title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-10 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Association between MTHFR gene polymorphisms and H-type hypertension in patients with ischemic stroke link: https://peerj.com/articles/20210 last-modified: 2025-10-10 description: BackgroundMethylenetetrahydrofolate reductase (MTHFR) is a key enzyme in homocysteine metabolism. Its 677C>T and 1298A>C polymorphisms can reduce enzyme activity, potentially elevating homocysteine levels. H-type hypertension (hypertension with homocysteine ≥10 μmol/L) is an important risk factor for ischemic stroke, and its synergistic effect exacerbates vascular damage. However, the association between these MTHFR polymorphisms and elevated homocysteine levels in patients with hypertension complicated by ischemic stroke remains unclear. This study aimed to investigate the association between MTHFR gene polymorphisms and H-type hypertension in patients with ischemic stroke.MethodsA total of 215 patients with ischemic stroke and hypertension admitted to the Department of Neurology at the Taian City Central Hospital from June 2021 to December 2022 were enrolled. General clinical data and biochemical indicators were collected. MTHFR genotyping was performed using a universal sequencing kit and a TL998A fluorescence detector. Linkage disequilibrium was analyzed via SHEsis software. Statistical analyses were conducted using SPSS 25.0. P < 0.05 indicates that the difference is statistically significant.ResultsAmong patients with ischemic stroke combined with hypertension in this region, the proportion of H-type hypertension was 89.3%. The proportion of males in the H-type hypertension group was significantly higher than in the non-H-type hypertension group (P < 0.05). The genotype and allele distributions of MTHFR(677C>T) (risk allele: T) differed significantly between groups (P < 0.05): the H-type group had a higher frequency of the TT genotype (47.4% vs. 17.4%) and T allele (67.2% vs. 50.0%). Multivariate logistic regression analysis showed that the MTHFR(677C>T) TT genotype was an independent risk factor for H-type hypertension (P = 0.021, OR = 2.615, 95%CI [1.154–5.926]). For haplotypes with a frequency >3%, there were three haplotypes of MTHFR(677C>T)/(1298A>C). The C-A haplotype was a protective factor for H-type hypertension (P = 0. 028, OR = 0.485, 95%CI [0.252–0.934]), while the T-A haplotype was a risk factor (P = 0.022, OR = 2.029, 95%CI [1.096–3.756]).ConclusionIn patients with ischemic stroke, the MTHFR(677C>T) TT genotype is an independent risk factor for H-type hypertension. For haplotypes with a frequency >3%, the C-A haplotype was a protective factor for H-type hypertension, whereas the T-A haplotype was a risk factor. creator: Bo Zhou creator: Tingting Yang creator: Shicang An creator: Qike Xu creator: Yuna Liang creator: Xiangyang An uri: https://doi.org/10.7717/peerj.20210 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhou et al. title: Risk factors for bronchopulmonary dysplasia in preterm infants: a systematic review and meta-analysis link: https://peerj.com/articles/20202 last-modified: 2025-10-10 description: BackgroundBronchopulmonary dysplasia (BPD) is the most common respiratory disease in preterm infants. As medical advancements have increased the survival rate of preterm infants, the prevalence of BPD has also increased, representing a significant societal burden. The pathogenesis of BPD is multifactorial, involving both genetic and environmental factors. Although numerous studies have examined risk factors for BPD, their findings are inconsistent. Few meta-analyses exist, yet most focus on risk factors for the development of pulmonary hypertension in infants with BPD. The primary aim of this study was to identify the risk factors for BPD.MethodsThe study protocol was registered with PROSPERO (CRD42024616871). A comprehensive literature search was conducted in the PubMed, Embase, Cochrane Library, and Web of Science databases for case-control and cohort studies investigating risk factors for BPD. The search was completed on 22 November 2024, and the data were analyzed using Review Manager 5.3.5 and Stata 15.1.ResultsA total of 23 studies were included in the analysis, encompassing 14,729 patients in the bronchopulmonary dysplasia (BPD) group and 19,101 in the non-bronchopulmonary dysplasia (non-BPD) group. The meta-analysis revealed that chorioamnionitis (CA) was associated with an increased risk of BPD (OR = 1.52, 95% CI [1.23–1.87]), as was premature rupture of membranes (PROM; OR = 1.42, 95% CI [1.02–1.98]). Additionally, hypertensive disorders of pregnancy (HDP) were identified as a significant risk factor for BPD (OR = 2.73, 95% CI [1.31–5.69]). Other notable risk factors included lower gestational