PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Prevalence and association testing of antinuclear antibodies and inflammatory bowel disease in Taiwan
items: A new species of Ampharete Malmgren, 1866 (Annelida: Ampharetidae) from Washington and redescription of A. cirrata Webster & Benedict, 1887 and A. labrops Hartman, 1961
items: Identification and characterization of novel SUMO genes in bread wheat
items: Understanding perceived exertion in power-aimed resistance training: the relationship between perceived exertion and muscle fatigue
items: Parasites influence the physiology and personality in a small mammal (Ochotona curzoniae)
items: Biochemical and molecular responses of maize to low and high temperatures in symbiosis with mixed arbuscular mycorrhizal fungi cultures
items: Evaluation of water quality and soil fertility in remediated farmland for protection of wetland ecology by planting different crops
items: Effects of monocropping soil on plant growth and rhizosphere microbial community structure of Salvia miltiorrhiza Bge
items: Effectiveness of respiratory muscle training on pulmonary function recovery in patients with spinal cord injury: a systematic review and meta-analysis
items: Genomics, population dynamics, immune evasion and resistance determinants foster the competence and global dissemination of Klebsiella pneumoniae
items: Structure and diversity of microbial communities in the rhizosphere soil of Trichosanthes kirilowii from different cultivation patterns
items: Long-term glycemic variability and the risk of heart failure: a meta-analysis
items: Retrospective analysis of cervical screening abnormalities in women with type 3 transformation zone without visible lesions
items: Effects of creatine supplementation on muscle strength gains—a meta-analysis and systematic review
items: Application analysis of two nucleic acid detection systems in blood detection of hepatitis B virus, hepatitis C virus and human immunodeficiency virus
items: Validity, reliability and minimal detectable change in the sit-to-stand test for synchronous and asynchronous tele-assessment in post-COVID-19 condition
items: Insights into the interactions between Deverra tortuosa and Schizomyia buboniae: phytochemicals, antioxidant capacity, and enzyme inhibitory effects
items: Patterns of pre-sleep music use and sleep quality: exploratory survey findings on state anxiety
items: Biological maturation, anthropometric, and physical fitness variables of youth breaking athletes with different competition levels
items: Efflux systems driving resistance and virulence across biological domains
items: Pelvis-Trunk coordination strategies differ a cross preparatory court movement distances during the tennis forehand
items: Mandibular form and function is more disparate in amniotes than in non-amniote tetrapods from the late Palaeozoic
items: Overexpression of ORAOV1 and its association with immunotherapy resistance in hepatocellular carcinoma
items: Resistance of cervical vertebrae in response to muscular stresses in pterosaurs: implications for foraging habits and skeletal pneumatization
items: Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)—induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies
items: Comparative efficacy of different exercise interventions in patients with ankylosing spondylitis: a systematic review and network meta-analysis
items: Coral reefs in the Mahafaly Seascape (SW Madagascar) as potential climate refugia following the 2024 mass bleaching event
items: Feasibility of a pulsed multiphase contrast media injection protocol in head and neck computed tomography angiography: a systematic retrospective study
items: Microgreens: nutritional properties, health benefits, production techniques, and food safety risks
items: Elemental pollution and risk assessment of soils and Gundelia tournefortii in a multi-sector industrial zone with a history of agricultural use
items: Bioinformatics-based identification of RAS disequilibrium involved in post-hemorrhagic shock mesenteric lymph return-mediated acute kidney injury in mice
items: Interaction of soil pH, organic matter, exchangeable acidity, and cation exchange capacity in a managed tea farm
items: Positive rates of total and specific immunoglobulin E in 7,824 adult patients with suspected allergic diseases in Liaoning Province, China: a retrospective study
items: Leaf-branch-root trait relationships in Quercus rehderiana across rocky and non-rocky desertification habitats in China
items: Patients with lower BMI are more likely to experience shoulder pain after single port laparoscopic myomectomy
items: Effects of virtual reality intervention dosage on gait performance in Parkinson’s disease: a systematic review and meta-analysis
items: Occurrence, composition, sources, and ecological-health risk assessment of polycyclic aromatic hydrocarbons in Chinese water bodies: a review
items: Carbon capture, photosynthesis, and leaf gas exchange of shade tree species and Arabica coffee varieties in coffee agroforestry systems in Veracruz state, Mexico
items: Utilization of soft pistachio hulls in Japanese quail diets for enhanced egg quality and yolk pigmentation
items: Evaluation study of effect of virtual care education on healthcare providers’ knowledge, confidence, and satisfaction
items: MAFF inhibits angiogenesis in non-small cell lung cancer by suppressing YAP1 nuclear translocation
items: Efficacy and safety of rivaroxaban in neonatal catheter-related thrombosis: a single-center retrospective study of 122 cases
items: The bee bread of honey bees is characterized by a core microbiota despite the application of miticide treatments and variation across space and time
items: Assessment of healing dynamics in dental extraction sockets among non-diabetic, prediabetic, and type 2 diabetic patients: a comparative clinical investigation
items: Hybrid contour and geometric partitioning for accurate plantar foot region segmentation
items: DHCR7: from sterol biosynthesis to oncogenic role in colorectal cancer
items: Unveiling the clinical profiles of critically ill COVID-19 patients: insights from Ezhou during the early spread
items: Selection and preliminary evaluation of superior individual plant in Camellia oleifera
items: Effectiveness of multi-component exercise in individuals with type 2 diabetes: a systematic review and meta-analysis
items: Effects of foliar applied asparagine, glycine and citric acid on cadmium uptake and yield in wheat
items: El Niño-driven phase shift to algal dominance on Isla del Caño’s coral reefs: implications for urgent restoration
items: Outcomes and safety of colonoscopy in elderly patients aged 80 years and older: a retrospective cohort study
items: Risk factors and predictive model for intrapartum cesarean delivery in women with epidural analgesia: a retrospective cohort study
items: Effect of quality sleep on basketball three-point shooting outcomes: the mediating role of athletic mental energy in a cross-sectional study of collegiate athletes
items: Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments
items: Cross-cultural adaptation and psychometric validation of the Chinese quality-of-life questionnaire for patients with systemic sclerosis
items: Dissecting antibody-dependent enhancement modulation by Fc-modified cross-neutralizing human monoclonal antibody
items: Comparison of anti-PD-1/PD-L1-based regimens in relapsed/refractory diffuse large B-cell lymphoma: a meta-analysis
items: Deciphering the role of Hat1 in spermatogenesis: Chromatin organization and beyond
items: A Bayesian model for assessing organic matter supply in complex marine food webs using amino acid stable isotope analysis
items: Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province
items: AIMP1: multifunctional regulator in physiology and pathology with therapeutic implications
items: Machine learning classification of mango maturity based on carotene content from Raman spectra
items: Identification of mitochondrial-related genes to evaluate the immune infiltration and prognosis of lung adenocarcinoma
items: Acute effect of short foot exercise on dynamic stability and foot kinematic in trail runners: a proof-of-concept study
items: Estuarine bivalve metabolic response mediated by environmental drivers
items: Effects of combined exercise training for adults with resistant major depression: a pilot study from the TRACE-RMD project
items: Tryptophan-kynurenine pathway: a possible new mechanism for the prevention and treatment of reproductive system-related diseases
items: Latitudinal variations in morphometric traits and bioenergetic status of adult red squat lobsters Grimothea monodon (H. Milne Edwards, 1837) in the Southeast Pacific Ocean
items: The effect of endoscopic polidocanol carbon dioxide foam for internal hemorrhoids: a retrospective study
items: Enhancing heatstroke prediction accuracy with interpretable machine learning: a multi-center data-driven approach
items: Feeding ecology and trophic interactions of the narrow-barred Spanish Mackerel (Scomberomorus commerson) in the Central Taiwan Strait

Prevalence and association testing of antinuclear antibodies and inflammatory bowel disease in Taiwan
type: item
type: AcademicArticle
description: Background Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are characterized by chronic inflammation of the gastrointestinal tract. Antinuclear antibodies (ANAs), which are autoantibodies directed against nuclear components, are commonly present in various autoimmune disorders. We investigated the prevalence and clinical significance of ANAs in Taiwanese patients with IBD. Methods From January 2017 to December 2024, ANA status was checked at initial diagnosis of IBD in patients from a medical center in central Taiwan. Risk factors for ANA positivity were evaluated. Results Of the 166 patients in this study, 57 had CD and 109 had UC. ANA test results were positive (titers of ≥ 1:160) in 26 patients (15.7%). Older age at disease diagnosis (p < 0.05) and a diagnosis of UC (p < 0.05) were statistically significant risk factors for ANA positivity. Gender (p = 0.31), use of advanced therapy (p = 0.66), and the presence of extraintestinal manifestations (EIMs) (p = 0.14) were not associated with ANA positivity. The response to anti-tumor necrosis factor therapy did not differ between ANA-positive and ANA-negative patients (p = 0.34). The most frequent ANA staining patterns were AC1, AC3, and AC4. Conclusions These findings suggest that although ANA positivity is relatively common among Taiwanese patients with IBD, particularly among older UC patients. Further validation is required to explore the clinical implications of ANA positivity in Asian population.
format: application/pdf
format: text/html
creator: Tsai-Min Yang
creator: Fang-Ting Lu
creator: Hsu-Heng Yen
creator: Yang-Yuan Chen
subject: Gastroenterology and Hepatology
subject: Rheumatology
description: doi:10.7717/peerj.20474
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: Background Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are characterized by chronic inflammation of the gastrointestinal tract. Antinuclear antibodies (ANAs), which are autoantibodies directed against nuclear components, are commonly present in various autoimmune disorders. We investigated the prevalence and clinical significance of ANAs in Taiwanese patients with IBD. Methods From January 2017 to December 2024, ANA status was checked at initial diagnosis of IBD in patients from a medical center in central Taiwan. Risk factors for ANA positivity were evaluated. Results Of the 166 patients in this study, 57 had CD and 109 had UC. ANA test results were positive (titers of ≥ 1:160) in 26 patients (15.7%). Older age at disease diagnosis (p < 0.05) and a diagnosis of UC (p < 0.05) were statistically significant risk factors for ANA positivity. Gender (p = 0.31), use of advanced therapy (p = 0.66), and the presence of extraintestinal manifestations (EIMs) (p = 0.14) were not associated with ANA positivity. The response to anti-tumor necrosis factor therapy did not differ between ANA-positive and ANA-negative patients (p = 0.34). The most frequent ANA staining patterns were AC1, AC3, and AC4. Conclusions These findings suggest that although ANA positivity is relatively common among Taiwanese patients with IBD, particularly among older UC patients. Further validation is required to explore the clinical implications of ANA positivity in Asian population.
bibliographic citation: Yang et al. (2025) Prevalence and association testing of antinuclear antibodies and inflammatory bowel disease in Taiwan. PeerJ 13:e20474 https://doi.org/10.7717/peerj.20474
date submitted: 2025-04-07
date accepted: 2025-11-04
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Tsai-Min
author list: Agent
  family name: Lu
  given name: Fang-Ting
author list: Agent
  family name: Yen
  given name: Hsu-Heng
author list: Agent
  family name: Chen
  given name: Yang-Yuan
doi: 10.7717/peerj.20474
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Yang et al.
attribution name: Yang et al.

A new species of Ampharete Malmgren, 1866 (Annelida: Ampharetidae) from Washington and redescription of A. cirrata Webster & Benedict, 1887 and A. labrops Hartman, 1961
type: item
type: AcademicArticle
description: Ampharete acutifrons (Grube, 1860), originally described from Greenland, has long been considered a widely distributed arctic-boreal species. However, recent morphological re-assessment of the holotype indicates that most previous records of A. acutifrons were misidentifications, and molecular sequence data also suggest that A. acutifrons is a multispecies complex. This study focuses on specimens of the A. acutifrons species complex from Washington, USA, with publicly available cytochrome c oxidase subunit I (COI) sequence data. Specimens from Washington belonging to the Invertebrate Zoology Collection of the Florida Museum of Natural History were examined. Additional specimens were examined for morphological comparison, including type material of A. cirrata Webster & Benedict, 1887, and A. labrops Hartman, 1961. Detailed morphological descriptions of specimens and photographs of the diagnostic characters were made. The molecular analysis includes 37 published COI sequences of Ampharete and Anobothrus species sourced from public databases. Redescriptions of type material of A. cirrata and A. labrops are provided. Ampharete paulayi n. sp. is described as a new species from Washington, USA, based on morphological and COI sequences data. Photographs of living specimens are presented, a hypothesis on the development of buccal tentacles in Ampharete species is proposed, and the use of Methyl green stain is recommended as a standard practice in future descriptions of ampharetids.
format: application/pdf
format: text/html
creator: Yessica Chávez-López
subject: Biodiversity
subject: Evolutionary Studies
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.20457
publisher: PeerJ Inc.
rights: © 2025 Chávez-López
abstract: Ampharete acutifrons (Grube, 1860), originally described from Greenland, has long been considered a widely distributed arctic-boreal species. However, recent morphological re-assessment of the holotype indicates that most previous records of A. acutifrons were misidentifications, and molecular sequence data also suggest that A. acutifrons is a multispecies complex. This study focuses on specimens of the A. acutifrons species complex from Washington, USA, with publicly available cytochrome c oxidase subunit I (COI) sequence data. Specimens from Washington belonging to the Invertebrate Zoology Collection of the Florida Museum of Natural History were examined. Additional specimens were examined for morphological comparison, including type material of A. cirrata Webster & Benedict, 1887, and A. labrops Hartman, 1961. Detailed morphological descriptions of specimens and photographs of the diagnostic characters were made. The molecular analysis includes 37 published COI sequences of Ampharete and Anobothrus species sourced from public databases. Redescriptions of type material of A. cirrata and A. labrops are provided. Ampharete paulayi n. sp. is described as a new species from Washington, USA, based on morphological and COI sequences data. Photographs of living specimens are presented, a hypothesis on the development of buccal tentacles in Ampharete species is proposed, and the use of Methyl green stain is recommended as a standard practice in future descriptions of ampharetids.
bibliographic citation: Chávez-López (2025) A new species of Ampharete Malmgren, 1866 (Annelida: Ampharetidae) from Washington and redescription of A. cirrata Webster & Benedict, 1887 and A. labrops Hartman, 1961. PeerJ 13:e20457 https://doi.org/10.7717/peerj.20457
date submitted: 2025-09-19
date accepted: 2025-10-31
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chávez-López
  given name: Yessica
doi: 10.7717/peerj.20457
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Chávez-López
attribution name: Chávez-López

Identification and characterization of novel SUMO genes in bread wheat
type: item
type: AcademicArticle
description: The small-ubiquitin-like-modifier (SUMO), composed of approximately 100 amino acid residues, regulates the cellular activity of several proteins by posttranslational modification. Almost all plant species express a family of SUMO isoforms. Nevertheless, the SUMO genes in wheat (TaSUMOs) have not undergone complete characterization, and the roles of TaSUMOs remain unidentified. The study identified four new SUMO genes in wheat, named TaSUMO4-7, in addition to the previously known TaSUMO1-3. These genes are part of the conserved SUMO family, as indicated by phylogenetic analysis. The genes contain the characteristic SUMO-acceptor site motif and the essential C-terminal diglycine motif for processing. Expression analysis showed that TaSUMO4-7 genes are expressed in various wheat tissues. Bioinformatics analysis predicted the biochemical properties and structures of the proteins, which were found to localize in the cytoplasm and nucleus. The study confirms that the new TaSUMO4-7 genes are functional members of the wheat SUMO family and lays the groundwork for further research into their specific roles.
format: application/pdf
format: text/html
creator: Eid I. Ibrahim
creator: Kotb A. Attia
creator: Abdelhalim Ghazy
creator: Itoh Kimiko
creator: Abdullah Al-Doss
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.20432
publisher: PeerJ Inc.
rights: © 2025 Ibrahim et al.
abstract: The small-ubiquitin-like-modifier (SUMO), composed of approximately 100 amino acid residues, regulates the cellular activity of several proteins by posttranslational modification. Almost all plant species express a family of SUMO isoforms. Nevertheless, the SUMO genes in wheat (TaSUMOs) have not undergone complete characterization, and the roles of TaSUMOs remain unidentified. The study identified four new SUMO genes in wheat, named TaSUMO4-7, in addition to the previously known TaSUMO1-3. These genes are part of the conserved SUMO family, as indicated by phylogenetic analysis. The genes contain the characteristic SUMO-acceptor site motif and the essential C-terminal diglycine motif for processing. Expression analysis showed that TaSUMO4-7 genes are expressed in various wheat tissues. Bioinformatics analysis predicted the biochemical properties and structures of the proteins, which were found to localize in the cytoplasm and nucleus. The study confirms that the new TaSUMO4-7 genes are functional members of the wheat SUMO family and lays the groundwork for further research into their specific roles.
bibliographic citation: Ibrahim et al. (2025) Identification and characterization of novel SUMO genes in bread wheat. PeerJ 13:e20432 https://doi.org/10.7717/peerj.20432
date submitted: 2025-02-25
date accepted: 2025-10-30
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ibrahim
  given name: Eid I.
author list: Agent
  family name: Attia
  given name: Kotb A.
author list: Agent
  family name: Ghazy
  given name: Abdelhalim
author list: Agent
  family name: Kimiko
  given name: Itoh
author list: Agent
  family name: Al-Doss
  given name: Abdullah
doi: 10.7717/peerj.20432
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: ©2025 Ibrahim et al.
attribution name: Ibrahim et al.

Understanding perceived exertion in power-aimed resistance training: the relationship between perceived exertion and muscle fatigue
type: item
type: AcademicArticle
description: Background Perceived exertion is an inevitable outcome of power-oriented resistance training. However, it remains unknown whether perceived exertion is dominated by central or peripheral responses during this type of training. This study examined the effect of neuromuscular responses on the determination of ratings of perceived exertion (RPE) during power bench press (BPress) exercise. Methods Sixteen trained males performed three BPress tasks with varying volumes (low, medium, high) at 65% of their one-repetition maximum. RPE, surface electromyography, and velocity loss were assessed across all conditions. Peak root mean square (RMS) and median frequency (MDF) were calculated from the surface electromyography data. Results Significant effects were observed across experimental conditions for overall RPE, average velocity loss, and average MDF (all p < 0.001), while no significant difference was found in average RMS. As the lifting tasks progressed, significant effects of repetition were observed in all measured variables (all p < 0.001). When comparing conditions, significant differences were found among the three in RPE, velocity loss, and MDF (all p < 0.001), whereas no significant effect of condition was observed in RMS. No significant relationship was found between MDF and velocity loss. Conclusions In power BPress, higher repetitions affected RPE, velocity loss, and MDF, while peak RMS was less responsive. These findings indicate that both athletic performance and RPE are primarily influenced by peripheral fatigue. However, velocity loss should be interpreted with caution as a fatigue marker in this context.
format: application/pdf
format: text/html
creator: Hanye Zhao
creator: Takanori Kurokawa
creator: Masayoshi Tajima
creator: Zijian Liu
creator: Junichi Okada
subject: Kinesiology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.20426
publisher: PeerJ Inc.
rights: © 2025 Zhao et al.
abstract: Background Perceived exertion is an inevitable outcome of power-oriented resistance training. However, it remains unknown whether perceived exertion is dominated by central or peripheral responses during this type of training. This study examined the effect of neuromuscular responses on the determination of ratings of perceived exertion (RPE) during power bench press (BPress) exercise. Methods Sixteen trained males performed three BPress tasks with varying volumes (low, medium, high) at 65% of their one-repetition maximum. RPE, surface electromyography, and velocity loss were assessed across all conditions. Peak root mean square (RMS) and median frequency (MDF) were calculated from the surface electromyography data. Results Significant effects were observed across experimental conditions for overall RPE, average velocity loss, and average MDF (all p < 0.001), while no significant difference was found in average RMS. As the lifting tasks progressed, significant effects of repetition were observed in all measured variables (all p < 0.001). When comparing conditions, significant differences were found among the three in RPE, velocity loss, and MDF (all p < 0.001), whereas no significant effect of condition was observed in RMS. No significant relationship was found between MDF and velocity loss. Conclusions In power BPress, higher repetitions affected RPE, velocity loss, and MDF, while peak RMS was less responsive. These findings indicate that both athletic performance and RPE are primarily influenced by peripheral fatigue. However, velocity loss should be interpreted with caution as a fatigue marker in this context.
bibliographic citation: Zhao et al. (2025) Understanding perceived exertion in power-aimed resistance training: the relationship between perceived exertion and muscle fatigue. PeerJ 13:e20426 https://doi.org/10.7717/peerj.20426
date submitted: 2025-06-18
date accepted: 2025-10-29
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Hanye
author list: Agent
  family name: Kurokawa
  given name: Takanori
author list: Agent
  family name: Tajima
  given name: Masayoshi
author list: Agent
  family name: Liu
  given name: Zijian
author list: Agent
  family name: Okada
  given name: Junichi
doi: 10.7717/peerj.20426
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: ©2025 Zhao et al.
attribution name: Zhao et al.

Parasites influence the physiology and personality in a small mammal (Ochotona curzoniae)
type: item
type: AcademicArticle
description: Background Parasites are prevalent in animals and have coexisted with their hosts over long evolutionary periods. However, the link between individual behavioral variations and parasitic infections remains unclear. Plateau pika (Ochotona curzoniae) is a keystone species on the Qinghai-Tibetan Plateau that is commonly infected with Eimeria spp., an intestinal parasite. Methods In this study, 30 adult pikas were assigned to three groups: infected with Eimeria spp. (PA+), administered normal saline (Ctrl), and treated with an anticoccidial drug (PA−). We examined changes in boldness, exploration, and docility, as well as variations in triiodothyronine (T3), thyroxine (T4), resting metabolic rate (RMR), and fecal cortisol (CORT) levels. Results The PA+ group exhibited significantly higher parasite load. Pikas showed increased boldness, exploration, and docility on day 5, when Eimeria spp. numbers were high. The T3 and T4 levels declined as parasite loads increased, whereas the CORT and RMR levels fluctuated at different experimental stages. These results suggest that parasite infection influences host behavior and physiology, providing insights into parasite-host interactions. Conclusion This study provides evidence that Eimeria spp. load modulates the behavior and physiology of plateau pikas. The specific behavioral shifts coinciding with peak infection, coupled with the suppression of thyroid hormones and metabolic responses, reveal a complex and integrated host adaptation strategy. As a keystone species on the Qinghai-Tibet Plateau, the behavior-physiology coupling mechanism in plateau pikas not only provides new evidence for host-parasite coevolution, but also offers critical insights into understanding the stability of regional ecosystems.
format: application/pdf
format: text/html
creator: Rong Wang
creator: Suqin Wang
creator: Jiapeng Qu
subject: Animal Behavior
subject: Ecology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.20420
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Background Parasites are prevalent in animals and have coexisted with their hosts over long evolutionary periods. However, the link between individual behavioral variations and parasitic infections remains unclear. Plateau pika (Ochotona curzoniae) is a keystone species on the Qinghai-Tibetan Plateau that is commonly infected with Eimeria spp., an intestinal parasite. Methods In this study, 30 adult pikas were assigned to three groups: infected with Eimeria spp. (PA+), administered normal saline (Ctrl), and treated with an anticoccidial drug (PA−). We examined changes in boldness, exploration, and docility, as well as variations in triiodothyronine (T3), thyroxine (T4), resting metabolic rate (RMR), and fecal cortisol (CORT) levels. Results The PA+ group exhibited significantly higher parasite load. Pikas showed increased boldness, exploration, and docility on day 5, when Eimeria spp. numbers were high. The T3 and T4 levels declined as parasite loads increased, whereas the CORT and RMR levels fluctuated at different experimental stages. These results suggest that parasite infection influences host behavior and physiology, providing insights into parasite-host interactions. Conclusion This study provides evidence that Eimeria spp. load modulates the behavior and physiology of plateau pikas. The specific behavioral shifts coinciding with peak infection, coupled with the suppression of thyroid hormones and metabolic responses, reveal a complex and integrated host adaptation strategy. As a keystone species on the Qinghai-Tibet Plateau, the behavior-physiology coupling mechanism in plateau pikas not only provides new evidence for host-parasite coevolution, but also offers critical insights into understanding the stability of regional ecosystems.
bibliographic citation: Wang et al. (2025) Parasites influence the physiology and personality in a small mammal (Ochotona curzoniae). PeerJ 13:e20420 https://doi.org/10.7717/peerj.20420
date submitted: 2025-09-05
date accepted: 2025-10-29
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Rong
author list: Agent
  family name: Wang
  given name: Suqin
author list: Agent
  family name: Qu
  given name: Jiapeng
doi: 10.7717/peerj.20420
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Wang et al.
attribution name: Wang et al.

Biochemical and molecular responses of maize to low and high temperatures in symbiosis with mixed arbuscular mycorrhizal fungi cultures
type: item
type: AcademicArticle
description: In this study, changes in mineral element concentrations, physiological parameters, and gene expression of heat shock proteins were investigated in maize plants subjected to mycorrhiza under low and high temperature stress. The application of seven different temperatures (5 °C, 10 °C, 15 °C, 25 °C, 35 °C, 40 °C, and 45 °C) under five different mixed arbuscular mycorrhizal fungi (AMF) culture treatments (M0, M1, M2, M3, and M4) constituted the factors of the experiment. With the application of mycorrhiza, the plant dry weight was found to be the highest at 25 °C, and the M3 group was applied. The highest values in mineral element concentrations were detected at 25 °C in the maize plant, where M4 had N, P, K, Ca, and Fe concentrations; M3 had Cu and Mn concentrations; and M2 had Mg and Zn concentrations. Lipid peroxidation gradually increased with temperature changes in all the applications, and the protective effect of proline was more pronounced at high temperatures than at low temperatures. Antioxidant enzyme activities were altered by applications of mycorrhiza and temperature. For all mycorrhiza applications, the expression of HSP70 and HSP90 reached a maximum at 10 °C, 40 °C, and 45 °C. It has been revealed that low- and high-temperature applications in maize plants cause serious changes in the mycorrhizal symbiosis on the basis of investigated parameters, and these changes occur at different levels depending on the temperature changes and the differences between mixed AMF cultures. However, it can be said that the M3 application has the capacity to facilitate the growth of maize even in conditions of low (−10 °C) and high (45 °C) temperature.
format: application/pdf
format: text/html
creator: Vedia Turudu
creator: Imren Kutlu
creator: Nurdilek Gulmezoglu
subject: Agricultural Science
description: doi:10.7717/peerj.20419
publisher: PeerJ Inc.
rights: © 2025 Turudu et al.
abstract: In this study, changes in mineral element concentrations, physiological parameters, and gene expression of heat shock proteins were investigated in maize plants subjected to mycorrhiza under low and high temperature stress. The application of seven different temperatures (5 °C, 10 °C, 15 °C, 25 °C, 35 °C, 40 °C, and 45 °C) under five different mixed arbuscular mycorrhizal fungi (AMF) culture treatments (M0, M1, M2, M3, and M4) constituted the factors of the experiment. With the application of mycorrhiza, the plant dry weight was found to be the highest at 25 °C, and the M3 group was applied. The highest values in mineral element concentrations were detected at 25 °C in the maize plant, where M4 had N, P, K, Ca, and Fe concentrations; M3 had Cu and Mn concentrations; and M2 had Mg and Zn concentrations. Lipid peroxidation gradually increased with temperature changes in all the applications, and the protective effect of proline was more pronounced at high temperatures than at low temperatures. Antioxidant enzyme activities were altered by applications of mycorrhiza and temperature. For all mycorrhiza applications, the expression of HSP70 and HSP90 reached a maximum at 10 °C, 40 °C, and 45 °C. It has been revealed that low- and high-temperature applications in maize plants cause serious changes in the mycorrhizal symbiosis on the basis of investigated parameters, and these changes occur at different levels depending on the temperature changes and the differences between mixed AMF cultures. However, it can be said that the M3 application has the capacity to facilitate the growth of maize even in conditions of low (−10 °C) and high (45 °C) temperature.
bibliographic citation: Turudu et al. (2025) Biochemical and molecular responses of maize to low and high temperatures in symbiosis with mixed arbuscular mycorrhizal fungi cultures. PeerJ 13:e20419 https://doi.org/10.7717/peerj.20419
date submitted: 2025-07-31
date accepted: 2025-10-28
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Turudu
  given name: Vedia
author list: Agent
  family name: Kutlu
  given name: Imren
author list: Agent
  family name: Gulmezoglu
  given name: Nurdilek
doi: 10.7717/peerj.20419
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Turudu et al.
attribution name: Turudu et al.

Evaluation of water quality and soil fertility in remediated farmland for protection of wetland ecology by planting different crops
type: item
type: AcademicArticle
description: Enhancements in water quality and soil characteristics of wetlands can improve the ecological environment of the area and enrich its biodiversity. The present study examined the effects of five distinct crops (i.e.: colza oil, mustard, Chinese cabbage, wheat, barley) cultivated in remediation plots, and evaluated their impact on water quality and soil fertility. The water quality within the remediated farmland was categorized as Class III (moderately polluted). The soil exhibited low total nitrogen and organic matter levels (the mean values were respectively 0.032% and 10.84 g/kg), and high readily available phosphorus and potassium concentration (the mean values were respectively 75.71 and 247.64 mg/kg). The soil fertility was comprehensively categorized as Class III (moderately polluted). Subsequently, the different components of bird droppings in the soil were investigated for their potential effects on soil fertility. The present research demonstrated that the remediation of farmland had the potential to enhance the quality of water and soil fertility in wetland. This, in turn, might result in an increased number of migratory birds inhabiting the area.
format: application/pdf
format: text/html
creator: Changqing Liu
creator: Zhongxiang Sun
creator: Hongyang Wang
creator: Tianwen Chen
creator: Lina Deng
creator: Li Zhang
creator: Huixing Liang
creator: Yuxiang Shen
creator: Hongshan Li
creator: Hai Cheng
subject: Plant Science
subject: Soil Science
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.20406
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Enhancements in water quality and soil characteristics of wetlands can improve the ecological environment of the area and enrich its biodiversity. The present study examined the effects of five distinct crops (i.e.: colza oil, mustard, Chinese cabbage, wheat, barley) cultivated in remediation plots, and evaluated their impact on water quality and soil fertility. The water quality within the remediated farmland was categorized as Class III (moderately polluted). The soil exhibited low total nitrogen and organic matter levels (the mean values were respectively 0.032% and 10.84 g/kg), and high readily available phosphorus and potassium concentration (the mean values were respectively 75.71 and 247.64 mg/kg). The soil fertility was comprehensively categorized as Class III (moderately polluted). Subsequently, the different components of bird droppings in the soil were investigated for their potential effects on soil fertility. The present research demonstrated that the remediation of farmland had the potential to enhance the quality of water and soil fertility in wetland. This, in turn, might result in an increased number of migratory birds inhabiting the area.
bibliographic citation: Liu et al. (2025) Evaluation of water quality and soil fertility in remediated farmland for protection of wetland ecology by planting different crops. PeerJ 13:e20406 https://doi.org/10.7717/peerj.20406
date submitted: 2025-01-14
date accepted: 2025-10-27
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Changqing
author list: Agent
  family name: Sun
  given name: Zhongxiang
author list: Agent
  family name: Wang
  given name: Hongyang
author list: Agent
  family name: Chen
  given name: Tianwen
author list: Agent
  family name: Deng
  given name: Lina
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Liang
  given name: Huixing
author list: Agent
  family name: Shen
  given name: Yuxiang
author list: Agent
  family name: Li
  given name: Hongshan
author list: Agent
  family name: Cheng
  given name: Hai
doi: 10.7717/peerj.20406
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: ©2025 Liu et al.
attribution name: Liu et al.

Effects of monocropping soil on plant growth and rhizosphere microbial community structure of Salvia miltiorrhiza Bge
type: item
type: AcademicArticle
description: Salvia miltiorrhiza (Danshen) is a commonly utilized remedy for various blood stasis syndromes, cardiovascular, and cerebrovascular diseases. The practice of continuous cropping presents a notable challenge to the production of high-quality S. miltiorrhiza due to the lack of rotation or soil remediation. Despite this, the precise mechanism, particularly the impact of alterations in the rhizosphere microbial community structure on the development of obstacles related to continuous cropping, remains obscure. The constitution of the rhizosphere microbial community plays a pivotal role in plant growth and has the potential to exacerbate issues associated with continuous cropping. This study aimed to comprehensively compare the impact of continuous vs. non-continuous cropping soils on the growth, physiological and biochemical characteristics, accumulation of active ingredients, and rhizosphere microbial community structure of S. miltiorrhiza seedlings to elucidate the microbial ecological mechanism behind continuous cropping challenges. A pot experiment was executed to assess the effects of continuous cropping on the morphological and physiological parameters of S. miltiorrhiza. High-throughput sequencing technology utilizing the NovaSeq platform was employed to sequence and analyze the V4 region of bacterial 16S rDNA and the ITS1 region of fungi in the rhizosphere. The findings revealed that continuous cropping soil led to a reduction in S. miltiorrhiza biomass, manifesting as wilting and stunted growth, diminished effective leaf area, main root length and diameter, reduced levels of total chlorophyll, carbohydrates, and active ingredients, as well as compromised photosynthesis. In the rhizosphere soil, both the composition and function of the fungal community have undergone significant changes, and the fungal diversity has shown a clear increasing trend; in contrast, the change in bacterial diversity is very slight. In conclusion, continuous cropping soil substantially…
format: application/pdf
format: text/html
creator: Ji Dong Ju
creator: Yuan Meng
creator: Bingqian Zhou
creator: Guohong Yang
creator: Xinyu Fu
creator: Wei Liu
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.20379
publisher: PeerJ Inc.
rights: © 2025 Ju et al.
abstract: Salvia miltiorrhiza (Danshen) is a commonly utilized remedy for various blood stasis syndromes, cardiovascular, and cerebrovascular diseases. The practice of continuous cropping presents a notable challenge to the production of high-quality S. miltiorrhiza due to the lack of rotation or soil remediation. Despite this, the precise mechanism, particularly the impact of alterations in the rhizosphere microbial community structure on the development of obstacles related to continuous cropping, remains obscure. The constitution of the rhizosphere microbial community plays a pivotal role in plant growth and has the potential to exacerbate issues associated with continuous cropping. This study aimed to comprehensively compare the impact of continuous vs. non-continuous cropping soils on the growth, physiological and biochemical characteristics, accumulation of active ingredients, and rhizosphere microbial community structure of S. miltiorrhiza seedlings to elucidate the microbial ecological mechanism behind continuous cropping challenges. A pot experiment was executed to assess the effects of continuous cropping on the morphological and physiological parameters of S. miltiorrhiza. High-throughput sequencing technology utilizing the NovaSeq platform was employed to sequence and analyze the V4 region of bacterial 16S rDNA and the ITS1 region of fungi in the rhizosphere. The findings revealed that continuous cropping soil led to a reduction in S. miltiorrhiza biomass, manifesting as wilting and stunted growth, diminished effective leaf area, main root length and diameter, reduced levels of total chlorophyll, carbohydrates, and active ingredients, as well as compromised photosynthesis. In the rhizosphere soil, both the composition and function of the fungal community have undergone significant changes, and the fungal diversity has shown a clear increasing trend; in contrast, the change in bacterial diversity is very slight. In conclusion, continuous cropping soil substantially…
bibliographic citation: Ju et al. (2025) Effects of monocropping soil on plant growth and rhizosphere microbial community structure of Salvia miltiorrhiza Bge. PeerJ 13:e20379 https://doi.org/10.7717/peerj.20379
date submitted: 2025-04-29
date accepted: 2025-10-21
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ju
  given name: Ji Dong
author list: Agent
  family name: Meng
  given name: Yuan
author list: Agent
  family name: Zhou
  given name: Bingqian
author list: Agent
  family name: Yang
  given name: Guohong
author list: Agent
  family name: Fu
  given name: Xinyu
author list: Agent
  family name: Liu
  given name: Wei
doi: 10.7717/peerj.20379
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Ju et al.
attribution name: Ju et al.

Effectiveness of respiratory muscle training on pulmonary function recovery in patients with spinal cord injury: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective This study conducted a thorough review and meta-analysis to examine how respiratory muscle training (RMT) affects lung function recovery in individuals with spinal cord injury (SCI). Methods We conducted a systematic review of Randomized Controlled Trials (RCTs) examining the effects of RMT on lung function in patients with SCI. The search included databases such as PubMed, Embase, The Cochrane Library, Scopus, and Web of Science up to October 2025. The experimental group received RMT as the main intervention, while the control group received either no treatment, a placebo, or conventional rehabilitation. Outcome measures included Forced Expiratory Volume in the first second (FEV1), Forced Vital Capacity (FVC), Maximum Inspiratory Pressure (MIP), Maximum Expiratory Pressure (MEP), Peak Expiratory Flow (PEF), Minute Ventilation Volume (MVV), Total Lung Capacity (TLC), Inspiratory Capacity (IC), and Vital Capacity (VC). Two reviewers independently screened, extracted data, and assessed bias. Meta-analysis was conducted using RevMan 5.3 software, and the quality of included studies was evaluated using the Cochrane bias risk assessment tool and the Physical Therapy Evidence Database scale. The reporting of this study followed the PRISMA guidelines and was registered with PROSPERO (ID: CRD42024627736). Results In this meta-analysis, 25 RCTs were included, comprising a total of 679 patients. The meta-analysis showed that compared with conventional rehabilitation, respiratory muscle training significantly improved FEV1 (p < 0.0001), FVC (p = 0.0001), MIP (p < 0.00001), MEP (p = 0.0004), PEF (p < 0.00001), MVV (p < 0.0001), TLC (p = 0.05), VC (p = 0.04), and their differences were statistically significant. However, IC (p = 0.40) was not statistically significant. Subgroup analyses showed that resistive training and surface electromyography biofeedback training were effective for improving FEV1 and FVC, while threshold training significantly improved MVV. Conclusi…
format: application/pdf
format: text/html
creator: Shuqi Yao
creator: Haozhe Guo
creator: Fuhai Ma
creator: Aiping Chi
subject: Kinesiology
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20373
publisher: PeerJ Inc.
rights: © 2025 Yao et al.
abstract: Objective This study conducted a thorough review and meta-analysis to examine how respiratory muscle training (RMT) affects lung function recovery in individuals with spinal cord injury (SCI). Methods We conducted a systematic review of Randomized Controlled Trials (RCTs) examining the effects of RMT on lung function in patients with SCI. The search included databases such as PubMed, Embase, The Cochrane Library, Scopus, and Web of Science up to October 2025. The experimental group received RMT as the main intervention, while the control group received either no treatment, a placebo, or conventional rehabilitation. Outcome measures included Forced Expiratory Volume in the first second (FEV1), Forced Vital Capacity (FVC), Maximum Inspiratory Pressure (MIP), Maximum Expiratory Pressure (MEP), Peak Expiratory Flow (PEF), Minute Ventilation Volume (MVV), Total Lung Capacity (TLC), Inspiratory Capacity (IC), and Vital Capacity (VC). Two reviewers independently screened, extracted data, and assessed bias. Meta-analysis was conducted using RevMan 5.3 software, and the quality of included studies was evaluated using the Cochrane bias risk assessment tool and the Physical Therapy Evidence Database scale. The reporting of this study followed the PRISMA guidelines and was registered with PROSPERO (ID: CRD42024627736). Results In this meta-analysis, 25 RCTs were included, comprising a total of 679 patients. The meta-analysis showed that compared with conventional rehabilitation, respiratory muscle training significantly improved FEV1 (p < 0.0001), FVC (p = 0.0001), MIP (p < 0.00001), MEP (p = 0.0004), PEF (p < 0.00001), MVV (p < 0.0001), TLC (p = 0.05), VC (p = 0.04), and their differences were statistically significant. However, IC (p = 0.40) was not statistically significant. Subgroup analyses showed that resistive training and surface electromyography biofeedback training were effective for improving FEV1 and FVC, while threshold training significantly improved MVV. Conclusi…
bibliographic citation: Yao et al. (2025) Effectiveness of respiratory muscle training on pulmonary function recovery in patients with spinal cord injury: a systematic review and meta-analysis. PeerJ 13:e20373 https://doi.org/10.7717/peerj.20373
date submitted: 2025-06-20
date accepted: 2025-10-20
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Shuqi
author list: Agent
  family name: Guo
  given name: Haozhe
author list: Agent
  family name: Ma
  given name: Fuhai
author list: Agent
  family name: Chi
  given name: Aiping
doi: 10.7717/peerj.20373
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: ©2025 Yao et al.
attribution name: Yao et al.

Genomics, population dynamics, immune evasion and resistance determinants foster the competence and global dissemination of Klebsiella pneumoniae
type: item
type: AcademicArticle
description: Background According to the World Health Organization (WHO), Klebsiella pneumoniae is a critical public health concern and an established ESKAPE (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp.) pathogen. Mounting incidence of MDR K. pneumoniae is worrisome across the globe. K. pneumoniae is an established ubiquitous pathogen and associated with various infections in a wide range of hosts. Methods The peer reviewed findings with given problem statements were thoroughly studied through literature review technique. Multiple antibiotic-resistance genes and virulence genes across various Klebsiella species were studied to explore their evolutionary dynamics and genetic diversity. Results Population dynamics revealed that the clonal group (CG) 258 and CG 14 are considered as global disseminated clones. The genome size (5.7 Mbps) of K. pneumoniae is reported to be larger than the other Enterobacteriaceae which allows K. pneumoniae to survive in diverse geographical niches. It has adequate resistome and virulence machinery to evade the host immune system and establish the infection. Due to the emergence of resistant variants K. pneumoniae needs appropriate alternative control measures. Conclusion The current review described the characteristics features of K. pneumoniae which are the key players in making this organism a credential pathogen. Additionally, it would be instructive and underpin the molecular insights that may aid in restraining this pathogen.
format: application/pdf
format: text/html
creator: Bilal Aslam
creator: Sulaiman F. Aljasir
subject: Microbiology
subject: Molecular Biology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.20296
publisher: PeerJ Inc.
rights: © 2025 Aslam and Aljasir
abstract: Background According to the World Health Organization (WHO), Klebsiella pneumoniae is a critical public health concern and an established ESKAPE (E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp.) pathogen. Mounting incidence of MDR K. pneumoniae is worrisome across the globe. K. pneumoniae is an established ubiquitous pathogen and associated with various infections in a wide range of hosts. Methods The peer reviewed findings with given problem statements were thoroughly studied through literature review technique. Multiple antibiotic-resistance genes and virulence genes across various Klebsiella species were studied to explore their evolutionary dynamics and genetic diversity. Results Population dynamics revealed that the clonal group (CG) 258 and CG 14 are considered as global disseminated clones. The genome size (5.7 Mbps) of K. pneumoniae is reported to be larger than the other Enterobacteriaceae which allows K. pneumoniae to survive in diverse geographical niches. It has adequate resistome and virulence machinery to evade the host immune system and establish the infection. Due to the emergence of resistant variants K. pneumoniae needs appropriate alternative control measures. Conclusion The current review described the characteristics features of K. pneumoniae which are the key players in making this organism a credential pathogen. Additionally, it would be instructive and underpin the molecular insights that may aid in restraining this pathogen.
bibliographic citation: Aslam et al. (2025) Genomics, population dynamics, immune evasion and resistance determinants foster the competence and global dissemination of Klebsiella pneumoniae. PeerJ 13:e20296 https://doi.org/10.7717/peerj.20296
date submitted: 2025-04-25
date accepted: 2025-10-06
issued: 2025-11-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aslam
  given name: Bilal
author list: Agent
  family name: Aljasir
  given name: Sulaiman F.
doi: 10.7717/peerj.20296
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-28
copyright: © 2025 Aslam and Aljasir
attribution name: Aslam and Aljasir

Structure and diversity of microbial communities in the rhizosphere soil of Trichosanthes kirilowii from different cultivation patterns
type: item
type: AcademicArticle
description: Background To analyze the effects of different cultivation patterns on the structure and diversity of the microbial community in the rhizosphere soil of Trichosanthes kirilowii (T. kirilowii) arms to establish reasonable and effective strategies to mitigate the continuous cropping barriers and promote the high-quality cultivation of T. kirilowii. Methods Three distinct cultivation patterns were investigated: open-field cultivation (TM1), film-mulched cultivation (TM2), and soybean intercropping cultivation (TM3). High-throughput sequencing and bioinformatic analyses were employed to evaluate the rhizosphere microbiome, and redundancy analysis was utilized to investigate the relationship between the microbial communities and soil nutrient indicators. Results TM2 and TM3 increased soil bacterial community diversity, reduced fungal community diversity, elevated the relative abundance of beneficial bacterial genera, and reduced the abundance of detrimental fungal genera in the rhizosphere soil. The relative abundance of Pseudarthrobacter, unclassified_Steroidobacteraceae, and Nocardioides in TM2 and TM3 was markedly higher than in TM1. Conversely, the relative abundance of Fusarium, Rhizoctonia, Ceratobasidium, and Plectosphaerella in TM2 and TM3 was significantly reduced compared to TM1. The contents of available potassium (AK), total nitrogen (TN), total phosphorus (TP), and pH in the rhizosphere soil of TM2 and TM3 were significantly higher than those in TM1. The distribution of soil bacterial genera was significantly influenced by the contents of TN and AK, while the distribution of soil fungal genera was significantly or extremely significantly impacted by the contents of TP, total potassium (TK), soil organic matter (SOM), and pH. The content of AK was extremely significantly positively correlated with the relative abundance of Nocardioides, whereas the content of TK showed an extremely negative correlation with the relative abundance of Ceratobasidium. Similarly,…
format: application/pdf
format: text/html
creator: Lei Zheng
creator: Huadong Wang
creator: Zhiqiang Zhang
creator: Jiulin Gu
creator: Yao Yin
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.20459
publisher: PeerJ Inc.
rights: © 2025 Zheng et al.
abstract: Background To analyze the effects of different cultivation patterns on the structure and diversity of the microbial community in the rhizosphere soil of Trichosanthes kirilowii (T. kirilowii) arms to establish reasonable and effective strategies to mitigate the continuous cropping barriers and promote the high-quality cultivation of T. kirilowii. Methods Three distinct cultivation patterns were investigated: open-field cultivation (TM1), film-mulched cultivation (TM2), and soybean intercropping cultivation (TM3). High-throughput sequencing and bioinformatic analyses were employed to evaluate the rhizosphere microbiome, and redundancy analysis was utilized to investigate the relationship between the microbial communities and soil nutrient indicators. Results TM2 and TM3 increased soil bacterial community diversity, reduced fungal community diversity, elevated the relative abundance of beneficial bacterial genera, and reduced the abundance of detrimental fungal genera in the rhizosphere soil. The relative abundance of Pseudarthrobacter, unclassified_Steroidobacteraceae, and Nocardioides in TM2 and TM3 was markedly higher than in TM1. Conversely, the relative abundance of Fusarium, Rhizoctonia, Ceratobasidium, and Plectosphaerella in TM2 and TM3 was significantly reduced compared to TM1. The contents of available potassium (AK), total nitrogen (TN), total phosphorus (TP), and pH in the rhizosphere soil of TM2 and TM3 were significantly higher than those in TM1. The distribution of soil bacterial genera was significantly influenced by the contents of TN and AK, while the distribution of soil fungal genera was significantly or extremely significantly impacted by the contents of TP, total potassium (TK), soil organic matter (SOM), and pH. The content of AK was extremely significantly positively correlated with the relative abundance of Nocardioides, whereas the content of TK showed an extremely negative correlation with the relative abundance of Ceratobasidium. Similarly,…
bibliographic citation: Zheng et al. (2025) Structure and diversity of microbial communities in the rhizosphere soil of Trichosanthes kirilowii from different cultivation patterns. PeerJ 13:e20459 https://doi.org/10.7717/peerj.20459
date submitted: 2025-09-24
date accepted: 2025-11-03
issued: 2025-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Lei
author list: Agent
  family name: Wang
  given name: Huadong
author list: Agent
  family name: Zhang
  given name: Zhiqiang
author list: Agent
  family name: Gu
  given name: Jiulin
author list: Agent
  family name: Yin
  given name: Yao
doi: 10.7717/peerj.20459
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-27
copyright: © 2025 Zheng et al.
attribution name: Zheng et al.

Long-term glycemic variability and the risk of heart failure: a meta-analysis
type: item
type: AcademicArticle
description: Background Long-term glycemic variability (GV) has emerged as a potential cardiovascular risk factor beyond average glycemic levels. However, its association with the risk of heart failure (HF) remains unclear. This meta-analysis evaluated the relationship between long-term GV and the incidence of HF in adults. Methods We systematically searched PubMed, Embase, and Web of Science from inception to January 31, 2025, for observational studies assessing the association between long-term GV—measured by variability indices of hemoglobin A1c (HbA1c) or fasting plasma glucose—and HF risk. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated using random-effects models by incorporating the influence of heterogeneity. Results Eleven datasets from 10 studies involving 4,229,377 adults were included. Compared with participants with low GV, those with high long-term GV had a significantly increased risk of incident HF (HR = 1.69; 95% CI [1.38–2.06]; p < 0.001; I2 = 92%). The association remained consistent in sensitivity analyses restricted to patients with type 2 diabetes, high-quality studies, and studies adjusting for mean hemoglobin A1c (HbA1c) levels (HR = 1.96, 1.78, and 1.95, respectively; all p < 0.001). Subgroup analyses revealed consistent findings across GV metrics, geographic regions, study designs, mean age, sex distribution, follow-up duration, and study quality (p for subgroup difference > 0.05). No significant publication bias was detected (Egger’s test, p = 0.29). Conclusion High long-term GV is independently associated with an increased risk of HF. These findings underscore the clinical relevance of GV monitoring in cardiovascular risk assessment, including risk stratification for the incidence of HF.
format: application/pdf
format: text/html
creator: Yong-Chao Li
creator: Ke-Er Mo
creator: Li-Shuai Zhang
creator: Qiang Zhao
creator: Ju Deng
creator: Li Li
subject: Cardiology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.20401
publisher: PeerJ Inc.
rights: © 2025 Li et al.
abstract: Background Long-term glycemic variability (GV) has emerged as a potential cardiovascular risk factor beyond average glycemic levels. However, its association with the risk of heart failure (HF) remains unclear. This meta-analysis evaluated the relationship between long-term GV and the incidence of HF in adults. Methods We systematically searched PubMed, Embase, and Web of Science from inception to January 31, 2025, for observational studies assessing the association between long-term GV—measured by variability indices of hemoglobin A1c (HbA1c) or fasting plasma glucose—and HF risk. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated using random-effects models by incorporating the influence of heterogeneity. Results Eleven datasets from 10 studies involving 4,229,377 adults were included. Compared with participants with low GV, those with high long-term GV had a significantly increased risk of incident HF (HR = 1.69; 95% CI [1.38–2.06]; p < 0.001; I2 = 92%). The association remained consistent in sensitivity analyses restricted to patients with type 2 diabetes, high-quality studies, and studies adjusting for mean hemoglobin A1c (HbA1c) levels (HR = 1.96, 1.78, and 1.95, respectively; all p < 0.001). Subgroup analyses revealed consistent findings across GV metrics, geographic regions, study designs, mean age, sex distribution, follow-up duration, and study quality (p for subgroup difference > 0.05). No significant publication bias was detected (Egger’s test, p = 0.29). Conclusion High long-term GV is independently associated with an increased risk of HF. These findings underscore the clinical relevance of GV monitoring in cardiovascular risk assessment, including risk stratification for the incidence of HF.
bibliographic citation: Li et al. (2025) Long-term glycemic variability and the risk of heart failure: a meta-analysis. PeerJ 13:e20401 https://doi.org/10.7717/peerj.20401
date submitted: 2025-06-25
date accepted: 2025-10-27
issued: 2025-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yong-Chao
author list: Agent
  family name: Mo
  given name: Ke-Er
author list: Agent
  family name: Zhang
  given name: Li-Shuai
author list: Agent
  family name: Zhao
  given name: Qiang
author list: Agent
  family name: Deng
  given name: Ju
author list: Agent
  family name: Li
  given name: Li
doi: 10.7717/peerj.20401
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-27
copyright: ©2025 Li et al.
attribution name: Li et al.

Retrospective analysis of cervical screening abnormalities in women with type 3 transformation zone without visible lesions
type: item
type: AcademicArticle
description: Objective Women with abnormal cervical screening but without visible lesions, particularly those with a type 3 transformation zone (TZ3), present a clinical challenge due to the non-visible squamocolumnar junction, increasing the risk of missed high-grade lesions. There is currently no consensus on optimal follow-up strategies for this group. This study aims to evaluate a risk-based management approach for these patients. Methods A cross-sectional study analyzed data from 4,648 women with TZ3 who underwent colposcopy and endocervical curettage (ECC) with or without cervical biopsies at Hunan Provincial Maternal and Child Health Care Hospital (2021–2024). Logistic regression with restricted cubic splines analyzed demographic, cytological and HPV data to identify HSIL+ predictors and age-risk thresholds. Results Among the study population, 3.1% (145 cases) of HSIL+ were identified despite negative colposcopy, although additional undetected cases may exist. Women with high-grade cytology (ASC-H/HSIL/AGC) had a consistently high HSIL+ risk (32.5%–37.2%) across all HPV subgroups. In low-grade cytology (NILM/ASCUS/LSIL), HPV 16/18 positivity increased HSIL+ risk (2.4%–5.0%) compared to non-HPV 16/18 cases (1.6%–1.8%), with the highest rate observed in LSIL cases (5.0%). In women with low-grade cytology and non-HPV 16/18 positivity, age and HSIL+ risk showed a nonlinear relationship (RCS P-nonlinear = 0.008). Threshold analysis identified 55 years as a critical cutoff, with a 10% annual increase in HSIL+ risk for women ≥ 55. (OR = 1.10, 95% CI [1.02–1.19]; P = 0.015). Further age-stratified analysis in this subgroup showed a clear upward trend: HSIL+ detection rates were 4.42% in women aged ≥ 65. Conclusion Among women with abnormal cervical screening and no visible lesions at type 3 transformation zone, HSIL+ risk varies by cytology, HPV genotype, and age. Our findings suggest that immediate diagnostic evaluation is warranted for those with high-grade cytology, HPV 16/18 …
format: application/pdf
format: text/html
creator: Jing Yang
creator: Qiao Liu
creator: Yi Tang
creator: Kui Huang
creator: Tianmin Chen
creator: Jing Zhao
subject: Gynecology and Obstetrics
subject: Oncology
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.20396
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: Objective Women with abnormal cervical screening but without visible lesions, particularly those with a type 3 transformation zone (TZ3), present a clinical challenge due to the non-visible squamocolumnar junction, increasing the risk of missed high-grade lesions. There is currently no consensus on optimal follow-up strategies for this group. This study aims to evaluate a risk-based management approach for these patients. Methods A cross-sectional study analyzed data from 4,648 women with TZ3 who underwent colposcopy and endocervical curettage (ECC) with or without cervical biopsies at Hunan Provincial Maternal and Child Health Care Hospital (2021–2024). Logistic regression with restricted cubic splines analyzed demographic, cytological and HPV data to identify HSIL+ predictors and age-risk thresholds. Results Among the study population, 3.1% (145 cases) of HSIL+ were identified despite negative colposcopy, although additional undetected cases may exist. Women with high-grade cytology (ASC-H/HSIL/AGC) had a consistently high HSIL+ risk (32.5%–37.2%) across all HPV subgroups. In low-grade cytology (NILM/ASCUS/LSIL), HPV 16/18 positivity increased HSIL+ risk (2.4%–5.0%) compared to non-HPV 16/18 cases (1.6%–1.8%), with the highest rate observed in LSIL cases (5.0%). In women with low-grade cytology and non-HPV 16/18 positivity, age and HSIL+ risk showed a nonlinear relationship (RCS P-nonlinear = 0.008). Threshold analysis identified 55 years as a critical cutoff, with a 10% annual increase in HSIL+ risk for women ≥ 55. (OR = 1.10, 95% CI [1.02–1.19]; P = 0.015). Further age-stratified analysis in this subgroup showed a clear upward trend: HSIL+ detection rates were 4.42% in women aged ≥ 65. Conclusion Among women with abnormal cervical screening and no visible lesions at type 3 transformation zone, HSIL+ risk varies by cytology, HPV genotype, and age. Our findings suggest that immediate diagnostic evaluation is warranted for those with high-grade cytology, HPV 16/18 …
bibliographic citation: Yang et al. (2025) Retrospective analysis of cervical screening abnormalities in women with type 3 transformation zone without visible lesions. PeerJ 13:e20396 https://doi.org/10.7717/peerj.20396
date submitted: 2025-04-21
date accepted: 2025-10-24
issued: 2025-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Jing
author list: Agent
  family name: Liu
  given name: Qiao
author list: Agent
  family name: Tang
  given name: Yi
author list: Agent
  family name: Huang
  given name: Kui
author list: Agent
  family name: Chen
  given name: Tianmin
author list: Agent
  family name: Zhao
  given name: Jing
doi: 10.7717/peerj.20396
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-27
copyright: ©2025 Yang et al.
attribution name: Yang et al.

Effects of creatine supplementation on muscle strength gains—a meta-analysis and systematic review
type: item
type: AcademicArticle
description: Creatine (Cr) is a widely utilized nutritional supplement. Empirical evidence indicates that Cr supplementation significantly elevates intramuscular Cr content, thereby providing an energy substrate reservoir for exercise performance and facilitating improvements in muscle strength. Although numerous studies have examined the relationship between Cr and muscle strength, comprehensive investigations into population-specific ergogenic responses, optimal Cr dosage, and concomitant training intensity remain limited. These parameters are critical determinants for maximizing the efficacy of Cr supplementation. Against this backdrop, this study adopts meta-analysis, integrating conventional and Robust Variance Estimation (RVE) models, to comprehensively evaluate the intervention effects of Cr supplementation across three dimensions: population applicability, dosage optimization, and training intensity (PROSPERO registration number: CRD42024547697). It aims to provide evidence-based support for precise clinical application and subsequent research directions. Results Results showed no statistical difference in baseline muscle strength between the Cr intervention group and the control group; after intervention, the Cr group exhibited significant strength gains. Further subgroup analysis revealed: untrained individuals had greater muscle strength improvements than trained ones; the low-to-moderate dose group showed better effects than the high-dose group; high-intensity training had more significant effect sizes than low-intensity training; and no definitive conclusion was reached on muscle strength improvements between middle-aged/elderly and young populations. Conclusion Cr supplementation significantly improves muscle strength in the general population. Specifically: untrained individuals show greater muscle strength improvements; low-dose supplementation combined with high-intensity exercise yields better effects; no definitive conclusion was reached on effect differences …
format: application/pdf
format: text/html
creator: Haoda Zhang
creator: Tian Lan
creator: Xueru Yan
creator: Haoran Gu
creator: Yanhong Li
creator: Enpeng He
subject: Anatomy and Physiology
subject: Kinesiology
subject: Nutrition
subject: Sports Medicine
description: doi:10.7717/peerj.20380
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Creatine (Cr) is a widely utilized nutritional supplement. Empirical evidence indicates that Cr supplementation significantly elevates intramuscular Cr content, thereby providing an energy substrate reservoir for exercise performance and facilitating improvements in muscle strength. Although numerous studies have examined the relationship between Cr and muscle strength, comprehensive investigations into population-specific ergogenic responses, optimal Cr dosage, and concomitant training intensity remain limited. These parameters are critical determinants for maximizing the efficacy of Cr supplementation. Against this backdrop, this study adopts meta-analysis, integrating conventional and Robust Variance Estimation (RVE) models, to comprehensively evaluate the intervention effects of Cr supplementation across three dimensions: population applicability, dosage optimization, and training intensity (PROSPERO registration number: CRD42024547697). It aims to provide evidence-based support for precise clinical application and subsequent research directions. Results Results showed no statistical difference in baseline muscle strength between the Cr intervention group and the control group; after intervention, the Cr group exhibited significant strength gains. Further subgroup analysis revealed: untrained individuals had greater muscle strength improvements than trained ones; the low-to-moderate dose group showed better effects than the high-dose group; high-intensity training had more significant effect sizes than low-intensity training; and no definitive conclusion was reached on muscle strength improvements between middle-aged/elderly and young populations. Conclusion Cr supplementation significantly improves muscle strength in the general population. Specifically: untrained individuals show greater muscle strength improvements; low-dose supplementation combined with high-intensity exercise yields better effects; no definitive conclusion was reached on effect differences …
bibliographic citation: Zhang et al. (2025) Effects of creatine supplementation on muscle strength gains—a meta-analysis and systematic review. PeerJ 13:e20380 https://doi.org/10.7717/peerj.20380
date submitted: 2024-08-13
date accepted: 2025-10-21
issued: 2025-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haoda
author list: Agent
  family name: Lan
  given name: Tian
author list: Agent
  family name: Yan
  given name: Xueru
author list: Agent
  family name: Gu
  given name: Haoran
author list: Agent
  family name: Li
  given name: Yanhong
author list: Agent
  family name: He
  given name: Enpeng
doi: 10.7717/peerj.20380
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-27
copyright: ©2025 Zhang et al.
attribution name: Zhang et al.

Application analysis of two nucleic acid detection systems in blood detection of hepatitis B virus, hepatitis C virus and human immunodeficiency virus
type: item
type: AcademicArticle
description: Objective This study aimed to compare the diagnostic efficacy between the Kehua and Roche nucleic acid testing (NAT) systems for detecting hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) in blood donation screening. Methods We analyzed retrospective data from 670,775 transient blood donation samples collected between 2016 and 2024. Key performance indicators (KPIs) included the types of reactive samples, effective split rate, effective reaction rate, single pool invalid number, batch invalid number, and pooling missing samples. Annual trends in cycle threshold (CT) value distributions and overall system performance were also evaluated. Results Among 419 reactive samples (Kehua: 202; Roche: 217), no significant differences were observed in the effective split rates (P > 0.05) or overall specimen reaction rates (P > 0.05) between the two systems. The HCV detection rate was significantly lower for the Kehua system (P < 0.05), while the detection rates for HBV and HIV showed no significant inter-system differences (P > 0.05). The separation efficiency of reactive pools varied significantly across different CT value ranges (P < 0.05). The Kehua system demonstrated stable annual effective split and reaction rates (P > 0.05), whereas the Roche system exhibited significant annual fluctuations in these metrics (P < 0.05). The Kehua system had significantly fewer single pool invalid numbers and pooling omissions than the Roche system (P < 0.05). Conclusion The Kehua and Roche NAT systems demonstrated comparable overall performance in blood screening, with Kehua proving non-inferior to Roche. Kehua’s advantages included fewer invalid tests and fewer pooling errors, which could reduce economic and time costs. The Roche system exhibited higher automation, supporting continuous batch processing. The observed CT value-dependent separation efficiency suggests potential for protocol optimization in detecting low viral load samples.
format: application/pdf
format: text/html
creator: Tao Wang
creator: Jianwei Zhang
subject: Molecular Biology
subject: Hematology
subject: HIV
subject: Immunology
description: doi:10.7717/peerj.20365
publisher: PeerJ Inc.
rights: © 2025 Wang and Zhang
abstract: Objective This study aimed to compare the diagnostic efficacy between the Kehua and Roche nucleic acid testing (NAT) systems for detecting hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) in blood donation screening. Methods We analyzed retrospective data from 670,775 transient blood donation samples collected between 2016 and 2024. Key performance indicators (KPIs) included the types of reactive samples, effective split rate, effective reaction rate, single pool invalid number, batch invalid number, and pooling missing samples. Annual trends in cycle threshold (CT) value distributions and overall system performance were also evaluated. Results Among 419 reactive samples (Kehua: 202; Roche: 217), no significant differences were observed in the effective split rates (P > 0.05) or overall specimen reaction rates (P > 0.05) between the two systems. The HCV detection rate was significantly lower for the Kehua system (P < 0.05), while the detection rates for HBV and HIV showed no significant inter-system differences (P > 0.05). The separation efficiency of reactive pools varied significantly across different CT value ranges (P < 0.05). The Kehua system demonstrated stable annual effective split and reaction rates (P > 0.05), whereas the Roche system exhibited significant annual fluctuations in these metrics (P < 0.05). The Kehua system had significantly fewer single pool invalid numbers and pooling omissions than the Roche system (P < 0.05). Conclusion The Kehua and Roche NAT systems demonstrated comparable overall performance in blood screening, with Kehua proving non-inferior to Roche. Kehua’s advantages included fewer invalid tests and fewer pooling errors, which could reduce economic and time costs. The Roche system exhibited higher automation, supporting continuous batch processing. The observed CT value-dependent separation efficiency suggests potential for protocol optimization in detecting low viral load samples.
bibliographic citation: Wang et al. (2025) Application analysis of two nucleic acid detection systems in blood detection of hepatitis B virus, hepatitis C virus and human immunodeficiency virus. PeerJ 13:e20365 https://doi.org/10.7717/peerj.20365
date submitted: 2025-02-26
date accepted: 2025-10-17
issued: 2025-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Zhang
  given name: Jianwei
doi: 10.7717/peerj.20365
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-27
copyright: ©2025 Wang and Zhang
attribution name: Wang and Zhang

Validity, reliability and minimal detectable change in the sit-to-stand test for synchronous and asynchronous tele-assessment in post-COVID-19 condition
type: item
type: AcademicArticle
description: Background Individuals with symptoms of long-term COVID-19 (coronavirus disease 2019) who presented mild infection without needing invasive ventilatory support require rehabilitation and performance and monitoring evaluations. The 1-minute sit-to-stand test (STS) is used to assess individuals with COVID-19 and might be an alternative for remote use in this population. Objective The current study aimed to validate the synchronous and asynchronous STS tele-assessment in individuals with post-COVID-19 condition to analyze the inter-evaluator reliability of the asynchronous STS, and identify the relationship between the participants’ self-reported asynchronous STS results and those of the evaluator. Methods Thirty-eight men and women with post-COVID syndrome who did not require invasive ventilator support were included in this study. The participants were assessed using STS in-person (STS-IP), synchronous (STS-S), and asynchronous (STS-A) tele-assessments. The participants also self-reported the total executed repetitions (STS-SR). The main outcomes were the number of repetitions performed in the STS-IP, STS-S, STS-A, and STS-SR. To verify STS-A reliability, the total repetitions registered between evaluators were compared. Results STS-IP showed significant correlations and lower total repetitions compared to STS-S and STS-A. STS-A repetitions were significantly lower compared to STS-SR; however, a significant correlation was observed. The STS-S and STS-A showed minimal detectable change values of 6.6 and 10.5, respectively. In terms of reliability, there were no significant differences in total repetitions or errors found between evaluators’ assessments of STS-A. Conclusion The study demonstrated good and moderate evidence of validity for synchronous and asynchronous remote STS assessments, respectively, highlighting the impact of the assessment protocol on STS performance interpretation. Asynchronous STS presented high reliability.
format: application/pdf
format: text/html
creator: Juliane Machado Marques
creator: Matheus Brasiliano da Paz
creator: Rodrigo Rodrigues Gomes Costa
creator: Frederico Ribeiro Neto
subject: Global Health
subject: Health Policy
subject: Public Health
subject: COVID-19
subject: Rehabilitation
description: doi:10.7717/peerj.20211
publisher: PeerJ Inc.
rights: © 2025 Machado Marques et al.
abstract: Background Individuals with symptoms of long-term COVID-19 (coronavirus disease 2019) who presented mild infection without needing invasive ventilatory support require rehabilitation and performance and monitoring evaluations. The 1-minute sit-to-stand test (STS) is used to assess individuals with COVID-19 and might be an alternative for remote use in this population. Objective The current study aimed to validate the synchronous and asynchronous STS tele-assessment in individuals with post-COVID-19 condition to analyze the inter-evaluator reliability of the asynchronous STS, and identify the relationship between the participants’ self-reported asynchronous STS results and those of the evaluator. Methods Thirty-eight men and women with post-COVID syndrome who did not require invasive ventilator support were included in this study. The participants were assessed using STS in-person (STS-IP), synchronous (STS-S), and asynchronous (STS-A) tele-assessments. The participants also self-reported the total executed repetitions (STS-SR). The main outcomes were the number of repetitions performed in the STS-IP, STS-S, STS-A, and STS-SR. To verify STS-A reliability, the total repetitions registered between evaluators were compared. Results STS-IP showed significant correlations and lower total repetitions compared to STS-S and STS-A. STS-A repetitions were significantly lower compared to STS-SR; however, a significant correlation was observed. The STS-S and STS-A showed minimal detectable change values of 6.6 and 10.5, respectively. In terms of reliability, there were no significant differences in total repetitions or errors found between evaluators’ assessments of STS-A. Conclusion The study demonstrated good and moderate evidence of validity for synchronous and asynchronous remote STS assessments, respectively, highlighting the impact of the assessment protocol on STS performance interpretation. Asynchronous STS presented high reliability.
bibliographic citation: Machado Marques et al. (2025) Validity, reliability and minimal detectable change in the sit-to-stand test for synchronous and asynchronous tele-assessment in post-COVID-19 condition. PeerJ 13:e20211 https://doi.org/10.7717/peerj.20211
date submitted: 2025-05-12
date accepted: 2025-09-19
issued: 2025-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Machado Marques
  given name: Juliane
author list: Agent
  family name: Brasiliano da Paz
  given name: Matheus
author list: Agent
  family name: Gomes Costa
  given name: Rodrigo Rodrigues
author list: Agent
  family name: Ribeiro Neto
  given name: Frederico
doi: 10.7717/peerj.20211
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-27
copyright: ©2025 Machado Marques et al.
attribution name: Machado Marques et al.

