PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparison of animal models for immune premature ovarian insufficiency
items: Geology correlates with gut microbial community composition in the Mountainsnails (Oreohelicidae: Oreohelix)
items: Diagnostic accuracy of the atherogenic index of plasma in metabolic syndrome: a diagnostic meta-analysis
items: Genetic modifiers of response to thalidomide in transfusion-dependent beta-thalassemia patients: a whole-exome sequence analysis
items: Soil storage temperature and air-drying did not significantly change bacterial taxa in the short-term
items: Bioinformatic analysis and experimental validation of hub autophagy-related genes as novel biomarkers for type 2 diabetes mellitus and Alzheimer’s disease
items: Factors influencing compliance with endoscopy final rinsing water standards: a study in a tertiary hospital setting
items: Knowledge and attitudes of university staff toward organ donation: a cross-sectional study in Oman
items: Trade-offs between aquatic and terrestrial locomotion and functional parallelism in Desmognathus salamanders
items: Predictive role of systemic immune-inflammation index in the prognosis of patients with advanced left-sided colorectal cancer: a retrospective study

Comparison of animal models for immune premature ovarian insufficiency
type: item
type: AcademicArticle
description: Premature ovarian insufficiency (POI) severely impacts women’s reproductive and overall health, yet effective treatments remain elusive. Research on its pathogenic mechanisms and therapeutic strategies is therefore critical. Due to the scarcity of ovarian samples from POI patients, animal models have become indispensable tools for investigation. Notably, immune-related POI accounts for an increasing proportion of cases, with over half of idiopathic POI cases hypothesized to involve immune dysregulation. Consequently, immune-mediated POI animal models are widely used to study immune-related mechanisms. This article compares the advantages, limitations, and applications of various immune-related POI animal models, aiming to guide researchers in selecting the most appropriate model for their specific research goals and experimental designs.
format: application/pdf
format: text/html
creator: Anchun Hu
creator: Yanli Mu
creator: Guanyou Huang
creator: Shuyun Zhao
subject: Biochemistry
subject: Cell Biology
subject: Zoology
subject: Immunology
subject: Women’s Health
description: doi:10.7717/peerj.20091
publisher: PeerJ Inc.
rights: © 2025 Hu et al.
abstract: Premature ovarian insufficiency (POI) severely impacts women’s reproductive and overall health, yet effective treatments remain elusive. Research on its pathogenic mechanisms and therapeutic strategies is therefore critical. Due to the scarcity of ovarian samples from POI patients, animal models have become indispensable tools for investigation. Notably, immune-related POI accounts for an increasing proportion of cases, with over half of idiopathic POI cases hypothesized to involve immune dysregulation. Consequently, immune-mediated POI animal models are widely used to study immune-related mechanisms. This article compares the advantages, limitations, and applications of various immune-related POI animal models, aiming to guide researchers in selecting the most appropriate model for their specific research goals and experimental designs.
bibliographic citation: Hu et al. (2025) Comparison of animal models for immune premature ovarian insufficiency. PeerJ 13:e20091 https://doi.org/10.7717/peerj.20091
date submitted: 2025-04-08
date accepted: 2025-08-26
issued: 2025-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Anchun
author list: Agent
  family name: Mu
  given name: Yanli
author list: Agent
  family name: Huang
  given name: Guanyou
author list: Agent
  family name: Zhao
  given name: Shuyun
doi: 10.7717/peerj.20091
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-07
copyright: ©2025 Hu et al.
attribution name: Hu et al.

Geology correlates with gut microbial community composition in the Mountainsnails (Oreohelicidae: Oreohelix)
type: item
type: AcademicArticle
description: Background Species that require soil mineral macronutrients for survival may depend on specific microbiome communities to aid in nutrient processing. Land snails, which utilize environmental minerals to synthesize a shell of calcium carbonate (CaCO3), may rely on or possess distinct gut microbiome communities depending on soil mineral characteristics. Here, we investigate whether the occurrence of calcareous vs. non-calcareous soils is associated with shifts the composition of the gut microbiome of the calciphilous and highly diverse land snail genus Oreohelix from the Western United States. Methods We collected snail and soil samples from nine sites in central Idaho: five near, and four away from calcium-rich geology. We sequenced the V4 region of the 16S rRNA gene of these samples to assess the gut microbiome compositions of Oreohelix land snails on and off calcium-rich substrates. After data clean-up and filtering we had 68 snail and 25 soil microbiome samples. Results We found that snail gut microbiomes differed significantly from the surface soil microbiome, with many amplicon sequence variants being unique and ubiquitous in the snails. We also found small, but significant, differences between snails on and off calcium-rich rocks. Our findings indicate that the gut microbial community assembly process of land snails is complex and does not reflect a simple relationship with the underlying soil microbiome. While we find a pattern of differences associated with the proximity of calcium-rich geology, the snail microbiome communities are likely forming based on a variety of other factors, including diet and host filtering. Furthermore, we found multiple microbial taxa that were ubiquitous in the snails and rare in the nearby substrate microbiomes. Future work should focus on disentangling the role of habitat and the functional importance (or lack thereof) of the microbial taxa that are common to almost every sampled snail.
