PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Study on the influence of TRX suspension training on the specific balance ability of surfers
items: LncRNACNVIntegrateR: a novel framework for correlating long non-coding RNAs with copy number variation abnormalities and disease progression
items: Estimating internal dissolved methane loading in rivers using a mass balance approach
items: Comparing the reliability of the single leg squat test using two, three, and four category ordinal rating scales
items: Evaluation of enamel integrity after clear aligner attachments removal: a risk–benefit comparison of one-step tools
items: Recognizing IgA-class endomysial antibody equivalent binding patterns on monkey liver substrate through EfficientNet architectures and deep learning
items: Effect of circadian rhythm disruption on benign prostatic hyperplasia in rats
items: Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles
items: Detection of terrestrial mammals using environmental DNA during heavy rainfall events and associated influencing factors
items: Comparison of IAA and amino acid profiles of the selected rootstocks and their accumulation in grafted scion of Cucumis sativus L.

Study on the influence of TRX suspension training on the specific balance ability of surfers
type: item
type: AcademicArticle
description: Objective To investigate the effects of total resistance exercise (TRX), suspension training on the specialized balance ability of surfing athletes. Methods A total of 32 Chinese National Surfing Team athletes were randomly assigned to TRX suspension training group (TRX group) and traditional balance training group (TB group), both undergoing an 8-week intervention training program consisting of three sessions per week lasting approximately 30 minutes each to improve balance ability. The balance board lateral squat specialized balance ability test was administered at different intervention phases to examine changes in participants’ specialized balance ability. Results Following the 8-week intervention, both training modalities demonstrated significant improvements in surfing specialized balance metrics relative to baseline (p < 0.01 for all comparisons). Inter-group comparisons revealed statistically superior outcomes for TRX suspension training, with marked divergence emerging at the 5-week assessment (p = 0.005 < 0.01, |d| = 1.062 > 0.8) that intensified through intervention completion (p = 0.000 < 0.01, |d| = 1.417 > 0.8). Conclusion Both 8 weeks of TRX suspension training and traditional balance training were effective in enhancing the specialized balance of surfers, but TRX suspension training was superior to traditional training in terms of enhancement, and this advantage was significantly demonstrated after 5 weeks and continued until the end of the training. TRX suspension training aligns with the balance demands of surfing, making it an effective training method. It is feasible for coaches to formulate customized TRX suspension training regimens tailored to surfers’ proficiency levels and core stability, integrating sport-specific movement patterns to enhance athletes’ neuromuscular adaptations for improved biomechanical control during dynamic wave navigation.
format: application/pdf
format: text/html
creator: Zhaoyi Wang
creator: Yong Ma
creator: Qian Huang
creator: Zhihao Guo
creator: Mengyao Ja
creator: Weitao Zheng
subject: Anatomy and Physiology
subject: Biomechanics
description: doi:10.7717/peerj.20180
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Objective To investigate the effects of total resistance exercise (TRX), suspension training on the specialized balance ability of surfing athletes. Methods A total of 32 Chinese National Surfing Team athletes were randomly assigned to TRX suspension training group (TRX group) and traditional balance training group (TB group), both undergoing an 8-week intervention training program consisting of three sessions per week lasting approximately 30 minutes each to improve balance ability. The balance board lateral squat specialized balance ability test was administered at different intervention phases to examine changes in participants’ specialized balance ability. Results Following the 8-week intervention, both training modalities demonstrated significant improvements in surfing specialized balance metrics relative to baseline (p < 0.01 for all comparisons). Inter-group comparisons revealed statistically superior outcomes for TRX suspension training, with marked divergence emerging at the 5-week assessment (p = 0.005 < 0.01, |d| = 1.062 > 0.8) that intensified through intervention completion (p = 0.000 < 0.01, |d| = 1.417 > 0.8). Conclusion Both 8 weeks of TRX suspension training and traditional balance training were effective in enhancing the specialized balance of surfers, but TRX suspension training was superior to traditional training in terms of enhancement, and this advantage was significantly demonstrated after 5 weeks and continued until the end of the training. TRX suspension training aligns with the balance demands of surfing, making it an effective training method. It is feasible for coaches to formulate customized TRX suspension training regimens tailored to surfers’ proficiency levels and core stability, integrating sport-specific movement patterns to enhance athletes’ neuromuscular adaptations for improved biomechanical control during dynamic wave navigation.
bibliographic citation: Wang et al. (2025) Study on the influence of TRX suspension training on the specific balance ability of surfers. PeerJ 13:e20180 https://doi.org/10.7717/peerj.20180
date submitted: 2024-10-31
date accepted: 2025-09-12
issued: 2025-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhaoyi
author list: Agent
  family name: Ma
  given name: Yong
author list: Agent
  family name: Huang
  given name: Qian
author list: Agent
  family name: Guo
  given name: Zhihao
author list: Agent
  family name: Ja
  given name: Mengyao
author list: Agent
  family name: Zheng
  given name: Weitao
doi: 10.7717/peerj.20180
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-16
copyright: ©2025 Wang et al.
attribution name: Wang et al.

