diagnosis, and impulsivity. PeerJ 14:e20725 https://doi.org/10.7717/peerj.20725
date submitted: 2025-08-13
date accepted: 2025-12-11
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vicentin
  given name: Stefano
author list: Agent
  family name: Chiriatti
  given name: Lavinia
author list: Agent
  family name: Cona
  given name: Giorgia
doi: 10.7717/peerj.20725
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Vicentin et al.
attribution name: Vicentin et al.

Quantitative image analysis applied to revise the taxonomy of the Palearctic Earophila badiata species group (Lepidoptera: Geometridae: Larentiinae)
type: item
type: AcademicArticle
description: The geometrid moth Earophila badiata (Denis & Schiffermüller, 1775), which occurs widely in the Palearctic realm, has rapidly filled a large gap in its range across southern Finland during the past two decades, prompting a re-evaluation of its taxonomy. Using an integrative taxonomic approach including a quantitative wing image analysis combined with genitalia morphology and mitochondrial DNA barcoding (mtCOI) analyses, we reassessed the status of the described taxa within the E. badiata species group. Quantitative analysis of forewing colours revealed strong sexual dimorphism and significant effects of specimen wear and age on colouration, but no consistent morphological differences between the nominotypical subspecies E. badiata badiata and taxon E. badiata fennokarelica (Kaisila, 1945). Comparative genitalia morphology, including micro-CT imaging, showed no diagnostic differences among closely related E. badiata, E. kolomietsi Vasilenko, 2003, and E. pseudobadiata Vasilenko, 2007, supporting the synonymy of these taxa. Molecular phylogeny and haplotype analysis confirmed monophyly among Eurasian samples with low genetic divergence (<0.63%), but implying a distinct lineage for North African E. badiata tellensis (Herbulot, 1957). Based on these findings, we propose synonymizing E. kolomietsi and E. pseudobadiata with E. badiata syn. n. and classify the E. badiata taxon fennokarelica as a morphological form of E. badiata below the subspecific rank. Our results challenge the current subspecies delineation and support a revision of taxonomic boundaries within this group, highlighting the value of integrative taxonomy for resolving complex relationships among closely related species.
format: application/pdf
format: text/html
creator: Mikael Englund
creator: George Hancock
creator: Elina Laiho
creator: Johanna Mappes
creator: Pasi Sihvonen
creator: Max Söderholm
creator: Alpo Turunen
creator: Kyung Min Lee
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Taxonomy
subject: Population Biology
description: doi:10.7717/peerj.20620
publisher: PeerJ Inc.
rights: © 2026 Englund et al.
abstract: The geometrid moth Earophila badiata (Denis & Schiffermüller, 1775), which occurs widely in the Palearctic realm, has rapidly filled a large gap in its range across southern Finland during the past two decades, prompting a re-evaluation of its taxonomy. Using an integrative taxonomic approach including a quantitative wing image analysis combined with genitalia morphology and mitochondrial DNA barcoding (mtCOI) analyses, we reassessed the status of the described taxa within the E. badiata species group. Quantitative analysis of forewing colours revealed strong sexual dimorphism and significant effects of specimen wear and age on colouration, but no consistent morphological differences between the nominotypical subspecies E. badiata badiata and taxon E. badiata fennokarelica (Kaisila, 1945). Comparative genitalia morphology, including micro-CT imaging, showed no diagnostic differences among closely related E. badiata, E. kolomietsi Vasilenko, 2003, and E. pseudobadiata Vasilenko, 2007, supporting the synonymy of these taxa. Molecular phylogeny and haplotype analysis confirmed monophyly among Eurasian samples with low genetic divergence (<0.63%), but implying a distinct lineage for North African E. badiata tellensis (Herbulot, 1957). Based on these findings, we propose synonymizing E. kolomietsi and E. pseudobadiata with E. badiata syn. n. and classify the E. badiata taxon fennokarelica as a morphological form of E. badiata below the subspecific rank. Our results challenge the current subspecies delineation and support a revision of taxonomic boundaries within this group, highlighting the value of integrative taxonomy for resolving complex relationships among closely related species.
bibliographic citation: Englund et al. (2026) Quantitative image analysis applied to revise the taxonomy of the Palearctic Earophila badiata species group (Lepidoptera: Geometridae: Larentiinae). PeerJ 14:e20620 https://doi.org/10.7717/peerj.20620
date submitted: 2025-09-26
date accepted: 2025-11-29
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Englund
  given name: Mikael
author list: Agent
  family name: Hancock
  given name: George
author list: Agent
  family name: Laiho
  given name: Elina
author list: Agent
  family name: Mappes
  given name: Johanna
author list: Agent
  family name: Sihvonen
  given name: Pasi
author list: Agent
  family name: Söderholm
  given name: Max
author list: Agent
  family name: Turunen
  given name: Alpo
author list: Agent
  family name: Lee
  given name: Kyung Min
doi: 10.7717/peerj.20620
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Englund et al.
attribution name: Englund et al.

Relationship between perceived risk and compliance with infection control measures during the first year of a pandemic
type: item
type: AcademicArticle
description: The way people perceive health risks is often assumed to influence how they adopt precautionary measures. However, people’s assessment of a given phenomenon’s risk may vary over time, and the relationship between perceived risk and compliance with protective measures may be dynamic and bi-directional. We measured the perceived risk of COVID-19 and compliance with infection control measures for a large representative sample at four time-points during the first year of the COVID-19 pandemic in Norway. We employed a cross-lagged panel analysis to investigate both the cross-sectional and the temporal association between perceived risk and compliance. We found cross-sectional associations between perceived risk and compliance at one of the time points. There were no temporal associations between risk at one time-point and compliance at the subsequent time-point. Neither was compliance associated with risk at the subsequent time-point. The results suggest that the relationship between perceived risk and compliance with COVID-19 infection control measures is negligible and stable over time. A multiverse analysis showed that the absence of a relationship between perceived risk and compliance was robust to different operationalizations of perceived risk. This highlights the need for a nuanced understanding of how risk perceptions impact behavior during a pandemic.
format: application/pdf
format: text/html
creator: Sebastian B. Bjørkheim
creator: Sigurd W. Hystad
creator: Bjørn Sætrevik
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.20554
publisher: PeerJ Inc.
rights: © 2026 Bjørkheim et al.
abstract: The way people perceive health risks is often assumed to influence how they adopt precautionary measures. However, people’s assessment of a given phenomenon’s risk may vary over time, and the relationship between perceived risk and compliance with protective measures may be dynamic and bi-directional. We measured the perceived risk of COVID-19 and compliance with infection control measures for a large representative sample at four time-points during the first year of the COVID-19 pandemic in Norway. We employed a cross-lagged panel analysis to investigate both the cross-sectional and the temporal association between perceived risk and compliance. We found cross-sectional associations between perceived risk and compliance at one of the time points. There were no temporal associations between risk at one time-point and compliance at the subsequent time-point. Neither was compliance associated with risk at the subsequent time-point. The results suggest that the relationship between perceived risk and compliance with COVID-19 infection control measures is negligible and stable over time. A multiverse analysis showed that the absence of a relationship between perceived risk and compliance was robust to different operationalizations of perceived risk. This highlights the need for a nuanced understanding of how risk perceptions impact behavior during a pandemic.
bibliographic citation: Bjørkheim et al. (2026) Relationship between perceived risk and compliance with infection control measures during the first year of a pandemic. PeerJ 14:e20554 https://doi.org/10.7717/peerj.20554
date submitted: 2025-11-13
date accepted: 2025-11-18
issued: 2026-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bjørkheim
  given name: Sebastian B.
author list: Agent
  family name: Hystad
  given name: Sigurd W.
author list: Agent
  family name: Sætrevik
  given name: Bjørn
doi: 10.7717/peerj.20554
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-19
copyright: ©2026 Bjørkheim et al.
attribution name: Bjørkheim et al.

Effect of Triton all-in-one irrigant on electronic working length determination using two apex locators: an in vitro study
type: item
type: AcademicArticle
description: Background This study evaluated whether Triton, a newly introduced all-in-one irrigant, affects the accuracy of electronic working length determination, and compared two electronic apex locators (Ai-Pex, Propex Pixi) under different irrigant conditions. Materials and Methods Forty-four extracted single-rooted human teeth were embedded in alginate. Actual working length was determined under a dental operating microscope. Specimens were assigned to four groups (Triton, 17% ethylenediaminetetraacetic acid, 10% citric acid, dry canal). Electronic working lengths were measured with Ai-Pex and Propex Pixi using #15 K-files. Statistical analyses were performed using one-way and two-way analysis of variance (ANOVA) following normality assessment, with statistical significance set at p < 0.05. Results No significant differences occurred among Triton, ethylenediaminetetraacetic acid, and citric acid groups (p > 0.05). Dry canal measurements were significantly longer than the actual working length measured under a dental operating microscope (p < 0.05). Both apex locators showed comparable accuracy. Conclusions Triton did not reduce apex locator precision, supporting its potential as a time-saving irrigant that permits simultaneous irrigation and measurement. Further clinical validation is required.
format: application/pdf
format: text/html
creator: Aybüke Karaca Sakallı
creator: İsen Güleç Koçyiğit
creator: Bilge Özcan
subject: Dentistry
subject: Drugs and Devices
description: doi:10.7717/peerj.20872
publisher: PeerJ Inc.
rights: © 2026 Karaca Sakallı et al.
abstract: Background This study evaluated whether Triton, a newly introduced all-in-one irrigant, affects the accuracy of electronic working length determination, and compared two electronic apex locators (Ai-Pex, Propex Pixi) under different irrigant conditions. Materials and Methods Forty-four extracted single-rooted human teeth were embedded in alginate. Actual working length was determined under a dental operating microscope. Specimens were assigned to four groups (Triton, 17% ethylenediaminetetraacetic acid, 10% citric acid, dry canal). Electronic working lengths were measured with Ai-Pex and Propex Pixi using #15 K-files. Statistical analyses were performed using one-way and two-way analysis of variance (ANOVA) following normality assessment, with statistical significance set at p < 0.05. Results No significant differences occurred among Triton, ethylenediaminetetraacetic acid, and citric acid groups (p > 0.05). Dry canal measurements were significantly longer than the actual working length measured under a dental operating microscope (p < 0.05). Both apex locators showed comparable accuracy. Conclusions Triton did not reduce apex locator precision, supporting its potential as a time-saving irrigant that permits simultaneous irrigation and measurement. Further clinical validation is required.
bibliographic citation: Karaca Sakallı et al. (2026) Effect of Triton all-in-one irrigant on electronic working length determination using two apex locators: an in vitro study. PeerJ 14:e20872 https://doi.org/10.7717/peerj.20872
date submitted: 2025-10-30
date accepted: 2026-01-09
issued: 2026-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karaca Sakallı
  given name: Aybüke
author list: Agent
  family name: Güleç Koçyiğit
  given name: İsen
author list: Agent
  family name: Özcan
  given name: Bilge
doi: 10.7717/peerj.20872
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-18
copyright: © 2026 Karaca Sakallı et al.
attribution name: Karaca Sakallı et al.

Quality, reliability and popularity assessment of Turkish YouTube videos on human papillomavirus and its vaccine: content analysis
type: item
type: AcademicArticle
description: Background Human papillomavirus (HPV) is among the most common sexually transmitted viral infections and is associated with significant health burdens, including genital warts and various cancers. YouTube has emerged as a frequently used platform for accessing health-related information, yet the quality and reliability of such content remain uncertain. Individuals seeking information about HPV and its vaccine frequently turn to YouTube, underscoring the need for systematic evaluation of online video content related to HPV vaccination, given its potential to directly influence public engagement and vaccine acceptance. Analyzing YouTube videos provides insight into the level of information users are exposed to, the potential risks of misinformation, and the overall reliability of health-related digital content. Such evaluations contribute to strengthening public health strategies and support efforts to enhance access to accurate and trustworthy information. Objective This study aimed to evaluate the information quality, reliability, and popularity of Turkish-language YouTube videos related to HPV and the HPV vaccine. Methods This cross-sectional study was conducted on the YouTube platform using the keywords ‘HPV,’ ‘HPV vaccine (“HPV aşısı”),’ and ‘human papillomavirus,’ and the videos were viewed between July 1 and 31, 2025. The first 200 videos for each keyword were screened, and those meeting the inclusion criteria were analyzed. Video characteristics (e.g., duration, views, likes, comments, like ratio) and content features (e.g., type, source, presentation format, narrator, purpose, citation of sources, recency, vaccine recommendations, anti-vaccine stance) were recorded. Information quality was assessed using the DISCERN instrument (16–80), reliability using the Journal of the American Medical Association (JAMA) Benchmark criteria (0–4), and popularity using the Video Power Index (VPI). Statistical analyses included descriptive statistics, t-tests, ANOVA, chi-squa…
format: application/pdf
format: text/html
creator: Hakan Gülmez
creator: Merve Ciftci
subject: Immunology
subject: Infectious Diseases
subject: Public Health
subject: Urology
subject: Women’s Health
description: doi:10.7717/peerj.20828
publisher: PeerJ Inc.
rights: © 2026 Gülmez et al.
abstract: Background Human papillomavirus (HPV) is among the most common sexually transmitted viral infections and is associated with significant health burdens, including genital warts and various cancers. YouTube has emerged as a frequently used platform for accessing health-related information, yet the quality and reliability of such content remain uncertain. Individuals seeking information about HPV and its vaccine frequently turn to YouTube, underscoring the need for systematic evaluation of online video content related to HPV vaccination, given its potential to directly influence public engagement and vaccine acceptance. Analyzing YouTube videos provides insight into the level of information users are exposed to, the potential risks of misinformation, and the overall reliability of health-related digital content. Such evaluations contribute to strengthening public health strategies and support efforts to enhance access to accurate and trustworthy information. Objective This study aimed to evaluate the information quality, reliability, and popularity of Turkish-language YouTube videos related to HPV and the HPV vaccine. Methods This cross-sectional study was conducted on the YouTube platform using the keywords ‘HPV,’ ‘HPV vaccine (“HPV aşısı”),’ and ‘human papillomavirus,’ and the videos were viewed between July 1 and 31, 2025. The first 200 videos for each keyword were screened, and those meeting the inclusion criteria were analyzed. Video characteristics (e.g., duration, views, likes, comments, like ratio) and content features (e.g., type, source, presentation format, narrator, purpose, citation of sources, recency, vaccine recommendations, anti-vaccine stance) were recorded. Information quality was assessed using the DISCERN instrument (16–80), reliability using the Journal of the American Medical Association (JAMA) Benchmark criteria (0–4), and popularity using the Video Power Index (VPI). Statistical analyses included descriptive statistics, t-tests, ANOVA, chi-squa…
bibliographic citation: Gülmez et al. (2026) Quality, reliability and popularity assessment of Turkish YouTube videos on human papillomavirus and its vaccine: content analysis. PeerJ 14:e20828 https://doi.org/10.7717/peerj.20828
date submitted: 2025-09-24
date accepted: 2025-12-31
issued: 2026-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gülmez
  given name: Hakan
author list: Agent
  family name: Ciftci
  given name: Merve
doi: 10.7717/peerj.20828
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-18
copyright: ©2026 Gülmez and Ciftci
attribution name: Gülmez et al.

Glacier boundary extraction and spatiotemporal variation analysis in Geladandong region
type: item
type: AcademicArticle
description: Glaciers, as sensitive indicators of global climate change, play a crucial role in influencing the global water cycle, sea level rise, and ecosystem dynamics. Understanding the interactive mechanisms between glacier boundary changes and multidimensional factors such as climate and topography is essential for revealing the complex relationships underlying the ecological functions supported by glacier systems. This study proposes a Remote Sensing Index–Random Forest fusion method (NDI-RF) to map glacial extent. The NDI-RF approach combines remote sensing index techniques with Random Forest modelling, ensuring the extraction accuracy of the Random Forest model while effectively enhancing boundary extraction precision in mosaic pixel scenarios. Then, the spatiotemporal changes in glacier extent and their response to climate change were analyzed. The experimental results indicate that the NDI-RF method can reduce spectral confusion on ice lakes and thin ice surfaces to a certain extent. The extraction results show Kappa coefficient, OA, F1-score, recall, and Precision values of 0.92, 0.94, 0.92, 0.88, and 0.93, respectively, all of which outperform the Normalized Difference Snow Index (NDSI) extraction method and the Random Forest model. From 2000 to 2024, glaciers in the Geladandong region have mainly been shrinking in area, with a total reduction in glacier area of 110.29 km2 and an average annual area change rate of 0.47%. Among these years, the period from 2010 to 2015 was marked by the most significant glacier retreat, with a reduction of 36.87 km2, and also saw the highest glacier area change rate. Analysis based on different terrain conditions showed that glaciers retreated more notably at altitudes below 5,250 m, with slopes greater than 45°, and on north-west facing slopes. Over the past 25 years, the average annual temperature and total precipitation have shown a fluctuating upward trend. The glacier area shows a negative correlation with the average annual tem…
format: application/pdf
format: text/html
creator: Haotian Liu
creator: Dongchuan Wang
creator: Tingrong Li
creator: Ang Yue
creator: Shuang Zhao
creator: Lihui Zhang
creator: Kai Ye
creator: Haotian Zhang
creator: Shuaizheng Ji
subject: Ecology
subject: Environmental Sciences
subject: Climate Change Biology
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20804
publisher: PeerJ Inc.
rights: © 2026 Liu et al.
abstract: Glaciers, as sensitive indicators of global climate change, play a crucial role in influencing the global water cycle, sea level rise, and ecosystem dynamics. Understanding the interactive mechanisms between glacier boundary changes and multidimensional factors such as climate and topography is essential for revealing the complex relationships underlying the ecological functions supported by glacier systems. This study proposes a Remote Sensing Index–Random Forest fusion method (NDI-RF) to map glacial extent. The NDI-RF approach combines remote sensing index techniques with Random Forest modelling, ensuring the extraction accuracy of the Random Forest model while effectively enhancing boundary extraction precision in mosaic pixel scenarios. Then, the spatiotemporal changes in glacier extent and their response to climate change were analyzed. The experimental results indicate that the NDI-RF method can reduce spectral confusion on ice lakes and thin ice surfaces to a certain extent. The extraction results show Kappa coefficient, OA, F1-score, recall, and Precision values of 0.92, 0.94, 0.92, 0.88, and 0.93, respectively, all of which outperform the Normalized Difference Snow Index (NDSI) extraction method and the Random Forest model. From 2000 to 2024, glaciers in the Geladandong region have mainly been shrinking in area, with a total reduction in glacier area of 110.29 km2 and an average annual area change rate of 0.47%. Among these years, the period from 2010 to 2015 was marked by the most significant glacier retreat, with a reduction of 36.87 km2, and also saw the highest glacier area change rate. Analysis based on different terrain conditions showed that glaciers retreated more notably at altitudes below 5,250 m, with slopes greater than 45°, and on north-west facing slopes. Over the past 25 years, the average annual temperature and total precipitation have shown a fluctuating upward trend. The glacier area shows a negative correlation with the average annual tem…
bibliographic citation: Liu et al. (2026) Glacier boundary extraction and spatiotemporal variation analysis in Geladandong region. PeerJ 14:e20804 https://doi.org/10.7717/peerj.20804
date submitted: 2025-07-23
date accepted: 2025-12-26
issued: 2026-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Haotian
author list: Agent
  family name: Wang
  given name: Dongchuan
author list: Agent
  family name: Li
  given name: Tingrong
author list: Agent
  family name: Yue
  given name: Ang
author list: Agent
  family name: Zhao
  given name: Shuang
author list: Agent
  family name: Zhang
  given name: Lihui
author list: Agent
  family name: Ye
  given name: Kai
author list: Agent
  family name: Zhang
  given name: Haotian
author list: Agent
  family name: Ji
  given name: Shuaizheng
doi: 10.7717/peerj.20804
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-18
copyright: ©2026 Liu et al.
attribution name: Liu et al.

Probiotic-infused activated charcoal/ hydroxyapatite microbeads: a novel strategy to disinfection
type: item
type: AcademicArticle
description: Objectives To develop a non-toxic, probiotic-infused activated charcoal/hydroxyapatite microbeads (PIMD) formulated with activated charcoal and hydroxyapatite. The formulation is designed to establish a stable probiotic biofilm on high-risk surfaces, such as medical sink basins and food cutting boards. Its dual mechanism aims to achieve rapid pathogen inhibition and long-term protection through sustained competitive exclusion, including against antibiotic-resistant microorganisms. Methods An applied study was conducted in the Al-Baha region of Saudi Arabia (January 2021–May 2025) employing probiotic-based biotechnology to engineer spatially segregated microenvironments using activated charcoal–hydroxyapatite microbeads. The study integrated ecological modeling concepts—including Gause’s competitive exclusion principle, Lotka–Volterra dynamics and agent-based cross-feeding simulations—with antimicrobial sensitivity assays and surface disinfection trials. Twelve probiotic strains capable of competitively excluding pathogens and producing antimicrobial compounds were encapsulated within activated charcoal and hydroxyapatite porous microbeads. The efficacy of the novel disinfectant was evaluated on stainless steel sink basins, food-grade cutting boards, and culture plates challenged with 43 pathogenic strains. Results The PIMD formulation remained physically stable under storage conditions, with probiotic viability largely preserved at –20 °C (0.46 log10 CFU/mL reduction) and 4 °C (0.89 log10 reduction) over 365 days. PIMD exhibited rapid broad-spectrum disinfection, reducing pathogen loads by ≥ 99.9% within 1 h, and maintained protective biofilm-mediated probiotic viability at ≥ 5.0 log10 CFU/cm2 for at least 21 days post-application across tested surfaces, including cutting boards, sink basins, and outdoor tiles. The mean inhibition zone diameter across 43 pathogens was 13.84 ± 1.23 mm, with a bactericidal outcome observed for 34.9% of tested strains. Conclusion PIMD …
format: application/pdf
format: text/html
creator: Mohammed A. Alqumber
subject: Biotechnology
subject: Microbiology
subject: Drugs and Devices
subject: Infectious Diseases
description: doi:10.7717/peerj.20803
publisher: PeerJ Inc.
rights: © 2026 Alqumber
abstract: Objectives To develop a non-toxic, probiotic-infused activated charcoal/hydroxyapatite microbeads (PIMD) formulated with activated charcoal and hydroxyapatite. The formulation is designed to establish a stable probiotic biofilm on high-risk surfaces, such as medical sink basins and food cutting boards. Its dual mechanism aims to achieve rapid pathogen inhibition and long-term protection through sustained competitive exclusion, including against antibiotic-resistant microorganisms. Methods An applied study was conducted in the Al-Baha region of Saudi Arabia (January 2021–May 2025) employing probiotic-based biotechnology to engineer spatially segregated microenvironments using activated charcoal–hydroxyapatite microbeads. The study integrated ecological modeling concepts—including Gause’s competitive exclusion principle, Lotka–Volterra dynamics and agent-based cross-feeding simulations—with antimicrobial sensitivity assays and surface disinfection trials. Twelve probiotic strains capable of competitively excluding pathogens and producing antimicrobial compounds were encapsulated within activated charcoal and hydroxyapatite porous microbeads. The efficacy of the novel disinfectant was evaluated on stainless steel sink basins, food-grade cutting boards, and culture plates challenged with 43 pathogenic strains. Results The PIMD formulation remained physically stable under storage conditions, with probiotic viability largely preserved at –20 °C (0.46 log10 CFU/mL reduction) and 4 °C (0.89 log10 reduction) over 365 days. PIMD exhibited rapid broad-spectrum disinfection, reducing pathogen loads by ≥ 99.9% within 1 h, and maintained protective biofilm-mediated probiotic viability at ≥ 5.0 log10 CFU/cm2 for at least 21 days post-application across tested surfaces, including cutting boards, sink basins, and outdoor tiles. The mean inhibition zone diameter across 43 pathogens was 13.84 ± 1.23 mm, with a bactericidal outcome observed for 34.9% of tested strains. Conclusion PIMD …
bibliographic citation: Alqumber (2026) Probiotic-infused activated charcoal/ hydroxyapatite microbeads: a novel strategy to disinfection. PeerJ 14:e20803 https://doi.org/10.7717/peerj.20803
date submitted: 2025-10-03
date accepted: 2025-12-24
issued: 2026-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alqumber
  given name: Mohammed A.
doi: 10.7717/peerj.20803
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-18
copyright: ©2026 Alqumber
attribution name: Alqumber

Immune-neural regulatory mechanism of osteoporosis induced by androgen deficiency
type: item
type: AcademicArticle
description: This article explores the pathophysiology of osteoporosis associated with androgen deficiency, a metabolic disorder characterized by inadequate levels of androgens or disruptions in androgen signaling. A focus is placed on the collaborative regulation of bone health by the immune and nervous systems. Notably, androgens are identified as critical modulators of immune responses, significantly influencing the development and progression of osteoporosis. The review highlights that androgens enhance erythropoietin (EPO) signaling, which exhibits dose-dependent effects on bone metabolism—physiological EPO levels promote osteoblast differentiation, while excessive EPO can induce osteoclastogenesis through the Janus kinase 2/Signal transducer and activator of transcription 5 (JAK2/STAT5) pathway. Importantly, the expression of EPO receptors (EPOR) is not confined to osteoblasts and osteoclasts but is also found on numerous immune cells, which suggests the potential for androgens to affect the EPO/EPOR signaling system and its implications for bone homeostasis. Additionally, androgens contribute to the management of osteoporosis by inhibiting osteoclastogenesis mediated by immune cells, promoting M2 macrophage polarization, decreasing Th17 cell differentiation, and lowering the Th1/Th2 ratio, ultimately leading to reduced Receptor Activator of Nuclear Factor Kappa-B Ligand (RANKL) expression. Furthermore, the central nervous system plays a pivotal role by mitigating the overactivation of the hypothalamic-pituitary-adrenal (HPA) axis, thereby lessening glucocorticoid-induced osteoblast apoptosis. In peripheral contexts, neuropeptides such as calcitonin gene-related peptide (CGRP) and Semaphorin 3A (Sema3A) promote osteogenesis. Moreover, androgens are shown to enhance neuromuscular junction functionality, providing additional mechanical stress that contributes to the maintenance of bone mass. This review aims to elucidate the intricate mechanisms governing bone homeostasis an…
format: application/pdf
format: text/html
creator: Jing Zhou
creator: Shuwen Li
creator: Huihui Yang
creator: Ning Ma
subject: Biochemistry
subject: Andrology
subject: Immunology
subject: Orthopedics
description: doi:10.7717/peerj.20737
publisher: PeerJ Inc.
rights: © 2026 Zhou et al.
abstract: This article explores the pathophysiology of osteoporosis associated with androgen deficiency, a metabolic disorder characterized by inadequate levels of androgens or disruptions in androgen signaling. A focus is placed on the collaborative regulation of bone health by the immune and nervous systems. Notably, androgens are identified as critical modulators of immune responses, significantly influencing the development and progression of osteoporosis. The review highlights that androgens enhance erythropoietin (EPO) signaling, which exhibits dose-dependent effects on bone metabolism—physiological EPO levels promote osteoblast differentiation, while excessive EPO can induce osteoclastogenesis through the Janus kinase 2/Signal transducer and activator of transcription 5 (JAK2/STAT5) pathway. Importantly, the expression of EPO receptors (EPOR) is not confined to osteoblasts and osteoclasts but is also found on numerous immune cells, which suggests the potential for androgens to affect the EPO/EPOR signaling system and its implications for bone homeostasis. Additionally, androgens contribute to the management of osteoporosis by inhibiting osteoclastogenesis mediated by immune cells, promoting M2 macrophage polarization, decreasing Th17 cell differentiation, and lowering the Th1/Th2 ratio, ultimately leading to reduced Receptor Activator of Nuclear Factor Kappa-B Ligand (RANKL) expression. Furthermore, the central nervous system plays a pivotal role by mitigating the overactivation of the hypothalamic-pituitary-adrenal (HPA) axis, thereby lessening glucocorticoid-induced osteoblast apoptosis. In peripheral contexts, neuropeptides such as calcitonin gene-related peptide (CGRP) and Semaphorin 3A (Sema3A) promote osteogenesis. Moreover, androgens are shown to enhance neuromuscular junction functionality, providing additional mechanical stress that contributes to the maintenance of bone mass. This review aims to elucidate the intricate mechanisms governing bone homeostasis an…
bibliographic citation: Zhou et al. (2026) Immune-neural regulatory mechanism of osteoporosis induced by androgen deficiency. PeerJ 14:e20737 https://doi.org/10.7717/peerj.20737
date submitted: 2025-08-10
date accepted: 2025-12-15
issued: 2026-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhou
  given name: Jing
author list: Agent
  family name: Li
  given name: Shuwen
author list: Agent
  family name: Yang
  given name: Huihui
author list: Agent
  family name: Ma
  given name: Ning
doi: 10.7717/peerj.20737
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-18
copyright: © 2026 Zhou et al.
attribution name: Zhou et al.

Association between myosteatosis and survival of patients with esophageal and gastro-esophageal junction cancer: a meta-analysis
type: item
type: AcademicArticle
description: Background Myosteatosis, a marker of fatty infiltration in skeletal muscle, has emerged as a potential prognostic factor in various cancers. However, its association with survival in patients with esophageal cancer (EC) or gastro-esophageal junction cancer (GEC) remains uncertain. This meta-analysis aimed to evaluate the predictive value of myosteatosis for survival of this patient population. Methods A systematic search of PubMed, Embase, and Web of Science was conducted through May 14, 2025. Studies reporting overall survival (OS) and/or progression-free survival (PFS) in patients with EC or GEC, with outcomes stratified by baseline myosteatosis status, were eligible for inclusion. To account for inter-study variability, pooled hazard ratios (HRs) and corresponding 95% confidence intervals (CIs) were estimated using random-effects models. Results Eleven cohort studies comprising 1,810 patients with EC or GEC were included. Myosteatosis was significantly associated with poorer OS (HR = 1.46, 95% CI [1.13–1.88], p = 0.004; I2 = 76%). Subgroup analyses indicated consistent associations across study design, cancer type, age, sex, treatment modality, and analytic models (p for subgroup differences > 0.05). A stronger effect was observed when myosteatosis was assessed using intramuscular adipose tissue content rather than muscle attenuation (HR = 2.29 vs. 1.30; p for subgroup difference = 0.02). Myosteatosis was not significantly associated with PFS (HR = 1.29, 95% CI [0.77–2.18], p = 0.34; I2 = 82%). Conclusion Baseline myosteatosis is associated with poorer OS in patients with EC or GEC. Muscle quality assessment may improve prognostic stratification in this population.
format: application/pdf
format: text/html
creator: Wu Wang
creator: Jinbiao Xie
creator: Tianbao Yang
creator: Shijie Huang
creator: Boyang Chen
subject: Evidence Based Medicine
subject: Oncology
subject: Pathology
subject: Radiology and Medical Imaging
subject: Metabolic Sciences
description: doi:10.7717/peerj.20825
publisher: PeerJ Inc.
rights: © 2026 Wang et al.
abstract: Background Myosteatosis, a marker of fatty infiltration in skeletal muscle, has emerged as a potential prognostic factor in various cancers. However, its association with survival in patients with esophageal cancer (EC) or gastro-esophageal junction cancer (GEC) remains uncertain. This meta-analysis aimed to evaluate the predictive value of myosteatosis for survival of this patient population. Methods A systematic search of PubMed, Embase, and Web of Science was conducted through May 14, 2025. Studies reporting overall survival (OS) and/or progression-free survival (PFS) in patients with EC or GEC, with outcomes stratified by baseline myosteatosis status, were eligible for inclusion. To account for inter-study variability, pooled hazard ratios (HRs) and corresponding 95% confidence intervals (CIs) were estimated using random-effects models. Results Eleven cohort studies comprising 1,810 patients with EC or GEC were included. Myosteatosis was significantly associated with poorer OS (HR = 1.46, 95% CI [1.13–1.88], p = 0.004; I2 = 76%). Subgroup analyses indicated consistent associations across study design, cancer type, age, sex, treatment modality, and analytic models (p for subgroup differences > 0.05). A stronger effect was observed when myosteatosis was assessed using intramuscular adipose tissue content rather than muscle attenuation (HR = 2.29 vs. 1.30; p for subgroup difference = 0.02). Myosteatosis was not significantly associated with PFS (HR = 1.29, 95% CI [0.77–2.18], p = 0.34; I2 = 82%). Conclusion Baseline myosteatosis is associated with poorer OS in patients with EC or GEC. Muscle quality assessment may improve prognostic stratification in this population.
bibliographic citation: Wang et al. (2026) Association between myosteatosis and survival of patients with esophageal and gastro-esophageal junction cancer: a meta-analysis. PeerJ 14:e20825 https://doi.org/10.7717/peerj.20825
date submitted: 2025-09-02
date accepted: 2025-12-30
issued: 2026-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Wu
author list: Agent
  family name: Xie
  given name: Jinbiao
author list: Agent
  family name: Yang
  given name: Tianbao
author list: Agent
  family name: Huang
  given name: Shijie
author list: Agent
  family name: Chen
  given name: Boyang
doi: 10.7717/peerj.20825
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-17
copyright: ©2026 Wang et al.
attribution name: Wang et al.

In vitro bioactivity and phytochemical characterization of a polyherbal extract with antioxidant and anticancer properties
type: item
type: AcademicArticle
description: Herbal extracts are increasingly recognized for their therapeutic potential due to their rich phytochemical composition and associated bioactivities. This study evaluates the antioxidant and anticancer properties of a compound extract derived from Sidr (Ziziphus spina-christi), Fenugreek (Trigonella foenum-graecum), and Black Seed (Nigella sativa), Quantitative phytochemical analysis revealed high total phenolic (89.35 ± 0.36 mg GAE/g) and tannin content (88.60 ± 0.51 mg GAE/g), along with moderate flavonoid (28.67 ± 0.09 mg QE/g) and flavonol (10.52 ± 0.51 mg QE/g) levels, indicative of robust antioxidant potential. The extract demonstrated notable free-radical scavenging activity, with IC50 values of 359.93 ± 9.91 µg/mL and 292.93 ± 4.24 µg/mL in the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) assays, respectively. Cytotoxicity evaluation against Caco-2 colorectal cancer cells showed an IC50 value of 103.40 ± 4.51 µg/mL, supporting its anticancer potential. UV–Vis spectral analysis identified a prominent peak at 323.14 nm, suggesting the presence of phenolic and aromatic compounds, while zeta potential analysis (−22.1 ± 6.92 mV) indicated moderate dispersion stability. These results provide preliminary evidence supporting the extract’s potential as a multifunctional bioactive formulation and offer a foundation for future mechanistic and in vivo investigations.
format: application/pdf
format: text/html
creator: Aiman Abdullah Ammari
creator: Hossam Mohammed Aljawdah
creator: Ramzi Ahmed Amran
creator: Ahmad Rashed Alhimaidi
subject: Biochemistry
subject: Plant Science
subject: Pharmacology
description: doi:10.7717/peerj.20824
publisher: PeerJ Inc.
rights: © 2026 Ammari et al.
abstract: Herbal extracts are increasingly recognized for their therapeutic potential due to their rich phytochemical composition and associated bioactivities. This study evaluates the antioxidant and anticancer properties of a compound extract derived from Sidr (Ziziphus spina-christi), Fenugreek (Trigonella foenum-graecum), and Black Seed (Nigella sativa), Quantitative phytochemical analysis revealed high total phenolic (89.35 ± 0.36 mg GAE/g) and tannin content (88.60 ± 0.51 mg GAE/g), along with moderate flavonoid (28.67 ± 0.09 mg QE/g) and flavonol (10.52 ± 0.51 mg QE/g) levels, indicative of robust antioxidant potential. The extract demonstrated notable free-radical scavenging activity, with IC50 values of 359.93 ± 9.91 µg/mL and 292.93 ± 4.24 µg/mL in the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) assays, respectively. Cytotoxicity evaluation against Caco-2 colorectal cancer cells showed an IC50 value of 103.40 ± 4.51 µg/mL, supporting its anticancer potential. UV–Vis spectral analysis identified a prominent peak at 323.14 nm, suggesting the presence of phenolic and aromatic compounds, while zeta potential analysis (−22.1 ± 6.92 mV) indicated moderate dispersion stability. These results provide preliminary evidence supporting the extract’s potential as a multifunctional bioactive formulation and offer a foundation for future mechanistic and in vivo investigations.
bibliographic citation: Ammari et al. (2026) In vitro bioactivity and phytochemical characterization of a polyherbal extract with antioxidant and anticancer properties. PeerJ 14:e20824 https://doi.org/10.7717/peerj.20824
date submitted: 2025-10-16
date accepted: 2025-12-29
issued: 2026-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ammari
  given name: Aiman Abdullah
author list: Agent
  family name: Aljawdah
  given name: Hossam Mohammed
author list: Agent
  family name: Amran
  given name: Ramzi Ahmed
author list: Agent
  family name: Alhimaidi
  given name: Ahmad Rashed
doi: 10.7717/peerj.20824
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-17
copyright: ©2026 Ammari et al.
attribution name: Ammari et al.

Test–retest reliability of kicking performance assessments over a 2-day interval in elite youth soccer players
type: item
type: AcademicArticle
description: Background Reliable assessment of kicking performance is critical for monitoring technical development in youth soccer players. This study examined the reliability of kicking performance assessments in skilled youth soccer players aged 14–18, focusing on maximum ball speed and accuracy. Method Using a test-retest design, fifty-three players from a Danish Super League academy completed standardised kicking tests on two occasions separated by 2 days. Maximum ball speed was assessed during penalty-style kicks with a stationary ball, while accuracy was assessed through target-directed kicks with a rolling ball. Two-way mixed-effects intraclass correlation coefficients (ICC) and limits of agreement (LoA) were used to assess reliability. Results Results indicated good reliability for maximum ball speed (ICC = 0.87; LoA = [−2.1, 2.5] m/s), consistent with previous studies. Conversely, kicking accuracy demonstrated poor to moderate reliability (ICC = 0.00–0.66; LoA = [−0.46, 0.48] m). Stratified analyses revealed the highest accuracy ICC within the U15 group. Exploratory error ellipse analyses suggested potential utility in assessing kicking distribution, showing good reliability for ellipse angle (ICC = 0.80; LoA = [−0.98, 0.92] rad), though other parameters displayed low reliability. These findings highlight the strengths and limitations of soccer technical assessments. While maximum ball speed tests are highly reliable, kicking accuracy assessments remain problematic and require methodological refinement to improve reliability. Future research should incorporate advanced analytical techniques to enhance test reliability and consistency in elite athlete evaluations.
format: application/pdf
format: text/html
creator: Jeppe Carstensen
creator: Thomas Bull Andersen
subject: Kinesiology
subject: Statistics
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.20806
publisher: PeerJ Inc.
rights: © 2026 Carstensen and Andersen
abstract: Background Reliable assessment of kicking performance is critical for monitoring technical development in youth soccer players. This study examined the reliability of kicking performance assessments in skilled youth soccer players aged 14–18, focusing on maximum ball speed and accuracy. Method Using a test-retest design, fifty-three players from a Danish Super League academy completed standardised kicking tests on two occasions separated by 2 days. Maximum ball speed was assessed during penalty-style kicks with a stationary ball, while accuracy was assessed through target-directed kicks with a rolling ball. Two-way mixed-effects intraclass correlation coefficients (ICC) and limits of agreement (LoA) were used to assess reliability. Results Results indicated good reliability for maximum ball speed (ICC = 0.87; LoA = [−2.1, 2.5] m/s), consistent with previous studies. Conversely, kicking accuracy demonstrated poor to moderate reliability (ICC = 0.00–0.66; LoA = [−0.46, 0.48] m). Stratified analyses revealed the highest accuracy ICC within the U15 group. Exploratory error ellipse analyses suggested potential utility in assessing kicking distribution, showing good reliability for ellipse angle (ICC = 0.80; LoA = [−0.98, 0.92] rad), though other parameters displayed low reliability. These findings highlight the strengths and limitations of soccer technical assessments. While maximum ball speed tests are highly reliable, kicking accuracy assessments remain problematic and require methodological refinement to improve reliability. Future research should incorporate advanced analytical techniques to enhance test reliability and consistency in elite athlete evaluations.
bibliographic citation: Carstensen et al. (2026) Test–retest reliability of kicking performance assessments over a 2-day interval in elite youth soccer players. PeerJ 14:e20806 https://doi.org/10.7717/peerj.20806
date submitted: 2025-09-10
date accepted: 2025-12-26
issued: 2026-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carstensen
  given name: Jeppe
author list: Agent
  family name: Andersen
  given name: Thomas Bull
doi: 10.7717/peerj.20806
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-17
copyright: ©2026 Carstensen and Andersen
attribution name: Carstensen and Andersen

Physiological dynamics of body temperature and heart rate during hibernation periods in male Japanese black bears (Ursus thibetanus japonicus)
type: item
type: AcademicArticle
description: Background The Japanese black bear (Ursus thibetanus japonicus) exhibits a profound seasonal metabolism shift, with a substantial increase in body weight in autumn and metabolic suppression during hibernation in winter. This species hibernates under the strict regulation of endogenous and environmental factors, making it a compelling subject for studies on the interrelationships between vital signs and metabolism. Studies continuously monitoring body temperature (Tb) and heart rate (HR) in Japanese black bears is limited, leaving gaps in understanding their synchronized fluctuations during hibernation. Methods Here, we conducted long-term monitoring to investigate changes in the Tb and HR of Japanese black bears across the pre-hibernation, hibernation-induction, hibernation, and post-hibernation periods. Subcutaneous Tb and HR loggers of six captive male bears were monitored for Tb and HR from October 2017 to May 2018. Results The Tb of male bears decreased gradually from the pre-hibernation period to the hibernation-induction period, experienced a predicted mean Tb of 35.2 °C (95% confidence interval (CI) [35.00–35.38]) during the hibernation period, and subsequently increased gradually during the post-hibernation period. The HR decreased rapidly at the end of the pre-hibernation and hibernation-induction periods, stabilized at a predicted mean of 44.76 bpm (95% CI [34.54–54.98]) bpm during the hibernation period, and subsequently increased rapidly at the beginning of the post-hibernation period. Tb and HR followed ~24-h cycles during the pre-and post-hibernation periods. Conversely, Tb and HR fluctuations exhibited synchronization with multi-day cycles during the hibernation periods. These results suggest that Japanese black bears exhibit a daily (24-h) rhythm of Tb and HR during the pre- and post-hibernation periods, while autonomic nervous system regulation predominates during hibernation period. We observed a difference between changes in Tb and HR, Tb decrease…
format: application/pdf
format: text/html
creator: Xiaofei Luo
creator: Alice C. C. Lau
creator: Michito Shimozuru
creator: Mariko Sashika
creator: Toshio Tsubota
subject: Animal Behavior
subject: Ecology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.20798
publisher: PeerJ Inc.
rights: © 2026 Luo et al.
abstract: Background The Japanese black bear (Ursus thibetanus japonicus) exhibits a profound seasonal metabolism shift, with a substantial increase in body weight in autumn and metabolic suppression during hibernation in winter. This species hibernates under the strict regulation of endogenous and environmental factors, making it a compelling subject for studies on the interrelationships between vital signs and metabolism. Studies continuously monitoring body temperature (Tb) and heart rate (HR) in Japanese black bears is limited, leaving gaps in understanding their synchronized fluctuations during hibernation. Methods Here, we conducted long-term monitoring to investigate changes in the Tb and HR of Japanese black bears across the pre-hibernation, hibernation-induction, hibernation, and post-hibernation periods. Subcutaneous Tb and HR loggers of six captive male bears were monitored for Tb and HR from October 2017 to May 2018. Results The Tb of male bears decreased gradually from the pre-hibernation period to the hibernation-induction period, experienced a predicted mean Tb of 35.2 °C (95% confidence interval (CI) [35.00–35.38]) during the hibernation period, and subsequently increased gradually during the post-hibernation period. The HR decreased rapidly at the end of the pre-hibernation and hibernation-induction periods, stabilized at a predicted mean of 44.76 bpm (95% CI [34.54–54.98]) bpm during the hibernation period, and subsequently increased rapidly at the beginning of the post-hibernation period. Tb and HR followed ~24-h cycles during the pre-and post-hibernation periods. Conversely, Tb and HR fluctuations exhibited synchronization with multi-day cycles during the hibernation periods. These results suggest that Japanese black bears exhibit a daily (24-h) rhythm of Tb and HR during the pre- and post-hibernation periods, while autonomic nervous system regulation predominates during hibernation period. We observed a difference between changes in Tb and HR, Tb decrease…
bibliographic citation: Luo et al. (2026) Physiological dynamics of body temperature and heart rate during hibernation periods in male Japanese black bears (Ursus thibetanus japonicus). PeerJ 14:e20798 https://doi.org/10.7717/peerj.20798
date submitted: 2025-09-01
date accepted: 2025-12-23
issued: 2026-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Xiaofei
author list: Agent
  family name: Lau
  given name: Alice C. C.
author list: Agent
  family name: Shimozuru
  given name: Michito
author list: Agent
  family name: Sashika
  given name: Mariko
author list: Agent
  family name: Tsubota
  given name: Toshio
doi: 10.7717/peerj.20798
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-17
copyright: © 2026 Luo et al.
attribution name: Luo et al.

Behavioral implications of an embedded tyrannosaurid tooth and associated tooth marks on an articulated skull of Edmontosaurus from the Hell Creek Formation, Montana
type: item
type: AcademicArticle
description: Because teeth can be taxonomically distinct, particularly for non-mammalian carnivores such as non-avian dinosaurs, teeth that have broken off in the bone of another animal during feeding, predation or antagonism can provide direct information on carnivore behaviour. Here, we report on a semi-complete, articulated adult Edmontosaurus skull (MOR 1627) from the Hell Creek Formation with an embedded theropod tooth in the nasal. To ascertain taxonomic identity of the preserved tooth tip, we compare standardized crown and denticle measurements as well as denticle descriptions of the embedded tooth to known non-avian theropods recovered from the Hell Creek Formation. We also use computed tomography (CT) scans to investigate the full extent and orientation of the embedded tooth. The apicobasal, labiolingual and mesiodistal dimensions of the tip as well as measured denticle densities and observed denticle characteristics indicate the embedded tooth is from a medium to large bodied tyrannosaurid. The curvature and ovoid cross-sectional shape of the tooth further suggests that the tooth is a maxillary tooth from a middle or posterior tooth position. The lack of reactive bone in the region surrounding the tooth suggests the animal died around the time the tooth became embedded in the nasal. Combined, this information suggests the tooth broke off when a tyrannosaurid bit the snout of the Edmontosaurus from the front at or near the time of death of the animal. Comparing observations of hunting and feeding behaviors of modern carnivores specializing in large-bodied prey, the scenario captured by MOR 1627 is most consistent with a bite inflicted during an attempt to control the struggling Edmontosaurus or deliver a killing blow followed by carcass consumption.
format: application/pdf
format: text/html
creator: Taia C.A. Wyenberg-Henzler
creator: John B. Scannella
subject: Animal Behavior
subject: Ecology
subject: Paleontology
description: doi:10.7717/peerj.20796
publisher: PeerJ Inc.
rights: © 2026 Wyenberg-Henzler and Scannella
abstract: Because teeth can be taxonomically distinct, particularly for non-mammalian carnivores such as non-avian dinosaurs, teeth that have broken off in the bone of another animal during feeding, predation or antagonism can provide direct information on carnivore behaviour. Here, we report on a semi-complete, articulated adult Edmontosaurus skull (MOR 1627) from the Hell Creek Formation with an embedded theropod tooth in the nasal. To ascertain taxonomic identity of the preserved tooth tip, we compare standardized crown and denticle measurements as well as denticle descriptions of the embedded tooth to known non-avian theropods recovered from the Hell Creek Formation. We also use computed tomography (CT) scans to investigate the full extent and orientation of the embedded tooth. The apicobasal, labiolingual and mesiodistal dimensions of the tip as well as measured denticle densities and observed denticle characteristics indicate the embedded tooth is from a medium to large bodied tyrannosaurid. The curvature and ovoid cross-sectional shape of the tooth further suggests that the tooth is a maxillary tooth from a middle or posterior tooth position. The lack of reactive bone in the region surrounding the tooth suggests the animal died around the time the tooth became embedded in the nasal. Combined, this information suggests the tooth broke off when a tyrannosaurid bit the snout of the Edmontosaurus from the front at or near the time of death of the animal. Comparing observations of hunting and feeding behaviors of modern carnivores specializing in large-bodied prey, the scenario captured by MOR 1627 is most consistent with a bite inflicted during an attempt to control the struggling Edmontosaurus or deliver a killing blow followed by carcass consumption.
bibliographic citation: Wyenberg-Henzler et al. (2026) Behavioral implications of an embedded tyrannosaurid tooth and associated tooth marks on an articulated skull of Edmontosaurus from the Hell Creek Formation, Montana. PeerJ 14:e20796 https://doi.org/10.7717/peerj.20796
date submitted: 2025-04-24
date accepted: 2025-12-23
issued: 2026-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wyenberg-Henzler
  given name: Taia C.A.
author list: Agent
  family name: Scannella
  given name: John B.
doi: 10.7717/peerj.20796
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-17
copyright: ©2026 Wyenberg-Henzler and Scannella
attribution name: Wyenberg-Henzler and Scannella

Digesting an ancient ecosystem: coprolites from the Grippia bonebed, Lower Triassic, Svalbard
type: item
type: AcademicArticle
description: The marine Grippia bonebed from Vikinghøgda Formation, Lower Triassic, Svalbard is composed of scattered skeletal remains, teeth and coprolites. From this, five coprolite morphotypes have been identified and described. In this study 97 coprolites were examined and classified based on their morphology and inclusions. Thin sections, scanning electron microscope (SEM) and micro-computed tomography (micro-CT) were used to analyze the inclusions revealing skeletal material, fish scales and notably the first observations of invertebrates in this locality. Among the invertebrate components were sponge spicules, a fragment of a cephalopod shell and numerous onychites. Potential coprolite producers are evaluated and likely include chondrichthyans, osteichthyes, ichthyopterygians and temnospondyls. Additionally, this research provides a CT-scanning method for identifying low-density inclusions such as onychites and contribute to a better understanding of the marine Early Triassic paleoecosystem and food web on Svalbard.
format: application/pdf
format: text/html
creator: Vanja Simonsen
creator: Aubrey Jane Roberts
creator: Victoria Sjøholt Engelschiøn
creator: Øyvind Hammer
creator: Jørn H. Hurum
subject: Ecology
subject: Paleontology
description: doi:10.7717/peerj.20746
publisher: PeerJ Inc.
rights: © 2026 Simonsen et al.
abstract: The marine Grippia bonebed from Vikinghøgda Formation, Lower Triassic, Svalbard is composed of scattered skeletal remains, teeth and coprolites. From this, five coprolite morphotypes have been identified and described. In this study 97 coprolites were examined and classified based on their morphology and inclusions. Thin sections, scanning electron microscope (SEM) and micro-computed tomography (micro-CT) were used to analyze the inclusions revealing skeletal material, fish scales and notably the first observations of invertebrates in this locality. Among the invertebrate components were sponge spicules, a fragment of a cephalopod shell and numerous onychites. Potential coprolite producers are evaluated and likely include chondrichthyans, osteichthyes, ichthyopterygians and temnospondyls. Additionally, this research provides a CT-scanning method for identifying low-density inclusions such as onychites and contribute to a better understanding of the marine Early Triassic paleoecosystem and food web on Svalbard.
bibliographic citation: Simonsen et al. (2026) Digesting an ancient ecosystem: coprolites from the Grippia bonebed, Lower Triassic, Svalbard. PeerJ 14:e20746 https://doi.org/10.7717/peerj.20746
date submitted: 2025-05-06
date accepted: 2025-12-16
issued: 2026-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simonsen
  given name: Vanja
author list: Agent
  family name: Roberts
  given name: Aubrey Jane
author list: Agent
  family name: Engelschiøn
  given name: Victoria Sjøholt
author list: Agent
  family name: Hammer
  given name: Øyvind
author list: Agent
  family name: Hurum
  given name: Jørn H.
doi: 10.7717/peerj.20746
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-17
copyright: ©2026 Simonsen et al.
attribution name: Simonsen et al.

The burden of neural tube defects in Southern Ethiopia: trends, hotspots, and public health implications
type: item
type: AcademicArticle
description: Background Neural tube defects (NTDs) are complex multifactorial disorders in the neurulation of the brain and spinal cord that occur between 21 and 28 days after conception. Limited evidence exists regarding the burden of NTDs in Ethiopia, particularly in southern areas. This study aimed to assess the burden, spatial and temporal distribution, and public health implications of neural tube defects in southern Ethiopia. Methods This multicenter retrospective study used a structured checklist to collect data from records of women who gave birth in the selected hospitals from January 2017 through December 2021. Birth prevalence of NTDs was calculated per 10,000 births, and temporal trends were assessed using the extended Mantel-Haenszel chi-square test. Spatial analysis was performed to identify hotspot areas. Data were analyzed using SPSS version 25 and ArcGIS version 10.1. Results A total of 199,353 babies were delivered at the selected hospitals during the study period, and 320 had NTDs. The overall prevalence of NTDs was 16.1 (95% CI [14.34–17.91]) per 10,000 births. Halaba Kulito General Hospital and Worabe Comprehensive Specialized Hospital reported the highest and second-highest prevalence, at 52.1 and 43.3 per 10,000 births, respectively. Anencephaly was the most frequent type (8.6 per 10,000), followed by spina bifida (6.5 per 10,000). Hotspot clusters, ranging from 16.0 to 46.1 per 10,000 births, were identified in the Halaba, Meskan, and Konso districts of southern Ethiopia. Only 36.6% of NTDs were diagnosed by ultrasound during pregnancy. NTDs were more common in females (61.3%) than males, and approximately three-quarters of affected babies were stillborn. Conclusion NTDs represent a significant public health concern in southern Ethiopia, with anencephaly and spina bifida being the most prevalent types. No significant linear trend was observed over the five-year period. Most hotspot districts are located within Ethiopia’s Great Rift Valley. Strengthening p…
format: application/pdf
format: text/html
creator: Beminet Moges Gebremariam
creator: Dejene Hailu Kassa
creator: Barbara J. Stoecker
creator: Afework Mulugeta
subject: Neurology
subject: Nutrition
subject: Pediatrics
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.20447
publisher: PeerJ Inc.
rights: © 2026 Gebremariam et al.
abstract: Background Neural tube defects (NTDs) are complex multifactorial disorders in the neurulation of the brain and spinal cord that occur between 21 and 28 days after conception. Limited evidence exists regarding the burden of NTDs in Ethiopia, particularly in southern areas. This study aimed to assess the burden, spatial and temporal distribution, and public health implications of neural tube defects in southern Ethiopia. Methods This multicenter retrospective study used a structured checklist to collect data from records of women who gave birth in the selected hospitals from January 2017 through December 2021. Birth prevalence of NTDs was calculated per 10,000 births, and temporal trends were assessed using the extended Mantel-Haenszel chi-square test. Spatial analysis was performed to identify hotspot areas. Data were analyzed using SPSS version 25 and ArcGIS version 10.1. Results A total of 199,353 babies were delivered at the selected hospitals during the study period, and 320 had NTDs. The overall prevalence of NTDs was 16.1 (95% CI [14.34–17.91]) per 10,000 births. Halaba Kulito General Hospital and Worabe Comprehensive Specialized Hospital reported the highest and second-highest prevalence, at 52.1 and 43.3 per 10,000 births, respectively. Anencephaly was the most frequent type (8.6 per 10,000), followed by spina bifida (6.5 per 10,000). Hotspot clusters, ranging from 16.0 to 46.1 per 10,000 births, were identified in the Halaba, Meskan, and Konso districts of southern Ethiopia. Only 36.6% of NTDs were diagnosed by ultrasound during pregnancy. NTDs were more common in females (61.3%) than males, and approximately three-quarters of affected babies were stillborn. Conclusion NTDs represent a significant public health concern in southern Ethiopia, with anencephaly and spina bifida being the most prevalent types. No significant linear trend was observed over the five-year period. Most hotspot districts are located within Ethiopia’s Great Rift Valley. Strengthening p…
bibliographic citation: Gebremariam et al. (2026) The burden of neural tube defects in Southern Ethiopia: trends, hotspots, and public health implications. PeerJ 14:e20447 https://doi.org/10.7717/peerj.20447
date submitted: 2025-02-17
date accepted: 2025-10-31
issued: 2026-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gebremariam
  given name: Beminet Moges
author list: Agent
  family name: Kassa
  given name: Dejene Hailu
author list: Agent
  family name: Stoecker
  given name: Barbara J.
author list: Agent
  family name: Mulugeta
  given name: Afework
doi: 10.7717/peerj.20447
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-17
copyright: ©2026 Gebremariam et al.
attribution name: Gebremariam et al.

Comprehensive efficacy of different prostate resection volumes for patients with benign prostatic hyperplasia: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Benign prostatic hyperplasia is one of the most common urological diseases in middle-aged and elderly men worldwide. The most effective treatment is surgery, and multiple surgical approaches, including traditional electroprostatectomy, laser vaporization, or steam ablation, have already been widely applied in clinical practice. However, few studies summarizing and reporting the comprehensive outcomes of whether different prostate resection volumes affect the efficacy of benign prostatic hyperplasia surgery exist. Thus, we conducted a systematic review and meta-analysis involving cohort studies and randomized controlled trials to compare the postoperative influence of different residual prostate volumes in patients with benign prostatic hyperplasia (BPH) to explore the best surgical treatment and minimize the recurrence rate and other complications. A total of 16 randomized controlled trials (RCTs) involving 2,164 patients who underwent prostate surgery were included in our analysis. In summary, compared with patients who had a smaller resected prostate volume, patients with more resected prostate tissue were more likely to have a lower International Prostate Symptom Score (IPSS), a lower postvoid residual urine volume (PVR), a higher quality of life (QoL) and maximal urinary flow rate (Qmax), and a decreased risk of bladder neck construction. However, patients with less resected prostate volume had advantages in terms of decreasing catheterization time, hospital stay, irrigation time, and the rates of blood transfusion and retrograde ejaculation. Moreover, the resected prostate volume was not correlated with the incidence of other complications. Given the limitations existing in our study, more primary studies are still needed in the future.
format: application/pdf
format: text/html
creator: Puze Wang
creator: Jinze Li
creator: Ziqiao Tang
creator: Liangren Liu
creator: Dong Lv
subject: Surgery and Surgical Specialties
subject: Urology
description: doi:10.7717/peerj.20819
publisher: PeerJ Inc.
rights: © 2026 Wang et al.
abstract: Benign prostatic hyperplasia is one of the most common urological diseases in middle-aged and elderly men worldwide. The most effective treatment is surgery, and multiple surgical approaches, including traditional electroprostatectomy, laser vaporization, or steam ablation, have already been widely applied in clinical practice. However, few studies summarizing and reporting the comprehensive outcomes of whether different prostate resection volumes affect the efficacy of benign prostatic hyperplasia surgery exist. Thus, we conducted a systematic review and meta-analysis involving cohort studies and randomized controlled trials to compare the postoperative influence of different residual prostate volumes in patients with benign prostatic hyperplasia (BPH) to explore the best surgical treatment and minimize the recurrence rate and other complications. A total of 16 randomized controlled trials (RCTs) involving 2,164 patients who underwent prostate surgery were included in our analysis. In summary, compared with patients who had a smaller resected prostate volume, patients with more resected prostate tissue were more likely to have a lower International Prostate Symptom Score (IPSS), a lower postvoid residual urine volume (PVR), a higher quality of life (QoL) and maximal urinary flow rate (Qmax), and a decreased risk of bladder neck construction. However, patients with less resected prostate volume had advantages in terms of decreasing catheterization time, hospital stay, irrigation time, and the rates of blood transfusion and retrograde ejaculation. Moreover, the resected prostate volume was not correlated with the incidence of other complications. Given the limitations existing in our study, more primary studies are still needed in the future.
bibliographic citation: Wang et al. (2026) Comprehensive efficacy of different prostate resection volumes for patients with benign prostatic hyperplasia: a systematic review and meta-analysis. PeerJ 14:e20819 https://doi.org/10.7717/peerj.20819
date submitted: 2025-07-29
date accepted: 2025-12-28
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Puze
author list: Agent
  family name: Li
  given name: Jinze
author list: Agent
  family name: Tang
  given name: Ziqiao
author list: Agent
  family name: Liu
  given name: Liangren
author list: Agent
  family name: Lv
  given name: Dong
doi: 10.7717/peerj.20819
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Wang et al.
attribution name: Wang et al.

https://peerj.com/articles/20801
type: item
type: AcademicArticle
title: Clinical effects and safety of proximal femur bionic nail versus proximal femoral nail anti-rotation or InterTAN for the treatment of intertrochanteric femoral fracture: a systematic review and meta-analysis
description: Objective To compare the clinical effects and safety of the proximal femur bionic nail (PFBN) with those of proximal femoral nail anti-rotation (PFNA) and InterTAN for the treatment of intertrochanteric femoral fracture (IFF). Methods Studies comparing the clinical efficacy of PFBN with that of PFNA and InterTAN in the treatment of IFF published before 16 December 2025 in the PubMed, Embase, Web of Science, Cochrane, CNKI, Wanfang, and VIP databases were retrieved. After the research data were extracted, Review Manager 5.4 (RevMan 5.4 ) was used for data analysis. Results A total of 15 studies involving 990 patients were included. The meta-analysis results indicated that the PFBN group had advantages over the control group in terms of the postoperative partial and full weight-bearing time, fracture healing time, fracture reduction quality, hospital stay, postoperative Harris score, intraoperative fluoroscopy time and postoperative complication rate (partial weight-bearing time: standardized mean difference (SMD) = −3.49, 95% confidence interval (CI) [−4.47 to −2.52], P < 0.00001; full weight-bearing time: SMD = −1.78, 95% CI [−2.86 to −0.70], P = 0.001; fracture healing time: SMD = −0.61, 95% CI −[0.86 to −0.37], P < 0.00001; fracture reduction quality: relative risk (RR) = 1.07, 95% CI [1.01∼1.13], P = 0.02; hospital stay: SMD = −0.44, 95% CI [−0.81 to −0.08], P = 0.02; postoperative complication rate: RR = 0.36, 95% CI [0.22∼0.59], P < 0.0001; postoperative Harris score: SMD = 0.32, 95% CI [0.04∼0.60], P = 0.02; intraoperative fluoroscopy time: SMD = 0.76, 95% CI [0.10∼1.42], P = 0.02). There was no significant difference between the two groups in terms of intraoperative blood loss, operation duration, postoperative hip range of motion, postoperative VAS score, or incision length (intraoperative blood loss: SMD = −0.30, 95% CI [−0.81∼0.21], P = 0.25; operation duration: SMD = 0.41, 95% CI [−0.03∼0.85], P = 0.07; postoperative flexion and extension motion: SMD = 0.…
format: application/pdf
format: text/html
creator: Wenbin Zhang
creator: Yulin Ma
creator: Feilong Lu
creator: Hao Song
creator: Xiaoming Du
creator: Zhaoxi Yang
creator: Yimei Hu
subject: Evidence Based Medicine
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.20801
publisher: PeerJ Inc.
rights: © 2026 Zhang et al.
abstract: Objective To compare the clinical effects and safety of the proximal femur bionic nail (PFBN) with those of proximal femoral nail anti-rotation (PFNA) and InterTAN for the treatment of intertrochanteric femoral fracture (IFF). Methods Studies comparing the clinical efficacy of PFBN with that of PFNA and InterTAN in the treatment of IFF published before 16 December 2025 in the PubMed, Embase, Web of Science, Cochrane, CNKI, Wanfang, and VIP databases were retrieved. After the research data were extracted, Review Manager 5.4 (RevMan 5.4 ) was used for data analysis. Results A total of 15 studies involving 990 patients were included. The meta-analysis results indicated that the PFBN group had advantages over the control group in terms of the postoperative partial and full weight-bearing time, fracture healing time, fracture reduction quality, hospital stay, postoperative Harris score, intraoperative fluoroscopy time and postoperative complication rate (partial weight-bearing time: standardized mean difference (SMD) = −3.49, 95% confidence interval (CI) [−4.47 to −2.52], P < 0.00001; full weight-bearing time: SMD = −1.78, 95% CI [−2.86 to −0.70], P = 0.001; fracture healing time: SMD = −0.61, 95% CI −[0.86 to −0.37], P < 0.00001; fracture reduction quality: relative risk (RR) = 1.07, 95% CI [1.01∼1.13], P = 0.02; hospital stay: SMD = −0.44, 95% CI [−0.81 to −0.08], P = 0.02; postoperative complication rate: RR = 0.36, 95% CI [0.22∼0.59], P < 0.0001; postoperative Harris score: SMD = 0.32, 95% CI [0.04∼0.60], P = 0.02; intraoperative fluoroscopy time: SMD = 0.76, 95% CI [0.10∼1.42], P = 0.02). There was no significant difference between the two groups in terms of intraoperative blood loss, operation duration, postoperative hip range of motion, postoperative VAS score, or incision length (intraoperative blood loss: SMD = −0.30, 95% CI [−0.81∼0.21], P = 0.25; operation duration: SMD = 0.41, 95% CI [−0.03∼0.85], P = 0.07; postoperative flexion and extension motion: SMD = 0.…
bibliographic citation: Zhang et al. (2026) Clinical effects and safety of proximal femur bionic nail versus proximal femoral nail anti-rotation or InterTAN for the treatment of intertrochanteric femoral fracture: a systematic review and meta-analysis. PeerJ 14:e20801 https://doi.org/10.7717/peerj.20801
date submitted: 2025-06-26
date accepted: 2025-12-24
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Wenbin
author list: Agent
  family name: Ma
  given name: Yulin
author list: Agent
  family name: Lu
  given name: Feilong
author list: Agent
  family name: Song
  given name: Hao
author list: Agent
  family name: Du
  given name: Xiaoming
author list: Agent
  family name: Yang
  given name: Zhaoxi
author list: Agent
  family name: Hu
  given name: Yimei
doi: 10.7717/peerj.20801
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Zhang et al.
attribution name: Zhang et al.