age (GA; MD = −1.86, 95% CI [−2.35 to −1.38]), male sex (OR = 1.41, 95% CI [1.14–1.75]), and being small for gestational age (SGA; OR = 3.14, 95% CI [1.03–9.60]). Furthermore, the analysis indicated that mechanical ventilation (MV; MD = 16.55, 95% CI [9.68–23.41]), oxygen administration (MD = 50.91, 95% CI [37.40–64.42]), and blood transfusion (OR = 1.38, 95% CI [1.06–1.81]) were significant risk factors for BPD. Other variables that were identified as significant risk factors included patent ductus arteriosus (PDA; OR = 1.75, 95% CI [1.35–2.27]), sepsis (OR = 1.88, 95% CI [1.44–2.46]), and respiratory distress syndrome (RDS; OR = 6.37, 95% CI [4.00–10.13]).ConclusionsSignificant risk factors for BPD include CA, PROM, HDP, lower GA, male sex, SGA, MV, oxygen administration, blood transfusions, PDA, sepsis, and RDS. These findings hold potential clinical significance for predicting BPD pathogenesis. creator: Ping Xiong creator: Lei Li creator: Zhangbin Yu creator: Yuanlin Pu creator: Hong Tang uri: https://doi.org/10.7717/peerj.20202 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xiong et al. title: Seasonally modulated nonlinear effects of PM2.5 on pediatric respiratory health: evidence from a time-series analysis in urban China link: https://peerj.com/articles/20187 last-modified: 2025-10-10 description: BackgroundAlthough many studies have shown that fine particulate matter (PM2.5) is associated with respiratory diseases (RDs) in children, fewer studies have examined this association in developing countries. We aimed to use the latest PM2.5 standards to investigate the interaction between PM2.5 and RDs among children in Guangzhou.MethodsWe included 18,291 pediatric inpatients aged 0–14 years with a primary diagnosis of RDs admitted to hospitals in Guangzhou, China, from January 1, 2018, to December 31, 2021. The association between PM2.5 and RDs was analysed using a non-linear distributed lag model, and additional subgroup analyses were performed based on sex and season.ResultsThe association of PM2.5 with RDs showed a zigzag shape. Specifically, the cumulative effects of PM2.5 at the 25th, 50th, and 75th percentiles, with a lag of 0–14 days, were associated with increases in the relative risk (RR) of RDs by 0.4% (95% confidence interval (CI) [1.000–1.007]), 3.4% (95% CI [1.004–1.065]), and 7.7% (95% CI [1.010–1.149]), respectively. Additionally, for each 10 µg/m3 increase in PM2.5 concentration, the on-the-day lagged effect on lag day 4 and lag day 7 was associated with an elevated risk of RDs, with RR of 1.018 (95% CI [1.002–1.034]) and 1.016 (95% CI [1.000–1.032]), respectively. Additionally, PM2.5 exposure significantly increased the risk of RDs in boys and elevated that risk in children during both summer and winter seasons.ConclusionsThis study reveals a significant effect of PM2.5 exposure on RDs in children, with notably elevated risks during summer and winter seasons. These findings underscore the critical importance of implementing air quality improvement measures to safeguard children’s health, particularly in developing countries. creator: Weiqi Liu creator: Bingqing Liu creator: Weiling Liu creator: Liuhong Qu creator: Cuiqing Qiu uri: https://doi.org/10.7717/peerj.20187 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Development and validation of the AUDEXCEL algorithm as a diagnostic tool for occupational noise-related hearing disorder link: https://peerj.com/articles/20149 last-modified: 2025-10-10 description: BackgroundOccupational noise-related hearing disorder (ONRHD) is an occupational disease that poses a significant challenge for workers both globally and locally. To address this, the study aimed to develop and validate AUDEXCEL, an Excel-based algorithm designed to diagnose ONRHD among workers in Malaysia.Materials & MethodsThis cross-sectional study involved audiograms from 320 workers. These audiograms were first analyzed by experienced occupational health doctors (OHDs) to establish a gold standard diagnosis. The same audiograms were then assessed using the AUDEXCEL algorithm, which was validated through 5-fold cross-validation. Validity (sensitivity, specificity, positive predictive value, and negative predictive value) and reliability (Cohen’s kappa coefficient) were evaluated for normal hearing, hearing loss, hearing impairment, permanent standard threshold shift (PSTS), temporary standard threshold shift (TSTS), and noise-induced hearing loss (NIHL).ResultsThe sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for normal hearing, hearing loss, PSTS, and TSTS were all 100.0%, with perfect agreement (κ = 1.000). For hearing impairment, sensitivity, specificity, PPV, and NPV were 100.0%, 99.5%, 99.5%, and 100.0%, respectively, with almost perfect agreement (κ = 0.994). For