Insights into the interactions between Deverra tortuosa and Schizomyia buboniae: phytochemicals, antioxidant capacity, and enzyme inhibitory effects
type: item
type: AcademicArticle
description: Schizomyia buboniae (Diptera: Cecidomyiidae) induces berry-like galls on the stems of Deverra tortuosa (Desf.) DC. It is also known as “Shabat El-Gabal” and is one of the most important aromatic medicinal plants in Egypt. Many researchers have reported the relationship between galling insects and plant secondary metabolites, but this relationship is not quantitative. This study investigated the impact of S. buboniae-induced galls on physiological traits, phytochemical profiles, antioxidant capacity, and antinutrient levels in D. tortuosa stems. Our results reported that photosynthetic pigment levels, including chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids significantly decreased in galled stems by 63%, 14%, 44%, and 53%, respectively (p < 0.05). Antioxidant enzyme activities such as polyphenol oxidase (PPO), peroxidase (POX), catalase (CAT) and superoxide dismutase (SOD) significantly increased in galled stems by 173%, 88%, 125% and 25%, respectively, indicating elevated oxidative stress response. The analysis of phytochemical compositions revealed that the galled stems of D. tortuosa contained significantly higher levels of total flavonoids, flavonols, saponins, steroids, tannins, alkaloids, cardiac glycosides, and total phenolic compounds compared to non-galled stems, suggesting enhanced production of secondary metabolites. Additionally, galled stems exhibited higher levels of phytates, oxalates, and cyanogenic glycosides than non-galled stems. Proximate contents, including lipids, carbohydrates and proteins, were also elevated in galled stems. Furthermore, galled stems exhibited significantly (p < 0.05) stronger antioxidant activity than non-galled stems. S. buboniae appears to modify the phenotype of D. tortuosa, inducing tissue differentiation and activating defense-related responses. These results reveal that gall composition alters key physiological and biochemical traits in D. tortuosa, possibly as a defense response or as a result of inse…
format: application/pdf
format: text/html
creator: Nashaat N. Mahmoud
creator: Abdulaziz R. Alqahtani
creator: Noura J. Alotaibi
creator: Muhammad I. Haggag
creator: Abdelatti I. Nowwar
creator: Sanad H. Ragab
subject: Biochemistry
subject: Ecology
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.20052
publisher: PeerJ Inc.
rights: © 2025 Mahmoud et al.
abstract: Schizomyia buboniae (Diptera: Cecidomyiidae) induces berry-like galls on the stems of Deverra tortuosa (Desf.) DC. It is also known as “Shabat El-Gabal” and is one of the most important aromatic medicinal plants in Egypt. Many researchers have reported the relationship between galling insects and plant secondary metabolites, but this relationship is not quantitative. This study investigated the impact of S. buboniae-induced galls on physiological traits, phytochemical profiles, antioxidant capacity, and antinutrient levels in D. tortuosa stems. Our results reported that photosynthetic pigment levels, including chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids significantly decreased in galled stems by 63%, 14%, 44%, and 53%, respectively (p < 0.05). Antioxidant enzyme activities such as polyphenol oxidase (PPO), peroxidase (POX), catalase (CAT) and superoxide dismutase (SOD) significantly increased in galled stems by 173%, 88%, 125% and 25%, respectively, indicating elevated oxidative stress response. The analysis of phytochemical compositions revealed that the galled stems of D. tortuosa contained significantly higher levels of total flavonoids, flavonols, saponins, steroids, tannins, alkaloids, cardiac glycosides, and total phenolic compounds compared to non-galled stems, suggesting enhanced production of secondary metabolites. Additionally, galled stems exhibited higher levels of phytates, oxalates, and cyanogenic glycosides than non-galled stems. Proximate contents, including lipids, carbohydrates and proteins, were also elevated in galled stems. Furthermore, galled stems exhibited significantly (p < 0.05) stronger antioxidant activity than non-galled stems. S. buboniae appears to modify the phenotype of D. tortuosa, inducing tissue differentiation and activating defense-related responses. These results reveal that gall composition alters key physiological and biochemical traits in D. tortuosa, possibly as a defense response or as a result of inse…
bibliographic citation: Mahmoud et al. (2025) Insights into the interactions between Deverra tortuosa and Schizomyia buboniae: phytochemicals, antioxidant capacity, and enzyme inhibitory effects. PeerJ 13:e20052 https://doi.org/10.7717/peerj.20052
date submitted: 2025-05-05
date accepted: 2025-08-17
issued: 2025-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mahmoud
  given name: Nashaat N.
author list: Agent
  family name: Alqahtani
  given name: Abdulaziz R.
author list: Agent
  family name: Alotaibi
  given name: Noura J.
author list: Agent
  family name: Haggag
  given name: Muhammad I.
author list: Agent
  family name: Nowwar
  given name: Abdelatti I.
author list: Agent
  family name: Ragab
  given name: Sanad H.
doi: 10.7717/peerj.20052
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-27
copyright: ©2025 Mahmoud et al.
attribution name: Mahmoud et al.

Patterns of pre-sleep music use and sleep quality: exploratory survey findings on state anxiety
type: item
type: AcademicArticle
description: Music listening is a widely used self-help approach that may influence psychological and physiological processes associated with sleep. This cross-sectional study explored patterns of pre-sleep music use in relation to psychological distress (state anxiety, mood disturbance, stress) and subjective sleep quality. Adults (N = 269, 52.6% female; Mage = 27.7, SD = 9.0) completed validated self-report measures of sleep quality (the Pittsburgh Sleep Quality Index (PSQI)) and psychological distress. Pre-sleep music use was modestly associated with poorer sleep quality (r = 0.23, p < 0.01). A borderline interaction between state anxiety and music use (β = −0.170, p = 0.050) suggested, but did not confirm, a possible buffering pattern in which the anxiety-sleep association appeared weaker among more frequent music users. No moderation effects were observed for mood or stress. These preliminary findings suggest that pre-sleep music use may reflect a coping-oriented effort among individuals experiencing anxiety. However, given the cross-sectional design, self-report measures, and borderline statistical support, the results should be viewed as descriptive and hypothesis-generating.
format: application/pdf
format: text/html
creator: Andrew Danso
creator: Mareike Ehlert
creator: Friederike Koehler
creator: Rory Kirk
creator: Nandhini Natarajan
creator: Shannon Eilyce Wright
creator: Renee Timmers
creator: Suvi Saarikallio
subject: Health Policy
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
subject: Healthcare Services
description: doi:10.7717/peerj.20444
publisher: PeerJ Inc.
rights: © 2025 Danso et al.
abstract: Music listening is a widely used self-help approach that may influence psychological and physiological processes associated with sleep. This cross-sectional study explored patterns of pre-sleep music use in relation to psychological distress (state anxiety, mood disturbance, stress) and subjective sleep quality. Adults (N = 269, 52.6% female; Mage = 27.7, SD = 9.0) completed validated self-report measures of sleep quality (the Pittsburgh Sleep Quality Index (PSQI)) and psychological distress. Pre-sleep music use was modestly associated with poorer sleep quality (r = 0.23, p < 0.01). A borderline interaction between state anxiety and music use (β = −0.170, p = 0.050) suggested, but did not confirm, a possible buffering pattern in which the anxiety-sleep association appeared weaker among more frequent music users. No moderation effects were observed for mood or stress. These preliminary findings suggest that pre-sleep music use may reflect a coping-oriented effort among individuals experiencing anxiety. However, given the cross-sectional design, self-report measures, and borderline statistical support, the results should be viewed as descriptive and hypothesis-generating.
bibliographic citation: Danso et al. (2025) Patterns of pre-sleep music use and sleep quality: exploratory survey findings on state anxiety. PeerJ 13:e20444 https://doi.org/10.7717/peerj.20444
date submitted: 2025-05-05
date accepted: 2025-10-31
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Danso
  given name: Andrew
author list: Agent
  family name: Ehlert
  given name: Mareike
author list: Agent
  family name: Koehler
  given name: Friederike
author list: Agent
  family name: Kirk
  given name: Rory
author list: Agent
  family name: Natarajan
  given name: Nandhini
author list: Agent
  family name: Wright
  given name: Shannon Eilyce
author list: Agent
  family name: Timmers
  given name: Renee
author list: Agent
  family name: Saarikallio
  given name: Suvi
doi: 10.7717/peerj.20444
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: © 2025 Danso et al.
attribution name: Danso et al.

Biological maturation, anthropometric, and physical fitness variables of youth breaking athletes with different competition levels
type: item
type: AcademicArticle
description: Purpose This study aimed to analyze differences in anthropometric characteristics and physical fitness performance based on chronological age, maturation status, and competition level among youth breaking athletes. Methods Morphological characteristics and selected physical fitness performances were assessed in 23 male youth breaking athletes (mean age: 14.47 ± 1.99 years). Biological maturity was estimated from anthropometric measures and expressed as age at peak height velocity (APHV) and maturity offset. All athletes were classified into two age groups (U14 and U18), three maturity groups (pre-peak height velocity (PHV), circum-PHV, and post-PHV) and two competition level groups (elite and sub-elite). Independent samples t-tests and analysis of variance (ANOVAs) were employed to examine group differences, and Pearson correlation analysis was conducted to investigate intragroup relationships between morphological and physical fitness variables. Results There was no difference in body fat percentage (P > 0.05) between U14 and U18 in terms of anthropometric measurement indicators. In contrast, significant differences (P < 0.05) were observed in most physical fitness indicators (T-test, standing long jump, 30-m sprint, p ull up and 400-m run), with the U18 athletes showing superior performance. No significant differences were observed between elite and sub-elite youth breaking athletes, except in the one-minute sit-up test (P = 0.028). Significant differences among different maturity groups were found in age (P < 0.01), maturity offset (P < 0.001), height (P < 0.001), body mass (P < 0.001), body mass index (BMI) (P < 0.001), sitting height (P < 0.001), leg length (P = 0.016), T-test (P = 0.029), standing long jump (P = 0.019), 30-m sprint (P = 0.006), 30s bodyweight squat (P = 0.030), and 400-m (P = 0.021). While chronological age and maturity status correlated with multiple physical performance indicators, body fat percentage (P > 0.05) showed no such association. C…
format: application/pdf
format: text/html
creator: Yifan Zhao
creator: Xiaobin Wei
creator: Kewei Zhao
subject: Anatomy and Physiology
subject: Sports Medicine
description: doi:10.7717/peerj.20383
publisher: PeerJ Inc.
rights: © 2025 Zhao et al.
abstract: Purpose This study aimed to analyze differences in anthropometric characteristics and physical fitness performance based on chronological age, maturation status, and competition level among youth breaking athletes. Methods Morphological characteristics and selected physical fitness performances were assessed in 23 male youth breaking athletes (mean age: 14.47 ± 1.99 years). Biological maturity was estimated from anthropometric measures and expressed as age at peak height velocity (APHV) and maturity offset. All athletes were classified into two age groups (U14 and U18), three maturity groups (pre-peak height velocity (PHV), circum-PHV, and post-PHV) and two competition level groups (elite and sub-elite). Independent samples t-tests and analysis of variance (ANOVAs) were employed to examine group differences, and Pearson correlation analysis was conducted to investigate intragroup relationships between morphological and physical fitness variables. Results There was no difference in body fat percentage (P > 0.05) between U14 and U18 in terms of anthropometric measurement indicators. In contrast, significant differences (P < 0.05) were observed in most physical fitness indicators (T-test, standing long jump, 30-m sprint, p ull up and 400-m run), with the U18 athletes showing superior performance. No significant differences were observed between elite and sub-elite youth breaking athletes, except in the one-minute sit-up test (P = 0.028). Significant differences among different maturity groups were found in age (P < 0.01), maturity offset (P < 0.001), height (P < 0.001), body mass (P < 0.001), body mass index (BMI) (P < 0.001), sitting height (P < 0.001), leg length (P = 0.016), T-test (P = 0.029), standing long jump (P = 0.019), 30-m sprint (P = 0.006), 30s bodyweight squat (P = 0.030), and 400-m (P = 0.021). While chronological age and maturity status correlated with multiple physical performance indicators, body fat percentage (P > 0.05) showed no such association. C…
bibliographic citation: Zhao et al. (2025) Biological maturation, anthropometric, and physical fitness variables of youth breaking athletes with different competition levels. PeerJ 13:e20383 https://doi.org/10.7717/peerj.20383
date submitted: 2025-05-08
date accepted: 2025-10-22
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yifan
author list: Agent
  family name: Wei
  given name: Xiaobin
author list: Agent
  family name: Zhao
  given name: Kewei
doi: 10.7717/peerj.20383
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: ©2025 Zhao et al.
attribution name: Zhao et al.

Efflux systems driving resistance and virulence across biological domains
type: item
type: AcademicArticle
description: Background Efflux pumps (EPs) are key contributors to multidrug resistance (MDR) in bacteria, fungi, and cancer cells. These membrane proteins actively extrude a variety of therapeutic agents, reducing their intracellular concentration and thus compromising the efficacy of treatment. Beyond resistance, EPs are also involved in virulence, biofilm formation, immune evasion, and environmental persistence. Aim This review aimed to provide a comprehensive and critical synthesis of the role of efflux pumps in antimicrobial and antitumoral resistance, as well as their contribution to virulence and persistence across biological domains. Methodology A narrative review was conducted following a structured search strategy in PubMed, Scopus, and Web of Science using combinations of terms related to efflux systems, efflux pumps, resistance mechanisms, virulence factors, detection methods, and inhibitors. The review integrates data from in vitro, in silico, and clinical studies, including both classical detection strategies and emerging technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based modulation, biosensors, and microfluidics. Results Efflux pumps from different families (e.g., resistance-nodulation-division (RND), ATP-binding cassette (ABC), major facilitator superfamily (MFS)) are implicated in the active extrusion of antimicrobial agents, facilitating MDR and treatment failure in pathogens such as E. coli, P. aeruginosa, M. tuberculosis, Candida albicans, and cancer cells. EPs also regulate biofilm formation, virulence factor secretion, and metabolic adaptation. Classical methods for detecting efflux (e.g., minimum inhibitory concentration (MIC) shifts with inhibitors, fluorometric assays) have technical limitations, while novel technologies offer improved precision. Several natural and synthetic efflux pump inhibitors (EPIs) have demonstrated efficacy in preclinical studies, yet few have progressed to clinical use due to toxicity a…
format: application/pdf
format: text/html
creator: Pedro Eduardo Almeida da Silva
creator: Andrea Von Groll
creator: Ivy Ramis
creator: Ana Julia Reis
creator: Daniela Ramos
creator: Miguel Viveiros
subject: Microbiology
subject: Mycology
subject: Infectious Diseases
description: doi:10.7717/peerj.20360
publisher: PeerJ Inc.
rights: © 2025 Almeida da Silva et al.
abstract: Background Efflux pumps (EPs) are key contributors to multidrug resistance (MDR) in bacteria, fungi, and cancer cells. These membrane proteins actively extrude a variety of therapeutic agents, reducing their intracellular concentration and thus compromising the efficacy of treatment. Beyond resistance, EPs are also involved in virulence, biofilm formation, immune evasion, and environmental persistence. Aim This review aimed to provide a comprehensive and critical synthesis of the role of efflux pumps in antimicrobial and antitumoral resistance, as well as their contribution to virulence and persistence across biological domains. Methodology A narrative review was conducted following a structured search strategy in PubMed, Scopus, and Web of Science using combinations of terms related to efflux systems, efflux pumps, resistance mechanisms, virulence factors, detection methods, and inhibitors. The review integrates data from in vitro, in silico, and clinical studies, including both classical detection strategies and emerging technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based modulation, biosensors, and microfluidics. Results Efflux pumps from different families (e.g., resistance-nodulation-division (RND), ATP-binding cassette (ABC), major facilitator superfamily (MFS)) are implicated in the active extrusion of antimicrobial agents, facilitating MDR and treatment failure in pathogens such as E. coli, P. aeruginosa, M. tuberculosis, Candida albicans, and cancer cells. EPs also regulate biofilm formation, virulence factor secretion, and metabolic adaptation. Classical methods for detecting efflux (e.g., minimum inhibitory concentration (MIC) shifts with inhibitors, fluorometric assays) have technical limitations, while novel technologies offer improved precision. Several natural and synthetic efflux pump inhibitors (EPIs) have demonstrated efficacy in preclinical studies, yet few have progressed to clinical use due to toxicity a…
bibliographic citation: Almeida da Silva et al. (2025) Efflux systems driving resistance and virulence across biological domains. PeerJ 13:e20360 https://doi.org/10.7717/peerj.20360
date submitted: 2025-07-09
date accepted: 2025-10-17
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almeida da Silva
  given name: Pedro Eduardo
author list: Agent
  family name: Von Groll
  given name: Andrea
author list: Agent
  family name: Ramis
  given name: Ivy
author list: Agent
  family name: Reis
  given name: Ana Julia
author list: Agent
  family name: Ramos
  given name: Daniela
author list: Agent
  family name: Viveiros
  given name: Miguel
doi: 10.7717/peerj.20360
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: ©2025 Almeida da Silva et al.
attribution name: Almeida da Silva et al.

Pelvis-Trunk coordination strategies differ a cross preparatory court movement distances during the tennis forehand
type: item
type: AcademicArticle
description: Objectives To examine the effects of on-court movement distances on pelvis-trunk coordination during forehand strokes. Methods Eighteen male college tennis athletes participated in this study. They performed forehand stroke task at three different preparatory court movement distances (minimum, medium and maximum movement distances). A one-way repeated-measures ANOVA with Statistical Parametric Mapping was used to determine differences in pelvis-trunk coordination in the transverse plane across the three movement distances, and Pearson’s correlation analysis was used to determine the relationships between each of the four pelvis-trunk coordination features on the dominant and non-dominant side and racket speed. Results Significant differences were observed for different movement distances in the non-dominant pelvis-trunk continuous relative phase (CRP) during 23–41% of the acceleration phase (p = 0.016, F2,34 = 5.901) and in the dominant pelvis-trunk CRP during 76–100% of the acceleration phase (p = 0.016, F2,34 = 5.946). For the minimum distance, significant correlations with racket speed were found in the mean CRP (r = − 0.889, p = 0.001) and peak CRP (r = − 0.488, p = 0.04) for the non-dominant side, and the mean CRP (r = − 0.478, p = 0.045) for the dominant side. Regarding medium distances, significant correlations with racket speed were observed for the non-dominant side in the mean CRP (r = − 0.493, p = 0.037), peak CRP (r = − 0.628, p = 0.005), and maximum positive CRP slope (r = 0.477, p = 0.046). For the dominant side, significant correlations with racket speed were noted for peak CRP (r = 0.551, p = 0.018) and maximum positive CRP slope (r = 0.514, p = 0.029). At the maximum distance, significant correlations with racket speed were identified for the dominant side in the maximum positive CRP slope (r = 0.580, p = 0.012) and maximum negative CRP slope (r = 0.566, p = 0.014); however, there was no significant difference in racket speed at impact when approach…
format: application/pdf
format: text/html
creator: Xiangwei Meng
creator: Youngsuk Kim
creator: Shuai Wang
creator: Sukwon Kim
creator: Ming Li
subject: Kinesiology
subject: Computational Science
subject: Biomechanics
description: doi:10.7717/peerj.20321
publisher: PeerJ Inc.
rights: © 2025 Meng et al.
abstract: Objectives To examine the effects of on-court movement distances on pelvis-trunk coordination during forehand strokes. Methods Eighteen male college tennis athletes participated in this study. They performed forehand stroke task at three different preparatory court movement distances (minimum, medium and maximum movement distances). A one-way repeated-measures ANOVA with Statistical Parametric Mapping was used to determine differences in pelvis-trunk coordination in the transverse plane across the three movement distances, and Pearson’s correlation analysis was used to determine the relationships between each of the four pelvis-trunk coordination features on the dominant and non-dominant side and racket speed. Results Significant differences were observed for different movement distances in the non-dominant pelvis-trunk continuous relative phase (CRP) during 23–41% of the acceleration phase (p = 0.016, F2,34 = 5.901) and in the dominant pelvis-trunk CRP during 76–100% of the acceleration phase (p = 0.016, F2,34 = 5.946). For the minimum distance, significant correlations with racket speed were found in the mean CRP (r = − 0.889, p = 0.001) and peak CRP (r = − 0.488, p = 0.04) for the non-dominant side, and the mean CRP (r = − 0.478, p = 0.045) for the dominant side. Regarding medium distances, significant correlations with racket speed were observed for the non-dominant side in the mean CRP (r = − 0.493, p = 0.037), peak CRP (r = − 0.628, p = 0.005), and maximum positive CRP slope (r = 0.477, p = 0.046). For the dominant side, significant correlations with racket speed were noted for peak CRP (r = 0.551, p = 0.018) and maximum positive CRP slope (r = 0.514, p = 0.029). At the maximum distance, significant correlations with racket speed were identified for the dominant side in the maximum positive CRP slope (r = 0.580, p = 0.012) and maximum negative CRP slope (r = 0.566, p = 0.014); however, there was no significant difference in racket speed at impact when approach…
bibliographic citation: Meng et al. (2025) Pelvis-Trunk coordination strategies differ a cross preparatory court movement distances during the tennis forehand. PeerJ 13:e20321 https://doi.org/10.7717/peerj.20321
date submitted: 2025-02-13
date accepted: 2025-10-10
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Meng
  given name: Xiangwei
author list: Agent
  family name: Kim
  given name: Youngsuk
author list: Agent
  family name: Wang
  given name: Shuai
author list: Agent
  family name: Kim
  given name: Sukwon
author list: Agent
  family name: Li
  given name: Ming
doi: 10.7717/peerj.20321
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: ©2025 Meng et al.
attribution name: Meng et al.

Mandibular form and function is more disparate in amniotes than in non-amniote tetrapods from the late Palaeozoic
type: item
type: AcademicArticle
description: Terrestrial tetrapods originated during the Middle Devonian, and the group rapidly diversified throughout the subsequent Carboniferous and Permian periods. Feeding in air rather than water is expected to require changes to tetrapod mandibular form and function. Previous biomechanical studies on jaw evolution, however, found that the increase in functional disparity lagged behind terrestrialisation by approximately 70 Myr, coinciding with the origin of amniotes and herbivory. We expand on a previous dataset composed primarily of non-amniote tetrapods to identify the drivers of this diversification, including representatives of all major amniote clades from the Permo-Carboniferous. First, we measured nine biomechanical traits from 111 tetrapod jaws in medial view. Second, we performed an Elliptical Fourier Analysis on 198 jaws in lateral view and 73 jaws in occlusal view. The first peak in jaw disparity, during the Pennsylvanian, occurs in carnivorous non-amniote tetrapods. However, the jaws of amniotes, particularly those inferred as herbivorous, are consistently more disparate than non-amniote tetrapods from the early Permian, especially in terms of jaw depth, symphysial length and force transmission. Functional and shape disparity of Palaeozoic tetrapod jaws follow a similar pattern that is explained by large-scale faunal turnovers and ecosystem structures.
format: application/pdf
format: text/html
creator: Jasper Ponstein
creator: Mark J. MacDougall
creator: Joep Schaeffer
creator: Christian F. Kammerer
creator: Jörg Fröbisch
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.20243
publisher: PeerJ Inc.
rights: © 2025 Ponstein et al.
abstract: Terrestrial tetrapods originated during the Middle Devonian, and the group rapidly diversified throughout the subsequent Carboniferous and Permian periods. Feeding in air rather than water is expected to require changes to tetrapod mandibular form and function. Previous biomechanical studies on jaw evolution, however, found that the increase in functional disparity lagged behind terrestrialisation by approximately 70 Myr, coinciding with the origin of amniotes and herbivory. We expand on a previous dataset composed primarily of non-amniote tetrapods to identify the drivers of this diversification, including representatives of all major amniote clades from the Permo-Carboniferous. First, we measured nine biomechanical traits from 111 tetrapod jaws in medial view. Second, we performed an Elliptical Fourier Analysis on 198 jaws in lateral view and 73 jaws in occlusal view. The first peak in jaw disparity, during the Pennsylvanian, occurs in carnivorous non-amniote tetrapods. However, the jaws of amniotes, particularly those inferred as herbivorous, are consistently more disparate than non-amniote tetrapods from the early Permian, especially in terms of jaw depth, symphysial length and force transmission. Functional and shape disparity of Palaeozoic tetrapod jaws follow a similar pattern that is explained by large-scale faunal turnovers and ecosystem structures.
bibliographic citation: Ponstein et al. (2025) Mandibular form and function is more disparate in amniotes than in non-amniote tetrapods from the late Palaeozoic. PeerJ 13:e20243 https://doi.org/10.7717/peerj.20243
date submitted: 2025-04-16
date accepted: 2025-09-24
issued: 2025-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ponstein
  given name: Jasper
author list: Agent
  family name: MacDougall
  given name: Mark J.
author list: Agent
  family name: Schaeffer
  given name: Joep
author list: Agent
  family name: Kammerer
  given name: Christian F.
author list: Agent
  family name: Fröbisch
  given name: Jörg
doi: 10.7717/peerj.20243
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-26
copyright: © 2025 Ponstein et al.
attribution name: Ponstein et al.

Overexpression of ORAOV1 and its association with immunotherapy resistance in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality globally. Previous studies have reported that oral cancer overexpression 1 (ORAOV1) is overexpressed in HCC and correlated with poor prognosis, yet its molecular mechanisms remain incompletely understood. In this study, ORAOV1 overexpression was confirmed in HCC tissues via tissue microarray analysis and functionally linked to tumor cell proliferation through a positive correlation with Ki-67 expression in the human HCC cell line MHCC-97L. Bioinformatics analyses using The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) HCC datasets further supported these findings. Multiple mechanisms appear to drive ORAOV1 upregulation, including promoter hypomethylation, amplification of the 11q13 region, and a putative ceRNA network involving AC005332.1, AC012615.1, and hsa-miR-100-5p. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses implicated ORAOV1 in various cellular processes, such as abnormal membrane channel function, extracellular matrix–receptor interactions, IL-17 signaling, and peroxisome proliferator-activated receptor (PPAR) signaling. Co-expression analysis identified significant associations between ORAOV1 and the oncogenes TPCN2 and CCND1. Additionally, ORAOV1 expression correlated with enhanced infiltration of immunosuppressive cells, including regulatory T cells, myeloid-derived suppressor cells, and cancer-associated fibroblasts, as well as upregulation of immune checkpoint markers (PD-1, PD-L1, and CTLA-4). These results indicate that ORAOV1 may modulate the immunosuppressive tumor microenvironment and contribute to resistance against immunotherapy, highlighting its potential as a therapeutic target in HCC.
format: application/pdf
format: text/html
creator: Yuzhen Huang
creator: Ni Yang
creator: Su Wen
creator: Ziwei Fang
creator: Yucong Zhang
creator: Zonghao Qian
creator: Yi Huang
creator: Tiejun Yin
creator: Cuntai Zhang
creator: Le Zhang
subject: Bioinformatics
subject: Genetics
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20390
publisher: PeerJ Inc.
rights: © 2025 Huang et al.
abstract: Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality globally. Previous studies have reported that oral cancer overexpression 1 (ORAOV1) is overexpressed in HCC and correlated with poor prognosis, yet its molecular mechanisms remain incompletely understood. In this study, ORAOV1 overexpression was confirmed in HCC tissues via tissue microarray analysis and functionally linked to tumor cell proliferation through a positive correlation with Ki-67 expression in the human HCC cell line MHCC-97L. Bioinformatics analyses using The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) HCC datasets further supported these findings. Multiple mechanisms appear to drive ORAOV1 upregulation, including promoter hypomethylation, amplification of the 11q13 region, and a putative ceRNA network involving AC005332.1, AC012615.1, and hsa-miR-100-5p. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses implicated ORAOV1 in various cellular processes, such as abnormal membrane channel function, extracellular matrix–receptor interactions, IL-17 signaling, and peroxisome proliferator-activated receptor (PPAR) signaling. Co-expression analysis identified significant associations between ORAOV1 and the oncogenes TPCN2 and CCND1. Additionally, ORAOV1 expression correlated with enhanced infiltration of immunosuppressive cells, including regulatory T cells, myeloid-derived suppressor cells, and cancer-associated fibroblasts, as well as upregulation of immune checkpoint markers (PD-1, PD-L1, and CTLA-4). These results indicate that ORAOV1 may modulate the immunosuppressive tumor microenvironment and contribute to resistance against immunotherapy, highlighting its potential as a therapeutic target in HCC.
bibliographic citation: Huang et al. (2025) Overexpression of ORAOV1 and its association with immunotherapy resistance in hepatocellular carcinoma. PeerJ 13:e20390 https://doi.org/10.7717/peerj.20390
date submitted: 2025-02-10
date accepted: 2025-10-24
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Yuzhen
author list: Agent
  family name: Yang
  given name: Ni
author list: Agent
  family name: Wen
  given name: Su
author list: Agent
  family name: Fang
  given name: Ziwei
author list: Agent
  family name: Zhang
  given name: Yucong
author list: Agent
  family name: Qian
  given name: Zonghao
author list: Agent
  family name: Huang
  given name: Yi
author list: Agent
  family name: Yin
  given name: Tiejun
author list: Agent
  family name: Zhang
  given name: Cuntai
author list: Agent
  family name: Zhang
  given name: Le
doi: 10.7717/peerj.20390
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Huang et al.
attribution name: Huang et al.

Resistance of cervical vertebrae in response to muscular stresses in pterosaurs: implications for foraging habits and skeletal pneumatization
type: item
type: AcademicArticle
description: The necks of pterosaurs were flexible and provided mobility for a relatively long skull. The varied morphologies and levels of pneumatization of their cervical vertebrae reflected differences in biomechanical behavior. Here, we examined the structural resistance of the cervical vertebrae to infer the most advantageous movements during the foraging behaviors of two pterodactyloid pterosaurs. We also examined the relationship between vertebral resistance and the presence of pneumatic foramina on the bone cortex. For this purpose, we analyzed three-dimensional models of the cervical vertebrae of Anhanguera piscator and Azhdarcho lancicollis, which are hypothesized to be aquatic and terrestrial predators, respectively, and employed Finite Element Analysis (FEA) to assess and quantify the stresses experienced by the vertebrae due to the performance of six different movement scenarios. We observed that the shorter vertebrae at the ends of the neck of both species favored the proliferation of larger stresses in these regions, especially in the posterior cervicals of Anhanguera piscator and in the atlas-axis of Azhdarcho lancicollis, and that their taller neural arches aided in absorbing stress. Larger stresses at the ends of the neck are consistent with the interior trabecular reinforcement of the atlas-axis and posterior cervical vertebrae, suggesting a link between biomechanical behavior and the level of pneumatization. Additionally, mechanical requirements may have also influenced the presence, size, and number of pneumatic foramina on the vertebral cortex, as evidenced by the large lateral foramen in Anhanguera piscator and the smaller and more numerous ones bordering the neural canal in Azhdarcho lancicollis. Our inferences corroborate the differences in foraging strategies hypothesized for anhanguerids and azhdarchids. The absorption of stresses resulting from ventral pitching of the head and neck indicates that the cervical vertebrae were well-adapted for making rap…
format: application/pdf
format: text/html
creator: Richard Buchmann
creator: Taissa Rodrigues
subject: Biophysics
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.20388
publisher: PeerJ Inc.
rights: © 2025 Buchmann and Rodrigues
abstract: The necks of pterosaurs were flexible and provided mobility for a relatively long skull. The varied morphologies and levels of pneumatization of their cervical vertebrae reflected differences in biomechanical behavior. Here, we examined the structural resistance of the cervical vertebrae to infer the most advantageous movements during the foraging behaviors of two pterodactyloid pterosaurs. We also examined the relationship between vertebral resistance and the presence of pneumatic foramina on the bone cortex. For this purpose, we analyzed three-dimensional models of the cervical vertebrae of Anhanguera piscator and Azhdarcho lancicollis, which are hypothesized to be aquatic and terrestrial predators, respectively, and employed Finite Element Analysis (FEA) to assess and quantify the stresses experienced by the vertebrae due to the performance of six different movement scenarios. We observed that the shorter vertebrae at the ends of the neck of both species favored the proliferation of larger stresses in these regions, especially in the posterior cervicals of Anhanguera piscator and in the atlas-axis of Azhdarcho lancicollis, and that their taller neural arches aided in absorbing stress. Larger stresses at the ends of the neck are consistent with the interior trabecular reinforcement of the atlas-axis and posterior cervical vertebrae, suggesting a link between biomechanical behavior and the level of pneumatization. Additionally, mechanical requirements may have also influenced the presence, size, and number of pneumatic foramina on the vertebral cortex, as evidenced by the large lateral foramen in Anhanguera piscator and the smaller and more numerous ones bordering the neural canal in Azhdarcho lancicollis. Our inferences corroborate the differences in foraging strategies hypothesized for anhanguerids and azhdarchids. The absorption of stresses resulting from ventral pitching of the head and neck indicates that the cervical vertebrae were well-adapted for making rap…
bibliographic citation: Buchmann et al. (2025) Resistance of cervical vertebrae in response to muscular stresses in pterosaurs: implications for foraging habits and skeletal pneumatization. PeerJ 13:e20388 https://doi.org/10.7717/peerj.20388
date submitted: 2025-07-22
date accepted: 2025-10-24
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buchmann
  given name: Richard
author list: Agent
  family name: Rodrigues
  given name: Taissa
doi: 10.7717/peerj.20388
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Buchmann and Rodrigues
attribution name: Buchmann and Rodrigues

Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)—induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies
type: item
type: AcademicArticle
description: Root rot disease is a globally significant threat to the health of diverse economically important crops. Understanding shifts in the plant microbiome during disease progression can aid in identifying beneficial microbes with disease-resistant potential and developing ecofriendly biocontrol strategies. However, microbiome changes during root rot progression in the medicinal plant Ligusticum chuanxiong remain poorly understood. This study aimed to investigate the response of host-associated microbiomes to pathogen stress (Fusarium oxysporum and F. solani syn. Neocosmospora solani) during L. chuanxiong root rot. The diversity, composition, function, and network interactions of bacterial and fungal communities were examined using high-throughput sequencing and network analysis in healthy rhizomes, healthy layers of diseased rhizomes, rotten layers of diseased rhizomes, and rhizosphere and non-rhizosphere soils. The bacterial diversity decreased as root rot progressed in end ophytic (from 0.72 to 0.38) and rhizosphere soils (from 0.80 to 0.68), whereas the fungal diversity showed no significant changes. The diseased samples were enriched with root rot pathogens and other potential pathogens, such as the soil bacterium Pectobacterium and the soil fungus Gibberella, whereas beneficial taxa, including endophytic Bacillus and Trichoderma, and soil-dwelling Candidatus_Solibacter and Beauveria, were significantly reduced. Notably, in the healthy layers of diseased rhizomes, which represent a “transitional phase”, fungal communities resembled those in rotten tissues with increased pathogenic taxa (e.g., Ceratocystis and Plectosphaerella), whereas bacterial communities were more similar to healthy rhizomes and enriched in beneficial genera (e.g., Microbacterium and Variovorax). Functional prediction indicated suppressed bacterial activity and enhanced fungal saprotrophy in rotten rhizomes. The cross-kingdom network complexity decreased in both endophytic and soil microbial commu…
format: application/pdf
format: text/html
creator: Weiping Gao
creator: Hai Wang
creator: Hongmei Jia
creator: Jianyun Zhang
creator: Zhuyun Yan
creator: Dongmei He
creator: Chuan Zheng
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.20369
publisher: PeerJ Inc.
rights: © 2025 Gao et al.
abstract: Root rot disease is a globally significant threat to the health of diverse economically important crops. Understanding shifts in the plant microbiome during disease progression can aid in identifying beneficial microbes with disease-resistant potential and developing ecofriendly biocontrol strategies. However, microbiome changes during root rot progression in the medicinal plant Ligusticum chuanxiong remain poorly understood. This study aimed to investigate the response of host-associated microbiomes to pathogen stress (Fusarium oxysporum and F. solani syn. Neocosmospora solani) during L. chuanxiong root rot. The diversity, composition, function, and network interactions of bacterial and fungal communities were examined using high-throughput sequencing and network analysis in healthy rhizomes, healthy layers of diseased rhizomes, rotten layers of diseased rhizomes, and rhizosphere and non-rhizosphere soils. The bacterial diversity decreased as root rot progressed in end ophytic (from 0.72 to 0.38) and rhizosphere soils (from 0.80 to 0.68), whereas the fungal diversity showed no significant changes. The diseased samples were enriched with root rot pathogens and other potential pathogens, such as the soil bacterium Pectobacterium and the soil fungus Gibberella, whereas beneficial taxa, including endophytic Bacillus and Trichoderma, and soil-dwelling Candidatus_Solibacter and Beauveria, were significantly reduced. Notably, in the healthy layers of diseased rhizomes, which represent a “transitional phase”, fungal communities resembled those in rotten tissues with increased pathogenic taxa (e.g., Ceratocystis and Plectosphaerella), whereas bacterial communities were more similar to healthy rhizomes and enriched in beneficial genera (e.g., Microbacterium and Variovorax). Functional prediction indicated suppressed bacterial activity and enhanced fungal saprotrophy in rotten rhizomes. The cross-kingdom network complexity decreased in both endophytic and soil microbial commu…
bibliographic citation: Gao et al. (2025) Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)—induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies. PeerJ 13:e20369 https://doi.org/10.7717/peerj.20369
date submitted: 2025-06-13
date accepted: 2025-10-18
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Gao
  given name: Weiping
author list: Agent
  family name: Wang
  given name: Hai
author list: Agent
  family name: Jia
  given name: Hongmei
author list: Agent
  family name: Zhang
  given name: Jianyun
author list: Agent
  family name: Yan
  given name: Zhuyun
author list: Agent
  family name: He
  given name: Dongmei
author list: Agent
  family name: Zheng
  given name: Chuan
doi: 10.7717/peerj.20369
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Gao et al.
attribution name: Gao et al.

Comparative efficacy of different exercise interventions in patients with ankylosing spondylitis: a systematic review and network meta-analysis
type: item
type: AcademicArticle
description: Background Exercise interventions have been widely applied as an adjunctive treatment for ankylosing spondylitis (AS), effectively alleviating pain, improving function, and enhancing quality of life. However, the efficacy of different exercise modalities remains inconclusive. This study aims to systematically compare the effects of various exercise interventions on clinical outcomes in AS patients using a network meta-analysis (NMA) to determine the optimal exercise regimen. Methods A comprehensive search was performed across six databases to identify studies assessing the impact of exercise interventions on AS. The primary outcomes analyzed included the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Metrology Index (BASMI), and Ankylosing Spondylitis Quality of Life (ASQoL). A network meta-analysis was conducted using the frequentist approach in STATA 18.0, while effect publication bias analysis used Review Manager 5.4. Results Forty-eight studies involving 3,140 participants were included, published between 2002 and 2024. Compared to the control group, all exercise interventions demonstrated varying degrees of benefit in improving BASDAI, BASFI, BASMI, and ASQoL scores. For BASDAI, the Aquatic Stretching Exercise (ASE) (−1.42, 95% CI [−2.51 to −0.33]), Land Aerobic Exercise (LAE) (−0.94, 95% CI [−1.41 to −0.47]), and Land Stretching Exercise (LSE) (−0.49, 95% CI [−0.94 to −0.04]) exhibited significant symptom relief, with ASE ranking highest (surface under the cumulative ranking curve (SUCRA) = 85.5). For BASFI, statistically significant improvements were observed with the Aquatic Aerobic Exercise (AAE) (−0.90, 95% CI [−1.50 to −0.29]), ASE (−1.74, 95% CI [−2.45 to −1.04]), LAE (−0.74, 95% CI [−1.05 to −0.43]), LSE (−0.54, 95% CI [−0.81 to −0.27]), and Muscle Exercise (ME) (−0.48, 95% CI [−0.83 to −0.13]). ASE had the highest SUCRA ranking (99.6). For BASMI, ASE (−1.06,…
format: application/pdf
format: text/html
creator: Lingkui Kong
creator: Chuanwen Yu
creator: Chaoxin Wang
creator: Zhanpeng Meng
subject: Evidence Based Medicine
subject: Kinesiology
subject: Sports Injury
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20336
publisher: PeerJ Inc.
rights: © 2025 Kong et al.
abstract: Background Exercise interventions have been widely applied as an adjunctive treatment for ankylosing spondylitis (AS), effectively alleviating pain, improving function, and enhancing quality of life. However, the efficacy of different exercise modalities remains inconclusive. This study aims to systematically compare the effects of various exercise interventions on clinical outcomes in AS patients using a network meta-analysis (NMA) to determine the optimal exercise regimen. Methods A comprehensive search was performed across six databases to identify studies assessing the impact of exercise interventions on AS. The primary outcomes analyzed included the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Metrology Index (BASMI), and Ankylosing Spondylitis Quality of Life (ASQoL). A network meta-analysis was conducted using the frequentist approach in STATA 18.0, while effect publication bias analysis used Review Manager 5.4. Results Forty-eight studies involving 3,140 participants were included, published between 2002 and 2024. Compared to the control group, all exercise interventions demonstrated varying degrees of benefit in improving BASDAI, BASFI, BASMI, and ASQoL scores. For BASDAI, the Aquatic Stretching Exercise (ASE) (−1.42, 95% CI [−2.51 to −0.33]), Land Aerobic Exercise (LAE) (−0.94, 95% CI [−1.41 to −0.47]), and Land Stretching Exercise (LSE) (−0.49, 95% CI [−0.94 to −0.04]) exhibited significant symptom relief, with ASE ranking highest (surface under the cumulative ranking curve (SUCRA) = 85.5). For BASFI, statistically significant improvements were observed with the Aquatic Aerobic Exercise (AAE) (−0.90, 95% CI [−1.50 to −0.29]), ASE (−1.74, 95% CI [−2.45 to −1.04]), LAE (−0.74, 95% CI [−1.05 to −0.43]), LSE (−0.54, 95% CI [−0.81 to −0.27]), and Muscle Exercise (ME) (−0.48, 95% CI [−0.83 to −0.13]). ASE had the highest SUCRA ranking (99.6). For BASMI, ASE (−1.06,…
bibliographic citation: Kong et al. (2025) Comparative efficacy of different exercise interventions in patients with ankylosing spondylitis: a systematic review and network meta-analysis. PeerJ 13:e20336 https://doi.org/10.7717/peerj.20336
date submitted: 2025-04-18
date accepted: 2025-10-13
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Lingkui
author list: Agent
  family name: Yu
  given name: Chuanwen
author list: Agent
  family name: Wang
  given name: Chaoxin
author list: Agent
  family name: Meng
  given name: Zhanpeng
doi: 10.7717/peerj.20336
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Kong et al.
attribution name: Kong et al.

Coral reefs in the Mahafaly Seascape (SW Madagascar) as potential climate refugia following the 2024 mass bleaching event
type: item
type: AcademicArticle
description: The southwesternmost coast of Madagascar, including the Mahafaly seascape, is home to some of the country’s most ecologically and culturally important coral reefs, which remain largely understudied. These ecosystems are facing growing pressure from a panel of disturbances, with climate-induced events such as marine heatwaves being among of the causes of coral bleaching. The decline of these reefs can directly threaten the livelihoods of the local communities, who depend heavily on the resources they provide. In this context, understanding how different disturbances impact coral reef condition and recovery is critical for developing effective management strategies and conservation for this vulnerable region. This study investigates coral bleaching dynamics in the Mahafaly seascape during and after the fourth mass coral bleaching event in 2024. Six reef locations within locally managed marine areas were surveyed, comprising a total of 11 stations, with 20 one-square-meter quadrats randomly deployed at each station during each sampling period. Average hard coral densities of 18.3 and 19.3 colonies m−2 were recorded during and after the event, respectively. Bleaching prevalence peaked during the event, affecting 38.8% of coral colonies, with a marked decrease to 6.0% afterward. However, coral mortality remained relatively low across the entire seascape, with a slight post-bleaching increase in dead colonies (+3.5%). Northern sites experienced the highest thermal stress, with Beheloke and Besambay reefs being the most susceptible to bleaching, whereas Ambola exhibited remarkable resilience. In the south, Ambohibola showed low vulnerability, Lembehitake moderate susceptibility, and Itampolo the highest bleaching prevalence despite lower thermal stress. Taxa-specific patterns were also evident, with thermally sensitive branching genera being most affected, contrasting with the relative tolerance of massive and encrusting corals. The heterogeneous coral bleaching patterns o…
format: application/pdf
format: text/html
creator: Mahery Randrianarivo
creator: Solotahiana Rakotomanga
creator: Fanja Razafindramasy
creator: Danny Kornelio Ravelojaona
creator: Tahiry Ranaivoson
creator: Domoina Rakotomalala
creator: Rémi Ratsimbazafy
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.20319
publisher: PeerJ Inc.
rights: © 2025 Randrianarivo et al.
abstract: The southwesternmost coast of Madagascar, including the Mahafaly seascape, is home to some of the country’s most ecologically and culturally important coral reefs, which remain largely understudied. These ecosystems are facing growing pressure from a panel of disturbances, with climate-induced events such as marine heatwaves being among of the causes of coral bleaching. The decline of these reefs can directly threaten the livelihoods of the local communities, who depend heavily on the resources they provide. In this context, understanding how different disturbances impact coral reef condition and recovery is critical for developing effective management strategies and conservation for this vulnerable region. This study investigates coral bleaching dynamics in the Mahafaly seascape during and after the fourth mass coral bleaching event in 2024. Six reef locations within locally managed marine areas were surveyed, comprising a total of 11 stations, with 20 one-square-meter quadrats randomly deployed at each station during each sampling period. Average hard coral densities of 18.3 and 19.3 colonies m−2 were recorded during and after the event, respectively. Bleaching prevalence peaked during the event, affecting 38.8% of coral colonies, with a marked decrease to 6.0% afterward. However, coral mortality remained relatively low across the entire seascape, with a slight post-bleaching increase in dead colonies (+3.5%). Northern sites experienced the highest thermal stress, with Beheloke and Besambay reefs being the most susceptible to bleaching, whereas Ambola exhibited remarkable resilience. In the south, Ambohibola showed low vulnerability, Lembehitake moderate susceptibility, and Itampolo the highest bleaching prevalence despite lower thermal stress. Taxa-specific patterns were also evident, with thermally sensitive branching genera being most affected, contrasting with the relative tolerance of massive and encrusting corals. The heterogeneous coral bleaching patterns o…
bibliographic citation: Randrianarivo et al. (2025) Coral reefs in the Mahafaly Seascape (SW Madagascar) as potential climate refugia following the 2024 mass bleaching event. PeerJ 13:e20319 https://doi.org/10.7717/peerj.20319
date submitted: 2025-03-18
date accepted: 2025-10-09
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Randrianarivo
  given name: Mahery
author list: Agent
  family name: Rakotomanga
  given name: Solotahiana
author list: Agent
  family name: Razafindramasy
  given name: Fanja
author list: Agent
  family name: Ravelojaona
  given name: Danny Kornelio
author list: Agent
  family name: Ranaivoson
  given name: Tahiry
author list: Agent
  family name: Rakotomalala
  given name: Domoina
author list: Agent
  family name: Ratsimbazafy
  given name: Rémi
doi: 10.7717/peerj.20319
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Randrianarivo et al.
attribution name: Randrianarivo et al.

Feasibility of a pulsed multiphase contrast media injection protocol in head and neck computed tomography angiography: a systematic retrospective study
type: item
type: AcademicArticle
description: Background This study aimed to evaluate the efficacy and value of a pulsed multiphase contrast media injection protocol in head and neck computed tomographic angiography (CTA). Information and Methodology A total of 522 patients who underwent head and neck CTA at the Second Hospital of Qiqihar Medical University between March 1, 2022, and March 31, 2024, were reviewed. After excluding 174 patients, 348 were included in the analysis. All scans were performed using a GE Revolution computed tomography (CT) scanner (256-row detector). In the conventional group (n = 179), patients received 60 mL of contrast agent followed by 40 mL of saline. In the pulse group (n = 169), patients received an initial 35 mL of contrast agent, followed by alternating injections of five mL contrast agent and five mL saline across four additional stages, and concluded with 40 mL of saline. Images were post-processed using a GE workstation with curved planar reformation (CPR), maximum intensity projection (MIP), and volume rendering (VR). CT values, contrast-to-noise ratio (CNR), and signal-to-noise ratio (SNR) were measured for target arteries and veins. Subjective image quality was assessed using a five-point scale. Results There were no significant differences in CT values, CNR, or SNR between the conventional and pulse groups. However, the pulse group showed significantly lower CT values in the subclavian vein (SCV) and superior vena cava (SVC) compared to the conventional group (P < 0.001). Both groups achieved image quality scores of three or higher, but a statistically significant difference in subjective image quality was observed (P < 0.001). Inter-rater agreement was moderate in the conventional group (Kappa = 0.573) and substantial in the pulse group (Kappa = 0.684). Radiation dose analysis revealed a significant reduction in the pulse group (P < 0.001), with mean dose-length product (DLP) and effective dose (ED) reduced by 67.58 mGy cm and 0.16 mSv, respectively. Conclusion The pul…
format: application/pdf
format: text/html
creator: Xinghao Yang
creator: Zheng Li
creator: Junyao Cai
creator: Lei Wu
creator: Jingyue Zhang
creator: Yihong Wu
creator: Hua Yao
creator: Shengkun Yuan
creator: Yantong Tao
creator: Kunrong Yu
creator: Shufeng Zhu
creator: Yuan Fang
creator: Dongxu Wang
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.20216
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: Background This study aimed to evaluate the efficacy and value of a pulsed multiphase contrast media injection protocol in head and neck computed tomographic angiography (CTA). Information and Methodology A total of 522 patients who underwent head and neck CTA at the Second Hospital of Qiqihar Medical University between March 1, 2022, and March 31, 2024, were reviewed. After excluding 174 patients, 348 were included in the analysis. All scans were performed using a GE Revolution computed tomography (CT) scanner (256-row detector). In the conventional group (n = 179), patients received 60 mL of contrast agent followed by 40 mL of saline. In the pulse group (n = 169), patients received an initial 35 mL of contrast agent, followed by alternating injections of five mL contrast agent and five mL saline across four additional stages, and concluded with 40 mL of saline. Images were post-processed using a GE workstation with curved planar reformation (CPR), maximum intensity projection (MIP), and volume rendering (VR). CT values, contrast-to-noise ratio (CNR), and signal-to-noise ratio (SNR) were measured for target arteries and veins. Subjective image quality was assessed using a five-point scale. Results There were no significant differences in CT values, CNR, or SNR between the conventional and pulse groups. However, the pulse group showed significantly lower CT values in the subclavian vein (SCV) and superior vena cava (SVC) compared to the conventional group (P < 0.001). Both groups achieved image quality scores of three or higher, but a statistically significant difference in subjective image quality was observed (P < 0.001). Inter-rater agreement was moderate in the conventional group (Kappa = 0.573) and substantial in the pulse group (Kappa = 0.684). Radiation dose analysis revealed a significant reduction in the pulse group (P < 0.001), with mean dose-length product (DLP) and effective dose (ED) reduced by 67.58 mGy cm and 0.16 mSv, respectively. Conclusion The pul…
bibliographic citation: Yang et al. (2025) Feasibility of a pulsed multiphase contrast media injection protocol in head and neck computed tomography angiography: a systematic retrospective study. PeerJ 13:e20216 https://doi.org/10.7717/peerj.20216
date submitted: 2025-05-01
date accepted: 2025-09-19
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Xinghao
author list: Agent
  family name: Li
  given name: Zheng
author list: Agent
  family name: Cai
  given name: Junyao
author list: Agent
  family name: Wu
  given name: Lei
author list: Agent
  family name: Zhang
  given name: Jingyue
author list: Agent
  family name: Wu
  given name: Yihong
author list: Agent
  family name: Yao
  given name: Hua
author list: Agent
  family name: Yuan
  given name: Shengkun
author list: Agent
  family name: Tao
  given name: Yantong
author list: Agent
  family name: Yu
  given name: Kunrong
author list: Agent
  family name: Zhu
  given name: Shufeng
author list: Agent
  family name: Fang
  given name: Yuan
author list: Agent
  family name: Wang
  given name: Dongxu
doi: 10.7717/peerj.20216
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Yang et al.
attribution name: Yang et al.

Microgreens: nutritional properties, health benefits, production techniques, and food safety risks
type: item
type: AcademicArticle
description: “Microgreens” is a hypothetical name given to a new class of edible plants that have become popular in recent years. Microgreens are plants that are larger than sprouts and smaller than baby greens, with an average height of 2–8 cm. They have some advantages, such as the microgreens are better than mature greens in terms of vitamins, minerals, antioxidants and phenolic compounds and the dense and digestible nutrient profile they contain. Microgreens appeal to vegan and vegetarian individuals and simple cultivation in a home environment. Industrial cultivation techniques are being developed under different environmental conditions to ensure that microgreens have a superior nutritional profile. Also, the current health benefits of microgreens are noteworthy. On the other hand, they may pose some food safety risks, especially due to cross-contamination which has created the need to establish suitable decontamination methods for microgreens. Microgreens have become a great topic of interest in the last 10 years, and studies in areas such as nutritional properties and health benefits, production techniques and food safety risks are increasing in the existing literature. This creates the need to bring together existing knowledge about microgreens. Therefore, the aim of this study is to conduct a very detailed literature review about microgreens.
format: application/pdf
format: text/html
creator: Seyda Kaya
creator: Hülya Yardımcı
subject: Food Science and Technology
subject: Global Health
subject: Nutrition
subject: Public Health
subject: Obesity
description: doi:10.7717/peerj.17938
publisher: PeerJ Inc.
rights: © 2025 Kaya and Yardımcı
abstract: “Microgreens” is a hypothetical name given to a new class of edible plants that have become popular in recent years. Microgreens are plants that are larger than sprouts and smaller than baby greens, with an average height of 2–8 cm. They have some advantages, such as the microgreens are better than mature greens in terms of vitamins, minerals, antioxidants and phenolic compounds and the dense and digestible nutrient profile they contain. Microgreens appeal to vegan and vegetarian individuals and simple cultivation in a home environment. Industrial cultivation techniques are being developed under different environmental conditions to ensure that microgreens have a superior nutritional profile. Also, the current health benefits of microgreens are noteworthy. On the other hand, they may pose some food safety risks, especially due to cross-contamination which has created the need to establish suitable decontamination methods for microgreens. Microgreens have become a great topic of interest in the last 10 years, and studies in areas such as nutritional properties and health benefits, production techniques and food safety risks are increasing in the existing literature. This creates the need to bring together existing knowledge about microgreens. Therefore, the aim of this study is to conduct a very detailed literature review about microgreens.
bibliographic citation: Kaya et al. (2025) Microgreens: nutritional properties, health benefits, production techniques, and food safety risks. PeerJ 13:e17938 https://doi.org/10.7717/peerj.17938
date submitted: 2023-08-25
date accepted: 2025-10-27
issued: 2025-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaya
  given name: Seyda
author list: Agent
  family name: Yardımcı
  given name: Hülya
doi: 10.7717/peerj.17938
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-25
copyright: ©2025 Kaya and Yardımcı
attribution name: Kaya and Yardımcı

Elemental pollution and risk assessment of soils and Gundelia tournefortii in a multi-sector industrial zone with a history of agricultural use
type: item
type: AcademicArticle
description: The study provides new insights into elemental enrichments in soil and Gundelia tournefortii (GT) parts in a complex land use region where intensive agricultural activities were carried out in the past and 343 industrial facilities from various sectors have been operating for the last 32 years. The levels of crustal elements (aluminum (Al), iron (Fe), potassium (K), sodium (Na), titanium (T)), heavy metals (cadmium (Cd), chromium (Cr), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), zinc (Zn)), sulfer (S) and phosphorus (P) were determined in the sample matrices, their possible sources and the health risks associated with their human consumption were investigated. Significant enrichments in Cr, Ni, Pb, and Zn were observed in the soils, with the exceptionally high Pb enrichment (EF: 81.34) being noteworthy. The soil pollution index values (PI:2.06–6.82) confirm significant anthropogenic contamination. Bioconcentration factors (BCF) for Cu, K, Na, Mg, P and S were found to be >1 in all roots and stems, Zn showed high accumulation in all roots and most stems, while Cd, Cr, Pb and Mn accumulated in a more limited number of samples. Principal component analysis (PCA) showed that the elements found in the geochemical composition of the region and those representing agricultural chemicals used throughout the long agricultural history overlap and form clusters that cannot be fully separated, while the analysis of the datasets from GT parts yielded similar results. However, the effects of industrial emissions and solid fuel use were clearly evident in the GT root and stem samples. High Nemerow Compound Pollution Index values (NCPIs) indicated contamination in plant parts. Estimated daily intake (EDI) values for Cu and Mn exceeded the tolerable upper intake level (TUIL) for children in many root and stem samples, while EDI values for Cr, Fe, and Zn also exceeded the limit value in several samples. Risk assessments for non-carcinogenic effects showed that numerous sample…
format: application/pdf
format: text/html
creator: Ayşenur Özuysal
creator: Fariborz Fadaeivash
creator: Görkem Akıncı
subject: Plant Science
subject: Soil Science
subject: Public Health
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.20374
publisher: PeerJ Inc.
rights: © 2025 Özuysal et al.
abstract: The study provides new insights into elemental enrichments in soil and Gundelia tournefortii (GT) parts in a complex land use region where intensive agricultural activities were carried out in the past and 343 industrial facilities from various sectors have been operating for the last 32 years. The levels of crustal elements (aluminum (Al), iron (Fe), potassium (K), sodium (Na), titanium (T)), heavy metals (cadmium (Cd), chromium (Cr), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), zinc (Zn)), sulfer (S) and phosphorus (P) were determined in the sample matrices, their possible sources and the health risks associated with their human consumption were investigated. Significant enrichments in Cr, Ni, Pb, and Zn were observed in the soils, with the exceptionally high Pb enrichment (EF: 81.34) being noteworthy. The soil pollution index values (PI:2.06–6.82) confirm significant anthropogenic contamination. Bioconcentration factors (BCF) for Cu, K, Na, Mg, P and S were found to be >1 in all roots and stems, Zn showed high accumulation in all roots and most stems, while Cd, Cr, Pb and Mn accumulated in a more limited number of samples. Principal component analysis (PCA) showed that the elements found in the geochemical composition of the region and those representing agricultural chemicals used throughout the long agricultural history overlap and form clusters that cannot be fully separated, while the analysis of the datasets from GT parts yielded similar results. However, the effects of industrial emissions and solid fuel use were clearly evident in the GT root and stem samples. High Nemerow Compound Pollution Index values (NCPIs) indicated contamination in plant parts. Estimated daily intake (EDI) values for Cu and Mn exceeded the tolerable upper intake level (TUIL) for children in many root and stem samples, while EDI values for Cr, Fe, and Zn also exceeded the limit value in several samples. Risk assessments for non-carcinogenic effects showed that numerous sample…
bibliographic citation: Özuysal et al. (2025) Elemental pollution and risk assessment of soils and Gundelia tournefortii in a multi-sector industrial zone with a history of agricultural use. PeerJ 13:e20374 https://doi.org/10.7717/peerj.20374
date submitted: 2024-12-20
date accepted: 2025-10-20
issued: 2025-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Özuysal
  given name: Ayşenur
author list: Agent
  family name: Fadaeivash
  given name: Fariborz
author list: Agent
  family name: Akıncı
  given name: Görkem
doi: 10.7717/peerj.20374
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-24
copyright: ©2025 Özuysal et al.
attribution name: Özuysal et al.

Bioinformatics-based identification of RAS disequilibrium involved in post-hemorrhagic shock mesenteric lymph return-mediated acute kidney injury in mice
type: item
type: AcademicArticle
description: Post-hemorrhagic shock mesenteric lymph (PHSML) return plays a critical role in the development of acute kidney injury (AKI). However, the molecular mechanism underlying PHSML-mediated AKI remains unclear. In this study, bioinformatics analysis identified key common targets of hemorrhagic shock and AKI, revealing significant enrichment in the renin-angiotensin system (RAS). To further investigate the role of RAS in PHSML-mediated AKI, we established mesenteric lymph duct ligation (MLDL) technology in mice and confirmed that MLDL alleviated hemorrhagic shock-induced AKI. Subsequently, male C57BL/6 mice subjected to hemorrhagic shock were treated with the angiotensin converting enzyme (ACE) inhibitor enalapril, angiotensin (1-7) (Ang (1-7)), and angiotensin II (Ang II) type 1 receptor (AT1R) inhibitor losartan. Additionally, mice with hemorrhage and MLDL were treated with Ang II, the Mas receptor (MasR) inhibitor A-779, or subjected to Ace2 knockout. Renal histomorphology, expression of ACE, ACE2, AT1R, and MasR, and levels of Ang II and Ang (1-7) were assessed 4 h after resuscitation. The results demonstrated that hemorrhagic shock upregulated ACE and AT1R, while downregulating ACE2 and MasR, accompanied by elevated Ang II and reduced Ang (1-7). These adverse effects were partially reversed by MLDL, enalapril, Ang-(1-7), or losartan. Conversely, the beneficial role of MLDL was abolished by Ace2 deficiency and the administration of Ang II and A-779. Collectively, these findings indicate that disequilibrium between the ACE-AngII-AT1R and ACE2-Ang (1-7)-MasR axes is implicated in PHSML-mediated AKI.
format: application/pdf
format: text/html
creator: Yujie Jin
creator: Jing Wang
creator: Shaoxuan Wang
creator: Yuting Li
creator: Kun Su
creator: Niuniu Feng
creator: Huibo Du
creator: Limin Zhang
creator: Xiuhong Yang
creator: Chun-Yu Niu
creator: Zi-Gang Zhao
subject: Biochemistry
subject: Nephrology
subject: Urology
subject: Histology
description: doi:10.7717/peerj.20359
publisher: PeerJ Inc.
rights: © 2025 Jin et al.
abstract: Post-hemorrhagic shock mesenteric lymph (PHSML) return plays a critical role in the development of acute kidney injury (AKI). However, the molecular mechanism underlying PHSML-mediated AKI remains unclear. In this study, bioinformatics analysis identified key common targets of hemorrhagic shock and AKI, revealing significant enrichment in the renin-angiotensin system (RAS). To further investigate the role of RAS in PHSML-mediated AKI, we established mesenteric lymph duct ligation (MLDL) technology in mice and confirmed that MLDL alleviated hemorrhagic shock-induced AKI. Subsequently, male C57BL/6 mice subjected to hemorrhagic shock were treated with the angiotensin converting enzyme (ACE) inhibitor enalapril, angiotensin (1-7) (Ang (1-7)), and angiotensin II (Ang II) type 1 receptor (AT1R) inhibitor losartan. Additionally, mice with hemorrhage and MLDL were treated with Ang II, the Mas receptor (MasR) inhibitor A-779, or subjected to Ace2 knockout. Renal histomorphology, expression of ACE, ACE2, AT1R, and MasR, and levels of Ang II and Ang (1-7) were assessed 4 h after resuscitation. The results demonstrated that hemorrhagic shock upregulated ACE and AT1R, while downregulating ACE2 and MasR, accompanied by elevated Ang II and reduced Ang (1-7). These adverse effects were partially reversed by MLDL, enalapril, Ang-(1-7), or losartan. Conversely, the beneficial role of MLDL was abolished by Ace2 deficiency and the administration of Ang II and A-779. Collectively, these findings indicate that disequilibrium between the ACE-AngII-AT1R and ACE2-Ang (1-7)-MasR axes is implicated in PHSML-mediated AKI.
bibliographic citation: Jin et al. (2025) Bioinformatics-based identification of RAS disequilibrium involved in post-hemorrhagic shock mesenteric lymph return-mediated acute kidney injury in mice. PeerJ 13:e20359 https://doi.org/10.7717/peerj.20359
date submitted: 2025-03-12
date accepted: 2025-10-16
issued: 2025-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Jin
  given name: Yujie
author list: Agent
  family name: Wang
  given name: Jing
author list: Agent
  family name: Wang
  given name: Shaoxuan
author list: Agent
  family name: Li
  given name: Yuting
author list: Agent
  family name: Su
  given name: Kun
author list: Agent
  family name: Feng
  given name: Niuniu
author list: Agent
  family name: Du
  given name: Huibo
author list: Agent
  family name: Zhang
  given name: Limin
author list: Agent
  family name: Yang
  given name: Xiuhong
author list: Agent
  family name: Niu
  given name: Chun-Yu
author list: Agent
  family name: Zhao
  given name: Zi-Gang
doi: 10.7717/peerj.20359
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-24
copyright: ©2025 Jin et al.
attribution name: Jin et al.

Interaction of soil pH, organic matter, exchangeable acidity, and cation exchange capacity in a managed tea farm
type: item
type: AcademicArticle
description: Background The Yangai tea farm was established in 1952, with a long history of cultivating tea plants. The tea plant can activate Al3+ of the soil and affect soil physicochemical properties. Understanding soil physicochemical properties is crucial for studying soil fertility, nutrient retention, and long-term agricultural sustainability. Therefore, we investigated the distribution characteristics of soil pH, exchangeable acid, soil organic matter (SOM), and cation exchange capacity (CEC) in the surface soil and soil profile to assess their interaction in the managed tea garden. Methods We collected surface soil and soil profile samples from the managed tea garden and three land-use types (i.e., managed tea garden, unmanaged tea garden, and Pinus massoniana forest), respectively. We measure soil pH value with a laboratory pH meter. We measured the SOM, soil exchangeable acid, and CEC content, respectively, with potassium dichromate heating, potassium chloride leaching, and spectrophotometric methods. Results The average soil pH value, exchangeable Al3+ content, and exchangeable H+ content were 4.50 (ranging from 3.95 to 5.88), 6.11 (0.04 to 9.32) cmol kg−1, and 0.30 (0.03 to 0.62) cmol kg−1, respectively. The surface soil acidification is severe, and the exchangeable acids in the tea garden were mainly exchangeable Al3+. The surface soil of the Yangai tea farm had a high ability to keep and supply fertilizer due to its enriching SOM content (average 55.94g kg−1) and soil CEC (24.06 cmol(+) kg−1). Surface soil exchangeable acid and CEC contents were higher after spring tea picking than before spring tea picking in the Yangai tea farm, while their SOM content was just the opposite. Therefore, it was recommended to supplement organic fertilizers after tea-picking because the surface SOM of the Yangai tea farm would decompose and be consumed more during the spring, summer, and autumn tea-picking periods than in winter. In addition, the SOM contents and soil pH values dec…
format: application/pdf
format: text/html
creator: Haijie Song
creator: Jing Shi
creator: Rou Wang
creator: Tao Jin
creator: Yishu Peng
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20341
publisher: PeerJ Inc.
rights: © 2025 Song et al.
abstract: Background The Yangai tea farm was established in 1952, with a long history of cultivating tea plants. The tea plant can activate Al3+ of the soil and affect soil physicochemical properties. Understanding soil physicochemical properties is crucial for studying soil fertility, nutrient retention, and long-term agricultural sustainability. Therefore, we investigated the distribution characteristics of soil pH, exchangeable acid, soil organic matter (SOM), and cation exchange capacity (CEC) in the surface soil and soil profile to assess their interaction in the managed tea garden. Methods We collected surface soil and soil profile samples from the managed tea garden and three land-use types (i.e., managed tea garden, unmanaged tea garden, and Pinus massoniana forest), respectively. We measure soil pH value with a laboratory pH meter. We measured the SOM, soil exchangeable acid, and CEC content, respectively, with potassium dichromate heating, potassium chloride leaching, and spectrophotometric methods. Results The average soil pH value, exchangeable Al3+ content, and exchangeable H+ content were 4.50 (ranging from 3.95 to 5.88), 6.11 (0.04 to 9.32) cmol kg−1, and 0.30 (0.03 to 0.62) cmol kg−1, respectively. The surface soil acidification is severe, and the exchangeable acids in the tea garden were mainly exchangeable Al3+. The surface soil of the Yangai tea farm had a high ability to keep and supply fertilizer due to its enriching SOM content (average 55.94g kg−1) and soil CEC (24.06 cmol(+) kg−1). Surface soil exchangeable acid and CEC contents were higher after spring tea picking than before spring tea picking in the Yangai tea farm, while their SOM content was just the opposite. Therefore, it was recommended to supplement organic fertilizers after tea-picking because the surface SOM of the Yangai tea farm would decompose and be consumed more during the spring, summer, and autumn tea-picking periods than in winter. In addition, the SOM contents and soil pH values dec…
bibliographic citation: Song et al. (2025) Interaction of soil pH, organic matter, exchangeable acidity, and cation exchange capacity in a managed tea farm. PeerJ 13:e20341 https://doi.org/10.7717/peerj.20341
date submitted: 2024-12-20
date accepted: 2025-10-14
issued: 2025-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Haijie
author list: Agent
  family name: Shi
  given name: Jing
author list: Agent
  family name: Wang
  given name: Rou
author list: Agent
  family name: Jin
  given name: Tao
author list: Agent
  family name: Peng
  given name: Yishu
doi: 10.7717/peerj.20341
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-24
copyright: ©2025 Song et al.
attribution name: Song et al.