Serum lncRNA H19/miR-675 /PPARα expression before middle gestation and their associations with macrosomia risk in singleton pregnancies without gestational diabetes mellitus: a preliminary study
type: item
type: AcademicArticle
description: Background The roles of maternal serum lncRNA H19, miR-675, and PPARα protein levels before mid-pregnancy in predicting macrosomia remain unclear. This study aimed to investigate whether the expression of these serum molecules is associated with the risk of macrosomia in singleton pregnancies without gestational diabetes mellitus. Methods A nested case-control study was conducted within a prospective cohort study of 898 women with singleton pregnancies. Mothers of liveborn macrosomic newborns constituted the case group, and a random sample of mothers of the normal-birthweight newborns, matched on gestational age at blood collection and delivery date, served as controls. Serum levels of lncRNA H19, miR-675, PPARα protein, and serum lipids were measured before 20 weeks’ gestation. Logistic regression, restricted cubic spline analysis, and stratified analysis were used to assess the associations. Predictive performance was explored using area under the receiver operating characteristic curve, net reclassification index (NRI), and integrated discrimination improvement (IDI). Results No significant differences were observed in lncRNA H19 (Z = − 0.344, P = 0.731), miR-675 (Z = − 1.376, P = 0.169), or PPARα protein levels (Z < 0, P = 0.999) between macrosomia and control groups. However, in women with pre-pregnancy BMI < 24 kg/m2, lower PPARα protein levels (tertile 2 vs. tertile 3) were associated with a 70% reduced risk of macrosomia (OR = 0.30, 95% CI [0.09–0.99], P = 0.049). The NRI and IDI of the combined model incorporating serum lncRNA H19, miR-675, and PPARα protein levels were statistically superior to lipid-based models (P < 0.05). Conclusions Serum lncRNA H19 and miR-675 were not associated with macrosomia risk. Lower serum PPARα protein levels in early pregnancy may be associated with a reduced risk of macrosomia, particularly in non-obese women. The combined biomarkers demonstrated preliminary predictive potential in exploratory analysis, but validation in lar…
format: application/pdf
format: text/html
creator: Qiuyan Yu
creator: Ming Min Jin
creator: Miao Miao Ding
creator: Bin Wei Cheng
creator: Xiao Xia He
creator: Xin Jun Yang
subject: Biochemistry
subject: Epidemiology
subject: Global Health
subject: Gynecology and Obstetrics
subject: Pediatrics
description: doi:10.7717/peerj.20793
publisher: PeerJ Inc.
rights: © 2026 Yu et al.
abstract: Background The roles of maternal serum lncRNA H19, miR-675, and PPARα protein levels before mid-pregnancy in predicting macrosomia remain unclear. This study aimed to investigate whether the expression of these serum molecules is associated with the risk of macrosomia in singleton pregnancies without gestational diabetes mellitus. Methods A nested case-control study was conducted within a prospective cohort study of 898 women with singleton pregnancies. Mothers of liveborn macrosomic newborns constituted the case group, and a random sample of mothers of the normal-birthweight newborns, matched on gestational age at blood collection and delivery date, served as controls. Serum levels of lncRNA H19, miR-675, PPARα protein, and serum lipids were measured before 20 weeks’ gestation. Logistic regression, restricted cubic spline analysis, and stratified analysis were used to assess the associations. Predictive performance was explored using area under the receiver operating characteristic curve, net reclassification index (NRI), and integrated discrimination improvement (IDI). Results No significant differences were observed in lncRNA H19 (Z = − 0.344, P = 0.731), miR-675 (Z = − 1.376, P = 0.169), or PPARα protein levels (Z < 0, P = 0.999) between macrosomia and control groups. However, in women with pre-pregnancy BMI < 24 kg/m2, lower PPARα protein levels (tertile 2 vs. tertile 3) were associated with a 70% reduced risk of macrosomia (OR = 0.30, 95% CI [0.09–0.99], P = 0.049). The NRI and IDI of the combined model incorporating serum lncRNA H19, miR-675, and PPARα protein levels were statistically superior to lipid-based models (P < 0.05). Conclusions Serum lncRNA H19 and miR-675 were not associated with macrosomia risk. Lower serum PPARα protein levels in early pregnancy may be associated with a reduced risk of macrosomia, particularly in non-obese women. The combined biomarkers demonstrated preliminary predictive potential in exploratory analysis, but validation in lar…
bibliographic citation: Yu et al. (2026) Serum lncRNA H19/miR-675 /PPARα expression before middle gestation and their associations with macrosomia risk in singleton pregnancies without gestational diabetes mellitus: a preliminary study. PeerJ 14:e20793 https://doi.org/10.7717/peerj.20793
date submitted: 2025-09-09
date accepted: 2025-12-23
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Qiuyan
author list: Agent
  family name: Jin
  given name: Ming Min
author list: Agent
  family name: Ding
  given name: Miao Miao
author list: Agent
  family name: Cheng
  given name: Bin Wei
author list: Agent
  family name: He
  given name: Xiao Xia
author list: Agent
  family name: Yang
  given name: Xin Jun
doi: 10.7717/peerj.20793
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Yu et al.
attribution name: Yu et al.

AKT1 but not AKT2 single nucleotide polymorphisms are associated with the risk of microscopic polyangiitis
type: item
type: AcademicArticle
description: Background Microscopic polyangiitis (MPA), a severe antineutrophil cytoplasmic antibody associated vasculitis (ANCA-associated vasculitis, AAV), demonstrates strong clinical association with myeloperoxidase/perinuclear anti-neutrophilic cytoplasmic antibodies (MPO/P-ANCA). While genetic factors are known to contribute to MPA susceptibility, the potential roles of AKT signaling components remain incompletely characterized, with limited data available for AKT1 and even less for its homologous gene AKT2 in this specific disease context. Methods This case-control analysis included 798 participants (202 MPA patients and 596 controls, the latter comprising 387 individuals from the 1,000 Genomes Project), with control groups pooled after confirmation of genetic homogeneity. Genotypes of seven single-nucleotidepolymorphisms (SNPs) (four in AKT1, three in AKT2) with divergent allele frequencies across populations were analyzed. Association analyses were conducted under multiple genetic models, with gene-level and set-based approaches employed to evaluate aggregate effects. Secondary analyses included haplotype reconstruction, SNP-SNP interaction testing, and functional characterization through expression quantitative trait locus (eQTL) mapping. Results Specific AKT1 variants (rs2498786 and rs1130233) demonstrated significant associations with reduced MPA risk, particularly in P-ANCA-positive patients. Gene-level analyses revealed a strong association for the AKT1 gene set (OR = 0.884, P = 0.002) but not for AKT2. Haplotype analysis identified protective AKT1 haplotypes, while interaction testing revealed high-risk genotype combinations. eQTL analysis indicated that protective alleles correlate with enhanced AKT1 expression in immune-relevant tissues, suggesting a potential regulatory mechanism. Conclusions AKT1 emerges from this study as a likely genetic contributor to MPA, with its influence potentially involving neutrophil regulatory functions and vascular maintenance. The…
format: application/pdf
format: text/html
creator: Lizhen Li
creator: Huifang Tan
creator: You Peng
creator: Liepeng Chu
creator: Jing Yang
creator: Wenlv Tang
creator: Kui Tan
creator: Shuangshuang Fu
creator: Meili Huang
creator: Meijun Xu
creator: Jinlan Rao
creator: Chao Xue
creator: Yinyin Chen
subject: Genetics
subject: Allergy and Clinical Immunology
subject: Immunology
subject: Rheumatology
subject: Medical Genetics
description: doi:10.7717/peerj.20791
publisher: PeerJ Inc.
rights: © 2026 Li et al.
abstract: Background Microscopic polyangiitis (MPA), a severe antineutrophil cytoplasmic antibody associated vasculitis (ANCA-associated vasculitis, AAV), demonstrates strong clinical association with myeloperoxidase/perinuclear anti-neutrophilic cytoplasmic antibodies (MPO/P-ANCA). While genetic factors are known to contribute to MPA susceptibility, the potential roles of AKT signaling components remain incompletely characterized, with limited data available for AKT1 and even less for its homologous gene AKT2 in this specific disease context. Methods This case-control analysis included 798 participants (202 MPA patients and 596 controls, the latter comprising 387 individuals from the 1,000 Genomes Project), with control groups pooled after confirmation of genetic homogeneity. Genotypes of seven single-nucleotidepolymorphisms (SNPs) (four in AKT1, three in AKT2) with divergent allele frequencies across populations were analyzed. Association analyses were conducted under multiple genetic models, with gene-level and set-based approaches employed to evaluate aggregate effects. Secondary analyses included haplotype reconstruction, SNP-SNP interaction testing, and functional characterization through expression quantitative trait locus (eQTL) mapping. Results Specific AKT1 variants (rs2498786 and rs1130233) demonstrated significant associations with reduced MPA risk, particularly in P-ANCA-positive patients. Gene-level analyses revealed a strong association for the AKT1 gene set (OR = 0.884, P = 0.002) but not for AKT2. Haplotype analysis identified protective AKT1 haplotypes, while interaction testing revealed high-risk genotype combinations. eQTL analysis indicated that protective alleles correlate with enhanced AKT1 expression in immune-relevant tissues, suggesting a potential regulatory mechanism. Conclusions AKT1 emerges from this study as a likely genetic contributor to MPA, with its influence potentially involving neutrophil regulatory functions and vascular maintenance. The…
bibliographic citation: Li et al. (2026) AKT1 but not AKT2 single nucleotide polymorphisms are associated with the risk of microscopic polyangiitis. PeerJ 14:e20791 https://doi.org/10.7717/peerj.20791
date submitted: 2025-05-28
date accepted: 2025-12-23
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Lizhen
author list: Agent
  family name: Tan
  given name: Huifang
author list: Agent
  family name: Peng
  given name: You
author list: Agent
  family name: Chu
  given name: Liepeng
author list: Agent
  family name: Yang
  given name: Jing
author list: Agent
  family name: Tang
  given name: Wenlv
author list: Agent
  family name: Tan
  given name: Kui
author list: Agent
  family name: Fu
  given name: Shuangshuang
author list: Agent
  family name: Huang
  given name: Meili
author list: Agent
  family name: Xu
  given name: Meijun
author list: Agent
  family name: Rao
  given name: Jinlan
author list: Agent
  family name: Xue
  given name: Chao
author list: Agent
  family name: Chen
  given name: Yinyin
doi: 10.7717/peerj.20791
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Li et al.
attribution name: Li et al.

Physical exercise programmes to improve insomnia or poor sleep quality in non-hospitalised elderly people: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Insomnia, or poor quality of sleep, among older people increasingly affects both physical and psychological health. This study aimed to evaluate the efficacy of physical exercise programs for improving sleep quality in non-hospitalized older adults, via objective methods such as actigraphy and polysomnography. Methods A systematic review and meta-analysis was conducted between January 1, 2025 and March 31, 2025 according to the standards of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guide. It has been registered in Prospero with the number CRD420251009838. The following databases were consulted: PubMed, Web of Science, CINAHL Complete and Scopus. The studies included groups of participants with a mean age above 60 years, who presented with sleep problems, insomnia or an interest in improving sleep quality. To assess the quality of the studies, the Rob-2 tool for randomized studies and crossover studies and the critical appraisal of the Joanna Briggs Institute were used. Results Seven experimental or quasi-experimental studies with intervention groups and/or controls published in the last decade were analyzed. Interventions included aerobic exercise, resistance training, tai chi, and aquatic activities. The results demonstrated improvements in sleep latency, sleep efficiency, total sleep time, and wake time after sleep onset. Meta-analyses confirmed statistically significant benefits, particularly in terms of sleep latency and efficiency. Conclusions The findings support the implementation of physical activity programs as cost-effective, safe, and practical interventions to enhance sleep quality in community and healthcare settings.
format: application/pdf
format: text/html
creator: Laura Pilar De Paz-Montón
creator: Juan Manuel Carmona-Torres
creator: Ángel López-Fernández-Roldán
creator: Rosa María Molina-Madueño
creator: Carlos Navarrete-Tejero
creator: José Alberto Laredo-Aguilera
subject: Evidence Based Medicine
subject: Nursing
subject: Public Health
subject: Sports Medicine
description: doi:10.7717/peerj.20764
publisher: PeerJ Inc.
rights: © 2026 De Paz-Montón et al.
abstract: Background Insomnia, or poor quality of sleep, among older people increasingly affects both physical and psychological health. This study aimed to evaluate the efficacy of physical exercise programs for improving sleep quality in non-hospitalized older adults, via objective methods such as actigraphy and polysomnography. Methods A systematic review and meta-analysis was conducted between January 1, 2025 and March 31, 2025 according to the standards of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guide. It has been registered in Prospero with the number CRD420251009838. The following databases were consulted: PubMed, Web of Science, CINAHL Complete and Scopus. The studies included groups of participants with a mean age above 60 years, who presented with sleep problems, insomnia or an interest in improving sleep quality. To assess the quality of the studies, the Rob-2 tool for randomized studies and crossover studies and the critical appraisal of the Joanna Briggs Institute were used. Results Seven experimental or quasi-experimental studies with intervention groups and/or controls published in the last decade were analyzed. Interventions included aerobic exercise, resistance training, tai chi, and aquatic activities. The results demonstrated improvements in sleep latency, sleep efficiency, total sleep time, and wake time after sleep onset. Meta-analyses confirmed statistically significant benefits, particularly in terms of sleep latency and efficiency. Conclusions The findings support the implementation of physical activity programs as cost-effective, safe, and practical interventions to enhance sleep quality in community and healthcare settings.
bibliographic citation: De Paz-Montón et al. (2026) Physical exercise programmes to improve insomnia or poor sleep quality in non-hospitalised elderly people: a systematic review and meta-analysis. PeerJ 14:e20764 https://doi.org/10.7717/peerj.20764
date submitted: 2025-07-27
date accepted: 2025-12-17
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Paz-Montón
  given name: Laura Pilar
author list: Agent
  family name: Carmona-Torres
  given name: Juan Manuel
author list: Agent
  family name: López-Fernández-Roldán
  given name: Ángel
author list: Agent
  family name: Molina-Madueño
  given name: Rosa María
author list: Agent
  family name: Navarrete-Tejero
  given name: Carlos
author list: Agent
  family name: Laredo-Aguilera
  given name: José Alberto
doi: 10.7717/peerj.20764
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: © 2026 De Paz-Montón et al.
attribution name: De Paz-Montón et al.

The soil depth determines soil multifunctionality via shaping the soil properties and microbial diversity
type: item
type: AcademicArticle
description: Background Soil microorganisms drive subsurface ecological processes and are shaped by soil properties, which in turn influence biogeochemical cycling. Although the link between biodiversity and soil multifunctionality (SMF) has received widespread attention, the relative roles of soil properties and microbial community structure in regulating SMF remain unclear. Methods Here, we investigated SMF and microbial communities in the humus layer and across the 0–80 cm depth of natural soil profiles in a subalpine grassland using high-throughput sequencing. Results Our findings revealed that SMF, microbial diversity and network complexity decreased significantly with soil depth. Microbial community structure was primarily determined by pH and soil water content (SWC). Soil properties were the primary drivers of SMF, predicting 47.24%–63.75% of its variance. Microbial diversity was a stronger predictor of SMF than network complexity, explaining 26.09–44.56% of its variation. Bacterial diversity was significantly positively correlated with soil nutrient, carbon and nitrogen multifunctionality, while fungal diversity was not significantly correlated with them. This finding provides critical data support for elucidating the relationship between biodiversity and ecosystem functioning.
format: application/pdf
format: text/html
creator: Xiaoxia Liang
creator: Yunxiao Zhao
creator: Yanhua Song
creator: Baofeng Chai
creator: Tong Jia
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Environmental Sciences
subject: Microbiology
description: doi:10.7717/peerj.20734
publisher: PeerJ Inc.
rights: © 2026 Liang et al.
abstract: Background Soil microorganisms drive subsurface ecological processes and are shaped by soil properties, which in turn influence biogeochemical cycling. Although the link between biodiversity and soil multifunctionality (SMF) has received widespread attention, the relative roles of soil properties and microbial community structure in regulating SMF remain unclear. Methods Here, we investigated SMF and microbial communities in the humus layer and across the 0–80 cm depth of natural soil profiles in a subalpine grassland using high-throughput sequencing. Results Our findings revealed that SMF, microbial diversity and network complexity decreased significantly with soil depth. Microbial community structure was primarily determined by pH and soil water content (SWC). Soil properties were the primary drivers of SMF, predicting 47.24%–63.75% of its variance. Microbial diversity was a stronger predictor of SMF than network complexity, explaining 26.09–44.56% of its variation. Bacterial diversity was significantly positively correlated with soil nutrient, carbon and nitrogen multifunctionality, while fungal diversity was not significantly correlated with them. This finding provides critical data support for elucidating the relationship between biodiversity and ecosystem functioning.
bibliographic citation: Liang et al. (2026) The soil depth determines soil multifunctionality via shaping the soil properties and microbial diversity. PeerJ 14:e20734 https://doi.org/10.7717/peerj.20734
date submitted: 2025-10-06
date accepted: 2025-12-12
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Xiaoxia
author list: Agent
  family name: Zhao
  given name: Yunxiao
author list: Agent
  family name: Song
  given name: Yanhua
author list: Agent
  family name: Chai
  given name: Baofeng
author list: Agent
  family name: Jia
  given name: Tong
doi: 10.7717/peerj.20734
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Liang et al.
attribution name: Liang et al.

Evaluation of phosphorus sources in tomato plants inoculated with plant growth-promoting rhizobacteria
type: item
type: AcademicArticle
description: Tomatoes are agriculturally and gastronomically significant and serve as model organisms in scientific research. This study examined plant-phosphorus interactions, evaluated two P sources for fertilization, and analyzed the effects of rhizobacteria on plant growth. Phosphorus (P) is an essential yet limited nutrient for plants. Microbial inoculants formulated with plant growth-promoting rhizobacteria (PGPR) enhance plant health and growth and improve P solubility. Tomato seedlings were inoculated with the following PGPR strains capable of P solubilization: Paenibacillus spp. BSP 1.1, Arthrobacter enclensis JN24, and Arthrobacter pokkalii JLB4. Morphological and physiological analyses were used to assess nitrogen (N) and P intake and developmental differences among treatments. The P source, bacterial strain, and their interactions influenced plant development differently. Plants treated with phosphate rock exhibited a higher greenness index and root volume, whereas those with soluble phosphate had increased leaf area when inoculated with BSP and JLB4. Strain JLB4 specifically increased leaf area when combined with soluble phosphate. P concentration was lower in phosphate rock-treated plants, although deficiency symptoms were absent. N concentrations and growth-related variables were diminished in the early stages but improved to the end of the experiment. In conclusion, P demand was constant, but its availability increased with the effect of P solubilization throughout the experiment. Therefore, the addition of phosphate rock as a source of P in soilless agriculture may be a viable alternative for tomato cultivation.
format: application/pdf
format: text/html
creator: Marco Polo Carballo-Sánchez
creator: Juan Jose Almaraz-Suarez
creator: Sara Monzerrat Ramírez-Olvera
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.20651
publisher: PeerJ Inc.
rights: © 2026 Carballo-Sánchez et al.
abstract: Tomatoes are agriculturally and gastronomically significant and serve as model organisms in scientific research. This study examined plant-phosphorus interactions, evaluated two P sources for fertilization, and analyzed the effects of rhizobacteria on plant growth. Phosphorus (P) is an essential yet limited nutrient for plants. Microbial inoculants formulated with plant growth-promoting rhizobacteria (PGPR) enhance plant health and growth and improve P solubility. Tomato seedlings were inoculated with the following PGPR strains capable of P solubilization: Paenibacillus spp. BSP 1.1, Arthrobacter enclensis JN24, and Arthrobacter pokkalii JLB4. Morphological and physiological analyses were used to assess nitrogen (N) and P intake and developmental differences among treatments. The P source, bacterial strain, and their interactions influenced plant development differently. Plants treated with phosphate rock exhibited a higher greenness index and root volume, whereas those with soluble phosphate had increased leaf area when inoculated with BSP and JLB4. Strain JLB4 specifically increased leaf area when combined with soluble phosphate. P concentration was lower in phosphate rock-treated plants, although deficiency symptoms were absent. N concentrations and growth-related variables were diminished in the early stages but improved to the end of the experiment. In conclusion, P demand was constant, but its availability increased with the effect of P solubilization throughout the experiment. Therefore, the addition of phosphate rock as a source of P in soilless agriculture may be a viable alternative for tomato cultivation.
bibliographic citation: Carballo-Sánchez et al. (2026) Evaluation of phosphorus sources in tomato plants inoculated with plant growth-promoting rhizobacteria. PeerJ 14:e20651 https://doi.org/10.7717/peerj.20651
date submitted: 2025-07-31
date accepted: 2025-12-02
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carballo-Sánchez
  given name: Marco Polo
author list: Agent
  family name: Almaraz-Suarez
  given name: Juan Jose
author list: Agent
  family name: Ramírez-Olvera
  given name: Sara Monzerrat
doi: 10.7717/peerj.20651
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Carballo-Sánchez et al.
attribution name: Carballo-Sánchez et al.

Research on the construction of growth models for dominant tree species in the Manas River Basin, Xinjiang
type: item
type: AcademicArticle
description: Research on forest growth models is not only crucial for regional ecological security and the optimal allocation of water and carbon resources but is also a key component in the study of carbon cycling in arid regions, holding scientific and practical significance for addressing climate change and promoting green sustainable development. Therefore, this study takes the Manas River Basin in Xinjiang as an example and based on the 2011 forest resource survey data from the Manas River Basin, constructs basic growth models for the diameter at breast height (DBH)-height and age-DBH relationships for five dominant tree types: Spruce, Poplar, Mixed wood, Sand jujube, and Populus euphratica. The optimal basic models for each types are selected. Secondly, climate factors (annual precipitation, Minimum of Daily Maximum Temperature, TXn) and topographic factors (Digital Elevation Model; DEM) are introduced into the optimal models to construct multivariate nonlinear forest growth models. Finally, deep learning is used to optimize the overall accuracy of the models. The results show that the optimal DBH-height models for Spruce, Poplar, Sand jujube, and Populus euphratica are S-curve models, while the optimal DBH-height model for Mixed wood is a logarithmic model. The optimal age-DBH models for Poplar and Populus euphratica are S-curve models, whereas the optimal age-DBH basic models for Spruce, Mixed wood, and Sand jujube are growth model, linear model, and logistics model, respectively. The overall accuracy of the multivariate nonlinear forest growth models is improved, with the highest R2 reaching 0.890 and the average RMSE increasing by 10.590, mainly due to the decrease in model accuracy for some tree types caused by random factors. Lastly, compared to the basic models and multivariate nonlinear forest growth models, the deep learning approach demonstrates the best performance, with the highest correlation coefficient reaching 0.960. Overall, by constructing forest growth m…
format: application/pdf
format: text/html
creator: ZhongQiong Zhao
creator: Mei Zan
creator: Jian Ke
creator: Jia Zhou
creator: Lili Zhai
creator: Cong Xue
creator: Shunfa Yang
creator: Yu Dong
creator: Yuntong Liu
subject: Ecology
subject: Natural Resource Management
subject: Environmental Impacts
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20650
publisher: PeerJ Inc.
rights: © 2026 Zhao et al.
abstract: Research on forest growth models is not only crucial for regional ecological security and the optimal allocation of water and carbon resources but is also a key component in the study of carbon cycling in arid regions, holding scientific and practical significance for addressing climate change and promoting green sustainable development. Therefore, this study takes the Manas River Basin in Xinjiang as an example and based on the 2011 forest resource survey data from the Manas River Basin, constructs basic growth models for the diameter at breast height (DBH)-height and age-DBH relationships for five dominant tree types: Spruce, Poplar, Mixed wood, Sand jujube, and Populus euphratica. The optimal basic models for each types are selected. Secondly, climate factors (annual precipitation, Minimum of Daily Maximum Temperature, TXn) and topographic factors (Digital Elevation Model; DEM) are introduced into the optimal models to construct multivariate nonlinear forest growth models. Finally, deep learning is used to optimize the overall accuracy of the models. The results show that the optimal DBH-height models for Spruce, Poplar, Sand jujube, and Populus euphratica are S-curve models, while the optimal DBH-height model for Mixed wood is a logarithmic model. The optimal age-DBH models for Poplar and Populus euphratica are S-curve models, whereas the optimal age-DBH basic models for Spruce, Mixed wood, and Sand jujube are growth model, linear model, and logistics model, respectively. The overall accuracy of the multivariate nonlinear forest growth models is improved, with the highest R2 reaching 0.890 and the average RMSE increasing by 10.590, mainly due to the decrease in model accuracy for some tree types caused by random factors. Lastly, compared to the basic models and multivariate nonlinear forest growth models, the deep learning approach demonstrates the best performance, with the highest correlation coefficient reaching 0.960. Overall, by constructing forest growth m…
bibliographic citation: Zhao et al. (2026) Research on the construction of growth models for dominant tree species in the Manas River Basin, Xinjiang. PeerJ 14:e20650 https://doi.org/10.7717/peerj.20650
date submitted: 2025-07-13
date accepted: 2025-12-01
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: ZhongQiong
author list: Agent
  family name: Zan
  given name: Mei
author list: Agent
  family name: Ke
  given name: Jian
author list: Agent
  family name: Zhou
  given name: Jia
author list: Agent
  family name: Zhai
  given name: Lili
author list: Agent
  family name: Xue
  given name: Cong
author list: Agent
  family name: Yang
  given name: Shunfa
author list: Agent
  family name: Dong
  given name: Yu
author list: Agent
  family name: Liu
  given name: Yuntong
doi: 10.7717/peerj.20650
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Zhao et al.
attribution name: Zhao et al.

Targetome profile of hsa-miR-93-5p is resistant to isoform formation in prostate adenocarcinoma
type: item
type: AcademicArticle
description: MicroRNAs (miRNAs) and their isoforms, known as isomiRs, are important regulators of tumorigenesis that act as post-transcriptional modulators of gene expression. Among these, 5’-isomiRs—generated through imprecise cleavage during miRNA biogenesis—exhibit altered seed regions compared to their canonical counterparts, potentially leading to distinct targetomes. Consequently, 5’-isomiRs may exert biological functions that differ substantially from those of the corresponding canonical miRNAs. Despite growing recognition of their potential significance, the functional roles of 5’-isomiRs remain largely uncharacterized for most miRNAs. In this study, we investigated the targetome divergence between canonical miRNAs and their 5’-isomiRs, focusing on hsa-miR-93-5p, a miRNA with a well-established oncogenic role in prostate adenocarcinoma. Target transcripts of the 5’-isomiRs were identified using a shRNA-based overexpression system. Bioinformatic analysis revealed a substantial overlap between the targets of the 5’-isomiRs and the canonical miRNA. This overlap was attributed to the co-occurrence of both canonical and shifted seed motifs within the same mRNA targets. Notably, hsa-miR-93-5p ranked among the top miRNAs with a relatively high number of targets transcripts containing both seed motifs, suggesting a unique dual-targeting capacity.
format: application/pdf
format: text/html
creator: Anton Zhiyanov
creator: Ivan Kirillov
creator: Roman Suvorov
creator: Diana Maltseva
creator: Alexander Tonevitsky
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.20642
publisher: PeerJ Inc.
rights: © 2026 Zhiyanov et al.
abstract: MicroRNAs (miRNAs) and their isoforms, known as isomiRs, are important regulators of tumorigenesis that act as post-transcriptional modulators of gene expression. Among these, 5’-isomiRs—generated through imprecise cleavage during miRNA biogenesis—exhibit altered seed regions compared to their canonical counterparts, potentially leading to distinct targetomes. Consequently, 5’-isomiRs may exert biological functions that differ substantially from those of the corresponding canonical miRNAs. Despite growing recognition of their potential significance, the functional roles of 5’-isomiRs remain largely uncharacterized for most miRNAs. In this study, we investigated the targetome divergence between canonical miRNAs and their 5’-isomiRs, focusing on hsa-miR-93-5p, a miRNA with a well-established oncogenic role in prostate adenocarcinoma. Target transcripts of the 5’-isomiRs were identified using a shRNA-based overexpression system. Bioinformatic analysis revealed a substantial overlap between the targets of the 5’-isomiRs and the canonical miRNA. This overlap was attributed to the co-occurrence of both canonical and shifted seed motifs within the same mRNA targets. Notably, hsa-miR-93-5p ranked among the top miRNAs with a relatively high number of targets transcripts containing both seed motifs, suggesting a unique dual-targeting capacity.
bibliographic citation: Zhiyanov et al. (2026) Targetome profile of hsa-miR-93-5p is resistant to isoform formation in prostate adenocarcinoma. PeerJ 14:e20642 https://doi.org/10.7717/peerj.20642
date submitted: 2025-07-16
date accepted: 2025-12-01
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhiyanov
  given name: Anton
author list: Agent
  family name: Kirillov
  given name: Ivan
author list: Agent
  family name: Suvorov
  given name: Roman
author list: Agent
  family name: Maltseva
  given name: Diana
author list: Agent
  family name: Tonevitsky
  given name: Alexander
doi: 10.7717/peerj.20642
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Zhiyanov et al.
attribution name: Zhiyanov et al.

Molecular classification and prognosis study of pancreatic ductal adenocarcinoma through multi-omics integrated clustering analysis
type: item
type: AcademicArticle
description: Background Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy characterized by significant heterogeneity. We conducted a multi-omics integrated clustering analysis to categorize PDAC molecular subtypes. Methods Multi-omics data from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA-PAAD) were integrated using ten clustering algorithms. Comparisons across PDAC subtypes were performed regarding prognosis, gene mutations, pathways, tumor microenvironment (TME), and chemotherapy sensitivity. A prognostic model was constructed utilizing Cox and Lasso regression based on subtype-related genes. Results Samples from the TCGA-PAAD cohort were classified into two subtypes. The CS1 subtype was identified as a high-risk, immunosilent subtype, while the CS2 subtype was characterized as a low-risk, immunoactive subtype. Compared to CS2 subtype, CS1 subtype exhibited shorter survival, higher frequency of genetic mutations, more aggressive tumor-promoting nature, lower TME immune score, and increased sensitivity to chemotherapy. The prognostic model related to PDAC subtypes displayed robust predictive efficiency; IL20RB gene emerged having superior predictive capability. Conclusions We successfully identified two distinct PDAC subtypes. The developed prognostic model exhibited strong predictive efficacy; and the upregulation of IL20RB was identified as a promising therapeutic target for PDAC.
format: application/pdf
format: text/html
creator: Guodong Zhong
creator: Lei Wang
creator: Peiling Fu
creator: Beibei Xi
creator: Houqiang Li
creator: Yanhong Cheng
creator: Jianlong Lin
creator: Linying Chen
subject: Bioinformatics
subject: Genetics
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.20619
publisher: PeerJ Inc.
rights: © 2026 Zhong et al.
abstract: Background Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy characterized by significant heterogeneity. We conducted a multi-omics integrated clustering analysis to categorize PDAC molecular subtypes. Methods Multi-omics data from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA-PAAD) were integrated using ten clustering algorithms. Comparisons across PDAC subtypes were performed regarding prognosis, gene mutations, pathways, tumor microenvironment (TME), and chemotherapy sensitivity. A prognostic model was constructed utilizing Cox and Lasso regression based on subtype-related genes. Results Samples from the TCGA-PAAD cohort were classified into two subtypes. The CS1 subtype was identified as a high-risk, immunosilent subtype, while the CS2 subtype was characterized as a low-risk, immunoactive subtype. Compared to CS2 subtype, CS1 subtype exhibited shorter survival, higher frequency of genetic mutations, more aggressive tumor-promoting nature, lower TME immune score, and increased sensitivity to chemotherapy. The prognostic model related to PDAC subtypes displayed robust predictive efficiency; IL20RB gene emerged having superior predictive capability. Conclusions We successfully identified two distinct PDAC subtypes. The developed prognostic model exhibited strong predictive efficacy; and the upregulation of IL20RB was identified as a promising therapeutic target for PDAC.
bibliographic citation: Zhong et al. (2026) Molecular classification and prognosis study of pancreatic ductal adenocarcinoma through multi-omics integrated clustering analysis. PeerJ 14:e20619 https://doi.org/10.7717/peerj.20619
date submitted: 2025-07-11
date accepted: 2025-11-29
issued: 2026-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Guodong
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Fu
  given name: Peiling
author list: Agent
  family name: Xi
  given name: Beibei
author list: Agent
  family name: Li
  given name: Houqiang
author list: Agent
  family name: Cheng
  given name: Yanhong
author list: Agent
  family name: Lin
  given name: Jianlong
author list: Agent
  family name: Chen
  given name: Linying
doi: 10.7717/peerj.20619
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-16
copyright: ©2026 Zhong et al.
attribution name: Zhong et al.

BCTI: a Bayesian network-based method for revealing critical transitions in complex biological systems
type: item
type: AcademicArticle
description: Background The identification of critical states during disease progression is essential yet challenging for preventing disease deterioration and developing precision therapies. Traditional methods often rely on the dynamic feature of coordinated molecular variation to provide early-warning signals of impending critical transitions. However, these methods typically overlook the causal relationships among variables, potentially limiting their interpretability in uncovering underlying molecular regulatory mechanisms. Methods With the rapid advancement of sequencing technologies and the surge in high-throughput data, we propose Bayesian Critical Transitions Inference (BCTI), inspired by the time-varying nature of gene regulatory networks. BCTI integrates mutual information and structural equation models to qualitatively capture dynamic changes in network topology and quantitatively evaluate system states through a network scoring mechanism, thereby enabling the efficient and robust dual detection of early-warning signals associated with critical transitions in disease progression. Results The proposed BCTI was validated by a series of applications on simulated and real datasets of complex biological systems. BCTI achieved superior or comparable accuracy to benchmark methods in inferring gene regulatory networks (GRNs) and detecting critical states. All the results demonstrate the high effectiveness of the proposed method in analyzing time-course/stage-course high-dimensional expression data, providing new insights into precision medicine for clinical applications and the underlying regulatory mechanisms of biological systems. Conclusions The proposed method enables effective detection of critical transitions and reveals dynamic regulatory mechanisms in complex biological systems, demonstrating strong potential for applications in systems biology, precision medicine, and the exploration of key molecular regulation driving disease progression and development.
format: application/pdf
format: text/html
creator: Yuyan Tong
creator: Renhao Hong
creator: Na Yang
creator: Pei Chen
creator: Hao Peng
creator: Hui Tang
creator: Rui Liu
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Mathematical Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20860
publisher: PeerJ Inc.
rights: © 2026 Tong et al.
abstract: Background The identification of critical states during disease progression is essential yet challenging for preventing disease deterioration and developing precision therapies. Traditional methods often rely on the dynamic feature of coordinated molecular variation to provide early-warning signals of impending critical transitions. However, these methods typically overlook the causal relationships among variables, potentially limiting their interpretability in uncovering underlying molecular regulatory mechanisms. Methods With the rapid advancement of sequencing technologies and the surge in high-throughput data, we propose Bayesian Critical Transitions Inference (BCTI), inspired by the time-varying nature of gene regulatory networks. BCTI integrates mutual information and structural equation models to qualitatively capture dynamic changes in network topology and quantitatively evaluate system states through a network scoring mechanism, thereby enabling the efficient and robust dual detection of early-warning signals associated with critical transitions in disease progression. Results The proposed BCTI was validated by a series of applications on simulated and real datasets of complex biological systems. BCTI achieved superior or comparable accuracy to benchmark methods in inferring gene regulatory networks (GRNs) and detecting critical states. All the results demonstrate the high effectiveness of the proposed method in analyzing time-course/stage-course high-dimensional expression data, providing new insights into precision medicine for clinical applications and the underlying regulatory mechanisms of biological systems. Conclusions The proposed method enables effective detection of critical transitions and reveals dynamic regulatory mechanisms in complex biological systems, demonstrating strong potential for applications in systems biology, precision medicine, and the exploration of key molecular regulation driving disease progression and development.
bibliographic citation: Tong et al. (2026) BCTI: a Bayesian network-based method for revealing critical transitions in complex biological systems. PeerJ 14:e20860 https://doi.org/10.7717/peerj.20860
date submitted: 2025-07-14
date accepted: 2026-01-07
issued: 2026-02-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tong
  given name: Yuyan
author list: Agent
  family name: Hong
  given name: Renhao
author list: Agent
  family name: Yang
  given name: Na
author list: Agent
  family name: Chen
  given name: Pei
author list: Agent
  family name: Peng
  given name: Hao
author list: Agent
  family name: Tang
  given name: Hui
author list: Agent
  family name: Liu
  given name: Rui
doi: 10.7717/peerj.20860
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-13
copyright: © 2026 Tong et al.
attribution name: Tong et al.

Proteome-wide analysis by liquid chromatography tandem mass spectrometry reveals the role of retinoic acid during adipogenesis in human bone mesenchymal stem cells
type: item
type: AcademicArticle
description: Objective Retinoic acid (RA), an active metabolite of vitamin A, may regulate adipogenesis and is associated with osteoporosis. To clarify the regulatory mechanism of RA in adipogenesis and its relationship with the occurrence and development of osteoporosis, we investigated the role of all-trans retinoic acid (ATRA) in protein expression profiling during human bone mesenchymal stem cells (hBMSCs) adipogenesis. Methods Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to determine the protein profile, and raw data were analyzed against the UniProt database using MaxQuant with the Andromeda search engine. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used for functional annotation of differentially expressed proteins (DEPs). The interaction relationships of DEPs were assessed using the STRING database, and Cytoscape was used to visualize the protein interaction network. Results A total of 5,611 proteins were identified by LC-MS/MS in 15 samples, of which 5,470 proteins showed quantifiable data. When treated with ATRA for seven and 14 days after adipogenic induction, 470 and 1,408 DEPs were upregulated and 508 and 1,345 DEPs were downregulated. Gene functional annotation of DEPs showed that ATRA upregulated classic signaling pathways, such as Wnt, Hippo, and MAPK, as well as cytoskeleton related pathways, including focal adhesion, extracellular matrix (ECM)-receptor interaction, and the regulation of actin cytoskeleton. ATRA downregulated many pathways related to metabolism, including the AMP-activated protein kinase (AMPK) and peroxisome proliferator activated receptor (PPAR) pathways, to repress adipocyte differentiation and lipid accumulation. Specifically, the inhibition of adipogenesis by ATRA was significantly attenuated when the Rho-associated protein kinase (ROCK) inhibitor Y27632 was used to block the regulation of actin cytoskeleton pathways. Conclusion Our study suggests that ATRA downregulates met…
format: application/pdf
format: text/html
creator: Jiaxin Peng
creator: Siyu Chen
creator: Shilei Nong
creator: Yifan Chen
creator: Zhenjie Wang
creator: Tao Wang
creator: Jun Cao
subject: Biochemistry
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.20846
publisher: PeerJ Inc.
rights: © 2026 Peng et al.
abstract: Objective Retinoic acid (RA), an active metabolite of vitamin A, may regulate adipogenesis and is associated with osteoporosis. To clarify the regulatory mechanism of RA in adipogenesis and its relationship with the occurrence and development of osteoporosis, we investigated the role of all-trans retinoic acid (ATRA) in protein expression profiling during human bone mesenchymal stem cells (hBMSCs) adipogenesis. Methods Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to determine the protein profile, and raw data were analyzed against the UniProt database using MaxQuant with the Andromeda search engine. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used for functional annotation of differentially expressed proteins (DEPs). The interaction relationships of DEPs were assessed using the STRING database, and Cytoscape was used to visualize the protein interaction network. Results A total of 5,611 proteins were identified by LC-MS/MS in 15 samples, of which 5,470 proteins showed quantifiable data. When treated with ATRA for seven and 14 days after adipogenic induction, 470 and 1,408 DEPs were upregulated and 508 and 1,345 DEPs were downregulated. Gene functional annotation of DEPs showed that ATRA upregulated classic signaling pathways, such as Wnt, Hippo, and MAPK, as well as cytoskeleton related pathways, including focal adhesion, extracellular matrix (ECM)-receptor interaction, and the regulation of actin cytoskeleton. ATRA downregulated many pathways related to metabolism, including the AMP-activated protein kinase (AMPK) and peroxisome proliferator activated receptor (PPAR) pathways, to repress adipocyte differentiation and lipid accumulation. Specifically, the inhibition of adipogenesis by ATRA was significantly attenuated when the Rho-associated protein kinase (ROCK) inhibitor Y27632 was used to block the regulation of actin cytoskeleton pathways. Conclusion Our study suggests that ATRA downregulates met…
bibliographic citation: Peng et al. (2026) Proteome-wide analysis by liquid chromatography tandem mass spectrometry reveals the role of retinoic acid during adipogenesis in human bone mesenchymal stem cells. PeerJ 14:e20846 https://doi.org/10.7717/peerj.20846
date submitted: 2025-08-05
date accepted: 2026-01-05
issued: 2026-02-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Jiaxin
author list: Agent
  family name: Chen
  given name: Siyu
author list: Agent
  family name: Nong
  given name: Shilei
author list: Agent
  family name: Chen
  given name: Yifan
author list: Agent
  family name: Wang
  given name: Zhenjie
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Cao
  given name: Jun
doi: 10.7717/peerj.20846
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-13
copyright: ©2026 Peng et al.
attribution name: Peng et al.

Characteristics and evolution of pelvic floor structures in female patients aged over 40 years with constipation—a retrospective cohort study
type: item
type: AcademicArticle
description: Background Pelvic floor dysfunction (PFD) is a common cause of chronic constipation which can reciprocally exacerbate pelvic floor burden. However, the characteristics and evolution of pelvic floor structures in patients with constipation remain unclear. This study investigates the characteristics and evolution of pelvic floor structures in constipated women aged over 40 years. Methods Clinical data were collected from female patients undergoing pelvic floor ultrasound at the Third Affiliated Hospital of Sun Yat-sen University from December 2020 to August 2023. Propensity score matching (PSM) minimized confounders between the constipation (n = 247) and non-constipation (n = 898) groups. We analyzed intergroup differences in ultrasound data and changes in pelvic floor structure over time among constipated patients. Results Significant intergroup differences emerged in uterine prolapse (P = 0.042), rectocele (P = 0.022), levator ani hiatus dilation (P=0.013), hiatus area (P < 0.01), the position of the uterus (P < 0.01), and rectal ampulla (P = 0.017) at maximal Valsalva maneuver (VM). Multivariate analysis identified rectocele (P = 0.023) and uterine descent at maximal VM (P = 0.026) as positively associated with constipation occurrence. Multiple ultrasonographic evaluations over two years revealed stable pelvic floor anatomy in non-constipated individuals but identified alterations in 78 constipated patients, including increased vesicocele (P = 0.039), uterine prolapse (P = 0.019), perineal hypermobility (P = 0.015), lower bladder (P < 0.001) and rectal ampulla (P < 0.01) positions at maximal VM, greater bladder descent (P < 0.01), and enlarged hiatus area (P < 0.01). Conclusion This study demonstrates that rectocele and uterine descent at maximal VM exhibit positive associations with constipation. Over time, further descent of the bladder, uterus, and rectum occurs in female patients with constipation, along with an increase in perineal mobility and levator ani hia…
format: application/pdf
format: text/html
creator: Jiarong You
creator: Ying Chen
creator: Rongpu Liang
creator: Li Lu
creator: Jianming Yang
creator: Jiannan Ren
creator: Guangchun Jiang
creator: Yuan Wang
creator: Runze Wu
creator: Xinling Zhang
creator: Bo Wei
subject: Anatomy and Physiology
subject: Gastroenterology and Hepatology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.20783
publisher: PeerJ Inc.
rights: © 2026 You et al.
abstract: Background Pelvic floor dysfunction (PFD) is a common cause of chronic constipation which can reciprocally exacerbate pelvic floor burden. However, the characteristics and evolution of pelvic floor structures in patients with constipation remain unclear. This study investigates the characteristics and evolution of pelvic floor structures in constipated women aged over 40 years. Methods Clinical data were collected from female patients undergoing pelvic floor ultrasound at the Third Affiliated Hospital of Sun Yat-sen University from December 2020 to August 2023. Propensity score matching (PSM) minimized confounders between the constipation (n = 247) and non-constipation (n = 898) groups. We analyzed intergroup differences in ultrasound data and changes in pelvic floor structure over time among constipated patients. Results Significant intergroup differences emerged in uterine prolapse (P = 0.042), rectocele (P = 0.022), levator ani hiatus dilation (P=0.013), hiatus area (P < 0.01), the position of the uterus (P < 0.01), and rectal ampulla (P = 0.017) at maximal Valsalva maneuver (VM). Multivariate analysis identified rectocele (P = 0.023) and uterine descent at maximal VM (P = 0.026) as positively associated with constipation occurrence. Multiple ultrasonographic evaluations over two years revealed stable pelvic floor anatomy in non-constipated individuals but identified alterations in 78 constipated patients, including increased vesicocele (P = 0.039), uterine prolapse (P = 0.019), perineal hypermobility (P = 0.015), lower bladder (P < 0.001) and rectal ampulla (P < 0.01) positions at maximal VM, greater bladder descent (P < 0.01), and enlarged hiatus area (P < 0.01). Conclusion This study demonstrates that rectocele and uterine descent at maximal VM exhibit positive associations with constipation. Over time, further descent of the bladder, uterus, and rectum occurs in female patients with constipation, along with an increase in perineal mobility and levator ani hia…
bibliographic citation: You et al. (2026) Characteristics and evolution of pelvic floor structures in female patients aged over 40 years with constipation—a retrospective cohort study. PeerJ 14:e20783 https://doi.org/10.7717/peerj.20783
date submitted: 2025-08-21
date accepted: 2025-12-22
issued: 2026-02-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: You
  given name: Jiarong
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: Liang
  given name: Rongpu
author list: Agent
  family name: Lu
  given name: Li
author list: Agent
  family name: Yang
  given name: Jianming
author list: Agent
  family name: Ren
  given name: Jiannan
author list: Agent
  family name: Jiang
  given name: Guangchun
author list: Agent
  family name: Wang
  given name: Yuan
author list: Agent
  family name: Wu
  given name: Runze
author list: Agent
  family name: Zhang
  given name: Xinling
author list: Agent
  family name: Wei
  given name: Bo
doi: 10.7717/peerj.20783
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-13
copyright: ©2026 You et al.
attribution name: You et al.

Risk prediction models for sepsis-associated encephalopathy: a systematic evaluation and meta-analysis
type: item
type: AcademicArticle
description: Background The number of risk prediction models for sepsis-associated encephalopathy (SAE) is increasing, while the quality and applicability of these models in clinical practice and future research remain uncertain. Objective To systematically review published studies on SAE risk prediction models. Design Systematic review and meta-analysis of observational studies. Methods A systematic search of PubMed, Web of Science, Embase, Wanfang, VIP, and CNKI databases was conducted from inception to April 2, 2025, to identify studies on SAE risk prediction models. Two independent reviewers screened the studies and extracted data. The Prediction model Risk Of Bias Assessment Tool (PROBAST) was applied to evaluate the risk of bias and applicability of the included studies. Results A total of 1,994 studies were identified, and 10 were included after screening. The reported incidence of SAE ranged from 15.16% to 63.3%. Age and Sequential Organ Failure Assessment (SOFA) score are the most frequently adopted factors with significant predictive value, both of which were incorporated into five models. Both the SOFA score and age were significantly associated with SAE. In studies with available data, the odds ratio (OR) for age ranged from 1.084 to 1.018, while that for SOFA score ranged from 1.246 to 2.416. The area under the receiver operating characteristic curve (AUC) for the 10 studies ranged from 0.743 to 0.975. All studies were found to have a high risk of bias, primarily due to inappropriate data sources and deficiencies in the analysis domain. The pooled AUC for the six validated models was 0.83 (95% confidence interval [0.77–0.89]), indicating fair discrimination. Conclusion Although the included studies reported some discrimination in the SAE prediction models, all were found to have a high risk of bias according to the PROBAST checklist. Registration This study protocol was registered on PROSPERO (registration number: CRD420251012485).
format: application/pdf
format: text/html
creator: Ting ting He
creator: Tuo quan Jiao
creator: Xue mei An
subject: Emergency and Critical Care
subject: Evidence Based Medicine
subject: Neurology
subject: Nursing
description: doi:10.7717/peerj.20770
publisher: PeerJ Inc.
rights: © 2026 He et al.
abstract: Background The number of risk prediction models for sepsis-associated encephalopathy (SAE) is increasing, while the quality and applicability of these models in clinical practice and future research remain uncertain. Objective To systematically review published studies on SAE risk prediction models. Design Systematic review and meta-analysis of observational studies. Methods A systematic search of PubMed, Web of Science, Embase, Wanfang, VIP, and CNKI databases was conducted from inception to April 2, 2025, to identify studies on SAE risk prediction models. Two independent reviewers screened the studies and extracted data. The Prediction model Risk Of Bias Assessment Tool (PROBAST) was applied to evaluate the risk of bias and applicability of the included studies. Results A total of 1,994 studies were identified, and 10 were included after screening. The reported incidence of SAE ranged from 15.16% to 63.3%. Age and Sequential Organ Failure Assessment (SOFA) score are the most frequently adopted factors with significant predictive value, both of which were incorporated into five models. Both the SOFA score and age were significantly associated with SAE. In studies with available data, the odds ratio (OR) for age ranged from 1.084 to 1.018, while that for SOFA score ranged from 1.246 to 2.416. The area under the receiver operating characteristic curve (AUC) for the 10 studies ranged from 0.743 to 0.975. All studies were found to have a high risk of bias, primarily due to inappropriate data sources and deficiencies in the analysis domain. The pooled AUC for the six validated models was 0.83 (95% confidence interval [0.77–0.89]), indicating fair discrimination. Conclusion Although the included studies reported some discrimination in the SAE prediction models, all were found to have a high risk of bias according to the PROBAST checklist. Registration This study protocol was registered on PROSPERO (registration number: CRD420251012485).
bibliographic citation: He et al. (2026) Risk prediction models for sepsis-associated encephalopathy: a systematic evaluation and meta-analysis. PeerJ 14:e20770 https://doi.org/10.7717/peerj.20770
date submitted: 2025-05-29
date accepted: 2025-12-18
issued: 2026-02-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Ting ting
author list: Agent
  family name: Jiao
  given name: Tuo quan
author list: Agent
  family name: An
  given name: Xue mei
doi: 10.7717/peerj.20770
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-13
copyright: ©2026 He et al.
attribution name: He et al.

Inclined treadmill walking kinetics of the non-paretic leg in early post-stroke survivors: an observational case-control study
type: item
type: AcademicArticle
description: Background Stroke remains the primary source of prolonged disability worldwide since it often results in gait asymmetry. Research shows compensatory mechanisms in chronic stroke patients’ non-paretic legs but lacks knowledge about these adaptations during the early post-stroke period when walking on inclines which mimic real-world mobility challenges. Objective This study sought to clarify the compensatory strategies in the non-paretic leg of early post-stroke survivors by analyzing the changes in vertical ground reaction force (GRF) profiles and respective variabilities during level (0%) and inclined (6%) treadmill walking, relative to healthy, matched controls. Methods The study included fourteen early post-stroke survivors who were three months post-event or less along with fourteen matched controls. Participants walked at their preferred speeds on treadmill at 0% and 6% grade incline settings. Researchers determined key vertical GRF profiles, including peak amplitudes (F1, F2, F3), impulses (J1–J4), timing to each peak, loading/unloading rates, and their respectively variabilities. Mixed two-way repeated measures Analysis of covariance (ANCOVA) were used and preferred walking speed was used as a covariate. Results Stroke survivors demonstrated significantly slower walking speeds compared to control participants (0.6 km/hr vs. 2.15 km/hr) while both groups shared similar demographic characteristics. It is worth mentioning that this study specifically focused on the non-paretic side; therefore, only GRF components corresponding to the non-paretic leg of the stroke survivors were investigated. During weight acceptance (F1) and push-off (F3) phases, stroke survivors showed lower vertical ground reaction force (VGRF) peak amplitudes (F1- control (C): 1.11 vs. patients (P): 1.04, F3 - C: 1.09 vs. P: 1.03) and impulse magnitudes (J1- C: 25.46 vs. P: 18.74, J2 - C: 21.37 vs. P: 13.46, J3- C: 22.38 vs. P: 15.71, J4 - C: 22.16 vs. P: 18.19) in their non-paretic leg compar…
format: application/pdf
format: text/html
creator: Jiani Lu
creator: Yun Miao
creator: Dingying Ma
creator: Lihua Chen
creator: Bo Yu
creator: Jung H. Chien
subject: Kinesiology
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.20766
publisher: PeerJ Inc.
rights: © 2026 Lu et al.
abstract: Background Stroke remains the primary source of prolonged disability worldwide since it often results in gait asymmetry. Research shows compensatory mechanisms in chronic stroke patients’ non-paretic legs but lacks knowledge about these adaptations during the early post-stroke period when walking on inclines which mimic real-world mobility challenges. Objective This study sought to clarify the compensatory strategies in the non-paretic leg of early post-stroke survivors by analyzing the changes in vertical ground reaction force (GRF) profiles and respective variabilities during level (0%) and inclined (6%) treadmill walking, relative to healthy, matched controls. Methods The study included fourteen early post-stroke survivors who were three months post-event or less along with fourteen matched controls. Participants walked at their preferred speeds on treadmill at 0% and 6% grade incline settings. Researchers determined key vertical GRF profiles, including peak amplitudes (F1, F2, F3), impulses (J1–J4), timing to each peak, loading/unloading rates, and their respectively variabilities. Mixed two-way repeated measures Analysis of covariance (ANCOVA) were used and preferred walking speed was used as a covariate. Results Stroke survivors demonstrated significantly slower walking speeds compared to control participants (0.6 km/hr vs. 2.15 km/hr) while both groups shared similar demographic characteristics. It is worth mentioning that this study specifically focused on the non-paretic side; therefore, only GRF components corresponding to the non-paretic leg of the stroke survivors were investigated. During weight acceptance (F1) and push-off (F3) phases, stroke survivors showed lower vertical ground reaction force (VGRF) peak amplitudes (F1- control (C): 1.11 vs. patients (P): 1.04, F3 - C: 1.09 vs. P: 1.03) and impulse magnitudes (J1- C: 25.46 vs. P: 18.74, J2 - C: 21.37 vs. P: 13.46, J3- C: 22.38 vs. P: 15.71, J4 - C: 22.16 vs. P: 18.19) in their non-paretic leg compar…
bibliographic citation: Lu et al. (2026) Inclined treadmill walking kinetics of the non-paretic leg in early post-stroke survivors: an observational case-control study. PeerJ 14:e20766 https://doi.org/10.7717/peerj.20766
date submitted: 2025-06-13
date accepted: 2025-12-17
issued: 2026-02-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Jiani
author list: Agent
  family name: Miao
  given name: Yun
author list: Agent
  family name: Ma
  given name: Dingying
author list: Agent
  family name: Chen
  given name: Lihua
author list: Agent
  family name: Yu
  given name: Bo
author list: Agent
  family name: Chien
  given name: Jung H.
doi: 10.7717/peerj.20766
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-13
copyright: ©2026 Lu et al.
attribution name: Lu et al.

Aging-related CD8+ T cell alterations and calcium/calmodulin dependent protein kinase 1D activation in the pathogenesis of diabetic kidney disease
type: item
type: AcademicArticle
description: Background Diabetic kidney disease (DKD) is a leading cause of end-stage renal disease (ESRD), accelerates age-related decline in estimated glomerular filtration rate (eGFR), leading to a markedly increased prevalence of DKD among elderly diabetic patients. Recent studies suggest that immune dysregulation plays a pivotal role in DKD progression; however, the cellular and molecular mechanisms linking aging, immune infiltration, and DKD remain unclear. Methods We used single-cell RNA sequencing (scRNA-seq) analysis to characterize immune cell dynamics between the young, the elderly and DKD patients. Based on the scRNA-seq analysis, Mendelian randomization (MR) analysis of differentially expressed genes (DEGs) in CD8+ T cells were conducted to explore the casual relationship between DEGs and DKD. Results The CD8+ T cell cluster was the predominant T cell subtype, but its proportion gradually declined from young individuals to elderly subjects and DKD patients. MR analysis of DEGs in CD8+ T cells suggested that calcium/calmodulin dependent protein kinase 1D (CAMK1D) exhibited strongest causal relationship with DKD. CAMK1D was upregulated in DKD kidney tissues, and its expression was localized to CD8+ T cells, as confirmed by immunofluorescence staining. Functional analysis indicated that CAMK1D+ CD8+ T cells engaged in pro-inflammatory and pro-fibrotic signaling with various renal cell types and showed enrichment in metabolic pathways related to DKD. Conclusion Our results highlighted the important role of CD8+ T cell in shaping the renal immune microenvironment in both DKD and aging. CAMK1D may serve as a shared molecular risk factor linking aging and diabetic renal injury.
format: application/pdf
format: text/html
creator: Peiqi Zhu
creator: Ruijie Tang
creator: Yaping Zhou
creator: Yining He
creator: Jing Zhao
creator: Zhengxin Liu
creator: Ying Zhao
creator: Weiming He
subject: Molecular Biology
subject: Geriatrics
subject: Immunology
subject: Nephrology
subject: Medical Genetics
description: doi:10.7717/peerj.20762
publisher: PeerJ Inc.
rights: © 2026 Zhu et al.
abstract: Background Diabetic kidney disease (DKD) is a leading cause of end-stage renal disease (ESRD), accelerates age-related decline in estimated glomerular filtration rate (eGFR), leading to a markedly increased prevalence of DKD among elderly diabetic patients. Recent studies suggest that immune dysregulation plays a pivotal role in DKD progression; however, the cellular and molecular mechanisms linking aging, immune infiltration, and DKD remain unclear. Methods We used single-cell RNA sequencing (scRNA-seq) analysis to characterize immune cell dynamics between the young, the elderly and DKD patients. Based on the scRNA-seq analysis, Mendelian randomization (MR) analysis of differentially expressed genes (DEGs) in CD8+ T cells were conducted to explore the casual relationship between DEGs and DKD. Results The CD8+ T cell cluster was the predominant T cell subtype, but its proportion gradually declined from young individuals to elderly subjects and DKD patients. MR analysis of DEGs in CD8+ T cells suggested that calcium/calmodulin dependent protein kinase 1D (CAMK1D) exhibited strongest causal relationship with DKD. CAMK1D was upregulated in DKD kidney tissues, and its expression was localized to CD8+ T cells, as confirmed by immunofluorescence staining. Functional analysis indicated that CAMK1D+ CD8+ T cells engaged in pro-inflammatory and pro-fibrotic signaling with various renal cell types and showed enrichment in metabolic pathways related to DKD. Conclusion Our results highlighted the important role of CD8+ T cell in shaping the renal immune microenvironment in both DKD and aging. CAMK1D may serve as a shared molecular risk factor linking aging and diabetic renal injury.
bibliographic citation: Zhu et al. (2026) Aging-related CD8+ T cell alterations and calcium/calmodulin dependent protein kinase 1D activation in the pathogenesis of diabetic kidney disease. PeerJ 14:e20762 https://doi.org/10.7717/peerj.20762
date submitted: 2025-07-31
date accepted: 2025-12-17
issued: 2026-02-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhu
  given name: Peiqi
author list: Agent
  family name: Tang
  given name: Ruijie
author list: Agent
  family name: Zhou
  given name: Yaping
author list: Agent
  family name: He
  given name: Yining
author list: Agent
  family name: Zhao
  given name: Jing
author list: Agent
  family name: Liu
  given name: Zhengxin
author list: Agent
  family name: Zhao
  given name: Ying
author list: Agent
  family name: He
  given name: Weiming
doi: 10.7717/peerj.20762
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-13
copyright: ©2026 Zhu et al.
attribution name: Zhu et al.

Seasonal abundance of six tephritid species and the fruiting phenology of their main hosts in northern Jiangxi, China
type: item
type: AcademicArticle
description: Several tephritid species have successfully invaded northern Jiangxi, China, posing a serious threat to regional fruit and vegetable production. This study presents a detailed report on the seasonal abundance of six tephritid species and the fruiting phenology of their main hosts across Nanchang, Yongxiu and Xiushui in northern Jiangxi from 2018 to 2021, using data from methyl eugenol (ME), cuelure (CUE), and sugar-wine-vinegar-water (SWVW)-baited traps and from fruits infested by tephritid larvae. A total of 18,875 tephritid specimens were captured by traps, representing six species, Bactrocera dorsalis (Hendel), B. scutellata (Hendel), B. minax (Enderlein), Zeugodacus tau (Walker), Z. cucurbitae (Coquillett), and Callantra trimacula (Wang). Notably, B. minax and C. trimacula were discovered for the first time in northern Jiangxi. In addition to B. minax (captured only in Xiushui) and Z. cucurbitae (captured only in Nanchang), B. dorsalis, B. scutellata, Z. tau and C. trimacula were captured in all three regions. Zeugodacus tau exhibited the highest population density, followed by B. dorsalis and B. scutellata, and C. trimacula densities were markedly lower. The diversity index of captured tephritid species was similar in Nanchang, Yongxiu and Xiushui, but varied significantly across different seasons from May to December. When tephritid adults were active, B. minax population density reached its maximum in mid-June, whereas B. scutellata, Z. tau and Z. cucurbitae peaked in August–September, and B. dorsalis peaked in September–October. Bactrocera dorsalis and B. minax share similar hosts, primarily those from the Rutaceae family, including Citrus sinensis (L.) Osbeck, C. reticulata Blanco, C. maxima (Burm) Merr., and C. grandis Tomentosa. However, B. scutellata, Z. tau and Z. cucurbitae have similar hosts, especially those from the Cucurbitaceae family, such as Cucurbita moschata (Duch. ex Lam.) Duch.ex Poiret, Luffa cylindrica (L.) Roem., Momordica charantia L., a…
format: application/pdf
format: text/html
creator: Haiyan Yang
creator: Weijun Li
creator: Xin Zhong
creator: Qingxiu Xie
creator: Xiaozhen Li
subject: Agricultural Science
subject: Biodiversity
subject: Entomology
subject: Population Biology
description: doi:10.7717/peerj.20751
publisher: PeerJ Inc.
rights: © 2026 Yang et al.
abstract: Several tephritid species have successfully invaded northern Jiangxi, China, posing a serious threat to regional fruit and vegetable production. This study presents a detailed report on the seasonal abundance of six tephritid species and the fruiting phenology of their main hosts across Nanchang, Yongxiu and Xiushui in northern Jiangxi from 2018 to 2021, using data from methyl eugenol (ME), cuelure (CUE), and sugar-wine-vinegar-water (SWVW)-baited traps and from fruits infested by tephritid larvae. A total of 18,875 tephritid specimens were captured by traps, representing six species, Bactrocera dorsalis (Hendel), B. scutellata (Hendel), B. minax (Enderlein), Zeugodacus tau (Walker), Z. cucurbitae (Coquillett), and Callantra trimacula (Wang). Notably, B. minax and C. trimacula were discovered for the first time in northern Jiangxi. In addition to B. minax (captured only in Xiushui) and Z. cucurbitae (captured only in Nanchang), B. dorsalis, B. scutellata, Z. tau and C. trimacula were captured in all three regions. Zeugodacus tau exhibited the highest population density, followed by B. dorsalis and B. scutellata, and C. trimacula densities were markedly lower. The diversity index of captured tephritid species was similar in Nanchang, Yongxiu and Xiushui, but varied significantly across different seasons from May to December. When tephritid adults were active, B. minax population density reached its maximum in mid-June, whereas B. scutellata, Z. tau and Z. cucurbitae peaked in August–September, and B. dorsalis peaked in September–October. Bactrocera dorsalis and B. minax share similar hosts, primarily those from the Rutaceae family, including Citrus sinensis (L.) Osbeck, C. reticulata Blanco, C. maxima (Burm) Merr., and C. grandis Tomentosa. However, B. scutellata, Z. tau and Z. cucurbitae have similar hosts, especially those from the Cucurbitaceae family, such as Cucurbita moschata (Duch. ex Lam.) Duch.ex Poiret, Luffa cylindrica (L.) Roem., Momordica charantia L., a…
bibliographic citation: Yang et al. (2026) Seasonal abundance of six tephritid species and the fruiting phenology of their main hosts in northern Jiangxi, China. PeerJ 14:e20751 https://doi.org/10.7717/peerj.20751
date submitted: 2025-08-13
date accepted: 2025-12-16
issued: 2026-02-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Haiyan
author list: Agent
  family name: Li
  given name: Weijun
author list: Agent
  family name: Zhong
  given name: Xin
author list: Agent
  family name: Xie
  given name: Qingxiu
author list: Agent
  family name: Li
  given name: Xiaozhen
doi: 10.7717/peerj.20751
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-13
copyright: ©2026 Yang et al.
attribution name: Yang et al.

Knowledge, attitudes, and practices regarding chronic sinusitis and its surgical treatment: a cross-sectional study in China
type: item
type: AcademicArticle
description: Background Chronic sinusitis is a common condition that can greatly affect patients’ quality of life. It is essential to understand patients’ knowledge, attitudes, and practices (KAP) regarding chronic sinusitis and its surgical treatment to enhance patient outcomes and optimize clinical management. This study aimed to investigate KAP among chronic sinusitis patients to identify areas for targeted intervention and improvement. Methods A cross-sectional study was conducted with chronic sinusitis patients at the Ear, Nose, and Throat Department of Liaocheng People’s Hospital from June 2019 to June 2022. Demographic data and KAP were collected using self-designed questionnaires. Results A total of 567 valid questionnaires were included, yielding a validity rate of 99.3%. Among the respondents, 314 were male (55.38%), and 260 individuals (45.86%) lived in urban areas. The mean scores for KAP were 7.86 ± 2.39 (possible range: 0–12), 17.69 ± 1.94 (possible range: 8–40), and 7.86 ± 2.39 (possible range: 7–35), respectively. Structural equation modeling demonstrated a direct impact of knowledge on attitude (β = −0.500, p < 0.001) and practice (β = 0.261, p = 0.001), and a direct impact of attitude on practice (β = 1.737, p < 0.001). Conclusion Patients with chronic sinusitis demonstrated insufficient knowledge and negative attitudes and practices towards both the condition and its surgical treatment. These findings highlight the need for targeted interventions to improve patient education and awareness. By addressing knowledge gaps and fostering positive attitudes towards treatment options, healthcare providers can empower patients to make informed decisions and enhance their management of chronic sinusitis.
format: application/pdf
format: text/html
creator: Maocai Li
creator: Tan Wang
creator: Lianqing Li
creator: Lili Gong
creator: Lingnan Bu
subject: Otorhinolaryngology
subject: Respiratory Medicine
description: doi:10.7717/peerj.20633
publisher: PeerJ Inc.
rights: © 2026 Li et al.
abstract: Background Chronic sinusitis is a common condition that can greatly affect patients’ quality of life. It is essential to understand patients’ knowledge, attitudes, and practices (KAP) regarding chronic sinusitis and its surgical treatment to enhance patient outcomes and optimize clinical management. This study aimed to investigate KAP among chronic sinusitis patients to identify areas for targeted intervention and improvement. Methods A cross-sectional study was conducted with chronic sinusitis patients at the Ear, Nose, and Throat Department of Liaocheng People’s Hospital from June 2019 to June 2022. Demographic data and KAP were collected using self-designed questionnaires. Results A total of 567 valid questionnaires were included, yielding a validity rate of 99.3%. Among the respondents, 314 were male (55.38%), and 260 individuals (45.86%) lived in urban areas. The mean scores for KAP were 7.86 ± 2.39 (possible range: 0–12), 17.69 ± 1.94 (possible range: 8–40), and 7.86 ± 2.39 (possible range: 7–35), respectively. Structural equation modeling demonstrated a direct impact of knowledge on attitude (β = −0.500, p < 0.001) and practice (β = 0.261, p = 0.001), and a direct impact of attitude on practice (β = 1.737, p < 0.001). Conclusion Patients with chronic sinusitis demonstrated insufficient knowledge and negative attitudes and practices towards both the condition and its surgical treatment. These findings highlight the need for targeted interventions to improve patient education and awareness. By addressing knowledge gaps and fostering positive attitudes towards treatment options, healthcare providers can empower patients to make informed decisions and enhance their management of chronic sinusitis.
bibliographic citation: Li et al. (2026) Knowledge, attitudes, and practices regarding chronic sinusitis and its surgical treatment: a cross-sectional study in China. PeerJ 14:e20633 https://doi.org/10.7717/peerj.20633
date submitted: 2025-05-08
date accepted: 2025-11-30
issued: 2026-02-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Maocai
author list: Agent
  family name: Wang
  given name: Tan
author list: Agent
  family name: Li
  given name: Lianqing
author list: Agent
  family name: Gong
  given name: Lili
author list: Agent
  family name: Bu
  given name: Lingnan
doi: 10.7717/peerj.20633
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-13
copyright: © 2026 Li et al.
attribution name: Li et al.

