title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=44 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Comparison of animal models for immune premature ovarian insufficiency link: https://peerj.com/articles/20091 last-modified: 2025-10-07 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. creator: Anchun Hu creator: Yanli Mu creator: Guanyou Huang creator: Shuyun Zhao uri: https://doi.org/10.7717/peerj.20091 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hu et al. title: Geology correlates with gut microbial community composition in the Mountainsnails (Oreohelicidae: Oreohelix) link: https://peerj.com/articles/20080 last-modified: 2025-10-07 description: BackgroundSpecies 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.MethodsWe 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.ResultsWe 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. creator: Ian M. Oiler creator: T. Mason Linscott creator: Christine E. Parent uri: https://doi.org/10.7717/peerj.20080 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Oiler et al. title: Diagnostic accuracy of the atherogenic index of plasma in metabolic syndrome: a diagnostic meta-analysis link: https://peerj.com/articles/20074 last-modified: 2025-10-07 description: ObjectiveThis 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.MethodsA 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.ResultsEleven 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.ConclusionsThis 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. creator: Yuge Gao creator: Chengcheng He creator: Jia Mi uri: https://doi.org/10.7717/peerj.20074 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gao et al. title: Genetic modifiers of response to thalidomide in transfusion-dependent beta-thalassemia patients: a whole-exome sequence analysis link: https://peerj.com/articles/20038 last-modified: 2025-10-07 description: BackgroundThalidomide 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 objectivesTo discover genetic variations that influence response to thalidomide in transfusion-dependent beta-thalassemia patients.MethodsTwenty 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.ResultsThe 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.ConclusionThis study shows a significant association of single-nucleotide polymorphisms rs880633, rs35132891, and rs10425763 with excellent response status, while rs7518979, rs75658797, rs4299484, and rs3207618 are associated with non-response status. 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 uri: https://doi.org/10.7717/peerj.20038 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bawazir et al. title: Soil storage temperature and air-drying did not significantly change bacterial taxa in the short-term link: https://peerj.com/articles/20162 last-modified: 2025-10-06 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. creator: Mingming Du creator: Peipei Xue creator: Budiman Minasny uri: https://doi.org/10.7717/peerj.20162 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Du et al. title: Bioinformatic analysis and experimental validation of hub autophagy-related genes as novel biomarkers for type 2 diabetes mellitus and Alzheimer’s disease link: https://peerj.com/articles/20143 last-modified: 2025-10-06 description: Background & ObjectivesAlzheimer’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.MethodsGene 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.ResultsA 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 the curve (AUC) exceeding 0.7 for T2DM in both training and validation sets. However, only MET and PFKFB3 demonstrated good diagnostic efficacy in AD patients. In animal models, qRT-PCR analysis revealed that the expression of ANXA5, BAG3, and MET was consistent with the bioinformatics results. In contrast, the expression of PFKFB3 and CDKN1A did not differ significantly between db/db model mice and db/m control mice.ConclusionsOur integrated bioinformatics analyses, supported by preliminary experimental validations, identified several hub ARGs shared between AD and T2DM. Among these, ANXA5, BAG3, and MET exhibited consistent expression trends across datasets and experimental models, while CDKN1A and PFKFB3 showed inconsistent expression patterns. These findings underscore the complexity of autophagy-related crosstalk in AD-T2DM comorbidity and highlight the need for further research to clarify their diagnostic and therapeutic potential. creator: Rui Zhang creator: Ruowei Wang creator: Shuna Zhai creator: Chunhong Shen creator: Yu An creator: Quanri Liu uri: https://doi.org/10.7717/peerj.20143 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Factors influencing compliance with endoscopy final rinsing water standards: a study in a tertiary hospital setting link: https://peerj.com/articles/20134 last-modified: 2025-10-06 description: BackgroundMaintaining 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.MethodsMonitoring 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.FindingsInitial 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).ConclusionThis 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. creator: Yuhua Yuan creator: Lihong Ye creator: Tianyi Lu creator: Baihuan Feng creator: Jin Zhao uri: https://doi.org/10.7717/peerj.20134 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yuan et al. title: Knowledge and attitudes of university staff toward organ donation: a cross-sectional study in Oman link: https://peerj.com/articles/20133 last-modified: 2025-10-06 description: BackgroundOrgan 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.MethodsA 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.ResultsThe 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 life (67.3%) and the most common reason for refusing organs was hesitation (45.7%).ConclusionsThe study revealed moderate knowledge about organ donation among university staff, with medical and academic staff showing higher levels. However, overall attitudes were less positive, and there was significant reliance on the internet for information. These findings emphasize the need for targeted awareness campaigns and educational programs to improve knowledge and attitudes, promoting a cultural shift towards increased organ donation. creator: Nasar Alwahaibi creator: Shahd Al Ghawi creator: Mohammed Al-Badi uri: https://doi.org/10.7717/peerj.20133 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alwahaibi et al. title: Trade-offs between aquatic and terrestrial locomotion and functional parallelism in Desmognathus salamanders link: https://peerj.com/articles/20111 last-modified: 2025-10-06 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 contributed to a consistent pattern of habitat partitioning during parallel speciation. creator: Benjamin M. Fitzpatrick uri: https://doi.org/10.7717/peerj.20111 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fitzpatrick title: Predictive role of systemic immune-inflammation index in the prognosis of patients with advanced left-sided colorectal cancer: a retrospective study link: https://peerj.com/articles/20095 last-modified: 2025-10-06 description: PurposeThis 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.MethodsA 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.ResultsUnivariable 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, and MLR, exhibiting the highest average C-index and the lowest MSE across 5-fold cross-validation. Patients with elevated pre-treatment SII had significantly worse OS compared to those with lower values.ConclusionSII is a robust prognostic marker in patients with advanced left-sided CRC receiving CAPEOX ± bevacizumab as first-line chemotherapy, demonstrating superior prognostic value compared to NLR, PLR, and MLR. Higher pre-treatment SII values were associated with worse OS, underscoring its clinical utility in prognostic stratification. creator: Jingyue Su creator: Shaokun Yu creator: Yanjie Xu creator: Jiemin Zhao creator: Wenwei Hu creator: Xuefeng Ni uri: https://doi.org/10.7717/peerj.20095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Su et al.