NIHL, sensitivity, specificity, PPV, and NPV were 90.3%, 98.0%, 95.0%, and 96.1%, respectively, also showing almost perfect agreement (κ = 0.922).ConclusionsAUDEXCEL demonstrated high validity and reliability in replicating expert diagnoses and may serve as a supportive diagnostic aid for ONRHD. However, its use should be complemented by clinical and occupational exposure assessments due to the inherent complexity of diagnosing ONRHD. creator: Sheng Qian Yew creator: Pothanantha Raja Pathmanathan uri: https://doi.org/10.7717/peerj.20149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yew and Raja Pathmanathan title: Antimicrobial activity of Andrographis paniculata intimate wash and commercial formulations against vaginal pathogens using the broth microdilution method link: https://peerj.com/articles/20144 last-modified: 2025-10-10 description: BackgroundThis study aims to evaluate the antimicrobial efficacy of a newly formulated Andrographis paniculata intimate wash in comparison with commercial brands (SebaMed®, Sumber Ayu, Lactacyd®, and Good Virtue & Co.) against vaginal pathogens. The antimicrobial activity of each formulation was tested against Streptococcus agalactiae, Escherichia coli, and Candida albicans. Additionally, Lactobacillus crispatus was tested to ensure the formulations did not inhibit normal vaginal flora.MethodsThe broth microdilution method was used to assess antimicrobial efficacy by calculating the percentage of microbial inhibition. Minimum inhibitory concentration (MIC) was determined for A. paniculata and commercial intimate washes against the tested pathogens, except for L. crispatus, due to the inability to observe turbidity. Minimum bactericidal concentration (MBC) was evaluated for the A. paniculata intimate wash against the same pathogens.ResultsThe A. paniculata intimate wash showed the highest percentage of microbial inhibition across all tested pathogens. It also recorded MIC and MBC values of 3.125 mg/ml against E. coli and C. albicans. Among commercial products, SebaMed® demonstrated the strongest antimicrobial effect against S. agalactiae at the same MIC concentration. The study concluded that the A. paniculata intimate wash is a potentially effective treatment for selected vaginal pathogens at higher concentrations and may promote the growth of L. crispatus. SebaMed®, a clinically established product, also exhibited notable antimicrobial properties. However, further in vivo and clinical trials are necessary to confirm efficacy and assess toxicity. The study highlights the need for continued research into the potential of herbal intimate washes for treating vaginal infections. creator: Nur Rina Alissa Razian creator: Tuan Noorkorina Tuan Kub creator: Nurdini Afiqah Suhaimi creator: Tuan Nadrah Naim Tuan Ismail creator: Muhamad Alojid Anis Amiera creator: Gayus Sale Dafur creator: Fatmawati Lambuk creator: Rohimah Mohamud creator: Ramlah Kadir creator: Norzila Ismail creator: Norhayati Yusop uri: https://doi.org/10.7717/peerj.20144 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Razian et al. title: Biomechanical analysis of iliosacral and transiliac–transsacral screw combinations for fixation of undisplaced Denis II vertical shear fractures in dysmorphic sacrum link: https://peerj.com/articles/20139 last-modified: 2025-10-10 description: BackgroundPercutaneous iliosacral screws (ISS) and transiliac-transsacral screws (TTS) are effective for treating posterior pelvic ring instability. However, the biomechanical stability of undisplaced sacral dysmorphism fractures remains underexplored. This study evaluated various ISS and TTS combinations to provide a clinical reference for fixing such fractures.MethodsA finite element model of a complete Denis type II dysmorphic sacral fracture (extending through the sacral foramen) was developed. The stability of the posterior pelvic ring was evaluated using seven fixation techniques: S1-ISS (Group 1), S2-ISS (Group 2), S1-ISS + S2-ISS (Group 3), S2-TTS (Group 4), anterior S1-ISS + S2-TTS (Group 5), middle S1-ISS + S2-TTS (Group 6), and posterior S1-ISS + S2-TTS (Group 7). In all models, the anterior pelvic ring was fixed with pubic ramus screws. The upper sacral surface was subjected to six loading modes to simulate physiological states: standing, forward flexion, left flexion, right flexion, left rotation, and right rotation. The following parameters were recorded and analyzed: vertical displacement and sagittal angular displacement of the upper sacral surface, relative displacement of five pairs of observation points on the anterior fracture line, and maximum Von Mises stress and deformation of the S1 and S2 screws.ResultsThe finite element analysis revealed that the maximum stress in all internal fixation groups across the six