Gene mapping and development of molecular markers for thousand-grain weight in rye based on bulked segregant analysis
type: item
type: AcademicArticle
description: Xinjiang wild rye (Secale cereale subsp. segetale) is a wild rye species that was discovered in Xinjiang Province of China in the 20th century. It is a relatively understudied cereal crop within the Poaceae family, and there is currently a lack of research on its yield-related traits. Mapping genes controlling thousand-grain weight (TGW) is crucial for developing high-yielding rye cultivars. In this study, bulk segregant analysis sequencing (BSA-seq) was performed on a cross-pollinated (CP) hybrid population derived from cultivated rye (Z837) and Xinjiang wild rye (90R13) to identify genomic regions associated with TGW. Molecular markers were then developed in the region of the initially mapped genes to further localize the TGW gene. BSA-seq analysis identified 10 candidate regions containing 68 single nucleotide polymorphism (SNP) loci across the seven chromosomes and unassembled chromosomal segments of rye. Molecular markers were designed for these loci and PCR-based validation was performed, yielding six high-quality Kompetitive allele-specific PCR (KASP) markers and one simple sequence repeat (SSR) marker. After evaluating amplification efficiency, a single KASP marker, TGW-16, proved highly effective for selecting germplasm with superior TGW. Functional annotation of the candidate gene ScWN7R01G304400 (linked to TGW-16) revealed that it encodes a protein containing an RNA recognition motif (RRM1) domain. These findings establish both genetic resources and methodological frameworks for marker-assisted breeding in rye, laying a solid foundation for cultivating elite varieties with optimized TGW performance.
format: application/pdf
format: text/html
creator: Lai Wei
creator: Zhenbo Zhai
creator: Yunjie Yang
creator: Yanping Yang
creator: Yonghe Che
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.20811
publisher: PeerJ Inc.
rights: © 2026 Wei et al.
abstract: Xinjiang wild rye (Secale cereale subsp. segetale) is a wild rye species that was discovered in Xinjiang Province of China in the 20th century. It is a relatively understudied cereal crop within the Poaceae family, and there is currently a lack of research on its yield-related traits. Mapping genes controlling thousand-grain weight (TGW) is crucial for developing high-yielding rye cultivars. In this study, bulk segregant analysis sequencing (BSA-seq) was performed on a cross-pollinated (CP) hybrid population derived from cultivated rye (Z837) and Xinjiang wild rye (90R13) to identify genomic regions associated with TGW. Molecular markers were then developed in the region of the initially mapped genes to further localize the TGW gene. BSA-seq analysis identified 10 candidate regions containing 68 single nucleotide polymorphism (SNP) loci across the seven chromosomes and unassembled chromosomal segments of rye. Molecular markers were designed for these loci and PCR-based validation was performed, yielding six high-quality Kompetitive allele-specific PCR (KASP) markers and one simple sequence repeat (SSR) marker. After evaluating amplification efficiency, a single KASP marker, TGW-16, proved highly effective for selecting germplasm with superior TGW. Functional annotation of the candidate gene ScWN7R01G304400 (linked to TGW-16) revealed that it encodes a protein containing an RNA recognition motif (RRM1) domain. These findings establish both genetic resources and methodological frameworks for marker-assisted breeding in rye, laying a solid foundation for cultivating elite varieties with optimized TGW performance.
bibliographic citation: Wei et al. (2026) Gene mapping and development of molecular markers for thousand-grain weight in rye based on bulked segregant analysis. PeerJ 14:e20811 https://doi.org/10.7717/peerj.20811
date submitted: 2025-06-26
date accepted: 2025-12-28
issued: 2026-02-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Lai
author list: Agent
  family name: Zhai
  given name: Zhenbo
author list: Agent
  family name: Yang
  given name: Yunjie
author list: Agent
  family name: Yang
  given name: Yanping
author list: Agent
  family name: Che
  given name: Yonghe
doi: 10.7717/peerj.20811
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-12
copyright: © 2026 Wei et al.
attribution name: Wei et al.

Pan-cancer multi-omics profiling of OAS3 reveals its immunological and prognostic associations across human cancers
type: item
type: AcademicArticle
description: Background The enzyme 2′-5′-oligoadenylate synthetase 3 (OAS3) plays a well-established role in antiviral immunity, but its involvement in cancer biology remains poorly understood. This study aimed to comprehensively investigate the expression patterns, mutation characteristics, prognostic significance, functional roles, and therapeutic potential of OAS3 across multiple cancer types. Methods Utilizing multi-omics data from public cancer databases, we analyzed OAS3 expression patterns, survival correlations, immune interactions, pathway enrichment, genomic associations, mutation profiles, and functional validation of OAS3 knockdown in THP-1 cells for apoptosis assays. Results OAS3 expression was significantly upregulated in 32 cancer types, highlighting its context-dependent roles as an oncogene. The expression patterns of OAS3 were found to be stage-specific and cancer-specific across multiple tumor types. Survival analysis revealed that high OAS3 expression was significantly associated with unfavorable prognosis in several cancers. Further analyses demonstrated that OAS3 expression was correlated with immune-related genes, immune checkpoints, tumor stemness, and immune cell infiltration across multiple tumor types. Moreover, gene set enrichment profiling revealed significant involvement of OAS3 in interferon response and immune regulation, with prominent enrichment in Janus kinase-signal transducer and activator of transcription (JAK-STAT) and Notch signaling pathways. Mutation analysis highlighted high mutation frequencies of OAS3 in several cancer types, especially in endometrial cancer and melanoma. Comprehensive molecular profiling further identified significant associations between OAS3 expression levels and key genomic features (tumor mutation burden, homologous recombination deficiency and RNA modification-related proteins). Besides, OAS3’s expression was associated with key processes such as cell cycle regulation and immune evasion, further underscoring its…
format: application/pdf
format: text/html
creator: Xi Zhang
creator: Hongyan Zhang
creator: Liang Zhong
creator: Wei Yang
creator: Chunhui Yang
creator: Yuqing Pan
creator: Beizhong Liu
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.20805
publisher: PeerJ Inc.
rights: © 2026 Zhang et al.
abstract: Background The enzyme 2′-5′-oligoadenylate synthetase 3 (OAS3) plays a well-established role in antiviral immunity, but its involvement in cancer biology remains poorly understood. This study aimed to comprehensively investigate the expression patterns, mutation characteristics, prognostic significance, functional roles, and therapeutic potential of OAS3 across multiple cancer types. Methods Utilizing multi-omics data from public cancer databases, we analyzed OAS3 expression patterns, survival correlations, immune interactions, pathway enrichment, genomic associations, mutation profiles, and functional validation of OAS3 knockdown in THP-1 cells for apoptosis assays. Results OAS3 expression was significantly upregulated in 32 cancer types, highlighting its context-dependent roles as an oncogene. The expression patterns of OAS3 were found to be stage-specific and cancer-specific across multiple tumor types. Survival analysis revealed that high OAS3 expression was significantly associated with unfavorable prognosis in several cancers. Further analyses demonstrated that OAS3 expression was correlated with immune-related genes, immune checkpoints, tumor stemness, and immune cell infiltration across multiple tumor types. Moreover, gene set enrichment profiling revealed significant involvement of OAS3 in interferon response and immune regulation, with prominent enrichment in Janus kinase-signal transducer and activator of transcription (JAK-STAT) and Notch signaling pathways. Mutation analysis highlighted high mutation frequencies of OAS3 in several cancer types, especially in endometrial cancer and melanoma. Comprehensive molecular profiling further identified significant associations between OAS3 expression levels and key genomic features (tumor mutation burden, homologous recombination deficiency and RNA modification-related proteins). Besides, OAS3’s expression was associated with key processes such as cell cycle regulation and immune evasion, further underscoring its…
bibliographic citation: Zhang et al. (2026) Pan-cancer multi-omics profiling of OAS3 reveals its immunological and prognostic associations across human cancers. PeerJ 14:e20805 https://doi.org/10.7717/peerj.20805
date submitted: 2025-06-13
date accepted: 2025-12-26
issued: 2026-02-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xi
author list: Agent
  family name: Zhang
  given name: Hongyan
author list: Agent
  family name: Zhong
  given name: Liang
author list: Agent
  family name: Yang
  given name: Wei
author list: Agent
  family name: Yang
  given name: Chunhui
author list: Agent
  family name: Pan
  given name: Yuqing
author list: Agent
  family name: Liu
  given name: Beizhong
doi: 10.7717/peerj.20805
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-12
copyright: ©2026 Zhang et al.
attribution name: Zhang et al.

In vitro polyploid induction in Allium grayi Regel using colchicine
type: item
type: AcademicArticle
description: Allium grayi Regel is a seasonally limited small perennial herb of the subfamily Allioideae, and is endemic to Matsu, Taiwan. The species possesses nutritious, ornamental value, and biological pharmacological activity. This study evaluated for the first time to induce polyploidy using the dissected bulb of A. grayi as explants in vitro, with the expectation of increasing the bulb size. Sterile bulbs were divided into four equal parts and pre-cultured under different durations before being soaked in a one g/L colchicine solution for 12 or 24 hours. Survival, regeneration, variation, and tetraploid induction rates were recorded, while ploidy levels were determined by flow cytometry and stomatal traits were measured microscopically. The results showed that pre-cultured treatment after dissecting the sterile bulbs increased the variation rate of the plants, with the group that was left static for 10 days before immersing in a one g/L colchicine liquid medium for 24 hours showing the best results. The variation rate reached 100%, and the induction rate of tetraploid plants reached 20% by flow cytometry examination. Among 123 regenerated shoots, 13 were chimeras and three stable tetraploid lines were established, all exhibiting larger stomata and lower stomatal density than diploids. These tetraploid lines provide great potential for future breeding and improvement of Matsu native shallot cultivars.
format: application/pdf
format: text/html
creator: Ting-Syuan Chen
creator: Wei-Hung Zhang
creator: Si-Yu Liu
creator: Cheng-Ying Hung
creator: Chien-Yuan Kao
subject: Agricultural Science
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.20790
publisher: PeerJ Inc.
rights: © 2026 Chen et al.
abstract: Allium grayi Regel is a seasonally limited small perennial herb of the subfamily Allioideae, and is endemic to Matsu, Taiwan. The species possesses nutritious, ornamental value, and biological pharmacological activity. This study evaluated for the first time to induce polyploidy using the dissected bulb of A. grayi as explants in vitro, with the expectation of increasing the bulb size. Sterile bulbs were divided into four equal parts and pre-cultured under different durations before being soaked in a one g/L colchicine solution for 12 or 24 hours. Survival, regeneration, variation, and tetraploid induction rates were recorded, while ploidy levels were determined by flow cytometry and stomatal traits were measured microscopically. The results showed that pre-cultured treatment after dissecting the sterile bulbs increased the variation rate of the plants, with the group that was left static for 10 days before immersing in a one g/L colchicine liquid medium for 24 hours showing the best results. The variation rate reached 100%, and the induction rate of tetraploid plants reached 20% by flow cytometry examination. Among 123 regenerated shoots, 13 were chimeras and three stable tetraploid lines were established, all exhibiting larger stomata and lower stomatal density than diploids. These tetraploid lines provide great potential for future breeding and improvement of Matsu native shallot cultivars.
bibliographic citation: Chen et al. (2026) In vitro polyploid induction in Allium grayi Regel using colchicine. PeerJ 14:e20790 https://doi.org/10.7717/peerj.20790
date submitted: 2025-07-22
date accepted: 2025-12-23
issued: 2026-02-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Ting-Syuan
author list: Agent
  family name: Zhang
  given name: Wei-Hung
author list: Agent
  family name: Liu
  given name: Si-Yu
author list: Agent
  family name: Hung
  given name: Cheng-Ying
author list: Agent
  family name: Kao
  given name: Chien-Yuan
doi: 10.7717/peerj.20790
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-12
copyright: ©2026 Chen et al.
attribution name: Chen et al.

Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community
type: item
type: AcademicArticle
description: Jellyfish are increasingly recognized as a significant contributor to marine organic matter (OM) on a global scale, with implications for ecosystem dynamics. While the role of jellyfish detritus in microbial nutrient cycling has been explored, the contribution of OM released by live jellyfish—primarily as mucus (hereinafter referred to as mucus-associated OM, or MAOM)—remains understudied. This study investigates the release of organic and inorganic nutrients through MAOM from live jellyfish and their effects on ambient microbial communities in the northern Adriatic Sea using a series of leaching and short-term microcosm experiments. Our results show that per gram of MAOM dry weight from the jellyfish Aurelia spp, approximatively 2 µmol of phosphate, 4 µmol of dissolved inorganic nitrogen, 18 µmol dissolved organic nitrogen, 134 µmol of dissolved organic carbon and 15 µmol of dissolved free amino acids can be released in the ambient seawater in 24 h. Almost half of the OM is released as dissolved OM (DOM), of which a substantial part is low molecular weight (<1 kDa) molecules. During the first 20 h, the DOM fraction of MAOM was rapidly consumed by the ambient microbial community without a corresponding increase in biomass, likely due to nitrogen limitation. In the subsequent 22 h, microbial growth accelerated to 0.19 ± 0.03 h−1 until phosphate became limiting, leading to a sharp decline in microbial production. Our metagenomics analysis revealed that the MAOM-degrading microbial community, dominated by Gammaproteobacteria opportunistic copiotrophs, exhibited increased functional capacity for nutrient assimilation and OM degradation, particularly in the transport and metabolism of amino acids (particularly glycine and taurine) and phosphorus. These traits mirror those found in detritus-degrading microbial communities, suggesting that jellyfish blooms promote the emergence of specialized microbial consortia with shared metabolic capabilities. Taken together, our findi…
format: application/pdf
format: text/html
creator: Nathan Hubot
creator: Sarah L.C. Giering
creator: Neža Orel
creator: Katja Klun
creator: Gerhard J. Herndl
creator: Felix Hohaus
creator: Cathy H. Lucas
creator: Tinkara Tinta
subject: Biochemistry
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.20784
publisher: PeerJ Inc.
rights: © 2026 Hubot et al.
abstract: Jellyfish are increasingly recognized as a significant contributor to marine organic matter (OM) on a global scale, with implications for ecosystem dynamics. While the role of jellyfish detritus in microbial nutrient cycling has been explored, the contribution of OM released by live jellyfish—primarily as mucus (hereinafter referred to as mucus-associated OM, or MAOM)—remains understudied. This study investigates the release of organic and inorganic nutrients through MAOM from live jellyfish and their effects on ambient microbial communities in the northern Adriatic Sea using a series of leaching and short-term microcosm experiments. Our results show that per gram of MAOM dry weight from the jellyfish Aurelia spp, approximatively 2 µmol of phosphate, 4 µmol of dissolved inorganic nitrogen, 18 µmol dissolved organic nitrogen, 134 µmol of dissolved organic carbon and 15 µmol of dissolved free amino acids can be released in the ambient seawater in 24 h. Almost half of the OM is released as dissolved OM (DOM), of which a substantial part is low molecular weight (<1 kDa) molecules. During the first 20 h, the DOM fraction of MAOM was rapidly consumed by the ambient microbial community without a corresponding increase in biomass, likely due to nitrogen limitation. In the subsequent 22 h, microbial growth accelerated to 0.19 ± 0.03 h−1 until phosphate became limiting, leading to a sharp decline in microbial production. Our metagenomics analysis revealed that the MAOM-degrading microbial community, dominated by Gammaproteobacteria opportunistic copiotrophs, exhibited increased functional capacity for nutrient assimilation and OM degradation, particularly in the transport and metabolism of amino acids (particularly glycine and taurine) and phosphorus. These traits mirror those found in detritus-degrading microbial communities, suggesting that jellyfish blooms promote the emergence of specialized microbial consortia with shared metabolic capabilities. Taken together, our findi…
bibliographic citation: Hubot et al. (2026) Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community. PeerJ 14:e20784 https://doi.org/10.7717/peerj.20784
date submitted: 2025-10-27
date accepted: 2025-12-22
issued: 2026-02-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hubot
  given name: Nathan
author list: Agent
  family name: Giering
  given name: Sarah L.C.
author list: Agent
  family name: Orel
  given name: Neža
author list: Agent
  family name: Klun
  given name: Katja
author list: Agent
  family name: Herndl
  given name: Gerhard J.
author list: Agent
  family name: Hohaus
  given name: Felix
author list: Agent
  family name: Lucas
  given name: Cathy H.
author list: Agent
  family name: Tinta
  given name: Tinkara
doi: 10.7717/peerj.20784
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-12
copyright: ©2026 Hubot et al.
attribution name: Hubot et al.

Epigenetic activation of SLC7A11 defines a ferroptosis—immune axis and enables robust DNA methylation-based diagnosis of lung squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Lung squamous cell carcinoma (LUSC) currently lacks reliable biomarkers for early diagnosis and precision therapy. While Solute Carrier Family 7 Member 11 (SLC7A11) plays key roles in ferroptosis resistance, redox homeostasis and tumor progression, its epigenetic regulation, diagnostic potential, and immunological functions in LUSC remain poorly understood. Methods Multi-omics data from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), Gene Expression Omnibus (GEO) and an in-house cohorts of 173 LUSC patients were integrated to characterize SLC7A11 DNA methylation, mRNA, and protein levels. Four methylation probes were utilized to construct diagnostic models, including Generalized Linear Model (GLM), Least Absolute Shrinkage and Selection Operator (LASSO), Random Forest (RF), and Extreme Gradient Boosting (XGB). These models were validated internally (via 10-fold cross-validation and bootsrtapping) and externally using the GSE121849 dataset. Model interpretability was examined through SHapley Additive exPlanations (SHAP). Additionally, immune infiltration, pathway enrichment and drug sensitivity analyses were performed to explore ferroptosis-associated and immunity-related mechanisms. Results SLC7A11 exhibited LUSC-specific epigenetic activation, characterized by promoter hypomethylation, mRNA upregulation, and protein overexpression across cohorts. The four-probe GLM diagnostic model achieved superior performance (AUC = 0.985 in TCGA; AUC = 1.000 in GSE121849), with SHAP identifying cg02102889 (TSS1500) as the most influential probe. While SLC7A11 expression and methylation were not significantly associated with survival in the overall cohort, high SLC7A11 predicted poorer outcomes in female patients and those with pathologic T3 & T4 stage disease. Mechanistically, SLC7A11-high tumors displayed ferroptosis-resistant and immunosuppressive phenotypes, including increased Programmed Death-Ligand 1 (PD-L1) expression and e…
format: application/pdf
format: text/html
creator: Hui-Ping Lu
creator: Kesong Nong
creator: Lingling Pang
creator: Yulu Tang
creator: Qi Li
creator: Zhendong Chen
creator: Li Xiao
creator: Liangqin Zhu
creator: Dongming Li
creator: Yiyang Chen
creator: Guoqiang Chen
creator: Jingwen Ling
creator: Jiandi Li
creator: Gang Chen
creator: Yi-Wu Dang
subject: Bioinformatics
subject: Immunology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.20686
publisher: PeerJ Inc.
rights: © 2026 Lu et al.
abstract: Background Lung squamous cell carcinoma (LUSC) currently lacks reliable biomarkers for early diagnosis and precision therapy. While Solute Carrier Family 7 Member 11 (SLC7A11) plays key roles in ferroptosis resistance, redox homeostasis and tumor progression, its epigenetic regulation, diagnostic potential, and immunological functions in LUSC remain poorly understood. Methods Multi-omics data from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), Gene Expression Omnibus (GEO) and an in-house cohorts of 173 LUSC patients were integrated to characterize SLC7A11 DNA methylation, mRNA, and protein levels. Four methylation probes were utilized to construct diagnostic models, including Generalized Linear Model (GLM), Least Absolute Shrinkage and Selection Operator (LASSO), Random Forest (RF), and Extreme Gradient Boosting (XGB). These models were validated internally (via 10-fold cross-validation and bootsrtapping) and externally using the GSE121849 dataset. Model interpretability was examined through SHapley Additive exPlanations (SHAP). Additionally, immune infiltration, pathway enrichment and drug sensitivity analyses were performed to explore ferroptosis-associated and immunity-related mechanisms. Results SLC7A11 exhibited LUSC-specific epigenetic activation, characterized by promoter hypomethylation, mRNA upregulation, and protein overexpression across cohorts. The four-probe GLM diagnostic model achieved superior performance (AUC = 0.985 in TCGA; AUC = 1.000 in GSE121849), with SHAP identifying cg02102889 (TSS1500) as the most influential probe. While SLC7A11 expression and methylation were not significantly associated with survival in the overall cohort, high SLC7A11 predicted poorer outcomes in female patients and those with pathologic T3 & T4 stage disease. Mechanistically, SLC7A11-high tumors displayed ferroptosis-resistant and immunosuppressive phenotypes, including increased Programmed Death-Ligand 1 (PD-L1) expression and e…
bibliographic citation: Lu et al. (2026) Epigenetic activation of SLC7A11 defines a ferroptosis—immune axis and enables robust DNA methylation-based diagnosis of lung squamous cell carcinoma. PeerJ 14:e20686 https://doi.org/10.7717/peerj.20686
date submitted: 2025-09-26
date accepted: 2025-12-05
issued: 2026-02-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Hui-Ping
author list: Agent
  family name: Nong
  given name: Kesong
author list: Agent
  family name: Pang
  given name: Lingling
author list: Agent
  family name: Tang
  given name: Yulu
author list: Agent
  family name: Li
  given name: Qi
author list: Agent
  family name: Chen
  given name: Zhendong
author list: Agent
  family name: Xiao
  given name: Li
author list: Agent
  family name: Zhu
  given name: Liangqin
author list: Agent
  family name: Li
  given name: Dongming
author list: Agent
  family name: Chen
  given name: Yiyang
author list: Agent
  family name: Chen
  given name: Guoqiang
author list: Agent
  family name: Ling
  given name: Jingwen
author list: Agent
  family name: Li
  given name: Jiandi
author list: Agent
  family name: Chen
  given name: Gang
author list: Agent
  family name: Dang
  given name: Yi-Wu
doi: 10.7717/peerj.20686
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-12
copyright: ©2026 Lu et al.
attribution name: Lu et al.

Interactions between dense seasonal macroalgal mats and oysters on natural and constructed shellfish reefs
type: item
type: AcademicArticle
description: Oysters are important coastal foundation species that provide valuable hard substrate for the recruitment of epibiotic organisms in environments otherwise dominated by soft sediment. Yet, their interactions with epibionts are relatively understudied. Despite the proliferation of macroalgal mats across the Southeastern United States in winter months, the relationship between oysters (Crassostrea virginica) and seasonal macroalgae is poorly understood. We conducted an observational field survey and two manipulative field experiments to document seasonal macroalgal dynamics on intertidal oyster reefs and to better understand the interaction between the oysters and algae. We found that algal mats in North Carolina were primarily composed of two genera, Ulva and Ectocarpus, which together reached extremely high cover (up to 100%) over large areas of reef. Macroalgae appeared in January and declined in May, with peak cover in February and March. Algal cover was significantly higher on constructed oyster reefs vs. natural oyster reefs. Our field experiments showed that algal cover was significantly higher on dead oyster mimics vs. live oysters, suggesting that the primary mechanism of algal facilitation is associated with the provisioning of hard substrate rather than fertilization. Reciprocally, we found no significant effects of macroalgae on oyster abundance or growth, likely due to relatively low algal cover in the experimental treatments. With a predicted proliferation of macroalgae under global change, our study highlights the important role that intertidal oyster reefs play in providing substrate for macroalgae, but more research on this key species interaction in intertidal areas of the Southeastern United States is needed.
format: application/pdf
format: text/html
creator: Carter S. Smith
creator: Michelle C. Brodeur
creator: Stephanie R. Valdez
creator: F. Joel Fodrie
creator: Y. Stacy Zhang
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.20682
publisher: PeerJ Inc.
rights: © 2026 Smith et al.
abstract: Oysters are important coastal foundation species that provide valuable hard substrate for the recruitment of epibiotic organisms in environments otherwise dominated by soft sediment. Yet, their interactions with epibionts are relatively understudied. Despite the proliferation of macroalgal mats across the Southeastern United States in winter months, the relationship between oysters (Crassostrea virginica) and seasonal macroalgae is poorly understood. We conducted an observational field survey and two manipulative field experiments to document seasonal macroalgal dynamics on intertidal oyster reefs and to better understand the interaction between the oysters and algae. We found that algal mats in North Carolina were primarily composed of two genera, Ulva and Ectocarpus, which together reached extremely high cover (up to 100%) over large areas of reef. Macroalgae appeared in January and declined in May, with peak cover in February and March. Algal cover was significantly higher on constructed oyster reefs vs. natural oyster reefs. Our field experiments showed that algal cover was significantly higher on dead oyster mimics vs. live oysters, suggesting that the primary mechanism of algal facilitation is associated with the provisioning of hard substrate rather than fertilization. Reciprocally, we found no significant effects of macroalgae on oyster abundance or growth, likely due to relatively low algal cover in the experimental treatments. With a predicted proliferation of macroalgae under global change, our study highlights the important role that intertidal oyster reefs play in providing substrate for macroalgae, but more research on this key species interaction in intertidal areas of the Southeastern United States is needed.
bibliographic citation: Smith et al. (2026) Interactions between dense seasonal macroalgal mats and oysters on natural and constructed shellfish reefs. PeerJ 14:e20682 https://doi.org/10.7717/peerj.20682
date submitted: 2025-08-01
date accepted: 2025-12-04
issued: 2026-02-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Carter S.
author list: Agent
  family name: Brodeur
  given name: Michelle C.
author list: Agent
  family name: Valdez
  given name: Stephanie R.
author list: Agent
  family name: Fodrie
  given name: F. Joel
author list: Agent
  family name: Zhang
  given name: Y. Stacy
doi: 10.7717/peerj.20682
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-12
copyright: © 2026 Smith et al.
attribution name: Smith et al.

Multiomics analysis of polyamine metabolism in colorectal cancer, highlighting the key role of extracellular putrescine in impairing CXCR6+CD8+ T cell anti-tumor activity
type: item
type: AcademicArticle
description: The contribution of putrescine (PUT) metabolism to impaired tumor immunosurveillance in colorectal cancer (CRC) requires a thorough examination of its biosynthesis, catabolism, and transport during tumor development. This study found, unexpectedly, that a better prognosis was associated with higher expression of the PUT biosynthesis genes ODC1 and AGMAT, while elevated expression of biosynthesis inhibitors and transport genes predicted worse outcomes. Two independent cohorts were deconvoluted by integrating data from 517,191 cells across 221 samples from 131 subjects. Higher percentages of epithelial subpopulations with low PUT transport scores were linked to improved prognosis. In contrast, greater proportions of T/natural killer/ILC cells with low biosynthesis but relatively higher transport scores were associated with poorer outcomes. PUT supplementation in HCT-116 and RKO cells promoted the tumor cell proliferation, but had no effect on cell migration or the expression of N-cadherin and E-cadherin. CXCR6+ CD8+ T cells, which were more prevalent in tumor tissue, exhibited significantly higher cytotoxicity compared to CXCR6− CD8+ T cells, as assessed using updated gene sets for T cell functional evaluation . However, CXCR6+CD8+ T cells also displayed elevated markers of exhaustion. Notably, higher CXCR6 expression and increased infiltration of CXCR6+ CD8+ T cells correlated with improved prognosis in both mismatch repair-proficient and mismatch repair-deficient CRC. To estimate the local accumulation of PUT around CXCR6+ CD8+ T cells, a novel “Pi value” was defined. A negative correlation was found between Pi values and both the cytotoxic activity and pro-inflammatory potential of these cells. Further investigation using a CRC tumor antigen-based in vitro system for the efficient induction of CXCR6+ CD8+ T cells revealed that extracellular PUT inhibits their cytotoxic function. Additionally, in a Dextran Sulfate Sodium (DSS)-induced colitis model combined with sin…
format: application/pdf
format: text/html
creator: Ziru Tan
creator: Yuqiang Zhang
creator: Cong pei jia
creator: Haifeng Lian
creator: Bin Wang
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Immunology
description: doi:10.7717/peerj.20663
publisher: PeerJ Inc.
rights: © 2026 Tan et al.
abstract: The contribution of putrescine (PUT) metabolism to impaired tumor immunosurveillance in colorectal cancer (CRC) requires a thorough examination of its biosynthesis, catabolism, and transport during tumor development. This study found, unexpectedly, that a better prognosis was associated with higher expression of the PUT biosynthesis genes ODC1 and AGMAT, while elevated expression of biosynthesis inhibitors and transport genes predicted worse outcomes. Two independent cohorts were deconvoluted by integrating data from 517,191 cells across 221 samples from 131 subjects. Higher percentages of epithelial subpopulations with low PUT transport scores were linked to improved prognosis. In contrast, greater proportions of T/natural killer/ILC cells with low biosynthesis but relatively higher transport scores were associated with poorer outcomes. PUT supplementation in HCT-116 and RKO cells promoted the tumor cell proliferation, but had no effect on cell migration or the expression of N-cadherin and E-cadherin. CXCR6+ CD8+ T cells, which were more prevalent in tumor tissue, exhibited significantly higher cytotoxicity compared to CXCR6− CD8+ T cells, as assessed using updated gene sets for T cell functional evaluation . However, CXCR6+CD8+ T cells also displayed elevated markers of exhaustion. Notably, higher CXCR6 expression and increased infiltration of CXCR6+ CD8+ T cells correlated with improved prognosis in both mismatch repair-proficient and mismatch repair-deficient CRC. To estimate the local accumulation of PUT around CXCR6+ CD8+ T cells, a novel “Pi value” was defined. A negative correlation was found between Pi values and both the cytotoxic activity and pro-inflammatory potential of these cells. Further investigation using a CRC tumor antigen-based in vitro system for the efficient induction of CXCR6+ CD8+ T cells revealed that extracellular PUT inhibits their cytotoxic function. Additionally, in a Dextran Sulfate Sodium (DSS)-induced colitis model combined with sin…
bibliographic citation: Tan et al. (2026) Multiomics analysis of polyamine metabolism in colorectal cancer, highlighting the key role of extracellular putrescine in impairing CXCR6+CD8+ T cell anti-tumor activity. PeerJ 14:e20663 https://doi.org/10.7717/peerj.20663
date submitted: 2025-05-06
date accepted: 2025-12-03
issued: 2026-02-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Ziru
author list: Agent
  family name: Zhang
  given name: Yuqiang
author list: Agent
  family name: pei jia
  given name: Cong
author list: Agent
  family name: Lian
  given name: Haifeng
author list: Agent
  family name: Wang
  given name: Bin
doi: 10.7717/peerj.20663
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-12
copyright: ©2026 Tan et al.
attribution name: Tan et al.

Chinese thyroid imaging reporting and data system with redefined marked hypoechogenicity for thyroid malignancy risk stratification demonstrates improved diagnostic accuracy
type: item
type: AcademicArticle
description: Purpose Using ultrasound to distinguish between benign and malignant thyroid nodules can be challenging. The purpose of this study was to evaluate the diagnostic performance of a modified Chinese Thyroid Imaging Reporting and Data System (C-TIRADS) that incorporates a redefined criterion for marked hypoechogenicity in stratifying the malignancy risk of thyroid nodules. Methods In this retrospective study, we analyzed patients with thyroid nodules who underwent ultrasound examination and subsequent biopsy or treatment at a tertiary hospital between January 2022 and December 2023. Interobserver agreement in identifying marked hypoechogenicity between two reviewers was assessed using kappa statistics. Using histopathology as the reference standard, the diagnostic performance of three classification systems, including the classical C-TIRADS, the modified C-TIRADS, and the 2021 K-TIRADS, was compared in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy, and the area under the receiver operating characteristic curve (AUC). Results The study included 1,219 patients with 1,721 thyroid nodules. After redefining marked hypoechogenicity, interobserver agreement (kappa) improved from 0.652 to 0.722. Compared to the original criterion, the redefined marked hypoechogenicity demonstrated significantly higher sensitivity (74.5% vs. 15.1%), accuracy (86.8% vs. 70.8%), and AUC (0.836 vs. 0.563) (all p < 0.05), with only a marginal reduction in specificity (92.6% vs. 97.4%, p > 0.05). The malignancy rates for the modified C-TIRADS categories were as follows: 12.0% (4a), 60.6% (4b), 85.8% (4c), and 93.3% (5). The optimal diagnostic thresholds were category 4b for both classical and modified C-TIRADS and category 4 for K-TIRADS. The modified C-TIRADS achieved superior accuracy (90.2% vs. 88.2% vs. 81.3%) and AUC (0.908 vs. 0.870 vs. 0.857) compared to the classical C-TIRADS and K-TIRADS, respectively (all pairwise p < 0.05). Co…
format: application/pdf
format: text/html
creator: Yingxue Bai
creator: Mingxin Yu
creator: Size Wu
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.20817
publisher: PeerJ Inc.
rights: © 2026 Bai et al.
abstract: Purpose Using ultrasound to distinguish between benign and malignant thyroid nodules can be challenging. The purpose of this study was to evaluate the diagnostic performance of a modified Chinese Thyroid Imaging Reporting and Data System (C-TIRADS) that incorporates a redefined criterion for marked hypoechogenicity in stratifying the malignancy risk of thyroid nodules. Methods In this retrospective study, we analyzed patients with thyroid nodules who underwent ultrasound examination and subsequent biopsy or treatment at a tertiary hospital between January 2022 and December 2023. Interobserver agreement in identifying marked hypoechogenicity between two reviewers was assessed using kappa statistics. Using histopathology as the reference standard, the diagnostic performance of three classification systems, including the classical C-TIRADS, the modified C-TIRADS, and the 2021 K-TIRADS, was compared in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy, and the area under the receiver operating characteristic curve (AUC). Results The study included 1,219 patients with 1,721 thyroid nodules. After redefining marked hypoechogenicity, interobserver agreement (kappa) improved from 0.652 to 0.722. Compared to the original criterion, the redefined marked hypoechogenicity demonstrated significantly higher sensitivity (74.5% vs. 15.1%), accuracy (86.8% vs. 70.8%), and AUC (0.836 vs. 0.563) (all p < 0.05), with only a marginal reduction in specificity (92.6% vs. 97.4%, p > 0.05). The malignancy rates for the modified C-TIRADS categories were as follows: 12.0% (4a), 60.6% (4b), 85.8% (4c), and 93.3% (5). The optimal diagnostic thresholds were category 4b for both classical and modified C-TIRADS and category 4 for K-TIRADS. The modified C-TIRADS achieved superior accuracy (90.2% vs. 88.2% vs. 81.3%) and AUC (0.908 vs. 0.870 vs. 0.857) compared to the classical C-TIRADS and K-TIRADS, respectively (all pairwise p < 0.05). Co…
bibliographic citation: Bai et al. (2026) Chinese thyroid imaging reporting and data system with redefined marked hypoechogenicity for thyroid malignancy risk stratification demonstrates improved diagnostic accuracy. PeerJ 14:e20817 https://doi.org/10.7717/peerj.20817
date submitted: 2025-05-28
date accepted: 2025-12-28
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Yingxue
author list: Agent
  family name: Yu
  given name: Mingxin
author list: Agent
  family name: Wu
  given name: Size
doi: 10.7717/peerj.20817
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Bai et al.
attribution name: Bai et al.

Effects of different cultivation methods on the rhizosphere microbial community and secondary metabolites of Houttuynia cordata Thunb.
type: item
type: AcademicArticle
description: This study aimed to investigate the effects of three distinct cultivation methods on the plant-soil system of Houttuynia cordata Thunb. specifically focusing on how they shape the rhizosphere microbial community and influence the accumulation of it is phenolic compounds. This study employed high-throughput sequencing of bacterial 16S rDNA and fungal ITS rDNA to assess the impact of three cultivation methods including in situ cultivation (ISC), indoor cultivation (IC), and tissue culture (TC) on the diversity and community structure of H. cordata rhizosphere soil microbes. Additionally, we explored the environmental drivers of phenotypic variations in secondary metabolite composition. Soil pH, urease (URA), total potassium (TK), and total nitrogen (TN) were significantly correlated with the accumulation of quercitrin, kaempferol-3-O-glucorhamnoside, isoquercitrin, and chlorogenic acid in H. cordata. Moreover, these environmental factors significantly influenced the rhizosphere microbial taxa Saitozyma, Lysobacter, Gemmata, and Penicillium. IC presents a sustainable approach for H. cordata cultivation, enhancing rhizosphere soil fertility and health. Furthermore, pH, URA, TK, and TN serve as key environmental drivers of secondary metabolite variation. These findings provide a foundation for establishing quality evaluation standards for H. cordata ensuring stable pharmacological efficacy, and facilitating further functional applications.
format: application/pdf
format: text/html
creator: Fangmei Song
creator: Die Fu
creator: Anping Wang
creator: Zhannan Yang
creator: Tianhua Yu
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.20797
publisher: PeerJ Inc.
rights: © 2026 Song et al.
abstract: This study aimed to investigate the effects of three distinct cultivation methods on the plant-soil system of Houttuynia cordata Thunb. specifically focusing on how they shape the rhizosphere microbial community and influence the accumulation of it is phenolic compounds. This study employed high-throughput sequencing of bacterial 16S rDNA and fungal ITS rDNA to assess the impact of three cultivation methods including in situ cultivation (ISC), indoor cultivation (IC), and tissue culture (TC) on the diversity and community structure of H. cordata rhizosphere soil microbes. Additionally, we explored the environmental drivers of phenotypic variations in secondary metabolite composition. Soil pH, urease (URA), total potassium (TK), and total nitrogen (TN) were significantly correlated with the accumulation of quercitrin, kaempferol-3-O-glucorhamnoside, isoquercitrin, and chlorogenic acid in H. cordata. Moreover, these environmental factors significantly influenced the rhizosphere microbial taxa Saitozyma, Lysobacter, Gemmata, and Penicillium. IC presents a sustainable approach for H. cordata cultivation, enhancing rhizosphere soil fertility and health. Furthermore, pH, URA, TK, and TN serve as key environmental drivers of secondary metabolite variation. These findings provide a foundation for establishing quality evaluation standards for H. cordata ensuring stable pharmacological efficacy, and facilitating further functional applications.
bibliographic citation: Song et al. (2026) Effects of different cultivation methods on the rhizosphere microbial community and secondary metabolites of Houttuynia cordata Thunb.. PeerJ 14:e20797 https://doi.org/10.7717/peerj.20797
date submitted: 2025-08-27
date accepted: 2025-12-23
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Fangmei
author list: Agent
  family name: Fu
  given name: Die
author list: Agent
  family name: Wang
  given name: Anping
author list: Agent
  family name: Yang
  given name: Zhannan
author list: Agent
  family name: Yu
  given name: Tianhua
doi: 10.7717/peerj.20797
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Song et al.
attribution name: Song et al.

https://peerj.com/articles/20780
type: item
type: AcademicArticle
title: The efficacy of tranexamic acid in reducing intraoperative bleeding during transurethral resection of the prostate for benign prostatic hyperplasia (BPH): a systematic review and meta-analysis of randomized controlled trials
description: Background Benign prostatic hyperplasia (BPH) is a common urinary system disease in elderly men, and transurethral resection of the prostate (TURP) is the gold standard for treating BPH. However, this surgery often leads to intraoperative and postoperative bleeding. Tranexamic acid (TXA) is an antifibrinolytic drug commonly used for hemostasis. This study aims to investigate the hemostatic effect of tranexamic acid in TURP surgery. Aim Evaluate the efficacy of tranexamic acid in TURP surgery. Methods We systematically searched the PubMed, Embase, EBSCO, Cochrane Library, and Web of Science databases for randomized controlled trials (RCTs) on TXA treatment for bleeding during transurethral resection of the prostate (TURP), published up to December 2025. Data analysis and management were performed using Review Manager version 5.3. Result After applying the predefined inclusion and exclusion criteria, a total of eight studies involving 611 patients were included in our meta-analysis. The results of our analysis indicated that the TXA group significantly outperformed the control group in three outcomes: intraoperative blood loss (P = 0.04), postoperative 24-hour hemoglobin levels (P < 0.001), and postoperative 24-hour hemoglobin difference (P = 0.02). However, no significant differences were observed between the TXA and control groups regarding surgical time (P = 0.28) and length of hospital stay (P = 0.08). Conclusions Compared to the control group, TXA significantly reduces intraoperative and postoperative bleeding in TURP surgery, making it valuable for anemic patients and in reducing surgical complications.
format: application/pdf
format: text/html
creator: Yanwei Zhang
creator: Ming Liu
creator: Fengze Sun
creator: Bin Wang
creator: Yicheng Guo
creator: Yuchen Qian
creator: Jitao Wu
subject: Clinical Trials
subject: Evidence Based Medicine
subject: Surgery and Surgical Specialties
subject: Urology
description: doi:10.7717/peerj.20780
publisher: PeerJ Inc.
rights: © 2026 Zhang et al.
abstract: Background Benign prostatic hyperplasia (BPH) is a common urinary system disease in elderly men, and transurethral resection of the prostate (TURP) is the gold standard for treating BPH. However, this surgery often leads to intraoperative and postoperative bleeding. Tranexamic acid (TXA) is an antifibrinolytic drug commonly used for hemostasis. This study aims to investigate the hemostatic effect of tranexamic acid in TURP surgery. Aim Evaluate the efficacy of tranexamic acid in TURP surgery. Methods We systematically searched the PubMed, Embase, EBSCO, Cochrane Library, and Web of Science databases for randomized controlled trials (RCTs) on TXA treatment for bleeding during transurethral resection of the prostate (TURP), published up to December 2025. Data analysis and management were performed using Review Manager version 5.3. Result After applying the predefined inclusion and exclusion criteria, a total of eight studies involving 611 patients were included in our meta-analysis. The results of our analysis indicated that the TXA group significantly outperformed the control group in three outcomes: intraoperative blood loss (P = 0.04), postoperative 24-hour hemoglobin levels (P < 0.001), and postoperative 24-hour hemoglobin difference (P = 0.02). However, no significant differences were observed between the TXA and control groups regarding surgical time (P = 0.28) and length of hospital stay (P = 0.08). Conclusions Compared to the control group, TXA significantly reduces intraoperative and postoperative bleeding in TURP surgery, making it valuable for anemic patients and in reducing surgical complications.
bibliographic citation: Zhang et al. (2026) The efficacy of tranexamic acid in reducing intraoperative bleeding during transurethral resection of the prostate for benign prostatic hyperplasia (BPH): a systematic review and meta-analysis of randomized controlled trials. PeerJ 14:e20780 https://doi.org/10.7717/peerj.20780
date submitted: 2025-08-12
date accepted: 2025-12-19
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yanwei
author list: Agent
  family name: Liu
  given name: Ming
author list: Agent
  family name: Sun
  given name: Fengze
author list: Agent
  family name: Wang
  given name: Bin
author list: Agent
  family name: Guo
  given name: Yicheng
author list: Agent
  family name: Qian
  given name: Yuchen
author list: Agent
  family name: Wu
  given name: Jitao
doi: 10.7717/peerj.20780
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Zhang et al.
attribution name: Zhang et al.

Effects of an 8-week liquid protein supplementation on resistance training adaptations in untrained healthy college students
type: item
type: AcademicArticle
description: This study investigates the effects of 8 weeks of liquid protein supplementation on resistance-training adaptations in healthy, untrained college students. Thirty untrained male participants were randomized into two groups: a protein supplement (resistance training exercise (RTE) + protein) and a control (RTE). Both groups underwent resistance training exercises (RTE) three times per week for 8 weeks. The RTE + protein consumed a protein liquid supplement post-exercise, while the RTE consumed water. The results showed a higher degree of change in chest circumference (mean difference = 6.10 cm vs 3.36 cm), maximal bench press strength (mean difference = 16.00 kg vs 8.93 kg, P = 0.007) and maximal squat strength (mean difference = 42.33 kg and 27.32 kg, P = 0.018) in the RTE + protein group compared to the RTE group. Both groups demonstrated increases in thigh circumference, muscle mass, and maximal bench press and deep squat repetitions, but no significant differences were observed between the two groups. These findings suggest that post-exercise protein liquid supplementation can enhance the benefits of RTE on muscle strength and body circumference in young untrained adults. The study highlights the importance of post-exercise protein supplementation for beginners seeking to improve muscle performance, and future research should explore the long-term effects and optimal dosages of protein supplementation in different forms. This trial was registered with ChiCTR under the registration number ChiCTR2300076750.
format: application/pdf
format: text/html
creator: Qisijing Liu
creator: Yi Guo
creator: Dancai Fan
creator: Bo Peng
creator: Jin Wang
creator: Ze Chen
creator: Wentao Gu
creator: Jian Wu
creator: Zhenhua Niu
creator: Shuo Wang
creator: Yanrong Zhao
subject: Nutrition
subject: Sports Medicine
description: doi:10.7717/peerj.20778
publisher: PeerJ Inc.
rights: © 2026 Liu et al.
abstract: This study investigates the effects of 8 weeks of liquid protein supplementation on resistance-training adaptations in healthy, untrained college students. Thirty untrained male participants were randomized into two groups: a protein supplement (resistance training exercise (RTE) + protein) and a control (RTE). Both groups underwent resistance training exercises (RTE) three times per week for 8 weeks. The RTE + protein consumed a protein liquid supplement post-exercise, while the RTE consumed water. The results showed a higher degree of change in chest circumference (mean difference = 6.10 cm vs 3.36 cm), maximal bench press strength (mean difference = 16.00 kg vs 8.93 kg, P = 0.007) and maximal squat strength (mean difference = 42.33 kg and 27.32 kg, P = 0.018) in the RTE + protein group compared to the RTE group. Both groups demonstrated increases in thigh circumference, muscle mass, and maximal bench press and deep squat repetitions, but no significant differences were observed between the two groups. These findings suggest that post-exercise protein liquid supplementation can enhance the benefits of RTE on muscle strength and body circumference in young untrained adults. The study highlights the importance of post-exercise protein supplementation for beginners seeking to improve muscle performance, and future research should explore the long-term effects and optimal dosages of protein supplementation in different forms. This trial was registered with ChiCTR under the registration number ChiCTR2300076750.
bibliographic citation: Liu et al. (2026) Effects of an 8-week liquid protein supplementation on resistance training adaptations in untrained healthy college students. PeerJ 14:e20778 https://doi.org/10.7717/peerj.20778
date submitted: 2025-05-26
date accepted: 2025-12-19
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Liu
  given name: Qisijing
author list: Agent
  family name: Guo
  given name: Yi
author list: Agent
  family name: Fan
  given name: Dancai
author list: Agent
  family name: Peng
  given name: Bo
author list: Agent
  family name: Wang
  given name: Jin
author list: Agent
  family name: Chen
  given name: Ze
author list: Agent
  family name: Gu
  given name: Wentao
author list: Agent
  family name: Wu
  given name: Jian
author list: Agent
  family name: Niu
  given name: Zhenhua
author list: Agent
  family name: Wang
  given name: Shuo
author list: Agent
  family name: Zhao
  given name: Yanrong
doi: 10.7717/peerj.20778
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Liu et al.
attribution name: Liu et al.

Psychological health outcomes of traditional Chinese exercises in older adults: a meta-analysis of randomized controlled trials
type: item
type: AcademicArticle
description: Background In recent years, an increasing number of systematic reviews and meta-analyses have examined the health benefits of traditional Chinese exercises (TCEs). However, most of the reviews and meta-analyses have just focused on their effects on physical function in older adults. This study conducts a meta-analysis of existing randomized controlled trials (RCTs) to investigate the effects of TCEs on psychological health outcomes. Methods Five Chinese and English databases were searched from their inception to July 2, 2025. RCTs were included if they used TCE interventions to improve psychological health outcomes in older adults, such as depression, anxiety, subjective well-being, general self-efficacy, and self-esteem. Study screening and data extraction were performed independently by two reviewers at all stages. Meta-analyses were conducted using Rev Man 5.4 and Stata 17.0. Pre-determined subgroups included the type of TCEs, mode of the intervention, duration of the intervention, frequency of exercise, duration of the single exercise session, and type of control condition. Result This study included 42 RCTs involving 4,317 participants. The meta-analysis revealed that, compared to control groups, TCEs are more effective in improving depression (SMD = −0.51, 95% CI [−0.72 to −0.29], p < 0.00001), anxiety (SMD = −0.39, 95% CI [−0.63 to −0.15], p = 0.002), and subjective well-being among older adults (SMD = 1.07, 95% CI [0.18–1.96], p = 0.02). TCEs also showed positive effects on general self-efficacy (SMD = 0.63, 95% CI [−0.05 to 1.31], p = 0.07) and self-esteem (SMD = 0.54, 95% CI [−0.06 to 1.13], p = 0.08), although these effects are not statistically significant. Despite the high heterogeneity in some outcomes, the studies with heterogeneity did not have a significant effect on the results. None of the included studies reported any injuries or adverse events among the participants. Conclusion TCEs represent an effective and safe intervention that can significa…
format: application/pdf
format: text/html
creator: Di Geng
creator: Xiaogang Li
creator: Yan Shi
subject: Geriatrics
subject: Psychiatry and Psychology
subject: Mental Health
subject: Sports Medicine
description: doi:10.7717/peerj.20773
publisher: PeerJ Inc.
rights: © 2026 Geng et al.
abstract: Background In recent years, an increasing number of systematic reviews and meta-analyses have examined the health benefits of traditional Chinese exercises (TCEs). However, most of the reviews and meta-analyses have just focused on their effects on physical function in older adults. This study conducts a meta-analysis of existing randomized controlled trials (RCTs) to investigate the effects of TCEs on psychological health outcomes. Methods Five Chinese and English databases were searched from their inception to July 2, 2025. RCTs were included if they used TCE interventions to improve psychological health outcomes in older adults, such as depression, anxiety, subjective well-being, general self-efficacy, and self-esteem. Study screening and data extraction were performed independently by two reviewers at all stages. Meta-analyses were conducted using Rev Man 5.4 and Stata 17.0. Pre-determined subgroups included the type of TCEs, mode of the intervention, duration of the intervention, frequency of exercise, duration of the single exercise session, and type of control condition. Result This study included 42 RCTs involving 4,317 participants. The meta-analysis revealed that, compared to control groups, TCEs are more effective in improving depression (SMD = −0.51, 95% CI [−0.72 to −0.29], p < 0.00001), anxiety (SMD = −0.39, 95% CI [−0.63 to −0.15], p = 0.002), and subjective well-being among older adults (SMD = 1.07, 95% CI [0.18–1.96], p = 0.02). TCEs also showed positive effects on general self-efficacy (SMD = 0.63, 95% CI [−0.05 to 1.31], p = 0.07) and self-esteem (SMD = 0.54, 95% CI [−0.06 to 1.13], p = 0.08), although these effects are not statistically significant. Despite the high heterogeneity in some outcomes, the studies with heterogeneity did not have a significant effect on the results. None of the included studies reported any injuries or adverse events among the participants. Conclusion TCEs represent an effective and safe intervention that can significa…
bibliographic citation: Geng et al. (2026) Psychological health outcomes of traditional Chinese exercises in older adults: a meta-analysis of randomized controlled trials. PeerJ 14:e20773 https://doi.org/10.7717/peerj.20773
date submitted: 2025-08-21
date accepted: 2025-12-18
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Geng
  given name: Di
author list: Agent
  family name: Li
  given name: Xiaogang
author list: Agent
  family name: Shi
  given name: Yan
doi: 10.7717/peerj.20773
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Geng et al.
attribution name: Geng et al.

A novel analysis workflow for simultaneous parsing prokaryotic and eukaryotic microbial genes from metagenomes
type: item
type: AcademicArticle
description: Accurately predicting coding genes from metagenomic samples containing a high proportion of eukaryotic content remains a significant challenge. Novel and reliable methods for the simultaneous prediction of prokaryotic and eukaryotic microbial genes are crucial to address this. We evaluated gene prediction accuracy of MetaGeneMark and MetaEuk using representative genomes from diverse organisms. Based on these findings, we developed an innovative analytical workflow. This approach involves an initial prediction of eukaryotic genes using MetaEuk, followed by the masking of these predicted eukaryotic genes and any co-identified partial prokaryotic genes using a custom Perl script. Remaining prokaryotic genes are then predicted from the masked metagenome using MetaGeneMark or metaProdigal. This integrated strategy achieved similar quantities and average lengths of eukaryotic genes compared to using MetaEuk alone. Notably, the quantity of predicted prokaryotic genes and viral genes using the new workflow was 14–18% higher than that obtained with standalone prokaryotic predictors. Furthermore, validation on a mixed prokaryotic-eukaryotic metagenome demonstrated that our workflow yielded genes with significantly higher average lengths, indicating reduced fragmentation and improved gene integrity. This novel workflow effectively enables the rapid and comprehensive retrieval of high-quality prokaryotic and eukaryotic coding sequences from diverse metagenomes.
format: application/pdf
format: text/html
creator: Wei Zhang
creator: Yanmei Zheng
creator: Guomin Han
creator: Xingbing He
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.20769
publisher: PeerJ Inc.
rights: © 2026 Zhang et al.
abstract: Accurately predicting coding genes from metagenomic samples containing a high proportion of eukaryotic content remains a significant challenge. Novel and reliable methods for the simultaneous prediction of prokaryotic and eukaryotic microbial genes are crucial to address this. We evaluated gene prediction accuracy of MetaGeneMark and MetaEuk using representative genomes from diverse organisms. Based on these findings, we developed an innovative analytical workflow. This approach involves an initial prediction of eukaryotic genes using MetaEuk, followed by the masking of these predicted eukaryotic genes and any co-identified partial prokaryotic genes using a custom Perl script. Remaining prokaryotic genes are then predicted from the masked metagenome using MetaGeneMark or metaProdigal. This integrated strategy achieved similar quantities and average lengths of eukaryotic genes compared to using MetaEuk alone. Notably, the quantity of predicted prokaryotic genes and viral genes using the new workflow was 14–18% higher than that obtained with standalone prokaryotic predictors. Furthermore, validation on a mixed prokaryotic-eukaryotic metagenome demonstrated that our workflow yielded genes with significantly higher average lengths, indicating reduced fragmentation and improved gene integrity. This novel workflow effectively enables the rapid and comprehensive retrieval of high-quality prokaryotic and eukaryotic coding sequences from diverse metagenomes.
bibliographic citation: Zhang et al. (2026) A novel analysis workflow for simultaneous parsing prokaryotic and eukaryotic microbial genes from metagenomes. PeerJ 14:e20769 https://doi.org/10.7717/peerj.20769
date submitted: 2025-03-13
date accepted: 2025-12-18
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Wei
author list: Agent
  family name: Zheng
  given name: Yanmei
author list: Agent
  family name: Han
  given name: Guomin
author list: Agent
  family name: He
  given name: Xingbing
doi: 10.7717/peerj.20769
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Zhang et al.
attribution name: Zhang et al.

Evaluation of problems encountered in daily living activities by ındividuals with colostomy: use of the Visual Analog Scale
type: item
type: AcademicArticle
description: Background Colostomy is a surgical intervention that affects physical and psychological health and can cause difficulties in areas such as personal care, hygiene, nutrition, mobility, and social interactions. Purpose To determine the severity of difficulties encountered in daily living activities by individuals with colostomy and to examine in which activities they experience the most difficulty. Methods The research was conducted with 94 patients using a cross-sectional and descriptive design based on the Model of Living. Data were collected using the “Patient Identification Information Form” and the “Daily Living Activities Difficulty Level Assessment Form” In the first stage, the “Patient Identification Information Form” was administered to the patients, and the “Daily Living Activities Difficulty Level Assessment Form” was introduced. In the second stage, patients were contacted by telephone 15 days after discharge, and the difficulties they experienced in daily living activities were evaluated within the framework of the Daily Living Model using scores ranging from 0 to 10. Results Patients experienced the most difficulty in areas such as excretion (8.0 ± 0.9) and anxieties about death and the future, quality of life, and meeting spiritual needs (7.0 ± 0.6), while activities with moderate difficulty were eating and drinking (4.0 ± 0.8), personal hygiene (6.0 ± 0.7), and sleep-rest (6.0 ± 0.5). The activities with the least difficulty were determined to be respiration (1.0 ± 0.4) and maintaining body temperature (2.0 ± 0.6). Patients with a higher level of education experienced less difficulty in sexual life activities. Single patients experienced less difficulty in providing a safe environment and engaging in work-leisure activities compared to married patients. Patients with temporary stomas reported experiencing less difficulty in eating and drinking activities compared to those with permanent stomas. Conclusion The study found that the daily living activitie…
format: application/pdf
format: text/html
creator: Muaz Gülşen
creator: Nursevim Aydıngülü
creator: Sevban Arslan
creator: Hülya Binokay
subject: Global Health
subject: Nursing
subject: Public Health
subject: Surgery and Surgical Specialties
subject: Healthcare Services
description: doi:10.7717/peerj.20763
publisher: PeerJ Inc.
rights: © 2026 Gülşen et al.
abstract: Background Colostomy is a surgical intervention that affects physical and psychological health and can cause difficulties in areas such as personal care, hygiene, nutrition, mobility, and social interactions. Purpose To determine the severity of difficulties encountered in daily living activities by individuals with colostomy and to examine in which activities they experience the most difficulty. Methods The research was conducted with 94 patients using a cross-sectional and descriptive design based on the Model of Living. Data were collected using the “Patient Identification Information Form” and the “Daily Living Activities Difficulty Level Assessment Form” In the first stage, the “Patient Identification Information Form” was administered to the patients, and the “Daily Living Activities Difficulty Level Assessment Form” was introduced. In the second stage, patients were contacted by telephone 15 days after discharge, and the difficulties they experienced in daily living activities were evaluated within the framework of the Daily Living Model using scores ranging from 0 to 10. Results Patients experienced the most difficulty in areas such as excretion (8.0 ± 0.9) and anxieties about death and the future, quality of life, and meeting spiritual needs (7.0 ± 0.6), while activities with moderate difficulty were eating and drinking (4.0 ± 0.8), personal hygiene (6.0 ± 0.7), and sleep-rest (6.0 ± 0.5). The activities with the least difficulty were determined to be respiration (1.0 ± 0.4) and maintaining body temperature (2.0 ± 0.6). Patients with a higher level of education experienced less difficulty in sexual life activities. Single patients experienced less difficulty in providing a safe environment and engaging in work-leisure activities compared to married patients. Patients with temporary stomas reported experiencing less difficulty in eating and drinking activities compared to those with permanent stomas. Conclusion The study found that the daily living activitie…
bibliographic citation: Gülşen et al. (2026) Evaluation of problems encountered in daily living activities by ındividuals with colostomy: use of the Visual Analog Scale. PeerJ 14:e20763 https://doi.org/10.7717/peerj.20763
date submitted: 2025-07-17
date accepted: 2025-12-17
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gülşen
  given name: Muaz
author list: Agent
  family name: Aydıngülü
  given name: Nursevim
author list: Agent
  family name: Arslan
  given name: Sevban
author list: Agent
  family name: Binokay
  given name: Hülya
doi: 10.7717/peerj.20763
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Gülşen et al.
attribution name: Gülşen et al.

A multi-omic analysis delineates a causal protective role for Bifidobacteriaceae and implicates key host genes in inflammatory bowel disease
type: item
type: AcademicArticle
description: Background While gut microbiota dysbiosis is a hallmark of inflammatory bowel disease (IBD), the causal microbial drivers and their host-mediated mechanisms remain elusive. This study leverages an integrated multi-omics approach, combining Mendelian randomization (MR) and transcriptome analysis, to bridge the gap from microbial causality to host molecular pathways. Methods We performed a two-sample MR analysis using large-scale genome-wide association study (GWAS) data to identify specific gut microbiota taxa with a causal effect on IBD risk. Subsequently, we conducted a multi-level bioinformatic analysis of IBD patient transcriptomes to elucidate the downstream host genes, regulatory networks, and immune cell interactions modulated by these causal microbes. Results Our MR analysis established a robust causal protective effect of the family Bifidobacteriaceae against IBD. Integrating this finding with transcriptomic data, we identified three key host genes as potential mediators acting through distinct mechanisms: LCT, whose regulation may foster a protective prebiotic niche; MCM6, which appears to function as a hub driving the proliferation of pathogenic immune infiltrates; and UBXN4, a critical regulator of cellular proteostasis, the failure of which can precipitate inflammatory stress. Conclusions This study moves beyond association to delineate a causal protective role for Bifidobacteriaceae in IBD and pinpoints specific host genes (LCT, MCM6, UBXN4) through which this effect is likely orchestrated. These findings provide a novel mechanistic framework for host-microbiota interactions and highlight new pathways for therapeutic intervention in IBD.
format: application/pdf
format: text/html
creator: Xia Leng
creator: Pengfei Liu
creator: Yi Gao
creator: Tongguo Shi
creator: Xingchao Zhu
creator: Fangjun Wang
creator: Qinhua Xi
subject: Bioinformatics
subject: Genomics
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.20742
publisher: PeerJ Inc.
rights: © 2026 Leng et al.
abstract: Background While gut microbiota dysbiosis is a hallmark of inflammatory bowel disease (IBD), the causal microbial drivers and their host-mediated mechanisms remain elusive. This study leverages an integrated multi-omics approach, combining Mendelian randomization (MR) and transcriptome analysis, to bridge the gap from microbial causality to host molecular pathways. Methods We performed a two-sample MR analysis using large-scale genome-wide association study (GWAS) data to identify specific gut microbiota taxa with a causal effect on IBD risk. Subsequently, we conducted a multi-level bioinformatic analysis of IBD patient transcriptomes to elucidate the downstream host genes, regulatory networks, and immune cell interactions modulated by these causal microbes. Results Our MR analysis established a robust causal protective effect of the family Bifidobacteriaceae against IBD. Integrating this finding with transcriptomic data, we identified three key host genes as potential mediators acting through distinct mechanisms: LCT, whose regulation may foster a protective prebiotic niche; MCM6, which appears to function as a hub driving the proliferation of pathogenic immune infiltrates; and UBXN4, a critical regulator of cellular proteostasis, the failure of which can precipitate inflammatory stress. Conclusions This study moves beyond association to delineate a causal protective role for Bifidobacteriaceae in IBD and pinpoints specific host genes (LCT, MCM6, UBXN4) through which this effect is likely orchestrated. These findings provide a novel mechanistic framework for host-microbiota interactions and highlight new pathways for therapeutic intervention in IBD.
bibliographic citation: Leng et al. (2026) A multi-omic analysis delineates a causal protective role for Bifidobacteriaceae and implicates key host genes in inflammatory bowel disease. PeerJ 14:e20742 https://doi.org/10.7717/peerj.20742
date submitted: 2025-09-09
date accepted: 2025-12-15
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Leng
  given name: Xia
author list: Agent
  family name: Liu
  given name: Pengfei
author list: Agent
  family name: Gao
  given name: Yi
author list: Agent
  family name: Shi
  given name: Tongguo
author list: Agent
  family name: Zhu
  given name: Xingchao
author list: Agent
  family name: Wang
  given name: Fangjun
author list: Agent
  family name: Xi
  given name: Qinhua
doi: 10.7717/peerj.20742
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Leng et al.
attribution name: Leng et al.