format: application/pdf
format: text/html
creator: Ian M. Oiler
creator: T. Mason Linscott
creator: Christine E. Parent
subject: Biodiversity
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.20080
publisher: PeerJ Inc.
rights: © 2025 Oiler et al.
abstract: Background Species that require soil mineral macronutrients for survival may depend on specific microbiome communities to aid in nutrient processing. Land snails, which utilize environmental minerals to synthesize a shell of calcium carbonate (CaCO3), may rely on or possess distinct gut microbiome communities depending on soil mineral characteristics. Here, we investigate whether the occurrence of calcareous vs. non-calcareous soils is associated with shifts the composition of the gut microbiome of the calciphilous and highly diverse land snail genus Oreohelix from the Western United States. Methods We collected snail and soil samples from nine sites in central Idaho: five near, and four away from calcium-rich geology. We sequenced the V4 region of the 16S rRNA gene of these samples to assess the gut microbiome compositions of Oreohelix land snails on and off calcium-rich substrates. After data clean-up and filtering we had 68 snail and 25 soil microbiome samples. Results We found that snail gut microbiomes differed significantly from the surface soil microbiome, with many amplicon sequence variants being unique and ubiquitous in the snails. We also found small, but significant, differences between snails on and off calcium-rich rocks. Our findings indicate that the gut microbial community assembly process of land snails is complex and does not reflect a simple relationship with the underlying soil microbiome. While we find a pattern of differences associated with the proximity of calcium-rich geology, the snail microbiome communities are likely forming based on a variety of other factors, including diet and host filtering. Furthermore, we found multiple microbial taxa that were ubiquitous in the snails and rare in the nearby substrate microbiomes. Future work should focus on disentangling the role of habitat and the functional importance (or lack thereof) of the microbial taxa that are common to almost every sampled snail.
bibliographic citation: Oiler et al. (2025) Geology correlates with gut microbial community composition in the Mountainsnails (Oreohelicidae: Oreohelix). PeerJ 13:e20080 https://doi.org/10.7717/peerj.20080
date submitted: 2024-09-12
date accepted: 2025-08-24
issued: 2025-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oiler
  given name: Ian M.
author list: Agent
  family name: Linscott
  given name: T. Mason
author list: Agent
  family name: Parent
  given name: Christine E.
doi: 10.7717/peerj.20080
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-07
copyright: ©2025 Oiler et al.
attribution name: Oiler et al.

Diagnostic accuracy of the atherogenic index of plasma in metabolic syndrome: a diagnostic meta-analysis
type: item
type: AcademicArticle
description: Objective This study aims to assess the diagnostic performance of the atherogenic index of plasma (AIP) in estimating the risk of metabolic syndrome (MetS) among adults across various geographic regions. Methods A comprehensive search was conducted across EMBASE, Web of Science, PubMed, and the Cochrane Library from their inception until September 29, 2024. Eligible studies were selected and evaluated for methodological quality using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) framework. Statistical analyses were performed using STATA 15.1. Sensitivity, specificity, diagnostic odds ratio, positive and negative likelihood ratios, the summary receiver operating characteristic (SROC), curve, and 95% confidence intervals (CI) were calculated to assess the diagnostic accuracy of AIP for MetS. Statistical significance was defined as a p-value < 0.05. Results Eleven observational studies involving 36,463 participants were included. The analysis showed that AIP is an effective biomarker for identifying the risk of MetS, with an area under the curve (AUC) of 0.84 (95% CI [0.81–0.87]). AIP demonstrated comparable diagnostic value in both males and females, with an AUC of 0.82, highlighting its potential utility in sex-specific assessments. Geographic region, diagnostic reference standards, and publication year were identified as potential sources of heterogeneity. Conclusions This study demonstrates that AIP is a relatively accurate tool for detecting MetS, supporting its role in prevention and in reducing the risk of associated chronic diseases. Further research with larger sample sizes and multi-center designs is needed to explore the combined use of AIP with other biomarkers to enhance diagnostic accuracy for MetS.
format: application/pdf
format: text/html
creator: Yuge Gao
creator: Chengcheng He
creator: Jia Mi
subject: Cardiology
subject: Diabetes and Endocrinology
subject: Evidence Based Medicine
subject: Metabolic Sciences
description: doi:10.7717/peerj.20074
publisher: PeerJ Inc.
rights: © 2025 Gao et al.
abstract: Objective This study aims to assess the diagnostic performance of the atherogenic index of plasma (AIP) in estimating the risk of metabolic syndrome (MetS) among adults across various geographic regions. Methods A comprehensive search was conducted across EMBASE, Web of Science, PubMed, and the Cochrane Library from their inception until September 29, 2024. Eligible studies were selected and evaluated for methodological quality using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) framework. Statistical analyses were performed using STATA 15.1. Sensitivity, specificity, diagnostic odds ratio, positive and negative likelihood ratios, the summary receiver operating characteristic (SROC), curve, and 95% confidence intervals (CI) were calculated to assess the diagnostic accuracy of AIP for MetS. Statistical significance was defined as a p-value < 0.05. Results Eleven observational studies involving 36,463 participants were included. The analysis showed that AIP is an effective biomarker for identifying the risk of MetS, with an area under the curve (AUC) of 0.84 (95% CI [0.81–0.87]). AIP demonstrated comparable diagnostic value in both males and females, with an AUC of 0.82, highlighting its potential utility in sex-specific assessments. Geographic region, diagnostic reference standards, and publication year were identified as potential sources of heterogeneity. Conclusions This study demonstrates that AIP is a relatively accurate tool for detecting MetS, supporting its role in prevention and in reducing the risk of associated chronic diseases. Further research with larger sample sizes and multi-center designs is needed to explore the combined use of AIP with other biomarkers to enhance diagnostic accuracy for MetS.
