PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The effects of naproxen sodium on the growth, reproduction, survival, and feeding of a freshwater pond snail
items: Prediction of ACL injury incidence and analysis of key features in basketball players based on multi-algorithm models
items: Metabarcoding analysis reveals hidden eukaryotic plankton biodiversity in the Ross Sea, Antarctica
items: Identification of diabetes related phenotype and diagnostic biomarkers in coronary artery disease
items: Comparison of supervised versus home-based exercise programs following platelet-rich plasma injections in knee osteoarthritis: clinical outcomes from quasi-experimental study
items: Metabolic profile alterations in juvenile rats with bladder overactivity induced by short-term high-fructose intake
items: rtpcr: a package for statistical analysis and graphical presentation of qPCR data in R
items: Extraction, identification and component analysis of exosome-like nanovesicles in Anoectochilus roxburghii (Wall.) Lindl.
items: Association of sociodemographic factors, lifestyle behaviors, anthropometric measures, and cardiometabolic health markers with blood pressure in adolescents: a cross-sectional analysis
items: Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor

The effects of naproxen sodium on the growth, reproduction, survival, and feeding of a freshwater pond snail
type: item
type: AcademicArticle
description: Over-the-counter drugs are emerging contaminants in the environment. These contaminants often affect aquatic communities, including freshwater invertebrates. Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly found in aquatic ecosystems worldwide and have documented negative effects on aquatic organisms. Naproxen is often suggested as a more environmentally friendly alternative due to less bioconcentration in fish. However, studies have yet to test the effects of naproxen on freshwater molluscs. This study exposed pond snails, Physa spp., to three nominal levels of naproxen sodium, 100 µg/L, 1,000 µg/L and 10,000 µg/L, along with a control, over a month-long experiment. We measured snail growth, survival, reproduction, and feeding. Naproxen reduced snail survival across all levels of naproxen exposure and the rate that snails fed at the highest level of naproxen. However, we did not detect an effect of naproxen on snail growth or reproduction rates, even at pollution levels well above those observed in natural systems. Naproxen reduced the grazing of Physa spp. only at our highest concentration, but reduced survival by at least 50% across all concentrations.
format: application/pdf
format: text/html
creator: Rachel Becker
creator: Elizabeth Hamman
subject: Ecology
subject: Ecotoxicology
subject: Freshwater Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.20163
publisher: PeerJ Inc.
rights: © 2025 Becker and Hamman
abstract: Over-the-counter drugs are emerging contaminants in the environment. These contaminants often affect aquatic communities, including freshwater invertebrates. Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly found in aquatic ecosystems worldwide and have documented negative effects on aquatic organisms. Naproxen is often suggested as a more environmentally friendly alternative due to less bioconcentration in fish. However, studies have yet to test the effects of naproxen on freshwater molluscs. This study exposed pond snails, Physa spp., to three nominal levels of naproxen sodium, 100 µg/L, 1,000 µg/L and 10,000 µg/L, along with a control, over a month-long experiment. We measured snail growth, survival, reproduction, and feeding. Naproxen reduced snail survival across all levels of naproxen exposure and the rate that snails fed at the highest level of naproxen. However, we did not detect an effect of naproxen on snail growth or reproduction rates, even at pollution levels well above those observed in natural systems. Naproxen reduced the grazing of Physa spp. only at our highest concentration, but reduced survival by at least 50% across all concentrations.
bibliographic citation: Becker et al. (2025) The effects of naproxen sodium on the growth, reproduction, survival, and feeding of a freshwater pond snail. PeerJ 13:e20163 https://doi.org/10.7717/peerj.20163
date submitted: 2024-12-04
date accepted: 2025-09-10
issued: 2025-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Becker
  given name: Rachel
author list: Agent
  family name: Hamman
  given name: Elizabeth
doi: 10.7717/peerj.20163
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-14
copyright: ©2025 Becker and Hamman
attribution name: Becker and Hamman

Prediction of ACL injury incidence and analysis of key features in basketball players based on multi-algorithm models
type: item
type: AcademicArticle
description: Background Basketball players are a high-risk group for anterior cruciate ligament (ACL) injuries. This study aimed to identify the critical factors contributing to ACL injuries in male basketball players and evaluate the performance of machine learning (ML) algorithms in injury prediction. Methodology This study protocol was registered with International Standard Registered Clinical/soCial sTudy Number (ISRCTN) (Registration number: 18009799). A total of 104 male collegiate basketball players volunteered to participate in this study. Data on the athletes’ profile, physical functions, basketball-specific skills, biomechanics, and electromyography (EMG) of seven lower limb muscles during unanticipated side-cutting maneuvers were collected. A 12-month follow-up was conducted to compare these variables between the injured (n = 11) and non-injured (n = 93) groups. Only the variables with significant differences between the groups were included in the predictive modeling. Results The performance of machine learning models in predicting ACL injury risk was assessed using the area under the curve (AUC) of the receiver operating characteristic (ROC). The AUC-ROC values ranged from 0.66 to 0.80, with the random forest algorithm achieving the highest performance (AUC-ROC = 0.80). The most influential predicting feature observed during the emergency stop phase, included a greater knee flexion moment, reduced knee flexion angle, increased backward ground reaction force, and increased activation of the vastus lateralis muscle. Conclusion The random forest model demonstrated superior predictive performance, providing valuable insights into the key risk factors associated with ACL injury among male basketball players. This study highlighted the importance of biomechanical testing based on sport-specific movements to accurately predict the ACL injury risk.