Does preferred technique influence how kinematics change during a run to exhaustion?—A cluster based approach
type: item
type: AcademicArticle
description: Fatigue-related changes in running technique may depend on a runner’s preferred style. Understanding these changes can inform targeted training to enhance performance. In previous work, we identified two technique-based clusters of runners: the “neutral pelvis” and the “tilted pelvis” clusters. This follow-up study examined whether fatigue induces cluster-specific technique adaptations. Sixty runners (neutral pelvis, n = 32; tilted pelvis, n = 28) completed a treadmill run to exhaustion at 5% above their individual lactate threshold speed. Stride frequency, duty factor, trunk and lower limb kinematics were compared between clusters at the start, middle, and end of the run using a 2-way repeated measures analysis of variance (ANOVA). All runners reached exhaustion in ∼20 minutes, covering ∼5 km. Runners from the tilted pelvis cluster consistently showed greater trunk-to-pelvis extension, more pelvic anterior tilt and greater hip flexion, and a smaller duty factor compared with the neutral pelvis cluster throughout the run. Fatigue-related adaptations were similar across clusters: reduced stride frequency, increased duty factor, greater trunk flexion during stance, increased plantar flexion, and higher coordination variability (trunk-to-pelvis–hip, hip–knee, knee–ankle) during swing. Although fatigue affected both groups similarly, the underlying technique differences suggest these adaptations may have distinct mechanical or performance consequences. Understanding such cluster-specific responses can help coaches tailor training and fatigue management strategies to individual running styles.
format: application/pdf
format: text/html
creator: Adrian R. Rivadulla
creator: Zak Sheehy
creator: Xi Chen
creator: Dario Cazzola
creator: Grant Trewartha
creator: Ezio Preatoni
subject: Data Science
subject: Biomechanics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.20673
publisher: PeerJ Inc.
rights: © 2026 Rivadulla et al.
abstract: Fatigue-related changes in running technique may depend on a runner’s preferred style. Understanding these changes can inform targeted training to enhance performance. In previous work, we identified two technique-based clusters of runners: the “neutral pelvis” and the “tilted pelvis” clusters. This follow-up study examined whether fatigue induces cluster-specific technique adaptations. Sixty runners (neutral pelvis, n = 32; tilted pelvis, n = 28) completed a treadmill run to exhaustion at 5% above their individual lactate threshold speed. Stride frequency, duty factor, trunk and lower limb kinematics were compared between clusters at the start, middle, and end of the run using a 2-way repeated measures analysis of variance (ANOVA). All runners reached exhaustion in ∼20 minutes, covering ∼5 km. Runners from the tilted pelvis cluster consistently showed greater trunk-to-pelvis extension, more pelvic anterior tilt and greater hip flexion, and a smaller duty factor compared with the neutral pelvis cluster throughout the run. Fatigue-related adaptations were similar across clusters: reduced stride frequency, increased duty factor, greater trunk flexion during stance, increased plantar flexion, and higher coordination variability (trunk-to-pelvis–hip, hip–knee, knee–ankle) during swing. Although fatigue affected both groups similarly, the underlying technique differences suggest these adaptations may have distinct mechanical or performance consequences. Understanding such cluster-specific responses can help coaches tailor training and fatigue management strategies to individual running styles.
bibliographic citation: Rivadulla et al. (2026) Does preferred technique influence how kinematics change during a run to exhaustion?—A cluster based approach. PeerJ 14:e20673 https://doi.org/10.7717/peerj.20673
date submitted: 2025-07-16
date accepted: 2025-12-04
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rivadulla
  given name: Adrian R.
author list: Agent
  family name: Sheehy
  given name: Zak
author list: Agent
  family name: Chen
  given name: Xi
author list: Agent
  family name: Cazzola
  given name: Dario
author list: Agent
  family name: Trewartha
  given name: Grant
author list: Agent
  family name: Preatoni
  given name: Ezio
doi: 10.7717/peerj.20673
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Rivadulla et al.
attribution name: Rivadulla et al.

Prediction of lymph node metastasis in T1 colorectal cancer based on machine learning
type: item
type: AcademicArticle
description: Background Colorectal cancer (CRC) ranks as the third most frequently diagnosed cancer. Early diagnosis and precise risk assessment for lymph node metastasis (LNM) of T1 CRC, characterized by tumor confined to the mucosa and submucosa, essential for enhancing patient outcomes and informing therapeutic strategies. This project aims to use machine learning in refining clinical decision-making processes for T1 CRC patients, thereby laying the groundwork for more personalized and efficacious treatment protocols. Methods In this study, we analyzed data from 210 patients with T1 CRC who underwent surgical resection at the First Affiliated Hospital of Chongqing Medical University from 2017 to 2023. The datasets encompassed clinical, endoscopic, and pathological parameters, which were examined to identify potential predictors of LNM. A range of machine learning algorithms, including boosted trees, decision trees, logistic regression, multilayer perceptron (MLP), naïve Bayes, k-nearest neighbors (K-NN), random forest and support vector machine (SVM), were leveraged to construct a predictive model for LNM in T1 CRC. Results Our research demonstrated that the random forest algorithm outperformed other models in predictive performance for the risk of LNM. Furthermore, the model identified seven key risk factors associated with LNM. We found four novel LNM predictive indicators for T1 CRC: tumor submucosal invasion area, percentage of tumors with invasive carcinoma, poorly differentiated tumor cell clusters, and serrated lesions. Conclusion This study developed a risk predictive model for LNM in T1 CRC patients by utilizing eight machine learning algorithms. Four novel predictive indicators were identified, improving the accuracy of LNM prediction.
format: application/pdf
format: text/html
creator: Suyujie Shi
creator: Xiongwu Li
creator: Linjun Li
creator: Haowen Zhong
creator: Ruoyan Wang
creator: Zhenyu Zhang
creator: Chuyi Liao
creator: Yun Mao
creator: Meijie Yang
creator: Yaying Yang
subject: Gastroenterology and Hepatology
subject: Global Health
subject: Health Policy
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.20500
publisher: PeerJ Inc.
rights: © 2026 Shi et al.
abstract: Background Colorectal cancer (CRC) ranks as the third most frequently diagnosed cancer. Early diagnosis and precise risk assessment for lymph node metastasis (LNM) of T1 CRC, characterized by tumor confined to the mucosa and submucosa, essential for enhancing patient outcomes and informing therapeutic strategies. This project aims to use machine learning in refining clinical decision-making processes for T1 CRC patients, thereby laying the groundwork for more personalized and efficacious treatment protocols. Methods In this study, we analyzed data from 210 patients with T1 CRC who underwent surgical resection at the First Affiliated Hospital of Chongqing Medical University from 2017 to 2023. The datasets encompassed clinical, endoscopic, and pathological parameters, which were examined to identify potential predictors of LNM. A range of machine learning algorithms, including boosted trees, decision trees, logistic regression, multilayer perceptron (MLP), naïve Bayes, k-nearest neighbors (K-NN), random forest and support vector machine (SVM), were leveraged to construct a predictive model for LNM in T1 CRC. Results Our research demonstrated that the random forest algorithm outperformed other models in predictive performance for the risk of LNM. Furthermore, the model identified seven key risk factors associated with LNM. We found four novel LNM predictive indicators for T1 CRC: tumor submucosal invasion area, percentage of tumors with invasive carcinoma, poorly differentiated tumor cell clusters, and serrated lesions. Conclusion This study developed a risk predictive model for LNM in T1 CRC patients by utilizing eight machine learning algorithms. Four novel predictive indicators were identified, improving the accuracy of LNM prediction.
bibliographic citation: Shi et al. (2026) Prediction of lymph node metastasis in T1 colorectal cancer based on machine learning. PeerJ 14:e20500 https://doi.org/10.7717/peerj.20500
date submitted: 2025-04-25
date accepted: 2025-11-10
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Suyujie
author list: Agent
  family name: Li
  given name: Xiongwu
author list: Agent
  family name: Li
  given name: Linjun
author list: Agent
  family name: Zhong
  given name: Haowen
author list: Agent
  family name: Wang
  given name: Ruoyan
author list: Agent
  family name: Zhang
  given name: Zhenyu
author list: Agent
  family name: Liao
  given name: Chuyi
author list: Agent
  family name: Mao
  given name: Yun
author list: Agent
  family name: Yang
  given name: Meijie
author list: Agent
  family name: Yang
  given name: Yaying
doi: 10.7717/peerj.20500
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: ©2026 Shi et al.
attribution name: Shi et al.

Optimization of environmental DNA-based methods: a case study for detecting brook trout (Salvelinus fontinalis)
type: item
type: AcademicArticle
description: The utility of eDNA for fish species and community monitoring is well-established using targeted amplification (i.e., qPCR and ddPCR) and sequencing approaches (i.e., metabarcoding). However, the lack of optimized and standardized methods across the eDNA workflow reduces the sensitivity of eDNA surveys and precludes the reliable comparison of findings across studies, respectively. DNA extraction is a prime target for optimization efforts because the extraction method is highly variable across eDNA studies despite being one of the most influential factors in detection efficiency across the entire post-collection workflow. Sequence analysis is arguably the least standardized step in the workflow, with new bioinformatics pipelines frequently emerging in the literature and being implemented with innumerable unique combinations of parameter values. The current study aimed to support the optimization and standardization of eDNA methods for fish detection by assessing two commercial DNA extraction kits. The kits, manufactured by Qiagen and Macherey-Nagel, were evaluated based on cost, time, and performance specifications and the success of brook trout detection by metabarcoding across three bioinformatics pipelines, qPCR, and ddPCR. Our protocols were effective in detecting brook trout in all 20 samples analyzed. Brook trout eDNA was detected by ddPCR in nine (90%) Qiagen extracts but only seven (70%) Macherey-Nagel extracts. The concentration of target DNA determined by ddPCR was significantly greater in Qiagen extracts. In comparison, detection success was equal across the two extraction kits using qPCR (70%) and metabarcoding (100% across all three bioinformatics pipelines). The concentration of target DNA determined by qPCR was not significantly different between Qiagen extracts and Macherey-Nagel extracts; however, the number of target DNA reads determined by metabarcoding was significantly greater in Qiagen extracts using MetaWorks, but no significant difference was …
format: application/pdf
format: text/html
creator: Erika Myler
creator: Yoamel Milián-García
creator: Tzitziki Loeza-Quintana
creator: Danielle Bourque
creator: Robert H. Hanner
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.20347
publisher: PeerJ Inc.
rights: © 2026 Myler et al.
abstract: The utility of eDNA for fish species and community monitoring is well-established using targeted amplification (i.e., qPCR and ddPCR) and sequencing approaches (i.e., metabarcoding). However, the lack of optimized and standardized methods across the eDNA workflow reduces the sensitivity of eDNA surveys and precludes the reliable comparison of findings across studies, respectively. DNA extraction is a prime target for optimization efforts because the extraction method is highly variable across eDNA studies despite being one of the most influential factors in detection efficiency across the entire post-collection workflow. Sequence analysis is arguably the least standardized step in the workflow, with new bioinformatics pipelines frequently emerging in the literature and being implemented with innumerable unique combinations of parameter values. The current study aimed to support the optimization and standardization of eDNA methods for fish detection by assessing two commercial DNA extraction kits. The kits, manufactured by Qiagen and Macherey-Nagel, were evaluated based on cost, time, and performance specifications and the success of brook trout detection by metabarcoding across three bioinformatics pipelines, qPCR, and ddPCR. Our protocols were effective in detecting brook trout in all 20 samples analyzed. Brook trout eDNA was detected by ddPCR in nine (90%) Qiagen extracts but only seven (70%) Macherey-Nagel extracts. The concentration of target DNA determined by ddPCR was significantly greater in Qiagen extracts. In comparison, detection success was equal across the two extraction kits using qPCR (70%) and metabarcoding (100% across all three bioinformatics pipelines). The concentration of target DNA determined by qPCR was not significantly different between Qiagen extracts and Macherey-Nagel extracts; however, the number of target DNA reads determined by metabarcoding was significantly greater in Qiagen extracts using MetaWorks, but no significant difference was …
bibliographic citation: Myler et al. (2026) Optimization of environmental DNA-based methods: a case study for detecting brook trout (Salvelinus fontinalis). PeerJ 14:e20347 https://doi.org/10.7717/peerj.20347
date submitted: 2025-04-17
date accepted: 2025-10-15
issued: 2026-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Myler
  given name: Erika
author list: Agent
  family name: Milián-García
  given name: Yoamel
author list: Agent
  family name: Loeza-Quintana
  given name: Tzitziki
author list: Agent
  family name: Bourque
  given name: Danielle
author list: Agent
  family name: Hanner
  given name: Robert H.
doi: 10.7717/peerj.20347
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-11
copyright: © 2026 Myler et al.
attribution name: Myler et al.

Retrospective assessment of the predictors of neonatal and infantile cholestasis with and without liver failure: an experience from Southeast China
type: item
type: AcademicArticle
description: Background Neonatal and infantile cholestasis with liver failure (LF) is a life-threatening condition. To identify predictive factors, it is essential to develop and validate novel nomograms for predicting neonatal and infantile cholestasis with LF separately in Southeast China. Methods The medical records of neonates and infants with cholestasis at Fujian Maternity and Child Health Hospital from April 27, 2012, to July 11, 2023, were retrospectively analyzed as the development cohort. An external validation cohort was assembled from Fujian Children’s Hospital during the same period. Univariate analysis was initially conducted on the relevant indices, then the least absolute shrinkage and selection operator was performed to assess independent predictive factors. Further multivariate logistic regression analysis was conducted to identify independent predictors and develop predictive nomograms. Area under the curve (AUC) of receiver operating characteristic, calibration curves and decision curve analysis (DCA) were used to evaluate and validate the model and subsequently confirmed with the external validation group. Results A total of 1,793 neonates and 583 infants were included in the development cohort, and 374 neonates and 232 infants in the external validation cohort. The neonatal nomogram included six variables that were significant independent predictors of LF: gestational age (p = 0.00), high-density lipoprotein (p = 0.008), red cell distribution width-standard deviation (p = 0.00), C-reactive protein (p = 0.00), albumin/fibrinogen (p = 0.00) and aspartate aminotransferase/platelets (p = 0.00). In the infant group, three variables, including vomiting (p = 0.005), lactate dehydrogenase (p = 0.00) and the albumin/fibrinogen (p = 0.00), were significant independent predictors of LF and were included in the infant nomogram. In the development cohort, the nomograms predicted LF with AUC values of 0.743 and 0.784 in the neonatal and infant groups, respectively. In th…
format: application/pdf
format: text/html
creator: Yijun Lin
creator: Rui Zhang
creator: Weijie Ou
creator: Hong Ye
subject: Gastroenterology and Hepatology
subject: Pediatrics
description: doi:10.7717/peerj.20800
publisher: PeerJ Inc.
rights: © 2026 Lin et al.
abstract: Background Neonatal and infantile cholestasis with liver failure (LF) is a life-threatening condition. To identify predictive factors, it is essential to develop and validate novel nomograms for predicting neonatal and infantile cholestasis with LF separately in Southeast China. Methods The medical records of neonates and infants with cholestasis at Fujian Maternity and Child Health Hospital from April 27, 2012, to July 11, 2023, were retrospectively analyzed as the development cohort. An external validation cohort was assembled from Fujian Children’s Hospital during the same period. Univariate analysis was initially conducted on the relevant indices, then the least absolute shrinkage and selection operator was performed to assess independent predictive factors. Further multivariate logistic regression analysis was conducted to identify independent predictors and develop predictive nomograms. Area under the curve (AUC) of receiver operating characteristic, calibration curves and decision curve analysis (DCA) were used to evaluate and validate the model and subsequently confirmed with the external validation group. Results A total of 1,793 neonates and 583 infants were included in the development cohort, and 374 neonates and 232 infants in the external validation cohort. The neonatal nomogram included six variables that were significant independent predictors of LF: gestational age (p = 0.00), high-density lipoprotein (p = 0.008), red cell distribution width-standard deviation (p = 0.00), C-reactive protein (p = 0.00), albumin/fibrinogen (p = 0.00) and aspartate aminotransferase/platelets (p = 0.00). In the infant group, three variables, including vomiting (p = 0.005), lactate dehydrogenase (p = 0.00) and the albumin/fibrinogen (p = 0.00), were significant independent predictors of LF and were included in the infant nomogram. In the development cohort, the nomograms predicted LF with AUC values of 0.743 and 0.784 in the neonatal and infant groups, respectively. In th…
bibliographic citation: Lin et al. (2026) Retrospective assessment of the predictors of neonatal and infantile cholestasis with and without liver failure: an experience from Southeast China. PeerJ 14:e20800 https://doi.org/10.7717/peerj.20800
date submitted: 2025-07-07
date accepted: 2025-12-24
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Yijun
author list: Agent
  family name: Zhang
  given name: Rui
author list: Agent
  family name: Ou
  given name: Weijie
author list: Agent
  family name: Ye
  given name: Hong
doi: 10.7717/peerj.20800
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Lin et al.
attribution name: Lin et al.

Study on the mortality risk and predictive model for COVID-19 inpatients with pneumonia manifestations
type: item
type: AcademicArticle
description: Background In 2020, COVID-19 posed a major threat to global public health in a remarkably short period. Although the WHO declared an end to the emergency phase in May 2023, a considerable proportion of recovered cases experience medium- and long-term effects, which pose ongoing health challenges to society. Therefore, it remains necessary to conduct relevant research in the post-epidemic era to explore the risk factors for death in COVID-19 inpatients. Methods We determined the mortality of COVID-19 inpatients with pneumonia manifestations through one-year follow-up, utilizing real-world data from three medical centers. Clinical characteristics associated with mortality risk were analyzed by logistic regression. Then, the dataset was randomly partitioned into three sets at a ratio of 4:2:4. Three machine learning algorithms were employed to develop and validate a mortality risk predictive model for COVID-19 inpatients, and a web-based visualization tool was created. Results There were 100 fatalities among the 1,693 samples included in this study. Meanwhile, we identified 37 factors correlated with increased mortality risk in COVID-19 inpatients with pneumonia manifestations. Ultimately, we developed a mortality risk predictive model using the random forest algorithm, which demonstrated superior predictive performance (AUC=0.907, 95% CI=0.849-0.957). Conclusions This study reports a mortality rate of 5.9% for COVID-19 inpatients with pneumonia manifestations. The high-performance mortality risk prediction model obtained in this study provides important practical guidance for monitoring the mortality risks of COVID-19 inpatients with pneumonia manifestations.
format: application/pdf
format: text/html
creator: Zhi Li
creator: Jiamin Liang
creator: Katie Lu
creator: Shuyu Tang
creator: Jinyi Huang
creator: Jinrong Zhang
creator: Jianjun Zou
creator: Dongsheng Huang
creator: Chenli Xie
creator: Linglong Zeng
creator: Zhiwei Wang
creator: Yibin Deng
creator: Jiachun Lu
subject: Epidemiology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.20795
publisher: PeerJ Inc.
rights: © 2026 Li et al.
abstract: Background In 2020, COVID-19 posed a major threat to global public health in a remarkably short period. Although the WHO declared an end to the emergency phase in May 2023, a considerable proportion of recovered cases experience medium- and long-term effects, which pose ongoing health challenges to society. Therefore, it remains necessary to conduct relevant research in the post-epidemic era to explore the risk factors for death in COVID-19 inpatients. Methods We determined the mortality of COVID-19 inpatients with pneumonia manifestations through one-year follow-up, utilizing real-world data from three medical centers. Clinical characteristics associated with mortality risk were analyzed by logistic regression. Then, the dataset was randomly partitioned into three sets at a ratio of 4:2:4. Three machine learning algorithms were employed to develop and validate a mortality risk predictive model for COVID-19 inpatients, and a web-based visualization tool was created. Results There were 100 fatalities among the 1,693 samples included in this study. Meanwhile, we identified 37 factors correlated with increased mortality risk in COVID-19 inpatients with pneumonia manifestations. Ultimately, we developed a mortality risk predictive model using the random forest algorithm, which demonstrated superior predictive performance (AUC=0.907, 95% CI=0.849-0.957). Conclusions This study reports a mortality rate of 5.9% for COVID-19 inpatients with pneumonia manifestations. The high-performance mortality risk prediction model obtained in this study provides important practical guidance for monitoring the mortality risks of COVID-19 inpatients with pneumonia manifestations.
bibliographic citation: Li et al. (2026) Study on the mortality risk and predictive model for COVID-19 inpatients with pneumonia manifestations. PeerJ 14:e20795 https://doi.org/10.7717/peerj.20795
date submitted: 2025-04-25
date accepted: 2025-12-23
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Zhi
author list: Agent
  family name: Liang
  given name: Jiamin
author list: Agent
  family name: Lu
  given name: Katie
author list: Agent
  family name: Tang
  given name: Shuyu
author list: Agent
  family name: Huang
  given name: Jinyi
author list: Agent
  family name: Zhang
  given name: Jinrong
author list: Agent
  family name: Zou
  given name: Jianjun
author list: Agent
  family name: Huang
  given name: Dongsheng
author list: Agent
  family name: Xie
  given name: Chenli
author list: Agent
  family name: Zeng
  given name: Linglong
author list: Agent
  family name: Wang
  given name: Zhiwei
author list: Agent
  family name: Deng
  given name: Yibin
author list: Agent
  family name: Lu
  given name: Jiachun
doi: 10.7717/peerj.20795
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Li et al.
attribution name: Li et al.

Genome-wide identification and drought-responsive root expression profiling of the VQ gene family in proso millet (Panicum miliaceum L.)
type: item
type: AcademicArticle
description: Background Proso millet (Panicum miliaceum L.) is a drought-tolerant cereal crop cultivated in arid and semi-arid regions. VQ proteins, a class of plant-specific proteins characterized by a conserved VQ motif (FxxxVQxxTG), are known to play critical roles in plant responses to abiotic stress. To elucidate the genetic basis of drought tolerance in proso millet, a genome-wide identification and characterization of the VQ gene family was undertaken. Methods This study involved the identification of all VQ family members from the proso millet genome, followed by comprehensive analyses including chromosomal localization, phylogenetic relationships, gene structure, conserved motifs, collinearity, and promoter cis-acting elements. Expression profiling was conducted using transcriptomics and Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) to investigate potential gene functions. Additionally, the drought tolerance of various germplasm materials was systematically assessed. Results A total of 70 VQ genes (PmVQ1–PmVQ70) were identified and classified into four distinct subfamilies. Based on the screening of root-preferential and drought-responsive candidate genes, combined with phenotypic and qRT-PCR analyses of drought-tolerant and drought-sensitive materials, four key candidate genes were identified. qRT-PCR analysis revealed that the four genes exhibited differential expression patterns between drought-tolerant and drought-sensitive materials, suggesting their potential roles as core regulators in proso millet’s drought response, particularly in root-specific regulatory pathways under drought stress. This study provides a systematic analysis of the VQ gene family in proso millet and offers valuable genetic resources for elucidating drought tolerance mechanisms and advancing molecular breeding.
format: application/pdf
format: text/html
creator: Qi Tan
creator: Yanan Liu
creator: Haotian Li
creator: Li Dong
creator: Guoqing Liu
creator: Yanmiao Jiang
creator: Haiquan Li
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.20792
publisher: PeerJ Inc.
rights: © 2026 Tan et al.
abstract: Background Proso millet (Panicum miliaceum L.) is a drought-tolerant cereal crop cultivated in arid and semi-arid regions. VQ proteins, a class of plant-specific proteins characterized by a conserved VQ motif (FxxxVQxxTG), are known to play critical roles in plant responses to abiotic stress. To elucidate the genetic basis of drought tolerance in proso millet, a genome-wide identification and characterization of the VQ gene family was undertaken. Methods This study involved the identification of all VQ family members from the proso millet genome, followed by comprehensive analyses including chromosomal localization, phylogenetic relationships, gene structure, conserved motifs, collinearity, and promoter cis-acting elements. Expression profiling was conducted using transcriptomics and Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) to investigate potential gene functions. Additionally, the drought tolerance of various germplasm materials was systematically assessed. Results A total of 70 VQ genes (PmVQ1–PmVQ70) were identified and classified into four distinct subfamilies. Based on the screening of root-preferential and drought-responsive candidate genes, combined with phenotypic and qRT-PCR analyses of drought-tolerant and drought-sensitive materials, four key candidate genes were identified. qRT-PCR analysis revealed that the four genes exhibited differential expression patterns between drought-tolerant and drought-sensitive materials, suggesting their potential roles as core regulators in proso millet’s drought response, particularly in root-specific regulatory pathways under drought stress. This study provides a systematic analysis of the VQ gene family in proso millet and offers valuable genetic resources for elucidating drought tolerance mechanisms and advancing molecular breeding.
bibliographic citation: Tan et al. (2026) Genome-wide identification and drought-responsive root expression profiling of the VQ gene family in proso millet (Panicum miliaceum L.). PeerJ 14:e20792 https://doi.org/10.7717/peerj.20792
date submitted: 2025-11-12
date accepted: 2025-12-23
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Tan
  given name: Qi
author list: Agent
  family name: Liu
  given name: Yanan
author list: Agent
  family name: Li
  given name: Haotian
author list: Agent
  family name: Dong
  given name: Li
author list: Agent
  family name: Liu
  given name: Guoqing
author list: Agent
  family name: Jiang
  given name: Yanmiao
author list: Agent
  family name: Li
  given name: Haiquan
doi: 10.7717/peerj.20792
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: © 2026 Tan et al.
attribution name: Tan et al.

Metabolomic profiling of follicular fluid reveals unique pathways in endometriosis and infertility etiologies: a pilot study
type: item
type: AcademicArticle
description: Purpose This study investigates metabolic profiles in follicular fluid of patients with endometriosis (EM), polycystic ovary syndrome (PCOS), tubal blockage (TB), and unexplained infertility (UEI), assessing their associations with follicular development and in vitro fertilization (IVF) outcomes. It aims to identify metabolic alterations and potential biomarkers for EM diagnosis and personalized reproductive strategies. Methods Follicular fluid samples were collected from 12 infertility patients (3 EM, 3 PCOS, 3 TB, and 3 UEI) undergoing IVF. Metabolomic profiling was performed using liquid chromatography-mass spectrometry (LC-MS), followed by pathway enrichment analysis to identify key metabolic pathways. Statistical analyses were conducted to compare metabolic profiles across groups, assess correlations with follicular development rate (FDR), and evaluate potential biomarkers for EM diagnosis. Results EM patients showed significant metabolic changes, including reduced steroid biosynthesis and elevated thiamine metabolism metabolites, linked to lower FDR. Oxidative stress markers (3-chloro-L-tyrosine, 8-oxoerythraline) were elevated and negatively correlated with FDR. A predictive model identified D-mannosamine, D-galacturonic acid, and 3-chloro-L-tyrosine as potential EM biomarkers with high diagnostic accuracy. Conclusion This study reveals distinct metabolic disruptions in the follicular fluid of EM patients, particularly in steroid biosynthesis and thiamine metabolism pathways, which are linked to impaired follicular development. The identification of specific metabolites as potential biomarkers for EM provides a foundation for developing diagnostic approaches that minimize the need for additional invasive procedures and support personalized assisted reproductive technology (ART) strategies. This pilot study requires further validation to confirm these findings and translate them into clinical practice.
format: application/pdf
format: text/html
creator: Ping Yu
creator: Dandan Chen
creator: Deshen Han
creator: Xin Jin
creator: Yuhong Li
creator: Fu Wei
creator: Yun Zhang
subject: Biochemistry
subject: Gynecology and Obstetrics
subject: Women’s Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.20786
publisher: PeerJ Inc.
rights: © 2026 Yu et al.
abstract: Purpose This study investigates metabolic profiles in follicular fluid of patients with endometriosis (EM), polycystic ovary syndrome (PCOS), tubal blockage (TB), and unexplained infertility (UEI), assessing their associations with follicular development and in vitro fertilization (IVF) outcomes. It aims to identify metabolic alterations and potential biomarkers for EM diagnosis and personalized reproductive strategies. Methods Follicular fluid samples were collected from 12 infertility patients (3 EM, 3 PCOS, 3 TB, and 3 UEI) undergoing IVF. Metabolomic profiling was performed using liquid chromatography-mass spectrometry (LC-MS), followed by pathway enrichment analysis to identify key metabolic pathways. Statistical analyses were conducted to compare metabolic profiles across groups, assess correlations with follicular development rate (FDR), and evaluate potential biomarkers for EM diagnosis. Results EM patients showed significant metabolic changes, including reduced steroid biosynthesis and elevated thiamine metabolism metabolites, linked to lower FDR. Oxidative stress markers (3-chloro-L-tyrosine, 8-oxoerythraline) were elevated and negatively correlated with FDR. A predictive model identified D-mannosamine, D-galacturonic acid, and 3-chloro-L-tyrosine as potential EM biomarkers with high diagnostic accuracy. Conclusion This study reveals distinct metabolic disruptions in the follicular fluid of EM patients, particularly in steroid biosynthesis and thiamine metabolism pathways, which are linked to impaired follicular development. The identification of specific metabolites as potential biomarkers for EM provides a foundation for developing diagnostic approaches that minimize the need for additional invasive procedures and support personalized assisted reproductive technology (ART) strategies. This pilot study requires further validation to confirm these findings and translate them into clinical practice.
bibliographic citation: Yu et al. (2026) Metabolomic profiling of follicular fluid reveals unique pathways in endometriosis and infertility etiologies: a pilot study. PeerJ 14:e20786 https://doi.org/10.7717/peerj.20786
date submitted: 2025-05-02
date accepted: 2025-12-22
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Ping
author list: Agent
  family name: Chen
  given name: Dandan
author list: Agent
  family name: Han
  given name: Deshen
author list: Agent
  family name: Jin
  given name: Xin
author list: Agent
  family name: Li
  given name: Yuhong
author list: Agent
  family name: Wei
  given name: Fu
author list: Agent
  family name: Zhang
  given name: Yun
doi: 10.7717/peerj.20786
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Yu et al.
attribution name: Yu et al.

A retrospective metatranscriptomic study of respiratory pathogens causing adult community-acquired pneumonia in Wuxi, China, before the pandemic
type: item
type: AcademicArticle
description: The COVID-19 pandemic has substantially altered respiratory pathogen circulation, underscoring the critical need for pre-pandemic baseline data to interpret current epidemiological trends. To establish this baseline, we employed metatranscriptomic sequencing to characterize the etiology of community-acquired pneumonia (CAP) in 20 adult patients hospitalized in Wuxi, China, during 2018–2019. Following ribosomal RNA depletion, sequencing data were analyzed using a stringent dual-filter strategy (RPM ≥ 100 and Z-score ≥ 2) to identify high-confidence pathogens. Our analysis revealed a complex, polymicrobial landscape. Bacterial pathogens predominated, with Streptococcus species detected in 25% of cases. The frequent co-occurrence of oral anaerobes (e.g., Prevotella, Veillonella, Rothia) suggested that aspiration-driven polymicrobial infections were a key pathogenic mechanism. Viral pathogens were also prominent, with Orthorubulavirus hominis and Human respirovirus 1 showing significant transcriptional activity. Notably, our approach enabled the discovery and characterization of two divergent viral strains: a novel Rhinovirus B strain (AP81) with only 90.52% nucleotide identity to its closest relative, and a picobirnavirus phylogenetically distinct from human strains (94.90% identity to a simian-derived virus). Fungal detection was minimal, with only Candida albicans meeting the criteria in a single case. In conclusion, this study provides a crucial pre-pandemic baseline of CAP etiology in Wuxi. It highlights the power of metatranscriptomics to not only define common etiological agents but also to uncover novel viral diversity and reveal the polymicrobial complexity of respiratory infections, offering critical insights for future surveillance and clinical management.
format: application/pdf
format: text/html
creator: Yan-Jun Kang
creator: Juan Liu
creator: Yumeng Gao
creator: Yujun Chen
creator: Yan Wang
creator: Chao Shi
creator: Yuan Shen
subject: Microbiology
subject: Infectious Diseases
subject: Public Health
subject: Respiratory Medicine
description: doi:10.7717/peerj.20774
publisher: PeerJ Inc.
rights: © 2026 Kang et al.
abstract: The COVID-19 pandemic has substantially altered respiratory pathogen circulation, underscoring the critical need for pre-pandemic baseline data to interpret current epidemiological trends. To establish this baseline, we employed metatranscriptomic sequencing to characterize the etiology of community-acquired pneumonia (CAP) in 20 adult patients hospitalized in Wuxi, China, during 2018–2019. Following ribosomal RNA depletion, sequencing data were analyzed using a stringent dual-filter strategy (RPM ≥ 100 and Z-score ≥ 2) to identify high-confidence pathogens. Our analysis revealed a complex, polymicrobial landscape. Bacterial pathogens predominated, with Streptococcus species detected in 25% of cases. The frequent co-occurrence of oral anaerobes (e.g., Prevotella, Veillonella, Rothia) suggested that aspiration-driven polymicrobial infections were a key pathogenic mechanism. Viral pathogens were also prominent, with Orthorubulavirus hominis and Human respirovirus 1 showing significant transcriptional activity. Notably, our approach enabled the discovery and characterization of two divergent viral strains: a novel Rhinovirus B strain (AP81) with only 90.52% nucleotide identity to its closest relative, and a picobirnavirus phylogenetically distinct from human strains (94.90% identity to a simian-derived virus). Fungal detection was minimal, with only Candida albicans meeting the criteria in a single case. In conclusion, this study provides a crucial pre-pandemic baseline of CAP etiology in Wuxi. It highlights the power of metatranscriptomics to not only define common etiological agents but also to uncover novel viral diversity and reveal the polymicrobial complexity of respiratory infections, offering critical insights for future surveillance and clinical management.
bibliographic citation: Kang et al. (2026) A retrospective metatranscriptomic study of respiratory pathogens causing adult community-acquired pneumonia in Wuxi, China, before the pandemic. PeerJ 14:e20774 https://doi.org/10.7717/peerj.20774
date submitted: 2025-03-29
date accepted: 2025-12-18
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kang
  given name: Yan-Jun
author list: Agent
  family name: Liu
  given name: Juan
author list: Agent
  family name: Gao
  given name: Yumeng
author list: Agent
  family name: Chen
  given name: Yujun
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Shi
  given name: Chao
author list: Agent
  family name: Shen
  given name: Yuan
doi: 10.7717/peerj.20774
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Kang et al.
attribution name: Kang et al.

Waist-to-height ratio, body fat, and macronutrient intake as predictors of lipid abnormalities in elite Turkish athletes: a comparative study
type: item
type: AcademicArticle
description: Background Regular physical activity can improve the blood lipid profile, yet athletes may still experience dyslipidemia. This study examined lipid profiles in Turkish endurance and strength athletes in relation to the dietary intake. Methods Eighty-four participants, including strength athletes (n = 45), endurance athletes (n = 20), and non-athletes (n = 19) were assessed for dietary intake (quantitative food-frequency questionnaire), body composition, and blood lipid profile. Results Endurance athletes had a lower body mass index (BMI), body fat (%), fat mass, waist-to-hip ratio, and waist-to-height ratio than strength athletes and non-athletes (p < 0.05). Endurance athletes derived a lower percentage of daily energy intake from protein and fat, a higher from carbohydrate, and consumed more dietary fiber (p < 0.05). Compared with endurance athletes, strength athletes showed higher serum low-density lipoprotein cholesterol (LDL-C) and apolipoprotein B (ApoB) levels, total cholesterol/high-density lipoprotein cholesterol (TC/HDL-C), LDL-C/HDL-C, and ApoB/ApoA-1 ratios, a higher atherogenic index, and lower levels of HDL-C and ApoA-1 (p < 0.05). Overall, athletes had lower serum triacylglycerol (TG), very low-density lipoprotein cholesterol (VLDL-C), and higher LDL-C levels than non-athletes (p < 0.05). Logistic regression models showed that waist-to-height ratio and body fat (%) were consistent predictors of adverse lipid outcomes, independent of dietary energy intake; strength athletes had higher odds of elevated LDL-C and ApoB, highlighting distinct lipid risks by sport group. Conclusion Endurance athletes displayed a more favorable lipid profile than strength athletes and non-athletes. Group differences in lipids likely reflect a combination of adiposity, dietary patterns, and sport-specific behaviors.
format: application/pdf
format: text/html
creator: Funda Tamer
creator: Betul Kisioglu Halis
creator: Pelin Bilgic
subject: Biochemistry
subject: Nutrition
description: doi:10.7717/peerj.20743
publisher: PeerJ Inc.
rights: © 2026 Tamer et al.
abstract: Background Regular physical activity can improve the blood lipid profile, yet athletes may still experience dyslipidemia. This study examined lipid profiles in Turkish endurance and strength athletes in relation to the dietary intake. Methods Eighty-four participants, including strength athletes (n = 45), endurance athletes (n = 20), and non-athletes (n = 19) were assessed for dietary intake (quantitative food-frequency questionnaire), body composition, and blood lipid profile. Results Endurance athletes had a lower body mass index (BMI), body fat (%), fat mass, waist-to-hip ratio, and waist-to-height ratio than strength athletes and non-athletes (p < 0.05). Endurance athletes derived a lower percentage of daily energy intake from protein and fat, a higher from carbohydrate, and consumed more dietary fiber (p < 0.05). Compared with endurance athletes, strength athletes showed higher serum low-density lipoprotein cholesterol (LDL-C) and apolipoprotein B (ApoB) levels, total cholesterol/high-density lipoprotein cholesterol (TC/HDL-C), LDL-C/HDL-C, and ApoB/ApoA-1 ratios, a higher atherogenic index, and lower levels of HDL-C and ApoA-1 (p < 0.05). Overall, athletes had lower serum triacylglycerol (TG), very low-density lipoprotein cholesterol (VLDL-C), and higher LDL-C levels than non-athletes (p < 0.05). Logistic regression models showed that waist-to-height ratio and body fat (%) were consistent predictors of adverse lipid outcomes, independent of dietary energy intake; strength athletes had higher odds of elevated LDL-C and ApoB, highlighting distinct lipid risks by sport group. Conclusion Endurance athletes displayed a more favorable lipid profile than strength athletes and non-athletes. Group differences in lipids likely reflect a combination of adiposity, dietary patterns, and sport-specific behaviors.
bibliographic citation: Tamer et al. (2026) Waist-to-height ratio, body fat, and macronutrient intake as predictors of lipid abnormalities in elite Turkish athletes: a comparative study. PeerJ 14:e20743 https://doi.org/10.7717/peerj.20743
date submitted: 2025-05-27
date accepted: 2025-12-15
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tamer
  given name: Funda
author list: Agent
  family name: Kisioglu Halis
  given name: Betul
author list: Agent
  family name: Bilgic
  given name: Pelin
doi: 10.7717/peerj.20743
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: © 2026 Tamer et al.
attribution name: Tamer et al.

Assessment of physicians’ awareness and clinical practice regarding gingival enlargement caused by calcium channel blockers
type: item
type: AcademicArticle
description: Background Gingival enlargement is a side effect of calcium channel blockers (CCBs), which are usually used to treat cardiovascular conditions. Physicians have an important role in identifying and managing the disease, but their level of awareness and ability to apply their knowledge in clinical practice remain unclear in Iraq. Objective This study aims to assess physicians’ knowledge of calcium channel blocker (CCB)-induced gingival enlargement and determine whether they apply this knowledge in their clinical practice. Methods A cross-sectional survey was conducted among 331 physicians working in Iraqi primary healthcare institutions to collect the data for this study. A Google Forms questionnaire was designed, created, and distributed via Facebook and WhatsApp (special groups for primary health centers in Iraq). The survey evaluated their understanding about gingival enlargement as a side effect of calcium channel blockers. Results The study analyzed responses to questions regarding awareness and management of gingival enlargement linked with calcium channel blocker (CCB) drugs. Only 58% of physicians reported that CCB use causes gingival enlargement as a side effect. However, fewer responders (33.5%) believed they informed patients about this risk. Furthermore, 57.7% of respondents said they do not regularly refer patients for gingival assessment related to CCB use. When asked about factors affecting the occurrence and severity of gingival enlargement, the majority (88.2%) identified a combination of individual susceptibility, dental hygiene levels, and specific medication as relevant factors for this. Most respondents (73.4%) approved that improving oral hygiene and professional cleanings assist in managing drug-induced gingival enlargement. Conclusion There is a gap between the knowledge of physicians regarding the role of calcium channel blockers in causing gingival enlargement and their clinical practice. Enhancing medical-dental collaboration and providing t…
format: application/pdf
format: text/html
creator: Banaz Jabbar Ali
creator: Al-Hussein Safaa Hussein
creator: Ban Karem Hassan
creator: Ola Shakir Fadhil
creator: Ammar Sh Ahmed
subject: Dentistry
subject: Pharmacology
subject: Science and Medical Education
description: doi:10.7717/peerj.20739
publisher: PeerJ Inc.
rights: © 2026 Ali et al.
abstract: Background Gingival enlargement is a side effect of calcium channel blockers (CCBs), which are usually used to treat cardiovascular conditions. Physicians have an important role in identifying and managing the disease, but their level of awareness and ability to apply their knowledge in clinical practice remain unclear in Iraq. Objective This study aims to assess physicians’ knowledge of calcium channel blocker (CCB)-induced gingival enlargement and determine whether they apply this knowledge in their clinical practice. Methods A cross-sectional survey was conducted among 331 physicians working in Iraqi primary healthcare institutions to collect the data for this study. A Google Forms questionnaire was designed, created, and distributed via Facebook and WhatsApp (special groups for primary health centers in Iraq). The survey evaluated their understanding about gingival enlargement as a side effect of calcium channel blockers. Results The study analyzed responses to questions regarding awareness and management of gingival enlargement linked with calcium channel blocker (CCB) drugs. Only 58% of physicians reported that CCB use causes gingival enlargement as a side effect. However, fewer responders (33.5%) believed they informed patients about this risk. Furthermore, 57.7% of respondents said they do not regularly refer patients for gingival assessment related to CCB use. When asked about factors affecting the occurrence and severity of gingival enlargement, the majority (88.2%) identified a combination of individual susceptibility, dental hygiene levels, and specific medication as relevant factors for this. Most respondents (73.4%) approved that improving oral hygiene and professional cleanings assist in managing drug-induced gingival enlargement. Conclusion There is a gap between the knowledge of physicians regarding the role of calcium channel blockers in causing gingival enlargement and their clinical practice. Enhancing medical-dental collaboration and providing t…
bibliographic citation: Ali et al. (2026) Assessment of physicians’ awareness and clinical practice regarding gingival enlargement caused by calcium channel blockers. PeerJ 14:e20739 https://doi.org/10.7717/peerj.20739
date submitted: 2025-05-05
date accepted: 2025-12-15
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ali
  given name: Banaz Jabbar
author list: Agent
  family name: Hussein
  given name: Al-Hussein Safaa
author list: Agent
  family name: Hassan
  given name: Ban Karem
author list: Agent
  family name: Fadhil
  given name: Ola Shakir
author list: Agent
  family name: Ahmed
  given name: Ammar Sh
doi: 10.7717/peerj.20739
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Ali et al.
attribution name: Ali et al.

Capg enhances proliferation, adipogenesis, and inflammatory response in preadipocytes: insights from bioinformatics analysis and functional validation
type: item
type: AcademicArticle
description: Background Various associations between adipose tissue and atherosclerosis (AS) have been revealed. This study aims to identify biomarkers in the epididymal adipose tissue of AS mice and to explore their effects on adipose tissue inflammation and adipogenesis. Methods The gene expression profiles of epididymal adipose tissue (GSE57659 and GSE76812) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEG) screened by Limma R package and genes searched by weighted gene correlation network analysis (WGCNA) were performed to classify common genes associated with AS. The Protein-Protein interaction (PPI) network was constructed by Cytoscape software, and hub genes were eventually determined by the Cytohubba plugin. Finally, one of these hub genes was selected. The cell proliferation ability was assessed using the CCK8 assay. Oil Red O staining and Western blot were employed to evaluate the lipid content in adipocytes. The extent of the inflammatory response in adipocytes was determined by Enzyme-Linked Immunosorbent Assay (ELISA). Results A total of 125 DEGs were identified between the control group and the atherosclerosis group. Among these, 34 genes were selected based on two key modules identified through WGCNA. Subsequently, five key nodes were identified, namely Capg, Timp1, Lgals3, Agt, and Mmp9. Capg was selected as the primary gene of interest for further investigation. Following the transfection of 3T3-L1 cells with lentivirus, Capg was overexpressed. Capping actin protein, gelsolin like (CAPG) significantly enhanced preadipocyte proliferation, as demonstrated by CCK-8 and upregulated expression of the Cyclin D1. Furthermore, Oil Red O staining revealed a marked elevation in intracellular lipid accumulation upon CAPG overexpression. Western blot analysis showed increased protein levels of PPAR γ and adiponectin. Furthermore, CAPG in 3T3-L1 cells resulted in a marked upregulation of IL-6 and MCP-1. Conclusion CAPG promotes t…
format: application/pdf
format: text/html
creator: Luyao Zhang
creator: Botao Sang
creator: Sainan Li
creator: Ying Li
creator: Dachuan Guo
creator: Qinan Ma
creator: Xiangfei Liu
creator: Xiaoshuo Li
creator: Beidong Chen
creator: Deping Liu
subject: Bioinformatics
subject: Cardiology
subject: Metabolic Sciences
description: doi:10.7717/peerj.20730
publisher: PeerJ Inc.
rights: © 2026 Zhang et al.
abstract: Background Various associations between adipose tissue and atherosclerosis (AS) have been revealed. This study aims to identify biomarkers in the epididymal adipose tissue of AS mice and to explore their effects on adipose tissue inflammation and adipogenesis. Methods The gene expression profiles of epididymal adipose tissue (GSE57659 and GSE76812) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEG) screened by Limma R package and genes searched by weighted gene correlation network analysis (WGCNA) were performed to classify common genes associated with AS. The Protein-Protein interaction (PPI) network was constructed by Cytoscape software, and hub genes were eventually determined by the Cytohubba plugin. Finally, one of these hub genes was selected. The cell proliferation ability was assessed using the CCK8 assay. Oil Red O staining and Western blot were employed to evaluate the lipid content in adipocytes. The extent of the inflammatory response in adipocytes was determined by Enzyme-Linked Immunosorbent Assay (ELISA). Results A total of 125 DEGs were identified between the control group and the atherosclerosis group. Among these, 34 genes were selected based on two key modules identified through WGCNA. Subsequently, five key nodes were identified, namely Capg, Timp1, Lgals3, Agt, and Mmp9. Capg was selected as the primary gene of interest for further investigation. Following the transfection of 3T3-L1 cells with lentivirus, Capg was overexpressed. Capping actin protein, gelsolin like (CAPG) significantly enhanced preadipocyte proliferation, as demonstrated by CCK-8 and upregulated expression of the Cyclin D1. Furthermore, Oil Red O staining revealed a marked elevation in intracellular lipid accumulation upon CAPG overexpression. Western blot analysis showed increased protein levels of PPAR γ and adiponectin. Furthermore, CAPG in 3T3-L1 cells resulted in a marked upregulation of IL-6 and MCP-1. Conclusion CAPG promotes t…
bibliographic citation: Zhang et al. (2026) Capg enhances proliferation, adipogenesis, and inflammatory response in preadipocytes: insights from bioinformatics analysis and functional validation. PeerJ 14:e20730 https://doi.org/10.7717/peerj.20730
date submitted: 2025-05-28
date accepted: 2025-12-12
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Luyao
author list: Agent
  family name: Sang
  given name: Botao
author list: Agent
  family name: Li
  given name: Sainan
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Guo
  given name: Dachuan
author list: Agent
  family name: Ma
  given name: Qinan
author list: Agent
  family name: Liu
  given name: Xiangfei
author list: Agent
  family name: Li
  given name: Xiaoshuo
author list: Agent
  family name: Chen
  given name: Beidong
author list: Agent
  family name: Liu
  given name: Deping
doi: 10.7717/peerj.20730
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Zhang et al.
attribution name: Zhang et al.

Pesticide residues on milkweed and strawberry at small farms and non-target effects of two fungicides on monarch butterfly caterpillars
type: item
type: AcademicArticle
description: Concern over insect declines has increased attention on the effects of pesticide residues on native insects. We collected strawberry (target) and common milkweed (non-target) foliage and flowers on two small Central New York farms, within crop fields as well as field margins, and analyzed the tissues for pesticide residues of 94 agrochemicals. We found quantifiable levels of 13 fungicides, herbicides, and insecticides, mostly at low concentrations (typically less than 200 ppb where detected), and more often on strawberry than milkweed. We generally found higher pesticide residue levels early in the season (June vs. July) and on leaves compared to flowers. Residue levels in fields did not differ strongly from margins but pesticide drift may have left low-level residues on milkweed leaves and flowers in margins. Given that non-target effects of fungicides are understudied, we selected two prevalent fungicides found in this study (cyprodinil and difenoconazole) and used them in laboratory assays to assess impacts on early instar monarch (Danaus plexippus) caterpillar feeding, growth, and growth efficiency on common milkweed, along with two other milkweed (Asclepias) species. We tested the hypothesis that exposure to pesticides may be most impactful on poor quality host plants. For both fungicides, exposure at the highest doses (>100,000 ppb) reduced feeding, with the strongest effect on Asclepias asperula, the lowest quality host plant. Effects on caterpillar growth were similarly negative and consistent across host plant species. Finally, effects of fungicides on gross growth efficiency of caterpillars were negative, but dependent on the fungicide. Effects of cyprodinil were stronger than difenoconazole, but at realistically low concentrations there was little effect of either fungicide. Nonetheless, higher concentrations of these chemicals, approximating those experienced directly after fungicide application, may impact non-target species. The observed interaction of…
format: application/pdf
format: text/html
creator: Amy P. Hastings
creator: Van Hniang Par
creator: Scott H. McArt
creator: Anurag A. Agrawal
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Ecotoxicology
description: doi:10.7717/peerj.20729
publisher: PeerJ Inc.
rights: © 2026 Hastings et al.
abstract: Concern over insect declines has increased attention on the effects of pesticide residues on native insects. We collected strawberry (target) and common milkweed (non-target) foliage and flowers on two small Central New York farms, within crop fields as well as field margins, and analyzed the tissues for pesticide residues of 94 agrochemicals. We found quantifiable levels of 13 fungicides, herbicides, and insecticides, mostly at low concentrations (typically less than 200 ppb where detected), and more often on strawberry than milkweed. We generally found higher pesticide residue levels early in the season (June vs. July) and on leaves compared to flowers. Residue levels in fields did not differ strongly from margins but pesticide drift may have left low-level residues on milkweed leaves and flowers in margins. Given that non-target effects of fungicides are understudied, we selected two prevalent fungicides found in this study (cyprodinil and difenoconazole) and used them in laboratory assays to assess impacts on early instar monarch (Danaus plexippus) caterpillar feeding, growth, and growth efficiency on common milkweed, along with two other milkweed (Asclepias) species. We tested the hypothesis that exposure to pesticides may be most impactful on poor quality host plants. For both fungicides, exposure at the highest doses (>100,000 ppb) reduced feeding, with the strongest effect on Asclepias asperula, the lowest quality host plant. Effects on caterpillar growth were similarly negative and consistent across host plant species. Finally, effects of fungicides on gross growth efficiency of caterpillars were negative, but dependent on the fungicide. Effects of cyprodinil were stronger than difenoconazole, but at realistically low concentrations there was little effect of either fungicide. Nonetheless, higher concentrations of these chemicals, approximating those experienced directly after fungicide application, may impact non-target species. The observed interaction of…
bibliographic citation: Hastings et al. (2026) Pesticide residues on milkweed and strawberry at small farms and non-target effects of two fungicides on monarch butterfly caterpillars. PeerJ 14:e20729 https://doi.org/10.7717/peerj.20729
date submitted: 2025-06-03
date accepted: 2025-12-11
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hastings
  given name: Amy P.
author list: Agent
  family name: Par
  given name: Van Hniang
author list: Agent
  family name: McArt
  given name: Scott H.
author list: Agent
  family name: Agrawal
  given name: Anurag A.
doi: 10.7717/peerj.20729
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Hastings et al.
attribution name: Hastings et al.

Photosynthetic responses of hydroponically grown basil (Ocimum basilicum L.) to drought and high-EC stress
type: item
type: AcademicArticle
description: Background Basil (Ocimum basilicum L.), a widely cultivated culinary and medicinal herb in the Lamiaceae family, is particularly vulnerable to various environmental stressors. This study examines how water deficit and elevated nutrient-solution electrical conductivity (EC) affect the photosynthetic efficiency of basil plants grown in an nutrient film technique (NFT) hydroponic system. Methods Chlorophyll fluorescence was assessed using both continuous-excitation and modulated pulse-amplitude-modulated (PAM) techniques. Fluorescence parameters were monitored in plants at two developmental stages, immature and mature, under drought and high–electrical-conductivity (EC) stress. Results Both stressors altered Photosystem II (PSII)—related fluorescence parameters, but high EC stress caused a wider spectrum of changes. In mature plants, those alterations were less pronounced, indicating enhanced tolerance likely due to more efficient electron transport and greater structural stability of the photosynthetic apparatus. The obtained results supported our hypothesis, that drought and high-EC stress would differentially impair photosynthetic efficiency, with drought imposing stronger osmotic limitations on photochemistry and high EC introducing additional ionic constraints. These stresses generated distinct physiological response patterns detectable by chlorophyll fluorescence measurements.
format: application/pdf
format: text/html
creator: Małgorzata Mirgos
creator: Piotr Dąbrowski
creator: Hazem Mohamed Kalaji
creator: Jacek Wróbel
creator: Janina Gajc-Wolska
creator: Bogumiła Pawluśkiewicz
creator: Małgorzata Kunka
creator: Katarzyna Kowalczyk
subject: Agricultural Science
subject: Biophysics
subject: Developmental Biology
subject: Plant Science
description: doi:10.7717/peerj.20728
publisher: PeerJ Inc.
rights: © 2026 Mirgos et al.
abstract: Background Basil (Ocimum basilicum L.), a widely cultivated culinary and medicinal herb in the Lamiaceae family, is particularly vulnerable to various environmental stressors. This study examines how water deficit and elevated nutrient-solution electrical conductivity (EC) affect the photosynthetic efficiency of basil plants grown in an nutrient film technique (NFT) hydroponic system. Methods Chlorophyll fluorescence was assessed using both continuous-excitation and modulated pulse-amplitude-modulated (PAM) techniques. Fluorescence parameters were monitored in plants at two developmental stages, immature and mature, under drought and high–electrical-conductivity (EC) stress. Results Both stressors altered Photosystem II (PSII)—related fluorescence parameters, but high EC stress caused a wider spectrum of changes. In mature plants, those alterations were less pronounced, indicating enhanced tolerance likely due to more efficient electron transport and greater structural stability of the photosynthetic apparatus. The obtained results supported our hypothesis, that drought and high-EC stress would differentially impair photosynthetic efficiency, with drought imposing stronger osmotic limitations on photochemistry and high EC introducing additional ionic constraints. These stresses generated distinct physiological response patterns detectable by chlorophyll fluorescence measurements.
bibliographic citation: Mirgos et al. (2026) Photosynthetic responses of hydroponically grown basil (Ocimum basilicum L.) to drought and high-EC stress. PeerJ 14:e20728 https://doi.org/10.7717/peerj.20728
date submitted: 2025-09-17
date accepted: 2025-12-11
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mirgos
  given name: Małgorzata
author list: Agent
  family name: Dąbrowski
  given name: Piotr
author list: Agent
  family name: Kalaji
  given name: Hazem Mohamed
author list: Agent
  family name: Wróbel
  given name: Jacek
author list: Agent
  family name: Gajc-Wolska
  given name: Janina
author list: Agent
  family name: Pawluśkiewicz
  given name: Bogumiła
author list: Agent
  family name: Kunka
  given name: Małgorzata
author list: Agent
  family name: Kowalczyk
  given name: Katarzyna
doi: 10.7717/peerj.20728
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Mirgos et al.
attribution name: Mirgos et al.

Cats, dogs, and sticky worms: invasion by land flatworms (Geoplanidae) is facilitated by household pets
type: item
type: AcademicArticle
description: Background It is well known that the main vector of invasion by land flatworms has been the export of potted plants from their countries of origin to the invaded country. Within the invaded country, transport to garden centres where the plants are sold, and transport to the buyer’s garden, are also carried out by humans. However, it is less clear how flatworms can then invade neighbouring gardens, given their slow movement rates. Methods We re-examined citizen science reports in metropolitan France received over more than 12 years (2013–2025), searching the 6500 original emails for keywords suggesting transport by pets. Results We found 15 citizen science observations of cats (13) or dogs (2) with flatworms stuck to their fur. Surprisingly, all reports concerned the species Caenoplana variegata, the two-tone planarian, even though this species is not the most abundant in gardens in France. Over the period 2020–2024, observations of C. variegata on dogs and cats represented 7.3% (10/137) of reports. Discussion We suspect that transport by domestic animals is a significant factor favouring invasion by C. variegata, which possesses a particularly sticky mucus adapted to arthropod predation. This is compounded by the fact that the species reproduces asexually in Europe, and therefore the transport of a single individual may be sufficient to facilitate an invasion. We calculated a conservative estimate of the distances travelled outdoors by all the dogs and cats in France, which was 18 billion km/year; if only a tiny proportion of these journeys involve pets carrying flatworms, this transport as a dispersal factor becomes entirely plausible. Conclusions We believe that animal transport is a significant factor favouring land flatworm invasion, but that this does not apply to all species. A citizen science initiative could provide a better understanding of the extent and importance of animal transport as a factor for land flatworm invasions in other countries.
format: application/pdf
format: text/html
creator: Jean-Lou Justine
creator: Leigh Winsor
subject: Biodiversity
subject: Soil Science
subject: Zoology
subject: Coupled Natural and Human Systems
subject: Biosphere Interactions
description: doi:10.7717/peerj.20713
publisher: PeerJ Inc.
rights: © 2026 Justine and Winsor
abstract: Background It is well known that the main vector of invasion by land flatworms has been the export of potted plants from their countries of origin to the invaded country. Within the invaded country, transport to garden centres where the plants are sold, and transport to the buyer’s garden, are also carried out by humans. However, it is less clear how flatworms can then invade neighbouring gardens, given their slow movement rates. Methods We re-examined citizen science reports in metropolitan France received over more than 12 years (2013–2025), searching the 6500 original emails for keywords suggesting transport by pets. Results We found 15 citizen science observations of cats (13) or dogs (2) with flatworms stuck to their fur. Surprisingly, all reports concerned the species Caenoplana variegata, the two-tone planarian, even though this species is not the most abundant in gardens in France. Over the period 2020–2024, observations of C. variegata on dogs and cats represented 7.3% (10/137) of reports. Discussion We suspect that transport by domestic animals is a significant factor favouring invasion by C. variegata, which possesses a particularly sticky mucus adapted to arthropod predation. This is compounded by the fact that the species reproduces asexually in Europe, and therefore the transport of a single individual may be sufficient to facilitate an invasion. We calculated a conservative estimate of the distances travelled outdoors by all the dogs and cats in France, which was 18 billion km/year; if only a tiny proportion of these journeys involve pets carrying flatworms, this transport as a dispersal factor becomes entirely plausible. Conclusions We believe that animal transport is a significant factor favouring land flatworm invasion, but that this does not apply to all species. A citizen science initiative could provide a better understanding of the extent and importance of animal transport as a factor for land flatworm invasions in other countries.
bibliographic citation: Justine et al. (2026) Cats, dogs, and sticky worms: invasion by land flatworms (Geoplanidae) is facilitated by household pets. PeerJ 14:e20713 https://doi.org/10.7717/peerj.20713
date submitted: 2025-06-16
date accepted: 2025-12-10
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Justine
  given name: Jean-Lou
author list: Agent
  family name: Winsor
  given name: Leigh
doi: 10.7717/peerj.20713
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Justine and Winsor
attribution name: Justine and Winsor

Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction
type: item
type: AcademicArticle
description: The Cas9 enzyme along with a single guide RNA molecule is a modular tool for genetic engineering and has shown effectiveness as a species-specific antimicrobial. The ability to accurately predict on-target cleavage is critical as activity varies by target. Using the sgRNA nucleotide sequence and an activity score, predictive models have been developed with the best performance resulting from deep learning architectures. Prior work has emphasized robust and novel architectures to improve predictive performance. Here, we explore the impact of a data-centric approach through optimization of the input target site adjacent nucleotide sequence length and the use of data filtering for read counts in the control conditions to improve input data utility. Using the existing crisprHAL architecture, we develop crisprHAL Tev, a bacterial SpCas9 prediction model with performance that generalizes across related species and across data types. During this process, we also rebuilt two prior Escherichia coli Cas9 datasets, demonstrating the importance of data quality, and resulting in the production of an improved bacterial eSpCas9 prediction model. The crisprHAL models are available through GitHub: https://github.com/tbrowne5/crisprHAL.
format: application/pdf
format: text/html
creator: Tyler S. Browne
creator: David R. Edgell
creator: Gregory B. Gloor
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
subject: Molecular Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20706
publisher: PeerJ Inc.
rights: © 2026 Browne et al.
abstract: The Cas9 enzyme along with a single guide RNA molecule is a modular tool for genetic engineering and has shown effectiveness as a species-specific antimicrobial. The ability to accurately predict on-target cleavage is critical as activity varies by target. Using the sgRNA nucleotide sequence and an activity score, predictive models have been developed with the best performance resulting from deep learning architectures. Prior work has emphasized robust and novel architectures to improve predictive performance. Here, we explore the impact of a data-centric approach through optimization of the input target site adjacent nucleotide sequence length and the use of data filtering for read counts in the control conditions to improve input data utility. Using the existing crisprHAL architecture, we develop crisprHAL Tev, a bacterial SpCas9 prediction model with performance that generalizes across related species and across data types. During this process, we also rebuilt two prior Escherichia coli Cas9 datasets, demonstrating the importance of data quality, and resulting in the production of an improved bacterial eSpCas9 prediction model. The crisprHAL models are available through GitHub: https://github.com/tbrowne5/crisprHAL.
bibliographic citation: Browne et al. (2026) Better data for better predictions: data curation improves deep learning for sgRNA/Cas9 prediction. PeerJ 14:e20706 https://doi.org/10.7717/peerj.20706
date submitted: 2025-07-21
date accepted: 2025-12-10
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Browne
  given name: Tyler S.
author list: Agent
  family name: Edgell
  given name: David R.
author list: Agent
  family name: Gloor
  given name: Gregory B.
doi: 10.7717/peerj.20706
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Browne et al.
attribution name: Browne et al.

Mastering cardiomyocyte mitophagy: molecular governance, pathological derailment and therapeutics
type: item
type: AcademicArticle
description: Mitophagy is a pivotal quality control pathway that maintains cardiac energy metabolism and structural stability by selectively removing damaged or senescent mitochondria, thereby keeping mitochondrial dynamics in balance. This process secures cardiomyocyte survival, calcium handling, and contractile function during both rest and stress. When mitophagic flux is inadequate, accumulation of reactive oxygen species, disruption of calcium homeostasis, and uncontrolled inflammation act together to drive pathological hypertrophy, heart failure, cardiac aging, and obesity-associated cardiomyopathy. Conversely, appropriate activation of mitophagy can lessen structural injury and restore pump performance during ischemia reperfusion, pressure overload, and metabolic stress. This review summarizes the central regulatory network of cardiac mitophagy and its pathological roles across cardiovascular disorders, emphasizing that careful modulation of flux is essential for preserving myocardial homeostasis. Recent experimental strategies that target mitophagy are also discussed, providing a theoretical foundation for the development of precise cardioprotective therapies.
format: application/pdf
format: text/html
creator: Pan Liu
creator: Haosheng Wu
creator: Huanhuan Ren
creator: Jing Wang
creator: Fan Yang
subject: Biochemistry
subject: Cell Biology
subject: Cardiology
description: doi:10.7717/peerj.20700
publisher: PeerJ Inc.
rights: © 2026 Liu et al.
abstract: Mitophagy is a pivotal quality control pathway that maintains cardiac energy metabolism and structural stability by selectively removing damaged or senescent mitochondria, thereby keeping mitochondrial dynamics in balance. This process secures cardiomyocyte survival, calcium handling, and contractile function during both rest and stress. When mitophagic flux is inadequate, accumulation of reactive oxygen species, disruption of calcium homeostasis, and uncontrolled inflammation act together to drive pathological hypertrophy, heart failure, cardiac aging, and obesity-associated cardiomyopathy. Conversely, appropriate activation of mitophagy can lessen structural injury and restore pump performance during ischemia reperfusion, pressure overload, and metabolic stress. This review summarizes the central regulatory network of cardiac mitophagy and its pathological roles across cardiovascular disorders, emphasizing that careful modulation of flux is essential for preserving myocardial homeostasis. Recent experimental strategies that target mitophagy are also discussed, providing a theoretical foundation for the development of precise cardioprotective therapies.
bibliographic citation: Liu et al. (2026) Mastering cardiomyocyte mitophagy: molecular governance, pathological derailment and therapeutics. PeerJ 14:e20700 https://doi.org/10.7717/peerj.20700
date submitted: 2025-07-31
date accepted: 2025-12-09
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Pan
author list: Agent
  family name: Wu
  given name: Haosheng
author list: Agent
  family name: Ren
  given name: Huanhuan
author list: Agent
  family name: Wang
  given name: Jing
author list: Agent
  family name: Yang
  given name: Fan
doi: 10.7717/peerj.20700
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: © 2026 Liu et al.
attribution name: Liu et al.

JGR-NMF: joint graph-regularized non-negative matrix factorization for spatial domain identification
type: item
type: AcademicArticle
description: The spatial transcriptomics technique provides an unprecedented perspective for analyzing the distribution patterns of cells within tissues and their functional tissue structures. To enhance the accuracy and robustness of spatial domain identification, we propose Joint Graph-Regularized Non-negative Matrix Factorization (JGR-NMF). An adaptive neighborhood graph construction strategy is introduced by applying an nth-power transformation to the spot adjacency probability matrix, thereby automatically optimizing the neighborhood size for individual spots. Furthermore, a JGR-NMF framework is developed, integrating this adaptively constructed kNN graph with the spatial adjacency matrix. Evaluations conducted on two breast cancer datasets, one Mouse Kidney dataset and one Mouse Embryo dataset, demonstrate that JGR-NMF significantly outperforms five state-of-the-art baseline methods in spatial domain identification. Systematic ablation studies further confirm the critical role of graph regularization in enhancing model performance.
format: application/pdf
format: text/html
creator: Juan Liang
creator: Jiuxi Huang
creator: Chenxi Xi
creator: Yun Wang
creator: Juntao Li
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20585
publisher: PeerJ Inc.
rights: © 2026 Liang et al.
abstract: The spatial transcriptomics technique provides an unprecedented perspective for analyzing the distribution patterns of cells within tissues and their functional tissue structures. To enhance the accuracy and robustness of spatial domain identification, we propose Joint Graph-Regularized Non-negative Matrix Factorization (JGR-NMF). An adaptive neighborhood graph construction strategy is introduced by applying an nth-power transformation to the spot adjacency probability matrix, thereby automatically optimizing the neighborhood size for individual spots. Furthermore, a JGR-NMF framework is developed, integrating this adaptively constructed kNN graph with the spatial adjacency matrix. Evaluations conducted on two breast cancer datasets, one Mouse Kidney dataset and one Mouse Embryo dataset, demonstrate that JGR-NMF significantly outperforms five state-of-the-art baseline methods in spatial domain identification. Systematic ablation studies further confirm the critical role of graph regularization in enhancing model performance.
bibliographic citation: Liang et al. (2026) JGR-NMF: joint graph-regularized non-negative matrix factorization for spatial domain identification. PeerJ 14:e20585 https://doi.org/10.7717/peerj.20585
date submitted: 2025-07-24
date accepted: 2025-11-24
issued: 2026-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Juan
author list: Agent
  family name: Huang
  given name: Jiuxi
author list: Agent
  family name: Xi
  given name: Chenxi
author list: Agent
  family name: Wang
  given name: Yun
author list: Agent
  family name: Li
  given name: Juntao
doi: 10.7717/peerj.20585
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-10
copyright: ©2026 Liang et al.
attribution name: Liang et al.