LncRNACNVIntegrateR: a novel framework for correlating long non-coding RNAs with copy number variation abnormalities and disease progression
type: item
type: AcademicArticle
description: Understanding complex biological systems and disease mechanisms necessitates the integration of multiple molecular layers, making multi-omics data integration a cornerstone of modern biomedical research. By combining datasets from different omics domains, researchers can uncover intricate molecular relationships, discover robust biomarkers, and advance precision medicine. Despite advancements in high-throughput technologies that have increased the availability of multi-omics datasets, challenges such as sample consistency and the development of reliable analytical frameworks hinder their full potential. Addressing these challenges is crucial for achieving a comprehensive understanding of biological systems and leveraging multi-omics data to drive breakthroughs in healthcare. lncRNACNVIntegrateR is an R package that facilitates multi-omics data integration to explore the interplay between long non-coding RNAs (lncRNAs) and copy number variations (CNVs). The package integrates transcriptomic data, CNV profiles, and clinical information from matched samples, providing a complete pipeline for data preprocessing, lncRNA-CNV correlation analysis, and identification of CNV-driven prognostic signatures. Additionally, the package supports the construction of risk score models based on CNV-associated lncRNAs and functional enrichment analyses to reveal the role of corresponding target genes in disease progression. We validated lncRNACNVIntegrateR using The Cancer Genome Atlas (TCGA) Glioblastoma (GBM) and Colorectal Adenocarcinoma (COAD) datasets. The risk score models developed by the package demonstrated promising predictive performance, achieving an area under the receiver operating characteristic curve (AUC) of 0.80 for GBM and 0.71 for COAD. Functional enrichment analyses further highlighted the biological significance of the identified prognostic CNV-driven lncRNA signatures, providing insights into disease progression, risk stratification, and potential therapeutic tar…
format: application/pdf
format: text/html
creator: Neetu Tyagi
creator: Shikha Roy
creator: Dinesh Gupta
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.20131
publisher: PeerJ Inc.
rights: © 2025 Tyagi et al.
abstract: Understanding complex biological systems and disease mechanisms necessitates the integration of multiple molecular layers, making multi-omics data integration a cornerstone of modern biomedical research. By combining datasets from different omics domains, researchers can uncover intricate molecular relationships, discover robust biomarkers, and advance precision medicine. Despite advancements in high-throughput technologies that have increased the availability of multi-omics datasets, challenges such as sample consistency and the development of reliable analytical frameworks hinder their full potential. Addressing these challenges is crucial for achieving a comprehensive understanding of biological systems and leveraging multi-omics data to drive breakthroughs in healthcare. lncRNACNVIntegrateR is an R package that facilitates multi-omics data integration to explore the interplay between long non-coding RNAs (lncRNAs) and copy number variations (CNVs). The package integrates transcriptomic data, CNV profiles, and clinical information from matched samples, providing a complete pipeline for data preprocessing, lncRNA-CNV correlation analysis, and identification of CNV-driven prognostic signatures. Additionally, the package supports the construction of risk score models based on CNV-associated lncRNAs and functional enrichment analyses to reveal the role of corresponding target genes in disease progression. We validated lncRNACNVIntegrateR using The Cancer Genome Atlas (TCGA) Glioblastoma (GBM) and Colorectal Adenocarcinoma (COAD) datasets. The risk score models developed by the package demonstrated promising predictive performance, achieving an area under the receiver operating characteristic curve (AUC) of 0.80 for GBM and 0.71 for COAD. Functional enrichment analyses further highlighted the biological significance of the identified prognostic CNV-driven lncRNA signatures, providing insights into disease progression, risk stratification, and potential therapeutic tar…
bibliographic citation: Tyagi et al. (2025) LncRNACNVIntegrateR: a novel framework for correlating long non-coding RNAs with copy number variation abnormalities and disease progression. PeerJ 13:e20131 https://doi.org/10.7717/peerj.20131
date submitted: 2025-04-26
date accepted: 2025-09-03
issued: 2025-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tyagi
  given name: Neetu
author list: Agent
  family name: Roy
  given name: Shikha
author list: Agent
  family name: Gupta
  given name: Dinesh
doi: 10.7717/peerj.20131
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-16
copyright: © 2025 Tyagi et al.
attribution name: Tyagi et al.