format: application/pdf
format: text/html
creator: Longfei Guo
creator: Zhilei Cui
creator: Wei Ping Loh
creator: Shazlin Shaharudin
subject: Data Mining and Machine Learning
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.20141
publisher: PeerJ Inc.
rights: © 2025 Guo et al.
abstract: Background Basketball players are a high-risk group for anterior cruciate ligament (ACL) injuries. This study aimed to identify the critical factors contributing to ACL injuries in male basketball players and evaluate the performance of machine learning (ML) algorithms in injury prediction. Methodology This study protocol was registered with International Standard Registered Clinical/soCial sTudy Number (ISRCTN) (Registration number: 18009799). A total of 104 male collegiate basketball players volunteered to participate in this study. Data on the athletes’ profile, physical functions, basketball-specific skills, biomechanics, and electromyography (EMG) of seven lower limb muscles during unanticipated side-cutting maneuvers were collected. A 12-month follow-up was conducted to compare these variables between the injured (n = 11) and non-injured (n = 93) groups. Only the variables with significant differences between the groups were included in the predictive modeling. Results The performance of machine learning models in predicting ACL injury risk was assessed using the area under the curve (AUC) of the receiver operating characteristic (ROC). The AUC-ROC values ranged from 0.66 to 0.80, with the random forest algorithm achieving the highest performance (AUC-ROC = 0.80). The most influential predicting feature observed during the emergency stop phase, included a greater knee flexion moment, reduced knee flexion angle, increased backward ground reaction force, and increased activation of the vastus lateralis muscle. Conclusion The random forest model demonstrated superior predictive performance, providing valuable insights into the key risk factors associated with ACL injury among male basketball players. This study highlighted the importance of biomechanical testing based on sport-specific movements to accurately predict the ACL injury risk.
bibliographic citation: Guo et al. (2025) Prediction of ACL injury incidence and analysis of key features in basketball players based on multi-algorithm models. PeerJ 13:e20141 https://doi.org/10.7717/peerj.20141
date submitted: 2025-02-17
date accepted: 2025-09-04
issued: 2025-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Longfei
author list: Agent
  family name: Cui
  given name: Zhilei
author list: Agent
  family name: Loh
  given name: Wei Ping
author list: Agent
  family name: Shaharudin
  given name: Shazlin
doi: 10.7717/peerj.20141
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-14
copyright: ©2025 Guo et al.
attribution name: Guo et al.

Metabarcoding analysis reveals hidden eukaryotic plankton biodiversity in the Ross Sea, Antarctica
type: item
type: AcademicArticle
description: Background Environmental DNA (eDNA) analysis is a highly sensitive, non-destructive method that enables the detection of various species through DNA shed into environmental samples without requiring direct organism collection. This study sought to investigate the biodiversity and community structure of eukaryotic plankton, including phytoplankton and zooplankton, in the Ross Sea marine protected area (RSR MPA) using eDNA metabarcoding analysis. By examining their spatial and vertical distributions, the study underscores the importance of continuous monitoring for the conservation of the RSR MPA. Methods We collected 48 seawater samples from 16 sites in the Ross Sea region for eDNA metabarcoding analysis, targeting the 18S rRNA gene region of eukaryotic plankton in Antarctica. Bioinformatic processing and taxonomic classification were conducted to assess the diversity and community composition of phytoplankton and zooplankton. Results Phytoplankton communities were primarily composed of six phyla with their distribution patterns and the grouping of samples with similar community structures was found to be shaped by the ocean currents of the RSR MPA and various environmental factors, such as salinity and dissolved oxygen levels. Zooplankton communities consisted of 18 major taxonomic groups, exhibiting distinct horizontal and vertical distribution patterns with differences in taxonomic community structure and species diversity across depth groups. Notably, previously undetected Antarctic species were identified in the Ross Sea region, demonstrating the effectiveness of eDNA in revealing hidden biodiversity. Conclusions Analyzing eukaryotic plankton communities in the vast and extreme Antarctic environment based on eDNA has proven to be highly efficient, enabling the detection of a greater number of species, including those that were difficult to identify in previous studies. It was observed that in the Ross Sea Marine Protected Area, various species form distinct comm…
format: application/pdf
format: text/html
creator: Soyun Choi
creator: Eunkyung Choi
creator: Minjoo Cho
creator: Seung Jae Lee
creator: Inseo Kim
creator: Doyoon Shin
creator: Jangyeon Kim
creator: Hyoung Sul La
creator: Jae-Sung Rhee
creator: Jeong-Hoon Kim
creator: Hyun Park
subject: Biodiversity
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.20118
publisher: PeerJ Inc.
rights: © 2025 Choi et al.