bibliographic citation: Gao et al. (2025) Diagnostic accuracy of the atherogenic index of plasma in metabolic syndrome: a diagnostic meta-analysis. PeerJ 13:e20074 https://doi.org/10.7717/peerj.20074
date submitted: 2025-02-11
date accepted: 2025-08-22
issued: 2025-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Yuge
author list: Agent
  family name: He
  given name: Chengcheng
author list: Agent
  family name: Mi
  given name: Jia
doi: 10.7717/peerj.20074
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-07
copyright: ©2025 Gao et al.
attribution name: Gao et al.

Genetic modifiers of response to thalidomide in transfusion-dependent beta-thalassemia patients: a whole-exome sequence analysis
type: item
type: AcademicArticle
description: Background Thalidomide induces fetal hemoglobin and renders most thalassemia patients transfusion-independent. Some patients, however, do not respond. Underlying genetic variations responsible for variable responses to thalidomide are unexplored. Aims and objectives To discover genetic variations that influence response to thalidomide in transfusion-dependent beta-thalassemia patients. Methods Twenty beta-thalassemia patients (14 excellent responders and six non-responders) who had received thalidomide were included in the study by a non-probability purposive sampling technique. Patients who showed a rise of >2 mg/dl in hemoglobin level and/or whose hemoglobin levels reached 9 gm/dl without blood transfusions were designated as excellent responders. Patients whose hemoglobin levels did not show an increment rise of >2 and/or whose hemoglobin levels did not rise above 5.9 gm/dl and needed blood transfusions to maintain optimal hemoglobin levels were designated as non-responders. DNA was extracted, and whole-exome sequencing was performed on an Illumina HiSeq System. Aligning and variant calling were done by the Sentieon software. Annotation was done by Annovar. Results The age of study participants ranged from 1–12 years, with a mean of 5.45 ± 3.81 years. There were 17 (85%) males and three (15%) females. A total of 222,180 germline variants were identified across 20 subjects, from which 24 candidate variants across 24 genes were identified. The three most common polymorphisms in the excellent responder group were found in the exon region of CHI3L1 (rs880633), NPNT (rs35132891), and ZNF 208 (rs10425763), which were found in 92%, 85%, and 71% cases, respectively. The commonest polymorphisms in the non-responder group were found in the PM20D1 gene (rs7518979), LGR6 (rs75658797), MYH15 (rs4299484), and RESF1 (rs3207618), each of which was found in 66.6% cases. Conclusion This study shows a significant association of single-nucleotide polymorphisms rs880633, rs35132891, …
format: application/pdf
format: text/html
creator: Waleed Mohammed Bawazir
creator: Muhammad Ihtesham Khan
creator: Mohannad Saeed Hazzazi
creator: Ammar Abdullah Basabrain
creator: Muhammad Tariq Masood Khan
creator: Sami Siraj
creator: Majed Naser Almashjary
creator: Osman Radhwi
creator: Steve Harakeh
creator: Yasar Mehmood Yousafzai
subject: Genetics
subject: Hematology
subject: Internal Medicine
subject: Pathology
subject: Medical Genetics
description: doi:10.7717/peerj.20038
publisher: PeerJ Inc.
rights: © 2025 Bawazir et al.