Positive rates of total and specific immunoglobulin E in 7,824 adult patients with suspected allergic diseases in Liaoning Province, China: a retrospective study
type: item
type: AcademicArticle
description: Background The escalating prevalence of allergic diseases poses a significant global health challenge. However, estimates of allergic disease prevalence in Liaoning Province, China, remain lacking. This study aimed to investigate total immunoglobulin E (tIgE) and specific immunoglobulin E (sIgE) levels in 7,824 patients with suspected allergic diseases and to identify factors associated with allergic conditions. Methods A total of 7,824 participants (3,180 males and 4,644 females) with a mean age of 53.63 years were included. tIgE and sIgE levels were measured using standard laboratory methods. The normal reference range for tIgE was stratified by age group, and sIgE results were categorized as positive or negative based on predefined thresholds. Statistical analysis was performed using SPSS 26.0. Results The overall tIgE positivity rate was 39.26%, with males showing a significantly higher rate (46.67%) than females (34.19%) (χ2 = 123.118, p < 0.001). The highest tIgE positivity was observed in the 18–44 age group (44.11%) and during the summer season (43.95%). No significant differences were found in sIgE positivity rates for inhaled and food allergens between sexes or seasons. Conclusions Male sex, younger and older age groups, and the summer season were identified as significant predictors of allergic diseases based on tIgE levels. These findings underscore the importance of sex and seasonal variations in allergic disease prevalence and highlight the need for targeted prevention and management strategies.
format: application/pdf
format: text/html
creator: Zan Sun
creator: Long Shao
creator: Peng Cao
creator: Hanqi Zhang
creator: Meng Chen
creator: Jingfang Wang
creator: Lin Zhou
subject: Biochemistry
subject: Allergy and Clinical Immunology
subject: Immunology
subject: Public Health
description: doi:10.7717/peerj.20394
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Background The escalating prevalence of allergic diseases poses a significant global health challenge. However, estimates of allergic disease prevalence in Liaoning Province, China, remain lacking. This study aimed to investigate total immunoglobulin E (tIgE) and specific immunoglobulin E (sIgE) levels in 7,824 patients with suspected allergic diseases and to identify factors associated with allergic conditions. Methods A total of 7,824 participants (3,180 males and 4,644 females) with a mean age of 53.63 years were included. tIgE and sIgE levels were measured using standard laboratory methods. The normal reference range for tIgE was stratified by age group, and sIgE results were categorized as positive or negative based on predefined thresholds. Statistical analysis was performed using SPSS 26.0. Results The overall tIgE positivity rate was 39.26%, with males showing a significantly higher rate (46.67%) than females (34.19%) (χ2 = 123.118, p < 0.001). The highest tIgE positivity was observed in the 18–44 age group (44.11%) and during the summer season (43.95%). No significant differences were found in sIgE positivity rates for inhaled and food allergens between sexes or seasons. Conclusions Male sex, younger and older age groups, and the summer season were identified as significant predictors of allergic diseases based on tIgE levels. These findings underscore the importance of sex and seasonal variations in allergic disease prevalence and highlight the need for targeted prevention and management strategies.
bibliographic citation: Sun et al. (2025) Positive rates of total and specific immunoglobulin E in 7,824 adult patients with suspected allergic diseases in Liaoning Province, China: a retrospective study. PeerJ 13:e20394 https://doi.org/10.7717/peerj.20394
date submitted: 2025-04-18
date accepted: 2025-10-24
issued: 2025-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Zan
author list: Agent
  family name: Shao
  given name: Long
author list: Agent
  family name: Cao
  given name: Peng
author list: Agent
  family name: Zhang
  given name: Hanqi
author list: Agent
  family name: Chen
  given name: Meng
author list: Agent
  family name: Wang
  given name: Jingfang
author list: Agent
  family name: Zhou
  given name: Lin
doi: 10.7717/peerj.20394
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-21
copyright: ©2025 Sun et al.
attribution name: Sun et al.

Leaf-branch-root trait relationships in Quercus rehderiana across rocky and non-rocky desertification habitats in China
type: item
type: AcademicArticle
description: Background Plant leaves, branches, and roots synergistically govern survival, growth, and reproduction. However, while interspecific and community-level studies have advanced our understanding of organ coordination, intraspecific trait covariation remains poorly understood due to limited evidence. Methodology This study investigated 28 functional traits across leaves, branches, and roots of Quercus rehderiana, a dominant species in rocky and non-rocky desertification forests, to evaluate intraspecific organ relationships. The traits, covering morphological, anatomical, and physiological aspects, reflect resource acquisition and utilization strategies. Standardized protocols were followed, with three replicates per individual for reliability. Results Our results revealed no significant correlations among leaf, branch, and root traits in either forest type. Principal component analysis (PCA) of leaf traits indicated that the first axis was positively associated with water storage and utilization strategies, showing positive correlations with leaf thickness (LT), palisade mesophyll thickness (PT), and spongy mesophyll thickness (ST). The second axis exhibited a positive relationship with leaf nitrogen concentration (LNC) and leaf phosphorus concentration (LPC). For branch traits, the first axis reflected water transport efficiency, demonstrating positive associations with theoretical hydraulic conductivity (Kt) and vessel density (VD). The second axis was positively correlated with branch N concentration (BNC) and branch phosphorus concentration (BPC). In root traits, the first axis aligned with root defense traits (positive correlation) but was inversely related to resource acquisition efficiency. The second axis showed a positive correlation with root N concentration (RNC) and root phosphorus concentration (RPC). Conclusions Organ-specific trait decoupling in Quercus rehderiana reveals independent above- and belowground adaptations to water and nutrient limitations, …
format: application/pdf
format: text/html
creator: Xiaolong Bai
creator: Shun Zou
creator: Tu Feng
creator: Dongpeng Lv
creator: Bin He
creator: Wangjun Li
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.20367
publisher: PeerJ Inc.
rights: © 2025 Bai et al.
abstract: Background Plant leaves, branches, and roots synergistically govern survival, growth, and reproduction. However, while interspecific and community-level studies have advanced our understanding of organ coordination, intraspecific trait covariation remains poorly understood due to limited evidence. Methodology This study investigated 28 functional traits across leaves, branches, and roots of Quercus rehderiana, a dominant species in rocky and non-rocky desertification forests, to evaluate intraspecific organ relationships. The traits, covering morphological, anatomical, and physiological aspects, reflect resource acquisition and utilization strategies. Standardized protocols were followed, with three replicates per individual for reliability. Results Our results revealed no significant correlations among leaf, branch, and root traits in either forest type. Principal component analysis (PCA) of leaf traits indicated that the first axis was positively associated with water storage and utilization strategies, showing positive correlations with leaf thickness (LT), palisade mesophyll thickness (PT), and spongy mesophyll thickness (ST). The second axis exhibited a positive relationship with leaf nitrogen concentration (LNC) and leaf phosphorus concentration (LPC). For branch traits, the first axis reflected water transport efficiency, demonstrating positive associations with theoretical hydraulic conductivity (Kt) and vessel density (VD). The second axis was positively correlated with branch N concentration (BNC) and branch phosphorus concentration (BPC). In root traits, the first axis aligned with root defense traits (positive correlation) but was inversely related to resource acquisition efficiency. The second axis showed a positive correlation with root N concentration (RNC) and root phosphorus concentration (RPC). Conclusions Organ-specific trait decoupling in Quercus rehderiana reveals independent above- and belowground adaptations to water and nutrient limitations, …
bibliographic citation: Bai et al. (2025) Leaf-branch-root trait relationships in Quercus rehderiana across rocky and non-rocky desertification habitats in China. PeerJ 13:e20367 https://doi.org/10.7717/peerj.20367
date submitted: 2025-04-05
date accepted: 2025-10-18
issued: 2025-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Xiaolong
author list: Agent
  family name: Zou
  given name: Shun
author list: Agent
  family name: Feng
  given name: Tu
author list: Agent
  family name: Lv
  given name: Dongpeng
author list: Agent
  family name: He
  given name: Bin
author list: Agent
  family name: Li
  given name: Wangjun
doi: 10.7717/peerj.20367
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-21
copyright: ©2025 Bai et al.
attribution name: Bai et al.

Patients with lower BMI are more likely to experience shoulder pain after single port laparoscopic myomectomy
type: item
type: AcademicArticle
description: Objective The aim of this study is to evaluate the incidence of shoulder pain after single port transumbilical laparoscopic myomectomy and analyze patient and operative specific factors associated with post-laparoscopy shoulder pain (PLSP). This information can inform preoperative risk assessment and intervention. Method This is a prospective cohort study. Two hundred and twenty patients undergoing elected single-port laparoscopic myomectomy under general anaesthesia were divided into two groups according to whether they had shoulder pain after surgery. Patient demographic data and duration of surgery, intraoperative blood loss volume, intraoperative carbon dioxide (CO2) usage volume, the usage of an abdominal drainage tube or not, the usage of patient-controlled intravenous analgesia (PCIA) or not were recorded. Statistical analyses were performed using SPSS. Data were compared using Student’s t-test or chi-square test. Risk factors were analyzed using logistic regression. Results The incidence of shoulder pain was 43.18%. The body mass index (BMI) of the shoulder pain group was significantly lower than that of the non-shoulder pain group (OR = 0.629, p < 0.05). Patients with BMI < 21.64 are more likely to experience postoperative shoulder pain. The use rate of abdominal drainage tubes was higher in the non-shoulder pain group (OR = 0.509, p < 0.05). Conclusion PLSP is more likely to occur in patients with lower BMI (<21.64), and placing an abdominal drainage tube can reduce the occurrence of shoulder pain.
format: application/pdf
format: text/html
creator: Xiubin Chen
creator: Min Guo
creator: Zheng Pei
subject: Anesthesiology and Pain Management
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.20362
publisher: PeerJ Inc.
rights: © 2025 Chen et al.
abstract: Objective The aim of this study is to evaluate the incidence of shoulder pain after single port transumbilical laparoscopic myomectomy and analyze patient and operative specific factors associated with post-laparoscopy shoulder pain (PLSP). This information can inform preoperative risk assessment and intervention. Method This is a prospective cohort study. Two hundred and twenty patients undergoing elected single-port laparoscopic myomectomy under general anaesthesia were divided into two groups according to whether they had shoulder pain after surgery. Patient demographic data and duration of surgery, intraoperative blood loss volume, intraoperative carbon dioxide (CO2) usage volume, the usage of an abdominal drainage tube or not, the usage of patient-controlled intravenous analgesia (PCIA) or not were recorded. Statistical analyses were performed using SPSS. Data were compared using Student’s t-test or chi-square test. Risk factors were analyzed using logistic regression. Results The incidence of shoulder pain was 43.18%. The body mass index (BMI) of the shoulder pain group was significantly lower than that of the non-shoulder pain group (OR = 0.629, p < 0.05). Patients with BMI < 21.64 are more likely to experience postoperative shoulder pain. The use rate of abdominal drainage tubes was higher in the non-shoulder pain group (OR = 0.509, p < 0.05). Conclusion PLSP is more likely to occur in patients with lower BMI (<21.64), and placing an abdominal drainage tube can reduce the occurrence of shoulder pain.
bibliographic citation: Chen et al. (2025) Patients with lower BMI are more likely to experience shoulder pain after single port laparoscopic myomectomy. PeerJ 13:e20362 https://doi.org/10.7717/peerj.20362
date submitted: 2025-05-08
date accepted: 2025-10-17
issued: 2025-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xiubin
author list: Agent
  family name: Guo
  given name: Min
author list: Agent
  family name: Pei
  given name: Zheng
doi: 10.7717/peerj.20362
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-21
copyright: ©2025 Chen et al.
attribution name: Chen et al.

Effects of virtual reality intervention dosage on gait performance in Parkinson’s disease: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective Gait impairment is a prevalent and disabling feature of Parkinson’s disease (PD) that is often insufficiently improved by conventional rehabilitation approaches. Virtual reality (VR)-based training has emerged as a novel therapeutic strategy; however, the overall efficacy of VR interventions on gait outcomes in PD remains inconclusive. This systematic review and meta-analysis aimed to (1) quantify the effects of VR-based rehabilitation on gait performance in individuals with PD, and (2) investigate whether treatment outcomes are moderated by intervention dosage parameters-such as training frequency, session duration, and total intervention period-as well as patient-related factors like disease duration and age. Methods Seven databases (Embase, Web of Science, PubMed, Cochrane Library, Wanfang Data, VIP, and CNKI) were searched from inception to December 2024. Randomized controlled trials (RCTs) investigating VR training for gait in PD were independently screened by two reviewers. Study quality was assessed using the PEDro scale. Meta-analyses were conducted with RevMan 5.4.1, and publication bias was examined using Stata 17.0. Effect sizes were calculated using standardized mean differences with 95% confidence intervals. The certainty of evidence was graded using the GRADE approach. Results A total of 13 RCTs, involving 541 patients with Parkinson’s disease, met the inclusion criteria. VR-based interventions demonstrated significant effects in improving composite gait function (SMD = 0.56; 95% CI [0.36–0.77]; P < 0.00001), indicating a moderate and clinically meaningful benefit. Gait function was evaluated using a range of clinical scales and spatiotemporal parameters, encompassing multiple dimensions such as dynamic stability, walking efficiency, and functional mobility. Subgroup analyses revealed greater improvements among patients with disease duration ≤8 years (SMD = 0.65), shorter intervention periods (≤4 weeks, SMD = 0.86), and shorter session durati…
format: application/pdf
format: text/html
creator: Shanan Yu
creator: Yu Zhu
creator: Yanfei Yang
subject: Evidence Based Medicine
subject: Geriatrics
subject: Global Health
description: doi:10.7717/peerj.20320
publisher: PeerJ Inc.
rights: © 2025 Yu et al.
abstract: Objective Gait impairment is a prevalent and disabling feature of Parkinson’s disease (PD) that is often insufficiently improved by conventional rehabilitation approaches. Virtual reality (VR)-based training has emerged as a novel therapeutic strategy; however, the overall efficacy of VR interventions on gait outcomes in PD remains inconclusive. This systematic review and meta-analysis aimed to (1) quantify the effects of VR-based rehabilitation on gait performance in individuals with PD, and (2) investigate whether treatment outcomes are moderated by intervention dosage parameters-such as training frequency, session duration, and total intervention period-as well as patient-related factors like disease duration and age. Methods Seven databases (Embase, Web of Science, PubMed, Cochrane Library, Wanfang Data, VIP, and CNKI) were searched from inception to December 2024. Randomized controlled trials (RCTs) investigating VR training for gait in PD were independently screened by two reviewers. Study quality was assessed using the PEDro scale. Meta-analyses were conducted with RevMan 5.4.1, and publication bias was examined using Stata 17.0. Effect sizes were calculated using standardized mean differences with 95% confidence intervals. The certainty of evidence was graded using the GRADE approach. Results A total of 13 RCTs, involving 541 patients with Parkinson’s disease, met the inclusion criteria. VR-based interventions demonstrated significant effects in improving composite gait function (SMD = 0.56; 95% CI [0.36–0.77]; P < 0.00001), indicating a moderate and clinically meaningful benefit. Gait function was evaluated using a range of clinical scales and spatiotemporal parameters, encompassing multiple dimensions such as dynamic stability, walking efficiency, and functional mobility. Subgroup analyses revealed greater improvements among patients with disease duration ≤8 years (SMD = 0.65), shorter intervention periods (≤4 weeks, SMD = 0.86), and shorter session durati…
bibliographic citation: Yu et al. (2025) Effects of virtual reality intervention dosage on gait performance in Parkinson’s disease: a systematic review and meta-analysis. PeerJ 13:e20320 https://doi.org/10.7717/peerj.20320
date submitted: 2025-04-28
date accepted: 2025-10-10
issued: 2025-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Shanan
author list: Agent
  family name: Zhu
  given name: Yu
author list: Agent
  family name: Yang
  given name: Yanfei
doi: 10.7717/peerj.20320
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-21
copyright: ©2025 Yu et al.
attribution name: Yu et al.

Occurrence, composition, sources, and ecological-health risk assessment of polycyclic aromatic hydrocarbons in Chinese water bodies: a review
type: item
type: AcademicArticle
description: Polycyclic aromatic hydrocarbons (PAHs) pose significant threats to aquatic ecosystems globally. This study conducted a comprehensive literature search (2015–2025) across Web of Science, ScienceDirect, and China National Knowledge Infrastructure (CNKI) databases to evaluate PAH contamination in diverse water bodies in China. Through an analysis of data from 69 distinct study areas, we synthesized concentration distributions, compositional profiles, pollution sources, and associated ecological and health risks. The results revealed significant spatiotemporal variations in PAH contamination across Chinese water bodies, with mean concentrations ranging from 17.4 to 3,856.68 ng/L, and an arithmetic mean of 498.3 ng/L. Northern industrial regions, eastern estuarine and coastal areas exhibited the highest pollution levels, while western remote areas remained less contaminated. Rivers showed the highest mean PAH concentrations, followed by lakes/reservoirs, coastal waters, and estuaries. Low-molecular-weight (LMW) PAHs dominated, accounting for 74.5–82.2% of total PAHs, though high-molecular-weight (HMW) compounds were enriched in industrial zones and deltas. Source apportionment indicated mixed contributions from fossil fuel combustion, petroleum spills, and traffic emissions, with distinct seasonal patterns: coal heating dominated in winter, while runoff inputs were major contributors in summer. Ecological risk assessment indicated high risk was prevalent, with risk quotient (RQ) values greatly exceeding 1 in severely polluted areas such as river basins and estuaries. Health risk evaluation showed that incremental lifetime cancer risk (ILCR) values in certain areas reach ed 4.6 × 10−3, exceeding the acceptable level (10−6) by orders of magnitude. These findings provide a scientific basis for formulating targeted PAH control strategies to better protect aquatic ecosystems and public health in China.
format: application/pdf
format: text/html
creator: Qu Chen
creator: Tianwen Song
creator: Jingjing Kong
creator: Jingjing Zhang
creator: Lei Zhu
creator: Hailong Li
creator: Yizhe Wang
creator: Di Xiao
creator: Tingting Tang
creator: Haili Zhang
creator: Zichu Zhao
creator: Qingli Zhang
subject: Toxicology
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.20300
publisher: PeerJ Inc.
rights: © 2025 Chen et al.
abstract: Polycyclic aromatic hydrocarbons (PAHs) pose significant threats to aquatic ecosystems globally. This study conducted a comprehensive literature search (2015–2025) across Web of Science, ScienceDirect, and China National Knowledge Infrastructure (CNKI) databases to evaluate PAH contamination in diverse water bodies in China. Through an analysis of data from 69 distinct study areas, we synthesized concentration distributions, compositional profiles, pollution sources, and associated ecological and health risks. The results revealed significant spatiotemporal variations in PAH contamination across Chinese water bodies, with mean concentrations ranging from 17.4 to 3,856.68 ng/L, and an arithmetic mean of 498.3 ng/L. Northern industrial regions, eastern estuarine and coastal areas exhibited the highest pollution levels, while western remote areas remained less contaminated. Rivers showed the highest mean PAH concentrations, followed by lakes/reservoirs, coastal waters, and estuaries. Low-molecular-weight (LMW) PAHs dominated, accounting for 74.5–82.2% of total PAHs, though high-molecular-weight (HMW) compounds were enriched in industrial zones and deltas. Source apportionment indicated mixed contributions from fossil fuel combustion, petroleum spills, and traffic emissions, with distinct seasonal patterns: coal heating dominated in winter, while runoff inputs were major contributors in summer. Ecological risk assessment indicated high risk was prevalent, with risk quotient (RQ) values greatly exceeding 1 in severely polluted areas such as river basins and estuaries. Health risk evaluation showed that incremental lifetime cancer risk (ILCR) values in certain areas reach ed 4.6 × 10−3, exceeding the acceptable level (10−6) by orders of magnitude. These findings provide a scientific basis for formulating targeted PAH control strategies to better protect aquatic ecosystems and public health in China.
bibliographic citation: Chen et al. (2025) Occurrence, composition, sources, and ecological-health risk assessment of polycyclic aromatic hydrocarbons in Chinese water bodies: a review. PeerJ 13:e20300 https://doi.org/10.7717/peerj.20300
date submitted: 2025-06-05
date accepted: 2025-10-06
issued: 2025-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Qu
author list: Agent
  family name: Song
  given name: Tianwen
author list: Agent
  family name: Kong
  given name: Jingjing
author list: Agent
  family name: Zhang
  given name: Jingjing
author list: Agent
  family name: Zhu
  given name: Lei
author list: Agent
  family name: Li
  given name: Hailong
author list: Agent
  family name: Wang
  given name: Yizhe
author list: Agent
  family name: Xiao
  given name: Di
author list: Agent
  family name: Tang
  given name: Tingting
author list: Agent
  family name: Zhang
  given name: Haili
author list: Agent
  family name: Zhao
  given name: Zichu
author list: Agent
  family name: Zhang
  given name: Qingli
doi: 10.7717/peerj.20300
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-21
copyright: © 2025 Chen et al.
attribution name: Chen et al.

Carbon capture, photosynthesis, and leaf gas exchange of shade tree species and Arabica coffee varieties in coffee agroforestry systems in Veracruz state, Mexico
type: item
type: AcademicArticle
description: Agroforestry systems with native vegetation enhance climate adaptation and mitigation by improving coffee farm resilience, carbon storage, and income diversification. Seven native tree species were pre-selected as shade providers for Veracruz coffee agroforestry systems based on ecological, cultural, and economic criteria. The present study evaluated their physiological performance through above-ground biomass, carbon stocks, and in-situ chlorophyll fluorescence and gas exchange measurements under controlled light and temperature conditions. Five Coffea arabica varieties were also assessed under these shade canopies using the same leaf-level parameters, and leaf nitrogen and moisture content. Erythrina americana and Persea schiedeana had the highest carbon sequestration per tree. E. americana showed the highest water-use efficiency, whereas P. schiedeana showed the lowest transpiration and stomatal conductance, indicating a water-saving strategy via stomatal restriction. These traits reflect their ecological adaptations to shade and microclimate conditions in agroforestry systems. Inga inicuil achieved the highest carbon capture per hectare due to high tree density, despite lower individual performance. Species-specific strategies were identified: Psidium guajava and P. schiedeana exhibited high transpiration but limited carbon gain. E. americana and Inga punctata formed a drought-resilient group, having a high carbon assimilation and low water loss. Intermediate species (Heliocarpus appendiculatus, Inga vera, I. inicuil) balanced moderate CO2 assimilation rates with adaptable stomatal response. Photochemical efficiency remained stable across species. Shaded Coffea arabica var. Oro Azteca had significantly higher leaf nitrogen, moisture, and water-use efficiency than unshaded ones. These differences coincided with lower PAR under shade, aligning with known variations in shaded versus unshaded coffee plants. Principal component analysis showed that PC1 correlated str…
format: application/pdf
format: text/html
creator: Daniel Cabrera-Santos
creator: Patricia Dávila
creator: Isela Rodríguez-Arévalo
creator: Anabel Ruiz-Flores
creator: Josefina Vázquez-Medrano
creator: Salvador Sampayo-Maldonado
creator: Cesar Ordoñez-Salanueva
creator: Maraeva Gianella
creator: Elizabeth Bell
creator: María Toledo-Garibaldi
creator: Robert Manson
creator: Flor G. Vázquez-Corzas
creator: Jazmin Cobos-Silva
creator: Cesar Mateo Flores Ortiz
creator: Tiziana Ulian
subject: Agricultural Science
subject: Plant Science
subject: Climate Change Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.20255
publisher: PeerJ Inc.
rights: © 2025 Cabrera-Santos et al.
abstract: Agroforestry systems with native vegetation enhance climate adaptation and mitigation by improving coffee farm resilience, carbon storage, and income diversification. Seven native tree species were pre-selected as shade providers for Veracruz coffee agroforestry systems based on ecological, cultural, and economic criteria. The present study evaluated their physiological performance through above-ground biomass, carbon stocks, and in-situ chlorophyll fluorescence and gas exchange measurements under controlled light and temperature conditions. Five Coffea arabica varieties were also assessed under these shade canopies using the same leaf-level parameters, and leaf nitrogen and moisture content. Erythrina americana and Persea schiedeana had the highest carbon sequestration per tree. E. americana showed the highest water-use efficiency, whereas P. schiedeana showed the lowest transpiration and stomatal conductance, indicating a water-saving strategy via stomatal restriction. These traits reflect their ecological adaptations to shade and microclimate conditions in agroforestry systems. Inga inicuil achieved the highest carbon capture per hectare due to high tree density, despite lower individual performance. Species-specific strategies were identified: Psidium guajava and P. schiedeana exhibited high transpiration but limited carbon gain. E. americana and Inga punctata formed a drought-resilient group, having a high carbon assimilation and low water loss. Intermediate species (Heliocarpus appendiculatus, Inga vera, I. inicuil) balanced moderate CO2 assimilation rates with adaptable stomatal response. Photochemical efficiency remained stable across species. Shaded Coffea arabica var. Oro Azteca had significantly higher leaf nitrogen, moisture, and water-use efficiency than unshaded ones. These differences coincided with lower PAR under shade, aligning with known variations in shaded versus unshaded coffee plants. Principal component analysis showed that PC1 correlated str…
bibliographic citation: Cabrera-Santos et al. (2025) Carbon capture, photosynthesis, and leaf gas exchange of shade tree species and Arabica coffee varieties in coffee agroforestry systems in Veracruz state, Mexico. PeerJ 13:e20255 https://doi.org/10.7717/peerj.20255
date submitted: 2025-03-27
date accepted: 2025-09-26
issued: 2025-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Cabrera-Santos
  given name: Daniel
author list: Agent
  family name: Dávila
  given name: Patricia
author list: Agent
  family name: Rodríguez-Arévalo
  given name: Isela
author list: Agent
  family name: Ruiz-Flores
  given name: Anabel
author list: Agent
  family name: Vázquez-Medrano
  given name: Josefina
author list: Agent
  family name: Sampayo-Maldonado
  given name: Salvador
author list: Agent
  family name: Ordoñez-Salanueva
  given name: Cesar
author list: Agent
  family name: Gianella
  given name: Maraeva
author list: Agent
  family name: Bell
  given name: Elizabeth
author list: Agent
  family name: Toledo-Garibaldi
  given name: María
author list: Agent
  family name: Manson
  given name: Robert
author list: Agent
  family name: Vázquez-Corzas
  given name: Flor G.
author list: Agent
  family name: Cobos-Silva
  given name: Jazmin
author list: Agent
  family name: Flores Ortiz
  given name: Cesar Mateo
author list: Agent
  family name: Ulian
  given name: Tiziana
doi: 10.7717/peerj.20255
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-21
copyright: ©2025 Cabrera-Santos et al.
attribution name: Cabrera-Santos et al.

Utilization of soft pistachio hulls in Japanese quail diets for enhanced egg quality and yolk pigmentation
type: item
type: AcademicArticle
description: Background Japanese quail (Coturnix coturnix japonica) offer rapid growth, early maturity and excellent feed conversion, but feed cost accounts for ∼70% of production expenses. This study evaluated soft pistachio hull (PH), an abundant agro-industrial by-product, as a low-cost dietary ingredient in laying quails. Methods Ninety-six female quails, seven weeks old age, were randomly distributed to four dietary groups (24 birds each; three replicates of eight birds). The treatment diets were based on a standard layer feed, with graded PH inclusion of 0%, 2%, 4%, and 6%, administered over a for five-week period. Parameters measured included live weight, feed intake, egg production rate, egg weight, feed conversion ratio, and a range of egg quality indicators, such as shape index, shell thickness, Haugh unit, albumen and yolk indices, and yolk color score, assessed at weeks 7 and 11. Results Final live weight followed a cubic trend (P = 0.05), with the 2% and 6% PH groups (356.5 g and 350.6 g, respectively) exceeding the control (333.9 g), while 4% PH yielded intermediate values. Although differences in egg production were not statistically conclusive, the 4% PH group showed the highest output (76.4%). Feed intake increased by 7.3% in birds fed 4% PH group (P < 0.05), with feed conversion efficiency slightly reduced in noth 2% and 6% PH treatments. Egg shape index improved significantly at 4% PH (+3.3%, P < 0.01), whereas shell thickness, albumen index and Haugh unit remained unchanged (P > 0.05). Yolk color score exhibited strong linear, quadratic and cubic increases (P < 0.01), with the 6% PH group scoring 11.43 (+38.9% vs. 8.23 control). Conclusion Pistachio hulls can be incorporated into laying quail diets up to 6% without adverse effects on egg quality. The 4% inclusion level appears optimal for egg shape and pruductivity, while 6% maximizes yolk coloration. Nonetheless, the observed decline in feed efficiency at some levels suggests that careful ration balancing is…
format: application/pdf
format: text/html
creator: Mehmet Çetin
subject: Agricultural Science
subject: Food Science and Technology
description: doi:10.7717/peerj.20204
publisher: PeerJ Inc.
rights: © 2025 Çetin
abstract: Background Japanese quail (Coturnix coturnix japonica) offer rapid growth, early maturity and excellent feed conversion, but feed cost accounts for ∼70% of production expenses. This study evaluated soft pistachio hull (PH), an abundant agro-industrial by-product, as a low-cost dietary ingredient in laying quails. Methods Ninety-six female quails, seven weeks old age, were randomly distributed to four dietary groups (24 birds each; three replicates of eight birds). The treatment diets were based on a standard layer feed, with graded PH inclusion of 0%, 2%, 4%, and 6%, administered over a for five-week period. Parameters measured included live weight, feed intake, egg production rate, egg weight, feed conversion ratio, and a range of egg quality indicators, such as shape index, shell thickness, Haugh unit, albumen and yolk indices, and yolk color score, assessed at weeks 7 and 11. Results Final live weight followed a cubic trend (P = 0.05), with the 2% and 6% PH groups (356.5 g and 350.6 g, respectively) exceeding the control (333.9 g), while 4% PH yielded intermediate values. Although differences in egg production were not statistically conclusive, the 4% PH group showed the highest output (76.4%). Feed intake increased by 7.3% in birds fed 4% PH group (P < 0.05), with feed conversion efficiency slightly reduced in noth 2% and 6% PH treatments. Egg shape index improved significantly at 4% PH (+3.3%, P < 0.01), whereas shell thickness, albumen index and Haugh unit remained unchanged (P > 0.05). Yolk color score exhibited strong linear, quadratic and cubic increases (P < 0.01), with the 6% PH group scoring 11.43 (+38.9% vs. 8.23 control). Conclusion Pistachio hulls can be incorporated into laying quail diets up to 6% without adverse effects on egg quality. The 4% inclusion level appears optimal for egg shape and pruductivity, while 6% maximizes yolk coloration. Nonetheless, the observed decline in feed efficiency at some levels suggests that careful ration balancing is…
bibliographic citation: Çetin (2025) Utilization of soft pistachio hulls in Japanese quail diets for enhanced egg quality and yolk pigmentation. PeerJ 13:e20204 https://doi.org/10.7717/peerj.20204
date submitted: 2025-06-06
date accepted: 2025-09-17
issued: 2025-11-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Çetin
  given name: Mehmet
doi: 10.7717/peerj.20204
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-21
copyright: ©2025 Çetin
attribution name: Çetin

Evaluation study of effect of virtual care education on healthcare providers’ knowledge, confidence, and satisfaction
type: item
type: AcademicArticle
description: Background Virtual care can increase access to healthcare and improve provider efficiency; however, many healthcare providers lack formal education in virtual care delivery, including skills in virtual communication, physical examination adaptations, confidentiality, and billing procedures. This training gap can result in reduced confidence and suboptimal patient care. To address this, an asynchronous continuing professional development (CPD) module was developed. The objective of this study was to evaluate the module’s efficacy regarding satisfaction and changes in knowledge and confidence. Methods The module covered key topics such as virtual visit etiquette, technology troubleshooting, adapted physical examinations, documentation, and remuneration processes. Interactive features included embedded videos, knowledge-check quizzes, and reflective questions. A single-group pre-post quasi-experimental design was used to evaluate its impact. Data were collected via electronic surveys administered at three time points (before, during, and post-module). Surveys included multiple choice questions assessing objective knowledge, and Likert-scale questions assessing confidence levels in virtual care delivery. Open-ended short answer questions captured qualitative feedback. Quantitative data were analyzed using descriptive statistics and paired t-tests or Wilcoxon signed-rank tests where appropriate. Qualitative data were analyzed thematically to identify learner-reported strengths and areas for improvement. Results A total of nine to 22 learners responded at each time point. Respondents were heterogeneous, with most identifying as male (66.7%), general practitioners (55.6%), practicing in hospital settings (55.6%), and in communities of 2,000 to 10,000 people (55.6%). Learners reported high satisfaction with the module’s content relevance, navigation, and interactive components, but requested more interactive components (e.g., case-based learning). Statistically significant …
format: application/pdf
format: text/html
creator: Megan Clemens
creator: Josheil Boparai
creator: Robert Glynn
creator: Gerry White
creator: Vernon Curran
subject: Science and Medical Education
subject: Healthcare Services
description: doi:10.7717/peerj.20414
publisher: PeerJ Inc.
rights: © 2025 Clemens et al.
abstract: Background Virtual care can increase access to healthcare and improve provider efficiency; however, many healthcare providers lack formal education in virtual care delivery, including skills in virtual communication, physical examination adaptations, confidentiality, and billing procedures. This training gap can result in reduced confidence and suboptimal patient care. To address this, an asynchronous continuing professional development (CPD) module was developed. The objective of this study was to evaluate the module’s efficacy regarding satisfaction and changes in knowledge and confidence. Methods The module covered key topics such as virtual visit etiquette, technology troubleshooting, adapted physical examinations, documentation, and remuneration processes. Interactive features included embedded videos, knowledge-check quizzes, and reflective questions. A single-group pre-post quasi-experimental design was used to evaluate its impact. Data were collected via electronic surveys administered at three time points (before, during, and post-module). Surveys included multiple choice questions assessing objective knowledge, and Likert-scale questions assessing confidence levels in virtual care delivery. Open-ended short answer questions captured qualitative feedback. Quantitative data were analyzed using descriptive statistics and paired t-tests or Wilcoxon signed-rank tests where appropriate. Qualitative data were analyzed thematically to identify learner-reported strengths and areas for improvement. Results A total of nine to 22 learners responded at each time point. Respondents were heterogeneous, with most identifying as male (66.7%), general practitioners (55.6%), practicing in hospital settings (55.6%), and in communities of 2,000 to 10,000 people (55.6%). Learners reported high satisfaction with the module’s content relevance, navigation, and interactive components, but requested more interactive components (e.g., case-based learning). Statistically significant …
bibliographic citation: Clemens et al. (2025) Evaluation study of effect of virtual care education on healthcare providers’ knowledge, confidence, and satisfaction. PeerJ 13:e20414 https://doi.org/10.7717/peerj.20414
date submitted: 2025-08-14
date accepted: 2025-10-28
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clemens
  given name: Megan
author list: Agent
  family name: Boparai
  given name: Josheil
author list: Agent
  family name: Glynn
  given name: Robert
author list: Agent
  family name: White
  given name: Gerry
author list: Agent
  family name: Curran
  given name: Vernon
doi: 10.7717/peerj.20414
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: © 2025 Clemens et al.
attribution name: Clemens et al.

MAFF inhibits angiogenesis in non-small cell lung cancer by suppressing YAP1 nuclear translocation
type: item
type: AcademicArticle
description: Objective To investigate the roles of MAFF and Yes-associated protein 1 (YAP1) in regulating angiogenesis in non-small cell lung cancer (NSCLC) and to explore the mechanism through which MAFF inhibits angiogenesis by suppressing YAP1 nuclear translocation. Methods Bioinformatics analysis was used to assess MAFF expression and its associated regulatory pathways. Clinical samples from NSCLC patients were analyzed by immunohistochemistry (IHC) to evaluate the correlation between MAFF expression and microvessel density (MVD). Cellular experiments were conducted to examine the effects of MAFF overexpression on proliferation, migration, and angiogenesis. Western blot (WB) and immunofluorescence (IF) analyses were performed to assess the expression of YAP1, vascular endothelial growth factor (VEGF), and connective tissue growth factor (CTGF). Tumor growth suppression was evaluated using nude mouse xenograft models. Results MAFF was significantly downregulated in NSCLC tissues and correlated with advanced T stage and higher MVD. Overexpression of MAFF inhibited NSCLC cell proliferation, migration, and angiogenesis, and downregulated the expression of YAP1, VEGF, and CTGF. IF confirmed that MAFF suppressed nuclear translocation of YAP1. In vivo, MAFF overexpression reduced tumor volume and weight, which was accompanied by inhibition of the YAP1 signaling pathway. Conclusion MAFF suppresses angiogenesis in NSCLC by blocking YAP1 nuclear translocation and downregulating VEGF and CTGF, highlighting its potential as a therapeutic target.
format: application/pdf
format: text/html
creator: Yao Ding
creator: Shizi Wang
creator: Rui Hu
creator: ZiYi Cao
creator: Yuting Zou
creator: Wei-ling Yang
creator: Weihang Ji
creator: Lin Liu
creator: Na Xiao
creator: Xiao lei Li
creator: Yi Zeng
subject: Cell Biology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.20395
publisher: PeerJ Inc.
rights: © 2025 Ding et al.
abstract: Objective To investigate the roles of MAFF and Yes-associated protein 1 (YAP1) in regulating angiogenesis in non-small cell lung cancer (NSCLC) and to explore the mechanism through which MAFF inhibits angiogenesis by suppressing YAP1 nuclear translocation. Methods Bioinformatics analysis was used to assess MAFF expression and its associated regulatory pathways. Clinical samples from NSCLC patients were analyzed by immunohistochemistry (IHC) to evaluate the correlation between MAFF expression and microvessel density (MVD). Cellular experiments were conducted to examine the effects of MAFF overexpression on proliferation, migration, and angiogenesis. Western blot (WB) and immunofluorescence (IF) analyses were performed to assess the expression of YAP1, vascular endothelial growth factor (VEGF), and connective tissue growth factor (CTGF). Tumor growth suppression was evaluated using nude mouse xenograft models. Results MAFF was significantly downregulated in NSCLC tissues and correlated with advanced T stage and higher MVD. Overexpression of MAFF inhibited NSCLC cell proliferation, migration, and angiogenesis, and downregulated the expression of YAP1, VEGF, and CTGF. IF confirmed that MAFF suppressed nuclear translocation of YAP1. In vivo, MAFF overexpression reduced tumor volume and weight, which was accompanied by inhibition of the YAP1 signaling pathway. Conclusion MAFF suppresses angiogenesis in NSCLC by blocking YAP1 nuclear translocation and downregulating VEGF and CTGF, highlighting its potential as a therapeutic target.
bibliographic citation: Ding et al. (2025) MAFF inhibits angiogenesis in non-small cell lung cancer by suppressing YAP1 nuclear translocation. PeerJ 13:e20395 https://doi.org/10.7717/peerj.20395
date submitted: 2025-07-08
date accepted: 2025-10-24
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ding
  given name: Yao
author list: Agent
  family name: Wang
  given name: Shizi
author list: Agent
  family name: Hu
  given name: Rui
author list: Agent
  family name: Cao
  given name: ZiYi
author list: Agent
  family name: Zou
  given name: Yuting
author list: Agent
  family name: Yang
  given name: Wei-ling
author list: Agent
  family name: Ji
  given name: Weihang
author list: Agent
  family name: Liu
  given name: Lin
author list: Agent
  family name: Xiao
  given name: Na
author list: Agent
  family name: Li
  given name: Xiao lei
author list: Agent
  family name: Zeng
  given name: Yi
doi: 10.7717/peerj.20395
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: © 2025 Ding et al.
attribution name: Ding et al.

Efficacy and safety of rivaroxaban in neonatal catheter-related thrombosis: a single-center retrospective study of 122 cases
type: item
type: AcademicArticle
description: Background To systematically evaluate the clinical efficacy of rivaroxaban in treating neonatal catheter-related thrombosis (CRT) and analyze risk factors affecting treatment outcomes. Methods Clinical data of 122 neonatal CRT patients treated with rivaroxaban from March 2022 to October 2024 at Fujian Provincial Maternal and Child Health Hospital were retrospectively analyzed. The primary outcome was the complete thrombus resolution rate. Multivariate logistic regression was used to analyze risk factors affecting treatment efficacy. Results Among 122 patients, the complete thrombus resolution rate was 71.31% (87/122) after 6 weeks of anticoagulation, which significantly increased to 88.52% (108/122) after extending to 3 months (p < 0.01). Multivariate logistic regression analysis showed that chemotherapy (OR = 5.48, 95% CI [1.04–28.73], P < 0.05) and difficult catheter placement (OR = 12.53, 95% CI [3.13–50.22], P < 0.05) were independent risk factors reducing the likelihood of complete thrombus resolution at 3 months. No anticoagulation-related bleeding or other complications were observed during the study period, though the sample size and follow-up period may limit the detection of rare events. Conclusion Retrospective data suggest that rivaroxaban is safe and effective in treating neonatal catheter-related thrombosis, with a higher complete thrombus resolution rate observed at 3 months compared to 6 weeks of anticoagulation therapy. Chemotherapy and difficult catheter placement were identified as independent risk factors affecting treatment efficacy. These findings, derived from a single-center retrospective study, require validation through multi-center, prospective, randomized controlled trials.
format: application/pdf
format: text/html
creator: Rong Zhang
creator: Gang Chen
creator: Wen Hong Cai
creator: Bin Yang
creator: Yun Feng Lin
creator: Teng Hui Zhan
subject: Cardiology
subject: Hematology
subject: Pediatrics
description: doi:10.7717/peerj.20375
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Background To systematically evaluate the clinical efficacy of rivaroxaban in treating neonatal catheter-related thrombosis (CRT) and analyze risk factors affecting treatment outcomes. Methods Clinical data of 122 neonatal CRT patients treated with rivaroxaban from March 2022 to October 2024 at Fujian Provincial Maternal and Child Health Hospital were retrospectively analyzed. The primary outcome was the complete thrombus resolution rate. Multivariate logistic regression was used to analyze risk factors affecting treatment efficacy. Results Among 122 patients, the complete thrombus resolution rate was 71.31% (87/122) after 6 weeks of anticoagulation, which significantly increased to 88.52% (108/122) after extending to 3 months (p < 0.01). Multivariate logistic regression analysis showed that chemotherapy (OR = 5.48, 95% CI [1.04–28.73], P < 0.05) and difficult catheter placement (OR = 12.53, 95% CI [3.13–50.22], P < 0.05) were independent risk factors reducing the likelihood of complete thrombus resolution at 3 months. No anticoagulation-related bleeding or other complications were observed during the study period, though the sample size and follow-up period may limit the detection of rare events. Conclusion Retrospective data suggest that rivaroxaban is safe and effective in treating neonatal catheter-related thrombosis, with a higher complete thrombus resolution rate observed at 3 months compared to 6 weeks of anticoagulation therapy. Chemotherapy and difficult catheter placement were identified as independent risk factors affecting treatment efficacy. These findings, derived from a single-center retrospective study, require validation through multi-center, prospective, randomized controlled trials.
bibliographic citation: Zhang et al. (2025) Efficacy and safety of rivaroxaban in neonatal catheter-related thrombosis: a single-center retrospective study of 122 cases. PeerJ 13:e20375 https://doi.org/10.7717/peerj.20375
date submitted: 2025-03-27
date accepted: 2025-10-20
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Rong
author list: Agent
  family name: Chen
  given name: Gang
author list: Agent
  family name: Cai
  given name: Wen Hong
author list: Agent
  family name: Yang
  given name: Bin
author list: Agent
  family name: Lin
  given name: Yun Feng
author list: Agent
  family name: Zhan
  given name: Teng Hui
doi: 10.7717/peerj.20375
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: ©2025 Zhang et al.
attribution name: Zhang et al.

The bee bread of honey bees is characterized by a core microbiota despite the application of miticide treatments and variation across space and time
type: item
type: AcademicArticle
description: Background Bee bread is composed of a mixture of pollen and nectar used as the main source of proteins and lipids for the development of bee larvae. Despite its important role in honey bee food preservation, relatively little is known about the composition of bee bread microbiota and the potential impact of beekeeping management of hives on these microbial systems. Methods Here, we evaluated whether (1) the bee bread of honey bees is characterized by a core microbiota and (2) miticide applications (formic acid and amitraz) affect the diversity and composition of the bee bread microbiota. We collected a total of 36 samples from six sites across two distinct geographic locations and sequenced the bee bread bacterial communities before and after miticide applications. Results Our results revealed a conserved bee bread core microbiota comprised of 15 taxa belonging to the phyla Proteobacteria (11 taxa), Firmicutes (two taxa), Actinobacteriota (one taxon), and Bacteroidota (one taxon). In addition, we found weak evidence of miticide treatments impacting the diversity of the bee bread microbiota, with a general trend of a decrease in the diversity of non-core taxa following the application of organic miticides. Conclusion Taken together, our results demonstrate that the bee bread of honey bees is characterized by a core microbiota despite variations associated with geographic location, sampling period, and miticide applications.
format: application/pdf
format: text/html
creator: Brooke L. Lawrence
creator: Gordon F. Custer
creator: Robyn M. Underwood
creator: Robert R. Dunn
creator: Francisco Dini-Andreote
creator: Margarita M. López-Uribe
subject: Agricultural Science
subject: Ecology
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.20366
publisher: PeerJ Inc.
rights: © 2025 Lawrence et al.
abstract: Background Bee bread is composed of a mixture of pollen and nectar used as the main source of proteins and lipids for the development of bee larvae. Despite its important role in honey bee food preservation, relatively little is known about the composition of bee bread microbiota and the potential impact of beekeeping management of hives on these microbial systems. Methods Here, we evaluated whether (1) the bee bread of honey bees is characterized by a core microbiota and (2) miticide applications (formic acid and amitraz) affect the diversity and composition of the bee bread microbiota. We collected a total of 36 samples from six sites across two distinct geographic locations and sequenced the bee bread bacterial communities before and after miticide applications. Results Our results revealed a conserved bee bread core microbiota comprised of 15 taxa belonging to the phyla Proteobacteria (11 taxa), Firmicutes (two taxa), Actinobacteriota (one taxon), and Bacteroidota (one taxon). In addition, we found weak evidence of miticide treatments impacting the diversity of the bee bread microbiota, with a general trend of a decrease in the diversity of non-core taxa following the application of organic miticides. Conclusion Taken together, our results demonstrate that the bee bread of honey bees is characterized by a core microbiota despite variations associated with geographic location, sampling period, and miticide applications.
bibliographic citation: Lawrence et al. (2025) The bee bread of honey bees is characterized by a core microbiota despite the application of miticide treatments and variation across space and time. PeerJ 13:e20366 https://doi.org/10.7717/peerj.20366
date submitted: 2024-11-14
date accepted: 2025-10-17
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lawrence
  given name: Brooke L.
author list: Agent
  family name: Custer
  given name: Gordon F.
author list: Agent
  family name: Underwood
  given name: Robyn M.
author list: Agent
  family name: Dunn
  given name: Robert R.
author list: Agent
  family name: Dini-Andreote
  given name: Francisco
author list: Agent
  family name: López-Uribe
  given name: Margarita M.
doi: 10.7717/peerj.20366
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: © 2025 Lawrence et al.
attribution name: Lawrence et al.

Assessment of healing dynamics in dental extraction sockets among non-diabetic, prediabetic, and type 2 diabetic patients: a comparative clinical investigation
type: item
type: AcademicArticle
description: Background Diabetes mellitus is a chronic metabolic disorder characterized by persistent hyperglycaemia, affecting various metabolic processes and leading to multiple complications, particularly in wound healing. This study aims to evaluate the impact of diabetes on the healing of extraction sockets in non-diabetic, prediabetic, and type 2 diabetic patients in Saudi Arabia. Methodology A prospective observational study was conducted with 72 participants who were divided equally (n = 24 for each group) into three groups, viz. non-diabetic, prediabetic, and diabetic groups based on glycated hemoglobin (HbA1c) and random blood glucose levels. Tooth extractions were performed by an experienced maxillofacial surgeon. Healing outcomes were assessed by measuring extraction socket size, post-operative pain, discharge, swelling, infection, erythema, dry socket occurrence, and analgesic consumption over one week. Initially descriptive statistics were calculated and one way Analysis of Variance (ANOVA) test was done to compare the reduction in socket size between groups. The level of statistical significance was set at P ≤ 0.05. Results Out of 275 screened participants, 104 provided informed consent, and 72 completed the study. Significant differences were found in socket size reduction, with non-diabetic patients showing a 62.5% reduction, prediabetic 56.4%, and diabetic 48.6% (p < 0.001). Diabetic patients experienced more post-operative pain (p = 0.039) and a higher incidence of complications such as swelling, infection, and discharge, although not statistically significant (p = 0.141). Conclusion Diabetes significantly affects post-operative healing in dental extractions, leading to less socket size reduction, higher pain levels, and increased complications. These findings underscore the necessity for specialized post-operative care for diabetic patients, including stringent infection control and pain management strategies. Further research with larger sample sizes and ext…
format: application/pdf
format: text/html
creator: Mohammed Saad Alqarni
subject: Dentistry
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.20361
publisher: PeerJ Inc.
rights: © 2025 Alqarni
abstract: Background Diabetes mellitus is a chronic metabolic disorder characterized by persistent hyperglycaemia, affecting various metabolic processes and leading to multiple complications, particularly in wound healing. This study aims to evaluate the impact of diabetes on the healing of extraction sockets in non-diabetic, prediabetic, and type 2 diabetic patients in Saudi Arabia. Methodology A prospective observational study was conducted with 72 participants who were divided equally (n = 24 for each group) into three groups, viz. non-diabetic, prediabetic, and diabetic groups based on glycated hemoglobin (HbA1c) and random blood glucose levels. Tooth extractions were performed by an experienced maxillofacial surgeon. Healing outcomes were assessed by measuring extraction socket size, post-operative pain, discharge, swelling, infection, erythema, dry socket occurrence, and analgesic consumption over one week. Initially descriptive statistics were calculated and one way Analysis of Variance (ANOVA) test was done to compare the reduction in socket size between groups. The level of statistical significance was set at P ≤ 0.05. Results Out of 275 screened participants, 104 provided informed consent, and 72 completed the study. Significant differences were found in socket size reduction, with non-diabetic patients showing a 62.5% reduction, prediabetic 56.4%, and diabetic 48.6% (p < 0.001). Diabetic patients experienced more post-operative pain (p = 0.039) and a higher incidence of complications such as swelling, infection, and discharge, although not statistically significant (p = 0.141). Conclusion Diabetes significantly affects post-operative healing in dental extractions, leading to less socket size reduction, higher pain levels, and increased complications. These findings underscore the necessity for specialized post-operative care for diabetic patients, including stringent infection control and pain management strategies. Further research with larger sample sizes and ext…
bibliographic citation: Alqarni (2025) Assessment of healing dynamics in dental extraction sockets among non-diabetic, prediabetic, and type 2 diabetic patients: a comparative clinical investigation. PeerJ 13:e20361 https://doi.org/10.7717/peerj.20361
date submitted: 2025-02-21
date accepted: 2025-10-17
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alqarni
  given name: Mohammed Saad
doi: 10.7717/peerj.20361
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: ©2025 Alqarni
attribution name: Alqarni

Hybrid contour and geometric partitioning for accurate plantar foot region segmentation
type: item
type: AcademicArticle
description: Background Precise segmentation of plantar foot regions is crucial for analyzing foot structure and pressure distribution, aiding in the diagnosis of pathologies and enabling preventive interventions. However, conventional segmentation approaches often struggle to accurately delineate key anatomical regions and detect their boundaries, particularly in the presence of foot abnormalities. Methods We created a dataset of plantar pressure images and proposed a hybrid algorithm that integrates edge contour detection techniques with dynamic geometric partitioning to address persistent challenges in plantar region segmentation. Our method first determines the lengths of the left and right feet using precise contour detection, then partitions the plantar surface into primary anatomical regions (forefoot, midfoot, and heel) based on standardized geometric proportions. Additionally, the methodology allows for finer subdivisions (e.g., inner/outer forefoot) that adapt to the unique morphology of each foot. This algorithm accommodates five foot types, including normal, low arch, high arch, inward heel tilt, and outward heel tilt. Results A comparative evaluation of three edge detection methods revealed that the Canny algorithm, when combined with geometric partitioning, yielded superior performance. On a dataset of 200 plantar pressure footprints encompassing both normal and abnormal feet, this hybrid approach achieved Intersection over Union (IoU) and mean Average Precision (mAP) scores exceeding 0.90 across all segmented regions (forefoot, midfoot, and heel). Furthermore, the results indicate that the proposed hybrid algorithm performs comparably across both normal and abnormal foot types, with no significant differences observed. Conclusions Our synergistic integration of contour detection and geometric partitioning yields an efficient technique for segmenting plantar regions from static plantar pressure images. Validation on a diverse dataset shows that the proposed approac…
format: application/pdf
format: text/html
creator: Shumei Zhang
creator: Xi Liang
creator: Minmin Wu
creator: Weiming Gu
subject: Computational Biology
subject: Data Science
subject: Biomechanics
description: doi:10.7717/peerj.20352
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Background Precise segmentation of plantar foot regions is crucial for analyzing foot structure and pressure distribution, aiding in the diagnosis of pathologies and enabling preventive interventions. However, conventional segmentation approaches often struggle to accurately delineate key anatomical regions and detect their boundaries, particularly in the presence of foot abnormalities. Methods We created a dataset of plantar pressure images and proposed a hybrid algorithm that integrates edge contour detection techniques with dynamic geometric partitioning to address persistent challenges in plantar region segmentation. Our method first determines the lengths of the left and right feet using precise contour detection, then partitions the plantar surface into primary anatomical regions (forefoot, midfoot, and heel) based on standardized geometric proportions. Additionally, the methodology allows for finer subdivisions (e.g., inner/outer forefoot) that adapt to the unique morphology of each foot. This algorithm accommodates five foot types, including normal, low arch, high arch, inward heel tilt, and outward heel tilt. Results A comparative evaluation of three edge detection methods revealed that the Canny algorithm, when combined with geometric partitioning, yielded superior performance. On a dataset of 200 plantar pressure footprints encompassing both normal and abnormal feet, this hybrid approach achieved Intersection over Union (IoU) and mean Average Precision (mAP) scores exceeding 0.90 across all segmented regions (forefoot, midfoot, and heel). Furthermore, the results indicate that the proposed hybrid algorithm performs comparably across both normal and abnormal foot types, with no significant differences observed. Conclusions Our synergistic integration of contour detection and geometric partitioning yields an efficient technique for segmenting plantar regions from static plantar pressure images. Validation on a diverse dataset shows that the proposed approac…
bibliographic citation: Zhang et al. (2025) Hybrid contour and geometric partitioning for accurate plantar foot region segmentation. PeerJ 13:e20352 https://doi.org/10.7717/peerj.20352
date submitted: 2025-02-19
date accepted: 2025-10-16
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shumei
author list: Agent
  family name: Liang
  given name: Xi
author list: Agent
  family name: Wu
  given name: Minmin
author list: Agent
  family name: Gu
  given name: Weiming
doi: 10.7717/peerj.20352
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: ©2025 Zhang et al.
attribution name: Zhang et al.

DHCR7: from sterol biosynthesis to oncogenic role in colorectal cancer
type: item
type: AcademicArticle
description: Objective 7-Dehydrocholesterol reductase (DHCR7) is an enzyme that plays a crucial regulatory role in sterol biosynthesis and has been implicated in tumorigenesis and progression. This study aims to elucidate the biological function of DHCR7 in the pathogenesis of colorectal cancer (CRC). Methods By integrating multi-omics data (including public genomic databases and mass spectrometry data from clinical samples) and establishing in vivo and in vitro experimental systems (encompassing animal models and CRC cell lines with gene overexpression and knockdown), we systematically investigated the functional role of DHCR7 in CRC. A multimodal research strategy combining bioinformatics analysis with molecular biology experiments (Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), western blotting, immunohistochemistry, etc.), proteomics analysis (liquid chromatography–mass spectrometry), and cellular functional assays (proliferation, apoptosis, migration, and invasion) was employed. Results Elevated levels of sterols were observed in CRC tumor tissues, and high cholesterol levels were found to promote the malignant phenotype of tumor cells. Mass spectrometry revealed that DHCR7 was significantly upregulated in CRC tissues and correlated with poor clinical prognosis. DHCR7 could modulate the cholesterol levels in CRC cells; overexpression of this gene enhanced cell proliferation, inhibited apoptosis, and promoted invasion and migration. Conversely, inhibition of DHCR7 expression abrogated these pro-tumorigenic effects, which was consistent with the inactivation of the PI3K/AKT/mTOR signaling pathway and confirmed by pathway reactivation experiments. DHCR7 deficiency significantly reduced tumorigenicity in vivo. Conclusion DHCR7 regulates the progression of CRC both in vitro and in vivo through the PI3K/AKT/mTOR signaling axis and affects the cholesterol levels in CRC.
format: application/pdf
format: text/html
creator: Chuan Zhou
creator: Jia Wang
creator: Han He
creator: Chao Wang
creator: YunFeng Zhang
creator: Wenbo Zhang
creator: Bin Wei
creator: Mingxu Da
creator: Minghui Pang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.20323
publisher: PeerJ Inc.
rights: © 2025 Zhou et al.
abstract: Objective 7-Dehydrocholesterol reductase (DHCR7) is an enzyme that plays a crucial regulatory role in sterol biosynthesis and has been implicated in tumorigenesis and progression. This study aims to elucidate the biological function of DHCR7 in the pathogenesis of colorectal cancer (CRC). Methods By integrating multi-omics data (including public genomic databases and mass spectrometry data from clinical samples) and establishing in vivo and in vitro experimental systems (encompassing animal models and CRC cell lines with gene overexpression and knockdown), we systematically investigated the functional role of DHCR7 in CRC. A multimodal research strategy combining bioinformatics analysis with molecular biology experiments (Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), western blotting, immunohistochemistry, etc.), proteomics analysis (liquid chromatography–mass spectrometry), and cellular functional assays (proliferation, apoptosis, migration, and invasion) was employed. Results Elevated levels of sterols were observed in CRC tumor tissues, and high cholesterol levels were found to promote the malignant phenotype of tumor cells. Mass spectrometry revealed that DHCR7 was significantly upregulated in CRC tissues and correlated with poor clinical prognosis. DHCR7 could modulate the cholesterol levels in CRC cells; overexpression of this gene enhanced cell proliferation, inhibited apoptosis, and promoted invasion and migration. Conversely, inhibition of DHCR7 expression abrogated these pro-tumorigenic effects, which was consistent with the inactivation of the PI3K/AKT/mTOR signaling pathway and confirmed by pathway reactivation experiments. DHCR7 deficiency significantly reduced tumorigenicity in vivo. Conclusion DHCR7 regulates the progression of CRC both in vitro and in vivo through the PI3K/AKT/mTOR signaling axis and affects the cholesterol levels in CRC.
bibliographic citation: Zhou et al. (2025) DHCR7: from sterol biosynthesis to oncogenic role in colorectal cancer. PeerJ 13:e20323 https://doi.org/10.7717/peerj.20323
date submitted: 2024-12-18
date accepted: 2025-10-10
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhou
  given name: Chuan
author list: Agent
  family name: Wang
  given name: Jia
author list: Agent
  family name: He
  given name: Han
author list: Agent
  family name: Wang
  given name: Chao
author list: Agent
  family name: Zhang
  given name: YunFeng
author list: Agent
  family name: Zhang
  given name: Wenbo
author list: Agent
  family name: Wei
  given name: Bin
author list: Agent
  family name: Da
  given name: Mingxu
author list: Agent
  family name: Pang
  given name: Minghui
doi: 10.7717/peerj.20323
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: © 2025 Zhou et al.
attribution name: Zhou et al.

Unveiling the clinical profiles of critically ill COVID-19 patients: insights from Ezhou during the early spread
type: item
type: AcademicArticle
description: The coronavirus disease 2019 (COVID-19) started in December 2019 in Wuhan. This article evaluated clinical characteristics, and imaging manifestations in Ezhou, an early locked-down city, 80 kilometers east of Wuhan. We analyzed data from 98 confirmed severe COVID-19 patients in Ezhou Central Hospital between February 1st and March 22nd, 2020. We compared patients’ laboratory results, imaging manifestations, and treatments between survival and death groups. Of these 98 confirmed COVID-19 patients, 24 individuals (24.6%) had chronic diseases. The main symptoms of critically ill patients were fever (86.7%), cough (83.7%), and dyspnea (59.1%). Common complications were acute respiratory distress syndrome (ARDS; 49%), acute kidney injury (37.7%), and multiple organ dysfunction syndrome (MODS; 32.6%). Computed tomography (CT) scans displayed ground-glass opacity at subpleural regions that were associated with interlobular septal thickening. Within 28 days, 39 (39.8%) patients died. Compared to survivors, the death group had a higher median age (69.8 vs. 61.3, p < 0.05), and were more prone to ARDS (100% vs. 15.2%) and MODS (76% vs. 3.4%). Our report showed that in the early days of the COVID-19 outbreak, there was a high mortality rate in critically ill patients. Elderly patients (>65 years) normally have an increased risk of complications and ARDS. Most non-survivors were highly dependent upon mechanical ventilation. CT scans with imaging manifestations showed abnormal conditions in the lower multiple bilateral lung lobes, which provides a useful characterization of this fatal disease by recognizing COVID-19 pneumonia and assessing its evolution for the target for intervention of the patient recovery.
format: application/pdf
format: text/html
creator: Guohui Yang
creator: Zewen Liu
creator: Tabitha Abraham
creator: Linwei Li
creator: Tingyang Zhou
creator: Qing Zhang
creator: Li Zuo
subject: Immunology
subject: Infectious Diseases
subject: Pathology
subject: COVID-19
description: doi:10.7717/peerj.20318
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: The coronavirus disease 2019 (COVID-19) started in December 2019 in Wuhan. This article evaluated clinical characteristics, and imaging manifestations in Ezhou, an early locked-down city, 80 kilometers east of Wuhan. We analyzed data from 98 confirmed severe COVID-19 patients in Ezhou Central Hospital between February 1st and March 22nd, 2020. We compared patients’ laboratory results, imaging manifestations, and treatments between survival and death groups. Of these 98 confirmed COVID-19 patients, 24 individuals (24.6%) had chronic diseases. The main symptoms of critically ill patients were fever (86.7%), cough (83.7%), and dyspnea (59.1%). Common complications were acute respiratory distress syndrome (ARDS; 49%), acute kidney injury (37.7%), and multiple organ dysfunction syndrome (MODS; 32.6%). Computed tomography (CT) scans displayed ground-glass opacity at subpleural regions that were associated with interlobular septal thickening. Within 28 days, 39 (39.8%) patients died. Compared to survivors, the death group had a higher median age (69.8 vs. 61.3, p < 0.05), and were more prone to ARDS (100% vs. 15.2%) and MODS (76% vs. 3.4%). Our report showed that in the early days of the COVID-19 outbreak, there was a high mortality rate in critically ill patients. Elderly patients (>65 years) normally have an increased risk of complications and ARDS. Most non-survivors were highly dependent upon mechanical ventilation. CT scans with imaging manifestations showed abnormal conditions in the lower multiple bilateral lung lobes, which provides a useful characterization of this fatal disease by recognizing COVID-19 pneumonia and assessing its evolution for the target for intervention of the patient recovery.
bibliographic citation: Yang et al. (2025) Unveiling the clinical profiles of critically ill COVID-19 patients: insights from Ezhou during the early spread. PeerJ 13:e20318 https://doi.org/10.7717/peerj.20318
date submitted: 2024-08-16
date accepted: 2025-10-09
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Guohui
author list: Agent
  family name: Liu
  given name: Zewen
author list: Agent
  family name: Abraham
  given name: Tabitha
author list: Agent
  family name: Li
  given name: Linwei
author list: Agent
  family name: Zhou
  given name: Tingyang
author list: Agent
  family name: Zhang
  given name: Qing
author list: Agent
  family name: Zuo
  given name: Li
doi: 10.7717/peerj.20318
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: ©2025 Yang et al.
attribution name: Yang et al.

Selection and preliminary evaluation of superior individual plant in Camellia oleifera
type: item
type: AcademicArticle
description: Camellia oleifera exhibits significant economic and ecological value as a woody oil crop. However, widespread low-yield stands persist due to suboptimal agricultural management and historical neglect of scientific cultivation practices. This study conducted a systematic characterization of 25 elite C. oleifera germplasms with high fruit set but phenotypic variability in fruit morphology and yield components. Multi-dimensional assessments were performed at late-stage fruit development, focusing on architecture traits (height, canopy area), fruit morphological parameters (size, weight, pericarp thickness), and key economic indices including yield potential and oil content. Multivariate analysis revealed H2 as the top-performing genotype, demonstrating superior performance across all evaluated traits. Genotypes H16, H5 and H6 ranked second tier but require optimized agronomic practices to maximize yield potential. Hierarchical cluster analysis based on 17 quantitative traits classified the elite trees into five distinct phenotypic groups. These findings provide a scientific framework for genotype selection in low-yield forest restoration programs. The identified superior trees offer potential for regional production enhancement, while the established trait correlation inform targeted breeding strategies.
format: application/pdf
format: text/html
creator: Wenpei Song
creator: Siqi Huang
creator: Fang Li
creator: Panfeng Tu
creator: Yongquan Li
creator: Bipei Zhang
creator: Yi Wang
creator: Jinghan Dou
creator: Caiqin Li
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20283
publisher: PeerJ Inc.
rights: © 2025 Song et al.
abstract: Camellia oleifera exhibits significant economic and ecological value as a woody oil crop. However, widespread low-yield stands persist due to suboptimal agricultural management and historical neglect of scientific cultivation practices. This study conducted a systematic characterization of 25 elite C. oleifera germplasms with high fruit set but phenotypic variability in fruit morphology and yield components. Multi-dimensional assessments were performed at late-stage fruit development, focusing on architecture traits (height, canopy area), fruit morphological parameters (size, weight, pericarp thickness), and key economic indices including yield potential and oil content. Multivariate analysis revealed H2 as the top-performing genotype, demonstrating superior performance across all evaluated traits. Genotypes H16, H5 and H6 ranked second tier but require optimized agronomic practices to maximize yield potential. Hierarchical cluster analysis based on 17 quantitative traits classified the elite trees into five distinct phenotypic groups. These findings provide a scientific framework for genotype selection in low-yield forest restoration programs. The identified superior trees offer potential for regional production enhancement, while the established trait correlation inform targeted breeding strategies.
bibliographic citation: Song et al. (2025) Selection and preliminary evaluation of superior individual plant in Camellia oleifera. PeerJ 13:e20283 https://doi.org/10.7717/peerj.20283
date submitted: 2025-04-26
date accepted: 2025-10-01
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Wenpei
author list: Agent
  family name: Huang
  given name: Siqi
author list: Agent
  family name: Li
  given name: Fang
author list: Agent
  family name: Tu
  given name: Panfeng
author list: Agent
  family name: Li
  given name: Yongquan
author list: Agent
  family name: Zhang
  given name: Bipei
author list: Agent
  family name: Wang
  given name: Yi
author list: Agent
  family name: Dou
  given name: Jinghan
author list: Agent
  family name: Li
  given name: Caiqin
doi: 10.7717/peerj.20283
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: ©2025 Song et al.
attribution name: Song et al.

Effectiveness of multi-component exercise in individuals with type 2 diabetes: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective This meta-analysis aimed to explore the effects of multi-component exercise interventions on glycemic and lipid metabolism, physical fitness, and cognitive function in individuals with type 2 diabetes mellitus (T2DM). Methods From inception to December 28, 2024, PubMed, Web of Science, Cochrane, and Elsevier databases were systematically searched for randomized controlled trials (RCTs) investigating multi-component exercise interventions for T2DM. A total of 37 articles, comprising 3,201 participants, were included. Primary and secondary outcome measures were categorized, summarized, and analyzed using RevMan 5.4 software. Results Compared to control groups, multi-component exercise interventions produced statistically significant improvements across all measured outcomes in individuals with T2DM: (1) Glycemic control: HbA1c (standard mean difference (SMD) = −0.52, 95% confidence interval (CI) [−0.76 to −0.28]); fasting blood glucose (SMD = −0.53, 95% CI [−0.93 to −0.12]). (2) Lipid metabolism: high density lipoprotein (HDL) (SMD = 0.32, 95% CI [0.21–0.44]); low density lipoprotein (LDL) (SMD = −0.21, 95% CI [−0.33 to −0.09]); triglycerides (SMD = −0.18, 95% CI [−0.30 to −0.06]). (3) Physical fitness: upper limb strength (SMD = 0.67, 95% CI [0.51–0.83]); lower limb strength (SMD = 0.56, 95% CI [0.10–1.02]); peak oxygen consumption (SMD = 0.62, 95% CI [0.31–0.93]); body mass index (BMI) (SMD = −0.38, 95% CI [−0.67 to −0.09]). (4) Cognitive function: overall cognitive performance (SMD = 0.34, 95% CI [0.18–0.50]). (5) Quality of life: vitality (SMD = 0.37, 95% CI [0.09–0.64]); physical functioning (SMD = 0.48, 95% CI [0.20–0.75]); mental health (SMD = 0.35, 95% CI [0.07–0.63]); general health (SMD = 0.34, 95% CI [0.06–0.61]). Quality assessment indicated that the included studies were of high overall quality. Egger’s regression analysis did not reveal significant publication bias. Conclusions Multi-component exercise interventions significantly improved glyce…
format: application/pdf
format: text/html
creator: Zhiyuan Sun
creator: Haiqing Zeng
creator: Hualei Liu
creator: Mengqi Hu
creator: Xuewen Tian
creator: Dewei Mao
creator: Rui Zhang
subject: Diabetes and Endocrinology
subject: Evidence Based Medicine
subject: Sports Medicine
description: doi:10.7717/peerj.20146
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Objective This meta-analysis aimed to explore the effects of multi-component exercise interventions on glycemic and lipid metabolism, physical fitness, and cognitive function in individuals with type 2 diabetes mellitus (T2DM). Methods From inception to December 28, 2024, PubMed, Web of Science, Cochrane, and Elsevier databases were systematically searched for randomized controlled trials (RCTs) investigating multi-component exercise interventions for T2DM. A total of 37 articles, comprising 3,201 participants, were included. Primary and secondary outcome measures were categorized, summarized, and analyzed using RevMan 5.4 software. Results Compared to control groups, multi-component exercise interventions produced statistically significant improvements across all measured outcomes in individuals with T2DM: (1) Glycemic control: HbA1c (standard mean difference (SMD) = −0.52, 95% confidence interval (CI) [−0.76 to −0.28]); fasting blood glucose (SMD = −0.53, 95% CI [−0.93 to −0.12]). (2) Lipid metabolism: high density lipoprotein (HDL) (SMD = 0.32, 95% CI [0.21–0.44]); low density lipoprotein (LDL) (SMD = −0.21, 95% CI [−0.33 to −0.09]); triglycerides (SMD = −0.18, 95% CI [−0.30 to −0.06]). (3) Physical fitness: upper limb strength (SMD = 0.67, 95% CI [0.51–0.83]); lower limb strength (SMD = 0.56, 95% CI [0.10–1.02]); peak oxygen consumption (SMD = 0.62, 95% CI [0.31–0.93]); body mass index (BMI) (SMD = −0.38, 95% CI [−0.67 to −0.09]). (4) Cognitive function: overall cognitive performance (SMD = 0.34, 95% CI [0.18–0.50]). (5) Quality of life: vitality (SMD = 0.37, 95% CI [0.09–0.64]); physical functioning (SMD = 0.48, 95% CI [0.20–0.75]); mental health (SMD = 0.35, 95% CI [0.07–0.63]); general health (SMD = 0.34, 95% CI [0.06–0.61]). Quality assessment indicated that the included studies were of high overall quality. Egger’s regression analysis did not reveal significant publication bias. Conclusions Multi-component exercise interventions significantly improved glyce…
bibliographic citation: Sun et al. (2025) Effectiveness of multi-component exercise in individuals with type 2 diabetes: a systematic review and meta-analysis. PeerJ 13:e20146 https://doi.org/10.7717/peerj.20146
date submitted: 2025-05-02
date accepted: 2025-09-05
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Zhiyuan
author list: Agent
  family name: Zeng
  given name: Haiqing
author list: Agent
  family name: Liu
  given name: Hualei
author list: Agent
  family name: Hu
  given name: Mengqi
author list: Agent
  family name: Tian
  given name: Xuewen
author list: Agent
  family name: Mao
  given name: Dewei
author list: Agent
  family name: Zhang
  given name: Rui
doi: 10.7717/peerj.20146
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: © 2025 Sun et al.
attribution name: Sun et al.