abstract: Background Environmental DNA (eDNA) analysis is a highly sensitive, non-destructive method that enables the detection of various species through DNA shed into environmental samples without requiring direct organism collection. This study sought to investigate the biodiversity and community structure of eukaryotic plankton, including phytoplankton and zooplankton, in the Ross Sea marine protected area (RSR MPA) using eDNA metabarcoding analysis. By examining their spatial and vertical distributions, the study underscores the importance of continuous monitoring for the conservation of the RSR MPA. Methods We collected 48 seawater samples from 16 sites in the Ross Sea region for eDNA metabarcoding analysis, targeting the 18S rRNA gene region of eukaryotic plankton in Antarctica. Bioinformatic processing and taxonomic classification were conducted to assess the diversity and community composition of phytoplankton and zooplankton. Results Phytoplankton communities were primarily composed of six phyla with their distribution patterns and the grouping of samples with similar community structures was found to be shaped by the ocean currents of the RSR MPA and various environmental factors, such as salinity and dissolved oxygen levels. Zooplankton communities consisted of 18 major taxonomic groups, exhibiting distinct horizontal and vertical distribution patterns with differences in taxonomic community structure and species diversity across depth groups. Notably, previously undetected Antarctic species were identified in the Ross Sea region, demonstrating the effectiveness of eDNA in revealing hidden biodiversity. Conclusions Analyzing eukaryotic plankton communities in the vast and extreme Antarctic environment based on eDNA has proven to be highly efficient, enabling the detection of a greater number of species, including those that were difficult to identify in previous studies. It was observed that in the Ross Sea Marine Protected Area, various species form distinct comm…
bibliographic citation: Choi et al. (2025) Metabarcoding analysis reveals hidden eukaryotic plankton biodiversity in the Ross Sea, Antarctica. PeerJ 13:e20118 https://doi.org/10.7717/peerj.20118
date submitted: 2025-05-27
date accepted: 2025-09-01
issued: 2025-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Soyun
author list: Agent
  family name: Choi
  given name: Eunkyung
author list: Agent
  family name: Cho
  given name: Minjoo
author list: Agent
  family name: Lee
  given name: Seung Jae
author list: Agent
  family name: Kim
  given name: Inseo
author list: Agent
  family name: Shin
  given name: Doyoon
author list: Agent
  family name: Kim
  given name: Jangyeon
author list: Agent
  family name: La
  given name: Hyoung Sul
author list: Agent
  family name: Rhee
  given name: Jae-Sung
author list: Agent
  family name: Kim
  given name: Jeong-Hoon
author list: Agent
  family name: Park
  given name: Hyun
doi: 10.7717/peerj.20118
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-14
copyright: ©2025 Choi et al.
attribution name: Choi et al.

Identification of diabetes related phenotype and diagnostic biomarkers in coronary artery disease
type: item
type: AcademicArticle
description: Background Diabetes mellitus (DM) and coronary artery disease (CAD) are closely interrelated clinical conditions. However, the combination analysis based on DM related CAD diagnostic model remains a gap. The primary objective of this study was to identify diagnostic models and diagnostic markers for CAD based on the association of diabetic phenotypes and attempt to explore them further in a mouse model. Methods We used data integration as well as multiple datasets for both coronary artery disease and diabetes to exclude bias as well as to improve reliability. We employed the least absolute shrinkage and selection operator (LASSO) regression algorithms to construct the CAD diagnostic model. Furthermore, we established mouse CAD model (low-density lipoprotein receptor deficient mice with high fat diet) to explore the crosstalk between the screened biomarkers and severe CAD progress. Results The intersecting genes from differential analysis and weighted correlation network analysis (WGCNA) results yielded 32 diabetes-related biomarkers. We then identified two diabetes-related phenotypes through the consensus clustering in CAD patients. Microenvironmental analysis revealed that phenotype 1 exhibited higher expression of most cytokines, inflammatory factors, interleukins, and related receptors. Immune cell composition in phenotype 1 showed increased infiltration compared to phenotype 2. The LASSO regression identified 16 diabetes-related genes and we further constructed a diagnostic model based on these genes, which the area under the curve (AUC) reached 0.8. Additionally, single cell immune analysis exhibited the location of these genes. KCNQ1, ATP6V1B1, MTDH, and ITPK1 were predominantly located in macrophages, indicating their potential in regulating macrophage during myocardial injury. Furthermore, We elucidated that KCNQ1 and ITPK1 exhibited high expression level in mouse CAD model in tissue level. exhibited similar expression trends with macrophage biomarkers (CD31…
format: application/pdf
format: text/html
creator: Gulandanmu Aihemaiti
creator: Abulikemu Abula
creator: Junyi Luo
creator: Qian Zhao
creator: Ning Song
creator: Fen Liu
creator: Niyaziaili Adili
creator: Yining Yang
creator: Xiaomei Li
subject: Bioinformatics
subject: Biotechnology
subject: Cardiology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.20117
publisher: PeerJ Inc.
rights: © 2025 Aihemaiti et al.