abstract: Background Thalidomide induces fetal hemoglobin and renders most thalassemia patients transfusion-independent. Some patients, however, do not respond. Underlying genetic variations responsible for variable responses to thalidomide are unexplored. Aims and objectives To discover genetic variations that influence response to thalidomide in transfusion-dependent beta-thalassemia patients. Methods Twenty beta-thalassemia patients (14 excellent responders and six non-responders) who had received thalidomide were included in the study by a non-probability purposive sampling technique. Patients who showed a rise of >2 mg/dl in hemoglobin level and/or whose hemoglobin levels reached 9 gm/dl without blood transfusions were designated as excellent responders. Patients whose hemoglobin levels did not show an increment rise of >2 and/or whose hemoglobin levels did not rise above 5.9 gm/dl and needed blood transfusions to maintain optimal hemoglobin levels were designated as non-responders. DNA was extracted, and whole-exome sequencing was performed on an Illumina HiSeq System. Aligning and variant calling were done by the Sentieon software. Annotation was done by Annovar. Results The age of study participants ranged from 1–12 years, with a mean of 5.45 ± 3.81 years. There were 17 (85%) males and three (15%) females. A total of 222,180 germline variants were identified across 20 subjects, from which 24 candidate variants across 24 genes were identified. The three most common polymorphisms in the excellent responder group were found in the exon region of CHI3L1 (rs880633), NPNT (rs35132891), and ZNF 208 (rs10425763), which were found in 92%, 85%, and 71% cases, respectively. The commonest polymorphisms in the non-responder group were found in the PM20D1 gene (rs7518979), LGR6 (rs75658797), MYH15 (rs4299484), and RESF1 (rs3207618), each of which was found in 66.6% cases. Conclusion This study shows a significant association of single-nucleotide polymorphisms rs880633, rs35132891, …
bibliographic citation: Bawazir et al. (2025) Genetic modifiers of response to thalidomide in transfusion-dependent beta-thalassemia patients: a whole-exome sequence analysis. PeerJ 13:e20038 https://doi.org/10.7717/peerj.20038
date submitted: 2025-06-04
date accepted: 2025-08-14
issued: 2025-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bawazir
  given name: Waleed Mohammed
author list: Agent
  family name: Khan
  given name: Muhammad Ihtesham
author list: Agent
  family name: Hazzazi
  given name: Mohannad Saeed
author list: Agent
  family name: Basabrain
  given name: Ammar Abdullah
author list: Agent
  family name: Khan
  given name: Muhammad Tariq Masood
author list: Agent
  family name: Siraj
  given name: Sami
author list: Agent
  family name: Almashjary
  given name: Majed Naser
author list: Agent
  family name: Radhwi
  given name: Osman
author list: Agent
  family name: Harakeh
  given name: Steve
author list: Agent
  family name: Yousafzai
  given name: Yasar Mehmood
doi: 10.7717/peerj.20038
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-07
copyright: © 2025 Bawazir et al.
attribution name: Bawazir et al.

Soil storage temperature and air-drying did not significantly change bacterial taxa in the short-term
type: item
type: AcademicArticle
description: Analysing soil microbial communities is vital for understanding ecosystem health, but samples from remote locations often require preservation before DNA can be extracted. In this study, we used the 16S rRNA amplicon sequencing to investigate how different storage methods affect soil microbial diversity over 4 weeks. We implemented storage temperature and moisture as two experimental factors. Three topsoils (sandy, silty loam, and clay loam) were collected and stored under four conditions: frozen at −20 °C, refrigerated at 4 °C, room temperature, and air-dried. DNA extractions and sequencing were performed at 1, 3, 7, 14, and 28 days. Our results revealed that storage temperature and moisture did not substantially change bacterial diversity and composition across all three soil types. Rare taxa showed a similar pattern to abundant taxa but were more variable in beta diversity. Overall, all tested methods effectively preserved both abundant and rare taxa in the short term. However, the long-term impacts of the sample storage, particularly on rare taxa, need further exploration.
format: application/pdf
format: text/html
creator: Mingming Du
creator: Peipei Xue
creator: Budiman Minasny
subject: Agricultural Science
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.20162
publisher: PeerJ Inc.
rights: © 2025 Du et al.
abstract: Analysing soil microbial communities is vital for understanding ecosystem health, but samples from remote locations often require preservation before DNA can be extracted. In this study, we used the 16S rRNA amplicon sequencing to investigate how different storage methods affect soil microbial diversity over 4 weeks. We implemented storage temperature and moisture as two experimental factors. Three topsoils (sandy, silty loam, and clay loam) were collected and stored under four conditions: frozen at −20 °C, refrigerated at 4 °C, room temperature, and air-dried. DNA extractions and sequencing were performed at 1, 3, 7, 14, and 28 days. Our results revealed that storage temperature and moisture did not substantially change bacterial diversity and composition across all three soil types. Rare taxa showed a similar pattern to abundant taxa but were more variable in beta diversity. Overall, all tested methods effectively preserved both abundant and rare taxa in the short term. However, the long-term impacts of the sample storage, particularly on rare taxa, need further exploration.
bibliographic citation: Du et al. (2025) Soil storage temperature and air-drying did not significantly change bacterial taxa in the short-term. PeerJ 13:e20162 https://doi.org/10.7717/peerj.20162
date submitted: 2025-07-11
date accepted: 2025-09-10
issued: 2025-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Mingming
author list: Agent
  family name: Xue
  given name: Peipei
author list: Agent
  family name: Minasny
  given name: Budiman
doi: 10.7717/peerj.20162
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-06
copyright: © 2025 Du et al.
attribution name: Du et al.