Effects of foliar applied asparagine, glycine and citric acid on cadmium uptake and yield in wheat
type: item
type: AcademicArticle
description: Cadmium (Cd) contamination is an important heavy metal that threatens agricultural production and food safety. This study investigates the potential of foliar applications of asparagine (Asn), glycine (Gly) and citric acid (CA) to reduce Cd uptake and improve the nutrient balance of wheat (Triticum durum L.). A pot experiment was conducted under controlled conditions with three different Cd concentrations (0, 3 and 12 mg Cd kg−1 soil). The mixture containing 0.5 mMg Gly, Asn, and CA was applied to the leaves a total of five times at 5-day intervals during the tillering, stem elongation, heading and flowering periods of wheat, starting 39 days after planting. The analysis showed that the application of Asn reduced the Cd concentration in the grains by 14.82%, 31.08% and 16.66%, respectively, while the application of Gly resulted in a reduction of 37.78%, 16.41% and 12.79% and the application of CA resulted in a reduction of 34.78%, 36.25% and −1.60% compared to the control (C0) group. In addition, grain yield increased in response to the amino acid applications, with Asn improving yield by 6.10%, 9.95% and 5.90%; glycine by 3.86%, 7.59% and 9.34%; CA by −2.64%, 6.16% and 3.44%, respectively. These amino acid treatments alleviated the growth limitations caused by Cd stress by increasing the grain yield of wheat. However, the effect of CA on Cd detoxification was lower compared to the amino acids. The results show that Asn and Gly not only reduce Cd accumulation in wheat but also improve nutrient balance and increase yield. Consequently, foliar application of these amino acids is a promising strategy to improve plant safety in Cd-contaminated agricultural soils.
format: application/pdf
format: text/html
creator: Özlem Ete Aydemir
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.20102
publisher: PeerJ Inc.
rights: © 2025 Ete Aydemir
abstract: Cadmium (Cd) contamination is an important heavy metal that threatens agricultural production and food safety. This study investigates the potential of foliar applications of asparagine (Asn), glycine (Gly) and citric acid (CA) to reduce Cd uptake and improve the nutrient balance of wheat (Triticum durum L.). A pot experiment was conducted under controlled conditions with three different Cd concentrations (0, 3 and 12 mg Cd kg−1 soil). The mixture containing 0.5 mMg Gly, Asn, and CA was applied to the leaves a total of five times at 5-day intervals during the tillering, stem elongation, heading and flowering periods of wheat, starting 39 days after planting. The analysis showed that the application of Asn reduced the Cd concentration in the grains by 14.82%, 31.08% and 16.66%, respectively, while the application of Gly resulted in a reduction of 37.78%, 16.41% and 12.79% and the application of CA resulted in a reduction of 34.78%, 36.25% and −1.60% compared to the control (C0) group. In addition, grain yield increased in response to the amino acid applications, with Asn improving yield by 6.10%, 9.95% and 5.90%; glycine by 3.86%, 7.59% and 9.34%; CA by −2.64%, 6.16% and 3.44%, respectively. These amino acid treatments alleviated the growth limitations caused by Cd stress by increasing the grain yield of wheat. However, the effect of CA on Cd detoxification was lower compared to the amino acids. The results show that Asn and Gly not only reduce Cd accumulation in wheat but also improve nutrient balance and increase yield. Consequently, foliar application of these amino acids is a promising strategy to improve plant safety in Cd-contaminated agricultural soils.
bibliographic citation: Ete Aydemir (2025) Effects of foliar applied asparagine, glycine and citric acid on cadmium uptake and yield in wheat. PeerJ 13:e20102 https://doi.org/10.7717/peerj.20102
date submitted: 2025-05-15
date accepted: 2025-08-27
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ete Aydemir
  given name: Özlem
doi: 10.7717/peerj.20102
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: ©2025 Ete Aydemir
attribution name: Ete Aydemir

El Niño-driven phase shift to algal dominance on Isla del Caño’s coral reefs: implications for urgent restoration
type: item
type: AcademicArticle
description: Background The 2023–24 El Niño event caused extreme marine heat stress and widespread coral bleaching. Coral reefs at the Reserva Biológica Isla del Caño and the northern coast of the Osa Peninsula, Costa Rica, underpin critical ecosystem services, including biodiversity conservation and marine tourism, and have previously withstood similar events with minimal coral loss. Evaluating the ecological impacts of the 2023–24 El Niño is essential to assess coral reef resilience and guide future management. Methods Coral Reef Watch sea surface temperature (SST) data (1985–2025; CoralTemp V3.1) were used to calculate long-term SST trends and degree heating weeks (DHW). Reef surveys were conducted at nine sites between 2019 and 2025, with primary benthic composition and coral health data collected in 2024–25. Benthic cover was assessed using point-intercept, line-intercept, and quadrat methods, while coral diversity, abundance, and health were measured via belt transects. Beta regression was used to assess the effect of temperature on coral cover, and multivariate analyses, including principal component analysis (PCA) and similarity percentage analysis (SIMPER), evaluated benthic community changes and bleaching patterns. An Ecological Recovery Feasibility Index (ERFI) was developed using PCA loadings and benthic indicators to rank sites by recovery potential. Results SST increased significantly over the past 40 years (∼0.23 °C/decade), with the 2023–24 El Niño recording peak SST (31.2 °C). Bleaching threshold exceedance days increased, while cool days declined. Twelve coral taxa were recorded; Pocillopora spp. and Porites lobata were present at all sites. Coral diversity varied, with Cueva and Ancla highest, and San Josecito lowest. Estimated baseline bleaching prevalence was ∼23%, highest in Pocillopora spp. (33.9%). SIMPER and PCA revealed a shift from coral to algal dominance: turf algae increased by 70.62%, dead coral declined 80.71%, and coral cover fell 40.44%. Major c…
format: application/pdf
format: text/html
creator: Caroline V. Palmer
creator: Shanttal Valeria Rodríguez Esquivel
creator: Christopher M. Parker
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.20088
publisher: PeerJ Inc.
rights: © 2025 Palmer et al.
abstract: Background The 2023–24 El Niño event caused extreme marine heat stress and widespread coral bleaching. Coral reefs at the Reserva Biológica Isla del Caño and the northern coast of the Osa Peninsula, Costa Rica, underpin critical ecosystem services, including biodiversity conservation and marine tourism, and have previously withstood similar events with minimal coral loss. Evaluating the ecological impacts of the 2023–24 El Niño is essential to assess coral reef resilience and guide future management. Methods Coral Reef Watch sea surface temperature (SST) data (1985–2025; CoralTemp V3.1) were used to calculate long-term SST trends and degree heating weeks (DHW). Reef surveys were conducted at nine sites between 2019 and 2025, with primary benthic composition and coral health data collected in 2024–25. Benthic cover was assessed using point-intercept, line-intercept, and quadrat methods, while coral diversity, abundance, and health were measured via belt transects. Beta regression was used to assess the effect of temperature on coral cover, and multivariate analyses, including principal component analysis (PCA) and similarity percentage analysis (SIMPER), evaluated benthic community changes and bleaching patterns. An Ecological Recovery Feasibility Index (ERFI) was developed using PCA loadings and benthic indicators to rank sites by recovery potential. Results SST increased significantly over the past 40 years (∼0.23 °C/decade), with the 2023–24 El Niño recording peak SST (31.2 °C). Bleaching threshold exceedance days increased, while cool days declined. Twelve coral taxa were recorded; Pocillopora spp. and Porites lobata were present at all sites. Coral diversity varied, with Cueva and Ancla highest, and San Josecito lowest. Estimated baseline bleaching prevalence was ∼23%, highest in Pocillopora spp. (33.9%). SIMPER and PCA revealed a shift from coral to algal dominance: turf algae increased by 70.62%, dead coral declined 80.71%, and coral cover fell 40.44%. Major c…
bibliographic citation: Palmer et al. (2025) El Niño-driven phase shift to algal dominance on Isla del Caño’s coral reefs: implications for urgent restoration. PeerJ 13:e20088 https://doi.org/10.7717/peerj.20088
date submitted: 2025-04-14
date accepted: 2025-08-26
issued: 2025-11-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palmer
  given name: Caroline V.
author list: Agent
  family name: Rodríguez Esquivel
  given name: Shanttal Valeria
author list: Agent
  family name: Parker
  given name: Christopher M.
doi: 10.7717/peerj.20088
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-20
copyright: ©2025 Palmer et al.
attribution name: Palmer et al.

Outcomes and safety of colonoscopy in elderly patients aged 80 years and older: a retrospective cohort study
type: item
type: AcademicArticle
description: Background The incidence of colorectal tumors increases with age. Colonoscopy is crucial for early detection, yet performing it on patients aged 80 and older poses challenges due to their complex health conditions. Methods This retrospective study included 447 elderly patients aged 80 years and older who underwent colorectal examinations at Peking University International Hospital from November 2015 to June 2024. Data on demographics, comorbidities, smoking and drinking history, and colonoscopy indications were collected. Risk factors for non-colorectal malignant tumors, colorectal malignant tumors, and colorectal advanced-stage tumors were compared. All patients received standard bowel preparation, and procedures were conducted by experienced endoscopists. Results A total of 364 patients (81.4%) completed the procedure successfully. The main reasons for failure were inadequate intestinal preparation and intestinal stenosis. A total of 37 (8.3%) had no significant abnormalities, 315 (70.5%) were diagnosed with colorectal polyps, and 110 (24.6%) had malignant tumors. The complication rate was 0.67%. Univariate analysis showed that patients with colorectal malignant tumors were older (P = 0.000) and had a higher prevalence of alcohol consumption history (P = 0.014). For advanced tumors, patients were also older (P = 0.000). Discussion Age is a significant risk factor for colorectal malignancies and advanced tumors. Although colonoscopy in elderly patients has acceptable safety, they face challenges in bowel preparation and examination techniques. The incidence of polyps and malignant tumors in this population is high. However, the study has limitations, such as its retrospective nature and reliance on incomplete electronic medical records. Conclusion Colonoscopy is effective and safe for elderly patients aged 80 and older. It is essential for detecting colorectal malignancies and polyps. Age-related risk factors highlight the importance of this procedure in this high-…
format: application/pdf
format: text/html
creator: Yiming Ding
creator: Xiangchun Lin
subject: Gastroenterology and Hepatology
subject: Geriatrics
subject: Internal Medicine
description: doi:10.7717/peerj.20404
publisher: PeerJ Inc.
rights: © 2025 Ding and Lin
abstract: Background The incidence of colorectal tumors increases with age. Colonoscopy is crucial for early detection, yet performing it on patients aged 80 and older poses challenges due to their complex health conditions. Methods This retrospective study included 447 elderly patients aged 80 years and older who underwent colorectal examinations at Peking University International Hospital from November 2015 to June 2024. Data on demographics, comorbidities, smoking and drinking history, and colonoscopy indications were collected. Risk factors for non-colorectal malignant tumors, colorectal malignant tumors, and colorectal advanced-stage tumors were compared. All patients received standard bowel preparation, and procedures were conducted by experienced endoscopists. Results A total of 364 patients (81.4%) completed the procedure successfully. The main reasons for failure were inadequate intestinal preparation and intestinal stenosis. A total of 37 (8.3%) had no significant abnormalities, 315 (70.5%) were diagnosed with colorectal polyps, and 110 (24.6%) had malignant tumors. The complication rate was 0.67%. Univariate analysis showed that patients with colorectal malignant tumors were older (P = 0.000) and had a higher prevalence of alcohol consumption history (P = 0.014). For advanced tumors, patients were also older (P = 0.000). Discussion Age is a significant risk factor for colorectal malignancies and advanced tumors. Although colonoscopy in elderly patients has acceptable safety, they face challenges in bowel preparation and examination techniques. The incidence of polyps and malignant tumors in this population is high. However, the study has limitations, such as its retrospective nature and reliance on incomplete electronic medical records. Conclusion Colonoscopy is effective and safe for elderly patients aged 80 and older. It is essential for detecting colorectal malignancies and polyps. Age-related risk factors highlight the importance of this procedure in this high-…
bibliographic citation: Ding et al. (2025) Outcomes and safety of colonoscopy in elderly patients aged 80 years and older: a retrospective cohort study. PeerJ 13:e20404 https://doi.org/10.7717/peerj.20404
date submitted: 2025-02-26
date accepted: 2025-10-27
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Yiming
author list: Agent
  family name: Lin
  given name: Xiangchun
doi: 10.7717/peerj.20404
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: © 2025 Ding and Lin
attribution name: Ding and Lin

Risk factors and predictive model for intrapartum cesarean delivery in women with epidural analgesia: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Labor epidural analgesia (LEA) is the gold standard for labor pain management, yet its association with intrapartum cesarean delivery (CD) remains controversial. This study aimed to identify risk factors and develop a predictive model for CD conversion in parturients receiving LEA. Methods A retrospective cohort study analyzed 1,896 parturients receiving LEA at Zhengzhou Central Hospital (2022–2023). Participants were categorized into vaginal delivery group (n = 1, 541) and cesarean delivery group (n = 355). The original dataset was randomly split into training/testing sets (7:3 ratio) for analytical purposes. Univariate analysis identified significant variables, followed by Least Absolute Shrinkage and Selection Operator (LASSO) regression and multivariate logistic regression to construct a predictive nomogram. Model performance was evaluated by area under the receiver operating characteristic curve (AUC), calibration curves, and decision curve analysis (DCA). Results The CD conversion rate was 18.7%. Eight independent predictors were identified: height, pre-pregnancy body mass index (BMI), gestational age ≥ 40 weeks, hypertension, meperidine use, cervical dilation at analgesia initiation, intrapartum fever (≥ 38.0 °C), and estimated fetal weight. The nomogram demonstrated good discrimination (training set area under the curve (AUC) = 0.729, 95% confidence interval (CI) [0.695–0.763]; testing set AUC = 0.722, 95% CI [0.670–0.774]) and calibration (Hosmer-Lemeshow P > 0.05). DCA confirmed clinical utility. Conclusions This model provides a tool for individualized labor management that aims to reduce unnecessary cesarean deliveries.
format: application/pdf
format: text/html
creator: Yu Feng
creator: Yili Zhao
creator: Rui Shao
creator: Yan Wang
creator: Pin Zhang
subject: Anesthesiology and Pain Management
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.20358
publisher: PeerJ Inc.
rights: © 2025 Feng et al.
abstract: Background Labor epidural analgesia (LEA) is the gold standard for labor pain management, yet its association with intrapartum cesarean delivery (CD) remains controversial. This study aimed to identify risk factors and develop a predictive model for CD conversion in parturients receiving LEA. Methods A retrospective cohort study analyzed 1,896 parturients receiving LEA at Zhengzhou Central Hospital (2022–2023). Participants were categorized into vaginal delivery group (n = 1, 541) and cesarean delivery group (n = 355). The original dataset was randomly split into training/testing sets (7:3 ratio) for analytical purposes. Univariate analysis identified significant variables, followed by Least Absolute Shrinkage and Selection Operator (LASSO) regression and multivariate logistic regression to construct a predictive nomogram. Model performance was evaluated by area under the receiver operating characteristic curve (AUC), calibration curves, and decision curve analysis (DCA). Results The CD conversion rate was 18.7%. Eight independent predictors were identified: height, pre-pregnancy body mass index (BMI), gestational age ≥ 40 weeks, hypertension, meperidine use, cervical dilation at analgesia initiation, intrapartum fever (≥ 38.0 °C), and estimated fetal weight. The nomogram demonstrated good discrimination (training set area under the curve (AUC) = 0.729, 95% confidence interval (CI) [0.695–0.763]; testing set AUC = 0.722, 95% CI [0.670–0.774]) and calibration (Hosmer-Lemeshow P > 0.05). DCA confirmed clinical utility. Conclusions This model provides a tool for individualized labor management that aims to reduce unnecessary cesarean deliveries.
bibliographic citation: Feng et al. (2025) Risk factors and predictive model for intrapartum cesarean delivery in women with epidural analgesia: a retrospective cohort study. PeerJ 13:e20358 https://doi.org/10.7717/peerj.20358
date submitted: 2025-06-20
date accepted: 2025-10-16
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Yu
author list: Agent
  family name: Zhao
  given name: Yili
author list: Agent
  family name: Shao
  given name: Rui
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Pin
doi: 10.7717/peerj.20358
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Feng et al.
attribution name: Feng et al.

Effect of quality sleep on basketball three-point shooting outcomes: the mediating role of athletic mental energy in a cross-sectional study of collegiate athletes
type: item
type: AcademicArticle
description: Introduction Quality sleep is crucial for optimal sports performance, yet the psychological mechanisms underpinning the sleep-sports performance relationship require further examination. Methods This cross-sectional study explored the effects of athletic mental energy (AME) and sleep quality on basketball three-point shooting outcomes with a particular emphasis on the mediating role of AME. One hundred and forty-five collegiate basketball athletes (71 males and 74 females; Mage = 19.62 ± 1.35) with highly trained levels were recruited to evaluate sleep quality, AME, and basketball three-point shooting performance and percentage. Data were collected through validated questionnaires and a standardized three-point shooting test, and analyzed using structural equation modeling (SEM) with bootstrapping. Results Sleep quality was positively associated with basketball three-point shooting performance (r = 0.22, p = 0.007) and shooting percentage (r = 0.22, p = 0.009). AME partially and fully mediated these associations (indirect effect = 0.18, p = 0.031, 95% bias-corrected CI [0.02–0.42] for shooting performance; indirect effect = 0.27, p = 0.019, 95% bias-corrected CI [0.04–0.60] for shooting percentage). Conclusions The findings contribute to the literature on the relationship between sleep and competition-relevant sports performance and suggest AME as one of the potential psychological mechanisms underlying these associations. These results highlight the importance of considering athletes’ sleep quality and AME in performance contexts, while further research is needed to strengthen and generalize these conclusions.
format: application/pdf
format: text/html
creator: Shu-Yueh Chan
creator: Wei-Jiun Shen
creator: Shin-Liang Lo
creator: Yun Che Hsieh
creator: Frank J.H. Lu
creator: Garry Kuan
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20355
publisher: PeerJ Inc.
rights: © 2025 Chan et al.
abstract: Introduction Quality sleep is crucial for optimal sports performance, yet the psychological mechanisms underpinning the sleep-sports performance relationship require further examination. Methods This cross-sectional study explored the effects of athletic mental energy (AME) and sleep quality on basketball three-point shooting outcomes with a particular emphasis on the mediating role of AME. One hundred and forty-five collegiate basketball athletes (71 males and 74 females; Mage = 19.62 ± 1.35) with highly trained levels were recruited to evaluate sleep quality, AME, and basketball three-point shooting performance and percentage. Data were collected through validated questionnaires and a standardized three-point shooting test, and analyzed using structural equation modeling (SEM) with bootstrapping. Results Sleep quality was positively associated with basketball three-point shooting performance (r = 0.22, p = 0.007) and shooting percentage (r = 0.22, p = 0.009). AME partially and fully mediated these associations (indirect effect = 0.18, p = 0.031, 95% bias-corrected CI [0.02–0.42] for shooting performance; indirect effect = 0.27, p = 0.019, 95% bias-corrected CI [0.04–0.60] for shooting percentage). Conclusions The findings contribute to the literature on the relationship between sleep and competition-relevant sports performance and suggest AME as one of the potential psychological mechanisms underlying these associations. These results highlight the importance of considering athletes’ sleep quality and AME in performance contexts, while further research is needed to strengthen and generalize these conclusions.
bibliographic citation: Chan et al. (2025) Effect of quality sleep on basketball three-point shooting outcomes: the mediating role of athletic mental energy in a cross-sectional study of collegiate athletes. PeerJ 13:e20355 https://doi.org/10.7717/peerj.20355
date submitted: 2025-05-14
date accepted: 2025-10-16
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chan
  given name: Shu-Yueh
author list: Agent
  family name: Shen
  given name: Wei-Jiun
author list: Agent
  family name: Lo
  given name: Shin-Liang
author list: Agent
  family name: Hsieh
  given name: Yun Che
author list: Agent
  family name: Lu
  given name: Frank J.H.
author list: Agent
  family name: Kuan
  given name: Garry
doi: 10.7717/peerj.20355
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Chan et al.
attribution name: Chan et al.

Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments
type: item
type: AcademicArticle
description: Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces—Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.
format: application/pdf
format: text/html
creator: Xuemei Han
creator: Huan Liu
creator: Xue Bai
creator: Diyan Li
creator: Tao Wang
creator: Hang Zhong
creator: Yongfang Yao
creator: Jing Sun
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.20348
publisher: PeerJ Inc.
rights: © 2025 Han et al.
abstract: Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces—Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.
bibliographic citation: Han et al. (2025) Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments. PeerJ 13:e20348 https://doi.org/10.7717/peerj.20348
date submitted: 2025-08-05
date accepted: 2025-10-15
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Xuemei
author list: Agent
  family name: Liu
  given name: Huan
author list: Agent
  family name: Bai
  given name: Xue
author list: Agent
  family name: Li
  given name: Diyan
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Zhong
  given name: Hang
author list: Agent
  family name: Yao
  given name: Yongfang
author list: Agent
  family name: Sun
  given name: Jing
doi: 10.7717/peerj.20348
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Han et al.
attribution name: Han et al.

Cross-cultural adaptation and psychometric validation of the Chinese quality-of-life questionnaire for patients with systemic sclerosis
type: item
type: AcademicArticle
description: Background Patients with systemic sclerosis (SSc) frequently experience symptoms such as pain, fatigue, and functional impairments, leading to a significant decline in their quality of life (QoL). Accurately evaluating the QoL of SSc patients is crucial for developing personalized treatment plans and enhancing prognosis. The Systemic Sclerosis Quality of Life Questionnaire (SScQoL), an internationally recognized SSc-specific tool, is commonly used for QoL assessment. However, this questionnaire has not undergone cross-cultural adaptation in China, and its reliability and validity require further validation. Objectives To localize the Systemic Sclerosis Quality of Life Questionnaire (SScQoL) into Chinese and assess its reliability and validity. Methods Following the principles of scale introduction, the Beaton model was employed to translate and back-translate the English version. The scale underwent cross-cultural adaptation through expert consultation, resulting in the Chinese version of the SScQoL test. From August 2023 to December 2024, a convenience sampling method was used to recruit 160 patients with systemic sclerosis from two hospitals for questionnaire surveys to evaluate questionnaire reliability and validity. Results SScQoL comprises five dimensions and 29 items. The content validity index (CVI) at the item level ranges from 0.83 to 1.00, and the CVI at the scale level is 0.97. Exploratory factor analysis identified five common factors, with a cumulative variance contribution rate of 65.761%. The Cronbach’s α coefficient for the total scale is 0.922, and the Cronbach’s α coefficients for the five dimensions range from 0.756 to 0.942. The test-retest reliability for the total scale is 0.969; for the five dimensions, it ranges from 0.710 to 0.961. Conclusions SScQoL is a reliable and effective tool for evaluating patients’ quality of life with systemic sclerosis. This tool can support nurses and researchers and help them formulate targeted strategies, there…
format: application/pdf
format: text/html
creator: Yinfeng Hu
creator: Wenjie Zhong
creator: Liqiong Zhou
subject: Global Health
subject: Nursing
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20331
publisher: PeerJ Inc.
rights: © 2025 Hu et al.
abstract: Background Patients with systemic sclerosis (SSc) frequently experience symptoms such as pain, fatigue, and functional impairments, leading to a significant decline in their quality of life (QoL). Accurately evaluating the QoL of SSc patients is crucial for developing personalized treatment plans and enhancing prognosis. The Systemic Sclerosis Quality of Life Questionnaire (SScQoL), an internationally recognized SSc-specific tool, is commonly used for QoL assessment. However, this questionnaire has not undergone cross-cultural adaptation in China, and its reliability and validity require further validation. Objectives To localize the Systemic Sclerosis Quality of Life Questionnaire (SScQoL) into Chinese and assess its reliability and validity. Methods Following the principles of scale introduction, the Beaton model was employed to translate and back-translate the English version. The scale underwent cross-cultural adaptation through expert consultation, resulting in the Chinese version of the SScQoL test. From August 2023 to December 2024, a convenience sampling method was used to recruit 160 patients with systemic sclerosis from two hospitals for questionnaire surveys to evaluate questionnaire reliability and validity. Results SScQoL comprises five dimensions and 29 items. The content validity index (CVI) at the item level ranges from 0.83 to 1.00, and the CVI at the scale level is 0.97. Exploratory factor analysis identified five common factors, with a cumulative variance contribution rate of 65.761%. The Cronbach’s α coefficient for the total scale is 0.922, and the Cronbach’s α coefficients for the five dimensions range from 0.756 to 0.942. The test-retest reliability for the total scale is 0.969; for the five dimensions, it ranges from 0.710 to 0.961. Conclusions SScQoL is a reliable and effective tool for evaluating patients’ quality of life with systemic sclerosis. This tool can support nurses and researchers and help them formulate targeted strategies, there…
bibliographic citation: Hu et al. (2025) Cross-cultural adaptation and psychometric validation of the Chinese quality-of-life questionnaire for patients with systemic sclerosis. PeerJ 13:e20331 https://doi.org/10.7717/peerj.20331
date submitted: 2025-04-23
date accepted: 2025-10-13
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Yinfeng
author list: Agent
  family name: Zhong
  given name: Wenjie
author list: Agent
  family name: Zhou
  given name: Liqiong
doi: 10.7717/peerj.20331
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: © 2025 Hu et al.
attribution name: Hu et al.

Dissecting antibody-dependent enhancement modulation by Fc-modified cross-neutralizing human monoclonal antibody
type: item
type: AcademicArticle
description: Background Dengue is a mosquito-borne disease caused by four dengue virus serotypes (DENV1 to DENV4). Secondary infections can generate flavivirus cross-reactive antibodies at sub-neutralizing levels. This phenomenon can significantly increase the severity of secondary infections through antibody-dependent enhancement (ADE). ADE is associated with a high risk of viral infection in immune effector cells, triggering cytokine cascades and activating the complement system, which can lead to severe symptoms. Despite extensive studies, therapeutic antibodies, particularly fully human monoclonal antibodies, which could serve as candidates for immune passive therapy, have not yet been discovered. Methodology This study generated LALA-mutated human monoclonal antibody clone B3B9 (LALA-B3B9 HuMAb) which can neutralize all four DENV serotypes without enhancing viral activity. The number of infected cells in the ADE assay was compared among the wild-type antibody (B3B9), LALA-B3B9 HuMAb, and an Fc modified variant at position N297Q (N297Q-B3B9), with or without complement proteins. Moreover, the therapeutic efficacy of these HuMAbs against ADE infection by competing with natural antibodies in patients with acute dengue was evaluated using the in vitro suppression-of-enhancement assay in K562 cells. Result Our novel Fc-modified antibody LALA-B3B9 (Leu234Ala/Leu235Ala mutations), exhibited neutralizing activity against all dengue virus serotypes without triggering ADE activity at any antibody concentration. This outcome was similar to that observed with the previously developed Fc-modified N297Q-B3B9 antibody (N297Q mutation). We further evaluated the effect of complement protein on the enhancing and neutralizing activities of our Fc-modified antibodies. The results showed that LALA-B3B9 and N297Q-B3B9 HuMAbs were complement-independent, meaning that the reduced binding between complement protein (C1q) and the Fc portion of the antibody left the neutralizing and enhancing activit…
format: application/pdf
format: text/html
creator: Subenya Injampa
creator: Surachet Benjathummarak
creator: Sujitra Keadsanti
creator: Rochanawan Sootichote
creator: Wilarat Puangmanee
creator: Atsushi Yamanaka
creator: Tadahiro Sasaki
creator: Pongrama Ramasoota
creator: Pannamthip Pitaksajjakul
subject: Biotechnology
subject: Virology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.20329
publisher: PeerJ Inc.
rights: © 2025 Injampa et al.
abstract: Background Dengue is a mosquito-borne disease caused by four dengue virus serotypes (DENV1 to DENV4). Secondary infections can generate flavivirus cross-reactive antibodies at sub-neutralizing levels. This phenomenon can significantly increase the severity of secondary infections through antibody-dependent enhancement (ADE). ADE is associated with a high risk of viral infection in immune effector cells, triggering cytokine cascades and activating the complement system, which can lead to severe symptoms. Despite extensive studies, therapeutic antibodies, particularly fully human monoclonal antibodies, which could serve as candidates for immune passive therapy, have not yet been discovered. Methodology This study generated LALA-mutated human monoclonal antibody clone B3B9 (LALA-B3B9 HuMAb) which can neutralize all four DENV serotypes without enhancing viral activity. The number of infected cells in the ADE assay was compared among the wild-type antibody (B3B9), LALA-B3B9 HuMAb, and an Fc modified variant at position N297Q (N297Q-B3B9), with or without complement proteins. Moreover, the therapeutic efficacy of these HuMAbs against ADE infection by competing with natural antibodies in patients with acute dengue was evaluated using the in vitro suppression-of-enhancement assay in K562 cells. Result Our novel Fc-modified antibody LALA-B3B9 (Leu234Ala/Leu235Ala mutations), exhibited neutralizing activity against all dengue virus serotypes without triggering ADE activity at any antibody concentration. This outcome was similar to that observed with the previously developed Fc-modified N297Q-B3B9 antibody (N297Q mutation). We further evaluated the effect of complement protein on the enhancing and neutralizing activities of our Fc-modified antibodies. The results showed that LALA-B3B9 and N297Q-B3B9 HuMAbs were complement-independent, meaning that the reduced binding between complement protein (C1q) and the Fc portion of the antibody left the neutralizing and enhancing activit…
bibliographic citation: Injampa et al. (2025) Dissecting antibody-dependent enhancement modulation by Fc-modified cross-neutralizing human monoclonal antibody. PeerJ 13:e20329 https://doi.org/10.7717/peerj.20329
date submitted: 2025-06-03
date accepted: 2025-10-13
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Injampa
  given name: Subenya
author list: Agent
  family name: Benjathummarak
  given name: Surachet
author list: Agent
  family name: Keadsanti
  given name: Sujitra
author list: Agent
  family name: Sootichote
  given name: Rochanawan
author list: Agent
  family name: Puangmanee
  given name: Wilarat
author list: Agent
  family name: Yamanaka
  given name: Atsushi
author list: Agent
  family name: Sasaki
  given name: Tadahiro
author list: Agent
  family name: Ramasoota
  given name: Pongrama
author list: Agent
  family name: Pitaksajjakul
  given name: Pannamthip
doi: 10.7717/peerj.20329
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Injampa et al.
attribution name: Injampa et al.

Comparison of anti-PD-1/PD-L1-based regimens in relapsed/refractory diffuse large B-cell lymphoma: a meta-analysis
type: item
type: AcademicArticle
description: Aim To evaluate the therapeutic value and find out potential combination agents of programmed death 1/programmed death-ligand 1 (PD-1/PD-L1) monoclonal antibody (mAb) in relapsed/refractory (r/r) diffuse large B-cell lymphoma (DLBCL). Methods We conducted a meta-analysis to assess the efficacy and safety of PD-1/PD-L1 mAb in r/r DLBCL, potential qualified studies were searched in PubMed, Embase, Web of Science, and ClinicalTrials.gov. This meta-analysis had been registered on the PROSPERO platform (CRD42023340031). Results After systematic screening, a total of 32 records involving 29 studies were included, pooled survival curves indicated better progression-free survival (PFS) (p < 0.0001; HR = 0.51, 95% CI [0.42–0.62]) and overall survival (OS) (p = 0.013; HR = 0.71, 95% CI [0.57–0.88]) for combination therapy compared with monotherapy. Combination therapy group also achieved a better pooled complete response rate (CRR) (14.6% vs. 3.0%; p < 0.001) and overall response rate (ORR) (30.5% vs. 10.3%; p < 0.001). Analysis of the incidence of adverse events (AEs) did not demonstrate additional toxicities of combination therapy. The limitation was the predominance of single-arm trials, precluding the direct comparison of combination versus partner agents alone. Conclusions These findings support further exploration of PD-1/PD-L1-mAb-based combination therapy to identify long-term survival benefits, while application of monotherapy in unselected DLBCL patients is not recommended.
format: application/pdf
format: text/html
creator: Wenxin Jiang
creator: Tingyu Wen
creator: Peng Liu
subject: Hematology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20314
publisher: PeerJ Inc.
rights: © 2025 Jiang et al.
abstract: Aim To evaluate the therapeutic value and find out potential combination agents of programmed death 1/programmed death-ligand 1 (PD-1/PD-L1) monoclonal antibody (mAb) in relapsed/refractory (r/r) diffuse large B-cell lymphoma (DLBCL). Methods We conducted a meta-analysis to assess the efficacy and safety of PD-1/PD-L1 mAb in r/r DLBCL, potential qualified studies were searched in PubMed, Embase, Web of Science, and ClinicalTrials.gov. This meta-analysis had been registered on the PROSPERO platform (CRD42023340031). Results After systematic screening, a total of 32 records involving 29 studies were included, pooled survival curves indicated better progression-free survival (PFS) (p < 0.0001; HR = 0.51, 95% CI [0.42–0.62]) and overall survival (OS) (p = 0.013; HR = 0.71, 95% CI [0.57–0.88]) for combination therapy compared with monotherapy. Combination therapy group also achieved a better pooled complete response rate (CRR) (14.6% vs. 3.0%; p < 0.001) and overall response rate (ORR) (30.5% vs. 10.3%; p < 0.001). Analysis of the incidence of adverse events (AEs) did not demonstrate additional toxicities of combination therapy. The limitation was the predominance of single-arm trials, precluding the direct comparison of combination versus partner agents alone. Conclusions These findings support further exploration of PD-1/PD-L1-mAb-based combination therapy to identify long-term survival benefits, while application of monotherapy in unselected DLBCL patients is not recommended.
bibliographic citation: Jiang et al. (2025) Comparison of anti-PD-1/PD-L1-based regimens in relapsed/refractory diffuse large B-cell lymphoma: a meta-analysis. PeerJ 13:e20314 https://doi.org/10.7717/peerj.20314
date submitted: 2025-07-16
date accepted: 2025-10-08
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Wenxin
author list: Agent
  family name: Wen
  given name: Tingyu
author list: Agent
  family name: Liu
  given name: Peng
doi: 10.7717/peerj.20314
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Jiang et al.
attribution name: Jiang et al.

Deciphering the role of Hat1 in spermatogenesis: Chromatin organization and beyond
type: item
type: AcademicArticle
description: Spermatogenesis, a core process for male fertility, relies heavily on chromatin organization regulated by histone acetyltransferases (HATs). However, the spatiotemporal expression pattern of histone acetyltransferase 1 (Hat1) in mouse testes and its specific role in spermatogenesis via chromatin organization remain unclear. This study employed RT-qPCR, Western blot, immunofluorescence localization, and bioinformatics to explore Hat1’s dynamic expression and regulatory mechanisms during mouse spermatogenesis. Results showed that both Hat1 mRNA and protein were significantly upregulated in the testes of 8-week-old (mature) mice compared to 3-week-old (immature) mice. Immunofluorescence revealed Hat1 was predominantly localized in the nuclei of male germ cells, with stage-specific expression: highest in spermatogonia and sperm, intermediate in primary spermatocytes, and lowest in secondary spermatocytes. Bioinformatics analysis (based on single-cell sequencing data GSE214315) identified 246 differentially expressed genes (DEGs) related to chromatin organization—these DEGs were screened between adjacent stages of male germ cell development during spermatogenesis, including comparisons of leptotene-zygotene vs. pachytene-diplotene cells, pachytene-diplotene vs. round spermatids, round spermatids vs. early elongating spermatids, and early elongating vs. late elongating spermatids (screening criteria: FDR < 0.05, |log2(FC)| ≥ 1). Additionally, 41 Hat1-interacting proteins encoded by these DEGs were identified. Functional enrichment indicated stage-specific roles of Hat1: in the leptotene-zygotene phase, it participated in transcription regulation to initiate meiosis; in round spermatids, it shifted to refined epigenetic regulation and chromatin assembly for subsequent spermiogenesis; in late spermiogenesis and sperm, it was involved in DNA repair and ATP-dependent chromatin remodeling to protect sperm genetic material. In summary, the stage-specific expression patterns of …
format: application/pdf
format: text/html
creator: Shenni Peng
creator: Yulian Tang
creator: Ruiqun Lu
creator: Shi Huang
creator: Yinyin Mo
creator: Hailing Huang
creator: Genliang Li
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.20240
publisher: PeerJ Inc.
rights: © 2025 Peng et al.
abstract: Spermatogenesis, a core process for male fertility, relies heavily on chromatin organization regulated by histone acetyltransferases (HATs). However, the spatiotemporal expression pattern of histone acetyltransferase 1 (Hat1) in mouse testes and its specific role in spermatogenesis via chromatin organization remain unclear. This study employed RT-qPCR, Western blot, immunofluorescence localization, and bioinformatics to explore Hat1’s dynamic expression and regulatory mechanisms during mouse spermatogenesis. Results showed that both Hat1 mRNA and protein were significantly upregulated in the testes of 8-week-old (mature) mice compared to 3-week-old (immature) mice. Immunofluorescence revealed Hat1 was predominantly localized in the nuclei of male germ cells, with stage-specific expression: highest in spermatogonia and sperm, intermediate in primary spermatocytes, and lowest in secondary spermatocytes. Bioinformatics analysis (based on single-cell sequencing data GSE214315) identified 246 differentially expressed genes (DEGs) related to chromatin organization—these DEGs were screened between adjacent stages of male germ cell development during spermatogenesis, including comparisons of leptotene-zygotene vs. pachytene-diplotene cells, pachytene-diplotene vs. round spermatids, round spermatids vs. early elongating spermatids, and early elongating vs. late elongating spermatids (screening criteria: FDR < 0.05, |log2(FC)| ≥ 1). Additionally, 41 Hat1-interacting proteins encoded by these DEGs were identified. Functional enrichment indicated stage-specific roles of Hat1: in the leptotene-zygotene phase, it participated in transcription regulation to initiate meiosis; in round spermatids, it shifted to refined epigenetic regulation and chromatin assembly for subsequent spermiogenesis; in late spermiogenesis and sperm, it was involved in DNA repair and ATP-dependent chromatin remodeling to protect sperm genetic material. In summary, the stage-specific expression patterns of …
bibliographic citation: Peng et al. (2025) Deciphering the role of Hat1 in spermatogenesis: Chromatin organization and beyond. PeerJ 13:e20240 https://doi.org/10.7717/peerj.20240
date submitted: 2025-06-04
date accepted: 2025-09-24
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Shenni
author list: Agent
  family name: Tang
  given name: Yulian
author list: Agent
  family name: Lu
  given name: Ruiqun
author list: Agent
  family name: Huang
  given name: Shi
author list: Agent
  family name: Mo
  given name: Yinyin
author list: Agent
  family name: Huang
  given name: Hailing
author list: Agent
  family name: Li
  given name: Genliang
doi: 10.7717/peerj.20240
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Peng et al.
attribution name: Peng et al.

A Bayesian model for assessing organic matter supply in complex marine food webs using amino acid stable isotope analysis
type: item
type: AcademicArticle
description: While several software packages have been developed to solve stable isotope mixing models, none are currently equipped to trace the flow of organic matter through the lower trophic levels of planktonic food webs. To address this gap, we have developed a new Bayesian mixing model tailored for use with δ15N values of individual amino acids. This model simultaneously estimates trophic relationships between consumers and organic matter sources at the base of the food web, determines the relative contributions of these basal organic matter sources to consumers, and accounts for trophic discrimination affecting amino acid δ15N values during protozoan and metazoan trophic steps. This “Organic Matter Supply Model” is uniquely suited for applications where food web structure is unknown and trophic intermediaries, such as protozoan and metazoan grazers with distinct amino acid trophic discrimination factors, play a critical role in nutrient transfer. In this paper, we describe the model’s basic structure, outline key considerations for adapting it to specific applications, evaluate its performance using simulated zooplankton data, discuss its strengths and limitations, and offer recommendations for its further development. By testing the model on simulated zooplankton amino acid δ15N data, we demonstrate that the Organic Matter Supply Model can enhance our understanding of the roles of small particles and diel vertical migration in deep-sea organic matter supply pathways. Furthermore, it provides a new framework for exploring the foundational role of heterotrophic protists in marine ecosystems. We find specific subsets of amino acids to be most useful as markers of trophic ecology (in this case including glutamic acid and proline) and to identify supply from basal organic matter sources (phenylalanine, lysine, and threonine). Other amino acids may be more ideal source tracers in other settings, although amino acids with inconsistent or poorly constrained isotope fractionation…
format: application/pdf
format: text/html
creator: Connor H.H. Shea
creator: Jeffrey C. Drazen
creator: Brian N. Popp
subject: Ecology
subject: Ecosystem Science
subject: Statistics
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.20220
publisher: PeerJ Inc.
rights: © 2025 Shea et al.
abstract: While several software packages have been developed to solve stable isotope mixing models, none are currently equipped to trace the flow of organic matter through the lower trophic levels of planktonic food webs. To address this gap, we have developed a new Bayesian mixing model tailored for use with δ15N values of individual amino acids. This model simultaneously estimates trophic relationships between consumers and organic matter sources at the base of the food web, determines the relative contributions of these basal organic matter sources to consumers, and accounts for trophic discrimination affecting amino acid δ15N values during protozoan and metazoan trophic steps. This “Organic Matter Supply Model” is uniquely suited for applications where food web structure is unknown and trophic intermediaries, such as protozoan and metazoan grazers with distinct amino acid trophic discrimination factors, play a critical role in nutrient transfer. In this paper, we describe the model’s basic structure, outline key considerations for adapting it to specific applications, evaluate its performance using simulated zooplankton data, discuss its strengths and limitations, and offer recommendations for its further development. By testing the model on simulated zooplankton amino acid δ15N data, we demonstrate that the Organic Matter Supply Model can enhance our understanding of the roles of small particles and diel vertical migration in deep-sea organic matter supply pathways. Furthermore, it provides a new framework for exploring the foundational role of heterotrophic protists in marine ecosystems. We find specific subsets of amino acids to be most useful as markers of trophic ecology (in this case including glutamic acid and proline) and to identify supply from basal organic matter sources (phenylalanine, lysine, and threonine). Other amino acids may be more ideal source tracers in other settings, although amino acids with inconsistent or poorly constrained isotope fractionation…
bibliographic citation: Shea et al. (2025) A Bayesian model for assessing organic matter supply in complex marine food webs using amino acid stable isotope analysis. PeerJ 13:e20220 https://doi.org/10.7717/peerj.20220
date submitted: 2025-05-30
date accepted: 2025-09-21
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shea
  given name: Connor H.H.
author list: Agent
  family name: Drazen
  given name: Jeffrey C.
author list: Agent
  family name: Popp
  given name: Brian N.
doi: 10.7717/peerj.20220
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Shea et al.
attribution name: Shea et al.

Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province
type: item
type: AcademicArticle
description: Background Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province. Methods Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing. Results The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal–Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative ab…
format: application/pdf
format: text/html
creator: Senquan Jia
creator: Wenpeng Gu
creator: Lili Jiang
creator: Yong Zhang
creator: Xiaoqing Fu
creator: Jianwen Yin
creator: Yongming Zhou
subject: Microbiology
subject: Global Health
subject: Public Health
subject: Environmental Contamination and Remediation
subject: Environmental Health
description: doi:10.7717/peerj.20199
publisher: PeerJ Inc.
rights: © 2025 Jia et al.
abstract: Background Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province. Methods Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing. Results The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal–Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative ab…
bibliographic citation: Jia et al. (2025) Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province. PeerJ 13:e20199 https://doi.org/10.7717/peerj.20199
date submitted: 2025-03-04
date accepted: 2025-09-16
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jia
  given name: Senquan
author list: Agent
  family name: Gu
  given name: Wenpeng
author list: Agent
  family name: Jiang
  given name: Lili
author list: Agent
  family name: Zhang
  given name: Yong
author list: Agent
  family name: Fu
  given name: Xiaoqing
author list: Agent
  family name: Yin
  given name: Jianwen
author list: Agent
  family name: Zhou
  given name: Yongming
doi: 10.7717/peerj.20199
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Jia et al.
attribution name: Jia et al.

AIMP1: multifunctional regulator in physiology and pathology with therapeutic implications
type: item
type: AcademicArticle
description: Aminoacyl tRNA synthetase complex interacting multifunctional protein 1 (AIMP1), also referred to as p43, serves as an auxiliary factor of the macromolecular aminoacyl tRNA synthetase complex. Beyond its classical role in the assembling the multisynthetase complex (MSC) for protein translation, growing evidence has elucidated that AIMP1 plays a pivotal role in regulating immune response, brain function and angiogenesis. Furthermore, accumulating studies have demonstrated that AIMP1 is involved in a spectrum of pathological processes, including cancer, immunity associated disorders, and neurological diseases. Herein, we summarize the current research regarding the functions of AIMP1 under both physiological and pathological conditions, with a particular focus on its therapeutic potential in these diseases.
format: application/pdf
format: text/html
creator: Xunan Yuan
creator: Xinmiao Wang
creator: Xiaodan Ma
creator: Yaping Mao
creator: Qinqin Wang
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Immunology
subject: Neurology
description: doi:10.7717/peerj.20334
publisher: PeerJ Inc.
rights: © 2025 Yuan et al.
abstract: Aminoacyl tRNA synthetase complex interacting multifunctional protein 1 (AIMP1), also referred to as p43, serves as an auxiliary factor of the macromolecular aminoacyl tRNA synthetase complex. Beyond its classical role in the assembling the multisynthetase complex (MSC) for protein translation, growing evidence has elucidated that AIMP1 plays a pivotal role in regulating immune response, brain function and angiogenesis. Furthermore, accumulating studies have demonstrated that AIMP1 is involved in a spectrum of pathological processes, including cancer, immunity associated disorders, and neurological diseases. Herein, we summarize the current research regarding the functions of AIMP1 under both physiological and pathological conditions, with a particular focus on its therapeutic potential in these diseases.
bibliographic citation: Yuan et al. (2025) AIMP1: multifunctional regulator in physiology and pathology with therapeutic implications. PeerJ 13:e20334 https://doi.org/10.7717/peerj.20334
date submitted: 2025-05-30
date accepted: 2025-10-13
issued: 2025-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yuan
  given name: Xunan
author list: Agent
  family name: Wang
  given name: Xinmiao
author list: Agent
  family name: Ma
  given name: Xiaodan
author list: Agent
  family name: Mao
  given name: Yaping
author list: Agent
  family name: Wang
  given name: Qinqin
doi: 10.7717/peerj.20334
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-18
copyright: © 2025 Yuan et al.
attribution name: Yuan et al.

Machine learning classification of mango maturity based on carotene content from Raman spectra
type: item
type: AcademicArticle
description: Determining mango ripeness is essential for ensuring its delicious taste, enticing aroma, and rich nutritional value. For farmers, harvesting mangoes too early can result in stunted fruit and lower yields compared to those harvested at a ripe stage. This study aims to develop a potentially non-invasive and efficient method for detecting mango ripeness using Raman spectroscopy. Traditional methods, which rely on human assessment and color evaluation with image processing, are inconsistent, inaccurate, and time-consuming due to variations in mango color and individual differences in vision and perception. To address these limitations, this study pursued three main objectives: extracting data characteristics of organic compounds in mangoes based on raw Raman spectrum data, identifying the correlation between carotene characteristics and mango ripeness levels, and evaluating the performance of machine learning models in classifying mango ripeness levels. A total of 29 mango fruit spectra were analyzed, with 13 samples selected to represent three ripeness categories: underripe, ripe, and overripe. Raman spectra peak signal analysis revealed that mango peel contains lycopene, β-carotene, lutein, and neoxanthin, all of which are derived from carotenoid molecules in the range of 1,480 cm−1 to 1,550 cm−1. Statistical analysis confirmed the significance (p < 0.05) of extracted Raman Peak Intensity features in distinguishing ripeness levels, supported by high correlation coefficients between carotenoid peak intensity and mango maturity. This study achieved 100% accuracy in classifying mango ripeness levels using three classifier models: the Medium Gaussian Support Vector Machine, the Cubic Support Vector Machine, and the Weighted K-Nearest Neighbors. Raman spectroscopy has proven to be a reliable and robust method, immune to external factors such as light, humidity, and noise, which makes it a promising approach for assessing mango ripeness.
format: application/pdf
format: text/html
creator: Ji Loun Tan
creator: Fazida Hanim Hashim
creator: Jahariah Sampe
creator: Aqilah Baseri Huddin
creator: Ghassan Maan Salim
creator: Sawal Hamid Md Ali
subject: Biochemistry
subject: Plant Science
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20288
publisher: PeerJ Inc.
rights: © 2025 Tan et al.
abstract: Determining mango ripeness is essential for ensuring its delicious taste, enticing aroma, and rich nutritional value. For farmers, harvesting mangoes too early can result in stunted fruit and lower yields compared to those harvested at a ripe stage. This study aims to develop a potentially non-invasive and efficient method for detecting mango ripeness using Raman spectroscopy. Traditional methods, which rely on human assessment and color evaluation with image processing, are inconsistent, inaccurate, and time-consuming due to variations in mango color and individual differences in vision and perception. To address these limitations, this study pursued three main objectives: extracting data characteristics of organic compounds in mangoes based on raw Raman spectrum data, identifying the correlation between carotene characteristics and mango ripeness levels, and evaluating the performance of machine learning models in classifying mango ripeness levels. A total of 29 mango fruit spectra were analyzed, with 13 samples selected to represent three ripeness categories: underripe, ripe, and overripe. Raman spectra peak signal analysis revealed that mango peel contains lycopene, β-carotene, lutein, and neoxanthin, all of which are derived from carotenoid molecules in the range of 1,480 cm−1 to 1,550 cm−1. Statistical analysis confirmed the significance (p < 0.05) of extracted Raman Peak Intensity features in distinguishing ripeness levels, supported by high correlation coefficients between carotenoid peak intensity and mango maturity. This study achieved 100% accuracy in classifying mango ripeness levels using three classifier models: the Medium Gaussian Support Vector Machine, the Cubic Support Vector Machine, and the Weighted K-Nearest Neighbors. Raman spectroscopy has proven to be a reliable and robust method, immune to external factors such as light, humidity, and noise, which makes it a promising approach for assessing mango ripeness.
bibliographic citation: Tan et al. (2025) Machine learning classification of mango maturity based on carotene content from Raman spectra. PeerJ 13:e20288 https://doi.org/10.7717/peerj.20288
date submitted: 2025-05-05
date accepted: 2025-10-03
issued: 2025-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Ji Loun
author list: Agent
  family name: Hashim
  given name: Fazida Hanim
author list: Agent
  family name: Sampe
  given name: Jahariah
author list: Agent
  family name: Baseri Huddin
  given name: Aqilah
author list: Agent
  family name: Salim
  given name: Ghassan Maan
author list: Agent
  family name: Md Ali
  given name: Sawal Hamid
doi: 10.7717/peerj.20288
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-18
copyright: ©2025 Tan et al.
attribution name: Tan et al.

Identification of mitochondrial-related genes to evaluate the immune infiltration and prognosis of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Mitochondrial dysfunction critically impacts lung adenocarcinoma (LUAD) progression and tumor microenvironment (TME) remodeling, highlighting the urgent need to identify predictive biomarkers with clinical utility. Methods RNA-seq data sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify mitochondrial-related (MTR) genes associated with LUAD progression. A three-gene prognostic signature, consisting of SFXN1, CPS1, and MTFR2, was developed through univariate, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. Functional enrichment, immune infiltration, and tumor mutation burden (TMB) analyses were performed to characterize the TME. Experimental studies were conducted in LUAD cell lines via siRNA-mediated knockdown, assessing mitochondrial dynamics, mitochondrial membrane potential (ΔΨm), reactive oxygen species (ROS) levels, and mitochondrial DNA (mtDNA) stability. Results The signature stratified patients into high-risk and low-risk groups with significant survival differences (TCGA: HR = 1.476, P < 0.001; GSE31210: P < 0.001; GSE30219: P = 0.001). High-risk patients exhibited features of immunosuppressive TME, including elevated tumor purity, higher TIDE scores, increased TMB, and immune checkpoint expression (CD274, CD276, PDCD1, RELT). Functional analyses revealed that siRNA-mediated knockdown of CPS1 triggered mitochondrial fission, as evidenced by ΔΨm↓/ROS↑. Conversely, SFXN1 knockdown induced mitochondrial fusion accompanied by hyperpolarization (ΔΨm↑/ROS↓). Notably, MTFR2 knockdown promoted mitochondrial fusion, contributing to ΔΨm↑/ROS↓. All three siRNA treatments compromised mtDNA integrity, with CPS1 knockdown uniquely inducing the release of cytosolic mtDNA. Conclusion This study has successfully established a mitochondrial-related prognostic signature that predicts survival outcomes and immune phenotypes of LUAD patients, providing a clinically …
format: application/pdf
format: text/html
creator: Yutong Ge
creator: Ao Sun
creator: Tao Yu
creator: Shaokun Yu
creator: Kaihua Lu
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20262
publisher: PeerJ Inc.
rights: © 2025 Ge et al.
abstract: Background Mitochondrial dysfunction critically impacts lung adenocarcinoma (LUAD) progression and tumor microenvironment (TME) remodeling, highlighting the urgent need to identify predictive biomarkers with clinical utility. Methods RNA-seq data sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify mitochondrial-related (MTR) genes associated with LUAD progression. A three-gene prognostic signature, consisting of SFXN1, CPS1, and MTFR2, was developed through univariate, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. Functional enrichment, immune infiltration, and tumor mutation burden (TMB) analyses were performed to characterize the TME. Experimental studies were conducted in LUAD cell lines via siRNA-mediated knockdown, assessing mitochondrial dynamics, mitochondrial membrane potential (ΔΨm), reactive oxygen species (ROS) levels, and mitochondrial DNA (mtDNA) stability. Results The signature stratified patients into high-risk and low-risk groups with significant survival differences (TCGA: HR = 1.476, P < 0.001; GSE31210: P < 0.001; GSE30219: P = 0.001). High-risk patients exhibited features of immunosuppressive TME, including elevated tumor purity, higher TIDE scores, increased TMB, and immune checkpoint expression (CD274, CD276, PDCD1, RELT). Functional analyses revealed that siRNA-mediated knockdown of CPS1 triggered mitochondrial fission, as evidenced by ΔΨm↓/ROS↑. Conversely, SFXN1 knockdown induced mitochondrial fusion accompanied by hyperpolarization (ΔΨm↑/ROS↓). Notably, MTFR2 knockdown promoted mitochondrial fusion, contributing to ΔΨm↑/ROS↓. All three siRNA treatments compromised mtDNA integrity, with CPS1 knockdown uniquely inducing the release of cytosolic mtDNA. Conclusion This study has successfully established a mitochondrial-related prognostic signature that predicts survival outcomes and immune phenotypes of LUAD patients, providing a clinically …
bibliographic citation: Ge et al. (2025) Identification of mitochondrial-related genes to evaluate the immune infiltration and prognosis of lung adenocarcinoma. PeerJ 13:e20262 https://doi.org/10.7717/peerj.20262
date submitted: 2025-04-23
date accepted: 2025-09-29
issued: 2025-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ge
  given name: Yutong
author list: Agent
  family name: Sun
  given name: Ao
author list: Agent
  family name: Yu
  given name: Tao
author list: Agent
  family name: Yu
  given name: Shaokun
author list: Agent
  family name: Lu
  given name: Kaihua
doi: 10.7717/peerj.20262
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-18
copyright: © 2025 Ge et al.
attribution name: Ge et al.

Acute effect of short foot exercise on dynamic stability and foot kinematic in trail runners: a proof-of-concept study
type: item
type: AcademicArticle
description: Background Trail runners face uneven terrains requiring optimal foot stability and postural control. The short foot exercise (SFE) may acutely enhance dynamic balance and foot arch height, potentially mitigating injury risk. This study aimed to evaluate the acute effects of the SFE on postural control and kinematics during a dynamic balance test in trail runners, considering the variations in the weekly training volumes of the participants. Methods Sixteen adult trail runners (mean age 36 ± 8.4 years; 50% male) with at least one year of trail running experience were evaluated. Dynamic balance was assessed using the Y-Balance Test (YBT), and kinematics of the foot arch were measured via the Arch Height Index (AHI) using a 3D motion capture system. Baseline measurements were taken, followed by an SFE protocol: the participants had to perform 12 repetitions of 5-second contractions, which they did in three sets with 2 minutes of rest between sets. Immediately afterward, YBT and AHI were reassessed. Results YBT showed significant improvements in all reach directions after the application of the SFE (p < 0.05). In contrast, no significant changes were observed in the AHI across reach directions (p > 0.05). Yet, subgroup analysis by weekly training volume revealed that participants with higher weekly volumes experienced a significant increase in anterior AHI (mean difference = −0.54 mm; 95% CI [−1.09 to 0.01]; p = 0.027; effect size = 0.13). The SFE may acutely improve foot kinematics and dynamic balance in trail runners; however, these effects are influenced by the weekly training volume of the participants. Conclusion This study suggests that a single session of the SFE may induce acute improvements in arch height and dynamic balance in trail runners, with differential responses depending on training volume. These preliminary results highlight the potential of the SFE as an acute activation strategy for the intrinsic foot muscles, but caution should be exercised when ex…
format: application/pdf
format: text/html
creator: Claudio Aguilar-Risco
creator: Mauricio San Martín-Correa
creator: Felipe Araya-Quintanilla
creator: Joaquín Calatayud
creator: Guillermo Mendez-Rebolledo
subject: Kinesiology
description: doi:10.7717/peerj.20364
publisher: PeerJ Inc.
rights: © 2025 Aguilar-Risco et al.
abstract: Background Trail runners face uneven terrains requiring optimal foot stability and postural control. The short foot exercise (SFE) may acutely enhance dynamic balance and foot arch height, potentially mitigating injury risk. This study aimed to evaluate the acute effects of the SFE on postural control and kinematics during a dynamic balance test in trail runners, considering the variations in the weekly training volumes of the participants. Methods Sixteen adult trail runners (mean age 36 ± 8.4 years; 50% male) with at least one year of trail running experience were evaluated. Dynamic balance was assessed using the Y-Balance Test (YBT), and kinematics of the foot arch were measured via the Arch Height Index (AHI) using a 3D motion capture system. Baseline measurements were taken, followed by an SFE protocol: the participants had to perform 12 repetitions of 5-second contractions, which they did in three sets with 2 minutes of rest between sets. Immediately afterward, YBT and AHI were reassessed. Results YBT showed significant improvements in all reach directions after the application of the SFE (p < 0.05). In contrast, no significant changes were observed in the AHI across reach directions (p > 0.05). Yet, subgroup analysis by weekly training volume revealed that participants with higher weekly volumes experienced a significant increase in anterior AHI (mean difference = −0.54 mm; 95% CI [−1.09 to 0.01]; p = 0.027; effect size = 0.13). The SFE may acutely improve foot kinematics and dynamic balance in trail runners; however, these effects are influenced by the weekly training volume of the participants. Conclusion This study suggests that a single session of the SFE may induce acute improvements in arch height and dynamic balance in trail runners, with differential responses depending on training volume. These preliminary results highlight the potential of the SFE as an acute activation strategy for the intrinsic foot muscles, but caution should be exercised when ex…
bibliographic citation: Aguilar-Risco et al. (2025) Acute effect of short foot exercise on dynamic stability and foot kinematic in trail runners: a proof-of-concept study. PeerJ 13:e20364 https://doi.org/10.7717/peerj.20364
date submitted: 2025-03-14
date accepted: 2025-10-17
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aguilar-Risco
  given name: Claudio
author list: Agent
  family name: San Martín-Correa
  given name: Mauricio
author list: Agent
  family name: Araya-Quintanilla
  given name: Felipe
author list: Agent
  family name: Calatayud
  given name: Joaquín
author list: Agent
  family name: Mendez-Rebolledo
  given name: Guillermo
doi: 10.7717/peerj.20364
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: ©2025 Aguilar-Risco et al.
attribution name: Aguilar-Risco et al.

Estuarine bivalve metabolic response mediated by environmental drivers
type: item
type: AcademicArticle
description: Humans are rapidly modifying environmental conditions in estuaries, which are among Earth’s most productive and dynamic ecosystems. Bivalve molluscs are key estuarine organisms, contributing to range of ecosystem functions and services, though human-induced environmental changes are affecting their behaviour, physiology, and fitness with implications at individual, population, community, and ecosystem levels. Understanding how estuarine bivalves respond and adapt to different environmental drivers will enable us to better predict change at multiple levels of biological organisation. In this study, we investigated the metabolites of a common and ecological important suspension-feeding bivalve in New Zealand, the cockle, Austrovenus stutchburyi. At seven of eight pre-established monitoring sites in a North Island estuary, we evaluated differences in cockle metabolite abundance, diversity, and composition, as well as relationships between cockle metabolites and environmental conditions. Our findings revealed differences in the abundance and diversity of cockle metabolites across sites, particularly in the metabolites alanine, aspartic acid, glutamic acid, glycine, proline, and succinic acid. The differences in metabolites across sites were mediated by the site-specific environmental conditions, in particular, the sediment’s mud content and organic matter. Differences in metabolites were most pronounced when comparing sites close to freshwater inputs versus sites located closer to the estuary mouth. In general, Austrovenus metabolite abundance was higher at sites with less signs of stress (i.e., close to the estuary mouth) and lower in sites with with higher mud content (i.e., close to freshwater inputs), while the metabolite diversity followed an inverse pattern. The metabolic responses of cockles appeared to be linked to processes such as feeding, oxygen regulation, and energy allocation. The observed metabolic trends highlight the complex interactions between cockles…
format: application/pdf
format: text/html
creator: Orlando Lam-Gordillo
creator: Emily J. Douglas
creator: Sarah F. Hailes
creator: Andrew M. Lohrer
subject: Ecology
subject: Marine Biology
subject: Metabolic Sciences
subject: Environmental Impacts
description: doi:10.7717/peerj.20357
publisher: PeerJ Inc.
rights: © 2025 Lam-Gordillo et al.
abstract: Humans are rapidly modifying environmental conditions in estuaries, which are among Earth’s most productive and dynamic ecosystems. Bivalve molluscs are key estuarine organisms, contributing to range of ecosystem functions and services, though human-induced environmental changes are affecting their behaviour, physiology, and fitness with implications at individual, population, community, and ecosystem levels. Understanding how estuarine bivalves respond and adapt to different environmental drivers will enable us to better predict change at multiple levels of biological organisation. In this study, we investigated the metabolites of a common and ecological important suspension-feeding bivalve in New Zealand, the cockle, Austrovenus stutchburyi. At seven of eight pre-established monitoring sites in a North Island estuary, we evaluated differences in cockle metabolite abundance, diversity, and composition, as well as relationships between cockle metabolites and environmental conditions. Our findings revealed differences in the abundance and diversity of cockle metabolites across sites, particularly in the metabolites alanine, aspartic acid, glutamic acid, glycine, proline, and succinic acid. The differences in metabolites across sites were mediated by the site-specific environmental conditions, in particular, the sediment’s mud content and organic matter. Differences in metabolites were most pronounced when comparing sites close to freshwater inputs versus sites located closer to the estuary mouth. In general, Austrovenus metabolite abundance was higher at sites with less signs of stress (i.e., close to the estuary mouth) and lower in sites with with higher mud content (i.e., close to freshwater inputs), while the metabolite diversity followed an inverse pattern. The metabolic responses of cockles appeared to be linked to processes such as feeding, oxygen regulation, and energy allocation. The observed metabolic trends highlight the complex interactions between cockles…
bibliographic citation: Lam-Gordillo et al. (2025) Estuarine bivalve metabolic response mediated by environmental drivers. PeerJ 13:e20357 https://doi.org/10.7717/peerj.20357
date submitted: 2025-07-28
date accepted: 2025-10-16
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lam-Gordillo
  given name: Orlando
author list: Agent
  family name: Douglas
  given name: Emily J.
author list: Agent
  family name: Hailes
  given name: Sarah F.
author list: Agent
  family name: Lohrer
  given name: Andrew M.
doi: 10.7717/peerj.20357
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: ©2025 Lam-Gordillo et al.
attribution name: Lam-Gordillo et al.

Effects of combined exercise training for adults with resistant major depression: a pilot study from the TRACE-RMD project
type: item
type: AcademicArticle
description: Background This pilot study analyzed the changes in body composition, cardiorespiratory fitness (CRF), biochemical profile, clinical symptoms, and quality of life (QoL) of adults with resistant major depression (RMD) following 12 weeks of combined exercise training. Methods Eighteen adults diagnosed with RMD (42.5 ± 9.9 years, 66.7% women) participated in a supervised exercise group (2 days/week). The combined exercise training consisted of low-to-moderate intensity aerobic interval exercise on a bicycle and strength-resistance exercises. All variables were assessed pre- and post-intervention, including clinical symptoms with the Montgomery-Åsberg Depression Rating Scale (MADRS), the Clinical Global Impressions Scale (CGI-S), the Sheehan Disability Scale (SDS), and health-related QoL with the Short Form-36. A symptom-limited cardiopulmonary exercise peak test was performed to evaluate CRF. Results The baseline results classified the participants as metabolically unhealthy with overweight/obesity, moderate depression, and low CRF and QoL. Following the intervention, there were no significant changes (P > 0.05) in body composition, the main CRF physiological variables, and the biochemical profile. However, regarding clinical symptoms, the MADRS (mean difference −8.31, 95% confidence interval (CI) [−15.1 to −1.5], P = 0.021), CGI-S (mean difference -1.17, 95% CI [−1.92 to −0.41], P = 0.006), and SDS (mean difference -5.46, 95% CI [−10.8 to −0.12], P = 0.046) scores decreased, and the domains of health-related QoL –general health (mean difference 13.8, 95% CI [2.9–24.8], P = 0.017), vitality (mean difference 10.4, 95% CI [0.26–20.5], P = 0.045), social functioning (mean difference 25.9, 95% CI [8.1–43.7], P = 0.008), and the mental component summary (mean difference 6.9, 95% CI [1.1–12.8], P = 0.024) increased. Conclusions A supervised combined exercise program in people with RMD may induce positive and beneficial changes in functionality and clinical and QoL variables,…
format: application/pdf
format: text/html
creator: Mikel Tous-Espelosin
creator: Cristóbal Pavón-Navajas
creator: José Etxaniz-Oses
creator: María Teresa Cañas-García
creator: Sara Maldonado-Martin
creator: Julene Orruño-Vivar
creator: Pablo Corres
creator: Nagore Iriarte-Yoller
subject: Clinical Trials
subject: Psychiatry and Psychology
subject: Mental Health
subject: Sports Medicine
description: doi:10.7717/peerj.20356
publisher: PeerJ Inc.
rights: © 2025 Tous-Espelosin et al.
abstract: Background This pilot study analyzed the changes in body composition, cardiorespiratory fitness (CRF), biochemical profile, clinical symptoms, and quality of life (QoL) of adults with resistant major depression (RMD) following 12 weeks of combined exercise training. Methods Eighteen adults diagnosed with RMD (42.5 ± 9.9 years, 66.7% women) participated in a supervised exercise group (2 days/week). The combined exercise training consisted of low-to-moderate intensity aerobic interval exercise on a bicycle and strength-resistance exercises. All variables were assessed pre- and post-intervention, including clinical symptoms with the Montgomery-Åsberg Depression Rating Scale (MADRS), the Clinical Global Impressions Scale (CGI-S), the Sheehan Disability Scale (SDS), and health-related QoL with the Short Form-36. A symptom-limited cardiopulmonary exercise peak test was performed to evaluate CRF. Results The baseline results classified the participants as metabolically unhealthy with overweight/obesity, moderate depression, and low CRF and QoL. Following the intervention, there were no significant changes (P > 0.05) in body composition, the main CRF physiological variables, and the biochemical profile. However, regarding clinical symptoms, the MADRS (mean difference −8.31, 95% confidence interval (CI) [−15.1 to −1.5], P = 0.021), CGI-S (mean difference -1.17, 95% CI [−1.92 to −0.41], P = 0.006), and SDS (mean difference -5.46, 95% CI [−10.8 to −0.12], P = 0.046) scores decreased, and the domains of health-related QoL –general health (mean difference 13.8, 95% CI [2.9–24.8], P = 0.017), vitality (mean difference 10.4, 95% CI [0.26–20.5], P = 0.045), social functioning (mean difference 25.9, 95% CI [8.1–43.7], P = 0.008), and the mental component summary (mean difference 6.9, 95% CI [1.1–12.8], P = 0.024) increased. Conclusions A supervised combined exercise program in people with RMD may induce positive and beneficial changes in functionality and clinical and QoL variables,…
bibliographic citation: Tous-Espelosin et al. (2025) Effects of combined exercise training for adults with resistant major depression: a pilot study from the TRACE-RMD project. PeerJ 13:e20356 https://doi.org/10.7717/peerj.20356
date submitted: 2025-02-17
date accepted: 2025-10-16
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tous-Espelosin
  given name: Mikel
author list: Agent
  family name: Pavón-Navajas
  given name: Cristóbal
author list: Agent
  family name: Etxaniz-Oses
  given name: José
author list: Agent
  family name: Cañas-García
  given name: María Teresa
author list: Agent
  family name: Maldonado-Martin
  given name: Sara
author list: Agent
  family name: Orruño-Vivar
  given name: Julene
author list: Agent
  family name: Corres
  given name: Pablo
author list: Agent
  family name: Iriarte-Yoller
  given name: Nagore
doi: 10.7717/peerj.20356
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: ©2025 Tous-Espelosin et al.
attribution name: Tous-Espelosin et al.