Estimating internal dissolved methane loading in rivers using a mass balance approach
type: item
type: AcademicArticle
description: The dynamics of dissolved methane concentration in rivers are influenced by losses through atmospheric emission and microbial oxidation, and by gains from internal (e.g., riverbed sediment) and external (e.g., groundwater) sources. Reducing riverine methane emissions, a key strategy for mitigating global warming, requires decreasing both internal and external loadings. To develop effective mitigation measures, it is essential to quantify these loadings separately. In this study, we estimated the internal methane loading in a river using a mass balance approach. We focused on river reaches without tributary inflow or significant discharge changes, assuming negligible external methane loading. Sampling was conducted at upstream and downstream sites of two short reaches (2.2 and 4.4 km) in the Kokai River, Japan, during 2022–23. Dissolved methane concentrations ranged from 237 ± 19 to 1,271 ± 6 nmol L–1, with changes from upstream to downstream ([CH4]downstream–[CH4]upstream) varying from –113 to 363 nmol L–1 . Methane oxidation rates and diffusive emission fluxes to the atmosphere were −1.2 ± 0.8~66 ± 19 µmol m–2 h–1 and 32 ± 10~199 ± 149 µmol m–2 h–1, respectively. The net flux of dissolved methane from the riverbed to the water varied from −33 to 160 µmol m–2 h–1. Compared to conventional methods, including benthic chambers and peeper sampling with model simulation, this approach is simple and facilitates methane flux measurements across multiple sites and diverse environmental gradients. By integrating the estimates from river reaches, the proposed method is applicable to large-scale assessments of internal methane loading in river systems.
format: application/pdf
format: text/html
creator: Kenji Tsuchiya
creator: Shingo Miura
creator: Ayato Kohzu
subject: Ecosystem Science
subject: Biosphere Interactions
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
subject: Ecohydrology
description: doi:10.7717/peerj.20238
publisher: PeerJ Inc.
rights: © 2025 Tsuchiya et al.
abstract: The dynamics of dissolved methane concentration in rivers are influenced by losses through atmospheric emission and microbial oxidation, and by gains from internal (e.g., riverbed sediment) and external (e.g., groundwater) sources. Reducing riverine methane emissions, a key strategy for mitigating global warming, requires decreasing both internal and external loadings. To develop effective mitigation measures, it is essential to quantify these loadings separately. In this study, we estimated the internal methane loading in a river using a mass balance approach. We focused on river reaches without tributary inflow or significant discharge changes, assuming negligible external methane loading. Sampling was conducted at upstream and downstream sites of two short reaches (2.2 and 4.4 km) in the Kokai River, Japan, during 2022–23. Dissolved methane concentrations ranged from 237 ± 19 to 1,271 ± 6 nmol L–1, with changes from upstream to downstream ([CH4]downstream–[CH4]upstream) varying from –113 to 363 nmol L–1 . Methane oxidation rates and diffusive emission fluxes to the atmosphere were −1.2 ± 0.8~66 ± 19 µmol m–2 h–1 and 32 ± 10~199 ± 149 µmol m–2 h–1, respectively. The net flux of dissolved methane from the riverbed to the water varied from −33 to 160 µmol m–2 h–1. Compared to conventional methods, including benthic chambers and peeper sampling with model simulation, this approach is simple and facilitates methane flux measurements across multiple sites and diverse environmental gradients. By integrating the estimates from river reaches, the proposed method is applicable to large-scale assessments of internal methane loading in river systems.
bibliographic citation: Tsuchiya et al. (2025) Estimating internal dissolved methane loading in rivers using a mass balance approach. PeerJ 13:e20238 https://doi.org/10.7717/peerj.20238
date submitted: 2025-04-25
date accepted: 2025-09-24
issued: 2025-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsuchiya
  given name: Kenji
author list: Agent
  family name: Miura
  given name: Shingo
author list: Agent
  family name: Kohzu
  given name: Ayato
doi: 10.7717/peerj.20238
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-15
copyright: © 2025 Tsuchiya et al.
attribution name: Tsuchiya et al.

Comparing the reliability of the single leg squat test using two, three, and four category ordinal rating scales
type: item
type: AcademicArticle
description: Background The single-leg squat test (SLST) is supported by evidence for reliability and validity across various visual rating methods, but the optimal number of ordinal categories for assessing movement quality remains unclear. The study aims to determine the most informative and reliable number of ordinal scoring categories for visually rating the SLST. Methods A total of 58 subjects with lower extremity injuries participated. A single therapist rated the SLST with a 1-week interval to establish intra-rater reliability. Two therapists independently rated the SLST at the same time point to establish inter-rater reliability. Two-, three-, and four-category ordinal scales were simultaneously used to evaluate SLST performance in rating the components of trunk deviation, hip adduction, and lower extremity internal rotation. Reliability was assessed using unweighted kappa (κ) values. Results The overall intra-rater reliability was κ = 0.60, 0.35, and 0.20, with inter-rater reliability being κ = 0.60, 0.61, and 0.33 for the two-, three-, and four-category scales, respectively. When specifically looking at the components of trunk deviation, hip adduction, and lower extremity internal rotation, intra-rater reliability was moderate to good for two-category scales (κ = 0.47–0.65), fair to good for three-category scales (κ = 0.3–0.7), and fair to good for four-category scales (κ = 0.36–0.65). Inter-rater reliability for the three components was good to excellent (κ = 0.65–0.86) for the two-category, good to excellent (κ = 0.69–0.86) for the three-category, and fair to excellent (κ = 0.55–0.76) for the four-category. Conclusion When applied to specific movement components, the three-category ordinal scale demonstrated the best balance between detailed assessment and reliability for visually rating trunk deviation, hip adduction, and lower extremity internal rotation during the SLST in patients with lower extremity injuries.