abstract: Background Diabetes mellitus (DM) and coronary artery disease (CAD) are closely interrelated clinical conditions. However, the combination analysis based on DM related CAD diagnostic model remains a gap. The primary objective of this study was to identify diagnostic models and diagnostic markers for CAD based on the association of diabetic phenotypes and attempt to explore them further in a mouse model. Methods We used data integration as well as multiple datasets for both coronary artery disease and diabetes to exclude bias as well as to improve reliability. We employed the least absolute shrinkage and selection operator (LASSO) regression algorithms to construct the CAD diagnostic model. Furthermore, we established mouse CAD model (low-density lipoprotein receptor deficient mice with high fat diet) to explore the crosstalk between the screened biomarkers and severe CAD progress. Results The intersecting genes from differential analysis and weighted correlation network analysis (WGCNA) results yielded 32 diabetes-related biomarkers. We then identified two diabetes-related phenotypes through the consensus clustering in CAD patients. Microenvironmental analysis revealed that phenotype 1 exhibited higher expression of most cytokines, inflammatory factors, interleukins, and related receptors. Immune cell composition in phenotype 1 showed increased infiltration compared to phenotype 2. The LASSO regression identified 16 diabetes-related genes and we further constructed a diagnostic model based on these genes, which the area under the curve (AUC) reached 0.8. Additionally, single cell immune analysis exhibited the location of these genes. KCNQ1, ATP6V1B1, MTDH, and ITPK1 were predominantly located in macrophages, indicating their potential in regulating macrophage during myocardial injury. Furthermore, We elucidated that KCNQ1 and ITPK1 exhibited high expression level in mouse CAD model in tissue level. exhibited similar expression trends with macrophage biomarkers (CD31…
bibliographic citation: Aihemaiti et al. (2025) Identification of diabetes related phenotype and diagnostic biomarkers in coronary artery disease. PeerJ 13:e20117 https://doi.org/10.7717/peerj.20117
date submitted: 2024-11-11
date accepted: 2025-09-01
issued: 2025-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Aihemaiti
  given name: Gulandanmu
author list: Agent
  family name: Abula
  given name: Abulikemu
author list: Agent
  family name: Luo
  given name: Junyi
author list: Agent
  family name: Zhao
  given name: Qian
author list: Agent
  family name: Song
  given name: Ning
author list: Agent
  family name: Liu
  given name: Fen
author list: Agent
  family name: Adili
  given name: Niyaziaili
author list: Agent
  family name: Yang
  given name: Yining
author list: Agent
  family name: Li
  given name: Xiaomei
doi: 10.7717/peerj.20117
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-14
copyright: ©2025 Aihemaiti et al.
attribution name: Aihemaiti et al.

Comparison of supervised versus home-based exercise programs following platelet-rich plasma injections in knee osteoarthritis: clinical outcomes from quasi-experimental study
type: item
type: AcademicArticle
description: Background Knee osteoarthritis (OA) is characterized by severe pain and decreased range of motion (ROM), mostly managed with conservative treatments. Therapies like platelet-rich plasma (PRP) intra-articular injections have gained fame for pain relief when surgery is a last resort. Objectives To compare the effectiveness of a supervised exercise program versus a home-based exercise program following PRP injections in terms of pain relief, ROM improvement, and disability reduction in knee osteoarthritis patients. Methods A quasi-experimental design was employed, enrolling 32 patients diagnosed with knee OA cases (age range: 40–60 years; 59% female), divided into two groups: a supervised exercise group (n = 16) and an unsupervised/home-based exercise group (n = 16). Both groups received two PRP injections spaced 15 days apart. The supervised group followed a structured exercise protocol, including cold packs post-injection for pain management. The program comprises three sessions per week for one month. The unsupervised group received similar exercises to be performed independently at home. Data analysis was conducted using parametric and non-parametric statistical methods based on data distribution. Results Both groups exhibited significant improvements from baseline to post-intervention in pain, ROM, and functional status (p < 0.05). The supervised exercise group demonstrated superior outcomes in pain reduction, knee flexion ROM, and Knee Injury and Osteoarthritis Outcome Score (KOOS). However, no significant difference was observed between groups for knee extension ROM (p = 0.378). Conclusion Both supervised and unsupervised exercise programs improved outcomes in knee OA patients following PRP injections; the supervised program showed greater pain relief, flexion ROM, and functional status. However, no significant difference was observed in knee extension ROM between the two groups.
format: application/pdf
format: text/html
creator: Ghalia Safdar
creator: Mubin Mustafa Kiyani
creator: Salman Ahmed Saleem
creator: Wajeeha Irfan Qureshi
creator: Shahid Bashir
creator: Turki Abualait
creator: Hamid Khan
creator: Abdul Ghafoor Sajjad
subject: Clinical Trials
subject: Orthopedics
subject: Rehabilitation
description: doi:10.7717/peerj.19971
publisher: PeerJ Inc.
rights: © 2025 Safdar et al.
abstract: Background Knee osteoarthritis (OA) is characterized by severe pain and decreased range of motion (ROM), mostly managed with conservative treatments. Therapies like platelet-rich plasma (PRP) intra-articular injections have gained fame for pain relief when surgery is a last resort. Objectives To compare the effectiveness of a supervised exercise program versus a home-based exercise program following PRP injections in terms of pain relief, ROM improvement, and disability reduction in knee osteoarthritis patients. Methods A quasi-experimental design was employed, enrolling 32 patients diagnosed with knee OA cases (age range: 40–60 years; 59% female), divided into two groups: a supervised exercise group (n = 16) and an unsupervised/home-based exercise group (n = 16). Both groups received two PRP injections spaced 15 days apart. The supervised group followed a structured exercise protocol, including cold packs post-injection for pain management. The program comprises three sessions per week for one month. The unsupervised group received similar exercises to be performed independently at home. Data analysis was conducted using parametric and non-parametric statistical methods based on data distribution. Results Both groups exhibited significant improvements from baseline to post-intervention in pain, ROM, and functional status (p < 0.05). The supervised exercise group demonstrated superior outcomes in pain reduction, knee flexion ROM, and Knee Injury and Osteoarthritis Outcome Score (KOOS). However, no significant difference was observed between groups for knee extension ROM (p = 0.378). Conclusion Both supervised and unsupervised exercise programs improved outcomes in knee OA patients following PRP injections; the supervised program showed greater pain relief, flexion ROM, and functional status. However, no significant difference was observed in knee extension ROM between the two groups.