Bioinformatic analysis and experimental validation of hub autophagy-related genes as novel biomarkers for type 2 diabetes mellitus and Alzheimer’s disease
type: item
type: AcademicArticle
description: Background & Objectives Alzheimer’s disease (AD) and type 2 diabetes mellitus (T2DM) share considerable similarities in their proposed patho mechanisms. Autophagy, an intrinsic cellular process involved in the degradation of dysfunctional organelles and abnormal proteins, has been implicated in the pathogenesis of both AD and T2DM. This study aims to identify potential shared biomarkers related to autophagy in AD and T2DM by analyzing hub differentially expressed autophagy-related genes (DEARGs) and examining their potential functions. Methods Gene expression profiles for AD and T2DM were acquired from the Gene Expression Omnibus (GEO) database (training sets: GSE109887 for AD and GSE104674 for T2DM; validation sets: GSE122063 for AD and GSE64998 for T2DM). Autophagy-related genes (ARGs) were extracted from multiple databases. DEARGs were identified and integrated with module genes derived from weighted gene co-expression network analysis (WGCNA) to determine key shared ARGs. Then, the STRING database was used to construct a protein-protein interaction (PPI) network, from which hub genes were identified. These hub genes were validated using independent microarray datasets through differential expression analysis, and ROC curves were generated to assess their diagnostic value. Moreover, the expression of the hub genes was validated in brain tissues of T2DM mouse models using qRT-PCR. Results A total of 33 shared DEARGs were identified, among which 12 were designated as hub genes (ANXA5, CCND1, MAP2K1, HSPB1, BNIP3, BAG3, YAP1, MET, FBXW7, CCL2, PFKFB3, CDKN1A) in both AD and T2DM patients. Validation using other datasets confirmed that ANXA5, BAG3, and CDKN1A remained significantly upregulated, while MET remained downregulated in both AD and T2DM patients. Additionally, PFKFB3 showed an inverse expression pattern between the two diseases. The diagnostic performance of these five hub genes was assessed using ROC curves, with all five exhibiting values of area under th…
format: application/pdf
format: text/html
creator: Rui Zhang
creator: Ruowei Wang
creator: Shuna Zhai
creator: Chunhong Shen
creator: Yu An
creator: Quanri Liu
subject: Bioinformatics
subject: Cognitive Disorders
subject: Diabetes and Endocrinology
subject: Neurology
subject: Metabolic Sciences
description: doi:10.7717/peerj.20143
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Background & Objectives Alzheimer’s disease (AD) and type 2 diabetes mellitus (T2DM) share considerable similarities in their proposed patho mechanisms. Autophagy, an intrinsic cellular process involved in the degradation of dysfunctional organelles and abnormal proteins, has been implicated in the pathogenesis of both AD and T2DM. This study aims to identify potential shared biomarkers related to autophagy in AD and T2DM by analyzing hub differentially expressed autophagy-related genes (DEARGs) and examining their potential functions. Methods Gene expression profiles for AD and T2DM were acquired from the Gene Expression Omnibus (GEO) database (training sets: GSE109887 for AD and GSE104674 for T2DM; validation sets: GSE122063 for AD and GSE64998 for T2DM). Autophagy-related genes (ARGs) were extracted from multiple databases. DEARGs were identified and integrated with module genes derived from weighted gene co-expression network analysis (WGCNA) to determine key shared ARGs. Then, the STRING database was used to construct a protein-protein interaction (PPI) network, from which hub genes were identified. These hub genes were validated using independent microarray datasets through differential expression analysis, and ROC curves were generated to assess their diagnostic value. Moreover, the expression of the hub genes was validated in brain tissues of T2DM mouse models using qRT-PCR. Results A total of 33 shared DEARGs were identified, among which 12 were designated as hub genes (ANXA5, CCND1, MAP2K1, HSPB1, BNIP3, BAG3, YAP1, MET, FBXW7, CCL2, PFKFB3, CDKN1A) in both AD and T2DM patients. Validation using other datasets confirmed that ANXA5, BAG3, and CDKN1A remained significantly upregulated, while MET remained downregulated in both AD and T2DM patients. Additionally, PFKFB3 showed an inverse expression pattern between the two diseases. The diagnostic performance of these five hub genes was assessed using ROC curves, with all five exhibiting values of area under th…
bibliographic citation: Zhang et al. (2025) Bioinformatic analysis and experimental validation of hub autophagy-related genes as novel biomarkers for type 2 diabetes mellitus and Alzheimer’s disease. PeerJ 13:e20143 https://doi.org/10.7717/peerj.20143
date submitted: 2025-04-25
date accepted: 2025-09-04
issued: 2025-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Rui
author list: Agent
  family name: Wang
  given name: Ruowei
author list: Agent
  family name: Zhai
  given name: Shuna
author list: Agent
  family name: Shen
  given name: Chunhong
author list: Agent
  family name: An
  given name: Yu
author list: Agent
  family name: Liu
  given name: Quanri
doi: 10.7717/peerj.20143
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-06
copyright: © 2025 Zhang et al.
attribution name: Zhang et al.