Preference for producer specific exudates shapes microbial communities in coral reefs
type: item
type: AcademicArticle
description: Exometabolites released by benthic primary producers (BPP) are an integral part of the coral reef food web. Depending on their origin and composition these complex mixtures of dissolved organic compounds support a distinct microbial community. Which exudate components are preferentially used by microbes, how this preference differs between exudate types, and what molecular features drive the microbial community differentiation is still poorly understood. Here we use an untargeted metabolomics approach (liquid chromatography-tandem mass spectrometry (LC/MS-MS)) to assess the microbial uptake of exudates produced by BPP (mixed coral community, macroalgae, turf algae, and coral-macroalgae, coral-turf algae). We can show that that exudate compounds and especially those unique to a specific BPP or mixed community are the most favored substrate for microbes in the respective communities. Our data suggests that in each BPP treatment the unique combination of organic compounds is the main driver selecting for a specific microbial community composition rather than a specific single substance. This emphasizes the complexity of mechanisms and metabolisms that constitute and structure communities in ecosystems as intricate as coral reefs.
format: application/pdf
format: text/html
creator: Milou G.I. Arts
creator: Benjamin Mueller
creator: Linda Wegley Kelly
creator: Craig E. Nelson
creator: Irina Koester
creator: Daniel Petras
creator: Ellen Hopmans
creator: Mark J.A. Vermeij
creator: Andreas F. Haas
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Biogeochemistry
description: doi:10.7717/peerj.20748
publisher: PeerJ Inc.
rights: © 2026 Arts et al.
abstract: Exometabolites released by benthic primary producers (BPP) are an integral part of the coral reef food web. Depending on their origin and composition these complex mixtures of dissolved organic compounds support a distinct microbial community. Which exudate components are preferentially used by microbes, how this preference differs between exudate types, and what molecular features drive the microbial community differentiation is still poorly understood. Here we use an untargeted metabolomics approach (liquid chromatography-tandem mass spectrometry (LC/MS-MS)) to assess the microbial uptake of exudates produced by BPP (mixed coral community, macroalgae, turf algae, and coral-macroalgae, coral-turf algae). We can show that that exudate compounds and especially those unique to a specific BPP or mixed community are the most favored substrate for microbes in the respective communities. Our data suggests that in each BPP treatment the unique combination of organic compounds is the main driver selecting for a specific microbial community composition rather than a specific single substance. This emphasizes the complexity of mechanisms and metabolisms that constitute and structure communities in ecosystems as intricate as coral reefs.
bibliographic citation: Arts et al. (2026) Preference for producer specific exudates shapes microbial communities in coral reefs. PeerJ 14:e20748 https://doi.org/10.7717/peerj.20748
date submitted: 2025-05-22
date accepted: 2025-12-16
issued: 2026-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arts
  given name: Milou G.I.
author list: Agent
  family name: Mueller
  given name: Benjamin
author list: Agent
  family name: Kelly
  given name: Linda Wegley
author list: Agent
  family name: Nelson
  given name: Craig E.
author list: Agent
  family name: Koester
  given name: Irina
author list: Agent
  family name: Petras
  given name: Daniel
author list: Agent
  family name: Hopmans
  given name: Ellen
author list: Agent
  family name: Vermeij
  given name: Mark J.A.
author list: Agent
  family name: Haas
  given name: Andreas F.
doi: 10.7717/peerj.20748
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-09
copyright: ©2026 Arts et al.
attribution name: Arts et al.

A retrospective study of a weight estimation model for hospitalized bedridden patients based on anthropometric parameters
type: item
type: AcademicArticle
description: Objective The aim of this study was to construct a weight estimation model for bedridden patients using anthropometric parameters that are readily obtainable during routine clinical care. Methods A retrospective study was conducted involving 494 bedridden inpatients from the Department of Endocrinology of a tertiary general hospital (February 2023–February 2024). Weight was measured via a calibrated wheelchair scale. Anthropometric parameters (age, height, wrist, lower limb, waist, and hip circumferences) were measured in the supine position by trained researchers using standardized tools and specific anatomical landmarks. The estimation models were developed using stepwise regression. Results The final models demonstrated excellent performance. The male model achieved an adjusted-R2 of 0.901 and Root Mean Square Error (RMSE) of 3.81 kg; the female model achieved an adjusted-R2 of 0.829 and RMSE of 3.81 kg. Bland-Altman analysis confirmed strong agreement between the actual and estimated weigh values, with a mean difference close to 0, no significant proportional bias, and most differences residing within the 95% limits of agreement. Conclusion The developed models provide a reliable, cost-effective method for weight estimation in bedridden patients, using parameters that can be integrated into routine clinical assessments, offering a practical alternative to specialized equipment in resource-limited settings.
format: application/pdf
format: text/html
creator: Ai Luo
creator: Zheng Tang
creator: Xiaojia Xu
creator: Guifen Guan
creator: Zehang Hong
creator: Dong Xiao
creator: Jieyi Xu
creator: Rongkui Wu
creator: Zhuoqing Hu
subject: Diabetes and Endocrinology
subject: Internal Medicine
subject: Nursing
subject: Rehabilitation
description: doi:10.7717/peerj.20698
publisher: PeerJ Inc.
rights: © 2026 Luo et al.
abstract: Objective The aim of this study was to construct a weight estimation model for bedridden patients using anthropometric parameters that are readily obtainable during routine clinical care. Methods A retrospective study was conducted involving 494 bedridden inpatients from the Department of Endocrinology of a tertiary general hospital (February 2023–February 2024). Weight was measured via a calibrated wheelchair scale. Anthropometric parameters (age, height, wrist, lower limb, waist, and hip circumferences) were measured in the supine position by trained researchers using standardized tools and specific anatomical landmarks. The estimation models were developed using stepwise regression. Results The final models demonstrated excellent performance. The male model achieved an adjusted-R2 of 0.901 and Root Mean Square Error (RMSE) of 3.81 kg; the female model achieved an adjusted-R2 of 0.829 and RMSE of 3.81 kg. Bland-Altman analysis confirmed strong agreement between the actual and estimated weigh values, with a mean difference close to 0, no significant proportional bias, and most differences residing within the 95% limits of agreement. Conclusion The developed models provide a reliable, cost-effective method for weight estimation in bedridden patients, using parameters that can be integrated into routine clinical assessments, offering a practical alternative to specialized equipment in resource-limited settings.
bibliographic citation: Luo et al. (2026) A retrospective study of a weight estimation model for hospitalized bedridden patients based on anthropometric parameters. PeerJ 14:e20698 https://doi.org/10.7717/peerj.20698
date submitted: 2025-04-28
date accepted: 2025-12-09
issued: 2026-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Ai
author list: Agent
  family name: Tang
  given name: Zheng
author list: Agent
  family name: Xu
  given name: Xiaojia
author list: Agent
  family name: Guan
  given name: Guifen
author list: Agent
  family name: Hong
  given name: Zehang
author list: Agent
  family name: Xiao
  given name: Dong
author list: Agent
  family name: Xu
  given name: Jieyi
author list: Agent
  family name: Wu
  given name: Rongkui
author list: Agent
  family name: Hu
  given name: Zhuoqing
doi: 10.7717/peerj.20698
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-09
copyright: ©2026 Luo et al.
attribution name: Luo et al.

Investigation of the relationship between pain, fear of movement and falling in geriatric patients
type: item
type: AcademicArticle
description: Background Falls among older adults represent a major public health concern and are strongly associated with pain, fear of falling, and fear of movement. Pain may increase fall risk in a dose-response manner, while fear of falling can limit mobility, further enhancing vulnerability. This study aimed to investigate the interrelationship between pain, kinesiophobia, and fear of falling in geriatric patients. Methods A descriptive cross-sectional study was conducted in the Physical Therapy Unit of Burdur State Hospital, Turkey, between March 2022 and March 2023. A total of 100 participants aged ≥65 years were recruited by random sampling. Data collection included sociodemographic characteristics, fall history, chronic diseases, and regular medication use. Pain was assessed using the Visual Analog Scale (VAS) and Verbal Category Scale, kinesiophobia using the Tampa Kinesiophobia Scale, and fear of falling using the Tinetti Falls Efficacy Scale. Data were analyzed using Statistical Package for the Social Sciences (SPSS version 23). Descriptive statistics, Student’s t-test, analysis of variance (ANOVA) with Tukey post-hoc, and Pearson correlation analyses were performed. Results The mean age of participants was 70.6 ± 4.5 years. The difference in VAS scores between genders was statistically significant (p < 0.05), with higher pain levels in women. A strong positive correlation was found between the Tampa and Tinetti scores (r = 0.704, p < 0.01), and a moderate positive correlation was observed between VAS and Verbal Category Scale scores (r = 0.535, p < 0.01). Other subgroup comparisons by education, marital status, and chronic disease were not statistically significant. Conclusions Pain, kinesiophobia, and fear of falling are interrelated in older adults and negatively affect daily functioning. Routine assessment of these factors is essential for personalized fall-prevention strategies. Interventions that encourage safe mobility and reduce fear of movement may improve qu…
format: application/pdf
format: text/html
creator: Ümmühan Meltem Öztürk
creator: Mümin Polat
subject: Geriatrics
subject: Global Health
subject: Public Health
subject: Mental Health
subject: Rehabilitation
description: doi:10.7717/peerj.20661
publisher: PeerJ Inc.
rights: © 2026 Öztürk and Polat
abstract: Background Falls among older adults represent a major public health concern and are strongly associated with pain, fear of falling, and fear of movement. Pain may increase fall risk in a dose-response manner, while fear of falling can limit mobility, further enhancing vulnerability. This study aimed to investigate the interrelationship between pain, kinesiophobia, and fear of falling in geriatric patients. Methods A descriptive cross-sectional study was conducted in the Physical Therapy Unit of Burdur State Hospital, Turkey, between March 2022 and March 2023. A total of 100 participants aged ≥65 years were recruited by random sampling. Data collection included sociodemographic characteristics, fall history, chronic diseases, and regular medication use. Pain was assessed using the Visual Analog Scale (VAS) and Verbal Category Scale, kinesiophobia using the Tampa Kinesiophobia Scale, and fear of falling using the Tinetti Falls Efficacy Scale. Data were analyzed using Statistical Package for the Social Sciences (SPSS version 23). Descriptive statistics, Student’s t-test, analysis of variance (ANOVA) with Tukey post-hoc, and Pearson correlation analyses were performed. Results The mean age of participants was 70.6 ± 4.5 years. The difference in VAS scores between genders was statistically significant (p < 0.05), with higher pain levels in women. A strong positive correlation was found between the Tampa and Tinetti scores (r = 0.704, p < 0.01), and a moderate positive correlation was observed between VAS and Verbal Category Scale scores (r = 0.535, p < 0.01). Other subgroup comparisons by education, marital status, and chronic disease were not statistically significant. Conclusions Pain, kinesiophobia, and fear of falling are interrelated in older adults and negatively affect daily functioning. Routine assessment of these factors is essential for personalized fall-prevention strategies. Interventions that encourage safe mobility and reduce fear of movement may improve qu…
bibliographic citation: Öztürk et al. (2026) Investigation of the relationship between pain, fear of movement and falling in geriatric patients. PeerJ 14:e20661 https://doi.org/10.7717/peerj.20661
date submitted: 2025-07-03
date accepted: 2025-12-02
issued: 2026-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Öztürk
  given name: Ümmühan Meltem
author list: Agent
  family name: Polat
  given name: Mümin
doi: 10.7717/peerj.20661
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-09
copyright: ©2026 Öztürk and Polat
attribution name: Öztürk and Polat

Systematic reviews of low-frequency repetitive transcranial magnetic stimulation on cognition and epileptiform discharge in patients with epilepsy
type: item
type: AcademicArticle
description: Background This systematic review investigates the efficacy of low-frequency repetitive transcranial magnetic stimulation (LF-rTMS) in improving cognitive function and reducing epileptiform discharges in patients with epilepsy. It further examines whether patient age moderates the treatment effect. Additionally, the review evaluates whether intervention parameters, including duration, frequency, session time, and stimulation site, positively influence the improvement of cognition and epileptiform discharges. Methods Seven databases were searched: Embase, Web of Science, PubMed, The Cochrane Library, Wanfang, VIP, and China National Knowledge Infrastructure. The search period was from database inception to September 2025. Two researchers independently screened the literature to identify randomized controlled trials (RCTs) that investigated the effects of TMS on cognition in patients with epilepsy. Quality assessment was performed using PEDro, and Meta-analysis and publication bias were tested using RevMan 5.4.1 and Stata 17.0, respectively. The quality of evidence for outcome indicators was evaluated using GRADEPro software. The standardized mean difference (SMD) and 95% CI were used as effect size statistics. Results This meta-analysis included 12 randomized controlled trials (n = 1,289 patients). Pooled results demonstrated that low-frequency rTMS (LF-rTMS) significantly improved cognitive function (SMD = 1.22, 95% CI [0.87–1.56], P < 0.0001; n = 861) and reduced epileptiform discharges (SMD = −0.68, 95% CI [−0.98 to −0.37], P < 0.00001; n = 428). Subgroup analyses identified key parameters associated with optimal outcomes. For cognitive improvement, greater effect sizes were observed in patients aged 45–60 years, with an LF-rTMS protocol of 1 Hz stimulation targeting the epileptogenic focus, session time >20 min, intervention duration >4 weeks, and frequency of ≤7 sessions/week, particularly when combined with levetiracetam. Conversely, a greater reduction in epil…
format: application/pdf
format: text/html
creator: Simin Xu
creator: Shufan Li
creator: Fen Yu
creator: Chen Wei
creator: Feng Ding
creator: Xing Wang
creator: Shihang Lin
subject: Cognitive Disorders
subject: Neurology
description: doi:10.7717/peerj.20637
publisher: PeerJ Inc.
rights: © 2026 Xu et al.
abstract: Background This systematic review investigates the efficacy of low-frequency repetitive transcranial magnetic stimulation (LF-rTMS) in improving cognitive function and reducing epileptiform discharges in patients with epilepsy. It further examines whether patient age moderates the treatment effect. Additionally, the review evaluates whether intervention parameters, including duration, frequency, session time, and stimulation site, positively influence the improvement of cognition and epileptiform discharges. Methods Seven databases were searched: Embase, Web of Science, PubMed, The Cochrane Library, Wanfang, VIP, and China National Knowledge Infrastructure. The search period was from database inception to September 2025. Two researchers independently screened the literature to identify randomized controlled trials (RCTs) that investigated the effects of TMS on cognition in patients with epilepsy. Quality assessment was performed using PEDro, and Meta-analysis and publication bias were tested using RevMan 5.4.1 and Stata 17.0, respectively. The quality of evidence for outcome indicators was evaluated using GRADEPro software. The standardized mean difference (SMD) and 95% CI were used as effect size statistics. Results This meta-analysis included 12 randomized controlled trials (n = 1,289 patients). Pooled results demonstrated that low-frequency rTMS (LF-rTMS) significantly improved cognitive function (SMD = 1.22, 95% CI [0.87–1.56], P < 0.0001; n = 861) and reduced epileptiform discharges (SMD = −0.68, 95% CI [−0.98 to −0.37], P < 0.00001; n = 428). Subgroup analyses identified key parameters associated with optimal outcomes. For cognitive improvement, greater effect sizes were observed in patients aged 45–60 years, with an LF-rTMS protocol of 1 Hz stimulation targeting the epileptogenic focus, session time >20 min, intervention duration >4 weeks, and frequency of ≤7 sessions/week, particularly when combined with levetiracetam. Conversely, a greater reduction in epil…
bibliographic citation: Xu et al. (2026) Systematic reviews of low-frequency repetitive transcranial magnetic stimulation on cognition and epileptiform discharge in patients with epilepsy. PeerJ 14:e20637 https://doi.org/10.7717/peerj.20637
date submitted: 2025-05-13
date accepted: 2025-11-30
issued: 2026-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Simin
author list: Agent
  family name: Li
  given name: Shufan
author list: Agent
  family name: Yu
  given name: Fen
author list: Agent
  family name: Wei
  given name: Chen
author list: Agent
  family name: Ding
  given name: Feng
author list: Agent
  family name: Wang
  given name: Xing
author list: Agent
  family name: Lin
  given name: Shihang
doi: 10.7717/peerj.20637
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-09
copyright: © 2026 Xu et al.
attribution name: Xu et al.

Myosin IXb is involved in multiple pathological conditions
type: item
type: AcademicArticle
description: Myosin IXb (Myo9b) is a single-headed motor protein in the myosin superfamily. It contains a unique Rho guanosine triphosphatase-activating protein domain, which enables it to regulate cytoskeletal dynamics and cell migration. Most studies on Myo9b are focused on epithelial repair, intestinal barrier function, and immune cell motility; however, its roles in immune regulation, inflammatory responses, tumorigenesis, and various autoimmune diseases have garnered notable attention in recent years. This study comprehensively reviews the structural characteristics, regulatory mechanisms, and biological functions of Myo9b, along with emphasizing its crucial roles in various pathological conditions and its potential as a therapeutic target.
format: application/pdf
format: text/html
creator: Shufeng Dong
creator: Kai Wang
creator: Feng-Shuang Yi
creator: Yonglei Hu
creator: Xin Zhang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20802
publisher: PeerJ Inc.
rights: © 2026 Dong et al.
abstract: Myosin IXb (Myo9b) is a single-headed motor protein in the myosin superfamily. It contains a unique Rho guanosine triphosphatase-activating protein domain, which enables it to regulate cytoskeletal dynamics and cell migration. Most studies on Myo9b are focused on epithelial repair, intestinal barrier function, and immune cell motility; however, its roles in immune regulation, inflammatory responses, tumorigenesis, and various autoimmune diseases have garnered notable attention in recent years. This study comprehensively reviews the structural characteristics, regulatory mechanisms, and biological functions of Myo9b, along with emphasizing its crucial roles in various pathological conditions and its potential as a therapeutic target.
bibliographic citation: Dong et al. (2026) Myosin IXb is involved in multiple pathological conditions. PeerJ 14:e20802 https://doi.org/10.7717/peerj.20802
date submitted: 2025-08-06
date accepted: 2025-12-24
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Dong
  given name: Shufeng
author list: Agent
  family name: Wang
  given name: Kai
author list: Agent
  family name: Yi
  given name: Feng-Shuang
author list: Agent
  family name: Hu
  given name: Yonglei
author list: Agent
  family name: Zhang
  given name: Xin
doi: 10.7717/peerj.20802
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: ©2026 Dong et al.
attribution name: Dong et al.

Remote ischemic preconditioning fails to enhance maximal accumulated oxygen deficit in well-trained college tennis players
type: item
type: AcademicArticle
description: Background Tennis, characterized by intermittent high-intensity bursts, demands both aerobic and anaerobic energy pathways for optimal performance. Remote ischemic preconditioning (RIPC) has emerged as a potential method to enhance athletic outcomes. This study aimed to explore the impact of RIPC on anaerobic capacity, specifically the maximal accumulated oxygen deficit (MAOD), in well-trained college tennis players. Methods In a single-blinded, randomized, controlled crossover design, 16 participants (eight men and eight women; age: 20.9 ± 1.4 years; height: 1.73 ± 0.76 m; weight: 63.5 ± 8.2 kg; BMI: 21.2 ± 1.4 kg/m2) completed supramaximal intensity tests across baseline, placebo, and RIPC conditions. RIPC involved alternating bilateral occlusion of 220 or 20 mmHg for 4 × 5 min applied to both arms. Subsequently, the subjects performed a supramaximal test on the treadmill at 110% VO2max intensity until exhaustion. Results The results indicated that RIPC had no discernible effect on time to exhaustion compared to baseline or placebo conditions (p > 0.05). Moreover, parameters including MAODALT (Alternative MAOD, derived from the fast component of excess post-exercise oxygen consumption and oxygen equivalent for blood lactate accumulation), lactic anaerobic capacity, alactic anaerobic capacity, and excess post-exercise oxygen uptake dynamics remained comparable across the three interventions (p > 0.05). Notably, a strong correlation was observed between MAOD and MAODALT (r = 0.739; p < 0.05). Conclusion In conclusion, this study provides evidence that remote ischemic preconditioning did not improve anaerobic capacity, as indicated by MAOD, among well-trained college tennis players. These findings emphasize the nuanced interplay of physiological factors in the context of RIPC and suggest that its impact on anaerobic capacity may be limited within this athletic cohort.
format: application/pdf
format: text/html
creator: Xinshi Zhao
creator: Yongji Yang
creator: Yameng Wang
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.20789
publisher: PeerJ Inc.
rights: © 2026 Zhao et al.
abstract: Background Tennis, characterized by intermittent high-intensity bursts, demands both aerobic and anaerobic energy pathways for optimal performance. Remote ischemic preconditioning (RIPC) has emerged as a potential method to enhance athletic outcomes. This study aimed to explore the impact of RIPC on anaerobic capacity, specifically the maximal accumulated oxygen deficit (MAOD), in well-trained college tennis players. Methods In a single-blinded, randomized, controlled crossover design, 16 participants (eight men and eight women; age: 20.9 ± 1.4 years; height: 1.73 ± 0.76 m; weight: 63.5 ± 8.2 kg; BMI: 21.2 ± 1.4 kg/m2) completed supramaximal intensity tests across baseline, placebo, and RIPC conditions. RIPC involved alternating bilateral occlusion of 220 or 20 mmHg for 4 × 5 min applied to both arms. Subsequently, the subjects performed a supramaximal test on the treadmill at 110% VO2max intensity until exhaustion. Results The results indicated that RIPC had no discernible effect on time to exhaustion compared to baseline or placebo conditions (p > 0.05). Moreover, parameters including MAODALT (Alternative MAOD, derived from the fast component of excess post-exercise oxygen consumption and oxygen equivalent for blood lactate accumulation), lactic anaerobic capacity, alactic anaerobic capacity, and excess post-exercise oxygen uptake dynamics remained comparable across the three interventions (p > 0.05). Notably, a strong correlation was observed between MAOD and MAODALT (r = 0.739; p < 0.05). Conclusion In conclusion, this study provides evidence that remote ischemic preconditioning did not improve anaerobic capacity, as indicated by MAOD, among well-trained college tennis players. These findings emphasize the nuanced interplay of physiological factors in the context of RIPC and suggest that its impact on anaerobic capacity may be limited within this athletic cohort.
bibliographic citation: Zhao et al. (2026) Remote ischemic preconditioning fails to enhance maximal accumulated oxygen deficit in well-trained college tennis players. PeerJ 14:e20789 https://doi.org/10.7717/peerj.20789
date submitted: 2025-04-14
date accepted: 2025-12-22
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Xinshi
author list: Agent
  family name: Yang
  given name: Yongji
author list: Agent
  family name: Wang
  given name: Yameng
doi: 10.7717/peerj.20789
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: © 2026 Zhao et al.
attribution name: Zhao et al.

Croton buiquensis (Euphorbiaceae), a new species from northeastern Brazil, its phylogenetic placement, and niche modeling
type: item
type: AcademicArticle
description: A new species of Croton, microendemic of the dry forests of northeastern Brazil in the state of Pernambuco, is here described. Morphological and ITS molecular data provide evidence for placing C. buiquensis sp. nov. as part of Croton section Pedicellati. Specimens of C. buiquensis had been previously identified in herbaria as C. pedicellatus, but the former can be distinguished from the latter by the hispid indumentum of the leaf blade, the ovate shape of the petals of staminate flowers, pistillate flowers with 4-fid to multifid styles, and a crossbow-shape caruncle. Evidence from ecological niche modeling points to other areas in the state of Pernambuco, specifically the “Agreste” region, as likely locations for the occurrence of the new species, which could be the target of future botanical surveys. Croton buiquensis is here provisionally considered as Critically Endangered based on IUCN criteria. This is the first record of multifid styles (more than six stigmatic tips) in C. sect. Pedicellati and also the first species of the section endemic to the state of Pernambuco.
format: application/pdf
format: text/html
creator: Joesili C.P. Oliveira
creator: Karen Y. Suarez-Contento
creator: Ricarda Riina
creator: Sarah M. Athiê-Souza
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.20718
publisher: PeerJ Inc.
rights: © 2026 Oliveira et al.
abstract: A new species of Croton, microendemic of the dry forests of northeastern Brazil in the state of Pernambuco, is here described. Morphological and ITS molecular data provide evidence for placing C. buiquensis sp. nov. as part of Croton section Pedicellati. Specimens of C. buiquensis had been previously identified in herbaria as C. pedicellatus, but the former can be distinguished from the latter by the hispid indumentum of the leaf blade, the ovate shape of the petals of staminate flowers, pistillate flowers with 4-fid to multifid styles, and a crossbow-shape caruncle. Evidence from ecological niche modeling points to other areas in the state of Pernambuco, specifically the “Agreste” region, as likely locations for the occurrence of the new species, which could be the target of future botanical surveys. Croton buiquensis is here provisionally considered as Critically Endangered based on IUCN criteria. This is the first record of multifid styles (more than six stigmatic tips) in C. sect. Pedicellati and also the first species of the section endemic to the state of Pernambuco.
bibliographic citation: Oliveira et al. (2026) Croton buiquensis (Euphorbiaceae), a new species from northeastern Brazil, its phylogenetic placement, and niche modeling. PeerJ 14:e20718 https://doi.org/10.7717/peerj.20718
date submitted: 2025-10-10
date accepted: 2025-12-11
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira
  given name: Joesili C.P.
author list: Agent
  family name: Suarez-Contento
  given name: Karen Y.
author list: Agent
  family name: Riina
  given name: Ricarda
author list: Agent
  family name: Athiê-Souza
  given name: Sarah M.
doi: 10.7717/peerj.20718
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: ©2026 Oliveira et al.
attribution name: Oliveira et al.

Normalized compression distance for DNA classification
type: item
type: AcademicArticle
description: Analyzing the origin and diversity of numerous genomic sequences, such as those sampled from the human microbiome, is an important first step in genomic analysis. The use of normalized compression distance (NCD) has demonstrated capabilities in the field of text classification as a low-resource alternative to deep neural networks (DNNs) by leveraging compression algorithms to approximate Kolmogorov information distance. In an effort to apply this technique toward genomics tasks akin to tools such as Many-against-Many sequence searching (MMseqs) and Kraken2, we have explored the use of a gzip-based NCD combination in both gene labeling of open reading frames (ORFs) and taxonomic classification of short reads. Our implementation achieved 0.89 accuracy and 0.88 macro-F1 on human gene classification, surpassing similar NCD-based approaches. In prokaryotic gene labeling tasks, NCD shows superior classification accuracy to traditional alignment or exact-match tools in out-of-distribution settings, while also outperforming comparable sequence-embedding methods in in-distribution classification. However, the computational complexity of O(MN) (in standard big-O notation, where M and N denote the sizes of the training and test databases, respectively) constrains scalability to very large datasets, though these findings nonetheless demonstrate that compression-based approaches provide an effective alternative for genomic sequence classification, particularly in low-data environments.
format: application/pdf
format: text/html
creator: Gavin Hearne
creator: Mohammadsaleh S. Refahi
creator: Haozhe (Neil) Duan
creator: James R. Brown
creator: Gail L. Rosen
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.20677
publisher: PeerJ Inc.
rights: © 2026 Hearne et al.
abstract: Analyzing the origin and diversity of numerous genomic sequences, such as those sampled from the human microbiome, is an important first step in genomic analysis. The use of normalized compression distance (NCD) has demonstrated capabilities in the field of text classification as a low-resource alternative to deep neural networks (DNNs) by leveraging compression algorithms to approximate Kolmogorov information distance. In an effort to apply this technique toward genomics tasks akin to tools such as Many-against-Many sequence searching (MMseqs) and Kraken2, we have explored the use of a gzip-based NCD combination in both gene labeling of open reading frames (ORFs) and taxonomic classification of short reads. Our implementation achieved 0.89 accuracy and 0.88 macro-F1 on human gene classification, surpassing similar NCD-based approaches. In prokaryotic gene labeling tasks, NCD shows superior classification accuracy to traditional alignment or exact-match tools in out-of-distribution settings, while also outperforming comparable sequence-embedding methods in in-distribution classification. However, the computational complexity of O(MN) (in standard big-O notation, where M and N denote the sizes of the training and test databases, respectively) constrains scalability to very large datasets, though these findings nonetheless demonstrate that compression-based approaches provide an effective alternative for genomic sequence classification, particularly in low-data environments.
bibliographic citation: Hearne et al. (2026) Normalized compression distance for DNA classification. PeerJ 14:e20677 https://doi.org/10.7717/peerj.20677
date submitted: 2025-06-11
date accepted: 2025-12-04
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hearne
  given name: Gavin
author list: Agent
  family name: S. Refahi
  given name: Mohammadsaleh
author list: Agent
  family name: Duan
  given name: Haozhe (Neil)
author list: Agent
  family name: Brown
  given name: James R.
author list: Agent
  family name: Rosen
  given name: Gail L.
doi: 10.7717/peerj.20677
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: ©2026 Hearne et al.
attribution name: Hearne et al.

Single cell atlas of the comorbidity mechanism between chronic obstructive pulmonary disease and lung adenocarcinoma: a study of multi-omics combined analysis
type: item
type: AcademicArticle
description: Purpose Chronic obstructive pulmonary disease (COPD) is a recognized risk factor for lung adenocarcinoma (LUAD), but the molecular mechanisms behind this association are still unclear. This study aims to reveal shared key genes and pathways involved in both COPD and LUAD, and identify potential biomarkers and therapeutic targets. Methods Two-sample Mendelian randomization (MR) analysis using Genome-Wide Association Study (GWAS) data was performed to evaluate genetic causality. Differential expression analysis was performed on GSE76925 (COPD) and GSE116959 (LUAD), followed by LASSO regression, enrichment analysis, immune cell infiltration analysis, RNA modification analysis, competing endogenous RNA (ceRNA) network construction, and drug sensitivity prediction. Single-cell RNA sequencing data (GSE270667, GSE189357) were used to explore cell-type-specific expression, and qPCR was performed to validate gene expression in patient blood samples. Results MR confirmed the genetic relationship between COPD and LUAD. Three key genes (FCRLA, GREM1, and MMP9) were significantly upregulated and involved in immune regulation, extracellular matrix (ECM) remodeling, and the PI3K-Akt signaling pathway. Single-cell analysis revealed that these genes were specifically expressed in B cells, T cells, and monocytes. Multiple omics analyses indicated epigenetic and RNA level regulation. Several candidate drugs have been identified. Conclusion FCRLA, GREM1, and MMP9 are inflammation-associated genes that may link the pathobiology of COPD and LUAD, and serve as valuable biomarkers with therapeutic potential in high-risk populations.
format: application/pdf
format: text/html
creator: Meng Li
creator: Binyu Wang
creator: Qian Peng
creator: Weiyun Shen
creator: Danfei Shi
creator: Xinmin Li
creator: Daojun Yu
creator: Yong Li
subject: Bioinformatics
subject: Immunology
subject: Oncology
subject: Respiratory Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20672
publisher: PeerJ Inc.
rights: © 2026 Li et al.
abstract: Purpose Chronic obstructive pulmonary disease (COPD) is a recognized risk factor for lung adenocarcinoma (LUAD), but the molecular mechanisms behind this association are still unclear. This study aims to reveal shared key genes and pathways involved in both COPD and LUAD, and identify potential biomarkers and therapeutic targets. Methods Two-sample Mendelian randomization (MR) analysis using Genome-Wide Association Study (GWAS) data was performed to evaluate genetic causality. Differential expression analysis was performed on GSE76925 (COPD) and GSE116959 (LUAD), followed by LASSO regression, enrichment analysis, immune cell infiltration analysis, RNA modification analysis, competing endogenous RNA (ceRNA) network construction, and drug sensitivity prediction. Single-cell RNA sequencing data (GSE270667, GSE189357) were used to explore cell-type-specific expression, and qPCR was performed to validate gene expression in patient blood samples. Results MR confirmed the genetic relationship between COPD and LUAD. Three key genes (FCRLA, GREM1, and MMP9) were significantly upregulated and involved in immune regulation, extracellular matrix (ECM) remodeling, and the PI3K-Akt signaling pathway. Single-cell analysis revealed that these genes were specifically expressed in B cells, T cells, and monocytes. Multiple omics analyses indicated epigenetic and RNA level regulation. Several candidate drugs have been identified. Conclusion FCRLA, GREM1, and MMP9 are inflammation-associated genes that may link the pathobiology of COPD and LUAD, and serve as valuable biomarkers with therapeutic potential in high-risk populations.
bibliographic citation: Li et al. (2026) Single cell atlas of the comorbidity mechanism between chronic obstructive pulmonary disease and lung adenocarcinoma: a study of multi-omics combined analysis. PeerJ 14:e20672 https://doi.org/10.7717/peerj.20672
date submitted: 2025-08-07
date accepted: 2025-12-04
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Meng
author list: Agent
  family name: Wang
  given name: Binyu
author list: Agent
  family name: Peng
  given name: Qian
author list: Agent
  family name: Shen
  given name: Weiyun
author list: Agent
  family name: Shi
  given name: Danfei
author list: Agent
  family name: Li
  given name: Xinmin
author list: Agent
  family name: Yu
  given name: Daojun
author list: Agent
  family name: Li
  given name: Yong
doi: 10.7717/peerj.20672
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: © 2026 Li et al.
attribution name: Li et al.

Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing
type: item
type: AcademicArticle
description: Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.
format: application/pdf
format: text/html
creator: Chakrit Bunyoo
creator: Juthaporn Phonmakham
creator: Masaaki Morikawa
creator: Arinthip Thamchaipenet
subject: Bioinformatics
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.20648
publisher: PeerJ Inc.
rights: © 2026 Bunyoo et al.
abstract: Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.
bibliographic citation: Bunyoo et al. (2026) Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing. PeerJ 14:e20648 https://doi.org/10.7717/peerj.20648
date submitted: 2025-08-21
date accepted: 2025-12-01
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bunyoo
  given name: Chakrit
author list: Agent
  family name: Phonmakham
  given name: Juthaporn
author list: Agent
  family name: Morikawa
  given name: Masaaki
author list: Agent
  family name: Thamchaipenet
  given name: Arinthip
doi: 10.7717/peerj.20648
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: ©2026 Bunyoo et al.
attribution name: Bunyoo et al.

Comparative efficacy and safety of Cohen versus Lich-Gregoir ureteral reimplantation in pediatric vesicoureteral reflux: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Cohen and Lich-Gregoir ureteral reimplantation techniques are the most commonly used surgical approaches for correcting vesicoureteral reflux (VUR) in children. While both techniques aim to restore the anti-reflux mechanism by lengthening the intramural ureter, their comparative efficacy and safety remain controversial. This meta-analysis aimed to systematically evaluate and compare the perioperative outcomes and postoperative complications of the Cohen and Lich-Gregoir procedures in pediatric patients with VUR. Methods A systematic search of PubMed, Embase, Cochrane Library, CNKI, Wanfang, and VIP databases was conducted in May 2025 following PRISMA guidelines, registered under PROSPERO (CRD420251058493). Studies comparing Cohen and Lich-Gregoir techniques in pediatric VUR were included. Meta-analysis was performed using RevMan 5.3. Subgroup analyses were conducted for unilateral and bilateral VUR. Results Eight retrospective studies involving 1,314 patients were included. Overall, the Lich-Gregoir technique was associated with shorter operative time (MD: 22.37 min, 95% CI [11.34–33.40]) and reduced hospital stay (MD: 2.65 days, 95% CI [1.59–3.71]). It also demonstrated lower risks of bladder spasms (OR: 5.93), hematuria (OR: 21.42), and overall complications. No significant differences were observed in postoperative catheter duration, persistent VUR, or urinary tract infection. Subgroup results were consistent with the overall findings. Conclusions Compared to the Cohen technique, Lich-Gregoir reimplantation may offer advantages in operative efficiency and complication profile, especially in bilateral cases. These findings provide clinical insight but require further confirmation through high-quality prospective studies.
format: application/pdf
format: text/html
creator: Min Wang
creator: Yu Xi
creator: Nanxiang Huang
creator: Li Zhang
creator: Jinlong Liu
subject: Evidence Based Medicine
subject: Pediatrics
subject: Surgery and Surgical Specialties
subject: Urology
description: doi:10.7717/peerj.20636
publisher: PeerJ Inc.
rights: © 2026 Wang et al.
abstract: Background Cohen and Lich-Gregoir ureteral reimplantation techniques are the most commonly used surgical approaches for correcting vesicoureteral reflux (VUR) in children. While both techniques aim to restore the anti-reflux mechanism by lengthening the intramural ureter, their comparative efficacy and safety remain controversial. This meta-analysis aimed to systematically evaluate and compare the perioperative outcomes and postoperative complications of the Cohen and Lich-Gregoir procedures in pediatric patients with VUR. Methods A systematic search of PubMed, Embase, Cochrane Library, CNKI, Wanfang, and VIP databases was conducted in May 2025 following PRISMA guidelines, registered under PROSPERO (CRD420251058493). Studies comparing Cohen and Lich-Gregoir techniques in pediatric VUR were included. Meta-analysis was performed using RevMan 5.3. Subgroup analyses were conducted for unilateral and bilateral VUR. Results Eight retrospective studies involving 1,314 patients were included. Overall, the Lich-Gregoir technique was associated with shorter operative time (MD: 22.37 min, 95% CI [11.34–33.40]) and reduced hospital stay (MD: 2.65 days, 95% CI [1.59–3.71]). It also demonstrated lower risks of bladder spasms (OR: 5.93), hematuria (OR: 21.42), and overall complications. No significant differences were observed in postoperative catheter duration, persistent VUR, or urinary tract infection. Subgroup results were consistent with the overall findings. Conclusions Compared to the Cohen technique, Lich-Gregoir reimplantation may offer advantages in operative efficiency and complication profile, especially in bilateral cases. These findings provide clinical insight but require further confirmation through high-quality prospective studies.
bibliographic citation: Wang et al. (2026) Comparative efficacy and safety of Cohen versus Lich-Gregoir ureteral reimplantation in pediatric vesicoureteral reflux: a systematic review and meta-analysis. PeerJ 14:e20636 https://doi.org/10.7717/peerj.20636
date submitted: 2025-07-02
date accepted: 2025-11-30
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Min
author list: Agent
  family name: Xi
  given name: Yu
author list: Agent
  family name: Huang
  given name: Nanxiang
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Liu
  given name: Jinlong
doi: 10.7717/peerj.20636
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: ©2026 Wang et al.
attribution name: Wang et al.

Localized low muscle mass is associated with hand dysfunction beyond inflammation in rheumatoid arthritis: a cross-sectional study
type: item
type: AcademicArticle
description: Background While systemic muscle loss is associated with physical dysfunction, the role of localized upper extremities muscle deterioration in hand disability remains unclear in rheumatoid arthritis (RA). We aimed to explore the impact of low muscle mass in upper extremities on hand dysfunction in patients with RA. Methods This cross-sectional study was conducted in a Chinese RA population and control subjects. Demographic and clinical data were collected. Hand function assessment included handgrip strength and hand disability according to the Stanford Health Assessment Questionnaire-Disability Index (HAQ-DI). Muscle mass was assessed using bioelectrical impedance analysis and muscle mass index of upper extremities (MMIUE) was calculated. Logistic regression analyses evaluated associations between MMIUE and hand dysfunction. Results A total of 1,104 RA patients and 3,281 control subjects were included in this study. RA patients exhibited lower MMIUE compared with controls (1.42 ± 0.32 vs. 1.73 ± 0.40 kg/m2, P < 0.001). The prevalence of low MMIUE was higher in RA patients (45.9%, 507/1104) than in controls (14.5%, 475/3,281, P < 0.001). Among RA patients, 57.2% (632/1,104) had low handgrip strength and 39.6% (437/1,104) had HAQ-DI hand disability. RA patients with low MMIUE showed significantly poorer hand function than those with normal MMIUE, including lower handgrip strength (14.59 ± 6.78 vs. 18.67 ± 8.14 kg), higher prevalence of low handgrip strength (70.0% vs. 46.4%) and HAQ-DI hand disability (46.9% vs. 33.3%, all P < 0.001) than those with normal MMIUE. Logistic regression analyses showed that RA patients with low MMIUE had higher risks of low handgrip strength (AOR = 2.44, 95% CI [1.84–3.23], P < 0.001) and HAQ-DI hand disability (AOR = 1.59, 95% CI [1.15–2.19], P = 0.005). Conclusions The present cross-sectional study demonstrates that localized low muscle mass of the upper extremities is associated with hand dysfunction in RA, independent of inflammation.…
format: application/pdf
format: text/html
creator: Ying Yang
creator: Yao-Wei Zou
creator: Ye Lu
creator: Tao Wu
creator: Zhi-Ming Ouyang
creator: Pei-Wen Jia
creator: Ya-Nan Cao
creator: Yu-Ting Fan
creator: PuiU Lam
creator: Ran Shi
creator: Jian-Zi Lin
creator: Kui-Min Yang
creator: Jian-Da Ma
creator: Lie Dai
subject: Nutrition
subject: Rheumatology
subject: Rehabilitation
description: doi:10.7717/peerj.20629
publisher: PeerJ Inc.
rights: © 2026 Yang et al.
abstract: Background While systemic muscle loss is associated with physical dysfunction, the role of localized upper extremities muscle deterioration in hand disability remains unclear in rheumatoid arthritis (RA). We aimed to explore the impact of low muscle mass in upper extremities on hand dysfunction in patients with RA. Methods This cross-sectional study was conducted in a Chinese RA population and control subjects. Demographic and clinical data were collected. Hand function assessment included handgrip strength and hand disability according to the Stanford Health Assessment Questionnaire-Disability Index (HAQ-DI). Muscle mass was assessed using bioelectrical impedance analysis and muscle mass index of upper extremities (MMIUE) was calculated. Logistic regression analyses evaluated associations between MMIUE and hand dysfunction. Results A total of 1,104 RA patients and 3,281 control subjects were included in this study. RA patients exhibited lower MMIUE compared with controls (1.42 ± 0.32 vs. 1.73 ± 0.40 kg/m2, P < 0.001). The prevalence of low MMIUE was higher in RA patients (45.9%, 507/1104) than in controls (14.5%, 475/3,281, P < 0.001). Among RA patients, 57.2% (632/1,104) had low handgrip strength and 39.6% (437/1,104) had HAQ-DI hand disability. RA patients with low MMIUE showed significantly poorer hand function than those with normal MMIUE, including lower handgrip strength (14.59 ± 6.78 vs. 18.67 ± 8.14 kg), higher prevalence of low handgrip strength (70.0% vs. 46.4%) and HAQ-DI hand disability (46.9% vs. 33.3%, all P < 0.001) than those with normal MMIUE. Logistic regression analyses showed that RA patients with low MMIUE had higher risks of low handgrip strength (AOR = 2.44, 95% CI [1.84–3.23], P < 0.001) and HAQ-DI hand disability (AOR = 1.59, 95% CI [1.15–2.19], P = 0.005). Conclusions The present cross-sectional study demonstrates that localized low muscle mass of the upper extremities is associated with hand dysfunction in RA, independent of inflammation.…
bibliographic citation: Yang et al. (2026) Localized low muscle mass is associated with hand dysfunction beyond inflammation in rheumatoid arthritis: a cross-sectional study. PeerJ 14:e20629 https://doi.org/10.7717/peerj.20629
date submitted: 2025-05-01
date accepted: 2025-11-30
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yang
  given name: Ying
author list: Agent
  family name: Zou
  given name: Yao-Wei
author list: Agent
  family name: Lu
  given name: Ye
author list: Agent
  family name: Wu
  given name: Tao
author list: Agent
  family name: Ouyang
  given name: Zhi-Ming
author list: Agent
  family name: Jia
  given name: Pei-Wen
author list: Agent
  family name: Cao
  given name: Ya-Nan
author list: Agent
  family name: Fan
  given name: Yu-Ting
author list: Agent
  family name: Lam
  given name: PuiU
author list: Agent
  family name: Shi
  given name: Ran
author list: Agent
  family name: Lin
  given name: Jian-Zi
author list: Agent
  family name: Yang
  given name: Kui-Min
author list: Agent
  family name: Ma
  given name: Jian-Da
author list: Agent
  family name: Dai
  given name: Lie
doi: 10.7717/peerj.20629
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: ©2026 Yang et al.
attribution name: Yang et al.

Difference in effects of open and closed motor skills on energy expenditure and after-burn effect in college student within physical classes
type: item
type: AcademicArticle
description: Introduction Metabolic health is closely related to physical activity, and different types of motor skills may induce distinct physiological responses. To investigate the differences in energy expenditure and substrate metabolic characteristics between university students engaged in closed motor skills and open motor skills physical education classes, and to provide exercise prescription and theoretical reference for metabolic health promotion. Methods Thirty-six male university students (n = 36, year = 20.83 ± 1.98) were recruited and asked to perform sequential open motor skills exercise (cricket practice, time = 40 min) and closed motor skills exercise (closed motor skills, time = 40 min) during university physical education classes. Resting energy expenditure (REE), exercise energy expenditure (EEE), energy expenditure rate (EER), respiratory quotient (RQ), fat energy supply rate (FESR), fat energy supply proportion (FESP), fat oxidation amount (FOA), fat oxidation rate (FOR), sugar energy supply rate (SESR), sugar energy supply proportion (SESP), sugar oxidation amount (SOA), sugar oxidation rate (SOR), rating of perceived exertion (RPE) and feeling scale (FS) was measured before exercise, during exercise in class, during a 3-h recovery period after class, and for 4 consecutive days after class. Results EEE, FOA, and FESP were significantly lower (P < 0.01) for open motor skills but higher (P < 0.01) for SESP than for closed motor skills during in-class practice. Within 3 h of recovery after class, EEE, FOA, FESP, and FS were significantly higher for open motor skills than for closed motor skills (P < 0.05), but lower for SOA, SOA, SESP, and RPE than for closed motor skills (P < 0.01). Within 4 consecutive days after training, the REE for open motor skills was higher than pre-training (P < 0.05) on days 1 and 2, and higher than closed motor skills (P < 0.05) on day 1. The RQ of open motor skills was lower than that of pre-exercise and closed motor skills on day…
format: application/pdf
format: text/html
creator: Xue Sun
creator: Kuo Li
creator: Yan Cao
creator: Tao Zhang
creator: Fang Yuan
subject: Kinesiology
subject: Nutrition
subject: Metabolic Sciences
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20562
publisher: PeerJ Inc.
rights: © 2026 Sun et al.
abstract: Introduction Metabolic health is closely related to physical activity, and different types of motor skills may induce distinct physiological responses. To investigate the differences in energy expenditure and substrate metabolic characteristics between university students engaged in closed motor skills and open motor skills physical education classes, and to provide exercise prescription and theoretical reference for metabolic health promotion. Methods Thirty-six male university students (n = 36, year = 20.83 ± 1.98) were recruited and asked to perform sequential open motor skills exercise (cricket practice, time = 40 min) and closed motor skills exercise (closed motor skills, time = 40 min) during university physical education classes. Resting energy expenditure (REE), exercise energy expenditure (EEE), energy expenditure rate (EER), respiratory quotient (RQ), fat energy supply rate (FESR), fat energy supply proportion (FESP), fat oxidation amount (FOA), fat oxidation rate (FOR), sugar energy supply rate (SESR), sugar energy supply proportion (SESP), sugar oxidation amount (SOA), sugar oxidation rate (SOR), rating of perceived exertion (RPE) and feeling scale (FS) was measured before exercise, during exercise in class, during a 3-h recovery period after class, and for 4 consecutive days after class. Results EEE, FOA, and FESP were significantly lower (P < 0.01) for open motor skills but higher (P < 0.01) for SESP than for closed motor skills during in-class practice. Within 3 h of recovery after class, EEE, FOA, FESP, and FS were significantly higher for open motor skills than for closed motor skills (P < 0.05), but lower for SOA, SOA, SESP, and RPE than for closed motor skills (P < 0.01). Within 4 consecutive days after training, the REE for open motor skills was higher than pre-training (P < 0.05) on days 1 and 2, and higher than closed motor skills (P < 0.05) on day 1. The RQ of open motor skills was lower than that of pre-exercise and closed motor skills on day…
bibliographic citation: Sun et al. (2026) Difference in effects of open and closed motor skills on energy expenditure and after-burn effect in college student within physical classes. PeerJ 14:e20562 https://doi.org/10.7717/peerj.20562
date submitted: 2025-05-22
date accepted: 2025-11-19
issued: 2026-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xue
author list: Agent
  family name: Li
  given name: Kuo
author list: Agent
  family name: Cao
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Tao
author list: Agent
  family name: Yuan
  given name: Fang
doi: 10.7717/peerj.20562
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-06
copyright: © 2026 Sun et al.
attribution name: Sun et al.

Effects of playing experience on joint kinetics and ball-release velocity in mid- and long-range basketball jump shots
type: item
type: AcademicArticle
description: Purpose This study investigated how playing experience influences joint kinetics and ball-release velocity during mid- and long-range jump shots. Wrist, elbow, shoulder and knee rate of torque development (RTD), peak power (Ppeak), and angular impulse (AI) were quantified, along with vertical release velocity (VV) and horizontal release velocity (HV) at release. Methods In a cross-sectional design, 15 experienced and 15 novice male collegiate basketball players each performed three made jump shots from 4.8 m and 6.75 m. A 3-D motion-capture system synchronised with force plates provided the data used to compute RTD, Ppeak, AI, VV and HV. Outcomes were compared with a two-way mixed ANOVA. Results Experienced players exhibited greater wrist AI (p < 0.001), elbow RTD (p = 0.002), Ppeak (p = 0.045) and AI (p < 0.001), knee Ppeak (p = 0.002) and VV (p < 0.001). Longer shooting distance increased shoulder Ppeak (p = 0.036) and HV (p = 0.018). Conclusions Collectively, these results show that experience enhances joint kinetic output, providing the mechanical foundation for more efficient and dependable shooting. For novice players, emphasising wrist-endurance work, explosive-power training for the elbow and knee, and targeted drills to raise VV is recommended to improve overall on-court shooting performance.
format: application/pdf
format: text/html
creator: Pengzhou Chen
creator: Tao Chen
creator: Xuan Tang
creator: Ming Li
creator: Xiangjun Miao
subject: Kinesiology
subject: Biomechanics
description: doi:10.7717/peerj.20757
publisher: PeerJ Inc.
rights: © 2026 Chen et al.
abstract: Purpose This study investigated how playing experience influences joint kinetics and ball-release velocity during mid- and long-range jump shots. Wrist, elbow, shoulder and knee rate of torque development (RTD), peak power (Ppeak), and angular impulse (AI) were quantified, along with vertical release velocity (VV) and horizontal release velocity (HV) at release. Methods In a cross-sectional design, 15 experienced and 15 novice male collegiate basketball players each performed three made jump shots from 4.8 m and 6.75 m. A 3-D motion-capture system synchronised with force plates provided the data used to compute RTD, Ppeak, AI, VV and HV. Outcomes were compared with a two-way mixed ANOVA. Results Experienced players exhibited greater wrist AI (p < 0.001), elbow RTD (p = 0.002), Ppeak (p = 0.045) and AI (p < 0.001), knee Ppeak (p = 0.002) and VV (p < 0.001). Longer shooting distance increased shoulder Ppeak (p = 0.036) and HV (p = 0.018). Conclusions Collectively, these results show that experience enhances joint kinetic output, providing the mechanical foundation for more efficient and dependable shooting. For novice players, emphasising wrist-endurance work, explosive-power training for the elbow and knee, and targeted drills to raise VV is recommended to improve overall on-court shooting performance.
bibliographic citation: Chen et al. (2026) Effects of playing experience on joint kinetics and ball-release velocity in mid- and long-range basketball jump shots. PeerJ 14:e20757 https://doi.org/10.7717/peerj.20757
date submitted: 2025-09-26
date accepted: 2025-12-17
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Pengzhou
author list: Agent
  family name: Chen
  given name: Tao
author list: Agent
  family name: Tang
  given name: Xuan
author list: Agent
  family name: Li
  given name: Ming
author list: Agent
  family name: Miao
  given name: Xiangjun
doi: 10.7717/peerj.20757
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Chen et al.
attribution name: Chen et al.

Litter thickness limits the seed germination and seedling growth of Rhododendron plants
type: item
type: AcademicArticle
description: Litter is considered a major constraint that affects the sexual reproduction and regeneration of populations of Rhododendron seedlings. In this study, we analyzed the effects of litter accumulation and its allelopathy on the regeneration potential of four Rhododendron species, and investigated the impacts of different litter amounts and coverage methods on Rhododendron seed germination through indoor pot experiments. The results showed that low amounts of litter promoted the rate of emergence of seedlings, while high amounts of litter inhibited this process. The rate of emergence of Rhododendron reached its maximum value when the amount of litter was between 200 and 400 g/m2 . The seeds of four species of Rhododendron began to germinate between days 7 and 8 of the experiment. The duration of germination for the four Rhododendron species ranged from 8 to 11 days. Extracts from different decomposition layers of litter had a “suppressive” effect or a “low promotion and high inhibition” effect on the germination rates of four species of Rhododendron. The litter extract inhibited the germination of Rhododendron decorum and Rhododendron delavayi at 2 mg/mL of extract, while it promoted the germination of Rhododendron irroratum and Rhododendron agastum seeds. Therefore, the presence of litter under Rhododendron shrubs in Northwest Guizhou Province, China, likely reduces the germination of the populations of Rhododendron and may limit their renewal through sexual reproduction. Thus, this study suggests that the presence of litter under Rhododendron shrubs in Northwest Guizhou Province may significantly limit their reproduction by seeds.
format: application/pdf
format: text/html
creator: Zijing Niu
creator: Yuefeng Wang
creator: Xuechun Zhao
subject: Biodiversity
subject: Conservation Biology
subject: Developmental Biology
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.20756
publisher: PeerJ Inc.
rights: © 2026 Niu et al.
abstract: Litter is considered a major constraint that affects the sexual reproduction and regeneration of populations of Rhododendron seedlings. In this study, we analyzed the effects of litter accumulation and its allelopathy on the regeneration potential of four Rhododendron species, and investigated the impacts of different litter amounts and coverage methods on Rhododendron seed germination through indoor pot experiments. The results showed that low amounts of litter promoted the rate of emergence of seedlings, while high amounts of litter inhibited this process. The rate of emergence of Rhododendron reached its maximum value when the amount of litter was between 200 and 400 g/m2 . The seeds of four species of Rhododendron began to germinate between days 7 and 8 of the experiment. The duration of germination for the four Rhododendron species ranged from 8 to 11 days. Extracts from different decomposition layers of litter had a “suppressive” effect or a “low promotion and high inhibition” effect on the germination rates of four species of Rhododendron. The litter extract inhibited the germination of Rhododendron decorum and Rhododendron delavayi at 2 mg/mL of extract, while it promoted the germination of Rhododendron irroratum and Rhododendron agastum seeds. Therefore, the presence of litter under Rhododendron shrubs in Northwest Guizhou Province, China, likely reduces the germination of the populations of Rhododendron and may limit their renewal through sexual reproduction. Thus, this study suggests that the presence of litter under Rhododendron shrubs in Northwest Guizhou Province may significantly limit their reproduction by seeds.
bibliographic citation: Niu et al. (2026) Litter thickness limits the seed germination and seedling growth of Rhododendron plants. PeerJ 14:e20756 https://doi.org/10.7717/peerj.20756
date submitted: 2025-09-23
date accepted: 2025-12-17
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Zijing
author list: Agent
  family name: Wang
  given name: Yuefeng
author list: Agent
  family name: Zhao
  given name: Xuechun
doi: 10.7717/peerj.20756
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: © 2026 Niu et al.
attribution name: Niu et al.

Effects of exercise interventions on memory in depression: a three-level meta-analysis
type: item
type: AcademicArticle
description: Background Patients with depression have memory impairment. Exercise can improve memory in people with depression. This study employs a three-level meta-analysis to investigate the interventional effects of exercise on verbal and visual memory in patients with depression. Methods A systematic electronic search was conducted in China National Knowledge Infrastructure, Wanfang Data, China Biomedicine, PubMed, EMBASE, the Cochrane Library, and Web of Science to identify randomized controlled trials investigating the effects of exercise interventions on memory in individuals with depression, up to July 18, 2024. A three-level meta-analysis based on a random-effects model was performed using R. The risk of bias of the included studies was assessed using the Cochrane Risk of Bias 2 (RoB 2) tool. Results A total of 16 studies were included in the analysis. The results indicated a statistically significant but small effect of exercise on verbal memory in patients with depression (g = 0.17, 95% confidence interval (CI) [0.02–0.32], p = 0.03); however, the 95% prediction interval crossed zero, suggesting that the effect may not be consistent across different settings or future studies; however, the 95% prediction interval crossed zero, suggesting that the effect may not be consistent across different settings or future studies (g = 0.27, 95% CI [−0.00–0.54], p = 0.05). Exercise intensity significantly moderated the effect of exercise on verbal memory in patients with depression (F = 3.39, p = 0.04), whereas exercise type, session time, duration, age, and intervention content of the experimental group were not moderating factors (p > 0.05). Low-to-moderate intensity (g = 0.43, p < 0.01), duration ≤12 weeks (g = 0.27, p < 0.01), and session time ≤60 minutes (g = 0.18, p = 0.03) of mind-body exercise (g = 0.43, p < 0.01) were most likely to improve verbal memory in patients with depression. The level of evidence was “moderate”. Conclusions Exercise may confer a small improvement…
format: application/pdf
format: text/html
creator: Xiaoling Zhu
creator: Yunong Zhang
creator: Cong Liu
creator: Xing Wang
subject: Cognitive Disorders
subject: Evidence Based Medicine
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20750
publisher: PeerJ Inc.
rights: © 2026 Zhu et al.
abstract: Background Patients with depression have memory impairment. Exercise can improve memory in people with depression. This study employs a three-level meta-analysis to investigate the interventional effects of exercise on verbal and visual memory in patients with depression. Methods A systematic electronic search was conducted in China National Knowledge Infrastructure, Wanfang Data, China Biomedicine, PubMed, EMBASE, the Cochrane Library, and Web of Science to identify randomized controlled trials investigating the effects of exercise interventions on memory in individuals with depression, up to July 18, 2024. A three-level meta-analysis based on a random-effects model was performed using R. The risk of bias of the included studies was assessed using the Cochrane Risk of Bias 2 (RoB 2) tool. Results A total of 16 studies were included in the analysis. The results indicated a statistically significant but small effect of exercise on verbal memory in patients with depression (g = 0.17, 95% confidence interval (CI) [0.02–0.32], p = 0.03); however, the 95% prediction interval crossed zero, suggesting that the effect may not be consistent across different settings or future studies; however, the 95% prediction interval crossed zero, suggesting that the effect may not be consistent across different settings or future studies (g = 0.27, 95% CI [−0.00–0.54], p = 0.05). Exercise intensity significantly moderated the effect of exercise on verbal memory in patients with depression (F = 3.39, p = 0.04), whereas exercise type, session time, duration, age, and intervention content of the experimental group were not moderating factors (p > 0.05). Low-to-moderate intensity (g = 0.43, p < 0.01), duration ≤12 weeks (g = 0.27, p < 0.01), and session time ≤60 minutes (g = 0.18, p = 0.03) of mind-body exercise (g = 0.43, p < 0.01) were most likely to improve verbal memory in patients with depression. The level of evidence was “moderate”. Conclusions Exercise may confer a small improvement…
bibliographic citation: Zhu et al. (2026) Effects of exercise interventions on memory in depression: a three-level meta-analysis. PeerJ 14:e20750 https://doi.org/10.7717/peerj.20750
date submitted: 2025-03-13
date accepted: 2025-12-16
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Xiaoling
author list: Agent
  family name: Zhang
  given name: Yunong
author list: Agent
  family name: Liu
  given name: Cong
author list: Agent
  family name: Wang
  given name: Xing
doi: 10.7717/peerj.20750
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Zhu et al.
attribution name: Zhu et al.

A network meta-analysis of interventions for anxiety and depression in PCOS
type: item
type: AcademicArticle
description: Background The study aimed to provide evidence to support optimal interventions for alleviating anxiety and depression symptoms in patients with polycystic ovarian syndrome (PCOS) through a systematic review and network meta-analysis. Methods A comprehensive literature search of PubMed, Embase, Cochrane Library, and Web of Science from their inceptions to January 2, 2025 was performed. The criteria for inclusion defined were as follows: (1) The study population consisted of female PCOS patients; (2) interventions included psychological therapy, exercise, drug treatment, or digital intervention; (3) studies that reported changes in anxiety and depression scores; and (4) randomized controlled trials (RCTs). Two reviewers independently screened the literature and extracted the data. Disagreements were resolved by consulting a third party. Standardized mean difference (SMD) was used for data recording in this study. The analysis of data was carried out based on a random-effects model, while network meta-analysis was implemented through R 4.4.0 and Just Another Gibbs Sampler (JAGS) 4.3.1. We conducted a Bayesian random-effects network meta-analysis (NMA) and ranked interventions using the surface under the cumulative ranking curve (SUCRA). Results This study included a total of 25 RCTs, involving 1,453 female PCOS patients, to evaluate the effects of various interventions in alleviating anxiety and depression symptoms. Effective interventions included emotion-focused therapy (EFT), peer support (PS), omega-3 plus vitamin E (O3+VE), and mindfulness stress management (MSM). Other interventions, such as metformin and vitamin D plus probiotics (VD+Pro), showed no significant benefit compared with control. Data on PS for anxiety were not analyzed in the present network meta-analysis because relevant trials could not be connected within the network structure. Conclusion Our study demonstrates that EFT and PS emerge as promising interventions in alleviating anxiety and depressi…
format: application/pdf
format: text/html
creator: Zuolin Tan
creator: Yunqing Li
creator: Jingyuan Liu
creator: Xinyin Hu
creator: Xuhan Su
creator: Yuhua Huang
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Women’s Health
description: doi:10.7717/peerj.20744
publisher: PeerJ Inc.
rights: © 2026 Tan et al.
abstract: Background The study aimed to provide evidence to support optimal interventions for alleviating anxiety and depression symptoms in patients with polycystic ovarian syndrome (PCOS) through a systematic review and network meta-analysis. Methods A comprehensive literature search of PubMed, Embase, Cochrane Library, and Web of Science from their inceptions to January 2, 2025 was performed. The criteria for inclusion defined were as follows: (1) The study population consisted of female PCOS patients; (2) interventions included psychological therapy, exercise, drug treatment, or digital intervention; (3) studies that reported changes in anxiety and depression scores; and (4) randomized controlled trials (RCTs). Two reviewers independently screened the literature and extracted the data. Disagreements were resolved by consulting a third party. Standardized mean difference (SMD) was used for data recording in this study. The analysis of data was carried out based on a random-effects model, while network meta-analysis was implemented through R 4.4.0 and Just Another Gibbs Sampler (JAGS) 4.3.1. We conducted a Bayesian random-effects network meta-analysis (NMA) and ranked interventions using the surface under the cumulative ranking curve (SUCRA). Results This study included a total of 25 RCTs, involving 1,453 female PCOS patients, to evaluate the effects of various interventions in alleviating anxiety and depression symptoms. Effective interventions included emotion-focused therapy (EFT), peer support (PS), omega-3 plus vitamin E (O3+VE), and mindfulness stress management (MSM). Other interventions, such as metformin and vitamin D plus probiotics (VD+Pro), showed no significant benefit compared with control. Data on PS for anxiety were not analyzed in the present network meta-analysis because relevant trials could not be connected within the network structure. Conclusion Our study demonstrates that EFT and PS emerge as promising interventions in alleviating anxiety and depressi…
bibliographic citation: Tan et al. (2026) A network meta-analysis of interventions for anxiety and depression in PCOS. PeerJ 14:e20744 https://doi.org/10.7717/peerj.20744
date submitted: 2025-03-21
date accepted: 2025-12-17
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Zuolin
author list: Agent
  family name: Li
  given name: Yunqing
author list: Agent
  family name: Liu
  given name: Jingyuan
author list: Agent
  family name: Hu
  given name: Xinyin
author list: Agent
  family name: Su
  given name: Xuhan
author list: Agent
  family name: Huang
  given name: Yuhua
doi: 10.7717/peerj.20744
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Tan et al.
attribution name: Tan et al.