bibliographic citation: Safdar et al. (2025) Comparison of supervised versus home-based exercise programs following platelet-rich plasma injections in knee osteoarthritis: clinical outcomes from quasi-experimental study. PeerJ 13:e19971 https://doi.org/10.7717/peerj.19971
date submitted: 2025-03-14
date accepted: 2025-07-31
issued: 2025-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Safdar
  given name: Ghalia
author list: Agent
  family name: Kiyani
  given name: Mubin Mustafa
author list: Agent
  family name: Saleem
  given name: Salman Ahmed
author list: Agent
  family name: Qureshi
  given name: Wajeeha Irfan
author list: Agent
  family name: Bashir
  given name: Shahid
author list: Agent
  family name: Abualait
  given name: Turki
author list: Agent
  family name: Khan
  given name: Hamid
author list: Agent
  family name: Sajjad
  given name: Abdul Ghafoor
doi: 10.7717/peerj.19971
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-14
copyright: ©2025 Safdar et al.
attribution name: Safdar et al.

Metabolic profile alterations in juvenile rats with bladder overactivity induced by short-term high-fructose intake
type: item
type: AcademicArticle
description: Background Overactive bladder syndrome (OAB) is a common condition that affects both adults and children, often causing significant discomfort and negatively impacting quality of life. This study aimed to preliminarily evaluate whether fructose exposure induces OAB-like symptoms in juvenile rats and to explore potential metabolic mechanisms involved. Methods Three-week-old female Sprague-Dawley rats were randomly assigned to two groups: a model group fed a 60% fructose diet for one week, and a control group fed a standard diet. Body weight, blood biochemical parameters, urination behavior, and urodynamic function were assessed. Bladder tissue was analyzed using hematoxylin and eosin staining, immunohistochemistry, and immunofluorescence. Molecular and metabolic changes were evaluated via Western blot and metabolomic analysis. Results Short-term high fructose intake led to significant metabolic and functional changes in juvenile rats. The model group showed reduced body weight and altered lipid metabolism, while glucose and insulin levels remained largely unchanged. Urodynamic assessments revealed increased non-voiding contractions, shortened intervals between contractions, and impaired bladder storage function. Open field tests indicated increased urinary frequency and open field test results. Histological analysis demonstrated disorganized bladder smooth muscle structure and elevated oxidative stress. Metabolomic profiling revealed marked alterations in energy metabolism, including enhanced glycolysis, pentose phosphate pathway activation, and accumulation of ATP and lactate. Western blot analysis confirmed activation of the CaMKK2/AMPK signaling pathway in bladder tissue. Conclusions Short-term high-fructose intake induces OAB-like symptoms in juvenile rats, accompanied by fructose toxicity, oxidative stress, calcium ion accumulation, and activation of the CaMKK2/AMPK signaling pathway. These findings highlight a potential link between fructose metabolism and blad…
format: application/pdf
format: text/html
creator: Xu Cui
creator: Zhiqiang Chen
creator: Longyao Xu
creator: Changwei Wu
creator: Chaoming Zhou
subject: Animal Behavior
subject: Biochemistry
subject: Toxicology
subject: Nutrition
subject: Urology
description: doi:10.7717/peerj.20186
publisher: PeerJ Inc.
rights: © 2025 Cui et al.
abstract: Background Overactive bladder syndrome (OAB) is a common condition that affects both adults and children, often causing significant discomfort and negatively impacting quality of life. This study aimed to preliminarily evaluate whether fructose exposure induces OAB-like symptoms in juvenile rats and to explore potential metabolic mechanisms involved. Methods Three-week-old female Sprague-Dawley rats were randomly assigned to two groups: a model group fed a 60% fructose diet for one week, and a control group fed a standard diet. Body weight, blood biochemical parameters, urination behavior, and urodynamic function were assessed. Bladder tissue was analyzed using hematoxylin and eosin staining, immunohistochemistry, and immunofluorescence. Molecular and metabolic changes were evaluated via Western blot and metabolomic analysis. Results Short-term high fructose intake led to significant metabolic and functional changes in juvenile rats. The model group showed reduced body weight and altered lipid metabolism, while glucose and insulin levels remained largely unchanged. Urodynamic assessments revealed increased non-voiding contractions, shortened intervals between contractions, and impaired bladder storage function. Open field tests indicated increased urinary frequency and open field test results. Histological analysis demonstrated disorganized bladder smooth muscle structure and elevated oxidative stress. Metabolomic profiling revealed marked alterations in energy metabolism, including enhanced glycolysis, pentose phosphate pathway activation, and accumulation of ATP and lactate. Western blot analysis confirmed activation of the CaMKK2/AMPK signaling pathway in bladder tissue. Conclusions Short-term high-fructose intake induces OAB-like symptoms in juvenile rats, accompanied by fructose toxicity, oxidative stress, calcium ion accumulation, and activation of the CaMKK2/AMPK signaling pathway. These findings highlight a potential link between fructose metabolism and blad…
bibliographic citation: Cui et al. (2025) Metabolic profile alterations in juvenile rats with bladder overactivity induced by short-term high-fructose intake. PeerJ 13:e20186 https://doi.org/10.7717/peerj.20186
date submitted: 2025-05-07
date accepted: 2025-09-15
issued: 2025-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Xu
author list: Agent
  family name: Chen
  given name: Zhiqiang
author list: Agent
  family name: Xu
  given name: Longyao
author list: Agent
  family name: Wu
  given name: Changwei
author list: Agent
  family name: Zhou
  given name: Chaoming
doi: 10.7717/peerj.20186
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-13
copyright: ©2025 Cui et al.
attribution name: Cui et al.