Factors influencing compliance with endoscopy final rinsing water standards: a study in a tertiary hospital setting
type: item
type: AcademicArticle
description: Background Maintaining a high compliance rate for final rinsing water is essential for patient safety and infection control in healthcare facilities. This study aims to investigate the causes of fluctuations in compliance rates at a tertiary hospital and evaluate the effectiveness of preventive measures. Methods Monitoring data from October 2022 to December 2023 were analyzed to assess microbial contamination in final rinse water. Environmental assessments and literature reviews were conducted to identify potential contributing factors. Strategic interventions were implemented, and their impact on water quality and infection control was systematically evaluated. Findings Initial assessments revealed fluctuating compliance rates, with faucet aerators identified as a potential source of contamination. Water samples collected before the aerator showed 100% compliance (6/6 samples), while colonies of Cupriavidus pauculus and Stenotrophomonas maltophilia were detected on aerator surfaces and in final rinse water. After removing the aerators and enhancing disinfection protocols, compliance improved significantly, with subsequent samples meeting infection control standards (≤10 CFU/100 mL). Conclusion This study suggests a potential link between fluctuations in endoscopy final rinsing water quality and the presence of faucet aerators. These findings support further research and the development of guidelines for the appropriate use of aerators in healthcare settings.
format: application/pdf
format: text/html
creator: Yuhua Yuan
creator: Lihong Ye
creator: Tianyi Lu
creator: Baihuan Feng
creator: Jin Zhao
subject: Microbiology
subject: Evidence Based Medicine
subject: Infectious Diseases
subject: Public Health
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.20134
publisher: PeerJ Inc.
rights: © 2025 Yuan et al.
abstract: Background Maintaining a high compliance rate for final rinsing water is essential for patient safety and infection control in healthcare facilities. This study aims to investigate the causes of fluctuations in compliance rates at a tertiary hospital and evaluate the effectiveness of preventive measures. Methods Monitoring data from October 2022 to December 2023 were analyzed to assess microbial contamination in final rinse water. Environmental assessments and literature reviews were conducted to identify potential contributing factors. Strategic interventions were implemented, and their impact on water quality and infection control was systematically evaluated. Findings Initial assessments revealed fluctuating compliance rates, with faucet aerators identified as a potential source of contamination. Water samples collected before the aerator showed 100% compliance (6/6 samples), while colonies of Cupriavidus pauculus and Stenotrophomonas maltophilia were detected on aerator surfaces and in final rinse water. After removing the aerators and enhancing disinfection protocols, compliance improved significantly, with subsequent samples meeting infection control standards (≤10 CFU/100 mL). Conclusion This study suggests a potential link between fluctuations in endoscopy final rinsing water quality and the presence of faucet aerators. These findings support further research and the development of guidelines for the appropriate use of aerators in healthcare settings.
bibliographic citation: Yuan et al. (2025) Factors influencing compliance with endoscopy final rinsing water standards: a study in a tertiary hospital setting. PeerJ 13:e20134 https://doi.org/10.7717/peerj.20134
date submitted: 2025-02-10
date accepted: 2025-09-03
issued: 2025-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Yuhua
author list: Agent
  family name: Ye
  given name: Lihong
author list: Agent
  family name: Lu
  given name: Tianyi
author list: Agent
  family name: Feng
  given name: Baihuan
author list: Agent
  family name: Zhao
  given name: Jin
doi: 10.7717/peerj.20134
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-06
copyright: ©2025 Yuan et al.
attribution name: Yuan et al.

Knowledge and attitudes of university staff toward organ donation: a cross-sectional study in Oman
type: item
type: AcademicArticle
description: Background Organ donation remains low when it is not accompanied by a good knowledge and positive attitude. Most published articles have evaluated organ donation knowledge and attitudes within single categories such as healthcare workers, students, or patients. Few studies have assessed these factors across various job categories. Therefore, this study aimed to fill that gap by evaluating knowledge and attitudes about organ donation among university staff from various job categories. Methods A cross-sectional study was conducted among university staff between June 2023 and January 2024 using an online validated self-designed questionnaire. University employees were divided into academic, medical, technical and administrative staff. The survey instrument included five distinct sections: study information, informed consent, demographic data, knowledge about organ donation, and attitudes toward organ donation. Analyses included descriptive statistics, Chi-square tests, and binary logistic regression. Results The study included 385 staff. 64.4% were females, and 52.2% were in the age group between 30–41 years old. The majority of participants demonstrated good knowledge about organ donation (67.5%) and brain death (63.9%), while a significant proportion (67.5%) exhibited a negative attitude toward organ donation. Medical staff have the highest knowledge and attitude with 94.7% and 60.5%, respectively. Multivariate analysis revealed that medical and academic staff were more likely than administrative staff to have good knowledge (AOR 9.244, 95% CI [2.143–39.871]; AOR 2.300, 95% CI [1.126–4.696], respectively) and a positive attitude (AOR 3.444, 95% CI [1.633–7.262]; AOR 2.636, 95% CI [1.266–5.491], respectively), while females were 2.026 times more likely (95% CI [1.246–3.295]) to have good knowledge compared to males. The most cited organ for organ donation was kidneys (94.5%). The most common reason for supporting donating organs among university students was to save a…
format: application/pdf
format: text/html
creator: Nasar Alwahaibi
creator: Shahd Al Ghawi
creator: Mohammed Al-Badi
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.20133
publisher: PeerJ Inc.
rights: © 2025 Alwahaibi et al.