Tryptophan-kynurenine pathway: a possible new mechanism for the prevention and treatment of reproductive system-related diseases
type: item
type: AcademicArticle
description: Tryptophan (Trp) is one of the essential amino acids, and its metabolic pathway is essential for the maintenance of normal human physiological activities. Among them, various metabolites and rate-limiting enzymes of the tryptophan-kynurenine metabolic pathway play important roles in inflammatory responses, immune regulation, energy metabolism, as well as neuroprotective and toxic effects. Abnormalities in tryptophan-kynurenine pathway metabolism thus inevitably lead to numerous pathological changes, such as reproductive disorders. It is noteworthy that the prevention and treatment of reproductive diseases are not currently focused on this pathway. In view of the increasing number of studies that have found abnormalities in the levels of key enzymes and metabolites of tryptophan-kynurenine in reproductive diseases, this article will focus on summarizing the molecular mechanisms and relevance of the pathway in reproductive diseases, as well as proposing new ideas for the prevention and treatment of reproductive diseases, including the use of inhibitors of the pathway and the regulation of tryptophan metabolism in the intestinal flora.
format: application/pdf
format: text/html
creator: Zhongkai Ou
creator: Aixia Xu
creator: Hua Su
creator: Yiting Liu
creator: Jia Li
subject: Biochemistry
subject: Andrology
subject: Gynecology and Obstetrics
subject: Women’s Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.20342
publisher: PeerJ Inc.
rights: © 2025 Ou et al.
abstract: Tryptophan (Trp) is one of the essential amino acids, and its metabolic pathway is essential for the maintenance of normal human physiological activities. Among them, various metabolites and rate-limiting enzymes of the tryptophan-kynurenine metabolic pathway play important roles in inflammatory responses, immune regulation, energy metabolism, as well as neuroprotective and toxic effects. Abnormalities in tryptophan-kynurenine pathway metabolism thus inevitably lead to numerous pathological changes, such as reproductive disorders. It is noteworthy that the prevention and treatment of reproductive diseases are not currently focused on this pathway. In view of the increasing number of studies that have found abnormalities in the levels of key enzymes and metabolites of tryptophan-kynurenine in reproductive diseases, this article will focus on summarizing the molecular mechanisms and relevance of the pathway in reproductive diseases, as well as proposing new ideas for the prevention and treatment of reproductive diseases, including the use of inhibitors of the pathway and the regulation of tryptophan metabolism in the intestinal flora.
bibliographic citation: Ou et al. (2025) Tryptophan-kynurenine pathway: a possible new mechanism for the prevention and treatment of reproductive system-related diseases. PeerJ 13:e20342 https://doi.org/10.7717/peerj.20342
date submitted: 2025-04-22
date accepted: 2025-10-15
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ou
  given name: Zhongkai
author list: Agent
  family name: Xu
  given name: Aixia
author list: Agent
  family name: Su
  given name: Hua
author list: Agent
  family name: Liu
  given name: Yiting
author list: Agent
  family name: Li
  given name: Jia
doi: 10.7717/peerj.20342
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: ©2025 Ou et al.
attribution name: Ou et al.

Latitudinal variations in morphometric traits and bioenergetic status of adult red squat lobsters Grimothea monodon (H. Milne Edwards, 1837) in the Southeast Pacific Ocean
type: item
type: AcademicArticle
description: Adults of the red squat lobster (Grimothea monodon) present two morphotypes (small-pelagic (SP) and large-benthic (LB)) in their wide geographic distribution range in the Southeastern Pacific Ocean (SEPO). In this marine ecosystem, they are exposed to conspicuous latitudinal variations in oceanographic and physicochemical parameters that affect their nutritional and fitness status. The objective of this study was to determine variations in the bioenergetic condition at the level of morphometric, sexual and biochemical traits of G. monodon, considering a wide spatial scale of their populations’ distribution along a latitudinal gradient (from 9°S to 36°S) in the SEPO. According to the environmental parameters, temperature and dissolved oxygen presented abrupt changes between 15°S–17°S, while chlorophyll and salinity showed a constant reduction along the latitudinal gradient. When environmental parameters were related to the size of the two morphotypes (SP, LB) of G. monodon, some trends of change were observed, while the relative condition factor showed significant differences along the latitudinal gradient. The biochemical condition of SP individuals showed an increasing trend in glucose from Chimbote to Chala, proteins showed abrupt changes in three zones (between Huacho-Lima, Lomitas, and Chala), and lipids showed a notable change between Lima-Cañete. In turn, in LB individual’s increases were recorded in all their biochemical constituents towards high latitudes. A slight variability in fatty acids was observed between SP individuals from the north (Chimbote, Huarmey, Huacho) and SP individuals from the south (Marcona, Chala, Planchada, Mollendo). In addition, significant latitudinal differences were observed in the fatty acids of the two morphotypes (SP, LP). The nutritional condition index (docosahexaenoic acid (DHA)/eicosapentaenoic acid (EPA) ratio) showed significant differences for the locality factor. Our findings revealed conspicuous differences in the bioe…
format: application/pdf
format: text/html
creator: Marco Quispe-Machaca
creator: Maximiliano Zilleruelo
creator: Pepe Espinoza
creator: Gabriela Torres
creator: Ángel Urzúa
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.20339
publisher: PeerJ Inc.
rights: © 2025 Quispe-Machaca et al.
abstract: Adults of the red squat lobster (Grimothea monodon) present two morphotypes (small-pelagic (SP) and large-benthic (LB)) in their wide geographic distribution range in the Southeastern Pacific Ocean (SEPO). In this marine ecosystem, they are exposed to conspicuous latitudinal variations in oceanographic and physicochemical parameters that affect their nutritional and fitness status. The objective of this study was to determine variations in the bioenergetic condition at the level of morphometric, sexual and biochemical traits of G. monodon, considering a wide spatial scale of their populations’ distribution along a latitudinal gradient (from 9°S to 36°S) in the SEPO. According to the environmental parameters, temperature and dissolved oxygen presented abrupt changes between 15°S–17°S, while chlorophyll and salinity showed a constant reduction along the latitudinal gradient. When environmental parameters were related to the size of the two morphotypes (SP, LB) of G. monodon, some trends of change were observed, while the relative condition factor showed significant differences along the latitudinal gradient. The biochemical condition of SP individuals showed an increasing trend in glucose from Chimbote to Chala, proteins showed abrupt changes in three zones (between Huacho-Lima, Lomitas, and Chala), and lipids showed a notable change between Lima-Cañete. In turn, in LB individual’s increases were recorded in all their biochemical constituents towards high latitudes. A slight variability in fatty acids was observed between SP individuals from the north (Chimbote, Huarmey, Huacho) and SP individuals from the south (Marcona, Chala, Planchada, Mollendo). In addition, significant latitudinal differences were observed in the fatty acids of the two morphotypes (SP, LP). The nutritional condition index (docosahexaenoic acid (DHA)/eicosapentaenoic acid (EPA) ratio) showed significant differences for the locality factor. Our findings revealed conspicuous differences in the bioe…
bibliographic citation: Quispe-Machaca et al. (2025) Latitudinal variations in morphometric traits and bioenergetic status of adult red squat lobsters Grimothea monodon (H. Milne Edwards, 1837) in the Southeast Pacific Ocean. PeerJ 13:e20339 https://doi.org/10.7717/peerj.20339
date submitted: 2024-10-14
date accepted: 2025-10-13
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quispe-Machaca
  given name: Marco
author list: Agent
  family name: Zilleruelo
  given name: Maximiliano
author list: Agent
  family name: Espinoza
  given name: Pepe
author list: Agent
  family name: Torres
  given name: Gabriela
author list: Agent
  family name: Urzúa
  given name: Ángel
doi: 10.7717/peerj.20339
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: ©2025 Quispe-Machaca et al.
attribution name: Quispe-Machaca et al.

The effect of endoscopic polidocanol carbon dioxide foam for internal hemorrhoids: a retrospective study
type: item
type: AcademicArticle
description: Aim This article aims to explore the effectiveness of polidocanol carbon dioxide foam as a therapy for internal hemorrhoids. Methods A retrospective analysis was conducted on 158 patients who received endoscopic polidocanol foam sclerotherapy for internal hemorrhoids between October 2022 and September 2023. Among the patients, 78 underwent endoscopic polidocanol sclerotherapy with polidocanol air foam (control group), while 80 received polidocanol carbon dioxide foam (study group). The primary outcomes of this study were clinical effect and the incidence of complications 1 month after surgery. Patient self-reports of anal bleeding and anal prolapse served as the foundation for establishing three categories of clinical efficacy criteria. The clinical effect was determined based on the efficacy index, which was employed to assess treatment effectiveness. The occurrence of several postoperative complications was documented, specifically including anal pain, anal swelling, urinary retention, perianal infection, ectopic embolization, and anal edema. Secondary outcomes encompassed the surgical cost, duration of hospital stay, and the administered dosage of polidocanol. Result The treatment success at the end of the sclerotherapy session in the study and control group were 85.0% and 83.3%, respectively (P = 0.829). One month following endoscopic sclerotherapy, the study group exhibited an effective rate of 98.8%, while the control group showed a rate of 98.0%. Compared with the clinical effects one month after surgery of the two groups of patients, postoperative complications, surgical cost, hospitalization time and the dosage of polidocanol, we found 11 patients with anal pain and 12 patients with anal swelling in the control group. Within the study group, three patients experienced anal pain, while four patients presented with anal swelling. The study group exhibited significantly fewer patients with anal pain and anal swelling compared to the control group (P < 0.05), a…
format: application/pdf
format: text/html
creator: Jiahui Xiang
creator: Shichao Li
creator: Tengjiang Yu
creator: Qingfeng Jiang
creator: Xia Jiang
creator: Yong Lan
subject: Clinical Trials
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.20252
publisher: PeerJ Inc.
rights: © 2025 Xiang et al.
abstract: Aim This article aims to explore the effectiveness of polidocanol carbon dioxide foam as a therapy for internal hemorrhoids. Methods A retrospective analysis was conducted on 158 patients who received endoscopic polidocanol foam sclerotherapy for internal hemorrhoids between October 2022 and September 2023. Among the patients, 78 underwent endoscopic polidocanol sclerotherapy with polidocanol air foam (control group), while 80 received polidocanol carbon dioxide foam (study group). The primary outcomes of this study were clinical effect and the incidence of complications 1 month after surgery. Patient self-reports of anal bleeding and anal prolapse served as the foundation for establishing three categories of clinical efficacy criteria. The clinical effect was determined based on the efficacy index, which was employed to assess treatment effectiveness. The occurrence of several postoperative complications was documented, specifically including anal pain, anal swelling, urinary retention, perianal infection, ectopic embolization, and anal edema. Secondary outcomes encompassed the surgical cost, duration of hospital stay, and the administered dosage of polidocanol. Result The treatment success at the end of the sclerotherapy session in the study and control group were 85.0% and 83.3%, respectively (P = 0.829). One month following endoscopic sclerotherapy, the study group exhibited an effective rate of 98.8%, while the control group showed a rate of 98.0%. Compared with the clinical effects one month after surgery of the two groups of patients, postoperative complications, surgical cost, hospitalization time and the dosage of polidocanol, we found 11 patients with anal pain and 12 patients with anal swelling in the control group. Within the study group, three patients experienced anal pain, while four patients presented with anal swelling. The study group exhibited significantly fewer patients with anal pain and anal swelling compared to the control group (P < 0.05), a…
bibliographic citation: Xiang et al. (2025) The effect of endoscopic polidocanol carbon dioxide foam for internal hemorrhoids: a retrospective study. PeerJ 13:e20252 https://doi.org/10.7717/peerj.20252
date submitted: 2024-10-31
date accepted: 2025-09-25
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiang
  given name: Jiahui
author list: Agent
  family name: Li
  given name: Shichao
author list: Agent
  family name: Yu
  given name: Tengjiang
author list: Agent
  family name: Jiang
  given name: Qingfeng
author list: Agent
  family name: Jiang
  given name: Xia
author list: Agent
  family name: Lan
  given name: Yong
doi: 10.7717/peerj.20252
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: © 2025 Xiang et al.
attribution name: Xiang et al.

Enhancing heatstroke prediction accuracy with interpretable machine learning: a multi-center data-driven approach
type: item
type: AcademicArticle
description: Background Heatstroke poses a significant threat to public health, frequently culminating in fatal outcomes. This study aimed to develop and validate an interpretable machine learning (ML) model to forecast heatstroke using clinical and laboratory data. Methods Data were collated from 24 hospitals spanning the years 2021 to 2023, with data from 2021 and 2022 comprising the training datasets and data from 2023 designated for validation. Model efficacy was quantified via the area under the receiver operating characteristic curve (AUROC) and calibration plots. Furthermore, the SHapley Additive exPlanations (SHAP) methodology was employed to elucidate the interpretability of the final model. Results The study encompassed 691 patients, with 176 in the training datasets and 80 in the testing datasets diagnosed with heatstroke. Among the nine ML models assessed, the gradient boosting machine (GBM) model demonstrated superior performance, achieving an AUROC of 0.971 in the training datasets and 0.836 in the testing datasets, and exhibiting substantial net benefits in decision curve analysis. Creatine kinase (CK)-MB was identified as the most impactful variable influencing the GBM model’s efficacy. Conclusion The ML model we developed demonstrates robust predictive capabilities for heatstroke, potentially aiding clinicians in the identification and management of patients at elevated risk.
format: application/pdf
format: text/html
creator: Qingbo Zeng
creator: Xingping Deng
creator: Longping He
creator: Lincui Zhong
creator: Qingwei Lin
creator: Nianqing Zhang
creator: Jingchun Song
subject: Emergency and Critical Care
subject: Public Health
subject: Sports Medicine
description: doi:10.7717/peerj.20377
publisher: PeerJ Inc.
rights: © 2025 Zeng et al.
abstract: Background Heatstroke poses a significant threat to public health, frequently culminating in fatal outcomes. This study aimed to develop and validate an interpretable machine learning (ML) model to forecast heatstroke using clinical and laboratory data. Methods Data were collated from 24 hospitals spanning the years 2021 to 2023, with data from 2021 and 2022 comprising the training datasets and data from 2023 designated for validation. Model efficacy was quantified via the area under the receiver operating characteristic curve (AUROC) and calibration plots. Furthermore, the SHapley Additive exPlanations (SHAP) methodology was employed to elucidate the interpretability of the final model. Results The study encompassed 691 patients, with 176 in the training datasets and 80 in the testing datasets diagnosed with heatstroke. Among the nine ML models assessed, the gradient boosting machine (GBM) model demonstrated superior performance, achieving an AUROC of 0.971 in the training datasets and 0.836 in the testing datasets, and exhibiting substantial net benefits in decision curve analysis. Creatine kinase (CK)-MB was identified as the most impactful variable influencing the GBM model’s efficacy. Conclusion The ML model we developed demonstrates robust predictive capabilities for heatstroke, potentially aiding clinicians in the identification and management of patients at elevated risk.
bibliographic citation: Zeng et al. (2025) Enhancing heatstroke prediction accuracy with interpretable machine learning: a multi-center data-driven approach. PeerJ 13:e20377 https://doi.org/10.7717/peerj.20377
date submitted: 2025-05-19
date accepted: 2025-10-20
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zeng
  given name: Qingbo
author list: Agent
  family name: Deng
  given name: Xingping
author list: Agent
  family name: He
  given name: Longping
author list: Agent
  family name: Zhong
  given name: Lincui
author list: Agent
  family name: Lin
  given name: Qingwei
author list: Agent
  family name: Zhang
  given name: Nianqing
author list: Agent
  family name: Song
  given name: Jingchun
doi: 10.7717/peerj.20377
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: © 2025 Zeng et al.
attribution name: Zeng et al.

Feeding ecology and trophic interactions of the narrow-barred Spanish Mackerel (Scomberomorus commerson) in the Central Taiwan Strait
type: item
type: AcademicArticle
description: Understanding the foraging ecology of marine predators is essential for ecosystem-based fisheries management. This study examined the diet of the narrow-barred Spanish mackerel (Scomberomorus commerson) in the Central Taiwan Strait using stomach content and stable isotope analyses integrated with an isotopic mixing model. A total of 1,733 specimens were collected between January 2017 and March 2022. Stomach content analysis revealed that 79.8% had empty stomachs, while the remainder mainly contained semi-digested fish remains. Among identifiable prey, composition varied by size and season. Sardinella lemuru, Decapterus spp., and Trichiurus spp. dominated the diet of smaller individuals, while larger fish primarily consumed Decapterus spp. and Mene maculata. Sardinella lemuru and Trichiurus spp. were more abundant in summer and autumn–winter, respectively. In the meanwhile, Decapterus spp. remained important year-round. Isotopic analysis further revealed that Sardinella lemuru, Etrumeus micropus, Decapterus macarellus and Penaeidae (Metapenaeopsis barbata) were dominant prey in smaller size classes, while Encrasicholina punctifer, D. macarellus, Evynnis cardinalis, Trichiurus spp. and Uroteuthis spp. were prevalent in intermediate and larger individuals. The estimated trophic position (3.8–4.3; mean = 4.0) confirms that S. commerson functions as a top predator with opportunistic feeding behavior. These findings improve understanding of regional trophic dynamics and support sustainable fisheries management in the Central Taiwan Strait.
format: application/pdf
format: text/html
creator: Li Chi Cheng
creator: Jia Shin He
creator: Chi Chang Lai
creator: Yen Hung Lee
creator: Jinn Shing Weng
creator: Hsing Han Huang
creator: Yi Shu Wu
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.20350
publisher: PeerJ Inc.
rights: © 2025 Cheng et al.
abstract: Understanding the foraging ecology of marine predators is essential for ecosystem-based fisheries management. This study examined the diet of the narrow-barred Spanish mackerel (Scomberomorus commerson) in the Central Taiwan Strait using stomach content and stable isotope analyses integrated with an isotopic mixing model. A total of 1,733 specimens were collected between January 2017 and March 2022. Stomach content analysis revealed that 79.8% had empty stomachs, while the remainder mainly contained semi-digested fish remains. Among identifiable prey, composition varied by size and season. Sardinella lemuru, Decapterus spp., and Trichiurus spp. dominated the diet of smaller individuals, while larger fish primarily consumed Decapterus spp. and Mene maculata. Sardinella lemuru and Trichiurus spp. were more abundant in summer and autumn–winter, respectively. In the meanwhile, Decapterus spp. remained important year-round. Isotopic analysis further revealed that Sardinella lemuru, Etrumeus micropus, Decapterus macarellus and Penaeidae (Metapenaeopsis barbata) were dominant prey in smaller size classes, while Encrasicholina punctifer, D. macarellus, Evynnis cardinalis, Trichiurus spp. and Uroteuthis spp. were prevalent in intermediate and larger individuals. The estimated trophic position (3.8–4.3; mean = 4.0) confirms that S. commerson functions as a top predator with opportunistic feeding behavior. These findings improve understanding of regional trophic dynamics and support sustainable fisheries management in the Central Taiwan Strait.
bibliographic citation: Cheng et al. (2025) Feeding ecology and trophic interactions of the narrow-barred Spanish Mackerel (Scomberomorus commerson) in the Central Taiwan Strait. PeerJ 13:e20350 https://doi.org/10.7717/peerj.20350
date submitted: 2025-05-07
date accepted: 2025-10-15
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Li Chi
author list: Agent
  family name: He
  given name: Jia Shin
author list: Agent
  family name: Lai
  given name: Chi Chang
author list: Agent
  family name: Lee
  given name: Yen Hung
author list: Agent
  family name: Weng
  given name: Jinn Shing
author list: Agent
  family name: Huang
  given name: Hsing Han
author list: Agent
  family name: Wu
  given name: Yi Shu
doi: 10.7717/peerj.20350
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: © 2025 Cheng et al.
attribution name: Cheng et al.

Does reef crest zone selection influence Acropora palmata (Lamarck, 1816) fragment survival and growth?
type: item
type: AcademicArticle
description: In this study, we evaluated the effects of the crest zones on the survival and growth of Acropora palmata fragments in four sites differentially impacted by multiple natural and anthropogenic stressors. The crests are in the northwest (Playa Baracoa and Rincón de Guanabo) and the south-central region (El Peruano and Mariflores in Jardines de la Reina National Park) of Cuba. We established a field-based experiment with 50 fragments placed in each crest, 25 fragments in the back crest zone and 25 in the fore crest zone, parallel to the shoreline. The water flow intensity was estimated in both crest zones, using the dissolution of plaster discs as an indicator. The survival and growth of fragments were significantly influenced by site-specific and microhabitat conditions. The survival of the A. palmata fragments was high (survival probability: >0.6) in all four crests. Fragments placed in the fore crest zone (p = 0.02) exhibited higher survival than those in the back crest zone. The growth rates were slower (−1.5 to 7.3 cm year−1) than those previously recorded for wild A. palmata colonies and were negatively affected (estimate = −6.1; p = 0.004) in the fore crest zone. The dissolution of the plaster discs did not indicate a marked gradient of water flow between the crest zones, during April and June, but it was significantly higher (p = 0.03) in the fore crest zone in December at El Peruano and Mariflores crests, indicating temporal variations during the monitoring periods. The dissolution of plaster discs, as a proxy for water flow, did not have a significant effect on fragment survival between zones. However, when the dissolution was below approximately 68%, growth declined slightly; above this threshold, growth increased, possibly by higher inferred water flow. At higher levels of water flow (dissolution of the plaster discs), the positive effect of temperature on growth was attenuated (p = 0.007), suggesting that under strong water flow heat may be dissipated. The…
format: application/pdf
format: text/html
creator: Amanda Ramos Romero
creator: Patricia González-Díaz
creator: Gabriela Aguilera Pérez
creator: Anastazia T. Banaszak
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.20303
publisher: PeerJ Inc.
rights: © 2025 Ramos Romero et al.
abstract: In this study, we evaluated the effects of the crest zones on the survival and growth of Acropora palmata fragments in four sites differentially impacted by multiple natural and anthropogenic stressors. The crests are in the northwest (Playa Baracoa and Rincón de Guanabo) and the south-central region (El Peruano and Mariflores in Jardines de la Reina National Park) of Cuba. We established a field-based experiment with 50 fragments placed in each crest, 25 fragments in the back crest zone and 25 in the fore crest zone, parallel to the shoreline. The water flow intensity was estimated in both crest zones, using the dissolution of plaster discs as an indicator. The survival and growth of fragments were significantly influenced by site-specific and microhabitat conditions. The survival of the A. palmata fragments was high (survival probability: >0.6) in all four crests. Fragments placed in the fore crest zone (p = 0.02) exhibited higher survival than those in the back crest zone. The growth rates were slower (−1.5 to 7.3 cm year−1) than those previously recorded for wild A. palmata colonies and were negatively affected (estimate = −6.1; p = 0.004) in the fore crest zone. The dissolution of the plaster discs did not indicate a marked gradient of water flow between the crest zones, during April and June, but it was significantly higher (p = 0.03) in the fore crest zone in December at El Peruano and Mariflores crests, indicating temporal variations during the monitoring periods. The dissolution of plaster discs, as a proxy for water flow, did not have a significant effect on fragment survival between zones. However, when the dissolution was below approximately 68%, growth declined slightly; above this threshold, growth increased, possibly by higher inferred water flow. At higher levels of water flow (dissolution of the plaster discs), the positive effect of temperature on growth was attenuated (p = 0.007), suggesting that under strong water flow heat may be dissipated. The…
bibliographic citation: Ramos Romero et al. (2025) Does reef crest zone selection influence Acropora palmata (Lamarck, 1816) fragment survival and growth?. PeerJ 13:e20303 https://doi.org/10.7717/peerj.20303
date submitted: 2025-04-07
date accepted: 2025-10-07
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramos Romero
  given name: Amanda
author list: Agent
  family name: González-Díaz
  given name: Patricia
author list: Agent
  family name: Aguilera Pérez
  given name: Gabriela
author list: Agent
  family name: Banaszak
  given name: Anastazia T.
doi: 10.7717/peerj.20303
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: ©2025 Ramos Romero et al.
attribution name: Ramos Romero et al.

Status and trends of giant clam populations demonstrate the effectiveness of village-based protection in American Sāmoa
type: item
type: AcademicArticle
description: Giant clams (subfamily Tridacninae) serve diverse ecological functions in coral reef ecosystems but have experienced severe populatiaon declines across much of their native ranges. Continued overharvesting, habitat degradation, and climate change impacts reinforce the need for updated population assessments and have prompted consideration for endangered species status. Here, we report a territory-wide evaluation of giant clam populations in American Sāmoa, integrating historical data (1994/95, 2002, and 2018) with new surveys conducted from 2022 to 2024 to assess the population status of these ecologically important bivalves. Using belt transects (50 m × 2 m at 10 m depth), we examined clam densities, size-class distributions, species composition, and population trends across six islands—Tutuila, Aunuʻu, Ofu, Olosega, Taʻū, and Muliāva. This study added 264 transects to the historical dataset and showed population densities of giant clams varied among islands but have remained relatively consistent over time. Using univariate and factorial ANOVAs of giant clam abundance and size data, we assessed spatial and temporal variation across American Sāmoa, and our analyses tested for effects of island, year, protection status, and their interactions. The lowest recent clam densities (83.5 individuals per hectare in 2022) were observed on the main island of Tutuila, where 98% of residents live. Mean clam density on Tutuila has increased from 14.1/ha in 1994/95, but the island has considerable variation amongst locations. Remote islands, such as Taʻū and Muliāva, showed higher densities, up to 812 and 1,166/ha, respectively. Most (96.7%) of giant clams found on transects were identified as Tridacna maxima, with infrequent occurrences of the cryptic species T. squamosa and T. noae, primarily within specific, village-managed protected areas. On Tutuila, surveys sites included a variety of jurisdictions and levels of management, with village protected areas and remote sites sup…
format: application/pdf
format: text/html
creator: Paolo Marra-Biggs
creator: Eric K. Brown
creator: Domingo Galgo Ochavillo
creator: Alison L. Green
creator: Alice Lawrence
creator: Carlos Tramonte
creator: Valentine Vaeoso
creator: Ian Moffitt
creator: Kersten Schnurle
creator: Nury Molina
creator: Robert J. Toonen
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
subject: Science Policy
description: doi:10.7717/peerj.20290
publisher: PeerJ Inc.
rights: © 2025 Marra-Biggs et al.
abstract: Giant clams (subfamily Tridacninae) serve diverse ecological functions in coral reef ecosystems but have experienced severe populatiaon declines across much of their native ranges. Continued overharvesting, habitat degradation, and climate change impacts reinforce the need for updated population assessments and have prompted consideration for endangered species status. Here, we report a territory-wide evaluation of giant clam populations in American Sāmoa, integrating historical data (1994/95, 2002, and 2018) with new surveys conducted from 2022 to 2024 to assess the population status of these ecologically important bivalves. Using belt transects (50 m × 2 m at 10 m depth), we examined clam densities, size-class distributions, species composition, and population trends across six islands—Tutuila, Aunuʻu, Ofu, Olosega, Taʻū, and Muliāva. This study added 264 transects to the historical dataset and showed population densities of giant clams varied among islands but have remained relatively consistent over time. Using univariate and factorial ANOVAs of giant clam abundance and size data, we assessed spatial and temporal variation across American Sāmoa, and our analyses tested for effects of island, year, protection status, and their interactions. The lowest recent clam densities (83.5 individuals per hectare in 2022) were observed on the main island of Tutuila, where 98% of residents live. Mean clam density on Tutuila has increased from 14.1/ha in 1994/95, but the island has considerable variation amongst locations. Remote islands, such as Taʻū and Muliāva, showed higher densities, up to 812 and 1,166/ha, respectively. Most (96.7%) of giant clams found on transects were identified as Tridacna maxima, with infrequent occurrences of the cryptic species T. squamosa and T. noae, primarily within specific, village-managed protected areas. On Tutuila, surveys sites included a variety of jurisdictions and levels of management, with village protected areas and remote sites sup…
bibliographic citation: Marra-Biggs et al. (2025) Status and trends of giant clam populations demonstrate the effectiveness of village-based protection in American Sāmoa. PeerJ 13:e20290 https://doi.org/10.7717/peerj.20290
date submitted: 2025-05-19
date accepted: 2025-10-03
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marra-Biggs
  given name: Paolo
author list: Agent
  family name: Brown
  given name: Eric K.
author list: Agent
  family name: Ochavillo
  given name: Domingo Galgo
author list: Agent
  family name: Green
  given name: Alison L.
author list: Agent
  family name: Lawrence
  given name: Alice
author list: Agent
  family name: Tramonte
  given name: Carlos
author list: Agent
  family name: Vaeoso
  given name: Valentine
author list: Agent
  family name: Moffitt
  given name: Ian
author list: Agent
  family name: Schnurle
  given name: Kersten
author list: Agent
  family name: Molina
  given name: Nury
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.20290
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: ©2025 Marra-Biggs et al.
attribution name: Marra-Biggs et al.

Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
type: item
type: AcademicArticle
description: Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies on multiple lines of evidence, including phylogenetic trees and metrics like the percentage of conserved proteins (POCP). POCP is widely used, but requires benchmarking in terms of both, computation and accuracy. We used 2,358,466 pairwise comparisons of proteomes derived from 4,767 genomes across 35 families to systematically assess POCP calculation and percentage of conserved proteins with unique matches (POCPu) which considers unique matches only. Both methods are 20x faster than the reference BLASTP when using the very-sensitive setting of DIAMOND. However, POCPu differentiates better within-genus from between-genera values, which improves bacterial genus assignment. This work facilitates comparative analysis of an increasingly larger number of genomes, providing a reliable metric to support genus delineation. The findings suggest that specific POCPu thresholds deviating from the reference 50% value are needed for certain families.
format: application/pdf
format: text/html
creator: Charlie Pauvert
creator: Thomas C.A. Hitch
creator: Thomas Clavel
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Taxonomy
subject: Data Science
description: doi:10.7717/peerj.20259
publisher: PeerJ Inc.
rights: © 2025 Pauvert et al.
abstract: Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies on multiple lines of evidence, including phylogenetic trees and metrics like the percentage of conserved proteins (POCP). POCP is widely used, but requires benchmarking in terms of both, computation and accuracy. We used 2,358,466 pairwise comparisons of proteomes derived from 4,767 genomes across 35 families to systematically assess POCP calculation and percentage of conserved proteins with unique matches (POCPu) which considers unique matches only. Both methods are 20x faster than the reference BLASTP when using the very-sensitive setting of DIAMOND. However, POCPu differentiates better within-genus from between-genera values, which improves bacterial genus assignment. This work facilitates comparative analysis of an increasingly larger number of genomes, providing a reliable metric to support genus delineation. The findings suggest that specific POCPu thresholds deviating from the reference 50% value are needed for certain families.
bibliographic citation: Pauvert et al. (2025) Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu). PeerJ 13:e20259 https://doi.org/10.7717/peerj.20259
date submitted: 2025-08-04
date accepted: 2025-09-29
issued: 2025-11-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pauvert
  given name: Charlie
author list: Agent
  family name: Hitch
  given name: Thomas C.A.
author list: Agent
  family name: Clavel
  given name: Thomas
doi: 10.7717/peerj.20259
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-14
copyright: ©2025 Pauvert et al.
attribution name: Pauvert et al.

Comparison of quadriceps and hamstring muscle size and strength between young athletes following knee surgery and healthy controls
type: item
type: AcademicArticle
description: Objectives This study compared the size and strength of the quadriceps and hamstring muscles in young athletes who had undergone previous knee surgery (POST) to sex- and age- matched, healthy controls (SAM). Methods A total of 18 (nine POST and nine SAM) participants volunteered to participate in the study’s procedures. Of the nine POST participants, six had underwent anterior cruciate ligament reconstruction, two underwent medial patellofemoral ligament reconstruction and one had undergone patellar tendon repair. Maximal voluntary isometric contractions assessed absolute strength (MVICABS) of the quadriceps and hamstrings. Muscle size was quantified as muscle cross-sectional area (mCSA) from panoramic ultrasound images. Relative strength (MVICREL) was calculated as a ratio of strength to muscle size. Separate 2-way mixed-factorial analyses of variance leg (operative or non-dominant (O-ND) vs. non-operative or dominant (NO-D)) and group (POST vs. SAM) assessed statistical differences at p ≤ 0.05. Results There were no significant two-way interactions (p-range: 0.142–0.74) for any variables. Further, there were no significant main effects for the quadriceps (p-range: 0.127–0.605) nor was there a main effect for leg in any hamstrings variables (p-range: 0.126–0.367). However, the POST group had greater MVICABS and MVICREL than SAM for the hamstrings by 69.8 ± 30.7 N (p = 0.037) and 2.21 ± 1.02 N cm−2 (p = 0.045). Conclusions These findings indicate that there was no difference in quadriceps muscle strength or size between the POST and SAM groups. However, the POST group had greater hamstrings strength than SAM yet no differences in muscle size. These results suggest that the rehabilitation program may have been effective in restoring quadriceps function and enhancing hamstrings strength in young athletes following knee surgery. However, future studies should continue to elucidate the physiological effects of knee surgeries in larger, more diverse samples to attenuate …
format: application/pdf
format: text/html
creator: Christopher J. Cleary
creator: Isaiah G. Roepe
creator: Christopher D. Bernard
creator: Traci Smiley
creator: John K. Veazey
creator: Kyle A. Martin
creator: Megan Bechtold
creator: Bryan G. Vopat
creator: Ashley A. Herda
subject: Kinesiology
subject: Orthopedics
subject: Sports Injury
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20330
publisher: PeerJ Inc.
rights: © 2025 Cleary et al.
abstract: Objectives This study compared the size and strength of the quadriceps and hamstring muscles in young athletes who had undergone previous knee surgery (POST) to sex- and age- matched, healthy controls (SAM). Methods A total of 18 (nine POST and nine SAM) participants volunteered to participate in the study’s procedures. Of the nine POST participants, six had underwent anterior cruciate ligament reconstruction, two underwent medial patellofemoral ligament reconstruction and one had undergone patellar tendon repair. Maximal voluntary isometric contractions assessed absolute strength (MVICABS) of the quadriceps and hamstrings. Muscle size was quantified as muscle cross-sectional area (mCSA) from panoramic ultrasound images. Relative strength (MVICREL) was calculated as a ratio of strength to muscle size. Separate 2-way mixed-factorial analyses of variance leg (operative or non-dominant (O-ND) vs. non-operative or dominant (NO-D)) and group (POST vs. SAM) assessed statistical differences at p ≤ 0.05. Results There were no significant two-way interactions (p-range: 0.142–0.74) for any variables. Further, there were no significant main effects for the quadriceps (p-range: 0.127–0.605) nor was there a main effect for leg in any hamstrings variables (p-range: 0.126–0.367). However, the POST group had greater MVICABS and MVICREL than SAM for the hamstrings by 69.8 ± 30.7 N (p = 0.037) and 2.21 ± 1.02 N cm−2 (p = 0.045). Conclusions These findings indicate that there was no difference in quadriceps muscle strength or size between the POST and SAM groups. However, the POST group had greater hamstrings strength than SAM yet no differences in muscle size. These results suggest that the rehabilitation program may have been effective in restoring quadriceps function and enhancing hamstrings strength in young athletes following knee surgery. However, future studies should continue to elucidate the physiological effects of knee surgeries in larger, more diverse samples to attenuate …
bibliographic citation: Cleary et al. (2025) Comparison of quadriceps and hamstring muscle size and strength between young athletes following knee surgery and healthy controls. PeerJ 13:e20330 https://doi.org/10.7717/peerj.20330
date submitted: 2025-04-17
date accepted: 2025-10-13
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cleary
  given name: Christopher J.
author list: Agent
  family name: Roepe
  given name: Isaiah G.
author list: Agent
  family name: Bernard
  given name: Christopher D.
author list: Agent
  family name: Smiley
  given name: Traci
author list: Agent
  family name: Veazey
  given name: John K.
author list: Agent
  family name: Martin
  given name: Kyle A.
author list: Agent
  family name: Bechtold
  given name: Megan
author list: Agent
  family name: Vopat
  given name: Bryan G.
author list: Agent
  family name: Herda
  given name: Ashley A.
doi: 10.7717/peerj.20330
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Cleary et al.
attribution name: Cleary et al.

Prevalence of poor sleep quality and its associated factors in patients with concurrent type 2 diabetes mellitus and hypertension
type: item
type: AcademicArticle
description: Background The coexistence of type 2 diabetes mellitus (T2DM) and hypertension can impair sleep quality, potentially leading to a wide range of adverse health outcomes. Therefore, this study aimed to evaluate sleep quality and its associated factors in patients with concurrent T2DM and hypertension in Hunan, China. Methods This cross-sectional study recruited patients with concurrent T2DM and hypertension who visited the Department of Endocrinology at the First People’s Hospital of Ruanjiang City, Hunan Province, China, between July 2022 and February 2023. Trained investigators conducted face-to-face interviews to collect data on sociodemographic, lifestyle, and disease-related factors, and assessed anxiety and sleep quality using the Generalized Anxiety Disorder-7 scale and the Pittsburgh Sleep Quality Index, respectively. Multivariable logistic regression analysis was performed to identify factors independently associated with sleep quality. A receiver operating characteristic (ROC) curve was generated to evaluate the predictive ability of the model, and the Hosmer–Lemeshow test was used to assess model calibration. Subgroup analyses were conducted by sex, educational level, and number of T2DM complications to test model robustness. Results A total of 475 patients with concurrent T2DM and hypertension were included. The prevalence of poor sleep quality was 59.4% (95% confidence interval (CI) [54.9%–63.9%]). Multivariable logistic regression analysis showed that advanced age (adjusted odds ratio (aOR) = 2.12, 95% CI [1.29–3.48]), history of stroke (aOR = 2.16, 95% CI [1.15–4.06]), and anxiety (aOR = 4.24, 95% CI [2.58–6.98]) were associated with higher odds of poor sleep quality. Regular physical activity was associated with lower odds (aOR = 0.53, 95% CI [0.34–0.84]). The area under the receiver operating characteristic (ROC) curve was 0.776 (95% CI [0.735–0.818]), and the Hosmer–Lemeshow test (P = 0.260) indicated good model calibration. Subgroup analyses yielded…
format: application/pdf
format: text/html
creator: Ziling Feng
creator: Hongying Liu
creator: Ni Xiong
creator: Leyao Tang
creator: Wenjie Dai
creator: Fang Yang
subject: Anthropology
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.20325
publisher: PeerJ Inc.
rights: © 2025 Feng et al.
abstract: Background The coexistence of type 2 diabetes mellitus (T2DM) and hypertension can impair sleep quality, potentially leading to a wide range of adverse health outcomes. Therefore, this study aimed to evaluate sleep quality and its associated factors in patients with concurrent T2DM and hypertension in Hunan, China. Methods This cross-sectional study recruited patients with concurrent T2DM and hypertension who visited the Department of Endocrinology at the First People’s Hospital of Ruanjiang City, Hunan Province, China, between July 2022 and February 2023. Trained investigators conducted face-to-face interviews to collect data on sociodemographic, lifestyle, and disease-related factors, and assessed anxiety and sleep quality using the Generalized Anxiety Disorder-7 scale and the Pittsburgh Sleep Quality Index, respectively. Multivariable logistic regression analysis was performed to identify factors independently associated with sleep quality. A receiver operating characteristic (ROC) curve was generated to evaluate the predictive ability of the model, and the Hosmer–Lemeshow test was used to assess model calibration. Subgroup analyses were conducted by sex, educational level, and number of T2DM complications to test model robustness. Results A total of 475 patients with concurrent T2DM and hypertension were included. The prevalence of poor sleep quality was 59.4% (95% confidence interval (CI) [54.9%–63.9%]). Multivariable logistic regression analysis showed that advanced age (adjusted odds ratio (aOR) = 2.12, 95% CI [1.29–3.48]), history of stroke (aOR = 2.16, 95% CI [1.15–4.06]), and anxiety (aOR = 4.24, 95% CI [2.58–6.98]) were associated with higher odds of poor sleep quality. Regular physical activity was associated with lower odds (aOR = 0.53, 95% CI [0.34–0.84]). The area under the receiver operating characteristic (ROC) curve was 0.776 (95% CI [0.735–0.818]), and the Hosmer–Lemeshow test (P = 0.260) indicated good model calibration. Subgroup analyses yielded…
bibliographic citation: Feng et al. (2025) Prevalence of poor sleep quality and its associated factors in patients with concurrent type 2 diabetes mellitus and hypertension. PeerJ 13:e20325 https://doi.org/10.7717/peerj.20325
date submitted: 2025-05-16
date accepted: 2025-10-13
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Ziling
author list: Agent
  family name: Liu
  given name: Hongying
author list: Agent
  family name: Xiong
  given name: Ni
author list: Agent
  family name: Tang
  given name: Leyao
author list: Agent
  family name: Dai
  given name: Wenjie
author list: Agent
  family name: Yang
  given name: Fang
doi: 10.7717/peerj.20325
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Feng et al.
attribution name: Feng et al.

Impact of preoperative underweight status on perioperative morbidity and mortality after liver resection for liver tumors: a meta-analysis
type: item
type: AcademicArticle
description: Background The impact of preoperative underweight status on the outcomes of liver resections for liver tumors is debated. We aimed at conducting a meta-analysis to evaluate the associations between underweight and short-term clinical outcomes after liver resection. Methods PubMed, Cochrane Library, Embase, Scopus , and Web of Science databases were searched from inception to September 14, 2024 (updated on April 21, 2025) to identify eligible studies. Risk ratios (RRs) or mean differences (MDs) and 95% confidence intervals (CI) were calculated. Results Seven studies were included, with a total of 3,835 patients (normal weight group: 3,412 patients; underweight group: 423 patients). Findings indicated that, relative to individuals of normal weight, underweight patients have longer operation time (MD, 7.73 mins; 95% CI [2.08–13.38], P = 0.007) and higher overall postoperative morbidity (RR 1.41 95% CI [1.06–1.88], P = 0.02), mortality (RR 2.98, 95% CI [1.4 3–6.20], P = 0.003), and surgical site infection (RR 2.00, 95% CI [1.03–3.88], P = 0.04). There were no significant differences in blood loss, length of stay, liver failure, bile leak, and blood transfusion between the normal weight and underweight groups. Conclusions Preoperative underweight status is associated with higher risk of morbidity and mortality after liver resection. Prospective studies or interventional trials, such as nutritional prehabilitation or stratification by cirrhosis and resection extent, are needed to confirm whether underweight represents a truly modifiable risk factor. This review is intended for professionals within the fields of hepatobiliary surgery.
format: application/pdf
format: text/html
creator: Xuan Tang
creator: Yunpeng Su
creator: Wenxi Li
creator: Li Wan
subject: Gastroenterology and Hepatology
subject: Nutrition
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.20324
publisher: PeerJ Inc.
rights: © 2025 Tang et al.
abstract: Background The impact of preoperative underweight status on the outcomes of liver resections for liver tumors is debated. We aimed at conducting a meta-analysis to evaluate the associations between underweight and short-term clinical outcomes after liver resection. Methods PubMed, Cochrane Library, Embase, Scopus , and Web of Science databases were searched from inception to September 14, 2024 (updated on April 21, 2025) to identify eligible studies. Risk ratios (RRs) or mean differences (MDs) and 95% confidence intervals (CI) were calculated. Results Seven studies were included, with a total of 3,835 patients (normal weight group: 3,412 patients; underweight group: 423 patients). Findings indicated that, relative to individuals of normal weight, underweight patients have longer operation time (MD, 7.73 mins; 95% CI [2.08–13.38], P = 0.007) and higher overall postoperative morbidity (RR 1.41 95% CI [1.06–1.88], P = 0.02), mortality (RR 2.98, 95% CI [1.4 3–6.20], P = 0.003), and surgical site infection (RR 2.00, 95% CI [1.03–3.88], P = 0.04). There were no significant differences in blood loss, length of stay, liver failure, bile leak, and blood transfusion between the normal weight and underweight groups. Conclusions Preoperative underweight status is associated with higher risk of morbidity and mortality after liver resection. Prospective studies or interventional trials, such as nutritional prehabilitation or stratification by cirrhosis and resection extent, are needed to confirm whether underweight represents a truly modifiable risk factor. This review is intended for professionals within the fields of hepatobiliary surgery.
bibliographic citation: Tang et al. (2025) Impact of preoperative underweight status on perioperative morbidity and mortality after liver resection for liver tumors: a meta-analysis. PeerJ 13:e20324 https://doi.org/10.7717/peerj.20324
date submitted: 2024-12-06
date accepted: 2025-10-10
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Xuan
author list: Agent
  family name: Su
  given name: Yunpeng
author list: Agent
  family name: Li
  given name: Wenxi
author list: Agent
  family name: Wan
  given name: Li
doi: 10.7717/peerj.20324
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Tang et al.
attribution name: Tang et al.

The CD8+/Foxp3+ ratio, but not the number of OX40+ TILs, is an independent predictor of tumor recurrence in non-muscle-invasive bladder cancer: a retrospective study
type: item
type: AcademicArticle
description: Non-muscle-invasive bladder cancer (NMIBC) frequently recurs and progresses into an aggressive and lethal entity within five years. The clinical management of recurrent tumors remains limited. Therefore, identifying individual patients who are at a high risk of recurrence is crucial for early clinical monitoring and appropriate medical intervention, which may lead to improved outcomes. OX40 is a dual modulator that stimulates effector T cells and suppresses Tregs. It appears to be an ideal molecule for predicting survival outcomes, surpassing the predictive power of single or combined T cell signatures. It has been shown to act as an independent tumor prognostic predictor in various cancers, including non-small cell lung cancer, melanoma, and colorectal cancer. However, its potential as a prognostic tool for tumor recurrence in NMIBC has yet to be investigated. The present study aimed to investigate the potential value of OX40 as a predictor of recurrence risk in patients with NMIBC. Additionally, its downstream effectors, Foxp3 and CD8, were also evaluated. Tissue samples were collected from a cohort of 110 patients diagnosed with NMIBC. Immunohistochemistry was performed to assess the density of stromal OX40+, Foxp3+, and CD8+ tumor infiltrating lymphocytes (TILs). Following survival analysis using the Kaplan-Meier method and log-rank test, we found that tumor recurrence was associated with a decreased density of OX40+ and CD8+ TILs, an elevated density of Foxp3+ TILs, and lower ratios of OX40+/Foxp3+ and CD8+/Foxp3+ TILs. However, after adjustment, multivariate COX regression analysis indicated that only the ratio of CD8+/Foxp3+ was an independent predictor of recurrence risk. The prediction power was assessed by a receiver operating characteristic (ROC) curve analysis. The results demonstrated that the AUC value for the CD8+/Foxp3+ ratio was better than the other predictive markers. Although the expression of OX40 in TILs was associated with tumor recurrence, ou…
format: application/pdf
format: text/html
creator: Ke Han
creator: Fenghou Wang
creator: Rong Wang
creator: Qingnuan Kong
subject: Oncology
subject: Pathology
subject: Urology
description: doi:10.7717/peerj.20322
publisher: PeerJ Inc.
rights: © 2025 Han et al.
abstract: Non-muscle-invasive bladder cancer (NMIBC) frequently recurs and progresses into an aggressive and lethal entity within five years. The clinical management of recurrent tumors remains limited. Therefore, identifying individual patients who are at a high risk of recurrence is crucial for early clinical monitoring and appropriate medical intervention, which may lead to improved outcomes. OX40 is a dual modulator that stimulates effector T cells and suppresses Tregs. It appears to be an ideal molecule for predicting survival outcomes, surpassing the predictive power of single or combined T cell signatures. It has been shown to act as an independent tumor prognostic predictor in various cancers, including non-small cell lung cancer, melanoma, and colorectal cancer. However, its potential as a prognostic tool for tumor recurrence in NMIBC has yet to be investigated. The present study aimed to investigate the potential value of OX40 as a predictor of recurrence risk in patients with NMIBC. Additionally, its downstream effectors, Foxp3 and CD8, were also evaluated. Tissue samples were collected from a cohort of 110 patients diagnosed with NMIBC. Immunohistochemistry was performed to assess the density of stromal OX40+, Foxp3+, and CD8+ tumor infiltrating lymphocytes (TILs). Following survival analysis using the Kaplan-Meier method and log-rank test, we found that tumor recurrence was associated with a decreased density of OX40+ and CD8+ TILs, an elevated density of Foxp3+ TILs, and lower ratios of OX40+/Foxp3+ and CD8+/Foxp3+ TILs. However, after adjustment, multivariate COX regression analysis indicated that only the ratio of CD8+/Foxp3+ was an independent predictor of recurrence risk. The prediction power was assessed by a receiver operating characteristic (ROC) curve analysis. The results demonstrated that the AUC value for the CD8+/Foxp3+ ratio was better than the other predictive markers. Although the expression of OX40 in TILs was associated with tumor recurrence, ou…
bibliographic citation: Han et al. (2025) The CD8+/Foxp3+ ratio, but not the number of OX40+ TILs, is an independent predictor of tumor recurrence in non-muscle-invasive bladder cancer: a retrospective study. PeerJ 13:e20322 https://doi.org/10.7717/peerj.20322
date submitted: 2025-05-28
date accepted: 2025-10-10
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Han
  given name: Ke
author list: Agent
  family name: Wang
  given name: Fenghou
author list: Agent
  family name: Wang
  given name: Rong
author list: Agent
  family name: Kong
  given name: Qingnuan
doi: 10.7717/peerj.20322
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Han et al.
attribution name: Han et al.

Assessment of serum diagnostic biomarkers for periprosthetic joint infection in hip and knee arthroplasty: a retrospective study
type: item
type: AcademicArticle
description: Background Periprosthetic joint infection (PJI) after total hip and knee arthroplasty is challenging to differentiate from similar afflictions. Platelet count-to-mean platelet volume (PC/MPV) ratio has been proposed, but requires validation. This study evaluated PC/MPV and other potential serological biomarkers for diagnosing PJI prior to reimplantation arthroplasty of the hip and knee. Material and Methods Medical records were retrospectively reviewed of patients who received hip and knee revision, and there were 88 PJI patients and 156 non-PJI patients met the modified 2018 criteria for inclusion. Receiver operating characteristic curves (ROCs) were used to analyze and compare the diagnostic performances of PC/MPV, fibrinogen (FIB), C-reactive protein (CRP), platelet count (PLT), erythrocyte sedimentation rate (ESR), and serum white blood cell (WBC) count. Results Compared with the control group, the patients with PJI had significantly higher PC/MPV, FIB, ESR, CRP, serum WBC, and PLT, respectively, and the areas under the ROC curve were 0.787, 0.917, 0.832, 0.934, 0.685, and 0.778; that of FIB and CRP were similar. Regarding PC/MPV, the optimal cutoff was 27.81, and the sensitivity, specificity, and positive and negative predictive values were 0.807, 0.673, 0.582, and 0.861. Conclusions The best diagnostic performance was achieved by CRP and FIB, and we recommend that these tests should be prioritized. Serum WBC, PC/MPV and PLT were insufficient to predict PJI prior to reimplantation arthroplasty of the hip and knee; however, CRP combined with FIB or PC/MPV best serves to obtain the most accurate prediction of PJI in our study.
format: application/pdf
format: text/html
creator: Zhiqiang Sun
creator: Qiqi Zhang
creator: Hui Ma
creator: Xiaohe Wang
creator: Changcheng Hua
creator: Fei Yang
subject: Orthopedics
subject: Surgery and Surgical Specialties
subject: Sports Medicine
description: doi:10.7717/peerj.20294
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Background Periprosthetic joint infection (PJI) after total hip and knee arthroplasty is challenging to differentiate from similar afflictions. Platelet count-to-mean platelet volume (PC/MPV) ratio has been proposed, but requires validation. This study evaluated PC/MPV and other potential serological biomarkers for diagnosing PJI prior to reimplantation arthroplasty of the hip and knee. Material and Methods Medical records were retrospectively reviewed of patients who received hip and knee revision, and there were 88 PJI patients and 156 non-PJI patients met the modified 2018 criteria for inclusion. Receiver operating characteristic curves (ROCs) were used to analyze and compare the diagnostic performances of PC/MPV, fibrinogen (FIB), C-reactive protein (CRP), platelet count (PLT), erythrocyte sedimentation rate (ESR), and serum white blood cell (WBC) count. Results Compared with the control group, the patients with PJI had significantly higher PC/MPV, FIB, ESR, CRP, serum WBC, and PLT, respectively, and the areas under the ROC curve were 0.787, 0.917, 0.832, 0.934, 0.685, and 0.778; that of FIB and CRP were similar. Regarding PC/MPV, the optimal cutoff was 27.81, and the sensitivity, specificity, and positive and negative predictive values were 0.807, 0.673, 0.582, and 0.861. Conclusions The best diagnostic performance was achieved by CRP and FIB, and we recommend that these tests should be prioritized. Serum WBC, PC/MPV and PLT were insufficient to predict PJI prior to reimplantation arthroplasty of the hip and knee; however, CRP combined with FIB or PC/MPV best serves to obtain the most accurate prediction of PJI in our study.
bibliographic citation: Sun et al. (2025) Assessment of serum diagnostic biomarkers for periprosthetic joint infection in hip and knee arthroplasty: a retrospective study. PeerJ 13:e20294 https://doi.org/10.7717/peerj.20294
date submitted: 2025-03-25
date accepted: 2025-10-03
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Zhiqiang
author list: Agent
  family name: Zhang
  given name: Qiqi
author list: Agent
  family name: Ma
  given name: Hui
author list: Agent
  family name: Wang
  given name: Xiaohe
author list: Agent
  family name: Hua
  given name: Changcheng
author list: Agent
  family name: Yang
  given name: Fei
doi: 10.7717/peerj.20294
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Sun et al.
attribution name: Sun et al.

Effects of arbuscular mycorrhizal fungi and earthworms on plant-soil systems of urban turf grasses
type: item
type: AcademicArticle
description: Background Arbuscular mycorrhizal fungi (AMF) and earthworms have been known to enhance plant growth and improve soil quality, but the results have shown some inconsistencies, exhibiting synergistic or independent effects under different studies. Methods In this study, we conducted a factorial experiment to investigate the effects of arbuscular mycorrhizal fungi and earthworms, both individually and in combination, on plant-soil systems of urban turf grasses. Five turf grass species of different functional groups (gramineous and leguminous) were inoculated with AMF (Glomus mosseae) and earthworms (Pheretima tschiliensis Michaelsen, 1928) in a pot culture experiment, and we comprehensively assessed the eco-physiological properties of both the plant and the soil. Results Inoculation with AMF and earthworms promoted the growth of five turf grass species. Specifically, AMF had a greater impact on the height and biomass of leguminous plants (white clover and alfalfa) compared to gramineous plants (ryegrass, early meadow grass, and tall fescue), while the effects of earthworms on two functional groups were opposite to those of AMF. AMF and earthworms had different dimensions of effects on the physical and chemical properties of the soil compared to the control, with AMF showing a better improvement in soil quality than earthworms. The results indicated that effects of AMF and earthworms on urban turf grasses and soil were dependent on different species. Dual inoculation with AMF and earthworms showed positive effects exclusively on the soil properties of five turf grass species, but only positive on the growth of gramineous plants. The comprehensive evaluation indicated that dual inoculation with AMF and earthworms did not improve the plant-soil system more effectively than AMF alone. Conversely, gramineous plants inoculated with AMF showed the greatest effective improvement in the soil-plant system. Therefore, dual inoculation with AMF and earthworms did not have a more …
format: application/pdf
format: text/html
creator: Ying Hou
creator: Zongying Zhang
creator: Yue Yuan
creator: Xinyu Zhu
creator: Jinping Ding
subject: Ecology
subject: Mycology
subject: Soil Science
subject: Zoology
description: doi:10.7717/peerj.20289
publisher: PeerJ Inc.
rights: © 2025 Hou et al.
abstract: Background Arbuscular mycorrhizal fungi (AMF) and earthworms have been known to enhance plant growth and improve soil quality, but the results have shown some inconsistencies, exhibiting synergistic or independent effects under different studies. Methods In this study, we conducted a factorial experiment to investigate the effects of arbuscular mycorrhizal fungi and earthworms, both individually and in combination, on plant-soil systems of urban turf grasses. Five turf grass species of different functional groups (gramineous and leguminous) were inoculated with AMF (Glomus mosseae) and earthworms (Pheretima tschiliensis Michaelsen, 1928) in a pot culture experiment, and we comprehensively assessed the eco-physiological properties of both the plant and the soil. Results Inoculation with AMF and earthworms promoted the growth of five turf grass species. Specifically, AMF had a greater impact on the height and biomass of leguminous plants (white clover and alfalfa) compared to gramineous plants (ryegrass, early meadow grass, and tall fescue), while the effects of earthworms on two functional groups were opposite to those of AMF. AMF and earthworms had different dimensions of effects on the physical and chemical properties of the soil compared to the control, with AMF showing a better improvement in soil quality than earthworms. The results indicated that effects of AMF and earthworms on urban turf grasses and soil were dependent on different species. Dual inoculation with AMF and earthworms showed positive effects exclusively on the soil properties of five turf grass species, but only positive on the growth of gramineous plants. The comprehensive evaluation indicated that dual inoculation with AMF and earthworms did not improve the plant-soil system more effectively than AMF alone. Conversely, gramineous plants inoculated with AMF showed the greatest effective improvement in the soil-plant system. Therefore, dual inoculation with AMF and earthworms did not have a more …
bibliographic citation: Hou et al. (2025) Effects of arbuscular mycorrhizal fungi and earthworms on plant-soil systems of urban turf grasses. PeerJ 13:e20289 https://doi.org/10.7717/peerj.20289
date submitted: 2025-04-14
date accepted: 2025-10-03
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Hou
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Zongying
author list: Agent
  family name: Yuan
  given name: Yue
author list: Agent
  family name: Zhu
  given name: Xinyu
author list: Agent
  family name: Ding
  given name: Jinping
doi: 10.7717/peerj.20289
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Hou et al.
attribution name: Hou et al.

The function and mechanisms of action of lysyl oxidase-like 3 (LOXL3) in cancers
type: item
type: AcademicArticle
description: Lysyl oxidase-like 3 (LOXL3) is a key member of the lysyl oxidase (LOX) family and belongs to the copper-dependent amine oxidase family. Its traditional core function is to catalyze the cross-linking of collagen and elastin in the extracellular matrix (ECM), thereby maintaining the structural integrity and normal physiological functions of the ECM. In recent years, studies on cancer molecular mechanisms have confirmed that LOXL3 exhibits abnormal expression in a variety of cancers: in common malignant tumors such as melanoma, liver cancer, gastric cancer, colorectal cancer, and breast cancer, its expression level is significantly higher than that in the corresponding normal tissues. Meanwhile, numerous prognostic analyses have demonstrated that high LOXL3 expression is an independent risk factor for poor prognosis in cancer patients. Such patients usually have shorter progression-free survival (PFS) and overall survival (OS), suggesting that LOXL3 may serve as a potential biomarker for evaluating cancer prognosis. At the functional and mechanistic level, the role of LOXL3 is not limited to ECM remodeling. It can directly affect key biological behaviors of cancer cells, including proliferation, invasion, metastatic potential, and sensitivity to chemotherapeutic drugs, by regulating a variety of intracellular signaling pathways. This article reviews the specific roles and potential molecular mechanisms of LOXL3 in cancer, covering its associations with key cancer pathological processes such as epithelial-mesenchymal transition, maintenance of genomic stability, and regulation of the tumor microenvironment. It focuses on clarifying the specific molecular pathways through which LOXL3 promotes pro-tumor activities in different tumors, as well as the regulatory effects of these pro-tumor activities on patients’ relevant prognosis.
format: application/pdf
format: text/html
creator: Dan Zhao
creator: Pu Su
creator: Xuan Peng
creator: Xue Cheng
creator: Bin Li
creator: Xi-min Tang
creator: Shaoyang Huang
creator: Zhengliang Li
creator: Huaize Cao
creator: Wei Xiong
subject: Molecular Biology
subject: Oncology
subject: Pathology
subject: Medical Genetics
description: doi:10.7717/peerj.20274
publisher: PeerJ Inc.
rights: © 2025 Zhao et al.
abstract: Lysyl oxidase-like 3 (LOXL3) is a key member of the lysyl oxidase (LOX) family and belongs to the copper-dependent amine oxidase family. Its traditional core function is to catalyze the cross-linking of collagen and elastin in the extracellular matrix (ECM), thereby maintaining the structural integrity and normal physiological functions of the ECM. In recent years, studies on cancer molecular mechanisms have confirmed that LOXL3 exhibits abnormal expression in a variety of cancers: in common malignant tumors such as melanoma, liver cancer, gastric cancer, colorectal cancer, and breast cancer, its expression level is significantly higher than that in the corresponding normal tissues. Meanwhile, numerous prognostic analyses have demonstrated that high LOXL3 expression is an independent risk factor for poor prognosis in cancer patients. Such patients usually have shorter progression-free survival (PFS) and overall survival (OS), suggesting that LOXL3 may serve as a potential biomarker for evaluating cancer prognosis. At the functional and mechanistic level, the role of LOXL3 is not limited to ECM remodeling. It can directly affect key biological behaviors of cancer cells, including proliferation, invasion, metastatic potential, and sensitivity to chemotherapeutic drugs, by regulating a variety of intracellular signaling pathways. This article reviews the specific roles and potential molecular mechanisms of LOXL3 in cancer, covering its associations with key cancer pathological processes such as epithelial-mesenchymal transition, maintenance of genomic stability, and regulation of the tumor microenvironment. It focuses on clarifying the specific molecular pathways through which LOXL3 promotes pro-tumor activities in different tumors, as well as the regulatory effects of these pro-tumor activities on patients’ relevant prognosis.
bibliographic citation: Zhao et al. (2025) The function and mechanisms of action of lysyl oxidase-like 3 (LOXL3) in cancers. PeerJ 13:e20274 https://doi.org/10.7717/peerj.20274
date submitted: 2025-05-22
date accepted: 2025-09-30
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Dan
author list: Agent
  family name: Su
  given name: Pu
author list: Agent
  family name: Peng
  given name: Xuan
author list: Agent
  family name: Cheng
  given name: Xue
author list: Agent
  family name: Li
  given name: Bin
author list: Agent
  family name: Tang
  given name: Xi-min
author list: Agent
  family name: Huang
  given name: Shaoyang
author list: Agent
  family name: Li
  given name: Zhengliang
author list: Agent
  family name: Cao
  given name: Huaize
author list: Agent
  family name: Xiong
  given name: Wei
doi: 10.7717/peerj.20274
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: © 2025 Zhao et al.
attribution name: Zhao et al.

Differential responses of hard coral Montipora digitata and soft coral Xenia umbellata to nutrient stoichiometry under heat stress
type: item
type: AcademicArticle
description: The nitrogen-to-phosphorus (N:P) ratio of dissolved inorganic nutrients may influence coral susceptibility to heat stress, but comparative studies on how different N:P ratios affect soft and hard corals do not exist. This study thus investigated the effects of two different N:P ratios on two common Indo-Pacific reef corals: the pulsating soft coral Xenia umbellata and the hard coral Montipora digitata. Corals were exposed for five weeks to N:P 19:1 (37 µM nitrate, two µM phosphate) and N:P 5:1 (37 µM nitrate, eight µM phosphate), relative to a low nutrient control (N:P 3:1, 0.003 µM nitrate, 0.001 µM phosphate). After two weeks, temperatures were gradually increased from 26 to 32 °C. Nutrient enrichment alone did not affect any response parameter for M. digitata, whereas for X. umbellata, 9% mortality was observed, along with a reduction in pulsation rates (−100% under 5:1 ratio, −58% under 19:1 ratio). Heat stress alone significantly reduced Symbiodiniaceae density and chlorophyll a content of M. digitata, while X. umbellata was unaffected. Combined factors significantly increased mortality for M. digitata (100% and 92%) and X. umbellata (87% and 33%) under the 5:1 and 19:1 ratio, respectively. Symbiodiniaceae density and chlorophyll a content in M. digitata showed the same response as under heat stress alone, while these parameters were unaffected for X. umbellata. Pulsation of X. umbellata was reduced by 100% in both combined treatments. Nutrient enrichment alone likely compromised X. umbellata’s metabolism through the energy-intensive reduction of nitrate to ammonium, halting pulsation. Yet, under combined warming and nutrient addition, X. umbellata showed better fitness than M. digitata, suggesting it may better cope with the predicted environmental changes. Still, both corals were negatively affected, particularly by the 5:1 N:P ratio. The stronger impact of this low ratio likely resulted from exacerbated energy depletion by nitrogen assimilation, while the im…
format: application/pdf
format: text/html
creator: Selma D. Mezger
creator: Sophie Littke
creator: Malte Ostendarp
creator: Mareike de Breuyn
creator: Christian Wild
subject: Ecology
subject: Marine Biology
subject: Biogeochemistry
description: doi:10.7717/peerj.20273
publisher: PeerJ Inc.
rights: © 2025 Mezger et al.
abstract: The nitrogen-to-phosphorus (N:P) ratio of dissolved inorganic nutrients may influence coral susceptibility to heat stress, but comparative studies on how different N:P ratios affect soft and hard corals do not exist. This study thus investigated the effects of two different N:P ratios on two common Indo-Pacific reef corals: the pulsating soft coral Xenia umbellata and the hard coral Montipora digitata. Corals were exposed for five weeks to N:P 19:1 (37 µM nitrate, two µM phosphate) and N:P 5:1 (37 µM nitrate, eight µM phosphate), relative to a low nutrient control (N:P 3:1, 0.003 µM nitrate, 0.001 µM phosphate). After two weeks, temperatures were gradually increased from 26 to 32 °C. Nutrient enrichment alone did not affect any response parameter for M. digitata, whereas for X. umbellata, 9% mortality was observed, along with a reduction in pulsation rates (−100% under 5:1 ratio, −58% under 19:1 ratio). Heat stress alone significantly reduced Symbiodiniaceae density and chlorophyll a content of M. digitata, while X. umbellata was unaffected. Combined factors significantly increased mortality for M. digitata (100% and 92%) and X. umbellata (87% and 33%) under the 5:1 and 19:1 ratio, respectively. Symbiodiniaceae density and chlorophyll a content in M. digitata showed the same response as under heat stress alone, while these parameters were unaffected for X. umbellata. Pulsation of X. umbellata was reduced by 100% in both combined treatments. Nutrient enrichment alone likely compromised X. umbellata’s metabolism through the energy-intensive reduction of nitrate to ammonium, halting pulsation. Yet, under combined warming and nutrient addition, X. umbellata showed better fitness than M. digitata, suggesting it may better cope with the predicted environmental changes. Still, both corals were negatively affected, particularly by the 5:1 N:P ratio. The stronger impact of this low ratio likely resulted from exacerbated energy depletion by nitrogen assimilation, while the im…
bibliographic citation: Mezger et al. (2025) Differential responses of hard coral Montipora digitata and soft coral Xenia umbellata to nutrient stoichiometry under heat stress. PeerJ 13:e20273 https://doi.org/10.7717/peerj.20273
date submitted: 2025-02-12
date accepted: 2025-09-30
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mezger
  given name: Selma D.
author list: Agent
  family name: Littke
  given name: Sophie
author list: Agent
  family name: Ostendarp
  given name: Malte
author list: Agent
  family name: de Breuyn
  given name: Mareike
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.20273
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Mezger et al.
attribution name: Mezger et al.