rtpcr: a package for statistical analysis and graphical presentation of qPCR data in R
type: item
type: AcademicArticle
description: Background Quantitative real-time polymerase chain reaction (qRT-PCR or qPCR) is widely used in molecular biology research. Various analysis methods are employed to interpret qPCR data and measure mRNA levels of target genes under different experimental conditions. Results The rtpcr package was developed for amplification efficiency calculation, statistical analysis, and graphical presentation of qPCR data in R. It uses a general calculation methodology that accommodates up to two reference genes and amplification efficiency values, including the Pfaffl method. Depending on the experimental design, rtpcr functions apply a t-test (for experiments with a two-level factor), analysis of variance (ANOVA), or analysis of covariance (ANCOVA) (for experiments with more than two levels or factors) to calculate fold change (FC) or relative expression (RE) of a target gene. The functions also provide standard errors and confidence intervals for the means and support statistical mean comparisons. To facilitate usage, the package includes example datasets. It also offers ggplot-based visualizations with customizable arguments, allowing users to tailor the graphical output. Conclusions In summary, the rtpcr package is a useful and user-friendly tool for analyzing real-time PCR data from experiments involving up to three different factors. Built on a general methodology, it provides robust calculations and comprehensive graphical outputs, making it a valuable resource for researchers working with qPCR data.
format: application/pdf
format: text/html
creator: Ghader Mirzaghaderi
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Computational Science
description: doi:10.7717/peerj.20185
publisher: PeerJ Inc.
rights: © 2025 Mirzaghaderi
abstract: Background Quantitative real-time polymerase chain reaction (qRT-PCR or qPCR) is widely used in molecular biology research. Various analysis methods are employed to interpret qPCR data and measure mRNA levels of target genes under different experimental conditions. Results The rtpcr package was developed for amplification efficiency calculation, statistical analysis, and graphical presentation of qPCR data in R. It uses a general calculation methodology that accommodates up to two reference genes and amplification efficiency values, including the Pfaffl method. Depending on the experimental design, rtpcr functions apply a t-test (for experiments with a two-level factor), analysis of variance (ANOVA), or analysis of covariance (ANCOVA) (for experiments with more than two levels or factors) to calculate fold change (FC) or relative expression (RE) of a target gene. The functions also provide standard errors and confidence intervals for the means and support statistical mean comparisons. To facilitate usage, the package includes example datasets. It also offers ggplot-based visualizations with customizable arguments, allowing users to tailor the graphical output. Conclusions In summary, the rtpcr package is a useful and user-friendly tool for analyzing real-time PCR data from experiments involving up to three different factors. Built on a general methodology, it provides robust calculations and comprehensive graphical outputs, making it a valuable resource for researchers working with qPCR data.
bibliographic citation: Mirzaghaderi (2025) rtpcr: a package for statistical analysis and graphical presentation of qPCR data in R. PeerJ 13:e20185 https://doi.org/10.7717/peerj.20185
date submitted: 2025-02-19
date accepted: 2025-09-15
issued: 2025-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mirzaghaderi
  given name: Ghader
doi: 10.7717/peerj.20185
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-13
copyright: ©2025 Mirzaghaderi
attribution name: Mirzaghaderi

Extraction, identification and component analysis of exosome-like nanovesicles in Anoectochilus roxburghii (Wall.) Lindl.
type: item
type: AcademicArticle
description: Objective This study aimed to investigate the presence of exosome-like nanovesicles in Anoectochilus roxburghii (Wall.) Lindl. (A. roxburghii) and the related active ingredients. Methods A. roxburghii-derived exosome-like nanovesicles (ARENVs) were extracted by the differential ultracentrifugation and characterized by transmission electron microscopy and nano-flow cytometry. The components in ARENVs derived from soil-cultured and hydroponic A. roxburghii were identified and quantified by liquid chromatography-mass spectrometry. Results Nanovesicles with typical exosome characteristics were successfully isolated from A. roxburghii. After analysis and identification, ARENVs were rich in multiple flavonoid components such as isoquercitrin, kaempferol, isorhamnetin, narcissoside, quercetin and rutin. The quantity of flavonoid compounds was higher in ARENVs derived from soil-cultured A. roxburghii than in those from hydroponic A. roxburghii. Conclusion A. roxburghii contains exosome-like nanovesicles, which are rich in active flavonoid ingredients. These active ingredients are more abundant in ARENVs derived from soil-cultured A. roxburghii than hydroponic counterparts. The findings may provide an innovative theoretical basis for further exploration of the medicinal value of A. roxburghii.
format: application/pdf
format: text/html
creator: Xuanzhe Zhou
creator: Xinglin Ruan
creator: Xue Mi
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.20182
publisher: PeerJ Inc.
rights: © 2025 Zhou et al.