abstract: Background Organ donation remains low when it is not accompanied by a good knowledge and positive attitude. Most published articles have evaluated organ donation knowledge and attitudes within single categories such as healthcare workers, students, or patients. Few studies have assessed these factors across various job categories. Therefore, this study aimed to fill that gap by evaluating knowledge and attitudes about organ donation among university staff from various job categories. Methods A cross-sectional study was conducted among university staff between June 2023 and January 2024 using an online validated self-designed questionnaire. University employees were divided into academic, medical, technical and administrative staff. The survey instrument included five distinct sections: study information, informed consent, demographic data, knowledge about organ donation, and attitudes toward organ donation. Analyses included descriptive statistics, Chi-square tests, and binary logistic regression. Results The study included 385 staff. 64.4% were females, and 52.2% were in the age group between 30–41 years old. The majority of participants demonstrated good knowledge about organ donation (67.5%) and brain death (63.9%), while a significant proportion (67.5%) exhibited a negative attitude toward organ donation. Medical staff have the highest knowledge and attitude with 94.7% and 60.5%, respectively. Multivariate analysis revealed that medical and academic staff were more likely than administrative staff to have good knowledge (AOR 9.244, 95% CI [2.143–39.871]; AOR 2.300, 95% CI [1.126–4.696], respectively) and a positive attitude (AOR 3.444, 95% CI [1.633–7.262]; AOR 2.636, 95% CI [1.266–5.491], respectively), while females were 2.026 times more likely (95% CI [1.246–3.295]) to have good knowledge compared to males. The most cited organ for organ donation was kidneys (94.5%). The most common reason for supporting donating organs among university students was to save a…
bibliographic citation: Alwahaibi et al. (2025) Knowledge and attitudes of university staff toward organ donation: a cross-sectional study in Oman. PeerJ 13:e20133 https://doi.org/10.7717/peerj.20133
date submitted: 2025-05-29
date accepted: 2025-09-03
issued: 2025-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alwahaibi
  given name: Nasar
author list: Agent
  family name: Al Ghawi
  given name: Shahd
author list: Agent
  family name: Al-Badi
  given name: Mohammed
doi: 10.7717/peerj.20133
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-06
copyright: © 2025 Alwahaibi et al.
attribution name: Alwahaibi et al.

Trade-offs between aquatic and terrestrial locomotion and functional parallelism in Desmognathus salamanders
type: item
type: AcademicArticle
description: A trade-off between aquatic and terrestrial locomotion is self-evident at broad phylogenetic scales. While the effects of more subtle trade-offs in the evolution of closely related species are less clear, they are hypothesized to drive ecological speciation and adaptive radiation. Amphibious animals strike a balance between aquatic and terrestrial activity, and the need to maintain performance in one medium is hypothesized to constrain evolution of high performance in the other (the running-swimming dilemma). Closely related species of Desmognathus salamanders partition local habitats along a gradient from mid-stream to stream edge to completely terrestrial. The trade-off hypothesis predicts that these species will differ in relative running vs. swimming performance depending on the relative importance of each mode of locomotion in their niches. Here, I show that primarily aquatic Desmognathus ecomorphs are superior swimmers and inferior runners relative to semi-aquatic ecomorphs using paired escape performance trials in aquatic and terrestrial arenas. I measured performance as the velocity of the fast-start response to simulated predator attack. I tested two species of each ecomorph, representing two divergent clades with parallel evolution of aquatic and semi-aquatic species. Notably, the different southern clade ecomorphs have been genetically isolated for millions of years, whereas the northern clade ecomorphs share a recent common ancestor and interbreed regularly. My results showed a negative correlation between aquatic and terrestrial performance, with aquatic ecomorphs being faster swimmers and semi-aquatic ecomorphs being faster runners. While there was a possible trend consistent with faster swimming speeds of northern forms relative to their southern counterparts, the functional differences between ecomorphs were similar in both clades. These results are consistent with the hypothesis that trade-offs between aquatic and terrestrial locomotion have contrib…
format: application/pdf
format: text/html
creator: Benjamin M. Fitzpatrick
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.20111
publisher: PeerJ Inc.
rights: © 2025 Fitzpatrick
abstract: A trade-off between aquatic and terrestrial locomotion is self-evident at broad phylogenetic scales. While the effects of more subtle trade-offs in the evolution of closely related species are less clear, they are hypothesized to drive ecological speciation and adaptive radiation. Amphibious animals strike a balance between aquatic and terrestrial activity, and the need to maintain performance in one medium is hypothesized to constrain evolution of high performance in the other (the running-swimming dilemma). Closely related species of Desmognathus salamanders partition local habitats along a gradient from mid-stream to stream edge to completely terrestrial. The trade-off hypothesis predicts that these species will differ in relative running vs. swimming performance depending on the relative importance of each mode of locomotion in their niches. Here, I show that primarily aquatic Desmognathus ecomorphs are superior swimmers and inferior runners relative to semi-aquatic ecomorphs using paired escape performance trials in aquatic and terrestrial arenas. I measured performance as the velocity of the fast-start response to simulated predator attack. I tested two species of each ecomorph, representing two divergent clades with parallel evolution of aquatic and semi-aquatic species. Notably, the different southern clade ecomorphs have been genetically isolated for millions of years, whereas the northern clade ecomorphs share a recent common ancestor and interbreed regularly. My results showed a negative correlation between aquatic and terrestrial performance, with aquatic ecomorphs being faster swimmers and semi-aquatic ecomorphs being faster runners. While there was a possible trend consistent with faster swimming speeds of northern forms relative to their southern counterparts, the functional differences between ecomorphs were similar in both clades. These results are consistent with the hypothesis that trade-offs between aquatic and terrestrial locomotion have contrib…
bibliographic citation: Fitzpatrick (2025) Trade-offs between aquatic and terrestrial locomotion and functional parallelism in Desmognathus salamanders. PeerJ 13:e20111 https://doi.org/10.7717/peerj.20111
date submitted: 2025-02-10
date accepted: 2025-08-29
issued: 2025-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fitzpatrick
  given name: Benjamin M.