format: application/pdf
format: text/html
creator: Yongni Zhang
creator: Yifan Liu
creator: Zhicheng Pan
creator: Hui Gao
creator: RobRoy L Martin
creator: Xinwei Huang
subject: Orthopedics
subject: Sports Injury
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.20218
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Background The single-leg squat test (SLST) is supported by evidence for reliability and validity across various visual rating methods, but the optimal number of ordinal categories for assessing movement quality remains unclear. The study aims to determine the most informative and reliable number of ordinal scoring categories for visually rating the SLST. Methods A total of 58 subjects with lower extremity injuries participated. A single therapist rated the SLST with a 1-week interval to establish intra-rater reliability. Two therapists independently rated the SLST at the same time point to establish inter-rater reliability. Two-, three-, and four-category ordinal scales were simultaneously used to evaluate SLST performance in rating the components of trunk deviation, hip adduction, and lower extremity internal rotation. Reliability was assessed using unweighted kappa (κ) values. Results The overall intra-rater reliability was κ = 0.60, 0.35, and 0.20, with inter-rater reliability being κ = 0.60, 0.61, and 0.33 for the two-, three-, and four-category scales, respectively. When specifically looking at the components of trunk deviation, hip adduction, and lower extremity internal rotation, intra-rater reliability was moderate to good for two-category scales (κ = 0.47–0.65), fair to good for three-category scales (κ = 0.3–0.7), and fair to good for four-category scales (κ = 0.36–0.65). Inter-rater reliability for the three components was good to excellent (κ = 0.65–0.86) for the two-category, good to excellent (κ = 0.69–0.86) for the three-category, and fair to excellent (κ = 0.55–0.76) for the four-category. Conclusion When applied to specific movement components, the three-category ordinal scale demonstrated the best balance between detailed assessment and reliability for visually rating trunk deviation, hip adduction, and lower extremity internal rotation during the SLST in patients with lower extremity injuries.
bibliographic citation: Zhang et al. (2025) Comparing the reliability of the single leg squat test using two, three, and four category ordinal rating scales. PeerJ 13:e20218 https://doi.org/10.7717/peerj.20218
date submitted: 2025-04-08
date accepted: 2025-09-20
issued: 2025-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yongni
author list: Agent
  family name: Liu
  given name: Yifan
author list: Agent
  family name: Pan
  given name: Zhicheng
author list: Agent
  family name: Gao
  given name: Hui
author list: Agent
  family name: Martin
  given name: RobRoy L
author list: Agent
  family name: Huang
  given name: Xinwei
doi: 10.7717/peerj.20218
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-15
copyright: ©2025 Zhang et al.
attribution name: Zhang et al.

Evaluation of enamel integrity after clear aligner attachments removal: a risk–benefit comparison of one-step tools
type: item
type: AcademicArticle
description: Background At the end of clear aligner treatment, attachment removal is essential to restore natural tooth morphology while preserving enamel integrity. This study aimed to compare the effects of seven different composite removal instruments on the enamel surface using a risk–benefit model. Materials The instruments assessed were: OneGloss, Enhance, SM 104, Sof-Lex disc (coarse grit), tungsten carbide bur, zirconia bur, and white stone bur. Seventy extracted premolar teeth were bonded with standardized condensable composite attachments (2 × 4 × 1 mm). Enamel integrity was quantitatively assessed by measuring surface roughness (µm) and enamel loss depth (mm), and qualitatively analyzed using scanning electron microscopy (SEM). The time required for attachment removal was recorded in seconds. A risk–benefit model was applied to compare enamel damage and time efficiency across tools. Results White stone bur exhibited higher surface roughness and greater enamel loss compared to other groups (p = 0.000). Aluminium oxide-based tools (OneGloss, Enhance, SM 104, and the Sof-Lex disc) resulted in less enamel loss than the tungsten carbide bur. The risk–benefit model indicated that OneGloss, Enhance, and SM 104 offered the best balance between enamel preservation and time efficiency. SEM analysis further confirmed that OneGloss and SM 104 produced smoother enamel surfaces compared to other instruments. Conclusion OneGloss and SM 104 demonstrated superior time efficiency and preservation of enamel integrity compared to other evaluated tools.
format: application/pdf
format: text/html
creator: Anh Viet Nguyen
creator: Trang Thi Nguyen
subject: Dentistry
subject: Orthopedics
description: doi:10.7717/peerj.20200
publisher: PeerJ Inc.