abstract: Objective This study aimed to investigate the presence of exosome-like nanovesicles in Anoectochilus roxburghii (Wall.) Lindl. (A. roxburghii) and the related active ingredients. Methods A. roxburghii-derived exosome-like nanovesicles (ARENVs) were extracted by the differential ultracentrifugation and characterized by transmission electron microscopy and nano-flow cytometry. The components in ARENVs derived from soil-cultured and hydroponic A. roxburghii were identified and quantified by liquid chromatography-mass spectrometry. Results Nanovesicles with typical exosome characteristics were successfully isolated from A. roxburghii. After analysis and identification, ARENVs were rich in multiple flavonoid components such as isoquercitrin, kaempferol, isorhamnetin, narcissoside, quercetin and rutin. The quantity of flavonoid compounds was higher in ARENVs derived from soil-cultured A. roxburghii than in those from hydroponic A. roxburghii. Conclusion A. roxburghii contains exosome-like nanovesicles, which are rich in active flavonoid ingredients. These active ingredients are more abundant in ARENVs derived from soil-cultured A. roxburghii than hydroponic counterparts. The findings may provide an innovative theoretical basis for further exploration of the medicinal value of A. roxburghii.
bibliographic citation: Zhou et al. (2025) Extraction, identification and component analysis of exosome-like nanovesicles in Anoectochilus roxburghii (Wall.) Lindl.. PeerJ 13:e20182 https://doi.org/10.7717/peerj.20182
date submitted: 2025-07-17
date accepted: 2025-09-15
issued: 2025-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Xuanzhe
author list: Agent
  family name: Ruan
  given name: Xinglin
author list: Agent
  family name: Mi
  given name: Xue
doi: 10.7717/peerj.20182
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-13
copyright: ©2025 Zhou et al.
attribution name: Zhou et al.

Association of sociodemographic factors, lifestyle behaviors, anthropometric measures, and cardiometabolic health markers with blood pressure in adolescents: a cross-sectional analysis
type: item
type: AcademicArticle
description: Introduction Evidence suggests that hypertension in adulthood may have its origins in childhood and adolescence. In this context, previous studies have demonstrated an association between lifestyle behaviors and nutritional status, both of which are linked to elevated blood pressure. Objective To examine the association between sociodemographic factors, subjective perception of health, lifestyle behaviors, anthropometric measurements, and cardiometabolic health markers with blood pressure in a sample of Brazilian adolescents. Methods A cross-sectional study was conducted with 273 adolescents (56% girls), aged 14–20 years, from Rio Branco, Acre, Amazon Region of Brazil. Data were collected using self-reported questionnaires and direct measurements, including anthropometric indices, cardiometabolic biomarkers, and blood pressure. Data were analyzed using chi-square tests and binary logistic regression models. Linear regression, adjusted by all variables, including dimension (sub-category) and age, was used to verify if the independent variables were associated with elevated blood pressure among adolescents. Results Significant associations were observed between elevated blood pressure and the male sex (OR = 2.56; 95% CI [1.11–5.86], p = 0.026) and rural residency (OR = 3.65; 95% CI [1.44–9.21], p = 0.006). Aerobic activity presented a significant association with elevated blood pressure (OR = 8.04; 95% CI [1.04–61.65], p = 0.045). Waist circumference increased the likelihood of elevated blood pressure (OR = 5.43; 95% CI [1.34–21.94], p = 0.018). Cardiometabolic markers, such as fasting glucose, demonstrated a significant association with elevated blood pressure (OR = 2.43; 95% CI [1.00–5.90], p = 0.048). No significant associations were found for muscle-strengthening activity, screen time, sleep duration, or food intake. Conclusion Our findings emphasize the crucial role of sociodemographic factors, especially the male sex and rural residency, in predicting elevated b…
format: application/pdf
format: text/html
creator: Fábio Nascimento-da-Silva
creator: João Rafael Valentim-Silva
creator: César Arruda Meschiari
creator: Ildercílio Mota de Souza Lima
creator: Dartagnan Pinto Guedes
creator: Juliano Casonatto
subject: Cardiology
subject: Pediatrics
description: doi:10.7717/peerj.20151
publisher: PeerJ Inc.
rights: © 2025 Nascimento-da-Silva et al.
abstract: Introduction Evidence suggests that hypertension in adulthood may have its origins in childhood and adolescence. In this context, previous studies have demonstrated an association between lifestyle behaviors and nutritional status, both of which are linked to elevated blood pressure. Objective To examine the association between sociodemographic factors, subjective perception of health, lifestyle behaviors, anthropometric measurements, and cardiometabolic health markers with blood pressure in a sample of Brazilian adolescents. Methods A cross-sectional study was conducted with 273 adolescents (56% girls), aged 14–20 years, from Rio Branco, Acre, Amazon Region of Brazil. Data were collected using self-reported questionnaires and direct measurements, including anthropometric indices, cardiometabolic biomarkers, and blood pressure. Data were analyzed using chi-square tests and binary logistic regression models. Linear regression, adjusted by all variables, including dimension (sub-category) and age, was used to verify if the independent variables were associated with elevated blood pressure among adolescents. Results Significant associations were observed between elevated blood pressure and the male sex (OR = 2.56; 95% CI [1.11–5.86], p = 0.026) and rural residency (OR = 3.65; 95% CI [1.44–9.21], p = 0.006). Aerobic activity presented a significant association with elevated blood pressure (OR = 8.04; 95% CI [1.04–61.65], p = 0.045). Waist circumference increased the likelihood of elevated blood pressure (OR = 5.43; 95% CI [1.34–21.94], p = 0.018). Cardiometabolic markers, such as fasting glucose, demonstrated a significant association with elevated blood pressure (OR = 2.43; 95% CI [1.00–5.90], p = 0.048). No significant associations were found for muscle-strengthening activity, screen time, sleep duration, or food intake. Conclusion Our findings emphasize the crucial role of sociodemographic factors, especially the male sex and rural residency, in predicting elevated b…
bibliographic citation: Nascimento-da-Silva et al. (2025) Association of sociodemographic factors, lifestyle behaviors, anthropometric measures, and cardiometabolic health markers with blood pressure in adolescents: a cross-sectional analysis. PeerJ 13:e20151 https://doi.org/10.7717/peerj.20151
date submitted: 2025-04-17
date accepted: 2025-09-08
issued: 2025-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nascimento-da-Silva
  given name: Fábio
author list: Agent
  family name: Valentim-Silva
  given name: João Rafael
author list: Agent
  family name: Meschiari
  given name: César Arruda
author list: Agent
  family name: Lima
  given name: Ildercílio Mota de Souza
author list: Agent
  family name: Guedes
  given name: Dartagnan Pinto
author list: Agent
  family name: Casonatto
  given name: Juliano
doi: 10.7717/peerj.20151
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-13
copyright: ©2025 Nascimento-da-Silva et al.