Development of a prediction model for lower limb deep vein thrombosis in critically ill patients after intracranial hemorrhage at high altitude: a retrospective study
type: item
type: AcademicArticle
description: Objective To analyze the risk factors for lower limb deep vein thrombosis (LDVT) in critically ill patients admitted to the intensive care unit (ICU) following intracranial hemorrhage at high altitude, and to establish a predictive model. Methods A retrospective analysis was conducted on 359 patients who underwent surgery for intracranial hemorrhage and were admitted to the ICU of Xizang Autonomous Region People’s Hospital between August 1, 2021, and December 31, 2023. Patients were categorized into an LDVT group (n = 86) and a non-LDVT group (n = 273) based on the occurrence of LDVT during their ICU stay. Demographic data, comorbidities, laboratory results, and treatment approaches were compared between the groups. Independent risk factors were identified through univariate and multivariate logistic regression analyses. A risk prediction model was developed using R software, and its performance was internally validated. Results Compared to the non-LDVT group, patients in the LDVT group had significantly longer ICU and overall hospital stays (p < 0.05). Multivariate logistic regression revealed hypoalbuminemia and elevated D-dimer levels as independent risk factors for LDVT, while aboriginal residency in high-altitude areas (≥ 4,500 m) was identified as a protective factor. A nomogram incorporating these variables was constructed. Internal validation demonstrated strong agreement between predicted and observed outcomes, with the area under the receiver operating characteristic (ROC) curve reaching 0.815 (95% CI [0.761–0.870]). The Hosmer-Lemeshow test indicated a good model fit (p = 0.088). Conclusion LDVT significantly prolongs ICU and hospital stays in critically ill patients. Hypoalbuminemia and elevated D-dimer levels are independent risk factors for LDVT, whereas aboriginal residency at high altitudes (≥ 4,500 m) serves as a protective factor. The developed risk prediction model shows strong predictive performance.
format: application/pdf
format: text/html
creator: Zhuoma Ciren
creator: Jianlei Fu
creator: Guoying Lin
creator: Qianwei Li
creator: Bin Wang
subject: Cardiology
subject: Emergency and Critical Care
subject: Neurology
description: doi:10.7717/peerj.20245
publisher: PeerJ Inc.
rights: © 2025 et al.
abstract: Objective To analyze the risk factors for lower limb deep vein thrombosis (LDVT) in critically ill patients admitted to the intensive care unit (ICU) following intracranial hemorrhage at high altitude, and to establish a predictive model. Methods A retrospective analysis was conducted on 359 patients who underwent surgery for intracranial hemorrhage and were admitted to the ICU of Xizang Autonomous Region People’s Hospital between August 1, 2021, and December 31, 2023. Patients were categorized into an LDVT group (n = 86) and a non-LDVT group (n = 273) based on the occurrence of LDVT during their ICU stay. Demographic data, comorbidities, laboratory results, and treatment approaches were compared between the groups. Independent risk factors were identified through univariate and multivariate logistic regression analyses. A risk prediction model was developed using R software, and its performance was internally validated. Results Compared to the non-LDVT group, patients in the LDVT group had significantly longer ICU and overall hospital stays (p < 0.05). Multivariate logistic regression revealed hypoalbuminemia and elevated D-dimer levels as independent risk factors for LDVT, while aboriginal residency in high-altitude areas (≥ 4,500 m) was identified as a protective factor. A nomogram incorporating these variables was constructed. Internal validation demonstrated strong agreement between predicted and observed outcomes, with the area under the receiver operating characteristic (ROC) curve reaching 0.815 (95% CI [0.761–0.870]). The Hosmer-Lemeshow test indicated a good model fit (p = 0.088). Conclusion LDVT significantly prolongs ICU and hospital stays in critically ill patients. Hypoalbuminemia and elevated D-dimer levels are independent risk factors for LDVT, whereas aboriginal residency at high altitudes (≥ 4,500 m) serves as a protective factor. The developed risk prediction model shows strong predictive performance.
bibliographic citation: Ciren et al. (2025) Development of a prediction model for lower limb deep vein thrombosis in critically ill patients after intracranial hemorrhage at high altitude: a retrospective study. PeerJ 13:e20245 https://doi.org/10.7717/peerj.20245
date submitted: 2025-03-14
date accepted: 2025-09-25
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ciren
  given name: Zhuoma
author list: Agent
  family name: Fu
  given name: Jianlei
author list: Agent
  family name: Lin
  given name: Guoying
author list: Agent
  family name: Li
  given name: Qianwei
author list: Agent
  family name: Wang
  given name: Bin
doi: 10.7717/peerj.20245
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 et al.
attribution name: et al.

Screening durum wheat cultivars for resistance traits against the stem-base pathogen Fusarium graminearum
type: item
type: AcademicArticle
description: Durum wheat is not a traditional crop in countries with a temperate climate, but the growing demand for semolina in the food processing industry has increased the popularity of this cereal species in the farming sector. The pathogens responsible for Fusarium crown rot (FCR), eyespot, and sharp eyespot contribute to lodging, disrupt the translocation of water and nutrients in plants, and decrease yields. The present study was conducted in several dozen locations in Poland to determine the severity of FCR, eyespot, and sharp eyespot in more than ten durum wheat cultivars, to identify stem-base pathogens, to analyze the virulence of Fusarium graminearum, and to evaluate the effectiveness of seed dressing in reducing the severity of infections in durum wheat seedlings. Durum wheat cultivars were screened in field and plot experiments in Poland. The virulence of F. graminearum and the effectiveness of biological and chemical seed dressing in reducing the incidence of FCR were determined in vivo. In the studied locations, symptoms of FCR and eyespot were observed on 16–76% and 1–36% of durum wheat stems, respectively, on average. Sharp eyespot was noted only in one year of the study in a single location (1–6%). The severity of the analyzed diseases was generally low. Fusarium avenaceum, F. culmorum, F. graminearum, F. oxysporum, F. poae, F. solani, and F. sporotrichioides were isolated from stems with symptoms of FCR. The number of F. graminearum and F. culmorum isolates was significantly positively correlated with the severity of FCR symptoms (r = 0.480 and r = 0.485, respectively). Fusarium graminearum was identified in 15 locations, and F. culmorum was detected in six locations. Seed treatment with triticonazole reduced the number of ungerminated kernels by 42.6% in comparison with the untreated control. Seed treatment involving Debaryomyces hansenii decreased the number of ungerminated kernels by 31.1% on average, but this effect was noted only in cv. Floradur. All du…
format: application/pdf
format: text/html
creator: Edyta Kwiatkowska
creator: Urszula Wachowska
creator: Weronika Giedrojć
creator: Agata Wachowska
creator: Dariusz Gontarz
subject: Mycology
description: doi:10.7717/peerj.20105
publisher: PeerJ Inc.
rights: © 2025 Kwiatkowska et al.
abstract: Durum wheat is not a traditional crop in countries with a temperate climate, but the growing demand for semolina in the food processing industry has increased the popularity of this cereal species in the farming sector. The pathogens responsible for Fusarium crown rot (FCR), eyespot, and sharp eyespot contribute to lodging, disrupt the translocation of water and nutrients in plants, and decrease yields. The present study was conducted in several dozen locations in Poland to determine the severity of FCR, eyespot, and sharp eyespot in more than ten durum wheat cultivars, to identify stem-base pathogens, to analyze the virulence of Fusarium graminearum, and to evaluate the effectiveness of seed dressing in reducing the severity of infections in durum wheat seedlings. Durum wheat cultivars were screened in field and plot experiments in Poland. The virulence of F. graminearum and the effectiveness of biological and chemical seed dressing in reducing the incidence of FCR were determined in vivo. In the studied locations, symptoms of FCR and eyespot were observed on 16–76% and 1–36% of durum wheat stems, respectively, on average. Sharp eyespot was noted only in one year of the study in a single location (1–6%). The severity of the analyzed diseases was generally low. Fusarium avenaceum, F. culmorum, F. graminearum, F. oxysporum, F. poae, F. solani, and F. sporotrichioides were isolated from stems with symptoms of FCR. The number of F. graminearum and F. culmorum isolates was significantly positively correlated with the severity of FCR symptoms (r = 0.480 and r = 0.485, respectively). Fusarium graminearum was identified in 15 locations, and F. culmorum was detected in six locations. Seed treatment with triticonazole reduced the number of ungerminated kernels by 42.6% in comparison with the untreated control. Seed treatment involving Debaryomyces hansenii decreased the number of ungerminated kernels by 31.1% on average, but this effect was noted only in cv. Floradur. All du…
bibliographic citation: Kwiatkowska et al. (2025) Screening durum wheat cultivars for resistance traits against the stem-base pathogen Fusarium graminearum. PeerJ 13:e20105 https://doi.org/10.7717/peerj.20105
date submitted: 2024-03-22
date accepted: 2025-08-28
issued: 2025-11-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kwiatkowska
  given name: Edyta
author list: Agent
  family name: Wachowska
  given name: Urszula
author list: Agent
  family name: Giedrojć
  given name: Weronika
author list: Agent
  family name: Wachowska
  given name: Agata
author list: Agent
  family name: Gontarz
  given name: Dariusz
doi: 10.7717/peerj.20105
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-13
copyright: ©2025 Kwiatkowska et al.
attribution name: Kwiatkowska et al.

Personality Assessment Inventory (PAI): obsolete norms identify psychopathology in nearly everyone
type: item
type: AcademicArticle
description: Background The Personality Assessment Inventory (PAI), a self-report personality test, is one of the frequently used measures to assess psychopathology in a wide variety of settings including in high stakes assessments, for example, in child custody disputes, employment settings and fitness for duty assessments. The PAI has never been normed on a Canadian population and the PAI users have simply assumed that the US norms also describe the Canadian population. Moreover, accumulated research demonstrates that the PAI’s 35 years outdated and obsolete norms no longer describe neither university students’ nor normal adult US populations. Method We administered the PAI to over 200 university students in a mid-size Canadian university. Results Our students scored on average in moderately elevated range (60T to 69T) on many of the PAI scales including anxiety (ANX), anxiety-related disorders (ARD), depression (DEP), schizophrenia (SCZ), and borderline features (BOR). Multivariate base rate analyses revealed that approximately 95% of our sample scored in elevated range on at least one out of the 22 PAI Scales. Furthermore, although some of the PAI reliabilities are adequate for research, the PAI reliabilities are too low for using the PAI in high stakes and forensic assessment, for example, in insurance benefits, child custody, employment, and fitness for duty assessments. Discussion We conclude that the PAI US norms are no longer appropriate for high-stakes assessments, ought to be withdrawn immediately, and new up-to-date norms ought to be established to prevent mislabelling and diagnostic misclassifications of and harm to examinees. Continued use of the PAI outdated norms in high stakes assessments carries ethical risks, is non-scientific, and likely amounts to malpractice.
format: application/pdf
format: text/html
creator: Bob Uttl
creator: Kiefer Sikma
creator: Mikayla Tat
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20340
publisher: PeerJ Inc.
rights: © 2025 Uttl et al.
abstract: Background The Personality Assessment Inventory (PAI), a self-report personality test, is one of the frequently used measures to assess psychopathology in a wide variety of settings including in high stakes assessments, for example, in child custody disputes, employment settings and fitness for duty assessments. The PAI has never been normed on a Canadian population and the PAI users have simply assumed that the US norms also describe the Canadian population. Moreover, accumulated research demonstrates that the PAI’s 35 years outdated and obsolete norms no longer describe neither university students’ nor normal adult US populations. Method We administered the PAI to over 200 university students in a mid-size Canadian university. Results Our students scored on average in moderately elevated range (60T to 69T) on many of the PAI scales including anxiety (ANX), anxiety-related disorders (ARD), depression (DEP), schizophrenia (SCZ), and borderline features (BOR). Multivariate base rate analyses revealed that approximately 95% of our sample scored in elevated range on at least one out of the 22 PAI Scales. Furthermore, although some of the PAI reliabilities are adequate for research, the PAI reliabilities are too low for using the PAI in high stakes and forensic assessment, for example, in insurance benefits, child custody, employment, and fitness for duty assessments. Discussion We conclude that the PAI US norms are no longer appropriate for high-stakes assessments, ought to be withdrawn immediately, and new up-to-date norms ought to be established to prevent mislabelling and diagnostic misclassifications of and harm to examinees. Continued use of the PAI outdated norms in high stakes assessments carries ethical risks, is non-scientific, and likely amounts to malpractice.
bibliographic citation: Uttl et al. (2025) Personality Assessment Inventory (PAI): obsolete norms identify psychopathology in nearly everyone. PeerJ 13:e20340 https://doi.org/10.7717/peerj.20340
date submitted: 2025-06-04
date accepted: 2025-10-14
issued: 2025-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uttl
  given name: Bob
author list: Agent
  family name: Sikma
  given name: Kiefer
author list: Agent
  family name: Tat
  given name: Mikayla
doi: 10.7717/peerj.20340
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-12
copyright: ©2025 Uttl et al.
attribution name: Uttl et al.

The effect of the erythropoietin resistance index on brain hemorrhage and infarction risk in maintenance hemodialysis patients: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Maintenance hemodialysis (MHD) is the main renal replacement therapy for patients with end-stage renal disease, and erythropoietin (EPO) is the main therapy for renal anemia in patients receiving maintenance hemodialysis. However, the risks of brain hemorrhage and infarction in patients on hemodialysis with erythropoietin therapy remain unclear. Methods Patients who underwent regular hemodialysis at the Blood Purification Center of the Northern Theater General Hospital from January 1, 2018, to January 1, 2022, were retrospectively selected. A total of 588 MHD patients were enrolled on the basis of the inclusion and exclusion criteria. The primary endpoint of follow-up was brain hemorrhage and infarction, or January 1, 2024. The secondary endpoint was all-cause death. The erythropoietin resistance index (ERI) was calculated as follows: erythropoiesis-stimulating agent (ESA) (IU/week)/body weight (kg)/hemoglobin level (g/dL). Patients were divided into four groups according to ERI quartile, and a Cox proportional risk model was applied to observe the associations between the ERI and the risks of brain hemorrhage and infarction and all-cause mortality. Results During a median follow-up of 6 years, brain hemorrhage events occurred in 41 (6.9%) MHD patients, and brain infarction events occurred in 61 (10.3%) MHD patients. According to the Kaplan–Meier curve, the incidence of brain hemorrhage and infarction was greater in the high-ERI subgroup than in the low-ERI subgroup (p < 0.001). Multivariate Cox regression analysis revealed that a high ERI was a significant predictor of brain hemorrhage (HR: 3.85, 95% CI [1.34–11.07], p = 0.012) and brain infarction (HR = 2.657, 95% CI [1.17–6.02], p = 0.020). A higher ERI was associated with an increased risk of all-cause death in MHD patients (HR: 1.72, 95% CI [1.05–2.82], p = 0.033). Conclusions Higher ERI scores were associated with brain hemorrhage and infarction in MHD patients.
format: application/pdf
format: text/html
creator: Mingyu Liu
creator: Kaiming Ren
creator: Qian Wang
creator: Chen Zhao
creator: Zhuo Ren
creator: Jiuxu Bai
creator: Ning Cao
subject: Cardiology
subject: Hematology
subject: Internal Medicine
subject: Nephrology
subject: Neurology
description: doi:10.7717/peerj.20326
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Maintenance hemodialysis (MHD) is the main renal replacement therapy for patients with end-stage renal disease, and erythropoietin (EPO) is the main therapy for renal anemia in patients receiving maintenance hemodialysis. However, the risks of brain hemorrhage and infarction in patients on hemodialysis with erythropoietin therapy remain unclear. Methods Patients who underwent regular hemodialysis at the Blood Purification Center of the Northern Theater General Hospital from January 1, 2018, to January 1, 2022, were retrospectively selected. A total of 588 MHD patients were enrolled on the basis of the inclusion and exclusion criteria. The primary endpoint of follow-up was brain hemorrhage and infarction, or January 1, 2024. The secondary endpoint was all-cause death. The erythropoietin resistance index (ERI) was calculated as follows: erythropoiesis-stimulating agent (ESA) (IU/week)/body weight (kg)/hemoglobin level (g/dL). Patients were divided into four groups according to ERI quartile, and a Cox proportional risk model was applied to observe the associations between the ERI and the risks of brain hemorrhage and infarction and all-cause mortality. Results During a median follow-up of 6 years, brain hemorrhage events occurred in 41 (6.9%) MHD patients, and brain infarction events occurred in 61 (10.3%) MHD patients. According to the Kaplan–Meier curve, the incidence of brain hemorrhage and infarction was greater in the high-ERI subgroup than in the low-ERI subgroup (p < 0.001). Multivariate Cox regression analysis revealed that a high ERI was a significant predictor of brain hemorrhage (HR: 3.85, 95% CI [1.34–11.07], p = 0.012) and brain infarction (HR = 2.657, 95% CI [1.17–6.02], p = 0.020). A higher ERI was associated with an increased risk of all-cause death in MHD patients (HR: 1.72, 95% CI [1.05–2.82], p = 0.033). Conclusions Higher ERI scores were associated with brain hemorrhage and infarction in MHD patients.
bibliographic citation: Liu et al. (2025) The effect of the erythropoietin resistance index on brain hemorrhage and infarction risk in maintenance hemodialysis patients: a retrospective cohort study. PeerJ 13:e20326 https://doi.org/10.7717/peerj.20326
date submitted: 2025-03-31
date accepted: 2025-10-13
issued: 2025-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Mingyu
author list: Agent
  family name: Ren
  given name: Kaiming
author list: Agent
  family name: Wang
  given name: Qian
author list: Agent
  family name: Zhao
  given name: Chen
author list: Agent
  family name: Ren
  given name: Zhuo
author list: Agent
  family name: Bai
  given name: Jiuxu
author list: Agent
  family name: Cao
  given name: Ning
doi: 10.7717/peerj.20326
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-12
copyright: ©2025 Liu et al.
attribution name: Liu et al.

Minos-mediated transgenesis in the pantry moth Plodia interpunctella
type: item
type: AcademicArticle
description: Transposon-mediated transgenesis has been widely used to study gene function in Lepidoptera, with piggyBac being the most commonly employed system. However, because the piggyBac transposase originates from a lepidopteran genome, it raises concerns about endogenous activation, remobilization, and silencing of transgenes, thus questioning its suitability as an optimal tool in Lepidoptera. As an alternative, we evaluated the dipteran-derived Minos transposase for stable germline transformation in the pantry moth, Plodia interpunctella. We injected syncytial embryos with transposase mRNA, along with donor plasmids encoding 3xP3::EGFP and 3xP3::mCherry markers of eye and glial tissues. Across multiple experiments, we found that G0 injectees could transmit Minos transgenes through the germline even in the absence of visible marker expression in the soma, and that large mating pools of G0 founders consistently produced transgenic offspring at efficiencies exceeding 10%. Using these methods, we generated transgenic lines with a dual expression plasmid, using 3xP3::mCherry for driving red fluorescence in eyes and glial tissues, as well as the Fibroin-L promoter expressing the recently developed mBaoJin fluorescent protein in the silk glands. This demonstrated the feasibility of screening two pairs of promoter activity in tissues of interest. Collectively, these results—along with previous findings in the silkworm Bombyx mori—demonstrate that Minos achieves robust germline integration of transgenes in Lepidoptera, offering a valuable pathway to the genetic modification of species where the remobilization or suppression of piggyBac elements might be rampant.
format: application/pdf
format: text/html
creator: Donya N. Shodja
creator: Luca Livraghi
creator: Arnaud Martin
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.20249
publisher: PeerJ Inc.
rights: © 2025 Shodja et al.
abstract: Transposon-mediated transgenesis has been widely used to study gene function in Lepidoptera, with piggyBac being the most commonly employed system. However, because the piggyBac transposase originates from a lepidopteran genome, it raises concerns about endogenous activation, remobilization, and silencing of transgenes, thus questioning its suitability as an optimal tool in Lepidoptera. As an alternative, we evaluated the dipteran-derived Minos transposase for stable germline transformation in the pantry moth, Plodia interpunctella. We injected syncytial embryos with transposase mRNA, along with donor plasmids encoding 3xP3::EGFP and 3xP3::mCherry markers of eye and glial tissues. Across multiple experiments, we found that G0 injectees could transmit Minos transgenes through the germline even in the absence of visible marker expression in the soma, and that large mating pools of G0 founders consistently produced transgenic offspring at efficiencies exceeding 10%. Using these methods, we generated transgenic lines with a dual expression plasmid, using 3xP3::mCherry for driving red fluorescence in eyes and glial tissues, as well as the Fibroin-L promoter expressing the recently developed mBaoJin fluorescent protein in the silk glands. This demonstrated the feasibility of screening two pairs of promoter activity in tissues of interest. Collectively, these results—along with previous findings in the silkworm Bombyx mori—demonstrate that Minos achieves robust germline integration of transgenes in Lepidoptera, offering a valuable pathway to the genetic modification of species where the remobilization or suppression of piggyBac elements might be rampant.
bibliographic citation: Shodja et al. (2025) Minos-mediated transgenesis in the pantry moth Plodia interpunctella. PeerJ 13:e20249 https://doi.org/10.7717/peerj.20249
date submitted: 2025-03-30
date accepted: 2025-09-25
issued: 2025-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shodja
  given name: Donya N.
author list: Agent
  family name: Livraghi
  given name: Luca
author list: Agent
  family name: Martin
  given name: Arnaud
doi: 10.7717/peerj.20249
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-12
copyright: © 2025 Shodja et al.
attribution name: Shodja et al.

The cuproptosis-related gene ITGB6 and LTBP1 may be associated with diabetic kidney disease progression and immune cell infiltration
type: item
type: AcademicArticle
description: Objective Cuproptosis, a newly discovered cell death mechanism, has been linked to the pathogenesis of multiple diseases. However, its role in diabetic kidney disease (DKD) remains unclear. Methods By analyzing datasets GPL17586 and GPL571 from the GEO database and applying machine learning, cuproptosis-related marker genes associated with DKD were identified. The expression levels of these genes were examined in Mouse Podocyte Cell Line (MPC5) podocytes cultured in vitro and treated with high glucose (30 mM) for 24, 48, and 72 h to explore their roles in the onset and progression of DKD. Results Key genes in the cuproptosis pathway, integrin β6 (ITGB6) and latent transforming growth factor beta-binding protein 1 (LTBP1), were significantly upregulated in DKD patients. Consistent with this, in high glucose-treated podocytes, the expression of ITGB6 and LTBP1 was significantly higher than in the control group at 24, 48, and 72 h. The area under the receiver operating characteristic (ROC) curve (AUC) for ITGB6 and LTBP1 in both the training set (GPL17586) and validation set (GPL571) exceeded 0.7, indicating good diagnostic efficacy for DKD. Furthermore, immune infiltration analysis further revealed that ITGB6 and LTBP1 were significantly positively correlated with activated B cells, central memory Cluster of Differentiation 4 (CD4) T cells, effector memory CD4 T cells, effector memory Cluster of Differentiation 8 (CD8) T cells, and immature B cells, while showing a significant negative correlation with neutrophils. Conclusion This study suggests that cuproptosis-related genes ITGB6 and LTBP1 may be associated with the progression of DKD through their potential role in immune cell infiltration, and could serve as potential novel targets for the prevention and diagnosis of DKD.
format: application/pdf
format: text/html
creator: Suying Hu
creator: Mengdi Tian
creator: Wenjia Hu
creator: Liang Yao
creator: Ying Tang
creator: Wei Shen
creator: Qing He
creator: Jing Xu
creator: Huan Yao
creator: Lei Ji
creator: Feifei Fan
creator: Shiqiang Liu
creator: Zhen Wang
subject: Bioinformatics
subject: Cell Biology
description: doi:10.7717/peerj.20346
publisher: PeerJ Inc.
rights: © 2025 Hu et al.
abstract: Objective Cuproptosis, a newly discovered cell death mechanism, has been linked to the pathogenesis of multiple diseases. However, its role in diabetic kidney disease (DKD) remains unclear. Methods By analyzing datasets GPL17586 and GPL571 from the GEO database and applying machine learning, cuproptosis-related marker genes associated with DKD were identified. The expression levels of these genes were examined in Mouse Podocyte Cell Line (MPC5) podocytes cultured in vitro and treated with high glucose (30 mM) for 24, 48, and 72 h to explore their roles in the onset and progression of DKD. Results Key genes in the cuproptosis pathway, integrin β6 (ITGB6) and latent transforming growth factor beta-binding protein 1 (LTBP1), were significantly upregulated in DKD patients. Consistent with this, in high glucose-treated podocytes, the expression of ITGB6 and LTBP1 was significantly higher than in the control group at 24, 48, and 72 h. The area under the receiver operating characteristic (ROC) curve (AUC) for ITGB6 and LTBP1 in both the training set (GPL17586) and validation set (GPL571) exceeded 0.7, indicating good diagnostic efficacy for DKD. Furthermore, immune infiltration analysis further revealed that ITGB6 and LTBP1 were significantly positively correlated with activated B cells, central memory Cluster of Differentiation 4 (CD4) T cells, effector memory CD4 T cells, effector memory Cluster of Differentiation 8 (CD8) T cells, and immature B cells, while showing a significant negative correlation with neutrophils. Conclusion This study suggests that cuproptosis-related genes ITGB6 and LTBP1 may be associated with the progression of DKD through their potential role in immune cell infiltration, and could serve as potential novel targets for the prevention and diagnosis of DKD.
bibliographic citation: Hu et al. (2025) The cuproptosis-related gene ITGB6 and LTBP1 may be associated with diabetic kidney disease progression and immune cell infiltration. PeerJ 13:e20346 https://doi.org/10.7717/peerj.20346
date submitted: 2025-06-17
date accepted: 2025-10-15
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Suying
author list: Agent
  family name: Tian
  given name: Mengdi
author list: Agent
  family name: Hu
  given name: Wenjia
author list: Agent
  family name: Yao
  given name: Liang
author list: Agent
  family name: Tang
  given name: Ying
author list: Agent
  family name: Shen
  given name: Wei
author list: Agent
  family name: He
  given name: Qing
author list: Agent
  family name: Xu
  given name: Jing
author list: Agent
  family name: Yao
  given name: Huan
author list: Agent
  family name: Ji
  given name: Lei
author list: Agent
  family name: Fan
  given name: Feifei
author list: Agent
  family name: Liu
  given name: Shiqiang
author list: Agent
  family name: Wang
  given name: Zhen
doi: 10.7717/peerj.20346
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: © 2025 Hu et al.
attribution name: Hu et al.

Decoding the bare necessities of decapod crustacean nomenclature through the ages
type: item
type: AcademicArticle
description: Though taxonomists have been classifying species since 1758, the methods and biases of their naming practices have recently come under scrutiny. Despite some compelling claims on e.g., historical imperialism in the published literature, the knowledge base for making such assertions is small, as nomenclatural trends have only been researched in a select few taxa. Here, we investigate naming practices in Decapoda, one of the most studied crustacean groups, thereby extending the knowledge base to the marine realm in contrast to a previously studied cohort of largely terrestrial taxa. To date almost 18,000 species of decapods are known, from which a total of 22,363 unique names are analysed, as neither nomenclatorial nor taxonomic status has any bearing on the naming process. Despite taxonomists being inspired by a multitude of cultural influences, historically the majority of names were derived from the morphology of the animals. This dominance declined in the Victorian era, with a concomitant rise in the use of both geographically inspired names and eponyms (species named after people). Post-1958, a near-even split is achieved between these three categories, while other etymological classifications stake a minority claim on the dataset. Although a historic and contemporary gender imbalance is present amongst eponyms honouring scientists, contrary to previous findings our results detect no actual bias in naming practices, instead indicating that female scientists have been honoured in proportion to their collective presence in the field. Though previous studies have flagged a significant proportion of eponyms named for colonialist figures, these were found in relatively small numbers among Decapoda.
format: application/pdf
format: text/html
creator: Sammy De Grave
creator: Elizabeth Cole
creator: Sancia E. T. van der Meij
subject: Biodiversity
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.20337
publisher: PeerJ Inc.
rights: © 2025 De Grave et al.
abstract: Though taxonomists have been classifying species since 1758, the methods and biases of their naming practices have recently come under scrutiny. Despite some compelling claims on e.g., historical imperialism in the published literature, the knowledge base for making such assertions is small, as nomenclatural trends have only been researched in a select few taxa. Here, we investigate naming practices in Decapoda, one of the most studied crustacean groups, thereby extending the knowledge base to the marine realm in contrast to a previously studied cohort of largely terrestrial taxa. To date almost 18,000 species of decapods are known, from which a total of 22,363 unique names are analysed, as neither nomenclatorial nor taxonomic status has any bearing on the naming process. Despite taxonomists being inspired by a multitude of cultural influences, historically the majority of names were derived from the morphology of the animals. This dominance declined in the Victorian era, with a concomitant rise in the use of both geographically inspired names and eponyms (species named after people). Post-1958, a near-even split is achieved between these three categories, while other etymological classifications stake a minority claim on the dataset. Although a historic and contemporary gender imbalance is present amongst eponyms honouring scientists, contrary to previous findings our results detect no actual bias in naming practices, instead indicating that female scientists have been honoured in proportion to their collective presence in the field. Though previous studies have flagged a significant proportion of eponyms named for colonialist figures, these were found in relatively small numbers among Decapoda.
bibliographic citation: De Grave et al. (2025) Decoding the bare necessities of decapod crustacean nomenclature through the ages. PeerJ 13:e20337 https://doi.org/10.7717/peerj.20337
date submitted: 2025-08-21
date accepted: 2025-10-13
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Grave
  given name: Sammy
author list: Agent
  family name: Cole
  given name: Elizabeth
author list: Agent
  family name: van der Meij
  given name: Sancia E. T.
doi: 10.7717/peerj.20337
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: © 2025 De Grave et al.
attribution name: De Grave et al.

Geographical and seasonal distribution of the Short-crested Coquette hummingbird: a microendemic and endangered species
type: item
type: AcademicArticle
description: Species movements along elevational or latitudinal gradients occur primarily due to climatic variations and food resource availability. However, the role of seasonal climatic conditions in species with highly restricted distributions has been poorly addressed. In this study, we analyzed the geographic distribution and seasonal climatic niche during the dry and rainy seasons of the Short-crested Coquette hummingbird (SCCH; Lophornis brachylophus), a species with high conservation priority at the global scale. We generated ecological niche and species distribution models for both seasons and used niche similarity tests to represent and compare their climatic differences. We recorded the availability of flowering and fruiting plants that the SCCH feeds on within its distribution area during both seasons and performed a kernel density analysis to evaluate the main peaks in food availability. Our results revealed that the potential distribution of the SCCH is larger (642 pixels) in the dry season than in the rainy season (487 pixels). In the dry season, the distribution of this hummingbird includes sites at lower elevations (reaching 780 m above sea level [masl]). In contrast, in the rainy season, it extends to higher elevations (up to 1,450 masl). This seasonal shift between the two seasons coincides with the availability of flowers and fruits along the elevational gradient. The climatic niche similarity between the dry and rainy seasons shows moderate overlap (Schoener’s D = 0.50) and is higher than expected by chance. Our results suggest that the SCCH moderate changes in its climatic niche throughout the year, with plant phenology being a primary driver of changes in its elevational range between seasons.
format: application/pdf
format: text/html
creator: Pablo Sierra-Morales
creator: Octavio R. Rojas-Soto
creator: Luis A. Sánchez-González
creator: Carina Gutiérrez-Flores
creator: R. Carlos Almazán-Núñez
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Zoology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20312
publisher: PeerJ Inc.
rights: © 2025 Sierra-Morales et al.
abstract: Species movements along elevational or latitudinal gradients occur primarily due to climatic variations and food resource availability. However, the role of seasonal climatic conditions in species with highly restricted distributions has been poorly addressed. In this study, we analyzed the geographic distribution and seasonal climatic niche during the dry and rainy seasons of the Short-crested Coquette hummingbird (SCCH; Lophornis brachylophus), a species with high conservation priority at the global scale. We generated ecological niche and species distribution models for both seasons and used niche similarity tests to represent and compare their climatic differences. We recorded the availability of flowering and fruiting plants that the SCCH feeds on within its distribution area during both seasons and performed a kernel density analysis to evaluate the main peaks in food availability. Our results revealed that the potential distribution of the SCCH is larger (642 pixels) in the dry season than in the rainy season (487 pixels). In the dry season, the distribution of this hummingbird includes sites at lower elevations (reaching 780 m above sea level [masl]). In contrast, in the rainy season, it extends to higher elevations (up to 1,450 masl). This seasonal shift between the two seasons coincides with the availability of flowers and fruits along the elevational gradient. The climatic niche similarity between the dry and rainy seasons shows moderate overlap (Schoener’s D = 0.50) and is higher than expected by chance. Our results suggest that the SCCH moderate changes in its climatic niche throughout the year, with plant phenology being a primary driver of changes in its elevational range between seasons.
bibliographic citation: Sierra-Morales et al. (2025) Geographical and seasonal distribution of the Short-crested Coquette hummingbird: a microendemic and endangered species. PeerJ 13:e20312 https://doi.org/10.7717/peerj.20312
date submitted: 2025-06-03
date accepted: 2025-10-08
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sierra-Morales
  given name: Pablo
author list: Agent
  family name: Rojas-Soto
  given name: Octavio R.
author list: Agent
  family name: Sánchez-González
  given name: Luis A.
author list: Agent
  family name: Gutiérrez-Flores
  given name: Carina
author list: Agent
  family name: Almazán-Núñez
  given name: R. Carlos
doi: 10.7717/peerj.20312
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: © 2025 Sierra-Morales et al.
attribution name: Sierra-Morales et al.

Modified STOP-Bang questionnaire for detecting obstructive sleep apnea in individuals with a body mass index below 35 kg/m2
type: item
type: AcademicArticle
description: Background Obstructive sleep apnea (OSA) is a common clinical condition. Due to its high prevalence, the waiting list for polysomnography is often long. A screening tool is needed to identify individuals at high risk for OSA who should undergo polysomnography. The STOP-Bang questionnaire is a widely used screening tool; however, it may require modification for individuals with a body mass index (BMI) below 35 kg/m2. This study aimed to evaluate whether the STOP-Bang questionnaire should be modified for patients with a BMI under 35 kg/m2. Methods This retrospective analytical study included adult patients suspected of having OSA who underwent polysomnography. Exclusion criteria included pregnancy and a BMI over 35 kg/m2 or meeting criteria for bariatric surgery. Patients were categorized into OSA and non-OSA groups. Logistic regression analysis was used to assess the predictive value of STOP-Bang factors for OSA. Results A total of 188 patients were included, of whom 158 (84.04%) were diagnosed with OSA. Among the eight STOP-Bang criteria, only age was independently associated with OSA after adjustment for other variables (adjusted odds ratio: 1.04; 95% CI [1.02–1.08]). Optimal cut-off points for predicting OSA were identified as age ≥ 40 years (sensitivity: 84.18%), BMI ≥ 23 kg/m2 (sensitivity: 82.91%), and neck circumference ≥ 35 cm (sensitivity: 86.08%). A modified STOP-Bang score incorporating these cut-offs showed improved sensitivity at a score of 3: 93.0% for apnea-hypopnea index (AHI) ≥ 5 events/hr, 95.9% for AHI ≥ 15 events/hr, and 97.6% for AHI ≥ 30 events/hr. In comparison, the original STOP-Bang score of 3 had sensitivities of 50.0%, 53.6%, and 56.1% for AHI ≥ 5 events/hr, AHI ≥ 15 events/hr, and AHI > 30 events/hr, respectively. Conclusions The STOP-Bang questionnaire may require modification for individuals with a BMI below 35 kg/m2 who are suspected of having OSA. Revised cut-off values for age, neck circumference, and BMI—40 years, 35 cm, and 23 kg/m2…
format: application/pdf
format: text/html
creator: Napassorn Sinsopa
creator: Viriya Tripakornkusol
creator: Sittichai Khamsai
creator: Kittisak Sawanyawisuth
subject: Internal Medicine
subject: Respiratory Medicine
subject: Obesity
description: doi:10.7717/peerj.20310
publisher: PeerJ Inc.
rights: © 2025 Sinsopa et al.
abstract: Background Obstructive sleep apnea (OSA) is a common clinical condition. Due to its high prevalence, the waiting list for polysomnography is often long. A screening tool is needed to identify individuals at high risk for OSA who should undergo polysomnography. The STOP-Bang questionnaire is a widely used screening tool; however, it may require modification for individuals with a body mass index (BMI) below 35 kg/m2. This study aimed to evaluate whether the STOP-Bang questionnaire should be modified for patients with a BMI under 35 kg/m2. Methods This retrospective analytical study included adult patients suspected of having OSA who underwent polysomnography. Exclusion criteria included pregnancy and a BMI over 35 kg/m2 or meeting criteria for bariatric surgery. Patients were categorized into OSA and non-OSA groups. Logistic regression analysis was used to assess the predictive value of STOP-Bang factors for OSA. Results A total of 188 patients were included, of whom 158 (84.04%) were diagnosed with OSA. Among the eight STOP-Bang criteria, only age was independently associated with OSA after adjustment for other variables (adjusted odds ratio: 1.04; 95% CI [1.02–1.08]). Optimal cut-off points for predicting OSA were identified as age ≥ 40 years (sensitivity: 84.18%), BMI ≥ 23 kg/m2 (sensitivity: 82.91%), and neck circumference ≥ 35 cm (sensitivity: 86.08%). A modified STOP-Bang score incorporating these cut-offs showed improved sensitivity at a score of 3: 93.0% for apnea-hypopnea index (AHI) ≥ 5 events/hr, 95.9% for AHI ≥ 15 events/hr, and 97.6% for AHI ≥ 30 events/hr. In comparison, the original STOP-Bang score of 3 had sensitivities of 50.0%, 53.6%, and 56.1% for AHI ≥ 5 events/hr, AHI ≥ 15 events/hr, and AHI > 30 events/hr, respectively. Conclusions The STOP-Bang questionnaire may require modification for individuals with a BMI below 35 kg/m2 who are suspected of having OSA. Revised cut-off values for age, neck circumference, and BMI—40 years, 35 cm, and 23 kg/m2…
bibliographic citation: Sinsopa et al. (2025) Modified STOP-Bang questionnaire for detecting obstructive sleep apnea in individuals with a body mass index below 35 kg/m2. PeerJ 13:e20310 https://doi.org/10.7717/peerj.20310
date submitted: 2024-05-23
date accepted: 2025-10-08
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sinsopa
  given name: Napassorn
author list: Agent
  family name: Tripakornkusol
  given name: Viriya
author list: Agent
  family name: Khamsai
  given name: Sittichai
author list: Agent
  family name: Sawanyawisuth
  given name: Kittisak
doi: 10.7717/peerj.20310
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: ©2025 Sinsopa et al.
attribution name: Sinsopa et al.

Effects of combined application of compound fertilizer and biochar on absorption and utilization of phosphorus by wheat
type: item
type: AcademicArticle
description: Unreasonable fertilization practices are still applied in agricultural production, resulting in reduced crop yields and wasting resources. Therefore, it is essential to optimize fertilization regimes to improve the nutrient absorption capacity of crops. However, the effects of combining nitrogen, phosphorus, and potassium (NPK) compound fertilizer with biochar on the uptake and utilization of phosphorus (P) by wheat and soil fertility remain poorly understood. Thus, we tested three biochar levels (0 quintal (q) ha−1 (B1), 75 q ha−1 (B2), and 150 q ha−1(B3)) and four compound fertilizer levels (0 q ha−1 (F1), 2.25 q ha –1(F2), 4.50 q ha−1 (F3), and 6.75 q ha−1 (F4)), and compared the effects of different experimental combinations across two years. The results showed that combined application could increase the wheat yield, soil P content, accumulated plant P, and P utilization efficiency. Among the different treatments, the wheat yields in both years were highest under B2F3, and the total soil P contents in the booting and flowering stages were also the highest. The soil available P contents in the jointing stage, booting stage, and flowering stage were highest under B3F3. The available P soil contents at maturity in both years were highest under B3F4. In addition, compared with B1F4, the accumulated plant P amounts in the booting and flowering stages were 17.6–77.3% and 17.0–87.3% higher, respectively, under B2F2, B2F3, B3F2, and B3F4 (P < 0.05). The accumulated plant P amounts in the maturity stage during the two years were highest under B2F3 (0.83 q ha−1) and B3F3 (0.42 q ha−1), respectively. Moreover, the partial factor productivity and agronomic use efficiency were significantly higher under B2F2, B2F3, B3F2, and B3F3 than B1F4. In summary, under the experimental conditions in this study, applying compound fertilizer at 4.50 q ha−1 combined with biochar at 75 q ha−1 is recommended as the optimal fertilization scheme.
format: application/pdf
format: text/html
creator: Yun Li
creator: Jiatong Wang
creator: Jiahui Lu
creator: Yanfei Feng
creator: Jingjing Li
creator: Zhenqing Guo
creator: Xiaohu Lin
creator: Yucui Han
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20308
publisher: PeerJ Inc.
rights: © 2025 Li et al.
abstract: Unreasonable fertilization practices are still applied in agricultural production, resulting in reduced crop yields and wasting resources. Therefore, it is essential to optimize fertilization regimes to improve the nutrient absorption capacity of crops. However, the effects of combining nitrogen, phosphorus, and potassium (NPK) compound fertilizer with biochar on the uptake and utilization of phosphorus (P) by wheat and soil fertility remain poorly understood. Thus, we tested three biochar levels (0 quintal (q) ha−1 (B1), 75 q ha−1 (B2), and 150 q ha−1(B3)) and four compound fertilizer levels (0 q ha−1 (F1), 2.25 q ha –1(F2), 4.50 q ha−1 (F3), and 6.75 q ha−1 (F4)), and compared the effects of different experimental combinations across two years. The results showed that combined application could increase the wheat yield, soil P content, accumulated plant P, and P utilization efficiency. Among the different treatments, the wheat yields in both years were highest under B2F3, and the total soil P contents in the booting and flowering stages were also the highest. The soil available P contents in the jointing stage, booting stage, and flowering stage were highest under B3F3. The available P soil contents at maturity in both years were highest under B3F4. In addition, compared with B1F4, the accumulated plant P amounts in the booting and flowering stages were 17.6–77.3% and 17.0–87.3% higher, respectively, under B2F2, B2F3, B3F2, and B3F4 (P < 0.05). The accumulated plant P amounts in the maturity stage during the two years were highest under B2F3 (0.83 q ha−1) and B3F3 (0.42 q ha−1), respectively. Moreover, the partial factor productivity and agronomic use efficiency were significantly higher under B2F2, B2F3, B3F2, and B3F3 than B1F4. In summary, under the experimental conditions in this study, applying compound fertilizer at 4.50 q ha−1 combined with biochar at 75 q ha−1 is recommended as the optimal fertilization scheme.
bibliographic citation: Li et al. (2025) Effects of combined application of compound fertilizer and biochar on absorption and utilization of phosphorus by wheat. PeerJ 13:e20308 https://doi.org/10.7717/peerj.20308
date submitted: 2025-05-02
date accepted: 2025-10-08
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yun
author list: Agent
  family name: Wang
  given name: Jiatong
author list: Agent
  family name: Lu
  given name: Jiahui
author list: Agent
  family name: Feng
  given name: Yanfei
author list: Agent
  family name: Li
  given name: Jingjing
author list: Agent
  family name: Guo
  given name: Zhenqing
author list: Agent
  family name: Lin
  given name: Xiaohu
author list: Agent
  family name: Han
  given name: Yucui
doi: 10.7717/peerj.20308
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: ©2025 Li et al.
attribution name: Li et al.

Impact of historical land use change on the brown bear habitat connectivity in the Polish Carpathians
type: item
type: AcademicArticle
description: Background Europe has undergone dynamic land use changes in recent decades that have affected the extent, quality, and connectivity of large carnivore habitats. However, the current distribution of large carnivores also depends on historical land use processes. In this article, we analyse the impact of historical land use changes on the potential connectivity of brown bear habitats in the region linking the western and eastern parts of the Carpathians, one of Europe’s biodiversity hotspots. Methods The analyses were conducted based on elevation, slope, and distance-based, land use-related variables representing four time periods: 1860s, 1930s, 1970s, and 2013, using cost surface and least-cost path analyses. We used two different approaches to create cost surfaces: weighted, where the weights differentiated between variables according to their relative importance, reflecting their role in either bear space selection or avoidance, and unweighted, where all the variables were treated as equally important. Results The results of both approaches showed a gradual improvement in habitat connectivity for brown bears over time, driven by the increase in forest cover observed over the whole analysed period. However, the dynamics of these changes were much higher after the forced post-war resettlement in the 1940s. These tragic events resulted in the removal of settlements over large areas, substantially reducing human pressure and allowing brown bears to spread into new territories, expanding their habitats and creating new connectivity opportunities. We found that up to 40% of the current corridor was stable since mid-19th century. Our analysis shows that the current population decline in many rural areas of Europe may have positive implications for the habitats and population connectivity of large carnivores, but careful planning is needed to avoid negative interactions with local communities.
format: application/pdf
format: text/html
creator: Anna Szwagierczak
creator: El.zbieta Ziółkowska
creator: Joanna Wąs
creator: Michał Jakiel
creator: Dominik Kaim
subject: Coupled Natural and Human Systems
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20295
publisher: PeerJ Inc.
rights: © 2025 Szwagierczak et al.
abstract: Background Europe has undergone dynamic land use changes in recent decades that have affected the extent, quality, and connectivity of large carnivore habitats. However, the current distribution of large carnivores also depends on historical land use processes. In this article, we analyse the impact of historical land use changes on the potential connectivity of brown bear habitats in the region linking the western and eastern parts of the Carpathians, one of Europe’s biodiversity hotspots. Methods The analyses were conducted based on elevation, slope, and distance-based, land use-related variables representing four time periods: 1860s, 1930s, 1970s, and 2013, using cost surface and least-cost path analyses. We used two different approaches to create cost surfaces: weighted, where the weights differentiated between variables according to their relative importance, reflecting their role in either bear space selection or avoidance, and unweighted, where all the variables were treated as equally important. Results The results of both approaches showed a gradual improvement in habitat connectivity for brown bears over time, driven by the increase in forest cover observed over the whole analysed period. However, the dynamics of these changes were much higher after the forced post-war resettlement in the 1940s. These tragic events resulted in the removal of settlements over large areas, substantially reducing human pressure and allowing brown bears to spread into new territories, expanding their habitats and creating new connectivity opportunities. We found that up to 40% of the current corridor was stable since mid-19th century. Our analysis shows that the current population decline in many rural areas of Europe may have positive implications for the habitats and population connectivity of large carnivores, but careful planning is needed to avoid negative interactions with local communities.
bibliographic citation: Szwagierczak et al. (2025) Impact of historical land use change on the brown bear habitat connectivity in the Polish Carpathians. PeerJ 13:e20295 https://doi.org/10.7717/peerj.20295
date submitted: 2025-05-13
date accepted: 2025-10-06
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Szwagierczak
  given name: Anna
author list: Agent
  family name: Ziółkowska
  given name: El.zbieta
author list: Agent
  family name: Wąs
  given name: Joanna
author list: Agent
  family name: Jakiel
  given name: Michał
author list: Agent
  family name: Kaim
  given name: Dominik
doi: 10.7717/peerj.20295
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: ©2025 Szwagierczak et al.
attribution name: Szwagierczak et al.

Integrated bioinformatics screening and experimental validation: construction of a LUAD prediction model based on Treg-related genes
type: item
type: AcademicArticle
description: Background The prognosis of lung adenocarcinoma (LUAD) is poor, and clinical treatment mainly comprises a combination of traditional therapy and immunotherapy. However, the role and mechanism of tumor-infiltrating regulatory T cells (Tregs) in immunotherapy remain controversial. Therefore, we aimed to determine the role of Tregs in LUAD and to construct a relevant prognostic model for future clinical treatment. Methods A LUAD dataset was downloaded from the Gene Expression Omnibus (GEO) database, screened, integrated, and divided into test and validation datasets. CIBERSORT and weighted correlation network analysis (WGCNA) algorithms were combined to screen for Treg cell-related modules. Minimum absolute contraction and selection operator (LASSO) and univariate and multivariate Cox regression analyses were used to screen genes in the key modules and construct Treg-related prognostic models. Then, the expression differences of genes in the prognostic model were analyzed, and the results were verified by Western blotting. Result Among all cluster modules, the correlation between the brown module and Treg s (R2 = 0.43, P = 1e − 30) was the highest. After LASSO and univariate and multivariate Cox regression screening, six genes (ADARB2, B3GALT, FER, LTB4R2, N6AMT1, and SCN9A) were selected to construct the prognosis model, and the prognosis of low-risk patients was found to be better than that of high-risk patients. Finally, the SCN9A gene with the highest correlation with the model was selected and verified using Western blot analysis. The results showed that the expression of Treg surface markers in LUAD cells was increased, and the expression of SCN9A was decreased compared with that in normal lung epithelial cells. Conclusion We identified the role of Treg-related genes in LUAD, constructed and verified a related prognostic model, and explored a potential therapeutic target, SCN9A, to provide a new perspective for the clinical treatment of LUAD.
format: application/pdf
format: text/html
creator: Tian Zhao
creator: Yan Yao
creator: Yan Sun
creator: Qingliang Lv
creator: Changgang Sun
creator: Yining Cheng
creator: Chundi Gao
creator: Jing Zhuang
subject: Bioinformatics
subject: Cell Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20287
publisher: PeerJ Inc.
rights: © 2025 Zhao et al.
abstract: Background The prognosis of lung adenocarcinoma (LUAD) is poor, and clinical treatment mainly comprises a combination of traditional therapy and immunotherapy. However, the role and mechanism of tumor-infiltrating regulatory T cells (Tregs) in immunotherapy remain controversial. Therefore, we aimed to determine the role of Tregs in LUAD and to construct a relevant prognostic model for future clinical treatment. Methods A LUAD dataset was downloaded from the Gene Expression Omnibus (GEO) database, screened, integrated, and divided into test and validation datasets. CIBERSORT and weighted correlation network analysis (WGCNA) algorithms were combined to screen for Treg cell-related modules. Minimum absolute contraction and selection operator (LASSO) and univariate and multivariate Cox regression analyses were used to screen genes in the key modules and construct Treg-related prognostic models. Then, the expression differences of genes in the prognostic model were analyzed, and the results were verified by Western blotting. Result Among all cluster modules, the correlation between the brown module and Treg s (R2 = 0.43, P = 1e − 30) was the highest. After LASSO and univariate and multivariate Cox regression screening, six genes (ADARB2, B3GALT, FER, LTB4R2, N6AMT1, and SCN9A) were selected to construct the prognosis model, and the prognosis of low-risk patients was found to be better than that of high-risk patients. Finally, the SCN9A gene with the highest correlation with the model was selected and verified using Western blot analysis. The results showed that the expression of Treg surface markers in LUAD cells was increased, and the expression of SCN9A was decreased compared with that in normal lung epithelial cells. Conclusion We identified the role of Treg-related genes in LUAD, constructed and verified a related prognostic model, and explored a potential therapeutic target, SCN9A, to provide a new perspective for the clinical treatment of LUAD.
bibliographic citation: Zhao et al. (2025) Integrated bioinformatics screening and experimental validation: construction of a LUAD prediction model based on Treg-related genes. PeerJ 13:e20287 https://doi.org/10.7717/peerj.20287
date submitted: 2025-05-09
date accepted: 2025-10-03
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhao
  given name: Tian
author list: Agent
  family name: Yao
  given name: Yan
author list: Agent
  family name: Sun
  given name: Yan
author list: Agent
  family name: Lv
  given name: Qingliang
author list: Agent
  family name: Sun
  given name: Changgang
author list: Agent
  family name: Cheng
  given name: Yining
author list: Agent
  family name: Gao
  given name: Chundi
author list: Agent
  family name: Zhuang
  given name: Jing
doi: 10.7717/peerj.20287
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: ©2025 Zhao et al.
attribution name: Zhao et al.

IPI score as a new prognostic index in extensive stage small cell lung cancer
type: item
type: AcademicArticle
description: Background Personalized prognostic assessment in extensive-stage small cell lung cancer (ES-SCLC) necessitates a comprehensive understanding of systemic inflammatory markers and their impact on survival outcomes. This study aimed to evaluate the prognostic significance of a novel Inflammatory Prognostic Index (IPI) score, derived from four inflammation-related biochemical markers—albumin, C-reactive protein (CRP), neutrophils, and lymphocytes—in patients with ES-SCLC. Methods Patients diagnosed with ES-SCLC were eligible if adequate clinical, pathological, and follow-up data were available. The IPI score was derived using the formula: C-reactive protein × neutrophil-to-lymphocyte ratio (NLR)/serum albumin. The threshold value for the IPI score was identified using receiver operating characteristic (ROC) curve analysis within the cohort and was applied in an exploratory manner. Based on the predefined cut-off, patients were stratified into low- and high-IPI groups. The log-rank test was used to compare survival times, while Kaplan–Meier curves and Cox regression analyses assessed variables associated with long-term survival. Overall survival (OS) served as the primary endpoint, and progression-free survival (PFS) was evaluated as a secondary endpoint. Results Patients with a high IPI score had a mean OS of 9 months (95% CI [4.8–13.2]), while those with a low IPI score had a mean OS of 23 months (95% CI [11.4–34.6]), a statistically significant difference (p = 0.005). The prognostic significance of IPI was confirmed in both univariate (p = 0.003) and multivariate (p = 0.012) analyses. Conclusion The IPI score in ES-SCLC patients was associated with prognosis, with a high IPI score indicating poorer OS. These findings should be considered hypothesis-generating and warrant validation in larger prospective cohorts.
format: application/pdf
format: text/html
creator: Ahmet Burak Ağaoğlu
creator: Ferhat Ekinci
creator: Mustafa Şahbazlar
creator: Atike Pınar Erdoğan
subject: Biochemistry
subject: Evidence Based Medicine
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.20343
publisher: PeerJ Inc.
rights: © 2025 Ağaoğlu et al.
abstract: Background Personalized prognostic assessment in extensive-stage small cell lung cancer (ES-SCLC) necessitates a comprehensive understanding of systemic inflammatory markers and their impact on survival outcomes. This study aimed to evaluate the prognostic significance of a novel Inflammatory Prognostic Index (IPI) score, derived from four inflammation-related biochemical markers—albumin, C-reactive protein (CRP), neutrophils, and lymphocytes—in patients with ES-SCLC. Methods Patients diagnosed with ES-SCLC were eligible if adequate clinical, pathological, and follow-up data were available. The IPI score was derived using the formula: C-reactive protein × neutrophil-to-lymphocyte ratio (NLR)/serum albumin. The threshold value for the IPI score was identified using receiver operating characteristic (ROC) curve analysis within the cohort and was applied in an exploratory manner. Based on the predefined cut-off, patients were stratified into low- and high-IPI groups. The log-rank test was used to compare survival times, while Kaplan–Meier curves and Cox regression analyses assessed variables associated with long-term survival. Overall survival (OS) served as the primary endpoint, and progression-free survival (PFS) was evaluated as a secondary endpoint. Results Patients with a high IPI score had a mean OS of 9 months (95% CI [4.8–13.2]), while those with a low IPI score had a mean OS of 23 months (95% CI [11.4–34.6]), a statistically significant difference (p = 0.005). The prognostic significance of IPI was confirmed in both univariate (p = 0.003) and multivariate (p = 0.012) analyses. Conclusion The IPI score in ES-SCLC patients was associated with prognosis, with a high IPI score indicating poorer OS. These findings should be considered hypothesis-generating and warrant validation in larger prospective cohorts.
bibliographic citation: Ağaoğlu et al. (2025) IPI score as a new prognostic index in extensive stage small cell lung cancer. PeerJ 13:e20343 https://doi.org/10.7717/peerj.20343
date submitted: 2025-04-21
date accepted: 2025-10-15
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ağaoğlu
  given name: Ahmet Burak
author list: Agent
  family name: Ekinci
  given name: Ferhat
author list: Agent
  family name: Şahbazlar
  given name: Mustafa
author list: Agent
  family name: Erdoğan
  given name: Atike Pınar
doi: 10.7717/peerj.20343
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: ©2025 Ağaoğlu et al.
attribution name: Ağaoğlu et al.

The association of maternal pre-pregnancy body mass index with macrosomia: a birth cohort study from China
type: item
type: AcademicArticle
description: Objective To investigate the association between pre-pregnancy body mass index (BMI) and the risk of macrosomia through a preconception-early pregnancy-birth cohort in China. Methods Among the 12,254 women initially recruited between July 2018 and December 2021, a total of 11,438 (drop out rate: 6.66%) mother–infant pairs were included in the final analysis after excluding participants with missing data on key variables or lost to follow-up. We collected basic demographic characteristics and lifestyle behavior information of the subjects through questionnaires and practical measurements, and conducted further follow-up for pregnancy outcomes. The study assessed the association between pre-pregnancy BMI-defined categories (underweight, normal weight, overweight, and obesity) and macrosomia using multivariable logistic regression models, adjusting for sociodemographic characteristics, lifestyle behaviors, and maternal clinical factors during pregnancy. A linear trend test was also conducted. Moreover, we utilized restricted cubic spline models with three knots (placed at the 10th, 50th, and 90th percentiles of BMI) and polynomial regression to investigate the non-linear relationship of pre-pregnancy BMI with macrosomia. Results A total of 11,438 subjects were included in this study, among whom 645 infants were diagnosed with macrosomia, resulting in a prevalence of 5.64%. The results indicated that, compared with the normal weight group, overweight women had a significantly higher risk of macrosomia (odds ratio (OR) = 1.66, 95% CI [1.35–2.01]), as did obese women (OR = 1.66, 95% CI [1.13–2.45]), while underweight women had a significantly lower risk (OR = 0.55, 95% CI [0.41–0.73]). A similar association pattern between pre-pregnancy BMI and grade 1 macrosomia was observed, consistent with that for overall macrosomia. The use of restricted cubic splines revealed that the prevalence of macrosomia/grade 1 macrosomia increased with rising pre-pregnancy BMI. Furthermore, w…
format: application/pdf
format: text/html
creator: Mingxin Yan
creator: Yunbo Zhang
creator: Doudou Zhao
creator: Yan Zhao
creator: Danmeng Liu
creator: Li Shan
creator: Yang Mi
creator: Leilei Pei
creator: Pengfei Qu
subject: Pediatrics
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.20332
publisher: PeerJ Inc.
rights: © 2025 Yan et al.
abstract: Objective To investigate the association between pre-pregnancy body mass index (BMI) and the risk of macrosomia through a preconception-early pregnancy-birth cohort in China. Methods Among the 12,254 women initially recruited between July 2018 and December 2021, a total of 11,438 (drop out rate: 6.66%) mother–infant pairs were included in the final analysis after excluding participants with missing data on key variables or lost to follow-up. We collected basic demographic characteristics and lifestyle behavior information of the subjects through questionnaires and practical measurements, and conducted further follow-up for pregnancy outcomes. The study assessed the association between pre-pregnancy BMI-defined categories (underweight, normal weight, overweight, and obesity) and macrosomia using multivariable logistic regression models, adjusting for sociodemographic characteristics, lifestyle behaviors, and maternal clinical factors during pregnancy. A linear trend test was also conducted. Moreover, we utilized restricted cubic spline models with three knots (placed at the 10th, 50th, and 90th percentiles of BMI) and polynomial regression to investigate the non-linear relationship of pre-pregnancy BMI with macrosomia. Results A total of 11,438 subjects were included in this study, among whom 645 infants were diagnosed with macrosomia, resulting in a prevalence of 5.64%. The results indicated that, compared with the normal weight group, overweight women had a significantly higher risk of macrosomia (odds ratio (OR) = 1.66, 95% CI [1.35–2.01]), as did obese women (OR = 1.66, 95% CI [1.13–2.45]), while underweight women had a significantly lower risk (OR = 0.55, 95% CI [0.41–0.73]). A similar association pattern between pre-pregnancy BMI and grade 1 macrosomia was observed, consistent with that for overall macrosomia. The use of restricted cubic splines revealed that the prevalence of macrosomia/grade 1 macrosomia increased with rising pre-pregnancy BMI. Furthermore, w…
bibliographic citation: Yan et al. (2025) The association of maternal pre-pregnancy body mass index with macrosomia: a birth cohort study from China. PeerJ 13:e20332 https://doi.org/10.7717/peerj.20332
date submitted: 2025-04-28
date accepted: 2025-10-13
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Mingxin
author list: Agent
  family name: Zhang
  given name: Yunbo
author list: Agent
  family name: Zhao
  given name: Doudou
author list: Agent
  family name: Zhao
  given name: Yan
author list: Agent
  family name: Liu
  given name: Danmeng
author list: Agent
  family name: Shan
  given name: Li
author list: Agent
  family name: Mi
  given name: Yang
author list: Agent
  family name: Pei
  given name: Leilei
author list: Agent
  family name: Qu
  given name: Pengfei
doi: 10.7717/peerj.20332
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: © 2025 Yan et al.
attribution name: Yan et al.

Research progress of tsRNAs in kidney diseases
type: item
type: AcademicArticle
description: Transfer RNA-derived small RNAs (tsRNAs) are a class of regulatory non-coding RNAs generated through enzymatic cleavage of precursor or mature tRNAs. In recent years, tsRNAs have garnered growing interest in nephrology due to their diverse biological functions and potential clinical significance. This review summarizes current research on the roles of tsRNAs in kidney diseases, including their involvement in gene expression regulation, signal transduction, apoptosis, and inflammation-related pathways. We further highlight their emerging mechanistic contributions in conditions such as acute kidney injury, chronic kidney disease, and glomerulonephritis. Finally, we discuss the prospects of tsRNAs as novel biomarkers for early diagnosis, prognosis assessment, and therapeutic targeting in renal disorders, aiming to offer new insights into kidney disease pathogenesis and management.
format: application/pdf
format: text/html
creator: Jialing Wang
creator: Yanzhe Wang
creator: Fengqin Li
creator: Xinmiao Xie
creator: Xinyue Chen
creator: Tong Wu
creator: Xiaoxia Wang
subject: Molecular Biology
subject: Internal Medicine
subject: Nephrology
description: doi:10.7717/peerj.20315
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Transfer RNA-derived small RNAs (tsRNAs) are a class of regulatory non-coding RNAs generated through enzymatic cleavage of precursor or mature tRNAs. In recent years, tsRNAs have garnered growing interest in nephrology due to their diverse biological functions and potential clinical significance. This review summarizes current research on the roles of tsRNAs in kidney diseases, including their involvement in gene expression regulation, signal transduction, apoptosis, and inflammation-related pathways. We further highlight their emerging mechanistic contributions in conditions such as acute kidney injury, chronic kidney disease, and glomerulonephritis. Finally, we discuss the prospects of tsRNAs as novel biomarkers for early diagnosis, prognosis assessment, and therapeutic targeting in renal disorders, aiming to offer new insights into kidney disease pathogenesis and management.
bibliographic citation: Wang et al. (2025) Research progress of tsRNAs in kidney diseases. PeerJ 13:e20315 https://doi.org/10.7717/peerj.20315
date submitted: 2025-05-02
date accepted: 2025-10-09
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jialing
author list: Agent
  family name: Wang
  given name: Yanzhe
author list: Agent
  family name: Li
  given name: Fengqin
author list: Agent
  family name: Xie
  given name: Xinmiao
author list: Agent
  family name: Chen
  given name: Xinyue
author list: Agent
  family name: Wu
  given name: Tong
author list: Agent
  family name: Wang
  given name: Xiaoxia
doi: 10.7717/peerj.20315
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: ©2025 Wang et al.
attribution name: Wang et al.

A preliminary assessment of population genetic structure of the common vampire bat (Desmodus rotundus) in Colombia
type: item
type: AcademicArticle
description: Rabies virus (RABV) is a neglected tropical pathogen in Latin America predominantly transmitted to mammals by the common vampire bat (Desmodus rotundus). Transmission of RABV among D. rotundus individuals and colonies is a function of individual dispersal between colonies, patterns of which can be inferred from population genetic structure. Nevertheless, a baseline assessment of population genetic structure among D. rotundus individuals has been lacking for some areas of South America, including Colombia, where RABV has impacted some areas more heavily than others. To assess individual dispersal and hence population structure of D. rotundus across heterogenous landscapes in Colombia, we conducted a cross-elevational assessment of population genetic variation using nuclear microsatellite DNA markers. We quantified genetic variance and geographic distribution of genetically clustered D. rotundus individuals across the landscape of Colombia with reference to a comparator group of individuals from Mexico. We found population-level differentiation and genetic structure within our collection of samples, and we inferred patterns of dispersal and genetically effective migration between D. rotundus populations. Analysis of molecular variance (AMOVA) showed considerable variation among inferred populations in Colombia (14.9% of genetic covariance, df = 2, Sum of Squares = 164.9, Sigma = 1.28, ϕ = 0.15, p = 0.01), with an associated G′ST of 0.34. Direct migrant identification suggested 15 likely first-generation migrants among sites. We found that there were no statistically significant differences between the landscapes occupied by the inferred populations, though our limited sampling size suggests a trend toward differences in relation to elevation (t = 1.91, df = 71.72, p = 0.06). These results indicate that D. rotundus is mobile within the region, potentially contributing to RABV transmission among colonies. Our results support previous hypotheses ecological resistance-med…
format: application/pdf
format: text/html
creator: Paige Van de Vuurst
creator: Analorena Cifuentes-Rincon
creator: Andrea S. Bertke
creator: Diego Soler-Tovar
creator: Nicolás Reyes-Amaya
creator: Fabiola Rodriguez Arévalo
creator: Julieth Stella Cárdenas Hincapié
creator: Jhon Rivera-Monroy
creator: Luis E. Escobar
creator: Eric Hallerman
subject: Biogeography
subject: Ecology
subject: Genetics
subject: Spatial and Geographic Information Science
subject: Population Biology
description: doi:10.7717/peerj.20306
publisher: PeerJ Inc.
rights: © 2025 Van de Vuurst et al.
abstract: Rabies virus (RABV) is a neglected tropical pathogen in Latin America predominantly transmitted to mammals by the common vampire bat (Desmodus rotundus). Transmission of RABV among D. rotundus individuals and colonies is a function of individual dispersal between colonies, patterns of which can be inferred from population genetic structure. Nevertheless, a baseline assessment of population genetic structure among D. rotundus individuals has been lacking for some areas of South America, including Colombia, where RABV has impacted some areas more heavily than others. To assess individual dispersal and hence population structure of D. rotundus across heterogenous landscapes in Colombia, we conducted a cross-elevational assessment of population genetic variation using nuclear microsatellite DNA markers. We quantified genetic variance and geographic distribution of genetically clustered D. rotundus individuals across the landscape of Colombia with reference to a comparator group of individuals from Mexico. We found population-level differentiation and genetic structure within our collection of samples, and we inferred patterns of dispersal and genetically effective migration between D. rotundus populations. Analysis of molecular variance (AMOVA) showed considerable variation among inferred populations in Colombia (14.9% of genetic covariance, df = 2, Sum of Squares = 164.9, Sigma = 1.28, ϕ = 0.15, p = 0.01), with an associated G′ST of 0.34. Direct migrant identification suggested 15 likely first-generation migrants among sites. We found that there were no statistically significant differences between the landscapes occupied by the inferred populations, though our limited sampling size suggests a trend toward differences in relation to elevation (t = 1.91, df = 71.72, p = 0.06). These results indicate that D. rotundus is mobile within the region, potentially contributing to RABV transmission among colonies. Our results support previous hypotheses ecological resistance-med…
bibliographic citation: Van de Vuurst et al. (2025) A preliminary assessment of population genetic structure of the common vampire bat (Desmodus rotundus) in Colombia. PeerJ 13:e20306 https://doi.org/10.7717/peerj.20306
date submitted: 2025-05-23
date accepted: 2025-10-07
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Van de Vuurst
  given name: Paige
author list: Agent
  family name: Cifuentes-Rincon
  given name: Analorena
author list: Agent
  family name: Bertke
  given name: Andrea S.
author list: Agent
  family name: Soler-Tovar
  given name: Diego
author list: Agent
  family name: Reyes-Amaya
  given name: Nicolás
author list: Agent
  family name: Rodriguez Arévalo
  given name: Fabiola
author list: Agent
  family name: Cárdenas Hincapié
  given name: Julieth Stella
author list: Agent
  family name: Rivera-Monroy
  given name: Jhon
author list: Agent
  family name: Escobar
  given name: Luis E.
author list: Agent
  family name: Hallerman
  given name: Eric
doi: 10.7717/peerj.20306
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: ©2025 Van de Vuurst et al.
attribution name: Van de Vuurst et al.

https://peerj.com/articles/20280
type: item
type: AcademicArticle
title: Development and validation of a functional assessment tool for Chinese inpatient rehabilitation: insights from a Delphi study based on the International Classification of Functioning, Disability, and Health (ICF)
description: Objectives To develop and validate a functional assessment tool for inpatient rehabilitation in China using the International Classification of Functioning, Disability, and Health (ICF) Rehabilitation Set (ICF-RS) framework and the Delphi method. Methods A three-round Delphi process engaged 15 experts to refine ICF-RS items via a 5-point importance questionnaire. Validation involved 2,574 inpatients assessed with a numerical rating scale. Reliability (Cronbach’s alpha) and structural validity (factor analysis) were evaluated. Results Through three rounds of Delphi meetings, 10, 2, and 1 ICF items with mean importance scores below the threshold were respectively removed, resulting in 17 ICF items achieving expert consensus for inclusion in the final assessment tool, named ICF-RS-17. Expert authority coefficient was 0.81. Cronbach’s alpha exceeded 0.9. Factor analysis identified two factors explaining 68.86% (admission) and 73.25% (discharge) of variance, confirming structural validity. Conclusions The study developed a 17-item functional assessment tool, ICF-RS-17, demonstrating strong reliability and validity for inpatient rehabilitation. These findings help promote the application of the ICF in clinical settings, enhance rehabilitation clinical management, and potentially support the further development of rehabilitation insurance policies.
format: application/pdf
format: text/html
creator: Jiahui Li
creator: Guangxu Xu
creator: Juan Jin
creator: Na Li
creator: Jianan Li
creator: Shouguo Liu
subject: Global Health
subject: Health Policy
subject: Healthcare Services
subject: Rehabilitation
description: doi:10.7717/peerj.20280
publisher: PeerJ Inc.
rights: © 2025 Li et al.
abstract: Objectives To develop and validate a functional assessment tool for inpatient rehabilitation in China using the International Classification of Functioning, Disability, and Health (ICF) Rehabilitation Set (ICF-RS) framework and the Delphi method. Methods A three-round Delphi process engaged 15 experts to refine ICF-RS items via a 5-point importance questionnaire. Validation involved 2,574 inpatients assessed with a numerical rating scale. Reliability (Cronbach’s alpha) and structural validity (factor analysis) were evaluated. Results Through three rounds of Delphi meetings, 10, 2, and 1 ICF items with mean importance scores below the threshold were respectively removed, resulting in 17 ICF items achieving expert consensus for inclusion in the final assessment tool, named ICF-RS-17. Expert authority coefficient was 0.81. Cronbach’s alpha exceeded 0.9. Factor analysis identified two factors explaining 68.86% (admission) and 73.25% (discharge) of variance, confirming structural validity. Conclusions The study developed a 17-item functional assessment tool, ICF-RS-17, demonstrating strong reliability and validity for inpatient rehabilitation. These findings help promote the application of the ICF in clinical settings, enhance rehabilitation clinical management, and potentially support the further development of rehabilitation insurance policies.
bibliographic citation: Li et al. (2025) Development and validation of a functional assessment tool for Chinese inpatient rehabilitation: insights from a Delphi study based on the International Classification of Functioning, Disability, and Health (ICF). PeerJ 13:e20280 https://doi.org/10.7717/peerj.20280
date submitted: 2025-06-09
date accepted: 2025-10-01
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiahui
author list: Agent
  family name: Xu
  given name: Guangxu
author list: Agent
  family name: Jin
  given name: Juan
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Li
  given name: Jianan
author list: Agent
  family name: Liu
  given name: Shouguo
doi: 10.7717/peerj.20280
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: ©2025 Li et al.
attribution name: Li et al.