rights: © 2025 Nguyen and Nguyen
abstract: Background At the end of clear aligner treatment, attachment removal is essential to restore natural tooth morphology while preserving enamel integrity. This study aimed to compare the effects of seven different composite removal instruments on the enamel surface using a risk–benefit model. Materials The instruments assessed were: OneGloss, Enhance, SM 104, Sof-Lex disc (coarse grit), tungsten carbide bur, zirconia bur, and white stone bur. Seventy extracted premolar teeth were bonded with standardized condensable composite attachments (2 × 4 × 1 mm). Enamel integrity was quantitatively assessed by measuring surface roughness (µm) and enamel loss depth (mm), and qualitatively analyzed using scanning electron microscopy (SEM). The time required for attachment removal was recorded in seconds. A risk–benefit model was applied to compare enamel damage and time efficiency across tools. Results White stone bur exhibited higher surface roughness and greater enamel loss compared to other groups (p = 0.000). Aluminium oxide-based tools (OneGloss, Enhance, SM 104, and the Sof-Lex disc) resulted in less enamel loss than the tungsten carbide bur. The risk–benefit model indicated that OneGloss, Enhance, and SM 104 offered the best balance between enamel preservation and time efficiency. SEM analysis further confirmed that OneGloss and SM 104 produced smoother enamel surfaces compared to other instruments. Conclusion OneGloss and SM 104 demonstrated superior time efficiency and preservation of enamel integrity compared to other evaluated tools.
bibliographic citation: Nguyen et al. (2025) Evaluation of enamel integrity after clear aligner attachments removal: a risk–benefit comparison of one-step tools. PeerJ 13:e20200 https://doi.org/10.7717/peerj.20200
date submitted: 2025-05-19
date accepted: 2025-09-16
issued: 2025-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nguyen
  given name: Anh Viet
author list: Agent
  family name: Nguyen
  given name: Trang Thi
doi: 10.7717/peerj.20200
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-15
copyright: ©2025 Nguyen and Nguyen
attribution name: Nguyen and Nguyen

Recognizing IgA-class endomysial antibody equivalent binding patterns on monkey liver substrate through EfficientNet architectures and deep learning
type: item
type: AcademicArticle
description: Deep learning offers promising potential for automating the interpretation of immunoglobulin A (IgA) endomysial antibody (EMA) tests, a critical serological test for the diagnosis of celiac disease that currently requires labor-intensive and subjective human interpretation. In this study, we employ and comprehensively evaluate the performance of the EfficientNet and EfficientNetV2 architectures in binary (positive vs negative, where all weak and strong positive signals were grouped as positive), three-class (negative, weak positive, strong positive), and four-class (negative, weak positive, strong positive and gray zone) classification scenarios using immunofluorescence images of IgA EMA equivalent (EMA-eq) tests. Our experiments on 368 clinical samples show high performance, with EfficientNetV2-S achieving an accuracy of 99.37% in binary classification, 95.28% in three-class classification, and 86.98% in the complex four-class scenario that introduces gray zone cases as a distinct interpretive category. Contrary to conventional assumptions, medium-sized deep architectures consistently outperformed their larger counterparts. The superior performance of the EfficientNet-V2 models can be attributed to their architectural innovations and higher input resolution (640 × 640 pixels), which proved critical for capturing subtle immunofluorescence patterns. We also incorporate HiRes-CAM (Class Activation Mapping), a convolutional neural network oriented visual explanation tool, to better understand the decisions of the underlying trained deep learning model in an explainable artificial intelligence (AI) manner. This study demonstrates that deep learning has the potential to achieve expert-level performance in EMA-eq test interpretation, offering a path toward more standardized, efficient and objective celiac disease diagnosis while reducing the burden on specialist medical staff.
format: application/pdf
format: text/html
creator: Mehmet Soylu
creator: Ahmet Selman Bozkir
subject: Computational Biology
subject: Radiology and Medical Imaging
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20191
publisher: PeerJ Inc.
rights: © 2025 Soylu and Bozkir
abstract: Deep learning offers promising potential for automating the interpretation of immunoglobulin A (IgA) endomysial antibody (EMA) tests, a critical serological test for the diagnosis of celiac disease that currently requires labor-intensive and subjective human interpretation. In this study, we employ and comprehensively evaluate the performance of the EfficientNet and EfficientNetV2 architectures in binary (positive vs negative, where all weak and strong positive signals were grouped as positive), three-class (negative, weak positive, strong positive), and four-class (negative, weak positive, strong positive and gray zone) classification scenarios using immunofluorescence images of IgA EMA equivalent (EMA-eq) tests. Our experiments on 368 clinical samples show high performance, with EfficientNetV2-S achieving an accuracy of 99.37% in binary classification, 95.28% in three-class classification, and 86.98% in the complex four-class scenario that introduces gray zone cases as a distinct interpretive category. Contrary to conventional assumptions, medium-sized deep architectures consistently outperformed their larger counterparts. The superior performance of the EfficientNet-V2 models can be attributed to their architectural innovations and higher input resolution (640 × 640 pixels), which proved critical for capturing subtle immunofluorescence patterns. We also incorporate HiRes-CAM (Class Activation Mapping), a convolutional neural network oriented visual explanation tool, to better understand the decisions of the underlying trained deep learning model in an explainable artificial intelligence (AI) manner. This study demonstrates that deep learning has the potential to achieve expert-level performance in EMA-eq test interpretation, offering a path toward more standardized, efficient and objective celiac disease diagnosis while reducing the burden on specialist medical staff.