doi: 10.7717/peerj.20111
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-06
copyright: ©2025 Fitzpatrick
attribution name: Fitzpatrick

Predictive role of systemic immune-inflammation index in the prognosis of patients with advanced left-sided colorectal cancer: a retrospective study
type: item
type: AcademicArticle
description: Purpose This study aimed to evaluate the prognostic value of the systemic immune-inflammation index (SII) in patients with advanced left-sided colorectal cancer (CRC) receiving CAPEOX ± bevacizumab as first-line chemotherapy. Methods A total of 231 patients with advanced left-sided CRC who received first-line CAPEOX ± bevacizumab therapy were included. Patients’ blood cell counts, clinical, and pathological data were collected before treatment, and systemic inflammatory indices were calculated, including neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), and SII. Optimal cutoffs for NLR, PLR, MLR, SII, and age were determined using X-Tile software, categorizing patients in to high- or low-value groups; clinicopathological characteristics were then compared between the high- and low-value groups within each systemic inflammatory index using chi-square tests. Survival curves were estimated using the Kaplan–Meier method, with log-rank tests applied to compare differences between groups. The Shapiro–Wilk test for normality and Spearman correlation analysis were used to evaluate the correlations among SII, NLR, PLR, and MLR. Univariable and multivariable analyses were performed with the Cox proportional hazards regression model. The prognostic value of systemic inflammatory indices was compared using the concordance index (C-index) and 5-fold cross-validation. The stability and generalizability of the C-index under varying data partitions were evaluated using mean square error (MSE). Interaction effects between treatment regimens and SII were further explored using multivariable Cox regression analysis. Results Univariable and multivariable Cox regression analyses identified age, primary tumor resection, SII, NLR, PLR, and MLR as independent prognostic factors for overall survival (OS). Comparative analysis of the C-index and MSE in the training and validation datasets demonstrated that SII outperformed NLR, PLR,…
format: application/pdf
format: text/html
creator: Jingyue Su
creator: Shaokun Yu
creator: Yanjie Xu
creator: Jiemin Zhao
creator: Wenwei Hu
creator: Xuefeng Ni
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.20095
publisher: PeerJ Inc.
rights: © 2025 Su et al.
abstract: Purpose This study aimed to evaluate the prognostic value of the systemic immune-inflammation index (SII) in patients with advanced left-sided colorectal cancer (CRC) receiving CAPEOX ± bevacizumab as first-line chemotherapy. Methods A total of 231 patients with advanced left-sided CRC who received first-line CAPEOX ± bevacizumab therapy were included. Patients’ blood cell counts, clinical, and pathological data were collected before treatment, and systemic inflammatory indices were calculated, including neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), and SII. Optimal cutoffs for NLR, PLR, MLR, SII, and age were determined using X-Tile software, categorizing patients in to high- or low-value groups; clinicopathological characteristics were then compared between the high- and low-value groups within each systemic inflammatory index using chi-square tests. Survival curves were estimated using the Kaplan–Meier method, with log-rank tests applied to compare differences between groups. The Shapiro–Wilk test for normality and Spearman correlation analysis were used to evaluate the correlations among SII, NLR, PLR, and MLR. Univariable and multivariable analyses were performed with the Cox proportional hazards regression model. The prognostic value of systemic inflammatory indices was compared using the concordance index (C-index) and 5-fold cross-validation. The stability and generalizability of the C-index under varying data partitions were evaluated using mean square error (MSE). Interaction effects between treatment regimens and SII were further explored using multivariable Cox regression analysis. Results Univariable and multivariable Cox regression analyses identified age, primary tumor resection, SII, NLR, PLR, and MLR as independent prognostic factors for overall survival (OS). Comparative analysis of the C-index and MSE in the training and validation datasets demonstrated that SII outperformed NLR, PLR,…
bibliographic citation: Su et al. (2025) Predictive role of systemic immune-inflammation index in the prognosis of patients with advanced left-sided colorectal cancer: a retrospective study. PeerJ 13:e20095 https://doi.org/10.7717/peerj.20095
date submitted: 2025-01-13
date accepted: 2025-08-27
issued: 2025-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Jingyue
author list: Agent
  family name: Yu
  given name: Shaokun
author list: Agent
  family name: Xu
  given name: Yanjie
author list: Agent
  family name: Zhao
  given name: Jiemin
author list: Agent
  family name: Hu
  given name: Wenwei
author list: Agent
  family name: Ni
  given name: Xuefeng
doi: 10.7717/peerj.20095
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-06
copyright: ©2025 Su et al.
attribution name: Su et al.

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