Divergent response of soil microbial community abundance and composition to fertilization in Camellia oleifera plantation, Southern China
type: item
type: AcademicArticle
description: Introduction Alterations in the composition and structure of the soil microbial community exert a substantial impact on soil nutrient cycling and fertility. Implementing sustainable land use strategies involves a deeper comprehension of the dynamics of the soil microbial community under different fertilization approaches. Methods Phospholipid fatty acid (PLFA) method was employed to characterize soil microbial community abundance and structure under four fertilization treatments (no fertilizer (CK), 100% mineral fertilizer (NPK), 30% organic fertilizer + 70% mineral fertilizer (LOM), and 60% organic fertilizer + 40% mineral fertilizer (HOM)) in a Camellia oleifera plantation area in southern China. Results Fertilization application substantially increased the Camellia oleifera yields, with the highest increment observed under the HOM treatment. Soil organic carbon and total nitrogen levels were significantly increased in LOM and HOM treatments as compared to CK. Total PLFAs absolute abundance in LOM and HOM treatments increased by 68.45% and 85.38%, respectively, compared to CK treatment. Furthermore, the absolute abundances of bacteria, fungi, and actinomycetes, as well as total PLFAs, were markedly enhanced in HOM and LOM treatments but not in the NPK treatment relative to CK treatment. There was less distinction observed in the microbial community structure than in microbial abundance across four fertilization treatments. Soil nutrients were identified as the primary factor affecting soil microbial abundance and crop yield. These findings imply that the combined application of organic and mineral fertilization than employing solely mineral fertilization may be more effective in improving soil nutrient levels, regulating soil microbial community composition and increasing crop yield in a Camellia oleifera plantation.
format: application/pdf
format: text/html
creator: Hanfang Luo
creator: Li Wen
creator: Chao Li
creator: Kaikai Cheng
creator: Lihong Shi
creator: Ke Wang
creator: Haiming Tang
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.20741
publisher: PeerJ Inc.
rights: © 2026 Luo et al.
abstract: Introduction Alterations in the composition and structure of the soil microbial community exert a substantial impact on soil nutrient cycling and fertility. Implementing sustainable land use strategies involves a deeper comprehension of the dynamics of the soil microbial community under different fertilization approaches. Methods Phospholipid fatty acid (PLFA) method was employed to characterize soil microbial community abundance and structure under four fertilization treatments (no fertilizer (CK), 100% mineral fertilizer (NPK), 30% organic fertilizer + 70% mineral fertilizer (LOM), and 60% organic fertilizer + 40% mineral fertilizer (HOM)) in a Camellia oleifera plantation area in southern China. Results Fertilization application substantially increased the Camellia oleifera yields, with the highest increment observed under the HOM treatment. Soil organic carbon and total nitrogen levels were significantly increased in LOM and HOM treatments as compared to CK. Total PLFAs absolute abundance in LOM and HOM treatments increased by 68.45% and 85.38%, respectively, compared to CK treatment. Furthermore, the absolute abundances of bacteria, fungi, and actinomycetes, as well as total PLFAs, were markedly enhanced in HOM and LOM treatments but not in the NPK treatment relative to CK treatment. There was less distinction observed in the microbial community structure than in microbial abundance across four fertilization treatments. Soil nutrients were identified as the primary factor affecting soil microbial abundance and crop yield. These findings imply that the combined application of organic and mineral fertilization than employing solely mineral fertilization may be more effective in improving soil nutrient levels, regulating soil microbial community composition and increasing crop yield in a Camellia oleifera plantation.
bibliographic citation: Luo et al. (2026) Divergent response of soil microbial community abundance and composition to fertilization in Camellia oleifera plantation, Southern China. PeerJ 14:e20741 https://doi.org/10.7717/peerj.20741
date submitted: 2025-07-11
date accepted: 2025-12-15
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Luo
  given name: Hanfang
author list: Agent
  family name: Wen
  given name: Li
author list: Agent
  family name: Li
  given name: Chao
author list: Agent
  family name: Cheng
  given name: Kaikai
author list: Agent
  family name: Shi
  given name: Lihong
author list: Agent
  family name: Wang
  given name: Ke
author list: Agent
  family name: Tang
  given name: Haiming
doi: 10.7717/peerj.20741
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Luo et al.
attribution name: Luo et al.

Strawberry atlas: Fragaria vesca gene expression atlas for strawberry genomics
type: item
type: AcademicArticle
description: Background Fragaria vesca (woodland strawberry) is a diploid model for cultivated strawberry (Fragaria × ananassa Duch. ex Rozier). While high-quality genome assemblies exist for key accessions such as Hawaii-4 (H4) and YW5AF7/Yellow Wonder (YW), a comprehensive understanding of transcriptional regulation across tissues and genotypes has been limited. Previous expression resources focused on select organs or individual studies, limiting tissue-level comparisons. Moreover, structural variants (SVs) and transposable elements (TEs), known to shape gene expression in other plants, remain understudied in F. vesca. An integrated gene expression resource spanning multiple tissues is needed to address these gaps and support functional genomics in strawberry research. Methods After quality control that removed mutant and infected samples, 233 high-quality RNA-seq libraries covering more than 50 tissues and developmental stages were retained. These libraries were consolidated into nine tissue categories: leaf, root, anther, carpel, flower bud, seed, stem, early fruit, and late fruit (mature fruit). In-house leaf libraries were used as a reference to validate data structure and batch correction. Transcript abundance was quantified against the latest F. vesca reference genome (v6), and dimensionality reduction via UMAP was used to assess tissue clustering. Tissue-specific (TS) and housekeeping (HK) genes were identified based on fold-change, adjusted p-values, and the tau tissue specificity index. To evaluate the relationship between genome structure and expression, SVs were detected between H4 and YW using assembly- and mapping-based approaches. Genes overlapping SVs were assessed for expression trends. A web interface was developed to facilitate interactive exploration. Results The resulting expression atlas captures a certain level of expression for ∼99% of 36,173 annotated genes that include TS genes. It also reveals robust clustering by tissue, underscoring the biological …
format: application/pdf
format: text/html
creator: Minto Odagiri
creator: Chonprakun Thagun
creator: Takeshi Kurokura
creator: Tomohiro Suzuki
creator: Yutaka Kodama
creator: Yoshinori Fukasawa
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.20740
publisher: PeerJ Inc.
rights: © 2026 Odagiri et al.
abstract: Background Fragaria vesca (woodland strawberry) is a diploid model for cultivated strawberry (Fragaria × ananassa Duch. ex Rozier). While high-quality genome assemblies exist for key accessions such as Hawaii-4 (H4) and YW5AF7/Yellow Wonder (YW), a comprehensive understanding of transcriptional regulation across tissues and genotypes has been limited. Previous expression resources focused on select organs or individual studies, limiting tissue-level comparisons. Moreover, structural variants (SVs) and transposable elements (TEs), known to shape gene expression in other plants, remain understudied in F. vesca. An integrated gene expression resource spanning multiple tissues is needed to address these gaps and support functional genomics in strawberry research. Methods After quality control that removed mutant and infected samples, 233 high-quality RNA-seq libraries covering more than 50 tissues and developmental stages were retained. These libraries were consolidated into nine tissue categories: leaf, root, anther, carpel, flower bud, seed, stem, early fruit, and late fruit (mature fruit). In-house leaf libraries were used as a reference to validate data structure and batch correction. Transcript abundance was quantified against the latest F. vesca reference genome (v6), and dimensionality reduction via UMAP was used to assess tissue clustering. Tissue-specific (TS) and housekeeping (HK) genes were identified based on fold-change, adjusted p-values, and the tau tissue specificity index. To evaluate the relationship between genome structure and expression, SVs were detected between H4 and YW using assembly- and mapping-based approaches. Genes overlapping SVs were assessed for expression trends. A web interface was developed to facilitate interactive exploration. Results The resulting expression atlas captures a certain level of expression for ∼99% of 36,173 annotated genes that include TS genes. It also reveals robust clustering by tissue, underscoring the biological …
bibliographic citation: Odagiri et al. (2026) Strawberry atlas: Fragaria vesca gene expression atlas for strawberry genomics. PeerJ 14:e20740 https://doi.org/10.7717/peerj.20740
date submitted: 2025-07-28
date accepted: 2025-12-15
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Odagiri
  given name: Minto
author list: Agent
  family name: Thagun
  given name: Chonprakun
author list: Agent
  family name: Kurokura
  given name: Takeshi
author list: Agent
  family name: Suzuki
  given name: Tomohiro
author list: Agent
  family name: Kodama
  given name: Yutaka
author list: Agent
  family name: Fukasawa
  given name: Yoshinori
doi: 10.7717/peerj.20740
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Odagiri et al.
attribution name: Odagiri et al.

Morphological characterization and RNA sequencing reveal adaptive strategies of Coix lacryma-jobi L. under waterlogging stress during the jointing stage
type: item
type: AcademicArticle
description: Background Coix lacryma-jobi L. is a vital medicinal and dual-purpose crop in Guizhou, requiring optimal cultivation conditions to preserve its therapeutic properties. Waterlogging stress significantly reduces its productivity, yet the underlying molecular mechanisms remain poorly understood. Methods We investigated the species’ adaptive responses using controlled waterlogging experiments on potted plants. Morphological alterations and key growth parameters (culm diameter, plant height, dry biomass) were quantified. We performed transcriptomic profiling by RNA-Seq to identify differentially expressed genes (DEGs). To elucidate the functional implications of these DEGs, we conducted systematic enrichment analyses using the clusters of orthologous groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Expression patterns of candidate genes were validated using Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Results Flooded plants exhibited significant morphological changes, with key growth parameters decreasing by 14.4–21.8%. A pronounced adaptive response was a 76.6% increase in adventitious root formation. RNA-Seq revealed 207 DEGs (133 upregulated, 74 downregulated). Enrichment analyses indicated these DEGs were predominantly involved in photosynthetic processes, carbohydrate dynamics, and signaling pathways. qRT-PCR confirmed consistent expression patterns for six candidate genes associated with photosynthesis and carbohydrate metabolism. These findings demonstrate that Coix lacryma-jobi L. activates coordinated molecular responses, including photosynthetic efficiency adjustment and metabolic pathway remodeling, to enhance waterlogging tolerance. This work identifies critical genetic components governing waterlogging adaptation, providing molecular markers for developing stress-tolerant cultivars through targeted breeding.
format: application/pdf
format: text/html
creator: Jing Yao
creator: Zhiqing Gong
creator: Weijie Tang
creator: Mei Yuan
creator: Yunyan He
creator: Yantao Liang
creator: Weizhong Li
creator: Ke Zhong
creator: Dandan Wang
creator: Peilong He
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.20731
publisher: PeerJ Inc.
rights: © 2026 Yao et al.
abstract: Background Coix lacryma-jobi L. is a vital medicinal and dual-purpose crop in Guizhou, requiring optimal cultivation conditions to preserve its therapeutic properties. Waterlogging stress significantly reduces its productivity, yet the underlying molecular mechanisms remain poorly understood. Methods We investigated the species’ adaptive responses using controlled waterlogging experiments on potted plants. Morphological alterations and key growth parameters (culm diameter, plant height, dry biomass) were quantified. We performed transcriptomic profiling by RNA-Seq to identify differentially expressed genes (DEGs). To elucidate the functional implications of these DEGs, we conducted systematic enrichment analyses using the clusters of orthologous groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Expression patterns of candidate genes were validated using Quantitative Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Results Flooded plants exhibited significant morphological changes, with key growth parameters decreasing by 14.4–21.8%. A pronounced adaptive response was a 76.6% increase in adventitious root formation. RNA-Seq revealed 207 DEGs (133 upregulated, 74 downregulated). Enrichment analyses indicated these DEGs were predominantly involved in photosynthetic processes, carbohydrate dynamics, and signaling pathways. qRT-PCR confirmed consistent expression patterns for six candidate genes associated with photosynthesis and carbohydrate metabolism. These findings demonstrate that Coix lacryma-jobi L. activates coordinated molecular responses, including photosynthetic efficiency adjustment and metabolic pathway remodeling, to enhance waterlogging tolerance. This work identifies critical genetic components governing waterlogging adaptation, providing molecular markers for developing stress-tolerant cultivars through targeted breeding.
bibliographic citation: Yao et al. (2026) Morphological characterization and RNA sequencing reveal adaptive strategies of Coix lacryma-jobi L. under waterlogging stress during the jointing stage. PeerJ 14:e20731 https://doi.org/10.7717/peerj.20731
date submitted: 2025-08-13
date accepted: 2025-12-12
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Jing
author list: Agent
  family name: Gong
  given name: Zhiqing
author list: Agent
  family name: Tang
  given name: Weijie
author list: Agent
  family name: Yuan
  given name: Mei
author list: Agent
  family name: He
  given name: Yunyan
author list: Agent
  family name: Liang
  given name: Yantao
author list: Agent
  family name: Li
  given name: Weizhong
author list: Agent
  family name: Zhong
  given name: Ke
author list: Agent
  family name: Wang
  given name: Dandan
author list: Agent
  family name: He
  given name: Peilong
doi: 10.7717/peerj.20731
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Yao et al.
attribution name: Yao et al.

Exercise alleviates allodynia and hyperalgesia concomitant with improvements in aberrant primary afferents and spinal circuit inhibition in the dorsal horn of rats with incomplete spinal cord injury
type: item
type: AcademicArticle
description: Neuropathic pain (NP) is a common complication following spinal cord injury (SCI), significantly impairing patients’ physical/mental health and quality of life. While activity—based exercise has demonstrated efficacy in alleviating SCI-NP in rodent models, the mechanisms underlying this effect remain unclear. Specifically, it requires investigation whether exercise mediates its benefits through the following mechanisms: improving aberrant primary afferents and circuit inhibition in the lumbar dorsal horn after thoracic contusion SCI. In this study, we implemented an exercise training protocol in rats with incomplete thoracic SCI. We evaluated its effects on several factors, including mechanical withdrawal thresholds (MWTs), thermal withdrawal latencies (TWLs), and rate-dependent depression (RDD) of H-reflex. Additionally, we examined the changes in vesicular glutamate transporter 1 (VGluT1, specifically labeled in myelinated primary afferent terminals), calcitonin gene-related peptide (CGRP)-labeled nociceptive unmyelinated primary afferents, glutamic acid decarboxylase 65+67 (GAD 65+67), and potassium-chloride cotransporter 2 (KCC2). Our results showed that exercise training significantly improved MWTs and TWLs, enhanced the RDD of H-reflex, increased the synthesis of VGluT1, GAD 65+67, and KCC2 within the spinal dorsal horn, while reducing the CGRP-labeled nociceptive unmyelinated primary afferents. These findings indicate that exercise alleviates mechanical allodynia and thermal hyperalgesia, which is paralleled by improvements in aberrant primary afferents, enhanced RDD of the H-reflex, and increased synthesis of GAD 65+67 and KCC2 in the lumbar dorsal horn following thoracic contusion SCI.
format: application/pdf
format: text/html
creator: Xiangzhe Li
creator: Jiahuan Wu
creator: Lu Fang
creator: Jiale Wang
creator: Sheng Wang
creator: Qinfeng Wu
creator: Tong Wang
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Neurology
subject: Rehabilitation
description: doi:10.7717/peerj.20699
publisher: PeerJ Inc.
rights: © 2026 Li et al.
abstract: Neuropathic pain (NP) is a common complication following spinal cord injury (SCI), significantly impairing patients’ physical/mental health and quality of life. While activity—based exercise has demonstrated efficacy in alleviating SCI-NP in rodent models, the mechanisms underlying this effect remain unclear. Specifically, it requires investigation whether exercise mediates its benefits through the following mechanisms: improving aberrant primary afferents and circuit inhibition in the lumbar dorsal horn after thoracic contusion SCI. In this study, we implemented an exercise training protocol in rats with incomplete thoracic SCI. We evaluated its effects on several factors, including mechanical withdrawal thresholds (MWTs), thermal withdrawal latencies (TWLs), and rate-dependent depression (RDD) of H-reflex. Additionally, we examined the changes in vesicular glutamate transporter 1 (VGluT1, specifically labeled in myelinated primary afferent terminals), calcitonin gene-related peptide (CGRP)-labeled nociceptive unmyelinated primary afferents, glutamic acid decarboxylase 65+67 (GAD 65+67), and potassium-chloride cotransporter 2 (KCC2). Our results showed that exercise training significantly improved MWTs and TWLs, enhanced the RDD of H-reflex, increased the synthesis of VGluT1, GAD 65+67, and KCC2 within the spinal dorsal horn, while reducing the CGRP-labeled nociceptive unmyelinated primary afferents. These findings indicate that exercise alleviates mechanical allodynia and thermal hyperalgesia, which is paralleled by improvements in aberrant primary afferents, enhanced RDD of the H-reflex, and increased synthesis of GAD 65+67 and KCC2 in the lumbar dorsal horn following thoracic contusion SCI.
bibliographic citation: Li et al. (2026) Exercise alleviates allodynia and hyperalgesia concomitant with improvements in aberrant primary afferents and spinal circuit inhibition in the dorsal horn of rats with incomplete spinal cord injury. PeerJ 14:e20699 https://doi.org/10.7717/peerj.20699
date submitted: 2025-04-08
date accepted: 2025-12-09
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Xiangzhe
author list: Agent
  family name: Wu
  given name: Jiahuan
author list: Agent
  family name: Fang
  given name: Lu
author list: Agent
  family name: Wang
  given name: Jiale
author list: Agent
  family name: Wang
  given name: Sheng
author list: Agent
  family name: Wu
  given name: Qinfeng
author list: Agent
  family name: Wang
  given name: Tong
doi: 10.7717/peerj.20699
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Li et al.
attribution name: Li et al.

Risk assessment and spatial-temporal distribution characteristics of nitrogen and phosphorus emissions from agricultural sources in the Yangtze River Economic Belt
type: item
type: AcademicArticle
description: Rapid socioeconomic development has intensified nitrogen and phosphorus pollution in the Yangtze River Economic Belt (YREB), posing severe threats to the water environment. Notably, agricultural sources have surpassed industrial sources to become the primary contributor to this pollution. To explore the spatiotemporal characteristics and impacts of agricultural nitrogen and phosphorus pollution in this region, this study constructed an improved output coefficient model. Using panel data from 11 provinces and municipalities in the YREB spanning 2005–2020, combined with Geographic Information System (GIS) spatial analysis tools, we calculated the pollution loads of agricultural nitrogen and phosphorus from three key sources: land use, rural domestic activities, and livestock and poultry breeding (LPB). The results show a consistent downward trend in total nitrogen (TN) and total phosphorus (TP) pollution loads from the three sources. Specifically, TN load decreased from 2,686.68 × 103 tons/yr in 2005 to 2,035.67 × 103 tons/yr in 2020, while TP load declined from 139.42 × 103 tons/yr to 102.52 × 103 tons/yr, with an average TN-to-TP pollution load ratio of approximately 19.40. GIS-generated spatial distribution maps confirm a widespread reduction in agricultural TN and TP pollution across the region. To effectively mitigate agricultural nitrogen and phosphorus pollution risks, we recommend strengthening research on fertilization techniques for major crops and exploring the establishment of centralized treatment stations for agricultural solid waste in regions within the YREB.
format: application/pdf
format: text/html
creator: Guang Wei Hu
creator: Ying Xu
creator: Yi Lan Ma
subject: Natural Resource Management
subject: Ecohydrology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.20687
publisher: PeerJ Inc.
rights: © 2026 Hu et al.
abstract: Rapid socioeconomic development has intensified nitrogen and phosphorus pollution in the Yangtze River Economic Belt (YREB), posing severe threats to the water environment. Notably, agricultural sources have surpassed industrial sources to become the primary contributor to this pollution. To explore the spatiotemporal characteristics and impacts of agricultural nitrogen and phosphorus pollution in this region, this study constructed an improved output coefficient model. Using panel data from 11 provinces and municipalities in the YREB spanning 2005–2020, combined with Geographic Information System (GIS) spatial analysis tools, we calculated the pollution loads of agricultural nitrogen and phosphorus from three key sources: land use, rural domestic activities, and livestock and poultry breeding (LPB). The results show a consistent downward trend in total nitrogen (TN) and total phosphorus (TP) pollution loads from the three sources. Specifically, TN load decreased from 2,686.68 × 103 tons/yr in 2005 to 2,035.67 × 103 tons/yr in 2020, while TP load declined from 139.42 × 103 tons/yr to 102.52 × 103 tons/yr, with an average TN-to-TP pollution load ratio of approximately 19.40. GIS-generated spatial distribution maps confirm a widespread reduction in agricultural TN and TP pollution across the region. To effectively mitigate agricultural nitrogen and phosphorus pollution risks, we recommend strengthening research on fertilization techniques for major crops and exploring the establishment of centralized treatment stations for agricultural solid waste in regions within the YREB.
bibliographic citation: Hu et al. (2026) Risk assessment and spatial-temporal distribution characteristics of nitrogen and phosphorus emissions from agricultural sources in the Yangtze River Economic Belt. PeerJ 14:e20687 https://doi.org/10.7717/peerj.20687
date submitted: 2025-03-19
date accepted: 2025-12-08
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Guang Wei
author list: Agent
  family name: Xu
  given name: Ying
author list: Agent
  family name: Ma
  given name: Yi Lan
doi: 10.7717/peerj.20687
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Hu et al.
attribution name: Hu et al.

The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus
type: item
type: AcademicArticle
description: Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa—highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for f…
format: application/pdf
format: text/html
creator: Peter F. Chuckran
creator: Steven J. Blazewicz
creator: Javier A. Ceja-Navarro
creator: Jennifer Pett-Ridge
creator: Egbert Schwartz
creator: Paul Dijkstra
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.20641
publisher: PeerJ Inc.
rights: © 2026 Chuckran et al.
abstract: Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa—highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for f…
bibliographic citation: Chuckran et al. (2026) The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus. PeerJ 14:e20641 https://doi.org/10.7717/peerj.20641
date submitted: 2025-03-20
date accepted: 2025-12-01
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chuckran
  given name: Peter F.
author list: Agent
  family name: Blazewicz
  given name: Steven J.
author list: Agent
  family name: Ceja-Navarro
  given name: Javier A.
author list: Agent
  family name: Pett-Ridge
  given name: Jennifer
author list: Agent
  family name: Schwartz
  given name: Egbert
author list: Agent
  family name: Dijkstra
  given name: Paul
doi: 10.7717/peerj.20641
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: © 2026 Chuckran et al.
attribution name: Chuckran et al.

Acute toxicity of TNT derivatives and hydrazine-based compounds from explosive and rocket fuel contamination to darkling beetles (Tenebrio molitor and Opatrum sabulosum)
type: item
type: AcademicArticle
description: The problem of toxic pollution of the environment by combustion products of explosives and rocket fuel is becoming increasingly important in the context of intensified military operations. In this study, the toxicity of TNT derivatives, hydrazine-based compounds, and nitroaromatic transformation products related to explosive and rocket fuel contamination was evaluated using the model organisms Tenebrio molitor Linnaeus, 1758 and Opatrum sabulosum (Linnaeus, 1761). We chose hydrazine derivatives, nitroanilines, benzene and naphthalene-based nitro compounds that can persist in the ground, water and atmosphere after explosions or incomplete combustion of rocket fuel. Topical dispersion was used to evaluate exposure of specified doses on the surface of containers containing larvae and imagoes of T. molitor and imagoes of O. sabulosum, followed by lethality counts and LC50 determination. The results indicate the high sensitivity of T. molitor larvae and imagoes and O. sabulosum imagoes to TNT derivatives, hydrazine compounds, and nitroaromatic contaminants commonly found in explosive-contaminated environments, which confirms the feasibility of introducing ecotoxicological monitoring of military-technological impact zones. The systematic toxicity assessment of these 29 explosive-related compounds provides essential baseline data for environmental risk modeling and ecotoxicological monitoring programs. The data obtained can be used for further modeling of environmental risk and development of bioindicator approaches to detect pollution as a result of military operations, for example, in Ukraine.
format: application/pdf
format: text/html
creator: Denis F. Rybalka
creator: Viktor V. Brygadyrenko
subject: Ecology
subject: Toxicology
subject: Zoology
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.20427
publisher: PeerJ Inc.
rights: © 2026 Rybalka and Brygadyrenko
abstract: The problem of toxic pollution of the environment by combustion products of explosives and rocket fuel is becoming increasingly important in the context of intensified military operations. In this study, the toxicity of TNT derivatives, hydrazine-based compounds, and nitroaromatic transformation products related to explosive and rocket fuel contamination was evaluated using the model organisms Tenebrio molitor Linnaeus, 1758 and Opatrum sabulosum (Linnaeus, 1761). We chose hydrazine derivatives, nitroanilines, benzene and naphthalene-based nitro compounds that can persist in the ground, water and atmosphere after explosions or incomplete combustion of rocket fuel. Topical dispersion was used to evaluate exposure of specified doses on the surface of containers containing larvae and imagoes of T. molitor and imagoes of O. sabulosum, followed by lethality counts and LC50 determination. The results indicate the high sensitivity of T. molitor larvae and imagoes and O. sabulosum imagoes to TNT derivatives, hydrazine compounds, and nitroaromatic contaminants commonly found in explosive-contaminated environments, which confirms the feasibility of introducing ecotoxicological monitoring of military-technological impact zones. The systematic toxicity assessment of these 29 explosive-related compounds provides essential baseline data for environmental risk modeling and ecotoxicological monitoring programs. The data obtained can be used for further modeling of environmental risk and development of bioindicator approaches to detect pollution as a result of military operations, for example, in Ukraine.
bibliographic citation: Rybalka et al. (2026) Acute toxicity of TNT derivatives and hydrazine-based compounds from explosive and rocket fuel contamination to darkling beetles (Tenebrio molitor and Opatrum sabulosum). PeerJ 14:e20427 https://doi.org/10.7717/peerj.20427
date submitted: 2025-07-18
date accepted: 2025-10-29
issued: 2026-02-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rybalka
  given name: Denis F.
author list: Agent
  family name: Brygadyrenko
  given name: Viktor V.
doi: 10.7717/peerj.20427
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-05
copyright: ©2026 Rybalka and Brygadyrenko
attribution name: Rybalka and Brygadyrenko

Temporal and spatial dynamics of Net Primary Productivity and prediction of wetland carbon sequestration potential on the Tibetan Plateau
type: item
type: AcademicArticle
description: Background Investigating the carbon sequestration potential of wetlands and the dynamics of net primary productivity (NPP) on the Tibetan Plateau of China enhances understanding of their contributions to global carbon emission reduction and their role in maintaining biodiversity and ecosystem stability. Vegetation NPP is a key indicator of carbon sequestration; however, existing research has largely focused on historical dynamics, with limited studies projecting future trends. This gap impedes proactive conservation and climate mitigation strategies. Methods Here, we predicted the spatial distribution of normalized difference vegetation index (NDVI) on the Tibetan Plateau for 2025–2030, employing a backpropagation neural network and Kriging interpolation fitting. We estimated spatial and temporal dynamics of NPP and wetland carbon sequestration potentials during the same period using the Carnegie-Ames-Stanford Approach model. Furthermore, we investigated the effects of land use and climate on NPP. Results Key findings were: (1) NDVI distribution was higher in the southeast than in the northwest, with temperature influencing its value. (2) Spatial distribution of NPP on the Tibetan Plateau exhibits a typical landscape pattern of “patch-corridor-matrix.” The maximum NPP of vegetation was 1,112.82 gC ⋅ m−2 ⋅ a−1 for 2025–2030. Projections of NPP for 2025–2030 suggest an increase of approximately 50% relative to current levels by 2045, indicating a substantial enhancement of the carbon sink potential over the coming two decades. (3) Carbon sequestration potential of wetlands on the Plateau ranges from 0 to 100 gC ⋅ m−2 ⋅ a−1, with high carbon sink potential concentrated near Palong Tsangpo, the largest tributary of the Yarlung Tsangpo River. (4) Woodland NPP has the highest mean value and rate of change. Furthermore, analysis of 2025 land use data shows that forestland and grassland are the dominant land cover types in the Yunnan, Sichuan, and Southeastern Xizang Sectio…
format: application/pdf
format: text/html
creator: Liang Cao
creator: Shi Dong
creator: Yuyan Wang
creator: Xingran Li
creator: Yonghua Zhao
creator: Danni Ma
creator: Zhuoma Pubu
creator: Hongmei Ma
creator: Wei Li
creator: Pengxi Cao
subject: Ecology
subject: Data Science
subject: Climate Change Biology
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20758
publisher: PeerJ Inc.
rights: © 2026 Cao et al.
abstract: Background Investigating the carbon sequestration potential of wetlands and the dynamics of net primary productivity (NPP) on the Tibetan Plateau of China enhances understanding of their contributions to global carbon emission reduction and their role in maintaining biodiversity and ecosystem stability. Vegetation NPP is a key indicator of carbon sequestration; however, existing research has largely focused on historical dynamics, with limited studies projecting future trends. This gap impedes proactive conservation and climate mitigation strategies. Methods Here, we predicted the spatial distribution of normalized difference vegetation index (NDVI) on the Tibetan Plateau for 2025–2030, employing a backpropagation neural network and Kriging interpolation fitting. We estimated spatial and temporal dynamics of NPP and wetland carbon sequestration potentials during the same period using the Carnegie-Ames-Stanford Approach model. Furthermore, we investigated the effects of land use and climate on NPP. Results Key findings were: (1) NDVI distribution was higher in the southeast than in the northwest, with temperature influencing its value. (2) Spatial distribution of NPP on the Tibetan Plateau exhibits a typical landscape pattern of “patch-corridor-matrix.” The maximum NPP of vegetation was 1,112.82 gC ⋅ m−2 ⋅ a−1 for 2025–2030. Projections of NPP for 2025–2030 suggest an increase of approximately 50% relative to current levels by 2045, indicating a substantial enhancement of the carbon sink potential over the coming two decades. (3) Carbon sequestration potential of wetlands on the Plateau ranges from 0 to 100 gC ⋅ m−2 ⋅ a−1, with high carbon sink potential concentrated near Palong Tsangpo, the largest tributary of the Yarlung Tsangpo River. (4) Woodland NPP has the highest mean value and rate of change. Furthermore, analysis of 2025 land use data shows that forestland and grassland are the dominant land cover types in the Yunnan, Sichuan, and Southeastern Xizang Sectio…
bibliographic citation: Cao et al. (2026) Temporal and spatial dynamics of Net Primary Productivity and prediction of wetland carbon sequestration potential on the Tibetan Plateau. PeerJ 14:e20758 https://doi.org/10.7717/peerj.20758
date submitted: 2025-04-29
date accepted: 2025-12-17
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Liang
author list: Agent
  family name: Dong
  given name: Shi
author list: Agent
  family name: Wang
  given name: Yuyan
author list: Agent
  family name: Li
  given name: Xingran
author list: Agent
  family name: Zhao
  given name: Yonghua
author list: Agent
  family name: Ma
  given name: Danni
author list: Agent
  family name: Pubu
  given name: Zhuoma
author list: Agent
  family name: Ma
  given name: Hongmei
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Cao
  given name: Pengxi
doi: 10.7717/peerj.20758
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: ©2026 Cao et al.
attribution name: Cao et al.

Development and optimization of mathematical models for uniform seed placement in precision black cumin seeding under laboratory conditions
type: item
type: AcademicArticle
description: Objectives The objective of the study was to quantify seed flow consistency and in-row spacing accuracy when using a conveyor belt-style metering device under varying operational parameters, to develop mathematical models, and to optimize the uniformity of seed placement for black cumin seeding. Methods Seed flow properties and the uniformity of in-row seed distribution uniformity were evaluated through weighing tests and sticky belt methods, respectively. The uniformity of the flow was assessed using coefficient of variation (CV) values, while the in-row seed distribution uniformity was evaluated by using the variation factor (Vf) and the goodness criterion (λ). The experiments were conducted based on Central Composite Design (CCD) under laboratory conditions. The forward speed, seed rate, and seed falling angle were chosen as independent variables. The experiments were conducted at five levels of forward speed (1.01, 1.4, 2.0, 2.6, and 3.01 m s−1), five levels of seed rate (6.6, 10, 15, 20 and 23.4 kg ha−1), and five levels of seed falling angle (1.36, 15, 35, 55 and 68.64°). Results The polynomial functions were developed and the Vf and λ models were optimized. Optimization reduced the variation factor (Vf) to 0.53 and improved the goodness criterion (λ) to 91.67%, indicating a substantial enhancement in seed placement uniformity. For the Vf model, the optimum forward speed was found to be 1.05 m s−1, with a seed rate of 12.35 kg ha−1 and a seed falling angle of 35°; whereas for the λ model, the corresponding values were calculated 1.55 m s−1, 21.1 kg ha−1, and 28.5°, respectively. The developed models showed high predictive accuracy, with an R2 value of 95.96% for the λ model. Based on the findings of this work, the seed rate was determined as the most important parameter for all models considered. Conclusions The results of the experiments also revealed that the conveyor belt metering unit could be used for the seeding process of black cumin seeds with great su…
format: application/pdf
format: text/html
creator: Gulin Turkusay
creator: Arzu Yazgi
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20755
publisher: PeerJ Inc.
rights: © 2026 Turkusay and Yazgi
abstract: Objectives The objective of the study was to quantify seed flow consistency and in-row spacing accuracy when using a conveyor belt-style metering device under varying operational parameters, to develop mathematical models, and to optimize the uniformity of seed placement for black cumin seeding. Methods Seed flow properties and the uniformity of in-row seed distribution uniformity were evaluated through weighing tests and sticky belt methods, respectively. The uniformity of the flow was assessed using coefficient of variation (CV) values, while the in-row seed distribution uniformity was evaluated by using the variation factor (Vf) and the goodness criterion (λ). The experiments were conducted based on Central Composite Design (CCD) under laboratory conditions. The forward speed, seed rate, and seed falling angle were chosen as independent variables. The experiments were conducted at five levels of forward speed (1.01, 1.4, 2.0, 2.6, and 3.01 m s−1), five levels of seed rate (6.6, 10, 15, 20 and 23.4 kg ha−1), and five levels of seed falling angle (1.36, 15, 35, 55 and 68.64°). Results The polynomial functions were developed and the Vf and λ models were optimized. Optimization reduced the variation factor (Vf) to 0.53 and improved the goodness criterion (λ) to 91.67%, indicating a substantial enhancement in seed placement uniformity. For the Vf model, the optimum forward speed was found to be 1.05 m s−1, with a seed rate of 12.35 kg ha−1 and a seed falling angle of 35°; whereas for the λ model, the corresponding values were calculated 1.55 m s−1, 21.1 kg ha−1, and 28.5°, respectively. The developed models showed high predictive accuracy, with an R2 value of 95.96% for the λ model. Based on the findings of this work, the seed rate was determined as the most important parameter for all models considered. Conclusions The results of the experiments also revealed that the conveyor belt metering unit could be used for the seeding process of black cumin seeds with great su…
bibliographic citation: Turkusay et al. (2026) Development and optimization of mathematical models for uniform seed placement in precision black cumin seeding under laboratory conditions. PeerJ 14:e20755 https://doi.org/10.7717/peerj.20755
date submitted: 2025-07-30
date accepted: 2025-12-17
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Turkusay
  given name: Gulin
author list: Agent
  family name: Yazgi
  given name: Arzu
doi: 10.7717/peerj.20755
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: ©2026 Turkusay and Yazgi
attribution name: Turkusay and Yazgi

Integrating agro-physiological traits and yield performance in soybean (Glycine max L.) resistance to fall armyworm (Spodoptera frugiperda) through genotype analysis
type: item
type: AcademicArticle
description: Fall armyworm (Spodoptera frugiperda) is a major invasive pest threatening soybean production, and identifying resistant genotypes is essential for sustainable crop protection. This study evaluated 36 soybean genotypes for their resistance to S. frugiperda based on leaf damage intensity and frequency, resistance classification, morphophysiological traits, and yield components. The research was conducted under field conditions using a randomized complete block design (RCBD) with three replications. Armyworm damage was assessed at 36 and 41 days after planting (DAP), and all quantitative data were analyzed using ANOVA followed by the Scott–Knott test at a 5% significance level. Data were presented as mean ± standard deviation (SD). Significant variation was evident among genotypes, with attack intensity at 41 DAP ranging from 18.31 ± 10.64% to 61.20 ± 11.39%, and attack frequency from 33.38 ± 16.92% to 95.49 ± 5.35%. Based on mean intensity values, one genotype was categorized as strongly resistant (SR) (UB 2), four as resistant (R) (UBASK24, UBASK35, GBG, TGM), and a broader set as moderately resistant (MR), while highly susceptible (HS) genotypes included UBASK15, UBASK62, UBASK64, UBASK32, UBASK36, and UBASK14. Morphophysiological traits exhibited wide variation, including leaf trichome density (13.56–42.11 trichomes 0.25 cm−2), plant height (38.42–78.67 cm), and flowering time (31–47 DAP), while yield traits identified TGM, UBASK35, UBASK24, and GBG as the highest-performing genotypes. Overall, UB 2, UBASK24, UBASK35, GBG, and TGM are promising parental candidates for breeding soybean resistance against S. frugiperda, integrating strong resistance expression with favorable agronomic performance.
format: application/pdf
format: text/html
creator: Anna Satyana Karyawati
creator: Demas Dharmawan
creator: Himma Rahmadillah
creator: Budi Waluyo
creator: Vina Mafazatul Ula
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20753
publisher: PeerJ Inc.
rights: © 2026 Satyana Karyawati et al.
abstract: Fall armyworm (Spodoptera frugiperda) is a major invasive pest threatening soybean production, and identifying resistant genotypes is essential for sustainable crop protection. This study evaluated 36 soybean genotypes for their resistance to S. frugiperda based on leaf damage intensity and frequency, resistance classification, morphophysiological traits, and yield components. The research was conducted under field conditions using a randomized complete block design (RCBD) with three replications. Armyworm damage was assessed at 36 and 41 days after planting (DAP), and all quantitative data were analyzed using ANOVA followed by the Scott–Knott test at a 5% significance level. Data were presented as mean ± standard deviation (SD). Significant variation was evident among genotypes, with attack intensity at 41 DAP ranging from 18.31 ± 10.64% to 61.20 ± 11.39%, and attack frequency from 33.38 ± 16.92% to 95.49 ± 5.35%. Based on mean intensity values, one genotype was categorized as strongly resistant (SR) (UB 2), four as resistant (R) (UBASK24, UBASK35, GBG, TGM), and a broader set as moderately resistant (MR), while highly susceptible (HS) genotypes included UBASK15, UBASK62, UBASK64, UBASK32, UBASK36, and UBASK14. Morphophysiological traits exhibited wide variation, including leaf trichome density (13.56–42.11 trichomes 0.25 cm−2), plant height (38.42–78.67 cm), and flowering time (31–47 DAP), while yield traits identified TGM, UBASK35, UBASK24, and GBG as the highest-performing genotypes. Overall, UB 2, UBASK24, UBASK35, GBG, and TGM are promising parental candidates for breeding soybean resistance against S. frugiperda, integrating strong resistance expression with favorable agronomic performance.
bibliographic citation: Satyana Karyawati et al. (2026) Integrating agro-physiological traits and yield performance in soybean (Glycine max L.) resistance to fall armyworm (Spodoptera frugiperda) through genotype analysis. PeerJ 14:e20753 https://doi.org/10.7717/peerj.20753
date submitted: 2025-02-14
date accepted: 2025-12-16
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Satyana Karyawati
  given name: Anna
author list: Agent
  family name: Dharmawan
  given name: Demas
author list: Agent
  family name: Rahmadillah
  given name: Himma
author list: Agent
  family name: Waluyo
  given name: Budi
author list: Agent
  family name: Ula
  given name: Vina Mafazatul
doi: 10.7717/peerj.20753
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: © 2026 Satyana Karyawati et al.
attribution name: Satyana Karyawati et al.

Admission serum tropomyosin 4 levels predict 1-year functional outcomes in acute ischemic stroke
type: item
type: AcademicArticle
description: Background Tropomyosin 4 (TPM4) regulates neurite outgrowth and vascular pathology but its role as a biomarker for predicting outcomes in stroke patients is unclear. This study investigated the association between serum TPM4 levels and 1-year functional outcomes in acute ischemic stroke (AIS) patients. Methods AIS patients admitted within 24 h post-onset from the Chengdu Stroke Registry were included. Serum TPM4 levels were measured by enzyme-linked immunosorbent assay (ELISA). Poor functional outcomes were defined as a modified Rankin Scale (mRS) score >2 at 1 year after stroke onset. Multivariate logistic regression assessed TPM4’s association with outcomes, with its predictive incremental value evaluated by discrimination, reclassification, and overall performance metrics. Results Among 181 patients (median age 66 years, 64.1% male), 59 (32.6%) experienced poor outcomes at 1 year, including 16 deaths (8.8%). Serum TPM4 levels on admission were negatively correlated with the National Institutes of Health Stroke Scale (NIHSS) score (r = −0.185, p = 0.013). Adjusted for confounders, lower serum TPM4 levels were independently associated with 1-year poor functional outcomes (adjusted OR 0.045, 95% CI [0.005–0.393], p = 0.005). Serum TPM4 levels had acceptable discriminative ability for predicting poor outcomes (AUROC 0.706, 95% CI [0.621–0.791], p < 0.0001). Incorporating TPM4 into the basic model significantly improved the predictive power for poor functional outcomes (net reclassification index: 31.87%, p = 0.041; integrated discrimination improvement: 5.01%, p = 0.008; Brier score decreased from 0.16 to 0.15, p = 0.012). Conclusions Lower serum TPM4 levels on admission were independently associated with poor functional outcomes at 1 year in AIS patients, suggesting that TPM4 may serve as a potential biomarker for long-term outcomes and offer insights into its potential role in stroke pathophysiology. These findings need to be further verified in external cohorts.
format: application/pdf
format: text/html
creator: Keying Wu
creator: Mingxi Chen
creator: Huan Wang
creator: Yuyi Zhu
creator: Yaqi Chen
creator: Shihong Zhang
creator: Xinyi Leng
creator: Zilong Hao
creator: Deren Wang
subject: Biochemistry
subject: Emergency and Critical Care
subject: Evidence Based Medicine
subject: Neurology
description: doi:10.7717/peerj.20745
publisher: PeerJ Inc.
rights: © 2026 Wu et al.
abstract: Background Tropomyosin 4 (TPM4) regulates neurite outgrowth and vascular pathology but its role as a biomarker for predicting outcomes in stroke patients is unclear. This study investigated the association between serum TPM4 levels and 1-year functional outcomes in acute ischemic stroke (AIS) patients. Methods AIS patients admitted within 24 h post-onset from the Chengdu Stroke Registry were included. Serum TPM4 levels were measured by enzyme-linked immunosorbent assay (ELISA). Poor functional outcomes were defined as a modified Rankin Scale (mRS) score >2 at 1 year after stroke onset. Multivariate logistic regression assessed TPM4’s association with outcomes, with its predictive incremental value evaluated by discrimination, reclassification, and overall performance metrics. Results Among 181 patients (median age 66 years, 64.1% male), 59 (32.6%) experienced poor outcomes at 1 year, including 16 deaths (8.8%). Serum TPM4 levels on admission were negatively correlated with the National Institutes of Health Stroke Scale (NIHSS) score (r = −0.185, p = 0.013). Adjusted for confounders, lower serum TPM4 levels were independently associated with 1-year poor functional outcomes (adjusted OR 0.045, 95% CI [0.005–0.393], p = 0.005). Serum TPM4 levels had acceptable discriminative ability for predicting poor outcomes (AUROC 0.706, 95% CI [0.621–0.791], p < 0.0001). Incorporating TPM4 into the basic model significantly improved the predictive power for poor functional outcomes (net reclassification index: 31.87%, p = 0.041; integrated discrimination improvement: 5.01%, p = 0.008; Brier score decreased from 0.16 to 0.15, p = 0.012). Conclusions Lower serum TPM4 levels on admission were independently associated with poor functional outcomes at 1 year in AIS patients, suggesting that TPM4 may serve as a potential biomarker for long-term outcomes and offer insights into its potential role in stroke pathophysiology. These findings need to be further verified in external cohorts.
bibliographic citation: Wu et al. (2026) Admission serum tropomyosin 4 levels predict 1-year functional outcomes in acute ischemic stroke. PeerJ 14:e20745 https://doi.org/10.7717/peerj.20745
date submitted: 2025-06-19
date accepted: 2025-12-15
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Keying
author list: Agent
  family name: Chen
  given name: Mingxi
author list: Agent
  family name: Wang
  given name: Huan
author list: Agent
  family name: Zhu
  given name: Yuyi
author list: Agent
  family name: Chen
  given name: Yaqi
author list: Agent
  family name: Zhang
  given name: Shihong
author list: Agent
  family name: Leng
  given name: Xinyi
author list: Agent
  family name: Hao
  given name: Zilong
author list: Agent
  family name: Wang
  given name: Deren
doi: 10.7717/peerj.20745
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: © 2026 Wu et al.
attribution name: Wu et al.

Time is of the essence: using archived samples in the development of a GT-seq panel to preserve continuity of ongoing genetic monitoring
type: item
type: AcademicArticle
description: Genotyping-in-Thousands by sequencing (GT-seq) is a promising tool for genetic monitoring. For the past 25 years, genetic monitoring of Rio Grande silvery minnow (Hybognathus amarus) has been conducted annually by surveying variation at microsatellite loci. This is the first study describing the development of a GT-seq panel using archived samples that maintains the analytical and inferential continuity of long-term genetic monitoring. A total of 2,983 microhaplotypes in 373 individuals were identified using nextRAD-seq from samples spanning 20 years and a conspecific reference genome. Using this data, estimates of genetic diversity and temporal genetic structure across the time-series were used as a baseline to test subsets of loci that effectively tracked those changes. A panel including 250 loci with higher FST across temporal samples and 250 loci selected randomly offered the highest power and was used for GT-seq optimization. A sex-linked marker validated previously was also included for sex assignment. The optimized GT-seq panel included 284 loci. Comparisons of genotypes from those loci obtained for the same samples with nextRAD-seq and GT-seq revealed high genotype accuracy (98.3%). Estimates of genetic diversity and patterns of temporal genetic structure were similar between datasets and accuracy of sex assignment was 100%. The utility of using a conspecific genome for both loci identification and primer design in the face of reduced genetic diversity, and the importance of temporal metrics representative of ongoing genetic monitoring is explored. The strategy used here, effectively preserved the long-term genetic monitoring of the endangered Rio Grande silvery minnow while transitioning to a more efficient and cost-effective marker system.
format: application/pdf
format: text/html
creator: Guilherme Caeiro-Dias
creator: Megan J. Osborne
creator: Thomas F. Turner
subject: Fisheries and Fish Science
subject: Bioinformatics
subject: Conservation Biology
subject: Genetics
subject: Freshwater Biology
description: doi:10.7717/peerj.20726
publisher: PeerJ Inc.
rights: © 2026 Caeiro-Dias et al.
abstract: Genotyping-in-Thousands by sequencing (GT-seq) is a promising tool for genetic monitoring. For the past 25 years, genetic monitoring of Rio Grande silvery minnow (Hybognathus amarus) has been conducted annually by surveying variation at microsatellite loci. This is the first study describing the development of a GT-seq panel using archived samples that maintains the analytical and inferential continuity of long-term genetic monitoring. A total of 2,983 microhaplotypes in 373 individuals were identified using nextRAD-seq from samples spanning 20 years and a conspecific reference genome. Using this data, estimates of genetic diversity and temporal genetic structure across the time-series were used as a baseline to test subsets of loci that effectively tracked those changes. A panel including 250 loci with higher FST across temporal samples and 250 loci selected randomly offered the highest power and was used for GT-seq optimization. A sex-linked marker validated previously was also included for sex assignment. The optimized GT-seq panel included 284 loci. Comparisons of genotypes from those loci obtained for the same samples with nextRAD-seq and GT-seq revealed high genotype accuracy (98.3%). Estimates of genetic diversity and patterns of temporal genetic structure were similar between datasets and accuracy of sex assignment was 100%. The utility of using a conspecific genome for both loci identification and primer design in the face of reduced genetic diversity, and the importance of temporal metrics representative of ongoing genetic monitoring is explored. The strategy used here, effectively preserved the long-term genetic monitoring of the endangered Rio Grande silvery minnow while transitioning to a more efficient and cost-effective marker system.
bibliographic citation: Caeiro-Dias et al. (2026) Time is of the essence: using archived samples in the development of a GT-seq panel to preserve continuity of ongoing genetic monitoring. PeerJ 14:e20726 https://doi.org/10.7717/peerj.20726
date submitted: 2025-10-02
date accepted: 2025-12-11
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caeiro-Dias
  given name: Guilherme
author list: Agent
  family name: Osborne
  given name: Megan J.
author list: Agent
  family name: Turner
  given name: Thomas F.
doi: 10.7717/peerj.20726
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: © 2026 Caeiro-Dias et al.
attribution name: Caeiro-Dias et al.

AI-based detection and sizing of saccular intracranial aneurysms: a single-center retrospective validation study using computed tomography angiography
type: item
type: AcademicArticle
description: Background Imaging advantages have raised intracranial aneurysm (IA) detection rates but have also increased radiologists’ workloads. Coupled with visual fatigue, this heavier burden heightens the risk of missed or erroneous diagnoses. Concurrently, artificial intelligence (AI) has shown great promise for analyzing medical images. This study aims to evaluate the diagnostic performance of AI software for IAs and to provide an initial, single-centre validation of its potential as a supportive tool in future deployment. Methods Between January 2019 and September 2023, 452 patients with 544 IAs diagnosed by head and neck computed tomography angiography (CTA) who also underwent digital subtraction angiography (DSA) were included. The AI’s ability to detect the presence, location, and size of IAs was recorded. Its results were compared with DSA, and the agreement between AI and radiologists in measuring IA size was evaluated. Results The AI software demonstrated a sensitivity of 88.97% (95% CI [0.861–0.963]) and an accuracy of 75.04% (95% CI [0.715–0.783]) for detecting IAs. Specifically, the accuracy and sensitivity of AI in detecting IAs that are smaller than three mm, between 3–5 mm, and larger than five mm are 58.46% (95% CI [0.462–0.698]) and 66.67% (95% CI [0.537–0.775]), 76.68% (95% CI [0.714–0.813]) and 88.93% (95% CI [0.843–0.924]), 77.10% (95% CI [0.720–0.816]) and 94.24% (95% CI [0.906–0.966]), respectively. There was good agreement between radiologists and DSA, between AI and DSA, and between radiologists and AI for identifying the location of IAs, with kappa values all greater than 0.75. The radiologists and AI also showed good consistency in measuring depth, width, height, and maximum diameter, with intraclass correlation coefficients (ICCs) all greater than 0.75, except for the neck width, which had an ICC of 0.492. Conclusions The AI software performs well in terms of detecting IAs that are larger than three mm and shows good agreement with radiologists in…
format: application/pdf
format: text/html
creator: Lu Zeng
creator: Xue-hua Zhang
creator: Wen-hao Li
creator: Bi-yao Qiao
creator: Jia-jia Chen
creator: Guang-xian Wang
subject: Neurology
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.20712
publisher: PeerJ Inc.
rights: © 2026 Zeng et al.
abstract: Background Imaging advantages have raised intracranial aneurysm (IA) detection rates but have also increased radiologists’ workloads. Coupled with visual fatigue, this heavier burden heightens the risk of missed or erroneous diagnoses. Concurrently, artificial intelligence (AI) has shown great promise for analyzing medical images. This study aims to evaluate the diagnostic performance of AI software for IAs and to provide an initial, single-centre validation of its potential as a supportive tool in future deployment. Methods Between January 2019 and September 2023, 452 patients with 544 IAs diagnosed by head and neck computed tomography angiography (CTA) who also underwent digital subtraction angiography (DSA) were included. The AI’s ability to detect the presence, location, and size of IAs was recorded. Its results were compared with DSA, and the agreement between AI and radiologists in measuring IA size was evaluated. Results The AI software demonstrated a sensitivity of 88.97% (95% CI [0.861–0.963]) and an accuracy of 75.04% (95% CI [0.715–0.783]) for detecting IAs. Specifically, the accuracy and sensitivity of AI in detecting IAs that are smaller than three mm, between 3–5 mm, and larger than five mm are 58.46% (95% CI [0.462–0.698]) and 66.67% (95% CI [0.537–0.775]), 76.68% (95% CI [0.714–0.813]) and 88.93% (95% CI [0.843–0.924]), 77.10% (95% CI [0.720–0.816]) and 94.24% (95% CI [0.906–0.966]), respectively. There was good agreement between radiologists and DSA, between AI and DSA, and between radiologists and AI for identifying the location of IAs, with kappa values all greater than 0.75. The radiologists and AI also showed good consistency in measuring depth, width, height, and maximum diameter, with intraclass correlation coefficients (ICCs) all greater than 0.75, except for the neck width, which had an ICC of 0.492. Conclusions The AI software performs well in terms of detecting IAs that are larger than three mm and shows good agreement with radiologists in…
bibliographic citation: Zeng et al. (2026) AI-based detection and sizing of saccular intracranial aneurysms: a single-center retrospective validation study using computed tomography angiography. PeerJ 14:e20712 https://doi.org/10.7717/peerj.20712
date submitted: 2025-08-21
date accepted: 2025-12-10
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zeng
  given name: Lu
author list: Agent
  family name: Zhang
  given name: Xue-hua
author list: Agent
  family name: Li
  given name: Wen-hao
author list: Agent
  family name: Qiao
  given name: Bi-yao
author list: Agent
  family name: Chen
  given name: Jia-jia
author list: Agent
  family name: Wang
  given name: Guang-xian
doi: 10.7717/peerj.20712
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: ©2026 Zeng et al.
attribution name: Zeng et al.

Cardioprotective effect of resveratrol in myocardial ischemia/reperfusion injury and myocardial infarction: a pre-clinical meta-analysis in animal studies
type: item
type: AcademicArticle
description: This meta-analysis aimed to assess the cardioprotective effect of resveratrol (RES) against myocardial ischemia/reperfusion injury (MIRI) and myocardial infarction (MI) in the animal. PubMed, Web of Science, and EMBASE were searched. Primary outcomes included myocardial infarct size (IS) and cardiac function. Secondary outcomes included cardiac injury enzyme, oxidative stress level, inflammatory cytokine, and apoptosis rate. Subgroup analysis, publication bias, sensitivity analysis, meta-regression, and dosage-efficacy analysis were used to evaluate the risk of bias. Fifty-seven studies were included involving 1,125 animals. The results showed that RES treatment decreased IS in animal models of MIRI (SMD: −5.44; 95% CI [−6.42 to −4.45]; P < 0.01; I2 = 86%) and MI (SMD: −3.41; 95% CI [−4.44 to −2.38]; P < 0.01; I2 = 75%). Moreover, RES treatment improved cardiac function, decreased cardiac injury enzymes, down-regulated oxidative stress levels, alleviated inflammatory cytokine levels, and reduced apoptosis rate in animal models of MIRI and MI. This meta-analysis of preclinical animal studies suggested that RES may have potential in alleviating MIRI and MI. However, the translational potential of RES remains uncertain, and additional preclinical studies with standardized protocols, comorbid models, and eventual clinical trials are needed to confirm these results.
format: application/pdf
format: text/html
creator: Shi-Jie Wei
creator: Qi-Hao Guo
creator: Xin-Yu Wei
creator: Si-Yu Chen
creator: Sheng Deng
creator: Liang An
creator: Wen-Jing Zeng
creator: Yi-Fan Zeng
subject: Cardiology
subject: Evidence Based Medicine
subject: Pathology
subject: Pharmacology
subject: Translational Medicine
description: doi:10.7717/peerj.20708
publisher: PeerJ Inc.
rights: © 2026 Wei et al.
abstract: This meta-analysis aimed to assess the cardioprotective effect of resveratrol (RES) against myocardial ischemia/reperfusion injury (MIRI) and myocardial infarction (MI) in the animal. PubMed, Web of Science, and EMBASE were searched. Primary outcomes included myocardial infarct size (IS) and cardiac function. Secondary outcomes included cardiac injury enzyme, oxidative stress level, inflammatory cytokine, and apoptosis rate. Subgroup analysis, publication bias, sensitivity analysis, meta-regression, and dosage-efficacy analysis were used to evaluate the risk of bias. Fifty-seven studies were included involving 1,125 animals. The results showed that RES treatment decreased IS in animal models of MIRI (SMD: −5.44; 95% CI [−6.42 to −4.45]; P < 0.01; I2 = 86%) and MI (SMD: −3.41; 95% CI [−4.44 to −2.38]; P < 0.01; I2 = 75%). Moreover, RES treatment improved cardiac function, decreased cardiac injury enzymes, down-regulated oxidative stress levels, alleviated inflammatory cytokine levels, and reduced apoptosis rate in animal models of MIRI and MI. This meta-analysis of preclinical animal studies suggested that RES may have potential in alleviating MIRI and MI. However, the translational potential of RES remains uncertain, and additional preclinical studies with standardized protocols, comorbid models, and eventual clinical trials are needed to confirm these results.
bibliographic citation: Wei et al. (2026) Cardioprotective effect of resveratrol in myocardial ischemia/reperfusion injury and myocardial infarction: a pre-clinical meta-analysis in animal studies. PeerJ 14:e20708 https://doi.org/10.7717/peerj.20708
date submitted: 2025-08-03
date accepted: 2025-12-10
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Shi-Jie
author list: Agent
  family name: Guo
  given name: Qi-Hao
author list: Agent
  family name: Wei
  given name: Xin-Yu
author list: Agent
  family name: Chen
  given name: Si-Yu
author list: Agent
  family name: Deng
  given name: Sheng
author list: Agent
  family name: An
  given name: Liang
author list: Agent
  family name: Zeng
  given name: Wen-Jing
author list: Agent
  family name: Zeng
  given name: Yi-Fan
doi: 10.7717/peerj.20708
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: ©2026 Wei et al.
attribution name: Wei et al.

Multifocal transcranial direct current stimulation enhances lower limb jump performance and neuromuscular adaptation in female collegiate basketball players
type: item
type: AcademicArticle
description: Background Transcranial direct current stimulation (tDCS) has been reported to enhance explosive strength in lower limb skeletal muscles. Nevertheless, findings regarding the impact of tDCS on jump performance remain inconclusive, potentially due to variations in stimulation montage and current intensity. Therefore, we aimed to elucidate the effects of multifocal tDCS on lower limb jump kinetics and neuromuscular adaptation. Methods Fourteen female collegiate basketball players were enrolled in a randomized, crossover, controlled trial. Each participant underwent three intervention sessions in a randomized sequence: 2 mA tDCS, 4 mA tDCS, and sham tDCS, all targeting the primary motor cortex (M1). After each stimulation session, countermovement jump (CMJ), squat jump (SJ), drop jump (DJ), and surface electromyography (EMG) data were collected. Statistical analysis was performed using one-way repeated measures ANOVA. Results The 4 mA multifocal tDCS condition produced a significant increase in jump height compared to baseline, sham, and the 2 mA condition. Similarly, the concentric impulse was markedly higher in the 4 mA group relative to all other conditions. Relative peak force was significantly improved in the 4 mA group versus baseline, and relative peak power was significantly greater under 4 mA tDCS compared to sham stimulation. The modified reactive strength index (RSImod) was also enhanced considerably following 4 mA tDCS, relative to both baseline and sham conditions. However, EMG analysis indicated that none of the tDCS interventions significantly affected the root mean square (RMS) values of lower limb muscle activation, including the rectus femoris (RF), vastus lateralis (VL), vastus medialis (VM), biceps femoris (BF), semitendinosus/semimembranosus (SEM), medial gastrocnemius (MG), lateral gastrocnemius (GL), and tibialis anterior (TA). Conclusion Multifocal anodal tDCS at an intensity of 4 mA significantly improves lower limb jump performance in female c…
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format: text/html
creator: Ruibo Chen
creator: Qingwei Wang
creator: Danyang Li
creator: Binbin Jia
subject: Neuroscience
subject: Kinesiology
subject: Neurology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.20705
publisher: PeerJ Inc.
rights: © 2026 Chen et al.
abstract: Background Transcranial direct current stimulation (tDCS) has been reported to enhance explosive strength in lower limb skeletal muscles. Nevertheless, findings regarding the impact of tDCS on jump performance remain inconclusive, potentially due to variations in stimulation montage and current intensity. Therefore, we aimed to elucidate the effects of multifocal tDCS on lower limb jump kinetics and neuromuscular adaptation. Methods Fourteen female collegiate basketball players were enrolled in a randomized, crossover, controlled trial. Each participant underwent three intervention sessions in a randomized sequence: 2 mA tDCS, 4 mA tDCS, and sham tDCS, all targeting the primary motor cortex (M1). After each stimulation session, countermovement jump (CMJ), squat jump (SJ), drop jump (DJ), and surface electromyography (EMG) data were collected. Statistical analysis was performed using one-way repeated measures ANOVA. Results The 4 mA multifocal tDCS condition produced a significant increase in jump height compared to baseline, sham, and the 2 mA condition. Similarly, the concentric impulse was markedly higher in the 4 mA group relative to all other conditions. Relative peak force was significantly improved in the 4 mA group versus baseline, and relative peak power was significantly greater under 4 mA tDCS compared to sham stimulation. The modified reactive strength index (RSImod) was also enhanced considerably following 4 mA tDCS, relative to both baseline and sham conditions. However, EMG analysis indicated that none of the tDCS interventions significantly affected the root mean square (RMS) values of lower limb muscle activation, including the rectus femoris (RF), vastus lateralis (VL), vastus medialis (VM), biceps femoris (BF), semitendinosus/semimembranosus (SEM), medial gastrocnemius (MG), lateral gastrocnemius (GL), and tibialis anterior (TA). Conclusion Multifocal anodal tDCS at an intensity of 4 mA significantly improves lower limb jump performance in female c…
bibliographic citation: Chen et al. (2026) Multifocal transcranial direct current stimulation enhances lower limb jump performance and neuromuscular adaptation in female collegiate basketball players. PeerJ 14:e20705 https://doi.org/10.7717/peerj.20705
date submitted: 2025-09-12
date accepted: 2025-12-10
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Ruibo
author list: Agent
  family name: Wang
  given name: Qingwei
author list: Agent
  family name: Li
  given name: Danyang
author list: Agent
  family name: Jia
  given name: Binbin
doi: 10.7717/peerj.20705
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: ©2026 Chen et al.
attribution name: Chen et al.

Effects of variable resistance training on lower limb explosive power in athletes: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objectives This study aims to investigate the effects of variable resistance training (VRT) on athletes’ lower limb explosive power through assessments of jumping, sprinting, and change of direction (COD) performance. Methods A systematic search was conducted across four electronic databases (Web of Science, PubMed, Scopus, ProQuest) from their inception until March 23, 2025. Study eligibility was assessed against the Population, Intervention, Comparison, Outcomes, Study design (PICOS) framework. Following data extraction, the methodological quality of the included studies was assessed using the Cochrane Risk of Bias tool. Data analysis was performed using Stata 15 software, with standardized mean differences (SMD) and 95% confidence intervals calculated as the pooled effect size measure. Results Fifteen articles involving 442 participants were included in the final analysis. The overall meta-analysis demonstrated that VRT was an effective method for enhancing athletes’ jumping performance (SMD = 0.81 cm, p < 0.001), sprint performance (SMD = −1.13 s, p < 0.001), and COD performance (SMD = −1.66 s, p < 0.001). Subgroup analyses indicated significant positive effects of VRT on vertical jump (VJ: SMD = 0.31 cm, p = 0.027), squat jump (SJ: SMD = 0.94 cm, p < 0.001), countermovement jump (CMJ: SMD = 1.01 cm, p < 0.001), 5-m sprint (SMD = −1.18 s, p < 0.001), 10-m sprint (SMD = −1.18 s, p < 0.001), 30-m sprint (SMD = −1.08 s, p = 0.013), T-test (SMD = −2.01 s, p < 0.001), repeated change of direction (RCOD: SMD = −2.01 s, p < 0.001), and Illinois test (SMD = −1.85 s, p < 0.001). Conclusion This systematic review suggests that VRT may serve as an effective training strategy for enhancing lower-limb explosive power in athletes. However, due to significant heterogeneity among the included studies and potential publication bias, the definitive benefits of VRT require further validation through additional high-quality research.
format: application/pdf
format: text/html
creator: Ziqi Xu
creator: Songpeng Su
creator: Zitong Xu
subject: Anatomy and Physiology
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.20644
publisher: PeerJ Inc.
rights: © 2026 Xu et al.
abstract: Objectives This study aims to investigate the effects of variable resistance training (VRT) on athletes’ lower limb explosive power through assessments of jumping, sprinting, and change of direction (COD) performance. Methods A systematic search was conducted across four electronic databases (Web of Science, PubMed, Scopus, ProQuest) from their inception until March 23, 2025. Study eligibility was assessed against the Population, Intervention, Comparison, Outcomes, Study design (PICOS) framework. Following data extraction, the methodological quality of the included studies was assessed using the Cochrane Risk of Bias tool. Data analysis was performed using Stata 15 software, with standardized mean differences (SMD) and 95% confidence intervals calculated as the pooled effect size measure. Results Fifteen articles involving 442 participants were included in the final analysis. The overall meta-analysis demonstrated that VRT was an effective method for enhancing athletes’ jumping performance (SMD = 0.81 cm, p < 0.001), sprint performance (SMD = −1.13 s, p < 0.001), and COD performance (SMD = −1.66 s, p < 0.001). Subgroup analyses indicated significant positive effects of VRT on vertical jump (VJ: SMD = 0.31 cm, p = 0.027), squat jump (SJ: SMD = 0.94 cm, p < 0.001), countermovement jump (CMJ: SMD = 1.01 cm, p < 0.001), 5-m sprint (SMD = −1.18 s, p < 0.001), 10-m sprint (SMD = −1.18 s, p < 0.001), 30-m sprint (SMD = −1.08 s, p = 0.013), T-test (SMD = −2.01 s, p < 0.001), repeated change of direction (RCOD: SMD = −2.01 s, p < 0.001), and Illinois test (SMD = −1.85 s, p < 0.001). Conclusion This systematic review suggests that VRT may serve as an effective training strategy for enhancing lower-limb explosive power in athletes. However, due to significant heterogeneity among the included studies and potential publication bias, the definitive benefits of VRT require further validation through additional high-quality research.
bibliographic citation: Xu et al. (2026) Effects of variable resistance training on lower limb explosive power in athletes: a systematic review and meta-analysis. PeerJ 14:e20644 https://doi.org/10.7717/peerj.20644
date submitted: 2025-09-06
date accepted: 2025-12-01
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Ziqi
author list: Agent
  family name: Su
  given name: Songpeng
author list: Agent
  family name: Xu
  given name: Zitong
doi: 10.7717/peerj.20644
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: ©2026 Xu et al.
attribution name: Xu et al.