bibliographic citation: Soylu et al. (2025) Recognizing IgA-class endomysial antibody equivalent binding patterns on monkey liver substrate through EfficientNet architectures and deep learning. PeerJ 13:e20191 https://doi.org/10.7717/peerj.20191
date submitted: 2025-05-05
date accepted: 2025-09-15
issued: 2025-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soylu
  given name: Mehmet
author list: Agent
  family name: Bozkir
  given name: Ahmet Selman
doi: 10.7717/peerj.20191
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-15
copyright: © 2025 Soylu and Bozkir
attribution name: Soylu and Bozkir

Effect of circadian rhythm disruption on benign prostatic hyperplasia in rats
type: item
type: AcademicArticle
description: Benign prostatic hyperplasia (BPH) is a common condition in middle-aged and elderly men. Disrupted circadian rhythms (CRD) can directly influence aging, inflammation, metabolic syndrome, and hormonal changes—all of which are closely linked to BPH. This study aimed to investigate whether CRD accelerates prostatic hyperplasia in rats. Twenty male Sprague-Dawley (SD) rats were divided into two batches. A BPH model was established using mixed slow-release pellets of testosterone (T) and estradiol (E2). CRD was induced by continuous light exposure (Cle), while a 12-hour light/12-hour dark cycle defined the control (Con) group. First batch Rats were divided into T+E2 and T+E2+Cle groups. Initial and final body weight, prostate weight, and prostate index (PI) were recorded. Hematoxylin and eosin (H&E) staining was performed. Serum levels of dihydrotestosterone (DHT) and estradiol (E2) were measured by ELISA, and mRNA expression of circadian rhythm genes was assessed via qRT-PCR. Second batch Rats were divided into Con and Cle groups. Body weight, prostate weight, and PI were recorded. H&E staining was used for pathological analysis. Ki-67 expression was assessed by immunohistochemistry (IHC). RNA sequencing (RNA-Seq) was used to investigate gene expression in prostate tissue, validated by qRT-PCR. Differentially expressed genes (DEGs) were analyzed using bioinformatics methods. First batch results CRD significantly increased prostate weight, PI, and epithelial thickness; elevated serum DHT levels; and reduced E2 levels. qRT-PCR confirmed that CRD altered circadian gene expression. Second batch results CRD significantly increased PI and Ki-67 expression in the prostate. GO analysis revealed significant enrichment in immune response, external side of plasma membrane, and carbohydrate binding (p < 0.001). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed enrichment in cytokine-cytokine receptor interaction, viral protein interaction with cytokine and rece…
format: application/pdf
format: text/html
creator: Xiaoxue Huang
creator: Xiaohu Tang
creator: Yuanzhao Xu
creator: Zhiyan Liu
creator: Guangheng Luo
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.20173
publisher: PeerJ Inc.
rights: © 2025 Huang et al.
abstract: Benign prostatic hyperplasia (BPH) is a common condition in middle-aged and elderly men. Disrupted circadian rhythms (CRD) can directly influence aging, inflammation, metabolic syndrome, and hormonal changes—all of which are closely linked to BPH. This study aimed to investigate whether CRD accelerates prostatic hyperplasia in rats. Twenty male Sprague-Dawley (SD) rats were divided into two batches. A BPH model was established using mixed slow-release pellets of testosterone (T) and estradiol (E2). CRD was induced by continuous light exposure (Cle), while a 12-hour light/12-hour dark cycle defined the control (Con) group. First batch Rats were divided into T+E2 and T+E2+Cle groups. Initial and final body weight, prostate weight, and prostate index (PI) were recorded. Hematoxylin and eosin (H&E) staining was performed. Serum levels of dihydrotestosterone (DHT) and estradiol (E2) were measured by ELISA, and mRNA expression of circadian rhythm genes was assessed via qRT-PCR. Second batch Rats were divided into Con and Cle groups. Body weight, prostate weight, and PI were recorded. H&E staining was used for pathological analysis. Ki-67 expression was assessed by immunohistochemistry (IHC). RNA sequencing (RNA-Seq) was used to investigate gene expression in prostate tissue, validated by qRT-PCR. Differentially expressed genes (DEGs) were analyzed using bioinformatics methods. First batch results CRD significantly increased prostate weight, PI, and epithelial thickness; elevated serum DHT levels; and reduced E2 levels. qRT-PCR confirmed that CRD altered circadian gene expression. Second batch results CRD significantly increased PI and Ki-67 expression in the prostate. GO analysis revealed significant enrichment in immune response, external side of plasma membrane, and carbohydrate binding (p < 0.001). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed enrichment in cytokine-cytokine receptor interaction, viral protein interaction with cytokine and rece…
bibliographic citation: Huang et al. (2025) Effect of circadian rhythm disruption on benign prostatic hyperplasia in rats. PeerJ 13:e20173 https://doi.org/10.7717/peerj.20173
date submitted: 2025-03-31
date accepted: 2025-09-11
issued: 2025-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Xiaoxue
author list: Agent
  family name: Tang
  given name: Xiaohu
author list: Agent
  family name: Xu
  given name: Yuanzhao
author list: Agent
  family name: Liu
  given name: Zhiyan
author list: Agent
  family name: Luo
  given name: Guangheng
doi: 10.7717/peerj.20173
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-15
copyright: ©2025 Huang et al.
attribution name: Huang et al.

Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles
type: item
type: AcademicArticle
description: As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds.
format: application/pdf
format: text/html
creator: Yonggang Dong
creator: Sitong Fan
creator: Shunfu He
creator: Wenxin Zhao
creator: Zhuoma Lancuo
creator: Kirill Sharshov
creator: Ying Li
creator: Wen Wang
subject: Microbiology
subject: Virology
subject: Zoology
description: doi:10.7717/peerj.20170
publisher: PeerJ Inc.
rights: © 2025 Dong et al.
abstract: As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds.
bibliographic citation: Dong et al. (2025) Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles. PeerJ 13:e20170 https://doi.org/10.7717/peerj.20170
date submitted: 2025-06-03
date accepted: 2025-09-11
issued: 2025-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Yonggang
author list: Agent
  family name: Fan
  given name: Sitong
author list: Agent
  family name: He
  given name: Shunfu
author list: Agent
  family name: Zhao
  given name: Wenxin
author list: Agent
  family name: Lancuo
  given name: Zhuoma
author list: Agent
  family name: Sharshov
  given name: Kirill
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Wang
  given name: Wen
doi: 10.7717/peerj.20170
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-15
copyright: ©2025 Dong et al.
attribution name: Dong et al.

Detection of terrestrial mammals using environmental DNA during heavy rainfall events and associated influencing factors
type: item
type: AcademicArticle
description: Recent developments in environmental DNA (eDNA) analyses have facilitated non-invasive and cost-effective ecological monitoring. Based on eDNA of terrestrial species released into water upon contact, simultaneous detection of aquatic and terrestrial species is feasible. However, an efficient sampling design for terrestrial vertebrate eDNA in aquatic environments has not yet been established because DNA is rarely released into these environments. In this study, we targeted eDNA transported from land to rivers through surface runoff during rainfall in three rivers and one irrigation channel within the Kiyotake River system, Japan. We quantified the eDNA concentration of a specific terrestrial vertebrate (Bos taurus) using digital polymerase chain reaction (PCR) and examined the efficiency of using filter papers with different pore sizes (0.7 µm and 2.7 µm). We also assessed the influence of various environmental factors (e.g., rainfall characteristics described by the parameters of Gaussian distribution, water turbidity) on eDNA detection across different rainfall events. During the surveys, target DNA was detected in 42 out of 47 samples, suggesting the feasibility of consistently detecting terrestrial mammals from stormwater runoff. Overall, compared with the glass fiber filter with larger pore size, the smaller pore size filter captured more eDNA. The generalized linear mixed model revealed that prolonged rainfall duration, turbidity, and pH had a significant positive effect on eDNA concentration, whereas the distance from the assumed point of entry into the river to the sampling point had a significant negative effect. These results suggest that the runoff and transport of eDNA from terrestrial areas to rivers are enhanced under prolonged rainfall conditions, although eDNA degrades while transported along a longer watercourse by biochemical decomposition and sedimentation.
format: application/pdf
format: text/html
creator: Chen Xu
creator: Kei Nukazawa
subject: Biodiversity
subject: Ecology
description: doi:10.7717/peerj.20166
publisher: PeerJ Inc.
rights: © 2025 Xu and Nukazawa
abstract: Recent developments in environmental DNA (eDNA) analyses have facilitated non-invasive and cost-effective ecological monitoring. Based on eDNA of terrestrial species released into water upon contact, simultaneous detection of aquatic and terrestrial species is feasible. However, an efficient sampling design for terrestrial vertebrate eDNA in aquatic environments has not yet been established because DNA is rarely released into these environments. In this study, we targeted eDNA transported from land to rivers through surface runoff during rainfall in three rivers and one irrigation channel within the Kiyotake River system, Japan. We quantified the eDNA concentration of a specific terrestrial vertebrate (Bos taurus) using digital polymerase chain reaction (PCR) and examined the efficiency of using filter papers with different pore sizes (0.7 µm and 2.7 µm). We also assessed the influence of various environmental factors (e.g., rainfall characteristics described by the parameters of Gaussian distribution, water turbidity) on eDNA detection across different rainfall events. During the surveys, target DNA was detected in 42 out of 47 samples, suggesting the feasibility of consistently detecting terrestrial mammals from stormwater runoff. Overall, compared with the glass fiber filter with larger pore size, the smaller pore size filter captured more eDNA. The generalized linear mixed model revealed that prolonged rainfall duration, turbidity, and pH had a significant positive effect on eDNA concentration, whereas the distance from the assumed point of entry into the river to the sampling point had a significant negative effect. These results suggest that the runoff and transport of eDNA from terrestrial areas to rivers are enhanced under prolonged rainfall conditions, although eDNA degrades while transported along a longer watercourse by biochemical decomposition and sedimentation.