Patient satisfaction after outpatient hysteroscopy: a retrospective descriptive study
type: item
type: AcademicArticle
description: Background The aim of the study is to analyse the overall satisfaction level of patients undergoing diagnostic and/or therapeutic hysteroscopy in an ambulatory setting and examine factors related to satisfaction. Methods A retrospective descriptive study was conducted to analyse outpatient hysteroscopies performed between January 2020 and June 2022 at the University Hospital of Igualada. Patient demographic and clinical data as well as hysteroscopic features were collected. A telephonic questionnaire on patient satisfaction was conducted retrospectively. Results A total of 435 hysteroscopies were analysed. Hysteroscopy was successful in 95.6% of them with a clinical remission in 69.8% of patients. The mean pain score was 3.33 (Visual Analogue Scale). An average overall satisfaction score of 9 was obtained. Pain was the main reason in patients with low satisfaction ratings. A positive correlation was found between the patient satisfaction score and the level of information received before the procedure. An inverse relationship was detected between the patient satisfaction score and the pain experienced during the hysteroscopy. Conclusions Outpatient diagnostic and/or therapeutic hysteroscopy is a technique accepted by the majority of patients and with a high level of satisfaction. Variables such as pain or the previous information received are important and directly related to the final satisfaction level of the procedure.
format: application/pdf
format: text/html
creator: Claudia Sanchez Carbonell
creator: Jennifer Rovira Pampalona
creator: Carla Oliveres Amor
creator: Alexandra Caballol Arteaga
creator: Maria Degollada
creator: Pere Brescó Torras
subject: Gynecology and Obstetrics
subject: Surgery and Surgical Specialties
subject: Women’s Health
description: doi:10.7717/peerj.20272
publisher: PeerJ Inc.
rights: © 2025 Sanchez Carbonell et al.
abstract: Background The aim of the study is to analyse the overall satisfaction level of patients undergoing diagnostic and/or therapeutic hysteroscopy in an ambulatory setting and examine factors related to satisfaction. Methods A retrospective descriptive study was conducted to analyse outpatient hysteroscopies performed between January 2020 and June 2022 at the University Hospital of Igualada. Patient demographic and clinical data as well as hysteroscopic features were collected. A telephonic questionnaire on patient satisfaction was conducted retrospectively. Results A total of 435 hysteroscopies were analysed. Hysteroscopy was successful in 95.6% of them with a clinical remission in 69.8% of patients. The mean pain score was 3.33 (Visual Analogue Scale). An average overall satisfaction score of 9 was obtained. Pain was the main reason in patients with low satisfaction ratings. A positive correlation was found between the patient satisfaction score and the level of information received before the procedure. An inverse relationship was detected between the patient satisfaction score and the pain experienced during the hysteroscopy. Conclusions Outpatient diagnostic and/or therapeutic hysteroscopy is a technique accepted by the majority of patients and with a high level of satisfaction. Variables such as pain or the previous information received are important and directly related to the final satisfaction level of the procedure.
bibliographic citation: Sanchez Carbonell et al. (2025) Patient satisfaction after outpatient hysteroscopy: a retrospective descriptive study. PeerJ 13:e20272 https://doi.org/10.7717/peerj.20272
date submitted: 2025-03-26
date accepted: 2025-09-30
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sanchez Carbonell
  given name: Claudia
author list: Agent
  family name: Rovira Pampalona
  given name: Jennifer
author list: Agent
  family name: Oliveres Amor
  given name: Carla
author list: Agent
  family name: Caballol Arteaga
  given name: Alexandra
author list: Agent
  family name: Degollada
  given name: Maria
author list: Agent
  family name: Brescó Torras
  given name: Pere
doi: 10.7717/peerj.20272
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: ©2025 Sanchez Carbonell et al.
attribution name: Sanchez Carbonell et al.

TSCytoPred: a deep learning framework for inferring cytokine expression trajectories from irregular longitudinal gene expression data to enhance multi-omics analyses
type: item
type: AcademicArticle
description: Cytokines play a crucial role in immune system regulation, mediating responses from pathogen defense to tissue-damaging inflammation. Excessive cytokine production is implicated in severe conditions such as cancer progression, hemophagocytic lymphohistiocytosis, and severe cases of Coronavirus disease-2019 (COVID-19). Studies have shown that cytokine expression profiles serve as biomarkers for disease severity and mortality prediction, with machine learning (ML) methods increasingly employed for predictive analysis. To improve patient outcome predictions, treatment adaptation, and survival rates, longitudinal analysis of cytokine profiles is essential. Time-series cytokine profiling has been linked to tumor response, overall survival in various cancers, and acute encephalopathy. Similarly, COVID-19 severity and patient outcomes correlate with cytokine expression dynamics over time. However, challenges remain due to the limited availability of time-series cytokine data, restricting broader experimental applications and robust predictive modeling. Recent advancements indicate that cytokine expression can be computationally inferred using gene expression data and transcription factor interactions. Inferring cytokine levels from existing gene expression datasets could enhance early disease detection and treatment response predictions while reducing profiling costs. This work proposes TSCytoPred, a deep learning-based model trained on time-series gene expression data to infer cytokine expression trajectories. TSCytoPred identifies genes relevant for predicting target cytokines through interaction relationships and high correlation. These identified genes are subsequently utilized in a neural network incorporating an interpolation block to estimate cytokine expression trajectories between observed time points. Performance evaluations using a COVID-19 dataset demonstrate that TSCytoPred significantly outperforms baseline regression methods, achieving the highest coefficien…
format: application/pdf
format: text/html
creator: Joung Min Choi
creator: Heejoon Chae
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.20270
publisher: PeerJ Inc.
rights: © 2025 Choi and Chae
abstract: Cytokines play a crucial role in immune system regulation, mediating responses from pathogen defense to tissue-damaging inflammation. Excessive cytokine production is implicated in severe conditions such as cancer progression, hemophagocytic lymphohistiocytosis, and severe cases of Coronavirus disease-2019 (COVID-19). Studies have shown that cytokine expression profiles serve as biomarkers for disease severity and mortality prediction, with machine learning (ML) methods increasingly employed for predictive analysis. To improve patient outcome predictions, treatment adaptation, and survival rates, longitudinal analysis of cytokine profiles is essential. Time-series cytokine profiling has been linked to tumor response, overall survival in various cancers, and acute encephalopathy. Similarly, COVID-19 severity and patient outcomes correlate with cytokine expression dynamics over time. However, challenges remain due to the limited availability of time-series cytokine data, restricting broader experimental applications and robust predictive modeling. Recent advancements indicate that cytokine expression can be computationally inferred using gene expression data and transcription factor interactions. Inferring cytokine levels from existing gene expression datasets could enhance early disease detection and treatment response predictions while reducing profiling costs. This work proposes TSCytoPred, a deep learning-based model trained on time-series gene expression data to infer cytokine expression trajectories. TSCytoPred identifies genes relevant for predicting target cytokines through interaction relationships and high correlation. These identified genes are subsequently utilized in a neural network incorporating an interpolation block to estimate cytokine expression trajectories between observed time points. Performance evaluations using a COVID-19 dataset demonstrate that TSCytoPred significantly outperforms baseline regression methods, achieving the highest coefficien…
bibliographic citation: Choi et al. (2025) TSCytoPred: a deep learning framework for inferring cytokine expression trajectories from irregular longitudinal gene expression data to enhance multi-omics analyses. PeerJ 13:e20270 https://doi.org/10.7717/peerj.20270
date submitted: 2025-05-06
date accepted: 2025-09-30
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Joung Min
author list: Agent
  family name: Chae
  given name: Heejoon
doi: 10.7717/peerj.20270
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: ©2025 Choi and Chae
attribution name: Choi and Chae

Assessment of distinct effects of Parinari curatellifolia Planch.ex Benth Ethanolic leaf extract on glucose transport in different cell types
type: item
type: AcademicArticle
description: Extracts of Parinari curatellifolia Planch.ex Benth have been used as a traditional medicine in Sub-Saharan Africa for the management of various ailments including diabetes and has been shown to reduce plasma glucose levels in rat models of diabetes. Treatment of a range of mammalian cell lines with P. curatellifolia ethanolic leaf extract (PCE) for 24–48 h, typically between 0 and 100 µg/mL, revealed different actions: in 3T3-L1 adipocytes, PCE markedly inhibited insulin-stimulated glucose transport (50% inhibition at 100 µg/mL), whereas by contrast PCE-treatment of Caco-2 cells, a model of the intestinal epithelia at the same concentration, increased glucose transport ∼2-fold. This effect was accompanied by increased glucose transporter-1 (GLUT1) levels but is independent of changes in the level of Akt, Adenosine monophosphate-activated protein kinase (AMPK) or p38. Our data suggest that the antidiabetic effects of extracts of P. curatellifolia may arise by increased absorption of glucose from the gut and thus distribution to other cells/tissues. Our data further highlight the importance of screening metabolic actions of plant extracts against multiple cell lines, as these can often exhibit distinct cell-type-specific responses, and further suggest that relatively low doses of PCE (up to 100 µg/mL) could warrant investigation in in vivo models of disease.
format: application/pdf
format: text/html
creator: Simeon Omale
creator: John C. Aguiyi
creator: Samuel Ede
creator: Layla Ryalls
creator: Runfei Ye
creator: Busra Basbaydar
creator: Gwyn W. Gould
creator: Shaun K. Bremner-Hart
subject: Biochemistry
subject: Cell Biology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.20269
publisher: PeerJ Inc.
rights: © 2025 Omale et al.
abstract: Extracts of Parinari curatellifolia Planch.ex Benth have been used as a traditional medicine in Sub-Saharan Africa for the management of various ailments including diabetes and has been shown to reduce plasma glucose levels in rat models of diabetes. Treatment of a range of mammalian cell lines with P. curatellifolia ethanolic leaf extract (PCE) for 24–48 h, typically between 0 and 100 µg/mL, revealed different actions: in 3T3-L1 adipocytes, PCE markedly inhibited insulin-stimulated glucose transport (50% inhibition at 100 µg/mL), whereas by contrast PCE-treatment of Caco-2 cells, a model of the intestinal epithelia at the same concentration, increased glucose transport ∼2-fold. This effect was accompanied by increased glucose transporter-1 (GLUT1) levels but is independent of changes in the level of Akt, Adenosine monophosphate-activated protein kinase (AMPK) or p38. Our data suggest that the antidiabetic effects of extracts of P. curatellifolia may arise by increased absorption of glucose from the gut and thus distribution to other cells/tissues. Our data further highlight the importance of screening metabolic actions of plant extracts against multiple cell lines, as these can often exhibit distinct cell-type-specific responses, and further suggest that relatively low doses of PCE (up to 100 µg/mL) could warrant investigation in in vivo models of disease.
bibliographic citation: Omale et al. (2025) Assessment of distinct effects of Parinari curatellifolia Planch.ex Benth Ethanolic leaf extract on glucose transport in different cell types. PeerJ 13:e20269 https://doi.org/10.7717/peerj.20269
date submitted: 2025-05-12
date accepted: 2025-09-30
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Omale
  given name: Simeon
author list: Agent
  family name: Aguiyi
  given name: John C.
author list: Agent
  family name: Ede
  given name: Samuel
author list: Agent
  family name: Ryalls
  given name: Layla
author list: Agent
  family name: Ye
  given name: Runfei
author list: Agent
  family name: Basbaydar
  given name: Busra
author list: Agent
  family name: Gould
  given name: Gwyn W.
author list: Agent
  family name: Bremner-Hart
  given name: Shaun K.
doi: 10.7717/peerj.20269
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: ©2025 Omale et al.
attribution name: Omale et al.

Impact of insular landscape features on the population genetics of a threatened climbing palm, Korthalsia rogersii Becc., endemic to the Andaman Islands
type: item
type: AcademicArticle
description: Despite the critical structural and functional roles of palms in tropical forest ecosystems and their importance in the local economy and livelihood, palms face significant threats from habitat loss and economic exploitation. Many endemic palms on tropical islands warrant conservation strategies aimed at augmenting the existing gene pool to support effective management and long-term protection of genetic diversity. This study investigated the genetic diversity and structure of Korthalsia rogersii, a threatened climbing palm (rattan) endemic to the Andaman Islands in the Bay of Bengal, across seven known populations (including recently identified ones) using microsatellite markers. The aim was to formulate informed conservation strategies by understanding how the island landscape influences the population genetic divergence of the species. Although heterozygosity and bottleneck analyses did not reveal significant genetic diversity loss, a positive correlation between population size and the number of observed alleles points to a potential ongoing decline. Moderate to high genetic differentiation was observed between populations, with geographical isolation contributing to divergence, particularly in the Interview island population. Notably, the South Andaman population (Chidiya Tapu) harbours the highest number of private alleles, despite exhibiting low overall genetic divergence, indicating it may serve as a reservoir of lost genetic diversity. Further, the Bakultala population shows significant within-population relatedness and reduced allelic diversity, indicative of genetic isolation and demographic decline. These findings provide preliminary insights into the role of the island landscapes in the Andaman archipelago in shaping population genetic divergence among plant taxa. Effective conservation strategies should target gene diversity, genetic structure and hotspots of unique alleles identified in the study, prioritising both population size enhancement and gene…
format: application/pdf
format: text/html
creator: Sarath Paremmal
creator: Modhumita Dasgupta
creator: Sreekumar VB
creator: Suma Dev
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.20265
publisher: PeerJ Inc.
rights: © 2025 Paremmal et al.
abstract: Despite the critical structural and functional roles of palms in tropical forest ecosystems and their importance in the local economy and livelihood, palms face significant threats from habitat loss and economic exploitation. Many endemic palms on tropical islands warrant conservation strategies aimed at augmenting the existing gene pool to support effective management and long-term protection of genetic diversity. This study investigated the genetic diversity and structure of Korthalsia rogersii, a threatened climbing palm (rattan) endemic to the Andaman Islands in the Bay of Bengal, across seven known populations (including recently identified ones) using microsatellite markers. The aim was to formulate informed conservation strategies by understanding how the island landscape influences the population genetic divergence of the species. Although heterozygosity and bottleneck analyses did not reveal significant genetic diversity loss, a positive correlation between population size and the number of observed alleles points to a potential ongoing decline. Moderate to high genetic differentiation was observed between populations, with geographical isolation contributing to divergence, particularly in the Interview island population. Notably, the South Andaman population (Chidiya Tapu) harbours the highest number of private alleles, despite exhibiting low overall genetic divergence, indicating it may serve as a reservoir of lost genetic diversity. Further, the Bakultala population shows significant within-population relatedness and reduced allelic diversity, indicative of genetic isolation and demographic decline. These findings provide preliminary insights into the role of the island landscapes in the Andaman archipelago in shaping population genetic divergence among plant taxa. Effective conservation strategies should target gene diversity, genetic structure and hotspots of unique alleles identified in the study, prioritising both population size enhancement and gene…
bibliographic citation: Paremmal et al. (2025) Impact of insular landscape features on the population genetics of a threatened climbing palm, Korthalsia rogersii Becc., endemic to the Andaman Islands. PeerJ 13:e20265 https://doi.org/10.7717/peerj.20265
date submitted: 2025-05-15
date accepted: 2025-09-29
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paremmal
  given name: Sarath
author list: Agent
  family name: Dasgupta
  given name: Modhumita
author list: Agent
  family name: VB
  given name: Sreekumar
author list: Agent
  family name: Dev
  given name: Suma
doi: 10.7717/peerj.20265
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: ©2025 Paremmal et al.
attribution name: Paremmal et al.

Multimodal system for recording individual-level behaviors in songbird groups
type: item
type: AcademicArticle
description: The implicit goal of longitudinal observations of animal groups is to identify individuals and to reliably detect their behaviors, including their vocalizations. Yet, to segment fast behaviors and to extract individual vocalizations from sound mixtures remain challenging problems. Promising approaches are systems that record behaviors with multiple cameras, microphones, and animal-borne wireless sensors. Good systems extract from such multimodal signals perfectly synchronized data streams. In this vein, we designed a modular system (BirdPark) for simultaneously recording small animals wearing custom low-power frequency-modulated radio transmitters. Our custom software-defined radio receiver makes use of a multi-antenna demodulation technique that eliminates data losses due to radio signal fading and that increases the signal-to-noise ratio of the received radio signals by 6.5 dB compared to demodulation from the best single-antenna. Digital acquisition of all data streams relies on a single clock, which offers accurate cross-modal redundancies that can be used to dissect rapid behaviors on time scales well below the video frame period. We demonstrate this feat by reconstructing the wing-stroke phases of free-flying songbirds and by separating the vocalizations among up to eight vocally interacting birds. In conclusion, our work paves the way for automatically dissecting complex social behaviors.
format: application/pdf
format: text/html
creator: Linus Rüttimann
creator: Yuhang Wang
creator: Jörg Rychen
creator: Tomas Tomka
creator: Heiko Hörster
creator: Richard H. R. Hahnloser
subject: Animal Behavior
subject: Computational Biology
subject: Zoology
subject: Statistics
description: doi:10.7717/peerj.20203
publisher: PeerJ Inc.
rights: © 2025 Rüttimann et al.
abstract: The implicit goal of longitudinal observations of animal groups is to identify individuals and to reliably detect their behaviors, including their vocalizations. Yet, to segment fast behaviors and to extract individual vocalizations from sound mixtures remain challenging problems. Promising approaches are systems that record behaviors with multiple cameras, microphones, and animal-borne wireless sensors. Good systems extract from such multimodal signals perfectly synchronized data streams. In this vein, we designed a modular system (BirdPark) for simultaneously recording small animals wearing custom low-power frequency-modulated radio transmitters. Our custom software-defined radio receiver makes use of a multi-antenna demodulation technique that eliminates data losses due to radio signal fading and that increases the signal-to-noise ratio of the received radio signals by 6.5 dB compared to demodulation from the best single-antenna. Digital acquisition of all data streams relies on a single clock, which offers accurate cross-modal redundancies that can be used to dissect rapid behaviors on time scales well below the video frame period. We demonstrate this feat by reconstructing the wing-stroke phases of free-flying songbirds and by separating the vocalizations among up to eight vocally interacting birds. In conclusion, our work paves the way for automatically dissecting complex social behaviors.
bibliographic citation: Rüttimann et al. (2025) Multimodal system for recording individual-level behaviors in songbird groups. PeerJ 13:e20203 https://doi.org/10.7717/peerj.20203
date submitted: 2025-02-10
date accepted: 2025-09-17
issued: 2025-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rüttimann
  given name: Linus
author list: Agent
  family name: Wang
  given name: Yuhang
author list: Agent
  family name: Rychen
  given name: Jörg
author list: Agent
  family name: Tomka
  given name: Tomas
author list: Agent
  family name: Hörster
  given name: Heiko
author list: Agent
  family name: Hahnloser
  given name: Richard H. R.
doi: 10.7717/peerj.20203
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-10
copyright: © 2025 Rüttimann et al.
attribution name: Rüttimann et al.

Risk factors of diastasis recti abdominis, and relationship with surface electromyography characteristics of pelvic floor muscles in early postpartum: a retrospective study
type: item
type: AcademicArticle
description: Objective This study aimed to identify the factors associated with diastasis recti abdominis (DRA) in early postpartum women and investigate any relationship with surface electromyography (sEMG) characteristics of pelvic floor muscles (PFM). Methods A total of 478 participants who visited Fujian Maternity and Child Health Hospital for postpartum re-examination between January and March 2023 were divided into two groups: DRA and Non-DRA. Basic demographic data were collected via self-reported questionnaires. Additionally, inter-recti distance (IRD) was measured using ultrasound imaging, and pelvic floor muscle activity was assessed using surface electromyography according to the Glazer protocols. Results There were no significant differences between the non-DRA and DRA groups in terms of weight gain during pregnancy, physical activity, number of fetuses, delivery mode, gestational diabetes, or urinary incontinence during pregnancy or postpartum. However, the DRA group was older and had a significantly lower level of education. Both pre-pregnancy and postpartum body mass index (BMI) were higher in the DRA group. The proportion of first-time mothers was greater in the non-DRA group, and fetal weight was lower in the non-DRA group compared to the DRA group. Multivariate logistic regression analysis revealed that older maternal age, lower education level, and a high number of deliveries were independently associated with an increased risk of DRA. No significant differences were observed in sEMG parameters between the two groups at the pre-baseline, flick contraction, tonic contraction, endurance contraction, and post-baseline stages. Conclusion Older maternal age, lower educational attainment, and higher parity were significantly associated with an increased risk of diastasis recti abdominis in early postpartum. No correlation was found between the sEMG characteristics of pelvic floor muscles and diastasis recti abdominis in the early postpartum period.
format: application/pdf
format: text/html
creator: Xiaojun He
creator: Yang Lin
creator: Sha He
creator: Juan Lin
subject: Anatomy and Physiology
subject: Evidence Based Medicine
subject: Gynecology and Obstetrics
subject: Women’s Health
subject: Rehabilitation
description: doi:10.7717/peerj.20299
publisher: PeerJ Inc.
rights: © 2025 He et al.
abstract: Objective This study aimed to identify the factors associated with diastasis recti abdominis (DRA) in early postpartum women and investigate any relationship with surface electromyography (sEMG) characteristics of pelvic floor muscles (PFM). Methods A total of 478 participants who visited Fujian Maternity and Child Health Hospital for postpartum re-examination between January and March 2023 were divided into two groups: DRA and Non-DRA. Basic demographic data were collected via self-reported questionnaires. Additionally, inter-recti distance (IRD) was measured using ultrasound imaging, and pelvic floor muscle activity was assessed using surface electromyography according to the Glazer protocols. Results There were no significant differences between the non-DRA and DRA groups in terms of weight gain during pregnancy, physical activity, number of fetuses, delivery mode, gestational diabetes, or urinary incontinence during pregnancy or postpartum. However, the DRA group was older and had a significantly lower level of education. Both pre-pregnancy and postpartum body mass index (BMI) were higher in the DRA group. The proportion of first-time mothers was greater in the non-DRA group, and fetal weight was lower in the non-DRA group compared to the DRA group. Multivariate logistic regression analysis revealed that older maternal age, lower education level, and a high number of deliveries were independently associated with an increased risk of DRA. No significant differences were observed in sEMG parameters between the two groups at the pre-baseline, flick contraction, tonic contraction, endurance contraction, and post-baseline stages. Conclusion Older maternal age, lower educational attainment, and higher parity were significantly associated with an increased risk of diastasis recti abdominis in early postpartum. No correlation was found between the sEMG characteristics of pelvic floor muscles and diastasis recti abdominis in the early postpartum period.
bibliographic citation: He et al. (2025) Risk factors of diastasis recti abdominis, and relationship with surface electromyography characteristics of pelvic floor muscles in early postpartum: a retrospective study. PeerJ 13:e20299 https://doi.org/10.7717/peerj.20299
date submitted: 2025-02-20
date accepted: 2025-10-06
issued: 2025-11-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Xiaojun
author list: Agent
  family name: Lin
  given name: Yang
author list: Agent
  family name: He
  given name: Sha
author list: Agent
  family name: Lin
  given name: Juan
doi: 10.7717/peerj.20299
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-07
copyright: ©2025 He et al.
attribution name: He et al.

Screening frost-tolerant sunflower hybrids: integrating physiological traits and electrolyte leakage analysis
type: item
type: AcademicArticle
description: Background Frost is an important environmental stress factor that adversely affects plant growth and development and can even threaten plant survival. Methods This study aimed to identify frost-tolerant sunflower hybrids by analyzing the changes in physiological characteristics after exposure to frost at two early growth stages. Fourteen sunflower hybrids were exposed to frost stress at −4 °C for 4 hours at developmental stages of V2 and V4. Chlorophyll content (SPAD), relative leaf water content, leaf temperature, and electrolyte leakage were measured. Additionally, the percentage of damaged and dead plants following frost stress was recorded. Principal component analysis was performed for classification of sunflower hybrids. Results Significant differences were observed among the sunflower hybrids for all parameters investigated. All parameters were significantly affected by genotype and frost treatment. Increased electrolyte leakage and decreased relative water content were identified in frost- stressed plants. Electrolyte leakage was found to be significantly correlated with the percentage of damaged and dead plants at the V4 stage. Frost susceptibility increased with the advancing growth stage, with a higher percentage of damaged and dead plants at the four-leaf stage. The dead plant rate increased from 4.1% at the V2 stage to 19.4% at the V4 stage. SY Roseta, P63LE113, P64LE121, and Sanbro MR had the lowest percentage of damaged and dead plants at the two-leaf stage, while Sanbro MR, LG 50.585, and LG 59.580 were at the V4 stage. Conclusions The study highlighted the crucial influence of the growth stage on frost tolerance, with earlier stages showing greater resilience. Sunflower hybrids P63LE113, SY Gibraltar, and P63MM54 appeared more tolerant to frost damage. At the V4 stage, chlorophyll content and electrolyte leakage can be employed as potential selection criteria for frost-tolerant genetic resources and hybrids.
format: application/pdf
format: text/html
creator: Mehmet Demir Kaya
creator: Engin Gökhan Kulan
creator: Nurgül Ergin
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20282
publisher: PeerJ Inc.
rights: © 2025 Kaya et al.
abstract: Background Frost is an important environmental stress factor that adversely affects plant growth and development and can even threaten plant survival. Methods This study aimed to identify frost-tolerant sunflower hybrids by analyzing the changes in physiological characteristics after exposure to frost at two early growth stages. Fourteen sunflower hybrids were exposed to frost stress at −4 °C for 4 hours at developmental stages of V2 and V4. Chlorophyll content (SPAD), relative leaf water content, leaf temperature, and electrolyte leakage were measured. Additionally, the percentage of damaged and dead plants following frost stress was recorded. Principal component analysis was performed for classification of sunflower hybrids. Results Significant differences were observed among the sunflower hybrids for all parameters investigated. All parameters were significantly affected by genotype and frost treatment. Increased electrolyte leakage and decreased relative water content were identified in frost- stressed plants. Electrolyte leakage was found to be significantly correlated with the percentage of damaged and dead plants at the V4 stage. Frost susceptibility increased with the advancing growth stage, with a higher percentage of damaged and dead plants at the four-leaf stage. The dead plant rate increased from 4.1% at the V2 stage to 19.4% at the V4 stage. SY Roseta, P63LE113, P64LE121, and Sanbro MR had the lowest percentage of damaged and dead plants at the two-leaf stage, while Sanbro MR, LG 50.585, and LG 59.580 were at the V4 stage. Conclusions The study highlighted the crucial influence of the growth stage on frost tolerance, with earlier stages showing greater resilience. Sunflower hybrids P63LE113, SY Gibraltar, and P63MM54 appeared more tolerant to frost damage. At the V4 stage, chlorophyll content and electrolyte leakage can be employed as potential selection criteria for frost-tolerant genetic resources and hybrids.
bibliographic citation: Kaya et al. (2025) Screening frost-tolerant sunflower hybrids: integrating physiological traits and electrolyte leakage analysis. PeerJ 13:e20282 https://doi.org/10.7717/peerj.20282
date submitted: 2024-12-24
date accepted: 2025-10-01
issued: 2025-11-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaya
  given name: Mehmet Demir
author list: Agent
  family name: Kulan
  given name: Engin Gökhan
author list: Agent
  family name: Ergin
  given name: Nurgül
doi: 10.7717/peerj.20282
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-07
copyright: ©2025 Kaya et al.
attribution name: Kaya et al.

Serum cystatin-C and all-cause mortality in patients with hypertrophic cardiomyopathy: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Numerous studies across various populations have revealed that elevated cystatin-C levels are associated with an excessive risk of mortality. However, the prognostic value of cystatin-C remains unidentified in hypertrophic cardiomyopathy (HCM) patients. The objective of this study was to investigate whether serum cystatin-C could predict all-cause mortality independently in HCM patients. Methods Data from 456 HCM patients treated at West China Hospital were collected and stratified into two groups based on the median baseline serum cystatin-C level. All-cause mortality was the primary outcome. Cox regression models were used to analyze the association between cystatin-C levels and mortality risk. Results A total of 90 deaths were recorded over a median follow-up period of 4.67 years. Patients with higher cystatin-C levels had an increased risk of all-cause mortality (adjusted hazard ratio (HR): 2.11, 95% CI [1.30–3.42], p = 0.003) compared to those with lower levels. Time-dependent area under the curves (AUC) of cystatin-C in different time points, ranging from initial measurement to follow-up, showed a relatively stable fluctuation between 0.70 and 0.80. In comparison, the commonly used renal function markers, estimated glomerular filtration rate (eGFR) and serum creatinine, yielded lower AUC values. Restricted cubic spline curves showed that with median value of cystatin-C (1.01 mg/L) as reference, there was a gradual rise in risk of all-cause mortality with cystatin-C increasing. Subgroup analyses in female, in the patients ≥ 58 years old, and in the patients with eGFR ≥ 60 mL/min/1.73 m2 consistently confirmed robustness of the main findings. Conclusion Elevated serum cystatin-C levels are associated with a higher risk of all-cause mortality in HCM patients, providing valuable prognostic information beyond traditional renal function markers such as eGFR and serum creatinine.
format: application/pdf
format: text/html
creator: Lu Liu
creator: Yi Zheng
creator: Haiyan Ruan
creator: Ziqiong Wang
creator: Xiaoping Chen
creator: Sen He
subject: Cardiology
subject: Epidemiology
subject: Internal Medicine
description: doi:10.7717/peerj.19631
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Numerous studies across various populations have revealed that elevated cystatin-C levels are associated with an excessive risk of mortality. However, the prognostic value of cystatin-C remains unidentified in hypertrophic cardiomyopathy (HCM) patients. The objective of this study was to investigate whether serum cystatin-C could predict all-cause mortality independently in HCM patients. Methods Data from 456 HCM patients treated at West China Hospital were collected and stratified into two groups based on the median baseline serum cystatin-C level. All-cause mortality was the primary outcome. Cox regression models were used to analyze the association between cystatin-C levels and mortality risk. Results A total of 90 deaths were recorded over a median follow-up period of 4.67 years. Patients with higher cystatin-C levels had an increased risk of all-cause mortality (adjusted hazard ratio (HR): 2.11, 95% CI [1.30–3.42], p = 0.003) compared to those with lower levels. Time-dependent area under the curves (AUC) of cystatin-C in different time points, ranging from initial measurement to follow-up, showed a relatively stable fluctuation between 0.70 and 0.80. In comparison, the commonly used renal function markers, estimated glomerular filtration rate (eGFR) and serum creatinine, yielded lower AUC values. Restricted cubic spline curves showed that with median value of cystatin-C (1.01 mg/L) as reference, there was a gradual rise in risk of all-cause mortality with cystatin-C increasing. Subgroup analyses in female, in the patients ≥ 58 years old, and in the patients with eGFR ≥ 60 mL/min/1.73 m2 consistently confirmed robustness of the main findings. Conclusion Elevated serum cystatin-C levels are associated with a higher risk of all-cause mortality in HCM patients, providing valuable prognostic information beyond traditional renal function markers such as eGFR and serum creatinine.
bibliographic citation: Liu et al. (2025) Serum cystatin-C and all-cause mortality in patients with hypertrophic cardiomyopathy: a retrospective cohort study. PeerJ 13:e19631 https://doi.org/10.7717/peerj.19631
date submitted: 2023-11-07
date accepted: 2025-05-30
issued: 2025-11-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Lu
author list: Agent
  family name: Zheng
  given name: Yi
author list: Agent
  family name: Ruan
  given name: Haiyan
author list: Agent
  family name: Wang
  given name: Ziqiong
author list: Agent
  family name: Chen
  given name: Xiaoping
author list: Agent
  family name: He
  given name: Sen
doi: 10.7717/peerj.19631
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-07
copyright: ©2025 Liu et al.
attribution name: Liu et al.

Prognostic implications of microRNA-107 in esophageal cancer: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Esophageal squamous cell carcinoma (ESCC) imposes a heavy disease burden in China, accounting for over 50% of global cases and approximately 301,000 annual deaths. Current prognostic markers inadequately predict recurrence in early-stage patients. This study investigates microRNA-107 (miR-107) as a novel prognostic biomarker for ESCC. Methods Tumor tissues (n = 66) and adjacent normal tissues (n = 28) were collected from ESCC patients undergoing radical surgery (2010–2012). miR-107 expression was quantified via reverse transcription quantitative polymerase chain reaction (RT-qPCR) (normalized to U6 snRNA). Clinicopathological correlations and survival outcomes were analyzed using χ2 tests, Kaplan–Meier/log-rank tests, and Cox regression. Comparative analysis of miR-107 levels was performed in human esophageal squamous cell carcinoma line 109 (EC109) cancer cells versus human esophageal epithelial cell (HEEC) normal epithelial cells. Results miR-107 expression was significantly lower in esophageal cancer tissues (0.801 ± 0.737) compared to adjacent non-cancerous tissues (1.390 ± 1.346), p = 0.006. Low miR-107 expression (cutoff = median) correlated with advanced tumor, node, metastasis stage (TNM stage) (I vs. V: 100% vs. 21.4%, P < 0.001), lymph node metastasis (73.1% vs. 35%, P < 0.001), and larger tumor size (70% vs. 33.3%, P < 0.001). Patients with low miR-107 had shorter median overall survival (10 vs. 59 months; Hazard Ratio (HR) = 0.475, 95% Confidence Interval (CI) [0.247–0.915]; P < 0.001). Multivariate Cox analysis confirmed miR-107 as an independent prognostic factor alongside TNM stage (HR = 3.586, 95% CI [2.253–5.708]; P < 0.001). Consistently, EC109 cells exhibited 59% lower miR-107 levels than HEEC (P = 0.029). Conclusions miR-107 downregulation is a robust predictor of aggressive ESCC phenotypes and poor survival. It holds promise as a clinical biomarker for risk stratification and personalized therapy. Future studies should validate these …
format: application/pdf
format: text/html
creator: Jie Sun
creator: Jin Zhang
creator: Jingwen Ye
creator: Yuqi Chen
creator: Caifeng Jiang
subject: Clinical Trials
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Oncology
description: doi:10.7717/peerj.20327
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Background Esophageal squamous cell carcinoma (ESCC) imposes a heavy disease burden in China, accounting for over 50% of global cases and approximately 301,000 annual deaths. Current prognostic markers inadequately predict recurrence in early-stage patients. This study investigates microRNA-107 (miR-107) as a novel prognostic biomarker for ESCC. Methods Tumor tissues (n = 66) and adjacent normal tissues (n = 28) were collected from ESCC patients undergoing radical surgery (2010–2012). miR-107 expression was quantified via reverse transcription quantitative polymerase chain reaction (RT-qPCR) (normalized to U6 snRNA). Clinicopathological correlations and survival outcomes were analyzed using χ2 tests, Kaplan–Meier/log-rank tests, and Cox regression. Comparative analysis of miR-107 levels was performed in human esophageal squamous cell carcinoma line 109 (EC109) cancer cells versus human esophageal epithelial cell (HEEC) normal epithelial cells. Results miR-107 expression was significantly lower in esophageal cancer tissues (0.801 ± 0.737) compared to adjacent non-cancerous tissues (1.390 ± 1.346), p = 0.006. Low miR-107 expression (cutoff = median) correlated with advanced tumor, node, metastasis stage (TNM stage) (I vs. V: 100% vs. 21.4%, P < 0.001), lymph node metastasis (73.1% vs. 35%, P < 0.001), and larger tumor size (70% vs. 33.3%, P < 0.001). Patients with low miR-107 had shorter median overall survival (10 vs. 59 months; Hazard Ratio (HR) = 0.475, 95% Confidence Interval (CI) [0.247–0.915]; P < 0.001). Multivariate Cox analysis confirmed miR-107 as an independent prognostic factor alongside TNM stage (HR = 3.586, 95% CI [2.253–5.708]; P < 0.001). Consistently, EC109 cells exhibited 59% lower miR-107 levels than HEEC (P = 0.029). Conclusions miR-107 downregulation is a robust predictor of aggressive ESCC phenotypes and poor survival. It holds promise as a clinical biomarker for risk stratification and personalized therapy. Future studies should validate these …
bibliographic citation: Sun et al. (2025) Prognostic implications of microRNA-107 in esophageal cancer: a retrospective cohort study. PeerJ 13:e20327 https://doi.org/10.7717/peerj.20327
date submitted: 2025-04-21
date accepted: 2025-10-13
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Jie
author list: Agent
  family name: Zhang
  given name: Jin
author list: Agent
  family name: Ye
  given name: Jingwen
author list: Agent
  family name: Chen
  given name: Yuqi
author list: Agent
  family name: Jiang
  given name: Caifeng
doi: 10.7717/peerj.20327
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Sun et al.
attribution name: Sun et al.

Effect of short-term exposure to air pollution on ischemic stroke incidence and mortality: a five-year time-series study in Jining, China
type: item
type: AcademicArticle
description: Background Short-term exposure to air pollutants is associated with an increased risk of ischemic stroke incidence and mortality. However, there is a lack of research based on data from disease surveillance systems. This study used disease surveillance system data to quantitatively analyze the association between air pollution and ischemic stroke incidence and mortality in Jining, China. Methods The stroke registration system of the Jining City Center for Disease Control and Prevention (CDC) includes information on confirmed stroke cases reported by all medical institutions in the jurisdiction, covering a population of 8.9 million. Generalized linear regression models combined with distributed lag nonlinear models (DLNM) were used to determine the association between air pollutants and ischemic stroke incidence and mortality. Stratified analyses by sex, age, and season were also conducted. Results During the study period (January 1, 2018, to December 31, 2022), there were 209,949 ischemic stroke incidence cases and 23,565 ischemic stroke-related deaths. There were more ischemic stroke incidence and death cases in males compared to females. The number of incidence cases was higher in the warm season (52.6%) than in the cold season (47.4%), while this pattern was reversed for the number of deaths, with a higher number of deaths in the cold season (55.9%) than in the warm season (44.1%). This study showed that exposure to particulate matter (PM2.5 and PM10), nitrogen dioxide (NO2), and carbon monoxide (CO) was associated with ischemic stroke incidence, and exposure to PM2.5, PM10, sulfur dioxide (SO2), and CO was associated with ischemic stroke mortality. The relative risks (RRs, with 95% CIs) for ischemic stroke incidence at the maximum single-lag effect day for each interquartile range (IQR) increment for PM2.5, PM10, NO2, and CO were 1.007 (1.001–1.014), 1.004 (1.000–1.008); 1.031 (1.011–1.051), and 1.008 (1.001–1.015), respectively. The RRs (with 95% CIs) for morta…
format: application/pdf
format: text/html
creator: Yaohui Kong
creator: Wenhua Duan
creator: Zi Zhang
creator: Peizhen Zhou
creator: Mei Wang
creator: Jing Zhang
creator: Wenjun Wang
subject: Neurology
subject: Public Health
subject: Environmental Health
description: doi:10.7717/peerj.20298
publisher: PeerJ Inc.
rights: © 2025 Kong et al.
abstract: Background Short-term exposure to air pollutants is associated with an increased risk of ischemic stroke incidence and mortality. However, there is a lack of research based on data from disease surveillance systems. This study used disease surveillance system data to quantitatively analyze the association between air pollution and ischemic stroke incidence and mortality in Jining, China. Methods The stroke registration system of the Jining City Center for Disease Control and Prevention (CDC) includes information on confirmed stroke cases reported by all medical institutions in the jurisdiction, covering a population of 8.9 million. Generalized linear regression models combined with distributed lag nonlinear models (DLNM) were used to determine the association between air pollutants and ischemic stroke incidence and mortality. Stratified analyses by sex, age, and season were also conducted. Results During the study period (January 1, 2018, to December 31, 2022), there were 209,949 ischemic stroke incidence cases and 23,565 ischemic stroke-related deaths. There were more ischemic stroke incidence and death cases in males compared to females. The number of incidence cases was higher in the warm season (52.6%) than in the cold season (47.4%), while this pattern was reversed for the number of deaths, with a higher number of deaths in the cold season (55.9%) than in the warm season (44.1%). This study showed that exposure to particulate matter (PM2.5 and PM10), nitrogen dioxide (NO2), and carbon monoxide (CO) was associated with ischemic stroke incidence, and exposure to PM2.5, PM10, sulfur dioxide (SO2), and CO was associated with ischemic stroke mortality. The relative risks (RRs, with 95% CIs) for ischemic stroke incidence at the maximum single-lag effect day for each interquartile range (IQR) increment for PM2.5, PM10, NO2, and CO were 1.007 (1.001–1.014), 1.004 (1.000–1.008); 1.031 (1.011–1.051), and 1.008 (1.001–1.015), respectively. The RRs (with 95% CIs) for morta…
bibliographic citation: Kong et al. (2025) Effect of short-term exposure to air pollution on ischemic stroke incidence and mortality: a five-year time-series study in Jining, China. PeerJ 13:e20298 https://doi.org/10.7717/peerj.20298
date submitted: 2025-02-05
date accepted: 2025-10-06
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Kong
  given name: Yaohui
author list: Agent
  family name: Duan
  given name: Wenhua
author list: Agent
  family name: Zhang
  given name: Zi
author list: Agent
  family name: Zhou
  given name: Peizhen
author list: Agent
  family name: Wang
  given name: Mei
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Wang
  given name: Wenjun
doi: 10.7717/peerj.20298
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Kong et al.
attribution name: Kong et al.

Are caves enough to represent karst groundwater biodiversity? Insights from geospatial analyses applied to European obligate groundwater-dwelling copepods
type: item
type: AcademicArticle
description: Caves are recognized as biodiversity hotspots for groundwater fauna, including obligate groundwater-dwelling copepods (Crustacea: Copepoda), exhibiting high species richness, endemism, and phylogenetic rarity. However, the extent to which caves alone provide a representative estimate of copepod species richness in karst areas remains uncertain. Taking advantage of the recently published EGCop dataset, the first expert-validated, Europe-wide occurrence dataset for obligate groundwater-dwelling copepods (hereinafter, GW copepods), this study investigates the distribution of GW copepods into karst areas, comparing species richness in caves versus other karst groundwater habitats (e.g., springs, karst streams, artificial wells), within and among the European karst units. The main aims are: (i) identifying karst areas which represent hotpots of GW copepod species richness; (ii) assessing to which extent caves, as open windows to the subterranean environments, contribute to define hotspots of GW copepods’ species richness into karst areas across Europe. EGCop comprises 6,986 records from 588 copepod species/subspecies distributed among four orders: Cyclopoida (3,664 records, 184 species), Harpacticoida (3,288 records, 395 species), Calanoida (32 records, seven species), and Gelyelloida (two records, two species). To perform geospatial analyses, we filtered the dataset by: (i) selecting only the records with spatial uncertainty in the associated coordinates lower than 10 km; (ii) searching for those records falling within, or very close to, the polygons representing European karst areas. Species richness hotspots were then estimated through geospatial analyses in geographic information system (GIS) environment. Within the selected records, those specifically referring to karst habitats (2,526 records, 369 species) are primarily represented by Harpacticoida (1,199 records, 228 species) and Cyclopoida (1,293 records, 132 species). Among species collected from karst habitats,…
format: application/pdf
format: text/html
creator: Emma Galmarini
creator: Mattia Di Cicco
creator: Barbara Fiasca
creator: Nataša Mori
creator: Mattia Iannella
creator: Tiziana Di Lorenzo
creator: Francesco Cerasoli
creator: Diana Maria Paola Galassi
subject: Biodiversity
subject: Conservation Biology
subject: Zoology
subject: Freshwater Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.20285
publisher: PeerJ Inc.
rights: © 2025 Galmarini et al.
abstract: Caves are recognized as biodiversity hotspots for groundwater fauna, including obligate groundwater-dwelling copepods (Crustacea: Copepoda), exhibiting high species richness, endemism, and phylogenetic rarity. However, the extent to which caves alone provide a representative estimate of copepod species richness in karst areas remains uncertain. Taking advantage of the recently published EGCop dataset, the first expert-validated, Europe-wide occurrence dataset for obligate groundwater-dwelling copepods (hereinafter, GW copepods), this study investigates the distribution of GW copepods into karst areas, comparing species richness in caves versus other karst groundwater habitats (e.g., springs, karst streams, artificial wells), within and among the European karst units. The main aims are: (i) identifying karst areas which represent hotpots of GW copepod species richness; (ii) assessing to which extent caves, as open windows to the subterranean environments, contribute to define hotspots of GW copepods’ species richness into karst areas across Europe. EGCop comprises 6,986 records from 588 copepod species/subspecies distributed among four orders: Cyclopoida (3,664 records, 184 species), Harpacticoida (3,288 records, 395 species), Calanoida (32 records, seven species), and Gelyelloida (two records, two species). To perform geospatial analyses, we filtered the dataset by: (i) selecting only the records with spatial uncertainty in the associated coordinates lower than 10 km; (ii) searching for those records falling within, or very close to, the polygons representing European karst areas. Species richness hotspots were then estimated through geospatial analyses in geographic information system (GIS) environment. Within the selected records, those specifically referring to karst habitats (2,526 records, 369 species) are primarily represented by Harpacticoida (1,199 records, 228 species) and Cyclopoida (1,293 records, 132 species). Among species collected from karst habitats,…
bibliographic citation: Galmarini et al. (2025) Are caves enough to represent karst groundwater biodiversity? Insights from geospatial analyses applied to European obligate groundwater-dwelling copepods. PeerJ 13:e20285 https://doi.org/10.7717/peerj.20285
date submitted: 2025-07-24
date accepted: 2025-10-02
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galmarini
  given name: Emma
author list: Agent
  family name: Di Cicco
  given name: Mattia
author list: Agent
  family name: Fiasca
  given name: Barbara
author list: Agent
  family name: Mori
  given name: Nataša
author list: Agent
  family name: Iannella
  given name: Mattia
author list: Agent
  family name: Di Lorenzo
  given name: Tiziana
author list: Agent
  family name: Cerasoli
  given name: Francesco
author list: Agent
  family name: Galassi
  given name: Diana Maria Paola
doi: 10.7717/peerj.20285
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Galmarini et al.
attribution name: Galmarini et al.

Breaking epigenetic shackles: targeting ARID1A methylation and the PI3K/AKT/mTOR-PD-L1 axis to overcome immune escape in gastric cancer
type: item
type: AcademicArticle
description: Objective AT-rich interaction domain 1A (ARID1A), is frequently mutated in cancer, leading to loss-of-function and posing challenges to therapeutic targeting. This study aimed to systematically explore epigenetic regulation of ARID1A, specifically promoter hypermethylation, in gastric cancer (GC) and its functional/immunological consequences. Methods We employed multi-omics bioinformatics analyses (UALCAN, cBioPortal, MEXPRESS and UCSC Xena) combined with in vitro functional validation in GC cell lines, including pharmacological demethylation using 5-Aza-2’-deoxycytidine (5-aza-CdR) and mechanistic interrogation via AKT agonism (SC79). Results Promoter hypermethylation was identified as a key mechanism silencing ARID1A transcriptional, showing a significant negative correlation between methylation β-values and mRNA expression (Spearman’s ρ = − 0.29, p = 2.06 × 10−8). 5-aza-CdR treatment restored ARID1A expression (p < 0.001), suppressed malignant phenotypes (proliferation, invasion, and apoptosis resistance), and revealed that ARID1A lose activates the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway (elevated p-AKT, p-mTOR) and upregulates PD-L1. Rescue experiments with SC79 reversed 5-aza-CdR’s effects, confirming the ARID1A-PI3K/AKT/mTOR-PD-L1 axis. Integrative analysis linked ARID1A hypermethylation to elevated immune/ESTIMATE scores (p < 0.05). Conclusion ARID1A promoter hypermethylation drives an epigenetic-immune checkpoint cascade in GC. Combined with its association with immune signatures and PD-L1 upregulation, ARID1A hypermethylation emerges as a candidate biomarker for predicting immune checkpoint blockade (ICB) responsiveness and patient stratification in GC. Future studies should evaluate 5-aza-CdR-ICB-AKT inhibitor regimens in advanced models to guide clinical translation.
format: application/pdf
format: text/html
creator: Xueqin Duan
creator: Xingfa Huo
creator: Yuming Zhang
creator: Hongwei Lan
creator: Fangfang Yang
creator: Xiaochun Zhang
creator: Na Zhou
subject: Cell Biology
subject: Molecular Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20251
publisher: PeerJ Inc.
rights: © 2025 Duan et al.
abstract: Objective AT-rich interaction domain 1A (ARID1A), is frequently mutated in cancer, leading to loss-of-function and posing challenges to therapeutic targeting. This study aimed to systematically explore epigenetic regulation of ARID1A, specifically promoter hypermethylation, in gastric cancer (GC) and its functional/immunological consequences. Methods We employed multi-omics bioinformatics analyses (UALCAN, cBioPortal, MEXPRESS and UCSC Xena) combined with in vitro functional validation in GC cell lines, including pharmacological demethylation using 5-Aza-2’-deoxycytidine (5-aza-CdR) and mechanistic interrogation via AKT agonism (SC79). Results Promoter hypermethylation was identified as a key mechanism silencing ARID1A transcriptional, showing a significant negative correlation between methylation β-values and mRNA expression (Spearman’s ρ = − 0.29, p = 2.06 × 10−8). 5-aza-CdR treatment restored ARID1A expression (p < 0.001), suppressed malignant phenotypes (proliferation, invasion, and apoptosis resistance), and revealed that ARID1A lose activates the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway (elevated p-AKT, p-mTOR) and upregulates PD-L1. Rescue experiments with SC79 reversed 5-aza-CdR’s effects, confirming the ARID1A-PI3K/AKT/mTOR-PD-L1 axis. Integrative analysis linked ARID1A hypermethylation to elevated immune/ESTIMATE scores (p < 0.05). Conclusion ARID1A promoter hypermethylation drives an epigenetic-immune checkpoint cascade in GC. Combined with its association with immune signatures and PD-L1 upregulation, ARID1A hypermethylation emerges as a candidate biomarker for predicting immune checkpoint blockade (ICB) responsiveness and patient stratification in GC. Future studies should evaluate 5-aza-CdR-ICB-AKT inhibitor regimens in advanced models to guide clinical translation.
bibliographic citation: Duan et al. (2025) Breaking epigenetic shackles: targeting ARID1A methylation and the PI3K/AKT/mTOR-PD-L1 axis to overcome immune escape in gastric cancer. PeerJ 13:e20251 https://doi.org/10.7717/peerj.20251
date submitted: 2025-05-28
date accepted: 2025-09-25
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duan
  given name: Xueqin
author list: Agent
  family name: Huo
  given name: Xingfa
author list: Agent
  family name: Zhang
  given name: Yuming
author list: Agent
  family name: Lan
  given name: Hongwei
author list: Agent
  family name: Yang
  given name: Fangfang
author list: Agent
  family name: Zhang
  given name: Xiaochun
author list: Agent
  family name: Zhou
  given name: Na
doi: 10.7717/peerj.20251
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Duan et al.
attribution name: Duan et al.

Retrospective study on the association between paternal occupational exposure to agrochemicals and childhood leukemia in Michoacán de Ocampo, México
type: item
type: AcademicArticle
description: Objectives The constant use of agrochemicals in avocado plantations, because of their susceptibility to pests and diseases, continuously exposes those who work or reside near these orchards to health risks. The purpose of this study was to investigate the association between childhood leukemia cases in Michoacán, paternal occupational exposure to agrochemicals, and environmental exposure due to residential proximity. Methods A retrospective observational cohort study was performed. We analyzed 430 cases of leukemia in children under 18 years of age diagnosed between 2010-2023. Logistic regression models were used to estimate odds ratios and 95% confidence intervals, adjusted for sociodemographic factors. Survival was analyzed using Kaplan-Meier curves. Results A total of 46.6% of the parents of children with leukemia in this study had jobs related to the use of agrochemicals (e.g., day laborers, peasants, farmers). Additionally, 65.4% of the leukemia cases occurred in municipalities producing avocado, the most important perennial crop in the state. Regarding the residential area analysis (mapping), many cases were found in contiguous zip codes and in areas densely occupied by avocado orchards. In addition, paternal occupations related to agrochemical use were associated with the avocado-growing zone, with an OR = 1.764 (95% CI [1.034–3.009], p = 0.0379). Interestingly, survival associated with agrochemical-related occupations has a higher mean survival (139.3 months) than all other parental occupations (p = 0.0148). Conclusions The epidemiologic evidence found in this study supports the association between paternal occupational exposure to agrochemicals and childhood leukemia. Furthermore, children with leukemia who live in avocado-growing regions have a higher survival rate.
format: application/pdf
format: text/html
creator: Paola Jiménez-Alcántar
creator: Anel Gómez-García
creator: Joel E. López-Meza
creator: Alejandra Ochoa-Zarzosa
creator: Luis Andrés Espino-Barajas
creator: Luis Miguel Morales-Manilla
creator: Eloy Pérez-Rivera
creator: Luz Yadira Zúñiga-Quijano
creator: Sergio Gutiérrez-Castellanos
subject: Epidemiology
subject: Hematology
subject: Oncology
subject: Pediatrics
subject: Environmental Health
description: doi:10.7717/peerj.20219
publisher: PeerJ Inc.
rights: © 2025 Jiménez-Alcántar et al.
abstract: Objectives The constant use of agrochemicals in avocado plantations, because of their susceptibility to pests and diseases, continuously exposes those who work or reside near these orchards to health risks. The purpose of this study was to investigate the association between childhood leukemia cases in Michoacán, paternal occupational exposure to agrochemicals, and environmental exposure due to residential proximity. Methods A retrospective observational cohort study was performed. We analyzed 430 cases of leukemia in children under 18 years of age diagnosed between 2010-2023. Logistic regression models were used to estimate odds ratios and 95% confidence intervals, adjusted for sociodemographic factors. Survival was analyzed using Kaplan-Meier curves. Results A total of 46.6% of the parents of children with leukemia in this study had jobs related to the use of agrochemicals (e.g., day laborers, peasants, farmers). Additionally, 65.4% of the leukemia cases occurred in municipalities producing avocado, the most important perennial crop in the state. Regarding the residential area analysis (mapping), many cases were found in contiguous zip codes and in areas densely occupied by avocado orchards. In addition, paternal occupations related to agrochemical use were associated with the avocado-growing zone, with an OR = 1.764 (95% CI [1.034–3.009], p = 0.0379). Interestingly, survival associated with agrochemical-related occupations has a higher mean survival (139.3 months) than all other parental occupations (p = 0.0148). Conclusions The epidemiologic evidence found in this study supports the association between paternal occupational exposure to agrochemicals and childhood leukemia. Furthermore, children with leukemia who live in avocado-growing regions have a higher survival rate.
bibliographic citation: Jiménez-Alcántar et al. (2025) Retrospective study on the association between paternal occupational exposure to agrochemicals and childhood leukemia in Michoacán de Ocampo, México. PeerJ 13:e20219 https://doi.org/10.7717/peerj.20219
date submitted: 2025-03-20
date accepted: 2025-09-20
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Jiménez-Alcántar
  given name: Paola
author list: Agent
  family name: Gómez-García
  given name: Anel
author list: Agent
  family name: López-Meza
  given name: Joel E.
author list: Agent
  family name: Ochoa-Zarzosa
  given name: Alejandra
author list: Agent
  family name: Espino-Barajas
  given name: Luis Andrés
author list: Agent
  family name: Morales-Manilla
  given name: Luis Miguel
author list: Agent
  family name: Pérez-Rivera
  given name: Eloy
author list: Agent
  family name: Zúñiga-Quijano
  given name: Luz Yadira
author list: Agent
  family name: Gutiérrez-Castellanos
  given name: Sergio
doi: 10.7717/peerj.20219
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Jiménez-Alcántar et al.
attribution name: Jiménez-Alcántar et al.

Auditory processing ability in Thai native speakers with the Gaps-In-Noise (GIN) test
type: item
type: AcademicArticle
description: Introduction Auditory processing disorder (APD) arises from dysfunctions within the central auditory nervous system (CANS). One key tool for assessing temporal auditory processing capabilities is the Gaps-In-Noise (GIN) test. While the GIN test serves as a critical tool, its accuracy may be influenced by linguistic factors. This research aims to establish preliminary normative data for the GIN test among young adult native Thai speakers and to compare potential performance differences across ears and various linguistic backgrounds. Methods This study included 52 native Thai speakers aged 18 to 25, all of whom had normal hearing confirmed through pure-tone audiometry, to examine auditory processing using the GIN test. The testing was conducted in an anechoic chamber to ensure standardized conditions. The results were analyzed based on the approximate gap-detection threshold (A.th.) value and the overall percent correct (OPC) value metrics. Results The study revealed that, among young adult native Thai speakers, the A.th. values were 5.12–0.81 milliseconds (ms.) in the right ear, 5.08–0.81 ms. in the left ear, and 5.04–0.68 ms. for both ears. The corresponding averages of OPC values were 69.94–7.66% for the right ear, 71.37–7.21% for the left ear, and 71.35–6.72% for both ears, respectively. While no significant differences were observed in the threshold between ears, a notable discrepancy in response accuracy was noted, with the right ear showing lower accuracy than the left ear. Significant differences were also found when compared to English, Korean, and Portuguese language users, but not when compared to Polish language users. Conclusion The study revealed comparable temporal processing abilities among young adult native Thai speakers, as indicated by similar A.th. values across both ears. However, differences in the OPC value responses suggest potential asymmetries in auditory processing mechanisms. Additionally, linguistic factors appeared to influence the outco…
format: application/pdf
format: text/html
creator: Supakarn Jeanbunjongkij
creator: Pawichaya Suphinnapong
creator: Patcharaorn Limkitisupasin
creator: Yuttana Roongthumskul
creator: Nattawan Utoomprurkporn
subject: Neuroscience
subject: Neurology
subject: Otorhinolaryngology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.20207
publisher: PeerJ Inc.
rights: © 2025 Jeanbunjongkij et al.
abstract: Introduction Auditory processing disorder (APD) arises from dysfunctions within the central auditory nervous system (CANS). One key tool for assessing temporal auditory processing capabilities is the Gaps-In-Noise (GIN) test. While the GIN test serves as a critical tool, its accuracy may be influenced by linguistic factors. This research aims to establish preliminary normative data for the GIN test among young adult native Thai speakers and to compare potential performance differences across ears and various linguistic backgrounds. Methods This study included 52 native Thai speakers aged 18 to 25, all of whom had normal hearing confirmed through pure-tone audiometry, to examine auditory processing using the GIN test. The testing was conducted in an anechoic chamber to ensure standardized conditions. The results were analyzed based on the approximate gap-detection threshold (A.th.) value and the overall percent correct (OPC) value metrics. Results The study revealed that, among young adult native Thai speakers, the A.th. values were 5.12–0.81 milliseconds (ms.) in the right ear, 5.08–0.81 ms. in the left ear, and 5.04–0.68 ms. for both ears. The corresponding averages of OPC values were 69.94–7.66% for the right ear, 71.37–7.21% for the left ear, and 71.35–6.72% for both ears, respectively. While no significant differences were observed in the threshold between ears, a notable discrepancy in response accuracy was noted, with the right ear showing lower accuracy than the left ear. Significant differences were also found when compared to English, Korean, and Portuguese language users, but not when compared to Polish language users. Conclusion The study revealed comparable temporal processing abilities among young adult native Thai speakers, as indicated by similar A.th. values across both ears. However, differences in the OPC value responses suggest potential asymmetries in auditory processing mechanisms. Additionally, linguistic factors appeared to influence the outco…
bibliographic citation: Jeanbunjongkij et al. (2025) Auditory processing ability in Thai native speakers with the Gaps-In-Noise (GIN) test. PeerJ 13:e20207 https://doi.org/10.7717/peerj.20207
date submitted: 2025-03-05
date accepted: 2025-09-18
issued: 2025-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jeanbunjongkij
  given name: Supakarn
author list: Agent
  family name: Suphinnapong
  given name: Pawichaya
author list: Agent
  family name: Limkitisupasin
  given name: Patcharaorn
author list: Agent
  family name: Roongthumskul
  given name: Yuttana
author list: Agent
  family name: Utoomprurkporn
  given name: Nattawan
doi: 10.7717/peerj.20207
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-06
copyright: ©2025 Jeanbunjongkij et al.
attribution name: Jeanbunjongkij et al.

Analysis of the chitin synthase gene family in Ganoderma lucidum: its structure, phylogeny, and expression patterns
type: item
type: AcademicArticle
description: Background Chitin synthases are essential enzymes in fungi, contributing to various biological processes such as hyphal growth, sporulation, and cell wall stability. Despite their well-documented functions in other fungal species, the specific roles of chitin synthases in Ganoderma lucidum remain unexplored. This investigation systematically characterized the complete chitin synthase gene family in Ganoderma lucidum. Methods A comprehensive analysis was conducted using bioinformatics tools to examine genomic localization, gene structure, conserved domains, and phylogenetic evolution. By employing bioinformatic approaches, the study investigated promoter cis-elements and expression patterns to elucidate the regulatory mechanisms of these genes in G. lucidum. Results In G. lucidum, eight chitin synthase (GlCS) family members were identified and phylogenetically classified into five distinct classes. Our investigation revealed stage-specific expression patterns of GlCS genes throughout the fungal development process. GlCS1, GlCS2, GlCS5, GlCS6, and GlCS8 exhibited significantly greater expression levels in the early fruiting body (EA) stage than in the other developmental phases. In the mature fruiting body (MA) stage, GlCS3 was predominantly expressed. In the primordium formation (PR) stage, GlCS7 exhibited peak expression levels. Six genes (GlCS1, GlCS3, GlCS4, GlCS6, GlCS7, and GlCS8) were markedly upregulated under 40 °C thermal stress, suggesting their potential roles in thermotolerance mechanisms. These findings demonstrate functional diversification among GlCS family members across different developmental stages and stress conditions.
format: application/pdf
format: text/html
creator: Linling Liu
creator: Yiming Yang
creator: Jintao Li
creator: Yanliang Gao
creator: Meixia Yan
subject: Agricultural Science
subject: Bioinformatics
subject: Mycology
description: doi:10.7717/peerj.20302
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Chitin synthases are essential enzymes in fungi, contributing to various biological processes such as hyphal growth, sporulation, and cell wall stability. Despite their well-documented functions in other fungal species, the specific roles of chitin synthases in Ganoderma lucidum remain unexplored. This investigation systematically characterized the complete chitin synthase gene family in Ganoderma lucidum. Methods A comprehensive analysis was conducted using bioinformatics tools to examine genomic localization, gene structure, conserved domains, and phylogenetic evolution. By employing bioinformatic approaches, the study investigated promoter cis-elements and expression patterns to elucidate the regulatory mechanisms of these genes in G. lucidum. Results In G. lucidum, eight chitin synthase (GlCS) family members were identified and phylogenetically classified into five distinct classes. Our investigation revealed stage-specific expression patterns of GlCS genes throughout the fungal development process. GlCS1, GlCS2, GlCS5, GlCS6, and GlCS8 exhibited significantly greater expression levels in the early fruiting body (EA) stage than in the other developmental phases. In the mature fruiting body (MA) stage, GlCS3 was predominantly expressed. In the primordium formation (PR) stage, GlCS7 exhibited peak expression levels. Six genes (GlCS1, GlCS3, GlCS4, GlCS6, GlCS7, and GlCS8) were markedly upregulated under 40 °C thermal stress, suggesting their potential roles in thermotolerance mechanisms. These findings demonstrate functional diversification among GlCS family members across different developmental stages and stress conditions.
bibliographic citation: Liu et al. (2025) Analysis of the chitin synthase gene family in Ganoderma lucidum: its structure, phylogeny, and expression patterns. PeerJ 13:e20302 https://doi.org/10.7717/peerj.20302
date submitted: 2025-07-09
date accepted: 2025-10-07
issued: 2025-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Linling
author list: Agent
  family name: Yang
  given name: Yiming
author list: Agent
  family name: Li
  given name: Jintao
author list: Agent
  family name: Gao
  given name: Yanliang
author list: Agent
  family name: Yan
  given name: Meixia
doi: 10.7717/peerj.20302
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-05
copyright: ©2025 Liu et al.
attribution name: Liu et al.

CD81 inhibits the proliferation of acute megakaryoblastic leukemia cells
type: item
type: AcademicArticle
description: CD81 is a cell surface protein that plays an important part in tumor development. Several studies have shown that CD81 plays a role in cancer cell proliferation, invasion, and metastasis, particularly in leukemia. It has been reported that CD81 is overexpressed in non-Down syndrome acute megakaryoblastic leukemia (non-DS AMKL). In this article, we hypothesize that CD81 may play a vital role in acute megakaryoblastic leukemia (AMKL). We constructed the CD81 knockdown cell line using shRNA and found that CD81 knockout can inhibit the proliferation of AMKL and increase the apoptosis of AMKL in vitro. Therefore, CD81 may be a target of AMKL.
format: application/pdf
format: text/html
creator: Narun Su
creator: Xiaohao Hu
subject: Cell Biology
subject: Molecular Biology
subject: Hematology
subject: Pediatrics
description: doi:10.7717/peerj.20286
publisher: PeerJ Inc.
rights: © 2025 Su and Hu
abstract: CD81 is a cell surface protein that plays an important part in tumor development. Several studies have shown that CD81 plays a role in cancer cell proliferation, invasion, and metastasis, particularly in leukemia. It has been reported that CD81 is overexpressed in non-Down syndrome acute megakaryoblastic leukemia (non-DS AMKL). In this article, we hypothesize that CD81 may play a vital role in acute megakaryoblastic leukemia (AMKL). We constructed the CD81 knockdown cell line using shRNA and found that CD81 knockout can inhibit the proliferation of AMKL and increase the apoptosis of AMKL in vitro. Therefore, CD81 may be a target of AMKL.
bibliographic citation: Su et al. (2025) CD81 inhibits the proliferation of acute megakaryoblastic leukemia cells. PeerJ 13:e20286 https://doi.org/10.7717/peerj.20286
date submitted: 2025-03-10
date accepted: 2025-10-02
issued: 2025-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Narun
author list: Agent
  family name: Hu
  given name: Xiaohao
doi: 10.7717/peerj.20286
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-05
copyright: ©2025 Su and Hu
attribution name: Su and Hu

Biocontrol-relevant diversity of wheat-associated Pseudomonas: prevalence of P. sivasensis and identification of the novel species P. arvensis sp. nov.
type: item
type: AcademicArticle
description: The role of microbial communities in plant health and productivity has become increasingly evident. In this study, we investigated the diversity and functional potential of Pseudomonas spp. associated with Belgian cereal crops, focusing on wheat and spelt. From 444 Pseudomonas isolates, we identified 11 species, with several strains exhibiting strong antagonistic activity against major wheat pathogens. Notably, we report the high prevalence and efficient colonization abilities of Pseudomonas sivasensis, including its capacity to translocate from seed to leaf and suppress Zymoseptoria tritici infection in planta. Furthermore, we describe Pseudomonas arvensis sp. nov., a newly characterized species within the wheat microbiome, with DR1PS3 designated as the type strain. Our results advance the understanding of beneficial plant-microbe interactions in cereals and highlight the promise of native Pseudomonas species as biocontrol agents for sustainable disease management.
format: application/pdf
format: text/html
creator: Mathieu Delitte
creator: Benjamin Dubois
creator: Louis Morandini
creator: Alain Bultreys
creator: Jacques Mahillon
creator: Frederic Debode
creator: Claude Bragard
subject: Agricultural Science
subject: Biodiversity
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.20177
publisher: PeerJ Inc.
rights: © 2025 Delitte et al.
abstract: The role of microbial communities in plant health and productivity has become increasingly evident. In this study, we investigated the diversity and functional potential of Pseudomonas spp. associated with Belgian cereal crops, focusing on wheat and spelt. From 444 Pseudomonas isolates, we identified 11 species, with several strains exhibiting strong antagonistic activity against major wheat pathogens. Notably, we report the high prevalence and efficient colonization abilities of Pseudomonas sivasensis, including its capacity to translocate from seed to leaf and suppress Zymoseptoria tritici infection in planta. Furthermore, we describe Pseudomonas arvensis sp. nov., a newly characterized species within the wheat microbiome, with DR1PS3 designated as the type strain. Our results advance the understanding of beneficial plant-microbe interactions in cereals and highlight the promise of native Pseudomonas species as biocontrol agents for sustainable disease management.
bibliographic citation: Delitte et al. (2025) Biocontrol-relevant diversity of wheat-associated Pseudomonas: prevalence of P. sivasensis and identification of the novel species P. arvensis sp. nov.. PeerJ 13:e20177 https://doi.org/10.7717/peerj.20177
date submitted: 2024-08-28
date accepted: 2025-09-12
issued: 2025-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Delitte
  given name: Mathieu
author list: Agent
  family name: Dubois
  given name: Benjamin
author list: Agent
  family name: Morandini
  given name: Louis
author list: Agent
  family name: Bultreys
  given name: Alain
author list: Agent
  family name: Mahillon
  given name: Jacques
author list: Agent
  family name: Debode
  given name: Frederic
author list: Agent
  family name: Bragard
  given name: Claude
doi: 10.7717/peerj.20177
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-05
copyright: ©2025 Delitte et al.
attribution name: Delitte et al.