Evidence-based practice among physiotherapists in India: a nationwide survey of knowledge, attitude, and implementation behavior
type: item
type: AcademicArticle
description: Background Physiotherapy services are often integrated within the broader healthcare system in India. Unlike in developed countries, physiotherapy is still limited to indirect access and needs a referral from other healthcare providers, which potentially limits physiotherapists. The purpose of this study was to explore the knowledge or skill, attitude, and behavior towards the implementation of evidence-based practice (EBP) in physiotherapy care. In addition, the physiotherapist’s perception of barriers in the implementation of EBP was inquired. Methods A cross-sectional study was conducted through an online survey involving two thousand nine hundred and ninety-six physiotherapists from 22 states/union territories in India. A 24-item EBP questionnaire (EBPQ) investigating knowledge, attitude, and behavior domains with a 1 to 7 Likert scale response for each item, with a higher score indicating a favorable response. A linear regression model was used to analyze the relationship between factors and evidence-based practice behavior among physiotherapists. Results The mean age of the participants was 35.8 ± 6.2 years, with a work experience of 13.25 ± 6.38 years. The overall EBPQ mean score of Indian physiotherapists was 3.6 ± 0.38, and the mean scores of the domains—knowledge, attitude, and implementation of EBP—were 3.59 ± 0.53, 4.29 ± 0.79, and 3.20 ± 0.62, respectively. The EBP domains were mainly determined by the educational attainment and workplace, which explained 46.1% of the variance. Lack of time and skills was identified as the top barrier influencing EBP among physiotherapists in India. The behavior dimension score of EBPQ is determined by 8 knowledge items and 2 attitude items, which explain 61.2% of the variance. Conclusions The Indian physiotherapists reported a positive attitude toward evidence-based practice; however, their knowledge and behavior were observed to be insufficient. Lack of time, limited skills, a shortage of resources, and limitations in…
format: application/pdf
format: text/html
creator: Mohammad Sidiq
creator: Jyoti Sharma
creator: Balamurugan Janakiraman
creator: Faizan Kashoo
creator: Aksh Chahal
creator: Ruchi Varshney
creator: Sumbul Ansari
creator: Akriti Pandey
creator: Richa Hirendra Rai
creator: Abdulqader Khormi
creator: Imran Khan
creator: Mohammed M. Alshehri
creator: Monira I. Aldhahi
subject: Evidence Based Medicine
subject: Global Health
subject: Science and Medical Education
subject: Healthcare Services
description: doi:10.7717/peerj.20632
publisher: PeerJ Inc.
rights: © 2026 Sidiq et al.
abstract: Background Physiotherapy services are often integrated within the broader healthcare system in India. Unlike in developed countries, physiotherapy is still limited to indirect access and needs a referral from other healthcare providers, which potentially limits physiotherapists. The purpose of this study was to explore the knowledge or skill, attitude, and behavior towards the implementation of evidence-based practice (EBP) in physiotherapy care. In addition, the physiotherapist’s perception of barriers in the implementation of EBP was inquired. Methods A cross-sectional study was conducted through an online survey involving two thousand nine hundred and ninety-six physiotherapists from 22 states/union territories in India. A 24-item EBP questionnaire (EBPQ) investigating knowledge, attitude, and behavior domains with a 1 to 7 Likert scale response for each item, with a higher score indicating a favorable response. A linear regression model was used to analyze the relationship between factors and evidence-based practice behavior among physiotherapists. Results The mean age of the participants was 35.8 ± 6.2 years, with a work experience of 13.25 ± 6.38 years. The overall EBPQ mean score of Indian physiotherapists was 3.6 ± 0.38, and the mean scores of the domains—knowledge, attitude, and implementation of EBP—were 3.59 ± 0.53, 4.29 ± 0.79, and 3.20 ± 0.62, respectively. The EBP domains were mainly determined by the educational attainment and workplace, which explained 46.1% of the variance. Lack of time and skills was identified as the top barrier influencing EBP among physiotherapists in India. The behavior dimension score of EBPQ is determined by 8 knowledge items and 2 attitude items, which explain 61.2% of the variance. Conclusions The Indian physiotherapists reported a positive attitude toward evidence-based practice; however, their knowledge and behavior were observed to be insufficient. Lack of time, limited skills, a shortage of resources, and limitations in…
bibliographic citation: Sidiq et al. (2026) Evidence-based practice among physiotherapists in India: a nationwide survey of knowledge, attitude, and implementation behavior. PeerJ 14:e20632 https://doi.org/10.7717/peerj.20632
date submitted: 2025-06-22
date accepted: 2025-11-30
issued: 2026-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sidiq
  given name: Mohammad
author list: Agent
  family name: Sharma
  given name: Jyoti
author list: Agent
  family name: Janakiraman
  given name: Balamurugan
author list: Agent
  family name: Kashoo
  given name: Faizan
author list: Agent
  family name: Chahal
  given name: Aksh
author list: Agent
  family name: Varshney
  given name: Ruchi
author list: Agent
  family name: Ansari
  given name: Sumbul
author list: Agent
  family name: Pandey
  given name: Akriti
author list: Agent
  family name: Rai
  given name: Richa Hirendra
author list: Agent
  family name: Khormi
  given name: Abdulqader
author list: Agent
  family name: Khan
  given name: Imran
author list: Agent
  family name: Alshehri
  given name: Mohammed M.
author list: Agent
  family name: Aldhahi
  given name: Monira I.
doi: 10.7717/peerj.20632
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-04
copyright: ©2026 Sidiq et al.
attribution name: Sidiq et al.

Machine learning-driven PET-CT and clinical pathology model for predicting mediastinal lymph node metastasis in non-small cell lung cancer: a retrospective cohort study
type: item
type: AcademicArticle
description: Objective This study aims to evaluate whether Positron Emission Tomography–Computed Tomography (PET-CT) imaging features of primary tumors and lymph nodes, combined with clinical and pathological data, can accurately predict mediastinal lymph node metastasis (MLNM) in resectable non-small cell lung cancer (NSCLC) using machine learning models. Methods A retrospective study was conducted on 390 NSCLC patients who underwent tumor resection and lymph node dissection between January 2017 and December 2023. All patients received 18F-fluorodeoxyglucose (18F-FDG) PET-CT scans within two weeks before surgery. Data from 390 primary tumors and 1,026 lymph node stations were analyzed. Clinical and PET-CT imaging features were extracted, and feature selection was performed using a random forest algorithm. Eight machine learning models were evaluated, including Logistic Regression, classification and regression tree (CART), support vector machine (SVM), gradient boosting decision tree (GBDT), Random Forest, multi-layer perceptron (MLP), extreme gradient boosting tree (XGBoost) and k-nearest neighbor algorithm (KNN). Three models were developed Tumor-Pathology-Clinical (TPC), Lymph-Pathology-Clinical (LPC), and Tumor-Lymph-Pathology-Clinical (TLPC). Model performance was assessed using Receiver Operating Characteristic (ROC) curves, Decision Curve Analysis (DCA), and confusion matrices. Results The TLPC model, based on the XGBoost algorithm, showed the best performance, with an Area Under the Curve (AUC) of 0.90 (95% CI [0.883–0.957]), specificity of 0.84, and sensitivity of 0.96 (P = 0.0069; significant at P < 0.05). In comparison, the TPC model achieved an AUC of 0.67 (95% CI [0.647–0.703]), specificity of 0.46, and sensitivity of 0.56 (P = 0.7037; not significant). The LPC model showed intermediate performance, with an AUC of 0.78 (95% CI [0.713–0.751]), specificity of 0.73, and sensitivity of 0.84 (P = 0.0269; significant at P < 0.05). All P-values were derived from DeLong’s …
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format: text/html
creator: Taiyu Bi
creator: Min Qiang
creator: Xiaotian Duan
creator: Yipeng Yin
creator: Wenyu Zhang
creator: Zhe Chen
creator: Xinjun Zhang
creator: Jianzun Ma
creator: Bowei Zhang
creator: Mingbo Tang
creator: Wei Liu
subject: Oncology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20788
publisher: PeerJ Inc.
rights: © 2026 Bi et al.
abstract: Objective This study aims to evaluate whether Positron Emission Tomography–Computed Tomography (PET-CT) imaging features of primary tumors and lymph nodes, combined with clinical and pathological data, can accurately predict mediastinal lymph node metastasis (MLNM) in resectable non-small cell lung cancer (NSCLC) using machine learning models. Methods A retrospective study was conducted on 390 NSCLC patients who underwent tumor resection and lymph node dissection between January 2017 and December 2023. All patients received 18F-fluorodeoxyglucose (18F-FDG) PET-CT scans within two weeks before surgery. Data from 390 primary tumors and 1,026 lymph node stations were analyzed. Clinical and PET-CT imaging features were extracted, and feature selection was performed using a random forest algorithm. Eight machine learning models were evaluated, including Logistic Regression, classification and regression tree (CART), support vector machine (SVM), gradient boosting decision tree (GBDT), Random Forest, multi-layer perceptron (MLP), extreme gradient boosting tree (XGBoost) and k-nearest neighbor algorithm (KNN). Three models were developed Tumor-Pathology-Clinical (TPC), Lymph-Pathology-Clinical (LPC), and Tumor-Lymph-Pathology-Clinical (TLPC). Model performance was assessed using Receiver Operating Characteristic (ROC) curves, Decision Curve Analysis (DCA), and confusion matrices. Results The TLPC model, based on the XGBoost algorithm, showed the best performance, with an Area Under the Curve (AUC) of 0.90 (95% CI [0.883–0.957]), specificity of 0.84, and sensitivity of 0.96 (P = 0.0069; significant at P < 0.05). In comparison, the TPC model achieved an AUC of 0.67 (95% CI [0.647–0.703]), specificity of 0.46, and sensitivity of 0.56 (P = 0.7037; not significant). The LPC model showed intermediate performance, with an AUC of 0.78 (95% CI [0.713–0.751]), specificity of 0.73, and sensitivity of 0.84 (P = 0.0269; significant at P < 0.05). All P-values were derived from DeLong’s …
bibliographic citation: Bi et al. (2026) Machine learning-driven PET-CT and clinical pathology model for predicting mediastinal lymph node metastasis in non-small cell lung cancer: a retrospective cohort study. PeerJ 14:e20788 https://doi.org/10.7717/peerj.20788
date submitted: 2025-07-23
date accepted: 2025-12-22
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bi
  given name: Taiyu
author list: Agent
  family name: Qiang
  given name: Min
author list: Agent
  family name: Duan
  given name: Xiaotian
author list: Agent
  family name: Yin
  given name: Yipeng
author list: Agent
  family name: Zhang
  given name: Wenyu
author list: Agent
  family name: Chen
  given name: Zhe
author list: Agent
  family name: Zhang
  given name: Xinjun
author list: Agent
  family name: Ma
  given name: Jianzun
author list: Agent
  family name: Zhang
  given name: Bowei
author list: Agent
  family name: Tang
  given name: Mingbo
author list: Agent
  family name: Liu
  given name: Wei
doi: 10.7717/peerj.20788
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: © 2026 Bi et al.
attribution name: Bi et al.

Effect of temperature acclimation period on upper thermal tolerance in a terrestrial salamander
type: item
type: AcademicArticle
description: Background Physiological traits, such as the critical thermal maximum (CTmax, defined as an individual’s upper thermal tolerance limit), can be important for understanding species’ vulnerability to climate and habitat change. A separate trait, thermal acclimation capacity, is defined as the physiological adjustment of organisms to temperature variation, which can influence phenotypic traits such as CTmax. The relationship between acclimation capacity and CTmax has been widely studied in ectotherms like fish, amphibians, and reptiles, and it is generally observed that CTmax increases with higher acclimation temperatures. However, there is a lack of information about whether amphibians respond differently to long- versus short-term acclimation. Understanding thermal acclimation capacity under rapid environmental change is important, as high acclimation capacity may reduce vulnerability. Here, we evaluated the thermal acclimation capacity of the Eastern Red-backed Salamander, Plethodon cinereus, in response to short- and long-term acclimation treatments in a laboratory setting. Methods We exposed salamanders to three different treatments: control animals were maintained at 15 °C for 30 days; animals in the short-term acclimation group were maintained at 15 °C for 28 days, and 23 °C for 48 hours before testing CTmax; and animals in the long-term acclimation group were maintained at 23 °C for 30 days. We measured the CTmax of all animals at the end of the experiment to determine whether tolerance to high temperatures varied depending on the length of exposure to warm conditions. Results Although we observed a slight increase in CTmax from the control treatment to the short-term (+0.93 °C) and long-term (+0.98 °C) acclimation treatments, the difference in CTmax between acclimation treatments was small (0.05 °C), and none of the differences were statistically significant. Discussion Several factors may explain the low variation in CTmax described in our study, including ph…
format: application/pdf
format: text/html
creator: Sandra C. Valderrama Robles
creator: Molly G. Russell
creator: Carl D. Anthony
creator: James I. Watling
subject: Conservation Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.20775
publisher: PeerJ Inc.
rights: © 2026 Valderrama Robles et al.
abstract: Background Physiological traits, such as the critical thermal maximum (CTmax, defined as an individual’s upper thermal tolerance limit), can be important for understanding species’ vulnerability to climate and habitat change. A separate trait, thermal acclimation capacity, is defined as the physiological adjustment of organisms to temperature variation, which can influence phenotypic traits such as CTmax. The relationship between acclimation capacity and CTmax has been widely studied in ectotherms like fish, amphibians, and reptiles, and it is generally observed that CTmax increases with higher acclimation temperatures. However, there is a lack of information about whether amphibians respond differently to long- versus short-term acclimation. Understanding thermal acclimation capacity under rapid environmental change is important, as high acclimation capacity may reduce vulnerability. Here, we evaluated the thermal acclimation capacity of the Eastern Red-backed Salamander, Plethodon cinereus, in response to short- and long-term acclimation treatments in a laboratory setting. Methods We exposed salamanders to three different treatments: control animals were maintained at 15 °C for 30 days; animals in the short-term acclimation group were maintained at 15 °C for 28 days, and 23 °C for 48 hours before testing CTmax; and animals in the long-term acclimation group were maintained at 23 °C for 30 days. We measured the CTmax of all animals at the end of the experiment to determine whether tolerance to high temperatures varied depending on the length of exposure to warm conditions. Results Although we observed a slight increase in CTmax from the control treatment to the short-term (+0.93 °C) and long-term (+0.98 °C) acclimation treatments, the difference in CTmax between acclimation treatments was small (0.05 °C), and none of the differences were statistically significant. Discussion Several factors may explain the low variation in CTmax described in our study, including ph…
bibliographic citation: Valderrama Robles et al. (2026) Effect of temperature acclimation period on upper thermal tolerance in a terrestrial salamander. PeerJ 14:e20775 https://doi.org/10.7717/peerj.20775
date submitted: 2025-10-20
date accepted: 2025-12-18
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valderrama Robles
  given name: Sandra C.
author list: Agent
  family name: Russell
  given name: Molly G.
author list: Agent
  family name: Anthony
  given name: Carl D.
author list: Agent
  family name: Watling
  given name: James I.
doi: 10.7717/peerj.20775
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Valderrama Robles et al.
attribution name: Valderrama Robles et al.

Nail structural alterations and zinc levels in the elderly: an observational cross-sectional study
type: item
type: AcademicArticle
description: Background Nails in the elderly undergo several structural changes related to aging with respect to surface, thickness, color, and growth pattern. The present study explores the potential association between nail alterations and zinc levels in this population. Methods A total of 64 subjects aged ≥60 years with or without nail changes were recruited from the Dermatology and Venereology Outpatient Clinic at Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia. Their nail features were observed clinically and evaluated utilizing dermoscopy, and nail clippings weighing a total of 200 milligrams were collected from each subject for nail zinc concentration measurement. Appropriate statistical tests were employed to determine the relationship between nail zinc levels and the structural alterations, as well as the patients’ comorbidities and medications, at a significance level of 0.05. Results Most subjects in our study showed altered nail profiles in multiple digits (75.0%) with a predilection for toenails (62.3%), and the first toenail was primarily affected. The commonest dermoscopic features displayed in altered nails include nail plate pigmentation (n = 64), distal edge thickening (n = 39), and surface changes (n = 34). The average nail zinc concentration was lower in the elderly with nail changes than in those without, albeit with no statistically significant differences (p = 0.687). Subgroup analyses according to comorbidities (hypertension, diabetes mellitus type 2, and dyslipidemia) and medications (antihypertensives, antidiabetics, antidyslipidemic drugs, and anticonvulsants) also exhibited no discrepancies. Conclusions This study highlights the complex interactions among nail structural changes, zinc levels, comorbidities, and medications; hence, further research is warranted to obtain a deeper understanding.
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creator: Shannaz Nadia Yusharyahya
creator: Chia-Yu Chu
creator: Roro Inge Ade Krisanti
creator: Lili Legiawati
creator: Rinadewi Astriningrum
creator: Levina Ameline Moelyono
creator: Viecky M.P. Betavani
creator: Valdi Ven Japranata
subject: Dermatology
subject: Geriatrics
subject: Global Health
description: doi:10.7717/peerj.20771
publisher: PeerJ Inc.
rights: © 2026 Yusharyahya et al.
abstract: Background Nails in the elderly undergo several structural changes related to aging with respect to surface, thickness, color, and growth pattern. The present study explores the potential association between nail alterations and zinc levels in this population. Methods A total of 64 subjects aged ≥60 years with or without nail changes were recruited from the Dermatology and Venereology Outpatient Clinic at Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia. Their nail features were observed clinically and evaluated utilizing dermoscopy, and nail clippings weighing a total of 200 milligrams were collected from each subject for nail zinc concentration measurement. Appropriate statistical tests were employed to determine the relationship between nail zinc levels and the structural alterations, as well as the patients’ comorbidities and medications, at a significance level of 0.05. Results Most subjects in our study showed altered nail profiles in multiple digits (75.0%) with a predilection for toenails (62.3%), and the first toenail was primarily affected. The commonest dermoscopic features displayed in altered nails include nail plate pigmentation (n = 64), distal edge thickening (n = 39), and surface changes (n = 34). The average nail zinc concentration was lower in the elderly with nail changes than in those without, albeit with no statistically significant differences (p = 0.687). Subgroup analyses according to comorbidities (hypertension, diabetes mellitus type 2, and dyslipidemia) and medications (antihypertensives, antidiabetics, antidyslipidemic drugs, and anticonvulsants) also exhibited no discrepancies. Conclusions This study highlights the complex interactions among nail structural changes, zinc levels, comorbidities, and medications; hence, further research is warranted to obtain a deeper understanding.
bibliographic citation: Yusharyahya et al. (2026) Nail structural alterations and zinc levels in the elderly: an observational cross-sectional study. PeerJ 14:e20771 https://doi.org/10.7717/peerj.20771
date submitted: 2025-09-06
date accepted: 2025-12-18
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yusharyahya
  given name: Shannaz Nadia
author list: Agent
  family name: Chu
  given name: Chia-Yu
author list: Agent
  family name: Krisanti
  given name: Roro Inge Ade
author list: Agent
  family name: Legiawati
  given name: Lili
author list: Agent
  family name: Astriningrum
  given name: Rinadewi
author list: Agent
  family name: Moelyono
  given name: Levina Ameline
author list: Agent
  family name: Betavani
  given name: Viecky M.P.
author list: Agent
  family name: Japranata
  given name: Valdi Ven
doi: 10.7717/peerj.20771
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Yusharyahya et al.
attribution name: Yusharyahya et al.

Retrospective dosimetric evaluation of the collapsed cone, AAA, and Acuros XB algorithms for lung cancer Halcyon VMAT plans
type: item
type: AcademicArticle
description: When RayStation is used for Halcyon treatment planning and the plan is transferred to the ARIA/Eclipse system for delivery verification, the dose must be recalculated using the Anisotropic Analytical Algorithm (AAA) or AcurosXB algorithm for compatibility. This study evaluated the dosimetric differences among the Collapsed Cone (CC), AAA, and AcurosXB algorithms for non-small cell lung cancer (NSCLC) volumetric modulated arc therapy (VMAT) plans on the Halcyon platform. Treatment plans for 60 lung cancer patients were initially generated using the CC algorithm in RayStation and then recalculated in Eclipse using AAA and AcurosXB without re-optimization or renormalization. Systematic variations were observed among the three algorithms. AcurosXB showed the largest reductions in target doses compared with CC (up to a 1.56% reduction in clinical target volume (CTV) D2%), while AAA demonstrated smaller differences. For planning target volume (PTV) metrics, both AAA and AcurosXB yielded lower doses than CC (AAA up to 2.16% in D95%; AcurosXB up to 1.58% in D2%). All variations in CTV and PTV metrics remained within approximately 1.7%. For organ-at-risk doses, AAA produced slightly lower values than CC, whereas AcurosXB yielded consistently lower doses across most parameters. Overall, this study shows that AAA and AcurosXB provide slightly lower dose estimates than CC for the same Halcyon plan, especially for PTV and organ-at-risk metrics. These results highlight the importance of consistent dose-calculation methodology in NSCLC radiotherapy, particularly in cross-platform workflows between RayStation and Eclipse.
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format: text/html
creator: Kainan Shao
creator: Fenglei Du
creator: Lingyun Qiu
creator: Yinghao Zhang
creator: Yucheng Li
creator: Jieni Ding
creator: Wenming Zhan
creator: Weijun Chen
subject: Biophysics
subject: Evidence Based Medicine
subject: Oncology
subject: Radiology and Medical Imaging
subject: Respiratory Medicine
description: doi:10.7717/peerj.20759
publisher: PeerJ Inc.
rights: © 2026 Shao et al.
abstract: When RayStation is used for Halcyon treatment planning and the plan is transferred to the ARIA/Eclipse system for delivery verification, the dose must be recalculated using the Anisotropic Analytical Algorithm (AAA) or AcurosXB algorithm for compatibility. This study evaluated the dosimetric differences among the Collapsed Cone (CC), AAA, and AcurosXB algorithms for non-small cell lung cancer (NSCLC) volumetric modulated arc therapy (VMAT) plans on the Halcyon platform. Treatment plans for 60 lung cancer patients were initially generated using the CC algorithm in RayStation and then recalculated in Eclipse using AAA and AcurosXB without re-optimization or renormalization. Systematic variations were observed among the three algorithms. AcurosXB showed the largest reductions in target doses compared with CC (up to a 1.56% reduction in clinical target volume (CTV) D2%), while AAA demonstrated smaller differences. For planning target volume (PTV) metrics, both AAA and AcurosXB yielded lower doses than CC (AAA up to 2.16% in D95%; AcurosXB up to 1.58% in D2%). All variations in CTV and PTV metrics remained within approximately 1.7%. For organ-at-risk doses, AAA produced slightly lower values than CC, whereas AcurosXB yielded consistently lower doses across most parameters. Overall, this study shows that AAA and AcurosXB provide slightly lower dose estimates than CC for the same Halcyon plan, especially for PTV and organ-at-risk metrics. These results highlight the importance of consistent dose-calculation methodology in NSCLC radiotherapy, particularly in cross-platform workflows between RayStation and Eclipse.
bibliographic citation: Shao et al. (2026) Retrospective dosimetric evaluation of the collapsed cone, AAA, and Acuros XB algorithms for lung cancer Halcyon VMAT plans. PeerJ 14:e20759 https://doi.org/10.7717/peerj.20759
date submitted: 2025-09-02
date accepted: 2025-12-17
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shao
  given name: Kainan
author list: Agent
  family name: Du
  given name: Fenglei
author list: Agent
  family name: Qiu
  given name: Lingyun
author list: Agent
  family name: Zhang
  given name: Yinghao
author list: Agent
  family name: Li
  given name: Yucheng
author list: Agent
  family name: Ding
  given name: Jieni
author list: Agent
  family name: Zhan
  given name: Wenming
author list: Agent
  family name: Chen
  given name: Weijun
doi: 10.7717/peerj.20759
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Shao et al.
attribution name: Shao et al.

Comparison of the performance of a Three-Dimensional Body Scanner and radiography in evaluating adult scoliosis
type: item
type: AcademicArticle
description: Background Adult scoliosis, which is characterized by a persistent lateral deviation of the spine of at least 10° in the frontal plane along with vertebral rotation in adulthood, can result from various causes, including degenerative changes, untreated childhood scoliosis, spinal trauma, and prior surgeries. Traditionally, spinal curvature is assessed by measuring the Cobb angle via radiographic imaging; however, concerns over radiation exposure have prompted exploration of alternative diagnostic tools. This study aims to evaluate the effectiveness of a newly developed three-dimensional (3D) body scanner, equipped with 12 depth cameras, in assessing spinal alignment and measuring the Cobb angle in patients with adult scoliosis, in comparison with radiographic imaging. Methods In this prospective cohort study, 40 patients with adult scoliosis—both idiopathic and degenerative—underwent evaluation using both radiographic imaging and 3D body scanning. Cobb angles were measured by both methods. Pearson and Spearman’s rank correlation coefficients were calculated to assess the linear and monotonic relationships between measurements. Measurement accuracy was quantified using the mean bias from Bland–Altman analysis and spatial agreement of spinal positions was further evaluated using the Intersection over Union (IoU) metric. Univariable and multivariable regression analyses were performed to assess whether body habitus (body mass index, waist circumference, waist-to-height ratio, age, and sex) influenced the absolute error between 3D body scanner-predicted and radiographic Cobb angles. Results Cobb angle measurements obtained from 3D body scanning were highly correlated with those from radiography (Pearson r = 0.92, P < 0.001; Spearman ρ = 0.85, P < 0.001), indicating strong linear and monotonic agreement. Bland–Altman analysis showed a small mean bias of −1.06 (95% limits of agreement: −10.25 to 8.12). The average IoU was 0.89, indicating substantial spatial agreement in …
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creator: Ting-Ju Kuo
creator: Chin-Yin Yu
creator: Jui-Chi Lin
creator: Chien-Min Lin
creator: Tsan-Hon Liou
creator: Chih-Wei Peng
creator: Hung-Chou Chen
subject: Bioengineering
subject: Anatomy and Physiology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.20752
publisher: PeerJ Inc.
rights: © 2026 Kuo et al.
abstract: Background Adult scoliosis, which is characterized by a persistent lateral deviation of the spine of at least 10° in the frontal plane along with vertebral rotation in adulthood, can result from various causes, including degenerative changes, untreated childhood scoliosis, spinal trauma, and prior surgeries. Traditionally, spinal curvature is assessed by measuring the Cobb angle via radiographic imaging; however, concerns over radiation exposure have prompted exploration of alternative diagnostic tools. This study aims to evaluate the effectiveness of a newly developed three-dimensional (3D) body scanner, equipped with 12 depth cameras, in assessing spinal alignment and measuring the Cobb angle in patients with adult scoliosis, in comparison with radiographic imaging. Methods In this prospective cohort study, 40 patients with adult scoliosis—both idiopathic and degenerative—underwent evaluation using both radiographic imaging and 3D body scanning. Cobb angles were measured by both methods. Pearson and Spearman’s rank correlation coefficients were calculated to assess the linear and monotonic relationships between measurements. Measurement accuracy was quantified using the mean bias from Bland–Altman analysis and spatial agreement of spinal positions was further evaluated using the Intersection over Union (IoU) metric. Univariable and multivariable regression analyses were performed to assess whether body habitus (body mass index, waist circumference, waist-to-height ratio, age, and sex) influenced the absolute error between 3D body scanner-predicted and radiographic Cobb angles. Results Cobb angle measurements obtained from 3D body scanning were highly correlated with those from radiography (Pearson r = 0.92, P < 0.001; Spearman ρ = 0.85, P < 0.001), indicating strong linear and monotonic agreement. Bland–Altman analysis showed a small mean bias of −1.06 (95% limits of agreement: −10.25 to 8.12). The average IoU was 0.89, indicating substantial spatial agreement in …
bibliographic citation: Kuo et al. (2026) Comparison of the performance of a Three-Dimensional Body Scanner and radiography in evaluating adult scoliosis. PeerJ 14:e20752 https://doi.org/10.7717/peerj.20752
date submitted: 2025-07-15
date accepted: 2025-12-16
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuo
  given name: Ting-Ju
author list: Agent
  family name: Yu
  given name: Chin-Yin
author list: Agent
  family name: Lin
  given name: Jui-Chi
author list: Agent
  family name: Lin
  given name: Chien-Min
author list: Agent
  family name: Liou
  given name: Tsan-Hon
author list: Agent
  family name: Peng
  given name: Chih-Wei
author list: Agent
  family name: Chen
  given name: Hung-Chou
doi: 10.7717/peerj.20752
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Kuo et al.
attribution name: Kuo et al.

Establishing a new methodology for annelid studies: a biometric study of the ragworm Hediste diversicolor (Müller, 1776)
type: item
type: AcademicArticle
description: In this study, we propose a new biometric methodology for annelids, based on the number of chaetiger segments as an indicator of growth (independent variable), relating to other structures, such as the number of paragnaths and parapodia, using the commercial species Hediste diversicolor (Müller, 1776) as a model. This species belongs to the family Nereididae, found in estuarine environments along the European Atlantic coast (DOI 10.11646/zootaxa.5696.1.2). This species has several appendages with sensory functions along the body that help the animal navigate in its environment. It also has specialised feeding structures in the peristomium that are essential for taxonomic identification, called paragnaths. The parapodium has distinct chaetal arrangements that distinguish it from other species in the same genus. Due to the importance of economic activities such as fishing and aquaculture, this ragworm is a typical protagonist for studies in multiple areas, with a well-documented life cycle. However, knowledge is lacking on the growth and evolution of individual structures and appendages of the body in this species during its life cycle. Our findings revealed a significant positive correlation between the number of chaetiger segments and most of the morphological structures analysed, evidencing a proportional growth of most of these features, related directly to the chaetigers segments. Simple chaetae, a specific type of chaeta only present in the genus Hediste, were only found in individuals with more than 25 chaetiger segments, possibly indicating a functional change as the worm matures. Simple chaetae tend to be found earlier along the body axis, closer to the median chaetiger as the organism matures. The results illustrate how H. diversicolor develops over time, highlighting the developmental processes and representing the first biometric study of nereidid polychaetes, based on chaetiger count as a proxy for biometric growth, to define new possible life cycle stage…
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format: text/html
creator: João Almeida
creator: Carlos Antunes
creator: Bruno Spacek Godoy
creator: Dimitri de Araujo Costa
subject: Developmental Biology
subject: Zoology
description: doi:10.7717/peerj.20736
publisher: PeerJ Inc.
rights: © 2026 Almeida et al.
abstract: In this study, we propose a new biometric methodology for annelids, based on the number of chaetiger segments as an indicator of growth (independent variable), relating to other structures, such as the number of paragnaths and parapodia, using the commercial species Hediste diversicolor (Müller, 1776) as a model. This species belongs to the family Nereididae, found in estuarine environments along the European Atlantic coast (DOI 10.11646/zootaxa.5696.1.2). This species has several appendages with sensory functions along the body that help the animal navigate in its environment. It also has specialised feeding structures in the peristomium that are essential for taxonomic identification, called paragnaths. The parapodium has distinct chaetal arrangements that distinguish it from other species in the same genus. Due to the importance of economic activities such as fishing and aquaculture, this ragworm is a typical protagonist for studies in multiple areas, with a well-documented life cycle. However, knowledge is lacking on the growth and evolution of individual structures and appendages of the body in this species during its life cycle. Our findings revealed a significant positive correlation between the number of chaetiger segments and most of the morphological structures analysed, evidencing a proportional growth of most of these features, related directly to the chaetigers segments. Simple chaetae, a specific type of chaeta only present in the genus Hediste, were only found in individuals with more than 25 chaetiger segments, possibly indicating a functional change as the worm matures. Simple chaetae tend to be found earlier along the body axis, closer to the median chaetiger as the organism matures. The results illustrate how H. diversicolor develops over time, highlighting the developmental processes and representing the first biometric study of nereidid polychaetes, based on chaetiger count as a proxy for biometric growth, to define new possible life cycle stage…
bibliographic citation: Almeida et al. (2026) Establishing a new methodology for annelid studies: a biometric study of the ragworm Hediste diversicolor (Müller, 1776). PeerJ 14:e20736 https://doi.org/10.7717/peerj.20736
date submitted: 2025-03-09
date accepted: 2025-12-15
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almeida
  given name: João
author list: Agent
  family name: Antunes
  given name: Carlos
author list: Agent
  family name: Godoy
  given name: Bruno Spacek
author list: Agent
  family name: Costa
  given name: Dimitri de Araujo
doi: 10.7717/peerj.20736
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Almeida et al.
attribution name: Almeida et al.

Comparative metabolomics reveals organ-specific discrepancy in TCMSP-predicted bioactive ingredients between two geographically distinct regions of Rehmannia chingii
type: item
type: AcademicArticle
description: Background The geographical region and organ-specific accumulation of metabolites in medicinal plants are critical determinants of their pharmaceutical efficacy. Rehmannia chingii, an endemic species native to eastern China and a significant member of the genus Rehmannia, exhibits multiple bioactive properties in both its leaves and roots. However, spatial distribution of its pharmaceutical ingredients across various geographical regions remains inadequately understood. Methods and Results This study combined widely targeted metabolomics with the Traditional Chinese Medicine System Drug Analysis Platform (TCMSP) to investigate the accumulation patterns of medicinal ingredients in the leaves and roots of fresh R. chingii from two distinct geographical regions. Among the 1,420 metabolites identified, four differential biomarkers were identified: p-coumaroylcadaverine and protocatechuic acid-4-o-glucoside, which were primarily associated with geographical differentiation, and 5, 6-dimethyl-2-benzofuran-1, 3-dione and daphnin, which were indicative of organ type classification. Additionally, 31 potential bioactive ingredients were prioritized via TCMSP screening. Metabolic profiling further revealed that multiple flavonoids were enriched in leaves, whereas roots accumulated higher levels of tangeretin, 6-o-p-coumaroylajugol, guanosine, virexilactone, and aucubin. Notably, coniferin and tangeretin, with oral bioavailability values ≥30% and drug-likeness values ≥0.18, were identified as key potential bioactive marker ingredients, and they were highly abundant in R. chingii from the Tianmu Mountain region of Hangzhou. Conclusion These findings highlight the critical role of geographic and organ-specific factors in determining the metabolic profiles of R. chingii, thereby advancing our understanding of its medicinal value and providing a theoretical basis for the rational exploitation and utilization of its medicinal resources.
format: application/pdf
format: text/html
creator: Wanbo Zhang
creator: Xinjie Jin
creator: Ying Zhang
creator: Luhan Peng
creator: Haifeng Wang
creator: Yongqun Chen
creator: Yonghua Zhang
subject: Agricultural Science
subject: Translational Medicine
subject: Metabolic Sciences
description: doi:10.7717/peerj.20722
publisher: PeerJ Inc.
rights: © 2026 Zhang et al.
abstract: Background The geographical region and organ-specific accumulation of metabolites in medicinal plants are critical determinants of their pharmaceutical efficacy. Rehmannia chingii, an endemic species native to eastern China and a significant member of the genus Rehmannia, exhibits multiple bioactive properties in both its leaves and roots. However, spatial distribution of its pharmaceutical ingredients across various geographical regions remains inadequately understood. Methods and Results This study combined widely targeted metabolomics with the Traditional Chinese Medicine System Drug Analysis Platform (TCMSP) to investigate the accumulation patterns of medicinal ingredients in the leaves and roots of fresh R. chingii from two distinct geographical regions. Among the 1,420 metabolites identified, four differential biomarkers were identified: p-coumaroylcadaverine and protocatechuic acid-4-o-glucoside, which were primarily associated with geographical differentiation, and 5, 6-dimethyl-2-benzofuran-1, 3-dione and daphnin, which were indicative of organ type classification. Additionally, 31 potential bioactive ingredients were prioritized via TCMSP screening. Metabolic profiling further revealed that multiple flavonoids were enriched in leaves, whereas roots accumulated higher levels of tangeretin, 6-o-p-coumaroylajugol, guanosine, virexilactone, and aucubin. Notably, coniferin and tangeretin, with oral bioavailability values ≥30% and drug-likeness values ≥0.18, were identified as key potential bioactive marker ingredients, and they were highly abundant in R. chingii from the Tianmu Mountain region of Hangzhou. Conclusion These findings highlight the critical role of geographic and organ-specific factors in determining the metabolic profiles of R. chingii, thereby advancing our understanding of its medicinal value and providing a theoretical basis for the rational exploitation and utilization of its medicinal resources.
bibliographic citation: Zhang et al. (2026) Comparative metabolomics reveals organ-specific discrepancy in TCMSP-predicted bioactive ingredients between two geographically distinct regions of Rehmannia chingii. PeerJ 14:e20722 https://doi.org/10.7717/peerj.20722
date submitted: 2025-06-24
date accepted: 2025-12-11
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Wanbo
author list: Agent
  family name: Jin
  given name: Xinjie
author list: Agent
  family name: Zhang
  given name: Ying
author list: Agent
  family name: Peng
  given name: Luhan
author list: Agent
  family name: Wang
  given name: Haifeng
author list: Agent
  family name: Chen
  given name: Yongqun
author list: Agent
  family name: Zhang
  given name: Yonghua
doi: 10.7717/peerj.20722
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Zhang et al.
attribution name: Zhang et al.

The effects of GLP-1 receptor agonists on metabolic inflammatory markers in patients with type 2 diabetes mellitus: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective This study aimed to evaluate the impact of GLP-1 receptor agonists (GLP-1 RAs) on metabolic inflammatory markers in patients with type 2 diabetes mellitus (T2DM), providing evidence-based insights for their potential application in anti-inflammatory therapy. Methods Research questions were developed using the PICOS framework, and the study strictly adhered to PRISMA guidelines. Comprehensive literature searches were conducted across PubMed, EBSCO, Embase, Web of Science, and the Cochrane Library. Data synthesis and subgroup analyses (focusing on GLP-1 RA subtypes, treatment duration, and administration frequency) were performed using RevMan 5.4 software. Results Out of 1,347 articles retrieved, 25 studies were ultimately included, comprising a total sample of 1,878 participants (879 in the experimental groups and 999 in the control groups). Quality assessment indicated that most studies exhibited a low risk of bias, with only one study rated as high risk and three studies showing some concerns. Meta-analysis results demonstrated that 18 studies reported a significant reduction in CRP levels in T2DM patients treated with GLP-1 RAs (SMD = −0.39, 95% CI [−0.72 to −0.06], P = 0.02, I2 = 88%). Although the results from 13 studies indicated a decreasing trend in IL-6 levels (SMD = −0.52), this change was not statistically significant (95% CI [−1.34 to 0.29], P = 0.21, I2 = 96%). Additionally, 14 studies showed that GLP-1 RAs significantly reduced TNF-α levels (SMD = −0.51, 95% CI [−0.81 to −0.20], P = 0.001, I2 = 81%). Subgroup analyses revealed that both the type of GLP-1 RA and a longer treatment duration (≥36 weeks) were associated with more pronounced improvements in inflammatory markers. Conclusion GLP-1 RAs exhibit a certain degree of anti-inflammatory effect in patients with T2DM, effectively reducing CRP and TNF-α levels. The anti-inflammatory efficacy appears to be influenced by both the type of drug used and the duration of treatment, with more pronoun…
format: application/pdf
format: text/html
creator: Fang Zhao
creator: Haoshu Wang
creator: Shenguang Li
creator: Hezhang Yun
creator: Wenbo Su
subject: Biochemistry
subject: Diabetes and Endocrinology
subject: Metabolic Sciences
subject: Obesity
description: doi:10.7717/peerj.20710
publisher: PeerJ Inc.
rights: © 2026 Zhao et al.
abstract: Objective This study aimed to evaluate the impact of GLP-1 receptor agonists (GLP-1 RAs) on metabolic inflammatory markers in patients with type 2 diabetes mellitus (T2DM), providing evidence-based insights for their potential application in anti-inflammatory therapy. Methods Research questions were developed using the PICOS framework, and the study strictly adhered to PRISMA guidelines. Comprehensive literature searches were conducted across PubMed, EBSCO, Embase, Web of Science, and the Cochrane Library. Data synthesis and subgroup analyses (focusing on GLP-1 RA subtypes, treatment duration, and administration frequency) were performed using RevMan 5.4 software. Results Out of 1,347 articles retrieved, 25 studies were ultimately included, comprising a total sample of 1,878 participants (879 in the experimental groups and 999 in the control groups). Quality assessment indicated that most studies exhibited a low risk of bias, with only one study rated as high risk and three studies showing some concerns. Meta-analysis results demonstrated that 18 studies reported a significant reduction in CRP levels in T2DM patients treated with GLP-1 RAs (SMD = −0.39, 95% CI [−0.72 to −0.06], P = 0.02, I2 = 88%). Although the results from 13 studies indicated a decreasing trend in IL-6 levels (SMD = −0.52), this change was not statistically significant (95% CI [−1.34 to 0.29], P = 0.21, I2 = 96%). Additionally, 14 studies showed that GLP-1 RAs significantly reduced TNF-α levels (SMD = −0.51, 95% CI [−0.81 to −0.20], P = 0.001, I2 = 81%). Subgroup analyses revealed that both the type of GLP-1 RA and a longer treatment duration (≥36 weeks) were associated with more pronounced improvements in inflammatory markers. Conclusion GLP-1 RAs exhibit a certain degree of anti-inflammatory effect in patients with T2DM, effectively reducing CRP and TNF-α levels. The anti-inflammatory efficacy appears to be influenced by both the type of drug used and the duration of treatment, with more pronoun…
bibliographic citation: Zhao et al. (2026) The effects of GLP-1 receptor agonists on metabolic inflammatory markers in patients with type 2 diabetes mellitus: a systematic review and meta-analysis. PeerJ 14:e20710 https://doi.org/10.7717/peerj.20710
date submitted: 2025-06-18
date accepted: 2025-12-10
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhao
  given name: Fang
author list: Agent
  family name: Wang
  given name: Haoshu
author list: Agent
  family name: Li
  given name: Shenguang
author list: Agent
  family name: Yun
  given name: Hezhang
author list: Agent
  family name: Su
  given name: Wenbo
doi: 10.7717/peerj.20710
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Zhao et al.
attribution name: Zhao et al.

Repetitive transcranial magnetic stimulation promotes the recovery of upper limb motor dysfunction in ischemic stroke patients: a DTI-based glymphatic system imaging prospective study
type: item
type: AcademicArticle
description: Background Repetitive transcranial magnetic stimulation (rTMS) is an effective tool for motor function recovery in patients with ischemic stroke (IS). Dysfunction of the glymphatic system is implicated in the pathological process of IS. However, it is still unclear whether the recovery of upper limb motor function in IS is affected by rTMS-driven modulation of glymphatic system function. This study aimed to investigate the potential utility of diffusion tensor imaging analysis along the perivascular space (DTI-ALPS) in assessing the impact of rTMS on IS recovery. Methods This prospective study recruited IS participants with upper limb motor disorders. A total of 35 participants were randomly assigned to receive either low-frequency rTMS (LF-rTMS) or high-frequency rTMS (HF-rTMS) for two weeks. HF-rTMS was conducted on the infarcted hemisphere M1 and the LF-rTMS was conducted on the non-infarcted hemisphere M1. The information collected from each patient included clinical characteristics, upper limb motor function score, and bilateral hemisphere DTI-ALPS index. Paired t-tests were used to evaluate longitudinal changes of the DTI-ALPS index in LF-rTMS and HF-rTMS groups. The DTI-ALPS index change rates were calculated, and their differences were compared between groups. Spearman’s correlation analyses were performed to assess the relationships between DTI-ALPS index changes and changes in upper limb motor function score. Results At baseline, no significant differences were observed in the DTI-ALPS index between the HF-rTMS and LF-rTMS groups. After two weeks of rTMS treatment, the DTI-ALPS index of the non-stimulated hemisphere in the HF-rTMS group significantly decreased (t = 2.42, P = 0.028), and the change rate of the DTI-ALPS index was negatively correlated with the recovery of upper limb motor function (r = − 0.42, P = 0.011). In the LF-rTMS group, longitudinal analysis showed improvement in upper limb motor function scores, but there was no significant change in…
format: application/pdf
format: text/html
creator: Yulan Dong
creator: Jing Liu
creator: Tianyao Wang
creator: Zhaoxiang Zhang
creator: Xiaoyue Hu
creator: Chengjia Zhu
creator: Meijuan Gao
creator: Ping Yan
creator: Hao Lei
creator: Jun Zhou
subject: Clinical Trials
subject: Neurology
subject: Radiology and Medical Imaging
subject: Rehabilitation
description: doi:10.7717/peerj.20709
publisher: PeerJ Inc.
rights: © 2026 Dong et al.
abstract: Background Repetitive transcranial magnetic stimulation (rTMS) is an effective tool for motor function recovery in patients with ischemic stroke (IS). Dysfunction of the glymphatic system is implicated in the pathological process of IS. However, it is still unclear whether the recovery of upper limb motor function in IS is affected by rTMS-driven modulation of glymphatic system function. This study aimed to investigate the potential utility of diffusion tensor imaging analysis along the perivascular space (DTI-ALPS) in assessing the impact of rTMS on IS recovery. Methods This prospective study recruited IS participants with upper limb motor disorders. A total of 35 participants were randomly assigned to receive either low-frequency rTMS (LF-rTMS) or high-frequency rTMS (HF-rTMS) for two weeks. HF-rTMS was conducted on the infarcted hemisphere M1 and the LF-rTMS was conducted on the non-infarcted hemisphere M1. The information collected from each patient included clinical characteristics, upper limb motor function score, and bilateral hemisphere DTI-ALPS index. Paired t-tests were used to evaluate longitudinal changes of the DTI-ALPS index in LF-rTMS and HF-rTMS groups. The DTI-ALPS index change rates were calculated, and their differences were compared between groups. Spearman’s correlation analyses were performed to assess the relationships between DTI-ALPS index changes and changes in upper limb motor function score. Results At baseline, no significant differences were observed in the DTI-ALPS index between the HF-rTMS and LF-rTMS groups. After two weeks of rTMS treatment, the DTI-ALPS index of the non-stimulated hemisphere in the HF-rTMS group significantly decreased (t = 2.42, P = 0.028), and the change rate of the DTI-ALPS index was negatively correlated with the recovery of upper limb motor function (r = − 0.42, P = 0.011). In the LF-rTMS group, longitudinal analysis showed improvement in upper limb motor function scores, but there was no significant change in…
bibliographic citation: Dong et al. (2026) Repetitive transcranial magnetic stimulation promotes the recovery of upper limb motor dysfunction in ischemic stroke patients: a DTI-based glymphatic system imaging prospective study. PeerJ 14:e20709 https://doi.org/10.7717/peerj.20709
date submitted: 2024-09-10
date accepted: 2025-12-10
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Yulan
author list: Agent
  family name: Liu
  given name: Jing
author list: Agent
  family name: Wang
  given name: Tianyao
author list: Agent
  family name: Zhang
  given name: Zhaoxiang
author list: Agent
  family name: Hu
  given name: Xiaoyue
author list: Agent
  family name: Zhu
  given name: Chengjia
author list: Agent
  family name: Gao
  given name: Meijuan
author list: Agent
  family name: Yan
  given name: Ping
author list: Agent
  family name: Lei
  given name: Hao
author list: Agent
  family name: Zhou
  given name: Jun
doi: 10.7717/peerj.20709
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Dong et al.
attribution name: Dong et al.

Study on biomarkers associated with epigenetic factors in endometriosis combining transcriptome with experimental validation
type: item
type: AcademicArticle
description: Background Endometriosis (EM) is a disease related to reproductive dysfunction. The mechanism of epigenetic factors (EF) in EM still needs to be studied. Emerging evidence suggests that EF plays a role in the development of EM. However, the specific molecular pathways through which they exert their effects remain incompletely understood, necessitating further in-depth research. This study aimed to explore the mechanisms underlying EF in EM. Methods In the study, the differentially expressed genes (DEGs) between EM and control were obtained by analyzing transcriptome data from public databases. Candidate genes were obtained by taking the intersection of DEGs and EF-related genes (EF-RGs), which were further screened using machine learning algorithms, receiver operating characteristic analysis, and expression levels in the EM and control samples to obtain biomarkers. The potential mechanisms of biomarkers in EF were further analyzed by constructing a nomogram model, gene set enrichment analysis (GSEA), immune infiltration analysis, expression profiling in tissues and cells, molecular regulatory networks, and drug prediction. The expression of these biomarkers was validated using in vitro experiments. Results Histone deacetylase 9 (HDAC9), YY1-associated factor 2 (YAF2), and cell division cycle 6 (CDC6) were identified as EF-associated biomarkers in EM. These biomarkers had excellent diagnostic ability for EM. HDAC9, CDC6, and YAF2 were respectively significantly enriched in focal adhesion and oxidative phosphorylation pathways. Four types of differentially distributed immune cells were identified between EM and control samples using immune infiltration analysis. The expression of these biomarkers in different tissues varied with age and menstrual cycle. The expression levels of biomarkers were higher in endothelial cells. Ten miRNAs and 24 lncRNAs that targeted these biomarkers were screened, and there were 12 transcription factors (TFs) in which all the biomarkers ac…
format: application/pdf
format: text/html
creator: Juan Du
creator: Zili Lv
creator: Xia Zheng
creator: Jinpeng Wang
creator: Hua Lu
subject: Gynecology and Obstetrics
subject: Immunology
subject: Women’s Health
description: doi:10.7717/peerj.20703
publisher: PeerJ Inc.
rights: © 2026 Du et al.
abstract: Background Endometriosis (EM) is a disease related to reproductive dysfunction. The mechanism of epigenetic factors (EF) in EM still needs to be studied. Emerging evidence suggests that EF plays a role in the development of EM. However, the specific molecular pathways through which they exert their effects remain incompletely understood, necessitating further in-depth research. This study aimed to explore the mechanisms underlying EF in EM. Methods In the study, the differentially expressed genes (DEGs) between EM and control were obtained by analyzing transcriptome data from public databases. Candidate genes were obtained by taking the intersection of DEGs and EF-related genes (EF-RGs), which were further screened using machine learning algorithms, receiver operating characteristic analysis, and expression levels in the EM and control samples to obtain biomarkers. The potential mechanisms of biomarkers in EF were further analyzed by constructing a nomogram model, gene set enrichment analysis (GSEA), immune infiltration analysis, expression profiling in tissues and cells, molecular regulatory networks, and drug prediction. The expression of these biomarkers was validated using in vitro experiments. Results Histone deacetylase 9 (HDAC9), YY1-associated factor 2 (YAF2), and cell division cycle 6 (CDC6) were identified as EF-associated biomarkers in EM. These biomarkers had excellent diagnostic ability for EM. HDAC9, CDC6, and YAF2 were respectively significantly enriched in focal adhesion and oxidative phosphorylation pathways. Four types of differentially distributed immune cells were identified between EM and control samples using immune infiltration analysis. The expression of these biomarkers in different tissues varied with age and menstrual cycle. The expression levels of biomarkers were higher in endothelial cells. Ten miRNAs and 24 lncRNAs that targeted these biomarkers were screened, and there were 12 transcription factors (TFs) in which all the biomarkers ac…
bibliographic citation: Du et al. (2026) Study on biomarkers associated with epigenetic factors in endometriosis combining transcriptome with experimental validation. PeerJ 14:e20703 https://doi.org/10.7717/peerj.20703
date submitted: 2025-07-03
date accepted: 2025-12-09
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Juan
author list: Agent
  family name: Lv
  given name: Zili
author list: Agent
  family name: Zheng
  given name: Xia
author list: Agent
  family name: Wang
  given name: Jinpeng
author list: Agent
  family name: Lu
  given name: Hua
doi: 10.7717/peerj.20703
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Du et al.
attribution name: Du et al.

Chronic obstructive pulmonary disease among former United States Department of Energy workers: comorbidities and lung function changes
type: item
type: AcademicArticle
description: Background Chronic Obstructive Pulmonary Disease (COPD) is a major cause of morbidity and mortality in the United States and is frequently associated with multiple comorbidities which lead to poor COPD outcomes in the general population. However, little is known regarding COPD comorbidities in occupational cohorts whose exposure experiences could result in differences in comorbidities compared to the general population. These differences may also be important for assessing COPD outcomes such as lung function changes or decline. Therefore, the objectives of this study were to: (1) identify and describe clusters of COPD comorbidities among Department of Energy (DOE) former workers; (2) assess if the attributes of the identified clusters differ from those identified among the general population based on the published literature, and (3) identify predictors of lung function changes and decline among DOE former workers. Methods Clinical, occupational, and sociodemographic data were obtained from the National Supplemental Screening Program. Imputation for missing values was performed using multiple imputation by chained equation. Comorbidity clusters were identified using hierarchical clustering. Regression and classification random forest models were used to identify predictors of changes in forced expiratory volume in one second (FEV1) and FEV1 decline. Variable importance scores were used to assess the predictive importance of the predictors. Results A total of 17,448 DOE former workers were included in this study, 20.9% of whom had COPD at their initial exam. Four comorbidity clusters were identified among those with COPD. Cluster 1 was composed of individuals with low prevalence of comorbidities, cluster 2 contained individuals with high prevalence of cardiovascular diseases, cluster 3 had those with high lung cancer prevalence, while cluster 4 had individuals with high prevalence of multiple comorbidities. There was no significant association between the clusters an…
format: application/pdf
format: text/html
creator: Sara Howard
creator: Louis Rocconi
creator: Agricola Odoi
subject: Epidemiology
subject: Public Health
subject: Respiratory Medicine
description: doi:10.7717/peerj.20696
publisher: PeerJ Inc.
rights: © 2026 Howard et al.
abstract: Background Chronic Obstructive Pulmonary Disease (COPD) is a major cause of morbidity and mortality in the United States and is frequently associated with multiple comorbidities which lead to poor COPD outcomes in the general population. However, little is known regarding COPD comorbidities in occupational cohorts whose exposure experiences could result in differences in comorbidities compared to the general population. These differences may also be important for assessing COPD outcomes such as lung function changes or decline. Therefore, the objectives of this study were to: (1) identify and describe clusters of COPD comorbidities among Department of Energy (DOE) former workers; (2) assess if the attributes of the identified clusters differ from those identified among the general population based on the published literature, and (3) identify predictors of lung function changes and decline among DOE former workers. Methods Clinical, occupational, and sociodemographic data were obtained from the National Supplemental Screening Program. Imputation for missing values was performed using multiple imputation by chained equation. Comorbidity clusters were identified using hierarchical clustering. Regression and classification random forest models were used to identify predictors of changes in forced expiratory volume in one second (FEV1) and FEV1 decline. Variable importance scores were used to assess the predictive importance of the predictors. Results A total of 17,448 DOE former workers were included in this study, 20.9% of whom had COPD at their initial exam. Four comorbidity clusters were identified among those with COPD. Cluster 1 was composed of individuals with low prevalence of comorbidities, cluster 2 contained individuals with high prevalence of cardiovascular diseases, cluster 3 had those with high lung cancer prevalence, while cluster 4 had individuals with high prevalence of multiple comorbidities. There was no significant association between the clusters an…
bibliographic citation: Howard et al. (2026) Chronic obstructive pulmonary disease among former United States Department of Energy workers: comorbidities and lung function changes. PeerJ 14:e20696 https://doi.org/10.7717/peerj.20696
date submitted: 2025-05-13
date accepted: 2025-12-08
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Howard
  given name: Sara
author list: Agent
  family name: Rocconi
  given name: Louis
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.20696
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Howard et al.
attribution name: Howard et al.

Hidden-break diversity in pancrustacean rRNA profiles
type: item
type: AcademicArticle
description: Background In the 28S rRNA molecule of many invertebrates, a hidden break splits this large subunit into two noncovalently associated fragments (28Sa and 28Sb), masking 28S in electrophoretic profiles and biasing the standard measurements of RNA quality in extracted tissue samples. Pancrustacean diversity in RNA hidden breaks remains incompletely surveyed, particularly for Oligostraca. Methods We sampled 12 species spanning Branchiopoda, Malacostraca, and Oligostraca around Valencia (Spain). RNA was stabilized with DNA/RNA Shield, extracted with Quick-RNA MagBead, and profiled on an Agilent 5200 Fragment Analyzer. Peaks were assigned to 18S and 28S fragments using BLAST-inferred gene lengths from reference genomes and annotated rDNA. We analyzed 28S secondary-structure domains (D-regions) using RNAfold and focusing on D3 and D7a. Results Oligostracans and most branchiopods analyzed showed the canonical single-peak profile consistent with 18S, 28Sa, and 28Sb of similar size. Malacostracans exhibited greater profile diversity, including multiple distinct peaks attributable to expansions that alter the relative sizes of 28Sa and b, including expansions near D7a. Comparative analyses indicate conserved D3/D7a architecture across Oligostraca/Branchiopoda and higher variability with frequent expansions in Malacostraca. Conclusions Our data extend RNA profile diversity to Oligostraca, refine fragment-size estimates with higher-resolution capillary electrophoresis, and link malacostracan profile heterogeneity to D7a and other expansions. We recommend rRNA-aware quality control for arthropod samples and targeted sequencing of poorly sampled lineages (e.g., Mystacocarida, Cephalocarida, Remipedia) to resolve mechanisms and the phylogenetic distribution of the hidden break.
format: application/pdf
format: text/html
creator: Aitana Casanova Gómez
creator: Francesc Mesquita-Joanes
creator: Ferran Palero
subject: Biodiversity
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.20693
publisher: PeerJ Inc.
rights: © 2026 Casanova Gómez et al.
abstract: Background In the 28S rRNA molecule of many invertebrates, a hidden break splits this large subunit into two noncovalently associated fragments (28Sa and 28Sb), masking 28S in electrophoretic profiles and biasing the standard measurements of RNA quality in extracted tissue samples. Pancrustacean diversity in RNA hidden breaks remains incompletely surveyed, particularly for Oligostraca. Methods We sampled 12 species spanning Branchiopoda, Malacostraca, and Oligostraca around Valencia (Spain). RNA was stabilized with DNA/RNA Shield, extracted with Quick-RNA MagBead, and profiled on an Agilent 5200 Fragment Analyzer. Peaks were assigned to 18S and 28S fragments using BLAST-inferred gene lengths from reference genomes and annotated rDNA. We analyzed 28S secondary-structure domains (D-regions) using RNAfold and focusing on D3 and D7a. Results Oligostracans and most branchiopods analyzed showed the canonical single-peak profile consistent with 18S, 28Sa, and 28Sb of similar size. Malacostracans exhibited greater profile diversity, including multiple distinct peaks attributable to expansions that alter the relative sizes of 28Sa and b, including expansions near D7a. Comparative analyses indicate conserved D3/D7a architecture across Oligostraca/Branchiopoda and higher variability with frequent expansions in Malacostraca. Conclusions Our data extend RNA profile diversity to Oligostraca, refine fragment-size estimates with higher-resolution capillary electrophoresis, and link malacostracan profile heterogeneity to D7a and other expansions. We recommend rRNA-aware quality control for arthropod samples and targeted sequencing of poorly sampled lineages (e.g., Mystacocarida, Cephalocarida, Remipedia) to resolve mechanisms and the phylogenetic distribution of the hidden break.
bibliographic citation: Casanova Gómez et al. (2026) Hidden-break diversity in pancrustacean rRNA profiles. PeerJ 14:e20693 https://doi.org/10.7717/peerj.20693
date submitted: 2025-09-25
date accepted: 2025-12-08
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Casanova Gómez
  given name: Aitana
author list: Agent
  family name: Mesquita-Joanes
  given name: Francesc
author list: Agent
  family name: Palero
  given name: Ferran
doi: 10.7717/peerj.20693
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Casanova Gómez et al.
attribution name: Casanova Gómez et al.

Exploring the mediating role of physical activity levels in the relationship between physical literacy and physical fitness in Chinese university students
type: item
type: AcademicArticle
description: Objective This study investigated the relationships between physical literacy (PL), physical activity levels (PALs), and physical fitness among Chinese university students, with a particular focus on the mediating role of PALs and the consistency of findings across various analytical methods. Methods Participants included 115 first-year students (79 males, 36 females) from Nanjing, China. PL was assessed using the Perceived Physical Literacy Instrument (PPLI-SC), PALs were measured using the Physical Activity Questionnaire for Adolescents (PAQ-A), and physical fitness was assessed through four indicators: body mass index (BMI), 50-m sprint, sit-and-reach, and 800/1,000-m run. Descriptive statistics, correlation, and regression analyses were conducted in SPSS 26.0. Mediation was tested using the PROCESS macro (Model 4, 5,000 bootstrap samples), and structural equation modeling (SEM) was applied using AMOS 26.0 for validation. Results Males outperformed females in the 50-m sprint, while females exhibited superior flexibility and cardiorespiratory endurance; BMI was significantly higher in males (p < 0.01). PL was positively correlated with PALs (r = 0.584, p < 0.01), and both were significantly associated with all fitness indicators except BMI. Mediation analyses indicated that PALs fully mediated the associations between PL and sprint performance, flexibility, and cardiorespiratory endurance. For BMI, the PROCESS macro suggested a weak indirect effect, whereas SEM results were nonsignificant, highlighting the sensitivity of the results to the analytical method used. Conclusion PL is strongly linked to physical fitness in Chinese university students, with PALs acting as a critical mediator. The inconsistent BMI findings underscore its complex determinants, which extend beyond physical activity. Promoting PL and PALs through university physical education programs may improve fitness outcomes. Future research should validate these findings using larger samples, longitud…
format: application/pdf
format: text/html
creator: Yingshuang Sun
creator: Donglin Hu
subject: Global Health
subject: Health Policy
subject: Public Health
subject: Mental Health
subject: Sports Medicine
description: doi:10.7717/peerj.20689
publisher: PeerJ Inc.
rights: © 2026 Sun and Hu
abstract: Objective This study investigated the relationships between physical literacy (PL), physical activity levels (PALs), and physical fitness among Chinese university students, with a particular focus on the mediating role of PALs and the consistency of findings across various analytical methods. Methods Participants included 115 first-year students (79 males, 36 females) from Nanjing, China. PL was assessed using the Perceived Physical Literacy Instrument (PPLI-SC), PALs were measured using the Physical Activity Questionnaire for Adolescents (PAQ-A), and physical fitness was assessed through four indicators: body mass index (BMI), 50-m sprint, sit-and-reach, and 800/1,000-m run. Descriptive statistics, correlation, and regression analyses were conducted in SPSS 26.0. Mediation was tested using the PROCESS macro (Model 4, 5,000 bootstrap samples), and structural equation modeling (SEM) was applied using AMOS 26.0 for validation. Results Males outperformed females in the 50-m sprint, while females exhibited superior flexibility and cardiorespiratory endurance; BMI was significantly higher in males (p < 0.01). PL was positively correlated with PALs (r = 0.584, p < 0.01), and both were significantly associated with all fitness indicators except BMI. Mediation analyses indicated that PALs fully mediated the associations between PL and sprint performance, flexibility, and cardiorespiratory endurance. For BMI, the PROCESS macro suggested a weak indirect effect, whereas SEM results were nonsignificant, highlighting the sensitivity of the results to the analytical method used. Conclusion PL is strongly linked to physical fitness in Chinese university students, with PALs acting as a critical mediator. The inconsistent BMI findings underscore its complex determinants, which extend beyond physical activity. Promoting PL and PALs through university physical education programs may improve fitness outcomes. Future research should validate these findings using larger samples, longitud…
bibliographic citation: Sun et al. (2026) Exploring the mediating role of physical activity levels in the relationship between physical literacy and physical fitness in Chinese university students. PeerJ 14:e20689 https://doi.org/10.7717/peerj.20689
date submitted: 2025-10-09
date accepted: 2025-12-08
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Yingshuang
author list: Agent
  family name: Hu
  given name: Donglin
doi: 10.7717/peerj.20689
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Sun and Hu
attribution name: Sun and Hu

No evidence for quorum sensing during egg hatching in the cestode Schistocephalus solidus
type: item
type: AcademicArticle
description: Schistocephalus solidus, a parasitic cestode with a multi-host life cycle, reproduces in its terminal host either by outcrossing with similarly sized individuals or selfing. Previous work found that selfing greatly depresses egg hatching rates, presumably as a result of inbreeding depression. We designed an experiment to test whether S. solidus evolved quorum sensing (QS) during hatching as a mechanism to facilitate synchronized infection, thereby increasing the opportunity for outcrossing in its terminal host. We also performed exploratory analyses to test whether QS varies across parasite populations and cross type (i.e., whether progeny were produced via outcrossing or selfing), though these had limited statistical power due to low sample sizes across treatments. We predicted that if QS was present, it would be common across all populations and that higher egg density within a small area would result in higher hatching rates. We also expected that outcrossed eggs would hatch at higher rates than those produced via selfing. While we found different hatching rates between populations, there was no evidence for QS. We also observed that selfed eggs hatched at lower rates than outcrossed eggs, replicating previous findings. Although we failed to find density dependent hatching within the scope of our sample size, we discuss the conditions that may either favor or disfavor QS evolution across S. solidus and other helminth populations.
format: application/pdf
format: text/html
creator: Emily V. Kerns
creator: Sara Engel
creator: Panna A. Codner
creator: Jesse N. Weber
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Parasitology
description: doi:10.7717/peerj.20667
publisher: PeerJ Inc.
rights: © 2026 Kerns et al.
abstract: Schistocephalus solidus, a parasitic cestode with a multi-host life cycle, reproduces in its terminal host either by outcrossing with similarly sized individuals or selfing. Previous work found that selfing greatly depresses egg hatching rates, presumably as a result of inbreeding depression. We designed an experiment to test whether S. solidus evolved quorum sensing (QS) during hatching as a mechanism to facilitate synchronized infection, thereby increasing the opportunity for outcrossing in its terminal host. We also performed exploratory analyses to test whether QS varies across parasite populations and cross type (i.e., whether progeny were produced via outcrossing or selfing), though these had limited statistical power due to low sample sizes across treatments. We predicted that if QS was present, it would be common across all populations and that higher egg density within a small area would result in higher hatching rates. We also expected that outcrossed eggs would hatch at higher rates than those produced via selfing. While we found different hatching rates between populations, there was no evidence for QS. We also observed that selfed eggs hatched at lower rates than outcrossed eggs, replicating previous findings. Although we failed to find density dependent hatching within the scope of our sample size, we discuss the conditions that may either favor or disfavor QS evolution across S. solidus and other helminth populations.
bibliographic citation: Kerns et al. (2026) No evidence for quorum sensing during egg hatching in the cestode Schistocephalus solidus. PeerJ 14:e20667 https://doi.org/10.7717/peerj.20667
date submitted: 2025-07-29
date accepted: 2025-12-04
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kerns
  given name: Emily V.
author list: Agent
  family name: Engel
  given name: Sara
author list: Agent
  family name: Codner
  given name: Panna A.
author list: Agent
  family name: Weber
  given name: Jesse N.
doi: 10.7717/peerj.20667
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Kerns et al.
attribution name: Kerns et al.