attribution name: Nascimento-da-Silva et al.

Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor
type: item
type: AcademicArticle
description: Background Nitrate (NO3−) can accumulate in closed-circuit ecosystems to a toxic level. Adding heterotrophic denitrification process to the water treatment is a strategy to reduce this level. This type of process usually requires the addition of a carbon source. Carbon-to-nitrogen ratio (C/N) is a key parameter known to influence both the function and the activity of microbial communities in bioprocesses. Few studies have examined the influence of C/N on denitrification systems operated under methylotrophic and marine conditions. Here we assessed the influence of C/N (methanol and NO3−) on the performance of a laboratory-scale, recirculating denitrifying reactor operated under marine conditions. We monitored the evolution of the bacterial community in the biofilm to assess its stability during the operating conditions. Finally, the relative gene expression profiles of Methylophaga nitratireducenticrescens strain GP59, the main denitrifier in the denitrifying biofilm, were determined during the operating conditions and compared with those of GP59 planktonic pure cultures. Methodology A 500-mL methanol-fed recirculating denitrification reactor operated under marine conditions and colonized by a naturally occurring multispecies denitrifying biofilm was subjected to eight different C/N. We monitored several physico-chemical parameters (denitrifying activities, methanol consumption, CO2 production) throughout the operating conditions. The evolution of the bacterial community in the biofilm during these conditions was determined by 16S rRNA gene amplicon sequencing. Metatranscriptomes were derived from the biofilm to determine (1) the relative gene expression profiles of strain GP59, and (2) the functional diversity of the active microorganisms in the biofilm. Results Changes in C/N did not correlate with the denitrification dynamics (NO3− and NO2− reduction rates, NO2− and N2O dynamics), but did correlate with the methanol consumption rates, and the CO2 production rates.…
format: application/pdf
format: text/html
creator: Livie Lestin
creator: Richard Villemur
subject: Bioengineering
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.20129
publisher: PeerJ Inc.
rights: © 2025 Lestin and Villemur
abstract: Background Nitrate (NO3−) can accumulate in closed-circuit ecosystems to a toxic level. Adding heterotrophic denitrification process to the water treatment is a strategy to reduce this level. This type of process usually requires the addition of a carbon source. Carbon-to-nitrogen ratio (C/N) is a key parameter known to influence both the function and the activity of microbial communities in bioprocesses. Few studies have examined the influence of C/N on denitrification systems operated under methylotrophic and marine conditions. Here we assessed the influence of C/N (methanol and NO3−) on the performance of a laboratory-scale, recirculating denitrifying reactor operated under marine conditions. We monitored the evolution of the bacterial community in the biofilm to assess its stability during the operating conditions. Finally, the relative gene expression profiles of Methylophaga nitratireducenticrescens strain GP59, the main denitrifier in the denitrifying biofilm, were determined during the operating conditions and compared with those of GP59 planktonic pure cultures. Methodology A 500-mL methanol-fed recirculating denitrification reactor operated under marine conditions and colonized by a naturally occurring multispecies denitrifying biofilm was subjected to eight different C/N. We monitored several physico-chemical parameters (denitrifying activities, methanol consumption, CO2 production) throughout the operating conditions. The evolution of the bacterial community in the biofilm during these conditions was determined by 16S rRNA gene amplicon sequencing. Metatranscriptomes were derived from the biofilm to determine (1) the relative gene expression profiles of strain GP59, and (2) the functional diversity of the active microorganisms in the biofilm. Results Changes in C/N did not correlate with the denitrification dynamics (NO3− and NO2− reduction rates, NO2− and N2O dynamics), but did correlate with the methanol consumption rates, and the CO2 production rates.…
bibliographic citation: Lestin et al. (2025) Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor. PeerJ 13:e20129 https://doi.org/10.7717/peerj.20129
date submitted: 2025-04-29
date accepted: 2025-09-02
issued: 2025-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lestin
  given name: Livie
author list: Agent
  family name: Villemur
  given name: Richard
doi: 10.7717/peerj.20129
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-13
copyright: ©2025 Lestin and Villemur
attribution name: Lestin and Villemur

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