Gardnerella species exhibit synergy in their ability to displace Lactobacillus crispatus adhered to HeLa cells
type: item
type: AcademicArticle
description: Background Bacterial vaginosis (BV) is the most common vaginal infection in reproductive-age women. It is associated with adverse pregnancy complications, such as preterm birth and low birth weight, in addition to an increased risk of acquisition of HIV and sexually transmitted infections. BV is characterized by a vaginal dysbiosis, involving loss of protective Lactobacillus species (including L. crispatus) and overgrowth of facultative and strict anaerobic bacteria, with Gardnerella species playing a predominant role. However, despite extensive research on BV pathogenesis, its etiology remains unclear, and the sequence of events leading to the displacement of lactobacilli by anaerobic bacteria in women has not yet been fully elucidated. Until 2019, all bacteria belonging to the Gardnerella genus were considered part of the species G. vaginalis. However, it is now recognized that different Gardnerella species exist, each with varying virulence potentials. Recent data have shown that multiple subgroups of Gardnerella spp. are frequently detected simultaneously in the vaginal microbiota of women with BV. With this in mind, we aimed to test the hypothesis that different combinations of known Gardnerella species, isolated from the vaginal microbiota of women with BV, have an enhanced ability to compete against Lactobacillus crispatus, pre-adhered to HeLa cells, thereby facilitating the early stages of BV development. Methods Adhesion assays of dual combinations of Gardnerella spp. (G. vaginalis, G. leopoldii, G. swidsinskii, G. piotii) were performed on an in vitro model of HeLa cells, covered with and without L. crispatus. Quantification of the species used in our assays was subsequently performed using quantitative polymerase chain reaction (qPCR). Results Our results revealed synergy between different Gardnerella spp., demonstrating their ability to overcome the presumed protective effect of L. crispatus, thereby creating favorable conditions for the development of a…
format: application/pdf
format: text/html
creator: Ângela Lima
creator: Joana Castro
creator: Christina A. Muzny
creator: Nuno Cerca
subject: Microbiology
subject: Gynecology and Obstetrics
subject: Infectious Diseases
description: doi:10.7717/peerj.20076
publisher: PeerJ Inc.
rights: © 2025 Lima et al.
abstract: Background Bacterial vaginosis (BV) is the most common vaginal infection in reproductive-age women. It is associated with adverse pregnancy complications, such as preterm birth and low birth weight, in addition to an increased risk of acquisition of HIV and sexually transmitted infections. BV is characterized by a vaginal dysbiosis, involving loss of protective Lactobacillus species (including L. crispatus) and overgrowth of facultative and strict anaerobic bacteria, with Gardnerella species playing a predominant role. However, despite extensive research on BV pathogenesis, its etiology remains unclear, and the sequence of events leading to the displacement of lactobacilli by anaerobic bacteria in women has not yet been fully elucidated. Until 2019, all bacteria belonging to the Gardnerella genus were considered part of the species G. vaginalis. However, it is now recognized that different Gardnerella species exist, each with varying virulence potentials. Recent data have shown that multiple subgroups of Gardnerella spp. are frequently detected simultaneously in the vaginal microbiota of women with BV. With this in mind, we aimed to test the hypothesis that different combinations of known Gardnerella species, isolated from the vaginal microbiota of women with BV, have an enhanced ability to compete against Lactobacillus crispatus, pre-adhered to HeLa cells, thereby facilitating the early stages of BV development. Methods Adhesion assays of dual combinations of Gardnerella spp. (G. vaginalis, G. leopoldii, G. swidsinskii, G. piotii) were performed on an in vitro model of HeLa cells, covered with and without L. crispatus. Quantification of the species used in our assays was subsequently performed using quantitative polymerase chain reaction (qPCR). Results Our results revealed synergy between different Gardnerella spp., demonstrating their ability to overcome the presumed protective effect of L. crispatus, thereby creating favorable conditions for the development of a…
bibliographic citation: Lima et al. (2025) Gardnerella species exhibit synergy in their ability to displace Lactobacillus crispatus adhered to HeLa cells. PeerJ 13:e20076 https://doi.org/10.7717/peerj.20076
date submitted: 2025-05-08
date accepted: 2025-08-22
issued: 2025-11-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lima
  given name: Ângela
author list: Agent
  family name: Castro
  given name: Joana
author list: Agent
  family name: Muzny
  given name: Christina A.
author list: Agent
  family name: Cerca
  given name: Nuno
doi: 10.7717/peerj.20076
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-05
copyright: ©2025 Lima et al.
attribution name: Lima et al.

MicroRNA-597-3p targets MACC1 to suppress proliferation and invasion of human ovarian cancer cells
type: item
type: AcademicArticle
description: Background Ovarian cancer is a lethal gynecological malignancy, largely due to late-stage diagnosis and poor prognosis. MicroRNA-597-3p (miR-597-3p) has been identified as a tumor suppressor in several cancers, while metastasis-associated colon cancer 1 (MACC1) functions as an oncogene that promotes metastasis. This study investigated the role of miR-597-3p and its regulation of MACC1 in ovarian cancer progression. Methods Ovarian cancer cell lines and the normal ovarian epithelial cell line IOSE-398 were used. Quantitative real-time PCR (qRT-PCR) measured the expression of miR-597-3p and MACC1. Functional assays (MTT, colony formation, AO/EB staining, and Transwell invasion) evaluated cell proliferation, cell death, and invasion. Dual-luciferase reporter assays confirmed the interaction between miR-597-3p and MACC1, while bioinformatics analysis identified potential targets. Western blotting was used to validate MACC1 and downstream proteins, MMP-2, and MMP-9 at the protein level. Results MiR-597-3p was significantly downregulated (P < 0.05) in ovarian cancer cells, whereas MACC1 was upregulated. Overexpression of miR-597-3p suppressed cell viability, colony formation, and invasion, and increased cell death with a pro-apoptotic shift in Bax/Bcl-2 expression. Mechanistically, miR-597-3p directly targeted MACC1, leading to reduced expression of MMP-2 and MMP-9 at both transcript and protein levels. Notably, MACC1 overexpression reversed the tumor-suppressive effects of miR-597-3p. Conclusions MiR-597-3p functions as a tumor suppressor in ovarian cancer by directly targeting MACC1, thereby inhibiting proliferation, invasion, and survival. These findings highlight the miR-597-3p/MACC1 axis as a potential therapeutic target and suggest miR-597-3p as a promising biomarker for ovarian cancer.
format: application/pdf
format: text/html
creator: Ahmed Abdullah Al Awadh
creator: Abdulaziz M.S. Alqahtani
creator: Fahad Alshahrani
creator: Mohammed Merae Alshahrani
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.20316
publisher: PeerJ Inc.
rights: © 2025 Al Awadh et al.
abstract: Background Ovarian cancer is a lethal gynecological malignancy, largely due to late-stage diagnosis and poor prognosis. MicroRNA-597-3p (miR-597-3p) has been identified as a tumor suppressor in several cancers, while metastasis-associated colon cancer 1 (MACC1) functions as an oncogene that promotes metastasis. This study investigated the role of miR-597-3p and its regulation of MACC1 in ovarian cancer progression. Methods Ovarian cancer cell lines and the normal ovarian epithelial cell line IOSE-398 were used. Quantitative real-time PCR (qRT-PCR) measured the expression of miR-597-3p and MACC1. Functional assays (MTT, colony formation, AO/EB staining, and Transwell invasion) evaluated cell proliferation, cell death, and invasion. Dual-luciferase reporter assays confirmed the interaction between miR-597-3p and MACC1, while bioinformatics analysis identified potential targets. Western blotting was used to validate MACC1 and downstream proteins, MMP-2, and MMP-9 at the protein level. Results MiR-597-3p was significantly downregulated (P < 0.05) in ovarian cancer cells, whereas MACC1 was upregulated. Overexpression of miR-597-3p suppressed cell viability, colony formation, and invasion, and increased cell death with a pro-apoptotic shift in Bax/Bcl-2 expression. Mechanistically, miR-597-3p directly targeted MACC1, leading to reduced expression of MMP-2 and MMP-9 at both transcript and protein levels. Notably, MACC1 overexpression reversed the tumor-suppressive effects of miR-597-3p. Conclusions MiR-597-3p functions as a tumor suppressor in ovarian cancer by directly targeting MACC1, thereby inhibiting proliferation, invasion, and survival. These findings highlight the miR-597-3p/MACC1 axis as a potential therapeutic target and suggest miR-597-3p as a promising biomarker for ovarian cancer.
bibliographic citation: Al Awadh et al. (2025) MicroRNA-597-3p targets MACC1 to suppress proliferation and invasion of human ovarian cancer cells. PeerJ 13:e20316 https://doi.org/10.7717/peerj.20316
date submitted: 2025-05-08
date accepted: 2025-10-09
issued: 2025-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Al Awadh
  given name: Ahmed Abdullah
author list: Agent
  family name: Alqahtani
  given name: Abdulaziz M.S.
author list: Agent
  family name: Alshahrani
  given name: Fahad
author list: Agent
  family name: Alshahrani
  given name: Mohammed Merae
doi: 10.7717/peerj.20316
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-04
copyright: ©2025 Al Awadh et al.
attribution name: Al Awadh et al.

Quantifying the scale dependence of primary productivity-species-richness relationships
type: item
type: AcademicArticle
description: Vegetation productivity is expected to correlate with species richness, but there is debate about whether the relationship form (non-existent, negative, positive, unimodal) of productivity-species-richness relationships (PSRR) depends on the spatial extent and productivity measure used. Previous assessments employed coarse distance categories to examine scale dependence and did not consider scale dependence for alternative productivity measures. I used spatially varying coefficient models to precisely estimate the distances over which PSRRs change and to map spatial patterns of form for breeding birds across the conterminous United States. I created separate models for three measures summarizing intra-annual estimates of gross primary productivity: sum, minimum, and seasonality (coefficient of variation). Models demonstrated that PSRRs were scale-dependent, and PSRR relationships changed at median distances ranging from 1,010 to 2,184 km depending on the productivity measure. Previously used coarse distance categories would not have resolved the modeled distance estimates. Differences in median distance estimates across productivity measures were not statistically important. Across measures, PSRR form generally alternated between non-existence and positive, but there were pockets where seasonality negatively related to species richness in the western United States. While spatial patterns of form differed across measures, species richness in a small region of the western United States displayed a positive association with all three measures. Spatial patterns were related to prevailing productivity conditions. For example, sum tended to have a positive association with bird species richness in areas characterized by low annual productivity. This study novelly applies spatially varying coefficient models to address the long-debated scale-dependence of PSRR form, and the same approach is broadly applicable across geographies and taxonomic groups.
format: application/pdf
format: text/html
creator: Brian G. Tavernia
subject: Biodiversity
subject: Ecology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20297
publisher: PeerJ Inc.
rights: © 2025 Tavernia
abstract: Vegetation productivity is expected to correlate with species richness, but there is debate about whether the relationship form (non-existent, negative, positive, unimodal) of productivity-species-richness relationships (PSRR) depends on the spatial extent and productivity measure used. Previous assessments employed coarse distance categories to examine scale dependence and did not consider scale dependence for alternative productivity measures. I used spatially varying coefficient models to precisely estimate the distances over which PSRRs change and to map spatial patterns of form for breeding birds across the conterminous United States. I created separate models for three measures summarizing intra-annual estimates of gross primary productivity: sum, minimum, and seasonality (coefficient of variation). Models demonstrated that PSRRs were scale-dependent, and PSRR relationships changed at median distances ranging from 1,010 to 2,184 km depending on the productivity measure. Previously used coarse distance categories would not have resolved the modeled distance estimates. Differences in median distance estimates across productivity measures were not statistically important. Across measures, PSRR form generally alternated between non-existence and positive, but there were pockets where seasonality negatively related to species richness in the western United States. While spatial patterns of form differed across measures, species richness in a small region of the western United States displayed a positive association with all three measures. Spatial patterns were related to prevailing productivity conditions. For example, sum tended to have a positive association with bird species richness in areas characterized by low annual productivity. This study novelly applies spatially varying coefficient models to address the long-debated scale-dependence of PSRR form, and the same approach is broadly applicable across geographies and taxonomic groups.
bibliographic citation: Tavernia (2025) Quantifying the scale dependence of primary productivity-species-richness relationships. PeerJ 13:e20297 https://doi.org/10.7717/peerj.20297
date submitted: 2025-07-12
date accepted: 2025-10-06
issued: 2025-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tavernia
  given name: Brian G.
doi: 10.7717/peerj.20297
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-04
copyright: ©2025 Tavernia
attribution name: Tavernia

Cognitive domain-specific impairments and associated risk factors in type 2 diabetes mellitus: a cross-sectional observational study based on neuropsychological assessment from Xiamen, China
type: item
type: AcademicArticle
description: Background Type 2 diabetes mellitus (T2DM) is associated with an increased risk of cognitive impairment, yet limited research has been conducted in subtropical regions of China. Objective To examine the characteristics of cognitive impairment and identify the potential risk factors in patients with T2DM in Xiamen. Methods This cross-sectional observational study included 84 patients with T2DM from Zhongshan Hospital Xiamen University. Patients were grouped based on their Montreal Cognitive Assessment (MoCA) scores into a cognitively impaired group (T2DM-CI group, n = 52) and a cognitively normal group (T2DM-NCI group, n = 32). Multivariate logistic regression was used to identify independent risk factors. Results Among the 52 patients in the T2DM-CI group, the most commonly affected cognitive domains were executive function (82.7%), language (75.0%), memory (61.5%), and attention (48.1%), with 59.6% exhibiting impairments in three or more domains. Compared with the T2DM-NCI group, the T2DM-CI group showed poorer performance in most MoCA subdomains—including visuospatial/executive function, language, delayed recall, abstraction, and orientation—as well as in individual cognitive domain tests (all P < 0.05), except for the Clock Drawing Test. Older age (OR = 1.167, 95% CI [1.045–1.303], P = 0.006) and higher lipoprotein (a) levels (OR = 1.109, 95% CI [1.020–1.205], P = 0.015) were independently associated with cognitive impairment in T2DM patients. Conclusion Cognitive impairment in T2DM affects multiple domains, with executive dysfunction most prominent. Age and elevated lipoprotein(a) may increase risk. Routine cognitive screening is warranted, particularly in older patients and those with vascular risk factors.
format: application/pdf
format: text/html
creator: Xueling Xiao
creator: Luling Chen
creator: Jingqi Liu
creator: Jiayan Cai
creator: Manxiang Deng
subject: Cognitive Disorders
subject: Diabetes and Endocrinology
subject: Neurology
subject: Metabolic Sciences
description: doi:10.7717/peerj.20292
publisher: PeerJ Inc.
rights: © 2025 Xiao et al.
abstract: Background Type 2 diabetes mellitus (T2DM) is associated with an increased risk of cognitive impairment, yet limited research has been conducted in subtropical regions of China. Objective To examine the characteristics of cognitive impairment and identify the potential risk factors in patients with T2DM in Xiamen. Methods This cross-sectional observational study included 84 patients with T2DM from Zhongshan Hospital Xiamen University. Patients were grouped based on their Montreal Cognitive Assessment (MoCA) scores into a cognitively impaired group (T2DM-CI group, n = 52) and a cognitively normal group (T2DM-NCI group, n = 32). Multivariate logistic regression was used to identify independent risk factors. Results Among the 52 patients in the T2DM-CI group, the most commonly affected cognitive domains were executive function (82.7%), language (75.0%), memory (61.5%), and attention (48.1%), with 59.6% exhibiting impairments in three or more domains. Compared with the T2DM-NCI group, the T2DM-CI group showed poorer performance in most MoCA subdomains—including visuospatial/executive function, language, delayed recall, abstraction, and orientation—as well as in individual cognitive domain tests (all P < 0.05), except for the Clock Drawing Test. Older age (OR = 1.167, 95% CI [1.045–1.303], P = 0.006) and higher lipoprotein (a) levels (OR = 1.109, 95% CI [1.020–1.205], P = 0.015) were independently associated with cognitive impairment in T2DM patients. Conclusion Cognitive impairment in T2DM affects multiple domains, with executive dysfunction most prominent. Age and elevated lipoprotein(a) may increase risk. Routine cognitive screening is warranted, particularly in older patients and those with vascular risk factors.
bibliographic citation: Xiao et al. (2025) Cognitive domain-specific impairments and associated risk factors in type 2 diabetes mellitus: a cross-sectional observational study based on neuropsychological assessment from Xiamen, China. PeerJ 13:e20292 https://doi.org/10.7717/peerj.20292
date submitted: 2025-02-18
date accepted: 2025-10-03
issued: 2025-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Xueling
author list: Agent
  family name: Chen
  given name: Luling
author list: Agent
  family name: Liu
  given name: Jingqi
author list: Agent
  family name: Cai
  given name: Jiayan
author list: Agent
  family name: Deng
  given name: Manxiang
doi: 10.7717/peerj.20292
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-04
copyright: ©2025 Xiao et al.
attribution name: Xiao et al.

A machine learning approach to managing game bird introductions
type: item
type: AcademicArticle
description: Effective management of introduced species requires a clear understanding of their habitat requirements. Species distribution models (SDMs) offer a powerful tool for addressing this challenge. We applied seven modeling techniques to predict a suitable habitat for the introduced Chukar Partridge (Alectoris chukar), including artificial neural networks, generalized additive models, k-nearest neighbor, random forests, support vector machines, extreme gradient boosting, and a weighted ensemble approach. Using site-level data on physiography, climate, land cover, and habitat range, we modeled Chukar distributions by simulating historical introduction efforts and extrapolating predictions into surrounding areas to assess cross-regional transferability. Model performance was evaluated using independent, geographically distinct validation datasets. Our results demonstrate that machine learning-based SDMs provide accurate and transferable predictions of Chukar habitat suitability. This study highlights the value of machine learning for predicting establishment success while emphasizing the importance of incorporating species movement behavior and site fidelity into SDM frameworks. Overall, our findings contribute to advancing conservation planning, species reintroductions, and adaptive management strategies.
format: application/pdf
format: text/html
creator: Austin M. Smith
creator: Wendell P. Cropper, Jr
creator: Michael P. Moulton
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Data Mining and Machine Learning
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20291
publisher: PeerJ Inc.
rights: © 2025 Smith et al.
abstract: Effective management of introduced species requires a clear understanding of their habitat requirements. Species distribution models (SDMs) offer a powerful tool for addressing this challenge. We applied seven modeling techniques to predict a suitable habitat for the introduced Chukar Partridge (Alectoris chukar), including artificial neural networks, generalized additive models, k-nearest neighbor, random forests, support vector machines, extreme gradient boosting, and a weighted ensemble approach. Using site-level data on physiography, climate, land cover, and habitat range, we modeled Chukar distributions by simulating historical introduction efforts and extrapolating predictions into surrounding areas to assess cross-regional transferability. Model performance was evaluated using independent, geographically distinct validation datasets. Our results demonstrate that machine learning-based SDMs provide accurate and transferable predictions of Chukar habitat suitability. This study highlights the value of machine learning for predicting establishment success while emphasizing the importance of incorporating species movement behavior and site fidelity into SDM frameworks. Overall, our findings contribute to advancing conservation planning, species reintroductions, and adaptive management strategies.
bibliographic citation: Smith et al. (2025) A machine learning approach to managing game bird introductions. PeerJ 13:e20291 https://doi.org/10.7717/peerj.20291
date submitted: 2025-07-03
date accepted: 2025-10-03
issued: 2025-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Austin M.
author list: Agent
  family name: Cropper, Jr
  given name: Wendell P.
author list: Agent
  family name: Moulton
  given name: Michael P.
doi: 10.7717/peerj.20291
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-04
copyright: ©2025 Smith et al.
attribution name: Smith et al.

Control of wind speed and contact angle on submicron particulate matter sampling
type: item
type: AcademicArticle
description: While particulate matter (PM) instruments are widely used for air quality monitoring and policy development, there is limited research on how wind speed (U0) and contact angle (θ) affect the measurement accuracy of submicron PM, or particles with their diameters ≤ one µm (PM1). This study addresses this gap by employing a wind tunnel experiment with a common sampling system featuring a customized thick-walled cylindrical metal inlet. The results reveal that wind-induced aerosol losses can reach up to 9%, and the sampling efficiency has a negative linear relationship with U0 and a third-order polynomial relationship with cos(θ). This model demonstrates a significant discrepancy with classic models in predicting sampling efficiency, which indicates the inapplicability of classic sampling efficiency models to submicron aerosols. The findings of this study can help correct wind-induced errors, improve sampling protocols, and develop new predictive models, which have implications for improving hazardous air quality warning systems and safeguarding public well-being.
format: application/pdf
format: text/html
creator: Bokun Sun
creator: Ziyang Wang
creator: Jiayun Huang
creator: Yumeng Li
creator: James R. Cooper
creator: Lei Han
creator: Bailiang Li
subject: Environmental Sciences
subject: Atmospheric Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.20235
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: While particulate matter (PM) instruments are widely used for air quality monitoring and policy development, there is limited research on how wind speed (U0) and contact angle (θ) affect the measurement accuracy of submicron PM, or particles with their diameters ≤ one µm (PM1). This study addresses this gap by employing a wind tunnel experiment with a common sampling system featuring a customized thick-walled cylindrical metal inlet. The results reveal that wind-induced aerosol losses can reach up to 9%, and the sampling efficiency has a negative linear relationship with U0 and a third-order polynomial relationship with cos(θ). This model demonstrates a significant discrepancy with classic models in predicting sampling efficiency, which indicates the inapplicability of classic sampling efficiency models to submicron aerosols. The findings of this study can help correct wind-induced errors, improve sampling protocols, and develop new predictive models, which have implications for improving hazardous air quality warning systems and safeguarding public well-being.
bibliographic citation: Sun et al. (2025) Control of wind speed and contact angle on submicron particulate matter sampling. PeerJ 13:e20235 https://doi.org/10.7717/peerj.20235
date submitted: 2025-02-18
date accepted: 2025-09-23
issued: 2025-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Bokun
author list: Agent
  family name: Wang
  given name: Ziyang
author list: Agent
  family name: Huang
  given name: Jiayun
author list: Agent
  family name: Li
  given name: Yumeng
author list: Agent
  family name: Cooper
  given name: James R.
author list: Agent
  family name: Han
  given name: Lei
author list: Agent
  family name: Li
  given name: Bailiang
doi: 10.7717/peerj.20235
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-04
copyright: ©2025 Sun et al.
attribution name: Sun et al.

Incidence, persistence, and clearance of cervical human papillomavirus infection among gynecological outpatients in Kunming, Yunnan, China, 2019–2023: a retrospective cohort study
type: item
type: AcademicArticle
description: Human papillomavirus (HPV), a leading sexually transmitted pathogen, is characterized by persistent infection, which represents a critical risk factor for cervical carcinogenesis. This retrospective cohort study investigated the epidemiology of HPV among 45,149 gynecological outpatients in Yunnan, China (2019–2023). The 12-month cumulative incidence of HPV infection was 36.84%, with the highest rates observed in the 30–49-year age group. HPV-52 was the predominant subtype, followed by HPV-51, -81, -58, and -16. Persistent infection was observed in 55.56% of cases, most frequently involving HPV-42, -52, -58, -81, and -56, with higher rates in individuals younger than 30 and older than 59 years. Overall clearance reached 74.43% and was inversely correlated with age. Rapid clearance was predominantly observed for HPV-26, -83, -11, -82, and -44, whereas high-risk HPV types (HPV-58, HPV-52, HPV-35) and low-risk types (HPV-42, HPV-81, HPV-43) exhibited prolonged persistence. Regional data indicate elevated risks of incident and persistent infections with HPV-58, HPV-52, HPV-42, and HPV-81, with older populations showing greater susceptibility to persistence and younger individuals demonstrating faster clearance. These findings underscore the age-specific dynamics of HPV infection and highlight priority subtypes for regional cervical cancer prevention strategies.
format: application/pdf
format: text/html
creator: Yafei Huang
creator: Xiangcong Wei
creator: Yan Guo
creator: Ting Su
creator: Qiuting Duan
creator: Xin Fan
creator: Jinxiu Wan
creator: Yufan Zhang
creator: Guiqian Zhang
creator: Yi Sun
creator: Ya Xu
subject: Epidemiology
subject: Global Health
subject: Gynecology and Obstetrics
subject: Infectious Diseases
subject: Women’s Health
description: doi:10.7717/peerj.20215
publisher: PeerJ Inc.
rights: © 2025 Huang et al.
abstract: Human papillomavirus (HPV), a leading sexually transmitted pathogen, is characterized by persistent infection, which represents a critical risk factor for cervical carcinogenesis. This retrospective cohort study investigated the epidemiology of HPV among 45,149 gynecological outpatients in Yunnan, China (2019–2023). The 12-month cumulative incidence of HPV infection was 36.84%, with the highest rates observed in the 30–49-year age group. HPV-52 was the predominant subtype, followed by HPV-51, -81, -58, and -16. Persistent infection was observed in 55.56% of cases, most frequently involving HPV-42, -52, -58, -81, and -56, with higher rates in individuals younger than 30 and older than 59 years. Overall clearance reached 74.43% and was inversely correlated with age. Rapid clearance was predominantly observed for HPV-26, -83, -11, -82, and -44, whereas high-risk HPV types (HPV-58, HPV-52, HPV-35) and low-risk types (HPV-42, HPV-81, HPV-43) exhibited prolonged persistence. Regional data indicate elevated risks of incident and persistent infections with HPV-58, HPV-52, HPV-42, and HPV-81, with older populations showing greater susceptibility to persistence and younger individuals demonstrating faster clearance. These findings underscore the age-specific dynamics of HPV infection and highlight priority subtypes for regional cervical cancer prevention strategies.
bibliographic citation: Huang et al. (2025) Incidence, persistence, and clearance of cervical human papillomavirus infection among gynecological outpatients in Kunming, Yunnan, China, 2019–2023: a retrospective cohort study. PeerJ 13:e20215 https://doi.org/10.7717/peerj.20215
date submitted: 2025-05-09
date accepted: 2025-09-19
issued: 2025-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Yafei
author list: Agent
  family name: Wei
  given name: Xiangcong
author list: Agent
  family name: Guo
  given name: Yan
author list: Agent
  family name: Su
  given name: Ting
author list: Agent
  family name: Duan
  given name: Qiuting
author list: Agent
  family name: Fan
  given name: Xin
author list: Agent
  family name: Wan
  given name: Jinxiu
author list: Agent
  family name: Zhang
  given name: Yufan
author list: Agent
  family name: Zhang
  given name: Guiqian
author list: Agent
  family name: Sun
  given name: Yi
author list: Agent
  family name: Xu
  given name: Ya
doi: 10.7717/peerj.20215
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-04
copyright: ©2025 Huang et al.
attribution name: Huang et al.

Knowledge and competence in vestibular rehabilitation: a cross-sectional study of physical therapy interns
type: item
type: AcademicArticle
description: Background Vestibular rehabilitation (VR) is a specialized physical therapy practice area that requires comprehensive knowledge and clinical competence to manage vestibular disorders effectively, which significantly impacts patients’ quality of life. Discrepancies between knowledge and competence among physical therapy interns remain under-researched. Addressing this gap is essential for identifying specific educational deficiencies, improving training programs, and enhancing clinical preparedness. Objective This study aimed to examine the knowledge and competence of Saudi physical therapist (PT) interns in VR. Methods A cross-sectional survey was conducted among PT interns (n = 233), and VR knowledge was assessed through self-reports and objective testing. The questionnaire, developed via the Delphi method, included items specifically designed to assess competence in and knowledge of VR. Statistical analyses included descriptive statistics, multiple response analysis, and multiple linear regression to explore demographic data, knowledge, and competence predictors. The data were analyzed via JASP 18.1.1. Results Competence showed a high mean score of 5.35 out of 8 (67%). In contrast, case report knowledge was low at 0.58/2 (29%), VR tests learned during academic years averaged 4.17 out of 20 (28%), while those learned during the internship averaged 2.43 out of 20 (17%). Similarly, treatment approaches and maneuvers for vestibular-related disorders learned during academic years averaged 2.47 out of 12 (25%), while those learned during the internship averaged 1.69 out of 12 (19%), indicating limited knowledge and skills in vestibular rehabilitation across both academic and clinical training phases. A simultaneous-entry multiple regression indicated that the predictor set significantly explained competence, F(12, 219) = 5.96, p < .001, accounting for 24.6% of the variance (adjusted R2 = .21, RMSE = 1.78). Internship vestibular-test knowledge (B = 0.25, β = .32, p < .00…
format: application/pdf
format: text/html
creator: Danah Alyahya
creator: Arwa Alharbi
creator: Faizan Kashoo
creator: Shaikha Alsaheli
creator: Faisal Mubarak AlMubarak
creator: Rehab Aljuhni
subject: Science and Medical Education
subject: Rehabilitation
description: doi:10.7717/peerj.20213
publisher: PeerJ Inc.
rights: © 2025 Alyahya et al.
abstract: Background Vestibular rehabilitation (VR) is a specialized physical therapy practice area that requires comprehensive knowledge and clinical competence to manage vestibular disorders effectively, which significantly impacts patients’ quality of life. Discrepancies between knowledge and competence among physical therapy interns remain under-researched. Addressing this gap is essential for identifying specific educational deficiencies, improving training programs, and enhancing clinical preparedness. Objective This study aimed to examine the knowledge and competence of Saudi physical therapist (PT) interns in VR. Methods A cross-sectional survey was conducted among PT interns (n = 233), and VR knowledge was assessed through self-reports and objective testing. The questionnaire, developed via the Delphi method, included items specifically designed to assess competence in and knowledge of VR. Statistical analyses included descriptive statistics, multiple response analysis, and multiple linear regression to explore demographic data, knowledge, and competence predictors. The data were analyzed via JASP 18.1.1. Results Competence showed a high mean score of 5.35 out of 8 (67%). In contrast, case report knowledge was low at 0.58/2 (29%), VR tests learned during academic years averaged 4.17 out of 20 (28%), while those learned during the internship averaged 2.43 out of 20 (17%). Similarly, treatment approaches and maneuvers for vestibular-related disorders learned during academic years averaged 2.47 out of 12 (25%), while those learned during the internship averaged 1.69 out of 12 (19%), indicating limited knowledge and skills in vestibular rehabilitation across both academic and clinical training phases. A simultaneous-entry multiple regression indicated that the predictor set significantly explained competence, F(12, 219) = 5.96, p < .001, accounting for 24.6% of the variance (adjusted R2 = .21, RMSE = 1.78). Internship vestibular-test knowledge (B = 0.25, β = .32, p < .00…
bibliographic citation: Alyahya et al. (2025) Knowledge and competence in vestibular rehabilitation: a cross-sectional study of physical therapy interns. PeerJ 13:e20213 https://doi.org/10.7717/peerj.20213
date submitted: 2025-02-20
date accepted: 2025-09-19
issued: 2025-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alyahya
  given name: Danah
author list: Agent
  family name: Alharbi
  given name: Arwa
author list: Agent
  family name: Kashoo
  given name: Faizan
author list: Agent
  family name: Alsaheli
  given name: Shaikha
author list: Agent
  family name: AlMubarak
  given name: Faisal Mubarak
author list: Agent
  family name: Aljuhni
  given name: Rehab
doi: 10.7717/peerj.20213
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-04
copyright: ©2025 Alyahya et al.
attribution name: Alyahya et al.

Geographic disparities and predictors of suicide mortality risk in Florida: spatial scan statistics and negative binomial modeling
type: item
type: AcademicArticle
description: Background Florida ranks 17th in suicide mortality risk in the United States, with 14.8 suicide deaths per 100,000 persons. Geographic disparities in suicide mortality across the US are well-documented and are partly attributed to the uneven distribution of risk factors. However, limited data exist on such disparities and associated predictors within Florida, despite their importance for guiding targeted prevention efforts. This study aimed to investigate county-level geographic disparities in suicide mortality risk in Florida and identify predictors of these disparities. Methods This retrospective ecological study used data from the Florida Department of Health. County-level age-adjusted suicide mortality risks and spatial empirical Bayesian-smoothed risks were calculated for three time periods: 2011–2013, 2014–2016, and 2017–2019. Tango’s spatial scan statistics were applied to identify high-risk clusters. A negative binomial regression model was used to examine county-level predictors of suicide mortality risk for the 2017–2019 period. Results Statewide age-adjusted suicide mortality risk increased from 22.6 to 24.3 per 100,000 persons over the study period. Counties in the northwest, northeast, southwest, and parts of central Florida consistently exhibited high mortality risks. Suicide mortality risk was significantly higher in counties with larger proportions of residents aged 45–64 years and ≥65 years, those reporting excessive drinking, frequent mental distress, or veteran status. Conclusion This study identified geographic disparities and key predictors of suicide mortality risk across Florida counties. These findings can inform policymakers, healthcare providers, and community organizations in designing and implementing targeted suicide prevention programs tailored to the specific needs of high-risk communities.
format: application/pdf
format: text/html
creator: Howard Onyuth
creator: Corey Day
creator: Nirmalendu Deb Nath
creator: Agricola Odoi
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.20075
publisher: PeerJ Inc.
rights: © 2025 Onyuth et al.
abstract: Background Florida ranks 17th in suicide mortality risk in the United States, with 14.8 suicide deaths per 100,000 persons. Geographic disparities in suicide mortality across the US are well-documented and are partly attributed to the uneven distribution of risk factors. However, limited data exist on such disparities and associated predictors within Florida, despite their importance for guiding targeted prevention efforts. This study aimed to investigate county-level geographic disparities in suicide mortality risk in Florida and identify predictors of these disparities. Methods This retrospective ecological study used data from the Florida Department of Health. County-level age-adjusted suicide mortality risks and spatial empirical Bayesian-smoothed risks were calculated for three time periods: 2011–2013, 2014–2016, and 2017–2019. Tango’s spatial scan statistics were applied to identify high-risk clusters. A negative binomial regression model was used to examine county-level predictors of suicide mortality risk for the 2017–2019 period. Results Statewide age-adjusted suicide mortality risk increased from 22.6 to 24.3 per 100,000 persons over the study period. Counties in the northwest, northeast, southwest, and parts of central Florida consistently exhibited high mortality risks. Suicide mortality risk was significantly higher in counties with larger proportions of residents aged 45–64 years and ≥65 years, those reporting excessive drinking, frequent mental distress, or veteran status. Conclusion This study identified geographic disparities and key predictors of suicide mortality risk across Florida counties. These findings can inform policymakers, healthcare providers, and community organizations in designing and implementing targeted suicide prevention programs tailored to the specific needs of high-risk communities.
bibliographic citation: Onyuth et al. (2025) Geographic disparities and predictors of suicide mortality risk in Florida: spatial scan statistics and negative binomial modeling. PeerJ 13:e20075 https://doi.org/10.7717/peerj.20075
date submitted: 2024-10-16
date accepted: 2025-08-22
issued: 2025-11-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Onyuth
  given name: Howard
author list: Agent
  family name: Day
  given name: Corey
author list: Agent
  family name: Deb Nath
  given name: Nirmalendu
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.20075
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-04
copyright: ©2025 Onyuth et al.
attribution name: Onyuth et al.

Serum growth differentiation factor 15 trajectory predicts 28-day mortality in critically ill patients: a multicenter cohort study
type: item
type: AcademicArticle
description: Background Growth differentiation factor 15 (GDF15) has been linked to critical illnesses, particularly cardiovascular and infectious diseases, but its dynamic patterns and prognostic value in critically ill patients remain unclear. This study investigates the predictive utility of serum GDF15 trajectories for 28-day mortality among patients in the intensive care unit (ICU). Methods In this multicenter, prospective cohort study, ICU patients were enrolled, and serum GDF15 trajectories during the first week were analyzed using group-based trajectory modeling (GBTM). The association between trajectory subtypes and 28-day mortality was assessed through hierarchically adjusted multivariable logistic regression. A cumulative index, “GDF15-load,” was introduced to quantify overall GDF15 exposure and compared with the Acute Physiology and Chronic Health Evaluation II (APACHE II) and Sequential Organ Failure Assessment (SOFA) scores. The correlation between initial GDF15 levels (GDF15-D1) and GDF15-load was evaluated using Spearman’s correlation test. Predictive performance was assessed via the area under the receiver operating characteristic curve (AUROC), and feature importance was interpreted using Shapley Additive Explanations (SHAP). Results Among 1,973 patients, 493 comprised the cohort for development with full serum profiles on days 1, 3, and 7. Four GDF15 trajectory subtypes were identified: low-maintenance (LM), medium-maintenance (MM), high-increase (HI), and high-persistent (HP). Trajectory subtypes showed significant differences in inflammatory markers, organ dysfunction, and 28-day mortality, with the HI and HP groups having the worst outcomes. GDF15-load increased progressively from LM to HP and emerged as the most important predictor of 28-day mortality, not inferior to APACHE II and SOFA scores. GDF15-D1 was strongly correlated with GDF15-load (Spearman r = 0.778) and demonstrated robust predictive value, particularly in postoperative ICU patients, where it…
format: application/pdf
format: text/html
creator: Qinxue Wang
creator: Jiawei Wang
creator: Yuhan Zhao
creator: Yuanze Ma
creator: Xiang Li
creator: Xinyi Chang
creator: Nan Zheng
creator: Yong Ji
creator: Yi Han
subject: Emergency and Critical Care
subject: Hematology
description: doi:10.7717/peerj.20317
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Background Growth differentiation factor 15 (GDF15) has been linked to critical illnesses, particularly cardiovascular and infectious diseases, but its dynamic patterns and prognostic value in critically ill patients remain unclear. This study investigates the predictive utility of serum GDF15 trajectories for 28-day mortality among patients in the intensive care unit (ICU). Methods In this multicenter, prospective cohort study, ICU patients were enrolled, and serum GDF15 trajectories during the first week were analyzed using group-based trajectory modeling (GBTM). The association between trajectory subtypes and 28-day mortality was assessed through hierarchically adjusted multivariable logistic regression. A cumulative index, “GDF15-load,” was introduced to quantify overall GDF15 exposure and compared with the Acute Physiology and Chronic Health Evaluation II (APACHE II) and Sequential Organ Failure Assessment (SOFA) scores. The correlation between initial GDF15 levels (GDF15-D1) and GDF15-load was evaluated using Spearman’s correlation test. Predictive performance was assessed via the area under the receiver operating characteristic curve (AUROC), and feature importance was interpreted using Shapley Additive Explanations (SHAP). Results Among 1,973 patients, 493 comprised the cohort for development with full serum profiles on days 1, 3, and 7. Four GDF15 trajectory subtypes were identified: low-maintenance (LM), medium-maintenance (MM), high-increase (HI), and high-persistent (HP). Trajectory subtypes showed significant differences in inflammatory markers, organ dysfunction, and 28-day mortality, with the HI and HP groups having the worst outcomes. GDF15-load increased progressively from LM to HP and emerged as the most important predictor of 28-day mortality, not inferior to APACHE II and SOFA scores. GDF15-D1 was strongly correlated with GDF15-load (Spearman r = 0.778) and demonstrated robust predictive value, particularly in postoperative ICU patients, where it…
bibliographic citation: Wang et al. (2025) Serum growth differentiation factor 15 trajectory predicts 28-day mortality in critically ill patients: a multicenter cohort study. PeerJ 13:e20317 https://doi.org/10.7717/peerj.20317
date submitted: 2025-03-25
date accepted: 2025-10-09
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qinxue
author list: Agent
  family name: Wang
  given name: Jiawei
author list: Agent
  family name: Zhao
  given name: Yuhan
author list: Agent
  family name: Ma
  given name: Yuanze
author list: Agent
  family name: Li
  given name: Xiang
author list: Agent
  family name: Chang
  given name: Xinyi
author list: Agent
  family name: Zheng
  given name: Nan
author list: Agent
  family name: Ji
  given name: Yong
author list: Agent
  family name: Han
  given name: Yi
doi: 10.7717/peerj.20317
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: © 2025 Wang et al.
attribution name: Wang et al.

Comparative dosimetric evaluation of single-beam dual-arc versus dual-beam single-arc volumetric modulated arc therapy strategies in lung stereotactic body radiotherapy using Monaco
type: item
type: AcademicArticle
description: Background and Objective In stereotactic body radiotherapy (SBRT) for lung cancer, the choice of volumetric modulated arc therapy (VMAT) optimization strategy is critical for achieving optimal target dose coverage while minimizing exposure to normal tissues. This study aims to compare the dosimetric performance and plan complexity of two VMAT optimization strategies in Monaco: single-beam dual-arc (1B2A) versus dual-beam single-arc (2B1A). Methods A retrospective analysis was conducted on 50 lung cancer patients treated with SBRT (prescription dose: 50 Gy in 5 fractions). Two VMAT plans were re-optimized using the Monaco treatment planning system: the 1B2A plan (single-beam dual-arc, collimator angle 10°) and the 2B1A plan (dual-beam single-arc, collimator angles 10° and 350°). Dosimetric parameters, including target dose coverage, conformity index (CI), and gradient index (GI), were evaluated for the internal target volume (ITV) and planning target volume (PTV). Dose metrics for organs at risk (OARs) were also analyzed. Plan complexity was assessed based on monitor units (MU), number of control points, complexity index, and integral dose to normal tissues. Results Significant dosimetric differences were observed between the two strategies. When normalized to ensure the prescribed 50 Gy isodose line covers 95% of the PTV volume, the high-dose parameters (D1%, D50%, Dmean) of the ITV and PTV were significantly lower in the 1B2A group compared to the 2B1A group (p < 0.001), indicating superior dose distribution with the 2B1A approach. Although the 1B2A plan exhibited marginally better CI, GI, and low-dose lung sparing (V5–V30), these differences were minimal and clinically insignicant. No substantial dierences were found in the dose sparing of other OARs, including the spinal cord, heart, and ribs. Additionally, the 1B2A plan required signicantly higher MU (+15.5%, p < 0.001) and had greater plan complexity (+9.47%, p < 0.001), suggesting lower treatment efficiency. C…
format: application/pdf
format: text/html
creator: Jieni Ding
creator: Yanqiu Huang
creator: Qiang Li
creator: Weijun Chen
creator: Kainan Shao
subject: Oncology
subject: Radiology and Medical Imaging
subject: Translational Medicine
description: doi:10.7717/peerj.20311
publisher: PeerJ Inc.
rights: © 2025 Ding et al.
abstract: Background and Objective In stereotactic body radiotherapy (SBRT) for lung cancer, the choice of volumetric modulated arc therapy (VMAT) optimization strategy is critical for achieving optimal target dose coverage while minimizing exposure to normal tissues. This study aims to compare the dosimetric performance and plan complexity of two VMAT optimization strategies in Monaco: single-beam dual-arc (1B2A) versus dual-beam single-arc (2B1A). Methods A retrospective analysis was conducted on 50 lung cancer patients treated with SBRT (prescription dose: 50 Gy in 5 fractions). Two VMAT plans were re-optimized using the Monaco treatment planning system: the 1B2A plan (single-beam dual-arc, collimator angle 10°) and the 2B1A plan (dual-beam single-arc, collimator angles 10° and 350°). Dosimetric parameters, including target dose coverage, conformity index (CI), and gradient index (GI), were evaluated for the internal target volume (ITV) and planning target volume (PTV). Dose metrics for organs at risk (OARs) were also analyzed. Plan complexity was assessed based on monitor units (MU), number of control points, complexity index, and integral dose to normal tissues. Results Significant dosimetric differences were observed between the two strategies. When normalized to ensure the prescribed 50 Gy isodose line covers 95% of the PTV volume, the high-dose parameters (D1%, D50%, Dmean) of the ITV and PTV were significantly lower in the 1B2A group compared to the 2B1A group (p < 0.001), indicating superior dose distribution with the 2B1A approach. Although the 1B2A plan exhibited marginally better CI, GI, and low-dose lung sparing (V5–V30), these differences were minimal and clinically insignicant. No substantial dierences were found in the dose sparing of other OARs, including the spinal cord, heart, and ribs. Additionally, the 1B2A plan required signicantly higher MU (+15.5%, p < 0.001) and had greater plan complexity (+9.47%, p < 0.001), suggesting lower treatment efficiency. C…
bibliographic citation: Ding et al. (2025) Comparative dosimetric evaluation of single-beam dual-arc versus dual-beam single-arc volumetric modulated arc therapy strategies in lung stereotactic body radiotherapy using Monaco. PeerJ 13:e20311 https://doi.org/10.7717/peerj.20311
date submitted: 2025-04-22
date accepted: 2025-10-08
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Jieni
author list: Agent
  family name: Huang
  given name: Yanqiu
author list: Agent
  family name: Li
  given name: Qiang
author list: Agent
  family name: Chen
  given name: Weijun
author list: Agent
  family name: Shao
  given name: Kainan
doi: 10.7717/peerj.20311
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Ding et al.
attribution name: Ding et al.

A comparison of spinal and lower extremity biomechanics during maximal and sub-maximal deadlifts among strength-trained women
type: item
type: AcademicArticle
description: Background Previous studies have examined changes in biomechanical variables in response to different deadlift loads, yet, the effect of sub-maximal and maximal loads on potential deviation in lifting technique remain inadequately understood. Methods Therefore, this study compared barbell and joint kinematics, net joint moments (NJMs), and surface electromyography (sEMG) amplitude during 70%, 90%, and 100% of three-repetition maximum (3RM) load using statistical parametric mapping. Twelve strength-trained women (age: 23.18 ± 3.46 years, height: 166.72 ± 2.90 cm, body mass: 68.18 ± 7.67 kg) lifted 72.5 ± 9.3 kg, 93.9 ± 16.6 kg, and 102.9 ± 17.6 kg s at 70%, 90%, and 100% of 3RM deadlifts, respectively. Results The main findings revealed that the maximal load resulted in a significant increase in lower thoracic flexion angles and erector spinae sEMG amplitudes compared to the sub-maximal loads. Additionally, significantly lower hip NJMs were observed with a 70% load compared to 90% and 100% loads. Conclusion Therefore, increasing loads beyond 90% of 3RM might not be necessary if the goal is to train hip extensor strength through deadlifting. Deadlifting loads beyond 90% of 3RM may be achieved by increasing spinal flexion. This posture may allow strength-trained women to lift beyond the strength capacity of their hip extensors during the final repetition of a 3RM deadlift.
format: application/pdf
format: text/html
creator: Andreas H. Gundersen
creator: Roland van den Tillaar
creator: Hallvard Falch
creator: Stian Larsen
subject: Kinesiology
subject: Women’s Health
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.20279
publisher: PeerJ Inc.
rights: © 2025 Gundersen et al.
abstract: Background Previous studies have examined changes in biomechanical variables in response to different deadlift loads, yet, the effect of sub-maximal and maximal loads on potential deviation in lifting technique remain inadequately understood. Methods Therefore, this study compared barbell and joint kinematics, net joint moments (NJMs), and surface electromyography (sEMG) amplitude during 70%, 90%, and 100% of three-repetition maximum (3RM) load using statistical parametric mapping. Twelve strength-trained women (age: 23.18 ± 3.46 years, height: 166.72 ± 2.90 cm, body mass: 68.18 ± 7.67 kg) lifted 72.5 ± 9.3 kg, 93.9 ± 16.6 kg, and 102.9 ± 17.6 kg s at 70%, 90%, and 100% of 3RM deadlifts, respectively. Results The main findings revealed that the maximal load resulted in a significant increase in lower thoracic flexion angles and erector spinae sEMG amplitudes compared to the sub-maximal loads. Additionally, significantly lower hip NJMs were observed with a 70% load compared to 90% and 100% loads. Conclusion Therefore, increasing loads beyond 90% of 3RM might not be necessary if the goal is to train hip extensor strength through deadlifting. Deadlifting loads beyond 90% of 3RM may be achieved by increasing spinal flexion. This posture may allow strength-trained women to lift beyond the strength capacity of their hip extensors during the final repetition of a 3RM deadlift.
bibliographic citation: Gundersen et al. (2025) A comparison of spinal and lower extremity biomechanics during maximal and sub-maximal deadlifts among strength-trained women. PeerJ 13:e20279 https://doi.org/10.7717/peerj.20279
date submitted: 2025-05-07
date accepted: 2025-10-01
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gundersen
  given name: Andreas H.
author list: Agent
  family name: van den Tillaar
  given name: Roland
author list: Agent
  family name: Falch
  given name: Hallvard
author list: Agent
  family name: Larsen
  given name: Stian
doi: 10.7717/peerj.20279
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Gundersen et al.
attribution name: Gundersen et al.

The role of pre-pregnancy overweight in gestational diabetes, hypertension, and macrosomia: a retrospective study
type: item
type: AcademicArticle
description: Purpose Adverse pregnancy outcomes, including gestational diabetes mellitus (GDM), gestational hypertension (GHp), macrosomia, preterm birth, and low birth weight, pose significant risks to maternal and neonatal health. Pre-pregnancy overweight is a modifiable risk factor for these outcomes. However, comprehensive analyses of multiple adverse outcomes and their dose-response relationships with pre-pregnancy body mass index (BMI) remain limited. Methods This retrospective cohort study included 748 women with singleton pregnancies who delivered at Yuyao Maternal and Child Health Hospital from January 1, 2022, to December 31, 2022. Participants were categorized into normal-weight and overweight groups based on pre-pregnancy BMI. Logistic regression models were used to evaluate associations between overweight and adverse pregnancy outcomes, adjusting for confounding variables. Restricted cubic spline (RCS) regression was employed to investigate dose-response relationships between BMI and pregnancy outcomes. Results Pre-pregnancy overweight was significantly associated with higher risks of GDM (adjusted OR = 3.122, 95% CI [1.754–5.557], p < 0.001), GHp (adjusted OR = 2.864, 95% CI [1.566–5.239], p = 0.001), and macrosomia (adjusted OR = 2.119, 95% CI [1.076–4.173], p = 0.030). No significant associations were observed with preterm birth or low birth weight. RCS analysis showed no evidence of nonlinear relationships, indicating that the risk of adverse outcomes increased linearly with BMI. Conclusion Pre-pregnancy overweight is a significant modifiable risk factor for adverse maternal and neonatal outcomes, particularly GDM, GHp, and macrosomia. These findings underscore the importance of integrating BMI monitoring and personalized weight management strategies into pre-pregnancy care programs to mitigate risks and improve maternal and neonatal health outcomes.
format: application/pdf
format: text/html
creator: Sisi Zhu
creator: LiFeng Chen
creator: LiJuan Shen
creator: Xiangxiang Fu
subject: Diabetes and Endocrinology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.20277
publisher: PeerJ Inc.
rights: © 2025 Zhu et al.
abstract: Purpose Adverse pregnancy outcomes, including gestational diabetes mellitus (GDM), gestational hypertension (GHp), macrosomia, preterm birth, and low birth weight, pose significant risks to maternal and neonatal health. Pre-pregnancy overweight is a modifiable risk factor for these outcomes. However, comprehensive analyses of multiple adverse outcomes and their dose-response relationships with pre-pregnancy body mass index (BMI) remain limited. Methods This retrospective cohort study included 748 women with singleton pregnancies who delivered at Yuyao Maternal and Child Health Hospital from January 1, 2022, to December 31, 2022. Participants were categorized into normal-weight and overweight groups based on pre-pregnancy BMI. Logistic regression models were used to evaluate associations between overweight and adverse pregnancy outcomes, adjusting for confounding variables. Restricted cubic spline (RCS) regression was employed to investigate dose-response relationships between BMI and pregnancy outcomes. Results Pre-pregnancy overweight was significantly associated with higher risks of GDM (adjusted OR = 3.122, 95% CI [1.754–5.557], p < 0.001), GHp (adjusted OR = 2.864, 95% CI [1.566–5.239], p = 0.001), and macrosomia (adjusted OR = 2.119, 95% CI [1.076–4.173], p = 0.030). No significant associations were observed with preterm birth or low birth weight. RCS analysis showed no evidence of nonlinear relationships, indicating that the risk of adverse outcomes increased linearly with BMI. Conclusion Pre-pregnancy overweight is a significant modifiable risk factor for adverse maternal and neonatal outcomes, particularly GDM, GHp, and macrosomia. These findings underscore the importance of integrating BMI monitoring and personalized weight management strategies into pre-pregnancy care programs to mitigate risks and improve maternal and neonatal health outcomes.
bibliographic citation: Zhu et al. (2025) The role of pre-pregnancy overweight in gestational diabetes, hypertension, and macrosomia: a retrospective study. PeerJ 13:e20277 https://doi.org/10.7717/peerj.20277
date submitted: 2025-05-16
date accepted: 2025-10-01
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhu
  given name: Sisi
author list: Agent
  family name: Chen
  given name: LiFeng
author list: Agent
  family name: Shen
  given name: LiJuan
author list: Agent
  family name: Fu
  given name: Xiangxiang
doi: 10.7717/peerj.20277
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Zhu et al.
attribution name: Zhu et al.

Investigation of spatiotemporal evolution and driving mechanisms of carbon sources and sinks in dry-hot valleys under extreme climate events: a case study of the Nu River dry-hot valley
type: item
type: AcademicArticle
description: Under global climate change, the rising frequency of extreme weather events profoundly affects ecosystem carbon cycles. However, in the ecologically fragile dry-hot valleys of Southwest China, the response of carbon source-sink dynamics to these extremes remains unclear, which hinders effective regional carbon management. This study investigates the Nu River dry-hot valley, using the Google Earth Engine platform to process multi-source remote sensing and meteorological data from 2001–2024. We established a framework of 15 extreme climate indices and applied Sen-Mann-Kendall trend analysis, Pearson correlation, and threshold regression models to explore the spatiotemporal evolution of carbon dynamics and their non-linear response to extreme climate. Our results show that: (1) The region’s carbon sink capacity displayed a fluctuating but overall increasing trend with significant spatial heterogeneity; areas of substantial increase were concentrated in the southern, low-altitude zones. (2) Extreme climate events triggered non-linear carbon cycle responses by altering hydrothermal conditions. The synergy of high temperatures and intense, short-duration precipitation weakened the carbon sink, whereas dispersed rainfall alleviated drought stress and enhanced carbon fixation. (3) Both extreme temperature and precipitation indices showed clear regulatory thresholds, above which their effects were significantly amplified; this reveals that the carbon cycle in the dry-hot valley is highly sensitive to extreme events and exhibits distinct threshold-driven responses. This research provides a theoretical basis for the mechanisms regulating carbon flux in dry-hot ecosystems under a variable climate and offers crucial scientific support for optimising regional pathways to carbon neutrality and implementing climate-adaptive management.
format: application/pdf
format: text/html
creator: Haojun Sun
creator: Shaoyun Zhang
creator: Shanshan Liu
creator: Liping Zhang
subject: Soil Science
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20268
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Under global climate change, the rising frequency of extreme weather events profoundly affects ecosystem carbon cycles. However, in the ecologically fragile dry-hot valleys of Southwest China, the response of carbon source-sink dynamics to these extremes remains unclear, which hinders effective regional carbon management. This study investigates the Nu River dry-hot valley, using the Google Earth Engine platform to process multi-source remote sensing and meteorological data from 2001–2024. We established a framework of 15 extreme climate indices and applied Sen-Mann-Kendall trend analysis, Pearson correlation, and threshold regression models to explore the spatiotemporal evolution of carbon dynamics and their non-linear response to extreme climate. Our results show that: (1) The region’s carbon sink capacity displayed a fluctuating but overall increasing trend with significant spatial heterogeneity; areas of substantial increase were concentrated in the southern, low-altitude zones. (2) Extreme climate events triggered non-linear carbon cycle responses by altering hydrothermal conditions. The synergy of high temperatures and intense, short-duration precipitation weakened the carbon sink, whereas dispersed rainfall alleviated drought stress and enhanced carbon fixation. (3) Both extreme temperature and precipitation indices showed clear regulatory thresholds, above which their effects were significantly amplified; this reveals that the carbon cycle in the dry-hot valley is highly sensitive to extreme events and exhibits distinct threshold-driven responses. This research provides a theoretical basis for the mechanisms regulating carbon flux in dry-hot ecosystems under a variable climate and offers crucial scientific support for optimising regional pathways to carbon neutrality and implementing climate-adaptive management.
bibliographic citation: Sun et al. (2025) Investigation of spatiotemporal evolution and driving mechanisms of carbon sources and sinks in dry-hot valleys under extreme climate events: a case study of the Nu River dry-hot valley. PeerJ 13:e20268 https://doi.org/10.7717/peerj.20268
date submitted: 2025-05-23
date accepted: 2025-09-30
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Haojun
author list: Agent
  family name: Zhang
  given name: Shaoyun
author list: Agent
  family name: Liu
  given name: Shanshan
author list: Agent
  family name: Zhang
  given name: Liping
doi: 10.7717/peerj.20268
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Sun et al.
attribution name: Sun et al.

From trace to trace maker: Oligocene–Miocene coprolites of southern Poland and their potential producers
type: item
type: AcademicArticle
description: In this paper we describe coprolites from deep-marine Oligocene sediments, shallow- and deep-marine Miocene deposits, as well as Miocene continental environments in southern and central Poland. The Oligocene and Miocene coprolites from marine environments (hereinafter referred to as M) are classified into six morphotypes: (M1) sinusoidal, (M2) elongated and straight, (M3) curved, (M4) irregular, (M5) S-shaped, and (M6) oval. Sinusoidal coprolites, previously interpreted as originating from predatory fish (e.g., Palimphyes, Oligophus, and indeterminate taxa), are reinterpreted here, based on actualistic observations, as crustacean (crab) faeces. Morphotypes (M2)–(M5) are attributed to fish, while the oval type (M6) is tentatively linked to columbid-like birds, although alternative producers cannot be excluded. Miocene deep-sea coprolites are represented by relatively long, complex fecal masses composed of constricted strings, suggesting holothurians or cephalopods as potential producers. Elongated Miocene coprolites from shallow-water environments are likely to have been produced by teleost fish - most likely Sparidae - or by sharks. However, other vertebrates, including toothed and toothless cetaceans and porpoises, cannot be ruled out. The terrestrial Miocene specimens include five morphotypes (hereinafter referred to as T-terrestrial, T1–T7): (T1) oval, (T2) sinusoidal, (T3) elongated with two submorphotypes (T3/1–siderite individuals and T3/2–apatite individuals), (T4) S-shaped, and (T5) irregular. They are interpreted as coprolites likely produced by snakes (T1–T3/1, T4, T5), and small mammals such as Sciuridae and/or Chiropteridae (T3/2). Overall, these data provide new insights into the diversity of post-Mesozoic coprolites and refine our understanding of their producers and associated ecosystems in Central Europe.
format: application/pdf
format: text/html
creator: Tomasz Brachaniec
creator: Dorota Środek
creator: Mateusz Salamon
creator: Michał Bugajski
creator: Piotr Duda
creator: Adam Danielak
creator: Magdalena Janiszewska
creator: Grzegorz Sadlok
creator: Wojciech Kuśnierczyk
subject: Ecology
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.20242
publisher: PeerJ Inc.
rights: © 2025 Brachaniec et al.
abstract: In this paper we describe coprolites from deep-marine Oligocene sediments, shallow- and deep-marine Miocene deposits, as well as Miocene continental environments in southern and central Poland. The Oligocene and Miocene coprolites from marine environments (hereinafter referred to as M) are classified into six morphotypes: (M1) sinusoidal, (M2) elongated and straight, (M3) curved, (M4) irregular, (M5) S-shaped, and (M6) oval. Sinusoidal coprolites, previously interpreted as originating from predatory fish (e.g., Palimphyes, Oligophus, and indeterminate taxa), are reinterpreted here, based on actualistic observations, as crustacean (crab) faeces. Morphotypes (M2)–(M5) are attributed to fish, while the oval type (M6) is tentatively linked to columbid-like birds, although alternative producers cannot be excluded. Miocene deep-sea coprolites are represented by relatively long, complex fecal masses composed of constricted strings, suggesting holothurians or cephalopods as potential producers. Elongated Miocene coprolites from shallow-water environments are likely to have been produced by teleost fish - most likely Sparidae - or by sharks. However, other vertebrates, including toothed and toothless cetaceans and porpoises, cannot be ruled out. The terrestrial Miocene specimens include five morphotypes (hereinafter referred to as T-terrestrial, T1–T7): (T1) oval, (T2) sinusoidal, (T3) elongated with two submorphotypes (T3/1–siderite individuals and T3/2–apatite individuals), (T4) S-shaped, and (T5) irregular. They are interpreted as coprolites likely produced by snakes (T1–T3/1, T4, T5), and small mammals such as Sciuridae and/or Chiropteridae (T3/2). Overall, these data provide new insights into the diversity of post-Mesozoic coprolites and refine our understanding of their producers and associated ecosystems in Central Europe.
bibliographic citation: Brachaniec et al. (2025) From trace to trace maker: Oligocene–Miocene coprolites of southern Poland and their potential producers. PeerJ 13:e20242 https://doi.org/10.7717/peerj.20242
date submitted: 2025-05-14
date accepted: 2025-09-24
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brachaniec
  given name: Tomasz
author list: Agent
  family name: Środek
  given name: Dorota
author list: Agent
  family name: Salamon
  given name: Mateusz
author list: Agent
  family name: Bugajski
  given name: Michał
author list: Agent
  family name: Duda
  given name: Piotr
author list: Agent
  family name: Danielak
  given name: Adam
author list: Agent
  family name: Janiszewska
  given name: Magdalena
author list: Agent
  family name: Sadlok
  given name: Grzegorz
author list: Agent
  family name: Kuśnierczyk
  given name: Wojciech
doi: 10.7717/peerj.20242
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Brachaniec et al.
attribution name: Brachaniec et al.

Hidden microalgae diversity in reef systems: reanalysis of coral microbiomes reveals spatial patterns of coral-associated plastid communities in the Southwestern Atlantic Ocean (SWAO)
type: item
type: AcademicArticle
description: The microbial community associated with corals plays a critical role in reef ecosystems, yet studies mainly focus on prokaryotes and Symbiodiniaceae, overlooking other oxygen-evolving photosynthetic eukaryotes. This leaves a knowledge gap regarding potentially important microbiome members. Here, we revisited coral microbiome datasets to investigate the diversity of plastid-bearing eukaryotes associated with Southwestern Atlantic Ocean (SWAO) corals. We compiled an inventory of plastid-bearing communities, uncovering their diversity and exploring ecological patterns. We further applied this approach to analyze the plastidiomes (plastid-bearing communities) of corals from the Abrolhos Bank, the largest reef system in the region, as a case study. A systematic literature review of 16S rDNA-based coral microbiome was conducted, excluding studies lacking plastid 16S sequences. The search made in PubMed resulted in 19 studies reporting corals sampled from 2009 to 2022, which were compiled and reanalyzed. Sequences of chloroplast origin (Silva 132) were further taxonomically classified by consensus-BLASTn search with the PR2 plastid 16S database. The dataset encompassed reef water and coral microbiomes from eight coral species, emphasizing the genus Mussismilia. A total of 272 amplicon libraries yielded 707,949 plastid sequences, identifying 196 algal genera across 41 classes. Reef water and coral plastid communities differed markedly. Ostreobium (81%) and Calliarthron (49%) were the most prevalent genera in coral samples. Diatoms were common (>40% of samples) in the water and in corals, whereas corallicolids were exclusive to corals (31.8%). The Abrolhos case study revealed geographic variation in Mussismilia harttii plastidiomes, which were less diverse than those in the water column. Coral indicator taxa included Ostreobium, corallicolids, Navicula, and Amphora. Our findings identify plastidiome variations and their implications for the coral host. Lipid-rich diatoms pre…
format: application/pdf
format: text/html
creator: Clara P. Pires
creator: Livia B. Villela
creator: Rodrigo L. Moura
creator: Paulo S. Salomon
creator: Arthur W. Silva-Lima
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.20116
publisher: PeerJ Inc.
rights: © 2025 Pires et al.
abstract: The microbial community associated with corals plays a critical role in reef ecosystems, yet studies mainly focus on prokaryotes and Symbiodiniaceae, overlooking other oxygen-evolving photosynthetic eukaryotes. This leaves a knowledge gap regarding potentially important microbiome members. Here, we revisited coral microbiome datasets to investigate the diversity of plastid-bearing eukaryotes associated with Southwestern Atlantic Ocean (SWAO) corals. We compiled an inventory of plastid-bearing communities, uncovering their diversity and exploring ecological patterns. We further applied this approach to analyze the plastidiomes (plastid-bearing communities) of corals from the Abrolhos Bank, the largest reef system in the region, as a case study. A systematic literature review of 16S rDNA-based coral microbiome was conducted, excluding studies lacking plastid 16S sequences. The search made in PubMed resulted in 19 studies reporting corals sampled from 2009 to 2022, which were compiled and reanalyzed. Sequences of chloroplast origin (Silva 132) were further taxonomically classified by consensus-BLASTn search with the PR2 plastid 16S database. The dataset encompassed reef water and coral microbiomes from eight coral species, emphasizing the genus Mussismilia. A total of 272 amplicon libraries yielded 707,949 plastid sequences, identifying 196 algal genera across 41 classes. Reef water and coral plastid communities differed markedly. Ostreobium (81%) and Calliarthron (49%) were the most prevalent genera in coral samples. Diatoms were common (>40% of samples) in the water and in corals, whereas corallicolids were exclusive to corals (31.8%). The Abrolhos case study revealed geographic variation in Mussismilia harttii plastidiomes, which were less diverse than those in the water column. Coral indicator taxa included Ostreobium, corallicolids, Navicula, and Amphora. Our findings identify plastidiome variations and their implications for the coral host. Lipid-rich diatoms pre…
bibliographic citation: Pires et al. (2025) Hidden microalgae diversity in reef systems: reanalysis of coral microbiomes reveals spatial patterns of coral-associated plastid communities in the Southwestern Atlantic Ocean (SWAO). PeerJ 13:e20116 https://doi.org/10.7717/peerj.20116
date submitted: 2024-07-18
date accepted: 2025-09-01
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pires
  given name: Clara P.
author list: Agent
  family name: Villela
  given name: Livia B.
author list: Agent
  family name: Moura
  given name: Rodrigo L.
author list: Agent
  family name: Salomon
  given name: Paulo S.
author list: Agent
  family name: Silva-Lima
  given name: Arthur W.
doi: 10.7717/peerj.20116
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: © 2025 Pires et al.
attribution name: Pires et al.

Predation experiments with 3D-printed lizard models yield limited responses in pheasants
type: item
type: AcademicArticle
description: Animal colouration has been viewed as an adaptation shaped by both abiotic and biotic factors, balancing sexual attractiveness against predation risk. In studying predator-prey dynamics, using 3D models as prey surrogates is common, but material constraints can affect outcomes in both natural and seminatural settings. Here, we utilized 3D-printed models representing three colour morphs of sand lizards (Lacerta agilis) to investigate interactions with captive-bred pheasants (Phasianus colchicus) utilizing forced exploration experiments in an outdoor arena fitted with a grass carpet. The models adequately represented the lizard colouration across a reflectance spectral range of 330–800 nm. Our findings indicate that the pheasants generally exhibited a minimal response to static models, with significant differences observed only in younger birds (7–12 weeks old), demonstrating a higher alert response than adults. No effects were found relating to the colour morph or sex of the lizard models. These results suggest that immobile 3D-printed prey models may be insufficient to trigger natural predator responses in this predator-prey system, highlighting potential limitations of static models in eliciting predator reaction.
format: application/pdf
format: text/html
creator: Radovan Smolinský
creator: Ivo Adam
creator: Zuzana Hiadlovská
creator: Shubhra Sau
creator: Pavel Škrabánek
creator: Natália Martínková
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.20103
publisher: PeerJ Inc.
rights: © 2025 Smolinský et al.
abstract: Animal colouration has been viewed as an adaptation shaped by both abiotic and biotic factors, balancing sexual attractiveness against predation risk. In studying predator-prey dynamics, using 3D models as prey surrogates is common, but material constraints can affect outcomes in both natural and seminatural settings. Here, we utilized 3D-printed models representing three colour morphs of sand lizards (Lacerta agilis) to investigate interactions with captive-bred pheasants (Phasianus colchicus) utilizing forced exploration experiments in an outdoor arena fitted with a grass carpet. The models adequately represented the lizard colouration across a reflectance spectral range of 330–800 nm. Our findings indicate that the pheasants generally exhibited a minimal response to static models, with significant differences observed only in younger birds (7–12 weeks old), demonstrating a higher alert response than adults. No effects were found relating to the colour morph or sex of the lizard models. These results suggest that immobile 3D-printed prey models may be insufficient to trigger natural predator responses in this predator-prey system, highlighting potential limitations of static models in eliciting predator reaction.
bibliographic citation: Smolinský et al. (2025) Predation experiments with 3D-printed lizard models yield limited responses in pheasants. PeerJ 13:e20103 https://doi.org/10.7717/peerj.20103
date submitted: 2025-06-20
date accepted: 2025-08-27
issued: 2025-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smolinský
  given name: Radovan
author list: Agent
  family name: Adam
  given name: Ivo
author list: Agent
  family name: Hiadlovská
  given name: Zuzana
author list: Agent
  family name: Sau
  given name: Shubhra
author list: Agent
  family name: Škrabánek
  given name: Pavel
author list: Agent
  family name: Martínková
  given name: Natália
doi: 10.7717/peerj.20103
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-03
copyright: ©2025 Smolinský et al.
attribution name: Smolinský et al.

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