Nano-scale silicon intervention for improving abiotic stress resilience in rice: mechanistic insights and practical applications
type: item
type: AcademicArticle
description: Rice, a global food staple, primary food source for half of the world’s population, is highly vulnerable to abiotic stresses such as drought, salinity, heat, and heavy metal toxicity. Silicon nanoparticles (SiNPs) have emerged as promising nano-interventions to enhance stress resilience by improving antioxidant defenses, photosynthesis, and ion homeostasis. Recent studies demonstrate that SiNPs modulate the expression of key transporter genes (OsHMA3, OsLsi1, OsABCC1) and activate transcription factors (DREB, NAC, WRKY) that regulate stress tolerance pathways. They also promote the accumulation of compatible solutes and phenolic compounds, reducing oxidative damage and metal toxicity. Omics-based research reveals that SiNPs influence redox signaling, hormonal balance, and epigenetic regulation, providing a clear understanding of their protective mechanisms at the physiological level. These effects are linked to enhanced structural integrity, reactive oxygen species (ROS) scavenging, and better nutrient uptake. However, rice-specific datasets remain limited, and field-scale validations are still scarce. SiNPs show strong potential as smart nanocarriers for nutrient delivery and gene modulation, integrating effectively with precision and sustainable agriculture practices. However, uncertainties regarding dosage, soil persistence, and food safety require careful evaluation before large-scale use. This review synthesizes physiological, molecular, and omics-based insights into SiNP-mediated abiotic stress tolerance in rice, emphasizing advances in understanding underlying resilience mechanisms. It also highlights environmental and regulatory challenges, identifies critical research gaps, and proposes future directions for safe and scalable applications of SiNPs in rice systems.
format: application/pdf
format: text/html
creator: Song Youliang
creator: Sher Muhammad
creator: Hu Ying
creator: Wang Lei
creator: Hua Zhimeng
creator: Zhou Xingyuan
creator: Zhao Pengke
creator: Li Fangzhen
creator: Xie Lu
creator: Ali Aslam
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.20599
publisher: PeerJ Inc.
rights: © 2026 Youliang et al.
abstract: Rice, a global food staple, primary food source for half of the world’s population, is highly vulnerable to abiotic stresses such as drought, salinity, heat, and heavy metal toxicity. Silicon nanoparticles (SiNPs) have emerged as promising nano-interventions to enhance stress resilience by improving antioxidant defenses, photosynthesis, and ion homeostasis. Recent studies demonstrate that SiNPs modulate the expression of key transporter genes (OsHMA3, OsLsi1, OsABCC1) and activate transcription factors (DREB, NAC, WRKY) that regulate stress tolerance pathways. They also promote the accumulation of compatible solutes and phenolic compounds, reducing oxidative damage and metal toxicity. Omics-based research reveals that SiNPs influence redox signaling, hormonal balance, and epigenetic regulation, providing a clear understanding of their protective mechanisms at the physiological level. These effects are linked to enhanced structural integrity, reactive oxygen species (ROS) scavenging, and better nutrient uptake. However, rice-specific datasets remain limited, and field-scale validations are still scarce. SiNPs show strong potential as smart nanocarriers for nutrient delivery and gene modulation, integrating effectively with precision and sustainable agriculture practices. However, uncertainties regarding dosage, soil persistence, and food safety require careful evaluation before large-scale use. This review synthesizes physiological, molecular, and omics-based insights into SiNP-mediated abiotic stress tolerance in rice, emphasizing advances in understanding underlying resilience mechanisms. It also highlights environmental and regulatory challenges, identifies critical research gaps, and proposes future directions for safe and scalable applications of SiNPs in rice systems.
bibliographic citation: Youliang et al. (2026) Nano-scale silicon intervention for improving abiotic stress resilience in rice: mechanistic insights and practical applications. PeerJ 14:e20599 https://doi.org/10.7717/peerj.20599
date submitted: 2025-10-08
date accepted: 2025-11-26
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Youliang
  given name: Song
author list: Agent
  family name: Muhammad
  given name: Sher
author list: Agent
  family name: Ying
  given name: Hu
author list: Agent
  family name: Lei
  given name: Wang
author list: Agent
  family name: Zhimeng
  given name: Hua
author list: Agent
  family name: Xingyuan
  given name: Zhou
author list: Agent
  family name: Pengke
  given name: Zhao
author list: Agent
  family name: Fangzhen
  given name: Li
author list: Agent
  family name: Lu
  given name: Xie
author list: Agent
  family name: Aslam
  given name: Ali
doi: 10.7717/peerj.20599
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Youliang et al.
attribution name: Youliang et al.

Risk factors for postpartum depression after cesarean section: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background The incidence of cesarean section (CS) is increasing each year and may be associated with an increased risk of postpartum depression (PPD). Although studies have examined the association between cesarean delivery and postpartum depression, the associated risk factors have not been fully investigated. This study aims to identify key risk factors for planned and emergency cesarean delivery through meta-analysis to help develop clinical prevention strategies. Methods We searched multiple databases, including CNKI, Wan Fang, VIP, PubMed, Embase, Scopus, Google Scholar, CINAHL, Cochrane Library, and Web of Science, for studies published from the inception of these databases through January 8, 2025. The quality of the studies was assessed using the Newcastle-Ottawa Scale (NOS), and standardized mean difference (SMD) and ratio of ratios (OR) were used to assess the strength of association between different risk factors and postpartum depression, when I2 > 50%, a random effects model was used for data analysis; when I2 < 50%, a fixed effects model was chosen for analysis. Result Nine articles (n = 3,338) were included in this study, meta-analysis results suggest that younger women (SMD = −0.16, 95% CI [−0.29 to −0.04], I2 = 0%), higher antenatal depression scores (SMD = 0.28, 95% CI [0.13–0.44], I2 = 15.1%), higher antenatal anxiety scores (SMD = 0.56, 95% CI [0.40–0.72], I2 = 35.6%) are more likely to experience postpartum depression, nulliparous (OR = 1.9, 95% CI [1.39–2.60], I2 = 0%) and elementary education level (OR = 1.34, 95% CI [1.05–1.72], I2 = 44.3%) were risk factor for postpartum depression after caesarean section. Conclusion In summary, age, first-time pregnancy status, education level, and antenatal depression and anxiety scores are important risk factors for postpartum depression following cesarean delivery. Identifying and addressing these factors could provide valuable insights for the prevention and management of postpartum depression.
format: application/pdf
format: text/html
creator: Yali Yu
creator: Hui Feng
creator: Peng Ma
subject: Global Health
subject: Gynecology and Obstetrics
subject: Psychiatry and Psychology
subject: Women’s Health
subject: Mental Health
description: doi:10.7717/peerj.20550
publisher: PeerJ Inc.
rights: © 2026 Yu et al.
abstract: Background The incidence of cesarean section (CS) is increasing each year and may be associated with an increased risk of postpartum depression (PPD). Although studies have examined the association between cesarean delivery and postpartum depression, the associated risk factors have not been fully investigated. This study aims to identify key risk factors for planned and emergency cesarean delivery through meta-analysis to help develop clinical prevention strategies. Methods We searched multiple databases, including CNKI, Wan Fang, VIP, PubMed, Embase, Scopus, Google Scholar, CINAHL, Cochrane Library, and Web of Science, for studies published from the inception of these databases through January 8, 2025. The quality of the studies was assessed using the Newcastle-Ottawa Scale (NOS), and standardized mean difference (SMD) and ratio of ratios (OR) were used to assess the strength of association between different risk factors and postpartum depression, when I2 > 50%, a random effects model was used for data analysis; when I2 < 50%, a fixed effects model was chosen for analysis. Result Nine articles (n = 3,338) were included in this study, meta-analysis results suggest that younger women (SMD = −0.16, 95% CI [−0.29 to −0.04], I2 = 0%), higher antenatal depression scores (SMD = 0.28, 95% CI [0.13–0.44], I2 = 15.1%), higher antenatal anxiety scores (SMD = 0.56, 95% CI [0.40–0.72], I2 = 35.6%) are more likely to experience postpartum depression, nulliparous (OR = 1.9, 95% CI [1.39–2.60], I2 = 0%) and elementary education level (OR = 1.34, 95% CI [1.05–1.72], I2 = 44.3%) were risk factor for postpartum depression after caesarean section. Conclusion In summary, age, first-time pregnancy status, education level, and antenatal depression and anxiety scores are important risk factors for postpartum depression following cesarean delivery. Identifying and addressing these factors could provide valuable insights for the prevention and management of postpartum depression.
bibliographic citation: Yu et al. (2026) Risk factors for postpartum depression after cesarean section: a systematic review and meta-analysis. PeerJ 14:e20550 https://doi.org/10.7717/peerj.20550
date submitted: 2025-03-04
date accepted: 2025-11-18
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Yali
author list: Agent
  family name: Feng
  given name: Hui
author list: Agent
  family name: Ma
  given name: Peng
doi: 10.7717/peerj.20550
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: © 2026 Yu et al.
attribution name: Yu et al.

A critical analysis of the global oases mapping
type: item
type: AcademicArticle
description: Oases are receiving particular attention for their capacity to provide different ecosystem services, and as examples of adaptation and resilience in the context of climate change. A 2025 study focusing on the global distribution of oases has been published by Hernández-Agüero et al. (DOI 10.7717/peerj.18884) reporting quantitative and spatial data about the global distribution of oases. An in-depth review of this global oases mapping found significantly inconsistent data with the risk of misinforming the scientific community and other relevant stakeholders about the global distribution of oases. The main critical issues are related to: (i) the oasis definition, (ii) not distinguishing between traditional and modern oases, (iii) methodological inconsistencies in the performed spatial analysis, and inadequate spatial resolution. While most common definitions of oases agree regarding the key role of (traditional) agricultural activities and practices for the oases’ origin, shaping, and preservation, the Hernández-Agüero et al. global oases mapping includes among the oases large portions of areas only characterized by natural vegetation of different types in arid areas. In addition, the global oases mapping includes intensive and, in the long term, unsustainable cultivations, and even urban areas. Traditional oases should be considered separately from intensive cultivation systems in arid areas, as only traditional oases are strictly related to high levels of agrobiodiversity, cultural values, traditional ecological knowledge, cultural landscapes, and sustainability. Oases, especially traditional ones, are characterized by different and complex characteristics with local high variability in terms of cultivated varieties, vertical and horizontal structure, and complexity of the landscape mosaic structure. An inaccurate mapping, together with the absence of a differentiation between modern and traditional oases, can lead to a misallocation of conservation resources or to …
format: application/pdf
format: text/html
creator: Antonio Santoro
creator: Francesco Piras
creator: Mauro Agnoletti
subject: Coupled Natural and Human Systems
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20508
publisher: PeerJ Inc.
rights: © 2026 Santoro et al.
abstract: Oases are receiving particular attention for their capacity to provide different ecosystem services, and as examples of adaptation and resilience in the context of climate change. A 2025 study focusing on the global distribution of oases has been published by Hernández-Agüero et al. (DOI 10.7717/peerj.18884) reporting quantitative and spatial data about the global distribution of oases. An in-depth review of this global oases mapping found significantly inconsistent data with the risk of misinforming the scientific community and other relevant stakeholders about the global distribution of oases. The main critical issues are related to: (i) the oasis definition, (ii) not distinguishing between traditional and modern oases, (iii) methodological inconsistencies in the performed spatial analysis, and inadequate spatial resolution. While most common definitions of oases agree regarding the key role of (traditional) agricultural activities and practices for the oases’ origin, shaping, and preservation, the Hernández-Agüero et al. global oases mapping includes among the oases large portions of areas only characterized by natural vegetation of different types in arid areas. In addition, the global oases mapping includes intensive and, in the long term, unsustainable cultivations, and even urban areas. Traditional oases should be considered separately from intensive cultivation systems in arid areas, as only traditional oases are strictly related to high levels of agrobiodiversity, cultural values, traditional ecological knowledge, cultural landscapes, and sustainability. Oases, especially traditional ones, are characterized by different and complex characteristics with local high variability in terms of cultivated varieties, vertical and horizontal structure, and complexity of the landscape mosaic structure. An inaccurate mapping, together with the absence of a differentiation between modern and traditional oases, can lead to a misallocation of conservation resources or to …
bibliographic citation: Santoro et al. (2026) A critical analysis of the global oases mapping. PeerJ 14:e20508 https://doi.org/10.7717/peerj.20508
date submitted: 2025-07-14
date accepted: 2025-11-10
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santoro
  given name: Antonio
author list: Agent
  family name: Piras
  given name: Francesco
author list: Agent
  family name: Agnoletti
  given name: Mauro
doi: 10.7717/peerj.20508
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: ©2026 Santoro et al.
attribution name: Santoro et al.

Pisinnocaris subconigera—a valid species of early Cambrian fuxianhuiid
type: item
type: AcademicArticle
description: Pisinnocaris subconigera was first described as a rare, small euarthropod from the early Cambrian Chengjiang biota, southwestern China. The taxonomic validity of this species was later challenged due to the lack of essential morphological details to differentiate it from Fuxianhuia protensa, especially from the juvenile perspective. Here, we examined the holotype and additional specimens of P. subconigera with multiple imaging techniques, such as microscope optical imaging, micro-CT scanning and computer-based 3D rendering, and revealed the previously unknown ventral organization of P. subconigera. New findings include four short prothoracic segments each bearing a pair of biramous appendages, four opisthothoracic segments each with four pairs of appendages, and four limbless abdominal segments. Both the small and large individuals exhibit unique and consistent morphological characteristics, indicating that P. subconigera does not represent the larval or juvenile form of any fuxianhuiid as previously proposed. Combined with phylogenetic analyses, our study suggests that P. subconigera remians as a valid member of the early Cambrian fuxianhuiids.
format: application/pdf
format: text/html
creator: Huijuan Mai
creator: Hong Chen
creator: Ailin Chen
creator: Jin Guo
creator: Xianguang Hou
creator: Yu Liu
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.20483
publisher: PeerJ Inc.
rights: © 2026 Mai et al.
abstract: Pisinnocaris subconigera was first described as a rare, small euarthropod from the early Cambrian Chengjiang biota, southwestern China. The taxonomic validity of this species was later challenged due to the lack of essential morphological details to differentiate it from Fuxianhuia protensa, especially from the juvenile perspective. Here, we examined the holotype and additional specimens of P. subconigera with multiple imaging techniques, such as microscope optical imaging, micro-CT scanning and computer-based 3D rendering, and revealed the previously unknown ventral organization of P. subconigera. New findings include four short prothoracic segments each bearing a pair of biramous appendages, four opisthothoracic segments each with four pairs of appendages, and four limbless abdominal segments. Both the small and large individuals exhibit unique and consistent morphological characteristics, indicating that P. subconigera does not represent the larval or juvenile form of any fuxianhuiid as previously proposed. Combined with phylogenetic analyses, our study suggests that P. subconigera remians as a valid member of the early Cambrian fuxianhuiids.
bibliographic citation: Mai et al. (2026) Pisinnocaris subconigera—a valid species of early Cambrian fuxianhuiid. PeerJ 14:e20483 https://doi.org/10.7717/peerj.20483
date submitted: 2025-04-26
date accepted: 2025-11-06
issued: 2026-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mai
  given name: Huijuan
author list: Agent
  family name: Chen
  given name: Hong
author list: Agent
  family name: Chen
  given name: Ailin
author list: Agent
  family name: Guo
  given name: Jin
author list: Agent
  family name: Hou
  given name: Xianguang
author list: Agent
  family name: Liu
  given name: Yu
doi: 10.7717/peerj.20483
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-03
copyright: © 2026 Mai et al.
attribution name: Mai et al.

Human-centered AI to promote youth mental health: a serendipitous natural experiment enabled by a digital health platform
type: item
type: AcademicArticle
description: Background Health systems are struggling to deliver timely preventive care, particularly for marginalized populations, necessitating integration across health, education, and social services. For Indigenous youth in rural communities, fragmented services, isolation, and limited culturally safe options worsen mental health disparities. Interactive technologies, particularly human-centered artificial intelligence (AI)-enabled digital health platforms grounded in human-computer interaction (HCI), can enable remote interaction with citizens and decision-makers. This study investigated a serendipitous natural experiment to assess varying levels of platform nudging on Indigenous youth compliance in a longitudinal intervention. Method This study emerged from the final year of a 5-year initiative embedding a culturally appropriate digital health intervention into school curricula in rural Indigenous communities. While the broader aim was to assess long-term mental health outcomes, an unexpected system disruption assessment of digital nudging on compliance. The platform featured two interfaces: a citizen-facing mobile app for ecological assessments and nudges, and a scientist dashboard for monitoring engagement and triggering nudges. Youth received three nudges: (1) daily system-triggered reminders to complete assessments, (2) weekly non-personalized messages (e.g., land-based activity reminders), and (3) weekly personalized “Best Picture” messages showcasing youth-submitted images. The disruption created four phases: Phase 1 included all nudges; Phase 2 removed non-personalized and personalized nudges; Phase 3 reintroduced them; Phase 4 removed only personalized nudges. Data were analyzed using one-way analysis of variance (ANOVA) with Tukey post hoc tests in R 4.4.2. Results Compliance, measured by completed mobile ecological prospective assessments (mEPAs), varied significantly across most phases. Comprehensive nudging (Phase 1) yielded the highest completion rates and fa…
format: application/pdf
format: text/html
creator: Tarun Reddy Katapally
creator: Nadine Elsahli
creator: Sheriff Tolulope Ibrahim
creator: Jasmin Bhawra
subject: Public Health
subject: Human-Computer Interaction
subject: Mental Health
description: doi:10.7717/peerj.20772
publisher: PeerJ Inc.
rights: © 2026 Katapally et al.
abstract: Background Health systems are struggling to deliver timely preventive care, particularly for marginalized populations, necessitating integration across health, education, and social services. For Indigenous youth in rural communities, fragmented services, isolation, and limited culturally safe options worsen mental health disparities. Interactive technologies, particularly human-centered artificial intelligence (AI)-enabled digital health platforms grounded in human-computer interaction (HCI), can enable remote interaction with citizens and decision-makers. This study investigated a serendipitous natural experiment to assess varying levels of platform nudging on Indigenous youth compliance in a longitudinal intervention. Method This study emerged from the final year of a 5-year initiative embedding a culturally appropriate digital health intervention into school curricula in rural Indigenous communities. While the broader aim was to assess long-term mental health outcomes, an unexpected system disruption assessment of digital nudging on compliance. The platform featured two interfaces: a citizen-facing mobile app for ecological assessments and nudges, and a scientist dashboard for monitoring engagement and triggering nudges. Youth received three nudges: (1) daily system-triggered reminders to complete assessments, (2) weekly non-personalized messages (e.g., land-based activity reminders), and (3) weekly personalized “Best Picture” messages showcasing youth-submitted images. The disruption created four phases: Phase 1 included all nudges; Phase 2 removed non-personalized and personalized nudges; Phase 3 reintroduced them; Phase 4 removed only personalized nudges. Data were analyzed using one-way analysis of variance (ANOVA) with Tukey post hoc tests in R 4.4.2. Results Compliance, measured by completed mobile ecological prospective assessments (mEPAs), varied significantly across most phases. Comprehensive nudging (Phase 1) yielded the highest completion rates and fa…
bibliographic citation: Katapally et al. (2026) Human-centered AI to promote youth mental health: a serendipitous natural experiment enabled by a digital health platform. PeerJ 14:e20772 https://doi.org/10.7717/peerj.20772
date submitted: 2025-05-06
date accepted: 2025-12-18
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Katapally
  given name: Tarun Reddy
author list: Agent
  family name: Elsahli
  given name: Nadine
author list: Agent
  family name: Ibrahim
  given name: Sheriff Tolulope
author list: Agent
  family name: Bhawra
  given name: Jasmin
doi: 10.7717/peerj.20772
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: © 2026 Katapally et al.
attribution name: Katapally et al.

Drivers of wolf depredation reporting and compensation use intentions by livestock producers
type: item
type: AcademicArticle
description: Background Across the western United States, compensation programs that pay livestock producers for losses seek to mitigate the impact of carnivore depredation on livestock. However, data suggest not all livestock producers report wolf depredations or utilize compensation programs. Understanding factors influencing producers to report depredations and to use compensation programs will be critical to program efficacy. Methods We designed a questionnaire expanding the Theory of Planned Behavior to explore which social-psychological and demographic factors most strongly correlate with compensation use and conflict reporting intentions. Our questionnaire was distributed across the inland western United States with confirmed wolf populations including Washington, Oregon, California, Idaho, Montana, Wyoming, Colorado, Arizona, and New Mexico, as well as Alberta, Canada. Results Perceptions of how commonly other producers were reporting wolf depredation (descriptive norms) and worry about future wolf depredation (perceptions of risk probability) were the strongest predictors of reporting intention. A lack of trust in state agencies, perceived financial risk without access to depredation compensation, descriptive norms, attitudes, age, and producer state of residence were the strongest predictors of compensation use intention. Our findings suggest that reducing operational financial vulnerability, building trust in agency personnel, and peer-to-peer knowledge sharing may be effective strategies for increasing reporting and compensation use. Though our sample size was relatively small, our results are informative and have important implications for compensation programs and reporting.
format: application/pdf
format: text/html
creator: Rae Nickerson
creator: Rebecca M. Niemiec
creator: Alexandra Few
creator: Dana Hoag
creator: Paul H. Evangelista
creator: Stewart W. Breck
subject: Anthropology
subject: Conservation Biology
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.20732
publisher: PeerJ Inc.
rights: © 2026 Nickerson et al.
abstract: Background Across the western United States, compensation programs that pay livestock producers for losses seek to mitigate the impact of carnivore depredation on livestock. However, data suggest not all livestock producers report wolf depredations or utilize compensation programs. Understanding factors influencing producers to report depredations and to use compensation programs will be critical to program efficacy. Methods We designed a questionnaire expanding the Theory of Planned Behavior to explore which social-psychological and demographic factors most strongly correlate with compensation use and conflict reporting intentions. Our questionnaire was distributed across the inland western United States with confirmed wolf populations including Washington, Oregon, California, Idaho, Montana, Wyoming, Colorado, Arizona, and New Mexico, as well as Alberta, Canada. Results Perceptions of how commonly other producers were reporting wolf depredation (descriptive norms) and worry about future wolf depredation (perceptions of risk probability) were the strongest predictors of reporting intention. A lack of trust in state agencies, perceived financial risk without access to depredation compensation, descriptive norms, attitudes, age, and producer state of residence were the strongest predictors of compensation use intention. Our findings suggest that reducing operational financial vulnerability, building trust in agency personnel, and peer-to-peer knowledge sharing may be effective strategies for increasing reporting and compensation use. Though our sample size was relatively small, our results are informative and have important implications for compensation programs and reporting.
bibliographic citation: Nickerson et al. (2026) Drivers of wolf depredation reporting and compensation use intentions by livestock producers. PeerJ 14:e20732 https://doi.org/10.7717/peerj.20732
date submitted: 2025-09-04
date accepted: 2025-12-12
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nickerson
  given name: Rae
author list: Agent
  family name: Niemiec
  given name: Rebecca M.
author list: Agent
  family name: Few
  given name: Alexandra
author list: Agent
  family name: Hoag
  given name: Dana
author list: Agent
  family name: Evangelista
  given name: Paul H.
author list: Agent
  family name: Breck
  given name: Stewart W.
doi: 10.7717/peerj.20732
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Nickerson et al.
attribution name: Nickerson et al.

Whole-genome and pangenome insights into Mycobacterium colombiense clinical isolates from human infections
type: item
type: AcademicArticle
description: Background Nontuberculous mycobacteria are opportunistic pathogens which cause infections in various tissues, with the Mycobacterium avium complex (MAC) being a major cause of pulmonary diseases. Among MAC members, Mycobacterium colombiense is a clinically significant species with recognized pathogenic potential; however, studies on its genomic structure and genetic diversity remain limited. Methods This study investigated the drug susceptibility profiles and performed whole-genome sequencing of 12 clinical M. colombiense isolates from the Clinical Microbiology Laboratory at Srinagarind Hospital, Khon Kaen University, Khon Kaen, Thailand. Results Based on minimum inhibitory concentration values, moxifloxacin resistance was most prevalent (100%), followed by linezolid (90%), clarithromycin (30%), and amikacin (30%). The presence of antibiotic resistance genes and virulence factors, including ESX secretion systems and efflux pumps, highlights the bacterium’s potential for immune evasion and survival under stress. Single nucleotide polymorphism-based phylogenetic analysis revealed a close genetic relatedness between the isolates. Pangenome analysis of 16 M. colombiense genomes (12 newly sequenced and four publicly available) identified 7,771 gene clusters, comprising 4,468 core genes, 1,834 accessory genes, and 1,469 unique genes, supporting a closed pangenome structure and indicating evolutionary conservation and low genetic variability among isolates. Conclusions This study provides valuable insight into the genomic diversity, antimicrobial resistance profiles, and virulence potential of M. colombiense isolates. These findings enhance understanding of the pathogen and may inform clinical management, targeted diagnostic development, and therapeutic strategies.
format: application/pdf
format: text/html
creator: Chutinthorn Oungbamnet
creator: Yothin Hinwan
creator: Nut Nithimongkolchai
creator: Vorthon Sawaswong
creator: Suwalak Chitcharoen
creator: Kiatichai Faksri
creator: Auttawit Sirichoat
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.20716
publisher: PeerJ Inc.
rights: © 2026 Oungbamnet et al.
abstract: Background Nontuberculous mycobacteria are opportunistic pathogens which cause infections in various tissues, with the Mycobacterium avium complex (MAC) being a major cause of pulmonary diseases. Among MAC members, Mycobacterium colombiense is a clinically significant species with recognized pathogenic potential; however, studies on its genomic structure and genetic diversity remain limited. Methods This study investigated the drug susceptibility profiles and performed whole-genome sequencing of 12 clinical M. colombiense isolates from the Clinical Microbiology Laboratory at Srinagarind Hospital, Khon Kaen University, Khon Kaen, Thailand. Results Based on minimum inhibitory concentration values, moxifloxacin resistance was most prevalent (100%), followed by linezolid (90%), clarithromycin (30%), and amikacin (30%). The presence of antibiotic resistance genes and virulence factors, including ESX secretion systems and efflux pumps, highlights the bacterium’s potential for immune evasion and survival under stress. Single nucleotide polymorphism-based phylogenetic analysis revealed a close genetic relatedness between the isolates. Pangenome analysis of 16 M. colombiense genomes (12 newly sequenced and four publicly available) identified 7,771 gene clusters, comprising 4,468 core genes, 1,834 accessory genes, and 1,469 unique genes, supporting a closed pangenome structure and indicating evolutionary conservation and low genetic variability among isolates. Conclusions This study provides valuable insight into the genomic diversity, antimicrobial resistance profiles, and virulence potential of M. colombiense isolates. These findings enhance understanding of the pathogen and may inform clinical management, targeted diagnostic development, and therapeutic strategies.
bibliographic citation: Oungbamnet et al. (2026) Whole-genome and pangenome insights into Mycobacterium colombiense clinical isolates from human infections. PeerJ 14:e20716 https://doi.org/10.7717/peerj.20716
date submitted: 2025-07-23
date accepted: 2025-12-10
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oungbamnet
  given name: Chutinthorn
author list: Agent
  family name: Hinwan
  given name: Yothin
author list: Agent
  family name: Nithimongkolchai
  given name: Nut
author list: Agent
  family name: Sawaswong
  given name: Vorthon
author list: Agent
  family name: Chitcharoen
  given name: Suwalak
author list: Agent
  family name: Faksri
  given name: Kiatichai
author list: Agent
  family name: Sirichoat
  given name: Auttawit
doi: 10.7717/peerj.20716
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: © 2026 Oungbamnet et al.
attribution name: Oungbamnet et al.

Comprehensive machine learning and experimental verification reveal the mechanism of action of autophagy-related genes FIZ1 and FBXO21 in acute kidney injury
type: item
type: AcademicArticle
description: Background Acute kidney injury (AKI) is a serious disease with a high incidence and easy induction. The search for innovative biomarkers and treatment methods is of great significance for improving the prognosis of patients. Autophagy is closely related to the occurrence and development of AKI. This study aims to explore the role of autophagy-related genes (ARGs) as potential biomarkers and therapeutic targets in AKI. Methods In this study, the gene microarray data of the GEO dataset were used to explore the molecular profile of AKI, and three machine learning algorithms were used to screen autophagy-related feature genes. To further validate the reliability of the screening results, we constructed a cisplatin-induced AKI rat model to validate potential biomarkers of machine learning screening. Results Machine learning analysis identified 17 differentially expressed ARGs and selected the core genes FIZ1 and FBXO21, with area under curve (AUC) values both exceeding 0.7 (95% CI [0.706–0.899]). Immune analysis revealed that the number of Mast cells resting significantly decreased in AKI samples compared to normal samples (P < 0.05). Electron microscopy observations of the cisplatin-induced AKI rat model indicated thickening of the basement membrane, fusion of foot processes, and swelling and rupture of mitochondria in the model group, suggesting a correlation between AKI and mitochondrial autophagy; Western blot results indicated a significant increase in the expression of FIZ1 and a significant decrease in FBXO21 in the AKI group (P < 0.01). The results of IHC staining were also consistent with those of Western blot results. Conclusion This study highlights the significant role of ARGs in AKI and identifies FIZ1 and FBXO21 as promising biomarkers with high diagnostic potential, offering new insights into the molecular mechanisms underlying AKI.
format: application/pdf
format: text/html
creator: Yunqi Bai
creator: Lili Zhang
creator: Bo Nie
creator: Yixin Su
creator: Jingwei Zhou
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Internal Medicine
subject: Nephrology
description: doi:10.7717/peerj.20707
publisher: PeerJ Inc.
rights: © 2026 Bai et al.
abstract: Background Acute kidney injury (AKI) is a serious disease with a high incidence and easy induction. The search for innovative biomarkers and treatment methods is of great significance for improving the prognosis of patients. Autophagy is closely related to the occurrence and development of AKI. This study aims to explore the role of autophagy-related genes (ARGs) as potential biomarkers and therapeutic targets in AKI. Methods In this study, the gene microarray data of the GEO dataset were used to explore the molecular profile of AKI, and three machine learning algorithms were used to screen autophagy-related feature genes. To further validate the reliability of the screening results, we constructed a cisplatin-induced AKI rat model to validate potential biomarkers of machine learning screening. Results Machine learning analysis identified 17 differentially expressed ARGs and selected the core genes FIZ1 and FBXO21, with area under curve (AUC) values both exceeding 0.7 (95% CI [0.706–0.899]). Immune analysis revealed that the number of Mast cells resting significantly decreased in AKI samples compared to normal samples (P < 0.05). Electron microscopy observations of the cisplatin-induced AKI rat model indicated thickening of the basement membrane, fusion of foot processes, and swelling and rupture of mitochondria in the model group, suggesting a correlation between AKI and mitochondrial autophagy; Western blot results indicated a significant increase in the expression of FIZ1 and a significant decrease in FBXO21 in the AKI group (P < 0.01). The results of IHC staining were also consistent with those of Western blot results. Conclusion This study highlights the significant role of ARGs in AKI and identifies FIZ1 and FBXO21 as promising biomarkers with high diagnostic potential, offering new insights into the molecular mechanisms underlying AKI.
bibliographic citation: Bai et al. (2026) Comprehensive machine learning and experimental verification reveal the mechanism of action of autophagy-related genes FIZ1 and FBXO21 in acute kidney injury. PeerJ 14:e20707 https://doi.org/10.7717/peerj.20707
date submitted: 2025-10-03
date accepted: 2025-12-10
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Yunqi
author list: Agent
  family name: Zhang
  given name: Lili
author list: Agent
  family name: Nie
  given name: Bo
author list: Agent
  family name: Su
  given name: Yixin
author list: Agent
  family name: Zhou
  given name: Jingwei
doi: 10.7717/peerj.20707
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Bai et al.
attribution name: Bai et al.

Change of direction and Repeated Sprint Ability with and without ball performance in young soccer players: a comparison across different age-categories
type: item
type: AcademicArticle
description: Background This study aimed to investigate age-related differences in anthropometric characteristics, change of direction (COD) and repeated sprint ability (RSA) performance, with and without ball control, in elite soccer players from U17, U19, and U23 categories. Methodology Seventy-two male players (age: 18.9 ± 2.23 years; height: 1.72 ± 0.08 m; body mass: 71.7 ± 5.04 kg; body mass index (BMI): 24.3 ± 2.61 kg/m2) from three professional soccer clubs were assessed (U17 = 24; U19 = 24; U23 = 24). After a two-month period of regular training and competition, anthropometric measures (height, body mass, body mass index) were recorded. In addition, players completed the New Multi-Change of Direction Agility Test (NMAT) and the Bangsbo RSA test, both performed with and without a ball. Testing was standardized for familiarization, warm-up, and environmental conditions. Results U23 players were taller and heavier than U17 and U19 players, and they showed superior COD performance without the ball compared to U17, whereas no statistically significant differences were found in COD with ball or RSA performance across age groups. Correlation analyses revealed moderate associations between anthropometric variables and COD performance (r = − 0.35 to −0.24), while higher BMI values were related to slower agility times (r = 0.24–0.26). Conclusions Age-related anthropometric characteristics were associated with better COD performance without the ball, whereas COD with ball and RSA performance appear less age-dependent and more influenced by training specificity. These findings highlight the importance of incorporating technical COD drills and RSA training early in player development to align physical and technical progression.
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format: text/html
creator: Mehdi Ben Brahim
creator: Farjana Akter Boby
creator: Ariadna Hernaiz-Sánchez
creator: Hussain Yasin
creator: Alejandro Sal-de-Rellán
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20691
publisher: PeerJ Inc.
rights: © 2026 Ben Brahim et al.
abstract: Background This study aimed to investigate age-related differences in anthropometric characteristics, change of direction (COD) and repeated sprint ability (RSA) performance, with and without ball control, in elite soccer players from U17, U19, and U23 categories. Methodology Seventy-two male players (age: 18.9 ± 2.23 years; height: 1.72 ± 0.08 m; body mass: 71.7 ± 5.04 kg; body mass index (BMI): 24.3 ± 2.61 kg/m2) from three professional soccer clubs were assessed (U17 = 24; U19 = 24; U23 = 24). After a two-month period of regular training and competition, anthropometric measures (height, body mass, body mass index) were recorded. In addition, players completed the New Multi-Change of Direction Agility Test (NMAT) and the Bangsbo RSA test, both performed with and without a ball. Testing was standardized for familiarization, warm-up, and environmental conditions. Results U23 players were taller and heavier than U17 and U19 players, and they showed superior COD performance without the ball compared to U17, whereas no statistically significant differences were found in COD with ball or RSA performance across age groups. Correlation analyses revealed moderate associations between anthropometric variables and COD performance (r = − 0.35 to −0.24), while higher BMI values were related to slower agility times (r = 0.24–0.26). Conclusions Age-related anthropometric characteristics were associated with better COD performance without the ball, whereas COD with ball and RSA performance appear less age-dependent and more influenced by training specificity. These findings highlight the importance of incorporating technical COD drills and RSA training early in player development to align physical and technical progression.
bibliographic citation: Ben Brahim et al. (2026) Change of direction and Repeated Sprint Ability with and without ball performance in young soccer players: a comparison across different age-categories. PeerJ 14:e20691 https://doi.org/10.7717/peerj.20691
date submitted: 2025-09-09
date accepted: 2025-12-08
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ben Brahim
  given name: Mehdi
author list: Agent
  family name: Boby
  given name: Farjana Akter
author list: Agent
  family name: Hernaiz-Sánchez
  given name: Ariadna
author list: Agent
  family name: Yasin
  given name: Hussain
author list: Agent
  family name: Sal-de-Rellán
  given name: Alejandro
doi: 10.7717/peerj.20691
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Ben Brahim et al.
attribution name: Ben Brahim et al.

Mitogenomes reveal the timing and distribution of divergence events among trans-Beringian birds
type: item
type: AcademicArticle
description: Glacial cycles operating across Beringia have repeatedly exposed large swathes of the Bering Land Bridge, intermittently isolating and reuniting North American and Eurasian taxa. In high-latitude birds, these cycles are hypothesized to have been important in driving divergence and speciation. These repeated events have resulted in multiple trans-Beringian avian sister populations of varying degrees of taxonomic depth distributed across modern Beringia. We asked how these cyclic pulses have affected the temporal distribution and number of overall divergence events across Beringia. We sequenced full mitogenomes at high depth from 39 lineage pairs of varying levels of divergence, totaling 432 individuals of seven orders, 14 families, and 49 species from both Eurasia and North America. We then used a hierarchical approximate Bayesian comparative (hABC) approach to estimate the number and distribution of divergence events between the population pairs, using subsampled datasets. Net nucleotide divergence (DA) and Jukes-Cantor distance (JC-distance) were also calculated for each pairwise comparison to estimate divergence dates between taxa, using calibrated rates appropriate for shallow avian divergence events. Average divergence times were 200,000 ya for population-level taxa (n = 16), 720,000 ya for subspecies (n = 12), and 1 Mya for species (n = 11), although we consider these dating estimates conservative because of a lack of appropriate calibration for data of this quality. We found eighteen taxon pairs to be significantly differentiated (p < 0.05) by FST or substantially differentiated by haplotype clade, bounding the number of potential overall divergence events from 1 to 18, and two subsets of the full mitogenomic dataset analyzed in MTML-msBayes strongly supported simultaneous divergence of all Beringian lineages. However, this finding of simultaneous divergence is biologically unusual given the substantial variation in divergence dates among taxa and might indica…
format: application/pdf
format: text/html
creator: Keiler A. Collier
creator: Travis C. Glenn
creator: Naoki Takebayashi
creator: Michael J. Hickerson
creator: Kevin Winker
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.20675
publisher: PeerJ Inc.
rights: © 2026 Collier et al.
abstract: Glacial cycles operating across Beringia have repeatedly exposed large swathes of the Bering Land Bridge, intermittently isolating and reuniting North American and Eurasian taxa. In high-latitude birds, these cycles are hypothesized to have been important in driving divergence and speciation. These repeated events have resulted in multiple trans-Beringian avian sister populations of varying degrees of taxonomic depth distributed across modern Beringia. We asked how these cyclic pulses have affected the temporal distribution and number of overall divergence events across Beringia. We sequenced full mitogenomes at high depth from 39 lineage pairs of varying levels of divergence, totaling 432 individuals of seven orders, 14 families, and 49 species from both Eurasia and North America. We then used a hierarchical approximate Bayesian comparative (hABC) approach to estimate the number and distribution of divergence events between the population pairs, using subsampled datasets. Net nucleotide divergence (DA) and Jukes-Cantor distance (JC-distance) were also calculated for each pairwise comparison to estimate divergence dates between taxa, using calibrated rates appropriate for shallow avian divergence events. Average divergence times were 200,000 ya for population-level taxa (n = 16), 720,000 ya for subspecies (n = 12), and 1 Mya for species (n = 11), although we consider these dating estimates conservative because of a lack of appropriate calibration for data of this quality. We found eighteen taxon pairs to be significantly differentiated (p < 0.05) by FST or substantially differentiated by haplotype clade, bounding the number of potential overall divergence events from 1 to 18, and two subsets of the full mitogenomic dataset analyzed in MTML-msBayes strongly supported simultaneous divergence of all Beringian lineages. However, this finding of simultaneous divergence is biologically unusual given the substantial variation in divergence dates among taxa and might indica…
bibliographic citation: Collier et al. (2026) Mitogenomes reveal the timing and distribution of divergence events among trans-Beringian birds. PeerJ 14:e20675 https://doi.org/10.7717/peerj.20675
date submitted: 2024-05-23
date accepted: 2025-12-04
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Collier
  given name: Keiler A.
author list: Agent
  family name: Glenn
  given name: Travis C.
author list: Agent
  family name: Takebayashi
  given name: Naoki
author list: Agent
  family name: Hickerson
  given name: Michael J.
author list: Agent
  family name: Winker
  given name: Kevin
doi: 10.7717/peerj.20675
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Collier et al.
attribution name: Collier et al.

Systemic serum protein alterations and molecular mechanisms in alcohol dependence
type: item
type: AcademicArticle
description: Introduction Most of the studies on alcohol dependence (AD) emphasize its impact on the nervous system and organ functions of the human body, but its molecular mechanism is largely unknown so far. This study determines serum protein changes in alcohol-dependent patients for the identification of biomarkers and the revelation of molecular mechanisms behind alcohol dependence. Methods Serum samples from seven newly diagnosed alcohol-dependent patients and four healthy controls are subjected to researcher-conducted proteomic analyses using data-independent acquisition (DIA) mass spectrometry. Functional enrichment analysis of gene activity and biological pathways is performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to reveal key processes related to alcohol dependence. The expression of Small Nuclear Ribonucleoprotein Polypeptide B (SNRPB) is evaluated to assess its potential as a biomarker, and survival analysis is performed to investigate its clinical relevance. Results The mass spectrometry detected a total of 1,249 and 1,020 proteins in the serum from alcohol-dependent patients and healthy controls, respectively. Biomarker analysis identified 195 proteins as potential markers with a differentially expressed pattern. Among them, 99 proteins are upregulated and 96 proteins downregulated in alcohol-dependent patients compared with controls. The GO and KEGG pathway analysis revealed that alcohol-dependent patients exhibit enhanced activity in pathways related to adenosine triphosphate (ATP)-dependent chromatin remodeling and immune responses but reduced activity in metabolic pathways. Alcohol-dependent patients exhibited significantly higher levels of the SNRPB protein, suggesting its potential role in immune system regulation and cell growth control. Survival analysis results indicated that higher levels of SNRPB are linked to worse outcomes in liver cancer patients, specifically those with liver hepatocellular carcinoma (LIHC), sugges…
format: application/pdf
format: text/html
creator: Xiao Ye
creator: Hui Sheng
creator: Yifan Ouyang
creator: Qian Wu
creator: Abulizi Abudula
creator: Aikebaier Reheman
subject: Biochemistry
subject: Genomics
subject: Molecular Biology
subject: Neurology
subject: Metabolic Sciences
description: doi:10.7717/peerj.20671
publisher: PeerJ Inc.
rights: © 2026 Ye et al.
abstract: Introduction Most of the studies on alcohol dependence (AD) emphasize its impact on the nervous system and organ functions of the human body, but its molecular mechanism is largely unknown so far. This study determines serum protein changes in alcohol-dependent patients for the identification of biomarkers and the revelation of molecular mechanisms behind alcohol dependence. Methods Serum samples from seven newly diagnosed alcohol-dependent patients and four healthy controls are subjected to researcher-conducted proteomic analyses using data-independent acquisition (DIA) mass spectrometry. Functional enrichment analysis of gene activity and biological pathways is performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to reveal key processes related to alcohol dependence. The expression of Small Nuclear Ribonucleoprotein Polypeptide B (SNRPB) is evaluated to assess its potential as a biomarker, and survival analysis is performed to investigate its clinical relevance. Results The mass spectrometry detected a total of 1,249 and 1,020 proteins in the serum from alcohol-dependent patients and healthy controls, respectively. Biomarker analysis identified 195 proteins as potential markers with a differentially expressed pattern. Among them, 99 proteins are upregulated and 96 proteins downregulated in alcohol-dependent patients compared with controls. The GO and KEGG pathway analysis revealed that alcohol-dependent patients exhibit enhanced activity in pathways related to adenosine triphosphate (ATP)-dependent chromatin remodeling and immune responses but reduced activity in metabolic pathways. Alcohol-dependent patients exhibited significantly higher levels of the SNRPB protein, suggesting its potential role in immune system regulation and cell growth control. Survival analysis results indicated that higher levels of SNRPB are linked to worse outcomes in liver cancer patients, specifically those with liver hepatocellular carcinoma (LIHC), sugges…
bibliographic citation: Ye et al. (2026) Systemic serum protein alterations and molecular mechanisms in alcohol dependence. PeerJ 14:e20671 https://doi.org/10.7717/peerj.20671
date submitted: 2025-06-02
date accepted: 2025-12-04
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ye
  given name: Xiao
author list: Agent
  family name: Sheng
  given name: Hui
author list: Agent
  family name: Ouyang
  given name: Yifan
author list: Agent
  family name: Wu
  given name: Qian
author list: Agent
  family name: Abudula
  given name: Abulizi
author list: Agent
  family name: Reheman
  given name: Aikebaier
doi: 10.7717/peerj.20671
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Ye et al.
attribution name: Ye et al.

Effects of sampling methods on bee pollinators observed in Cucurbita pepo
type: item
type: AcademicArticle
description: This study was performed to compare catch abundance of three commonly used bee sampling methods within pumpkin and squash (Cucurbita pepo) fields. The three methods of sampling included visual sampling, vacuum sampling, and bowl trapping. Cucurbita pepo require bee pollinators to move pollen from male flower to female flower for fruit to set. In Cucurbita pepo the three major expected bee types that should be observed are squash bees Xenoglossa pruinosa Say (formerly Eucera (Peponapis) pruinosa) [Hymenoptera: Apidae], bumble bees (Bombus spp.) [Hymenoptera: Apidae], and honey bees (Apis mellifera L. [Hymenoptera: Apidae]). Knowing what bees are present in a grower’s field could help them to make field management decisions and potentially reduce input costs, thus we chose methods where collected specimens could be submitted to experts for identification. We used visual observations as our control as we could confirm these bees were contacting flower reproductive segments, and this method is widely adopted in literature. Through this study, a total of 2,502 bees were observed, of which 82% were squash bees, 3.4% were honey bees and 2.4% were bumble bees. Bowl sampling differed significantly from visual observations for all three major bee types, having significantly fewer catches. Vacuum sampling recovered no bumble bees. Vacuum sampling was not significantly different from visual observation for honey bees but caught fewer squash bees relative to visual sampling. This study also looked at other collected morphotaxa of bees, particularly in bowl trapping, however bees beyond the three taxa presented above had limited presence in visual observations, and as such were not considered to play a major role in the pollination of these plants. This study indicates that visual observation of flowers provides a more reliable estimate of active pollinators in C. pepo fields than the two other bee sampling methods, vacuum sampling and bowl trapping, and they should likely not be…
format: application/pdf
format: text/html
creator: Courtney Walls
creator: Thomas Kuhar
creator: T’ai Roulston
creator: James Wilson
subject: Agricultural Science
subject: Entomology
description: doi:10.7717/peerj.20649
publisher: PeerJ Inc.
rights: © 2026 Walls et al.
abstract: This study was performed to compare catch abundance of three commonly used bee sampling methods within pumpkin and squash (Cucurbita pepo) fields. The three methods of sampling included visual sampling, vacuum sampling, and bowl trapping. Cucurbita pepo require bee pollinators to move pollen from male flower to female flower for fruit to set. In Cucurbita pepo the three major expected bee types that should be observed are squash bees Xenoglossa pruinosa Say (formerly Eucera (Peponapis) pruinosa) [Hymenoptera: Apidae], bumble bees (Bombus spp.) [Hymenoptera: Apidae], and honey bees (Apis mellifera L. [Hymenoptera: Apidae]). Knowing what bees are present in a grower’s field could help them to make field management decisions and potentially reduce input costs, thus we chose methods where collected specimens could be submitted to experts for identification. We used visual observations as our control as we could confirm these bees were contacting flower reproductive segments, and this method is widely adopted in literature. Through this study, a total of 2,502 bees were observed, of which 82% were squash bees, 3.4% were honey bees and 2.4% were bumble bees. Bowl sampling differed significantly from visual observations for all three major bee types, having significantly fewer catches. Vacuum sampling recovered no bumble bees. Vacuum sampling was not significantly different from visual observation for honey bees but caught fewer squash bees relative to visual sampling. This study also looked at other collected morphotaxa of bees, particularly in bowl trapping, however bees beyond the three taxa presented above had limited presence in visual observations, and as such were not considered to play a major role in the pollination of these plants. This study indicates that visual observation of flowers provides a more reliable estimate of active pollinators in C. pepo fields than the two other bee sampling methods, vacuum sampling and bowl trapping, and they should likely not be…
bibliographic citation: Walls et al. (2026) Effects of sampling methods on bee pollinators observed in Cucurbita pepo. PeerJ 14:e20649 https://doi.org/10.7717/peerj.20649
date submitted: 2025-09-18
date accepted: 2025-12-01
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Walls
  given name: Courtney
author list: Agent
  family name: Kuhar
  given name: Thomas
author list: Agent
  family name: Roulston
  given name: T’ai
author list: Agent
  family name: Wilson
  given name: James
doi: 10.7717/peerj.20649
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Walls et al.
attribution name: Walls et al.

Autotrophic methylotrophy with no methanol dehydrogenase (MDH) in a strain of fluorescent Pseudomonas
type: item
type: AcademicArticle
description: Background Very few true Pseudomonas methylotrophic strains have been described, and in none of them have the pathways for one-carbon (C1) substrate metabolism been elucidated. Methods The genomes of three Pseudomonas strains able to grow on methanol as the sole source of carbon (C) and energy (E) were sequenced and analyzed, and one of the strains was further characterized at the proteomic and physiological level. Results None of the three strains possesses a classic methanol dehydrogenase enzyme, and they apparently employ generalist type-I alcohol dehydrogenases (ADHs) to catabolize methanol to formaldehyde. In two of the strains’ genomes, the only complete route encoded for incorporating methylotrophic carbon is the Calvin-Benson-Bassham (CBB) cycle, while other more typical pathways for C1-carbon assimilation (serine cycle, ribulose monophosphate cycle) appear incomplete. The indispensability of the QedA1 alcohol dehydrogenase and of ribulose bisphosphate carboxylase for growth on methanol was demonstrated by insertion mutagenesis of the qedA1 and cbbL genes in one of the strains. Discussion To the author’s knowledge, all wild-type methylotrophic Pseudomonadota (i.e., “Gram-negative bacteria”) so far described employ a specific dehydrogenase distinctively adapted to using methanol as a substrate (MxaFI, XoxFI, or Mdh2). The methylotrophic Pseudomonas strains described here lack MDH and employ generalist ADHs, thus demoting methanol dehydrogenase (MDH) from the position of a critical enzyme for methanol utilization and expanding the range of enzymes (and genes) that enable methylotrophy in nature. The second remarkable result of this work is the discovery of the utilization of the CBB cycle by a Pseudomonas strain during methylotrophic growth, an absolute novelty for this very relevant bacterial genus.
format: application/pdf
format: text/html
creator: Paolo De Marco
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.20614
publisher: PeerJ Inc.
rights: © 2026 De Marco
abstract: Background Very few true Pseudomonas methylotrophic strains have been described, and in none of them have the pathways for one-carbon (C1) substrate metabolism been elucidated. Methods The genomes of three Pseudomonas strains able to grow on methanol as the sole source of carbon (C) and energy (E) were sequenced and analyzed, and one of the strains was further characterized at the proteomic and physiological level. Results None of the three strains possesses a classic methanol dehydrogenase enzyme, and they apparently employ generalist type-I alcohol dehydrogenases (ADHs) to catabolize methanol to formaldehyde. In two of the strains’ genomes, the only complete route encoded for incorporating methylotrophic carbon is the Calvin-Benson-Bassham (CBB) cycle, while other more typical pathways for C1-carbon assimilation (serine cycle, ribulose monophosphate cycle) appear incomplete. The indispensability of the QedA1 alcohol dehydrogenase and of ribulose bisphosphate carboxylase for growth on methanol was demonstrated by insertion mutagenesis of the qedA1 and cbbL genes in one of the strains. Discussion To the author’s knowledge, all wild-type methylotrophic Pseudomonadota (i.e., “Gram-negative bacteria”) so far described employ a specific dehydrogenase distinctively adapted to using methanol as a substrate (MxaFI, XoxFI, or Mdh2). The methylotrophic Pseudomonas strains described here lack MDH and employ generalist ADHs, thus demoting methanol dehydrogenase (MDH) from the position of a critical enzyme for methanol utilization and expanding the range of enzymes (and genes) that enable methylotrophy in nature. The second remarkable result of this work is the discovery of the utilization of the CBB cycle by a Pseudomonas strain during methylotrophic growth, an absolute novelty for this very relevant bacterial genus.
bibliographic citation: De Marco (2026) Autotrophic methylotrophy with no methanol dehydrogenase (MDH) in a strain of fluorescent Pseudomonas. PeerJ 14:e20614 https://doi.org/10.7717/peerj.20614
date submitted: 2025-09-01
date accepted: 2025-11-28
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Marco
  given name: Paolo
doi: 10.7717/peerj.20614
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 De Marco
attribution name: De Marco

The relationship between physical fitness and drop vertical jump biomechanics in male college basketball players
type: item
type: AcademicArticle
description: Background Studies have shown that vertical jump biomechanics or patterns may be related to physical fitness. This study investigated the relationship between physical fitness and drop vertical jump (DVJ) biomechanics in male college basketball players. Methods Health-related physical fitness was measured by 20s sit-up, core endurance and flexibility test; whilst athletic-related physical fitness by Y-balance test and dominant extremity single-leg hop distance test. Kinetics and kinematics during DVJ were evaluated by VICON. Results Five-level side bridge correlated negatively with angle displacement of hip adduction (p = 0.014) and positively with moment of knee flexion (p = 0.033); 8-level abdominal bridge correlated positively with moment of knee flexion (p = 0.01); ankle dorsiflexion range of motion correlated negatively with mediolateral ground reaction force (p = 0.025), angle displacement of knee flexion (p = 0.004), moment of ankle plantarflexion (p = 0.009), and positively with angle displacement of ankle plantarflexion (p = 0.015); ankle plantarflexion ROM correlated negatively with angle of knee flexion (p = 0.012); trunk flexion ROM correlated negatively with moment of ankle plantarflexion (p = 0.014). Conclusion Health-related physical fitness could be the alternatives for DVJ biomechanics assessment.
format: application/pdf
format: text/html
creator: Liang Guo
creator: Kaiyuan Qu
creator: Jing Zhang
creator: Yufeng Zhang
creator: Zhiye Zhang
creator: Ying Wu
creator: Dan Wang
subject: Biomechanics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.20613
publisher: PeerJ Inc.
rights: © 2026 Guo et al.
abstract: Background Studies have shown that vertical jump biomechanics or patterns may be related to physical fitness. This study investigated the relationship between physical fitness and drop vertical jump (DVJ) biomechanics in male college basketball players. Methods Health-related physical fitness was measured by 20s sit-up, core endurance and flexibility test; whilst athletic-related physical fitness by Y-balance test and dominant extremity single-leg hop distance test. Kinetics and kinematics during DVJ were evaluated by VICON. Results Five-level side bridge correlated negatively with angle displacement of hip adduction (p = 0.014) and positively with moment of knee flexion (p = 0.033); 8-level abdominal bridge correlated positively with moment of knee flexion (p = 0.01); ankle dorsiflexion range of motion correlated negatively with mediolateral ground reaction force (p = 0.025), angle displacement of knee flexion (p = 0.004), moment of ankle plantarflexion (p = 0.009), and positively with angle displacement of ankle plantarflexion (p = 0.015); ankle plantarflexion ROM correlated negatively with angle of knee flexion (p = 0.012); trunk flexion ROM correlated negatively with moment of ankle plantarflexion (p = 0.014). Conclusion Health-related physical fitness could be the alternatives for DVJ biomechanics assessment.
bibliographic citation: Guo et al. (2026) The relationship between physical fitness and drop vertical jump biomechanics in male college basketball players. PeerJ 14:e20613 https://doi.org/10.7717/peerj.20613
date submitted: 2025-03-08
date accepted: 2025-11-28
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Liang
author list: Agent
  family name: Qu
  given name: Kaiyuan
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Yufeng
author list: Agent
  family name: Zhang
  given name: Zhiye
author list: Agent
  family name: Wu
  given name: Ying
author list: Agent
  family name: Wang
  given name: Dan
doi: 10.7717/peerj.20613
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Guo et al.
attribution name: Guo et al.

The osteology, taxonomy, and phylogenetic affinities of the Early Jurassic plesiosaur Lusonectes sauvagei
type: item
type: AcademicArticle
description: The transition from the Early to the Middle Jurassic was marked by significant restructuring of plesiosaur communities. While knowledge of the earliest Middle Jurassic plesiosaurs is generally limited, Toarcian plesiosaur occurrences are abundant, though the vast majority of specimens have been unearthed in the United Kingdom and Germany. Here, we reassess Lusonectes sauvagei, an early-diverging plesiosaur from the lower to middle upper Toarcian of the São Gião Formation in Portugal. Originally described as Plesiosaurus sp., it was later established as a distinct taxon closely related to taxa currently encompassed within Microcleididae. Our firsthand examination of the holotype of L. sauvagei resulted in differing interpretations of certain aspects of its morphology, prompting a detailed osteological, taxonomic, and phylogenetic reevaluation. We provide a redescription of L. sauvagei, propose a new diagnosis, and investigate its phylogenetic affinities. Although the specimen is fragmentary and poorly preserved, our study suggests that, contrary to the original interpretation, L. sauvagei is not affiliated with Microcleidus spp. The taxon remains problematic and may represent either an early-diverging pliosaurid or a plesiosauroid. Lusonectes is one of the few diagnosable plesiosaurs from the upper Lower Jurassic found outside the classic British and German localities and thus offers insights into the diversity of plesiosaurs just prior to a major event in the evolutionary history of the clade.
format: application/pdf
format: text/html
creator: Sven Sachs
creator: Daniel Madzia
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.20611
publisher: PeerJ Inc.
rights: © 2026 Sachs and Madzia
abstract: The transition from the Early to the Middle Jurassic was marked by significant restructuring of plesiosaur communities. While knowledge of the earliest Middle Jurassic plesiosaurs is generally limited, Toarcian plesiosaur occurrences are abundant, though the vast majority of specimens have been unearthed in the United Kingdom and Germany. Here, we reassess Lusonectes sauvagei, an early-diverging plesiosaur from the lower to middle upper Toarcian of the São Gião Formation in Portugal. Originally described as Plesiosaurus sp., it was later established as a distinct taxon closely related to taxa currently encompassed within Microcleididae. Our firsthand examination of the holotype of L. sauvagei resulted in differing interpretations of certain aspects of its morphology, prompting a detailed osteological, taxonomic, and phylogenetic reevaluation. We provide a redescription of L. sauvagei, propose a new diagnosis, and investigate its phylogenetic affinities. Although the specimen is fragmentary and poorly preserved, our study suggests that, contrary to the original interpretation, L. sauvagei is not affiliated with Microcleidus spp. The taxon remains problematic and may represent either an early-diverging pliosaurid or a plesiosauroid. Lusonectes is one of the few diagnosable plesiosaurs from the upper Lower Jurassic found outside the classic British and German localities and thus offers insights into the diversity of plesiosaurs just prior to a major event in the evolutionary history of the clade.
bibliographic citation: Sachs et al. (2026) The osteology, taxonomy, and phylogenetic affinities of the Early Jurassic plesiosaur Lusonectes sauvagei. PeerJ 14:e20611 https://doi.org/10.7717/peerj.20611
date submitted: 2025-03-31
date accepted: 2025-11-28
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sachs
  given name: Sven
author list: Agent
  family name: Madzia
  given name: Daniel
doi: 10.7717/peerj.20611
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Sachs and Madzia
attribution name: Sachs and Madzia

Identification of novel metagenomic lipases through integrated structural and sequence-based analysis
type: item
type: AcademicArticle
description: Enzymes, as key biocatalysts, are essential for advancing sustainable green technologies across diverse industrial sectors. The discovery of novel enzymes is essential for expanding their applications. In this study, we identified new lipases using an integrated screening strategy. This approach combines both structural and sequence-based methods on a large-scale metagenomic database. This strategy enabled the identification of new lipases with low sequence identity to known reference proteins. Our approach, therefore, circumvents the limitations of traditional sequence-only methods, which often fail to identify functionally similar enzymes with low sequence similarity. We first used Foldseek, a state-of-the-art structural homology search tool, to rapidly screen the database for proteins with structures similar to widely used lipases. This was followed by a rigorous sequence similarity filtering against public protein databases, yielding 711 putative novel lipases. We selected and experimentally validated three candidates, confirming their lipase activity. Further biochemical characterization revealed their notable properties including thermostability with optimal activity at 50–55 °C, and distinct alkaline activity profiles, maximal at pH of 8.0–9.0. Their unique properties, including high activity at elevated temperatures and alkaline pH, suggest potential for applications in detergent formulations, bioremediation, and industrial biocatalysis. Beyond identifying these promising enzymes, this study demonstrates the power of a combined structural and sequence-based approach for finding novel biocatalysts. This methodological innovation has broad implications for future enzyme discovery from metagenomic resources.
format: application/pdf
format: text/html
creator: Nongluck Jaito
creator: Nattha Kaewsawat
creator: Kamollak Sangawthong
creator: Tanaporn Uengwetwanit
subject: Bioinformatics
subject: Biotechnology
description: doi:10.7717/peerj.20462
publisher: PeerJ Inc.
rights: © 2026 Jaito et al.
abstract: Enzymes, as key biocatalysts, are essential for advancing sustainable green technologies across diverse industrial sectors. The discovery of novel enzymes is essential for expanding their applications. In this study, we identified new lipases using an integrated screening strategy. This approach combines both structural and sequence-based methods on a large-scale metagenomic database. This strategy enabled the identification of new lipases with low sequence identity to known reference proteins. Our approach, therefore, circumvents the limitations of traditional sequence-only methods, which often fail to identify functionally similar enzymes with low sequence similarity. We first used Foldseek, a state-of-the-art structural homology search tool, to rapidly screen the database for proteins with structures similar to widely used lipases. This was followed by a rigorous sequence similarity filtering against public protein databases, yielding 711 putative novel lipases. We selected and experimentally validated three candidates, confirming their lipase activity. Further biochemical characterization revealed their notable properties including thermostability with optimal activity at 50–55 °C, and distinct alkaline activity profiles, maximal at pH of 8.0–9.0. Their unique properties, including high activity at elevated temperatures and alkaline pH, suggest potential for applications in detergent formulations, bioremediation, and industrial biocatalysis. Beyond identifying these promising enzymes, this study demonstrates the power of a combined structural and sequence-based approach for finding novel biocatalysts. This methodological innovation has broad implications for future enzyme discovery from metagenomic resources.
bibliographic citation: Jaito et al. (2026) Identification of novel metagenomic lipases through integrated structural and sequence-based analysis. PeerJ 14:e20462 https://doi.org/10.7717/peerj.20462
date submitted: 2025-07-25
date accepted: 2025-11-03
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jaito
  given name: Nongluck
author list: Agent
  family name: Kaewsawat
  given name: Nattha
author list: Agent
  family name: Sangawthong
  given name: Kamollak
author list: Agent
  family name: Uengwetwanit
  given name: Tanaporn
doi: 10.7717/peerj.20462
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Jaito et al.
attribution name: Jaito et al.

Diversification in the steppe rat snake Elaphe dione (Pallas, 1773) coincides with the Mid-Pleistocene climatic transition of Eurasia
type: item
type: AcademicArticle
description: Background The steppe rat snake, Elaphe dione, has one of the broadest terrestrial distributions among snakes. Its distribution spans from the Azov Sea and the Caucasus to the Pacific coast of Far East Asia. The steppe rat snake is one of the few reptile species with an extensive distribution in both the Western and Eastern Palearctic, making its evolutionary history of particular interest in understanding biogeographical patterns and connections between these regions. However, knowledge of its genetic variability and phylogeography remains limited. In this study, we examined the phylogeographic structure of E. dione to shed light on its genetic diversity and diversification history in the Western and Eastern Palearctic. Methods We reconstructed phylogenies and analyzed the genetic structure of E. dione populations originating from most of its geographic range using three mitochondrial DNA gene fragments (12S rRNA, COI, ND4+tRNAs). In total, we analyzed sequences from 130 E. dione specimens from 100 locations. We used maximum likelihood and Bayesian inference methods to reconstruct phylogenetic trees, supplemented by an analysis of haplotype networks, molecular clocks, and a neutrality test for historical demography. Results We identified 11 phylogeographic lineages grouped into three broader clades that diverged during the Late Miocene-Pliocene. The average uncorrected genetic distance between these 11 lineages ranged from 0.7% to 6.7% based on sequences of the COI fragment. Most of the contemporary range of E. dione is occupied by a single clade, with lineages distributed west and east of the Central Asian mountains. This west-east split in the clade occurred approximately 1.7 million years ago (Mya), followed by vicariant radiation in the Western and Eastern Palearctic during the Mid-Pleistocene era. Spatial patterns of mtDNA variation identified areas of post-last glacial maximum (LGM) dispersal and secondary contact zones of several lineages in the Altai and th…
format: application/pdf
format: text/html
creator: Evgeniy Simonov
creator: Polina Chernigova
creator: Artem Lisachov
creator: Kazhmurat Akhmedenov
creator: Oleg Ermakov
creator: Anastasia Klenina
creator: Andrey Bakiev
creator: Roman Nazarov
creator: Sayagul Akhmedenova
creator: Daniel Jablonski
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.20351
publisher: PeerJ Inc.
rights: © 2026 Simonov et al.
abstract: Background The steppe rat snake, Elaphe dione, has one of the broadest terrestrial distributions among snakes. Its distribution spans from the Azov Sea and the Caucasus to the Pacific coast of Far East Asia. The steppe rat snake is one of the few reptile species with an extensive distribution in both the Western and Eastern Palearctic, making its evolutionary history of particular interest in understanding biogeographical patterns and connections between these regions. However, knowledge of its genetic variability and phylogeography remains limited. In this study, we examined the phylogeographic structure of E. dione to shed light on its genetic diversity and diversification history in the Western and Eastern Palearctic. Methods We reconstructed phylogenies and analyzed the genetic structure of E. dione populations originating from most of its geographic range using three mitochondrial DNA gene fragments (12S rRNA, COI, ND4+tRNAs). In total, we analyzed sequences from 130 E. dione specimens from 100 locations. We used maximum likelihood and Bayesian inference methods to reconstruct phylogenetic trees, supplemented by an analysis of haplotype networks, molecular clocks, and a neutrality test for historical demography. Results We identified 11 phylogeographic lineages grouped into three broader clades that diverged during the Late Miocene-Pliocene. The average uncorrected genetic distance between these 11 lineages ranged from 0.7% to 6.7% based on sequences of the COI fragment. Most of the contemporary range of E. dione is occupied by a single clade, with lineages distributed west and east of the Central Asian mountains. This west-east split in the clade occurred approximately 1.7 million years ago (Mya), followed by vicariant radiation in the Western and Eastern Palearctic during the Mid-Pleistocene era. Spatial patterns of mtDNA variation identified areas of post-last glacial maximum (LGM) dispersal and secondary contact zones of several lineages in the Altai and th…
bibliographic citation: Simonov et al. (2026) Diversification in the steppe rat snake Elaphe dione (Pallas, 1773) coincides with the Mid-Pleistocene climatic transition of Eurasia. PeerJ 14:e20351 https://doi.org/10.7717/peerj.20351
date submitted: 2025-06-26
date accepted: 2025-10-15
issued: 2026-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simonov
  given name: Evgeniy
author list: Agent
  family name: Chernigova
  given name: Polina
author list: Agent
  family name: Lisachov
  given name: Artem
author list: Agent
  family name: Akhmedenov
  given name: Kazhmurat
author list: Agent
  family name: Ermakov
  given name: Oleg
author list: Agent
  family name: Klenina
  given name: Anastasia
author list: Agent
  family name: Bakiev
  given name: Andrey
author list: Agent
  family name: Nazarov
  given name: Roman
author list: Agent
  family name: Akhmedenova
  given name: Sayagul
author list: Agent
  family name: Jablonski
  given name: Daniel
doi: 10.7717/peerj.20351
volume: 14
issn: 2167-8359
publication name: PeerJ
publication date: 2026-02-02
copyright: ©2026 Simonov et al.
attribution name: Simonov et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359