bibliographic citation: Xu et al. (2025) Detection of terrestrial mammals using environmental DNA during heavy rainfall events and associated influencing factors. PeerJ 13:e20166 https://doi.org/10.7717/peerj.20166
date submitted: 2025-06-25
date accepted: 2025-09-11
issued: 2025-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Chen
author list: Agent
  family name: Nukazawa
  given name: Kei
doi: 10.7717/peerj.20166
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-15
copyright: ©2025 Xu and Nukazawa
attribution name: Xu and Nukazawa

Comparison of IAA and amino acid profiles of the selected rootstocks and their accumulation in grafted scion of Cucumis sativus L.
type: item
type: AcademicArticle
description: Finding a suitable rootstock for Cucumis sativus L. is an important area of research, as it is aimed at extending the fruiting period and increasing the yield. In such studies, it is important to evaluate various biochemical parameters in addition to morphometric data, such as amino acid and auxin content, which will reflect the effectiveness of the rootstock for scion growth. In this research, we tested 56 genotypes and lines from four species of the Cucurbitaceae family as potential candidates for grafting cucumber rootstock: Cucurbita ficifolia Bouché, Cucurbita moschata L., Cucurbita pepo L. and Cucurbita maxima Duch. The study focused on the study of morphometric parameters, amino acid and indoleacetic acid (IAA) accumulation in rootstocks at the age of 2 and 4 weeks. Based on the results of the work, the Dunganskaya otb 3 variety of C. maxima was selected as a rootstock for cucumber, since it showed the largest plant and root weight, as well as the highest content of amino acids and IAA. Further, an optimized tongue grafting method was used for grafting cucumber with the selected variety of C. maxima, which in turn contributed to the rapid healing and adaptation of the scion. Also, a significant increase in the amino acids L-valine, L-threonine, L-alanine, L-tyrosine by 28.8; 38.8; 42.5; 98%, respectively and IAA by 39% in the scions compared to the control cucumber plants were observed at the end of the fourth week after grafting. The yield of grafted cucumber plants per plant and per square meter showed an increase of 23% compared to the control. In conclusion, from the obtained data, it can be assumed that grafting of C. sativus onto C. maxima plants is the most suitable and can be recommended for production.
format: application/pdf
format: text/html
creator: Serik Jantassov
creator: Alima Shoibekova
creator: Aigerim Jantassova
creator: Ali Samatov
creator: Bulat Kuluev
creator: Yakov Mineev
creator: Izat Smekenov
creator: Maxat Toishimanov
creator: Gabit Bari
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
description: doi:10.7717/peerj.20159
publisher: PeerJ Inc.
rights: © 2025 Jantassov et al.
abstract: Finding a suitable rootstock for Cucumis sativus L. is an important area of research, as it is aimed at extending the fruiting period and increasing the yield. In such studies, it is important to evaluate various biochemical parameters in addition to morphometric data, such as amino acid and auxin content, which will reflect the effectiveness of the rootstock for scion growth. In this research, we tested 56 genotypes and lines from four species of the Cucurbitaceae family as potential candidates for grafting cucumber rootstock: Cucurbita ficifolia Bouché, Cucurbita moschata L., Cucurbita pepo L. and Cucurbita maxima Duch. The study focused on the study of morphometric parameters, amino acid and indoleacetic acid (IAA) accumulation in rootstocks at the age of 2 and 4 weeks. Based on the results of the work, the Dunganskaya otb 3 variety of C. maxima was selected as a rootstock for cucumber, since it showed the largest plant and root weight, as well as the highest content of amino acids and IAA. Further, an optimized tongue grafting method was used for grafting cucumber with the selected variety of C. maxima, which in turn contributed to the rapid healing and adaptation of the scion. Also, a significant increase in the amino acids L-valine, L-threonine, L-alanine, L-tyrosine by 28.8; 38.8; 42.5; 98%, respectively and IAA by 39% in the scions compared to the control cucumber plants were observed at the end of the fourth week after grafting. The yield of grafted cucumber plants per plant and per square meter showed an increase of 23% compared to the control. In conclusion, from the obtained data, it can be assumed that grafting of C. sativus onto C. maxima plants is the most suitable and can be recommended for production.
bibliographic citation: Jantassov et al. (2025) Comparison of IAA and amino acid profiles of the selected rootstocks and their accumulation in grafted scion of Cucumis sativus L.. PeerJ 13:e20159 https://doi.org/10.7717/peerj.20159
date submitted: 2025-04-21
date accepted: 2025-09-10
issued: 2025-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jantassov
  given name: Serik
author list: Agent
  family name: Shoibekova
  given name: Alima
author list: Agent
  family name: Jantassova
  given name: Aigerim
author list: Agent
  family name: Samatov
  given name: Ali
author list: Agent
  family name: Kuluev
  given name: Bulat
author list: Agent
  family name: Mineev
  given name: Yakov
author list: Agent
  family name: Smekenov
  given name: Izat
author list: Agent
  family name: Toishimanov
  given name: Maxat
author list: Agent
  family name: Bari
  given name: Gabit
doi: 10.7717/peerj.20159
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-15
copyright: ©2025 Jantassov et al.
attribution name: Jantassov et al.

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