loading modes was below the yield strength of titanium alloy, indicating no risk of implant failure. Screw deformation was highest in G1 and lowest in G5 for the S1 segment, and highest in G2 and lowest in G 5 for the S2 segment. G5 also exhibited the minimum vertical and angular displacements of the sacral upper surface in all motion states.ConclusionThis study demonstrates that S1-ISS combined with S2-TTS fixation provides excellent biomechanical stability for undisplaced vertical fractures of the sacral dysmorphism, particularly the combination of anterior S1-ISS and S2-TTS. This fixation method offers a promising clinical treatment option. creator: Peishuai Zhao creator: Chengfei Peng creator: Honghu Lin creator: Ying Ji creator: Weiyi Pang creator: Chaoyong Bei uri: https://doi.org/10.7717/peerj.20139 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Characterizing programmed cell death features in osteoarthritis through integrative multiomics and machine learning analysis link: https://peerj.com/articles/20104 last-modified: 2025-10-10 description: BackgroundProgrammed cell death (PCD) is an essential biological process in maintaining tissue homeostasis and eliminating damaged or unnecessary cells. Signaling molecules profoundly affect cellular metabolism and are crucial in various diseases; however, their role in osteoarthritis (OA) remains unclear. This study aimed to systematically evaluate the predictive value, genetic alterations, and therapeutic implications of PCD-associated genes in OA.MethodsWe performed multiomics analyses, integrating transcriptomic and single-cell transcriptome data. The biological importance of PCD genes was investigated using differential expression analysis, functional enrichment analysis, pathway analysis, weighted gene co-expression network analysis, and many machine learning models. Additionally, we evaluated diagnostic efficacy, immune infiltration, and competing endogenous RNA networks associated with these genes. We established an in vitro OA model using hypoxic treatment of ATDC5 chondrocyte cells and conducted extensive research on the expression and function of key PCD-related genes.ResultsThe key PCD gene was identified as markedly dysregulated in OA. Elevated expression of S100A9, PMAIP1, and EDA2R was observed in OA samples, indicating these genes as potential risk factors for OA. However, FASN expression was reduced in OA samples compared to the normal group, indicating its potential role as a protective gene in OA. Furthermore, PCD emerged as a reliable diagnostic marker with improved predictive accuracy. Functional experimental studies demonstrated that S100A9, PMAIP1, and EDA2R downregulation through small interfering RNA, alongside FASN gene overexpression through plasmid transfection, significantly ameliorated hypoxia-induced reductions in cell viability, decreased hyaluronan secretion, and increased secretion of inflammatory cytokines (tumor necrosis factor-alpha and interleukin-6).ConclusionUtilizing a multi-model synergistic artificial intelligence framework, we demonstrated the remarkable potential of PCD to provide individualized vulnerability assessments and customized recommendations for metabolic and immunotherapeutic interventions in OA. We identified abnormal expression of four hub genes associated with PCD and examined their biological functions, thereby facilitating new avenues for research into the role of PCD in OA and other immune-mediated diseases. creator: Qinchao Sun creator: Ye Zhong creator: Gaoxiang Huang creator: Yongpei Lin uri: https://doi.org/10.7717/peerj.20104 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sun et al. title: Contrasting microbial assembly patterns in the woody endosphere of hybrid and non-hybrid Populus trees link: https://peerj.com/articles/20073 last-modified: 2025-10-10 description: Endophytes asymptomatically infect virtually all plant species, yet little is known about endophyte community assembly and diversity within the woody tissues of forest trees. We utilised phylogenetic null models of alpha (ses.MNTDab and ses.MPDab) and beta diversity (ses.βMNTDab and ses.βMPDab) to infer the role of deterministic and stochastic ecological processes in structuring bacterial and fungal endophyte communities in the woody tissues of Populus deltoides and the naturally occurring P. × jackii hybrid complex (P. deltoides × P. balsamifera). Microbial communities were characterised through Illumina amplicon sequencing (MiSeq) of the ITS and 16S rRNA gene. We detected 227 fungal ASVs, which were mainly classified as Ascomycota (92.4%). Among the 667 bacterial ASVs detected, the majority were classified as phylum Actinobacteriota (47.6%) and Proteobacteria (44.9%). We predicted that hybridisation could lead to a host environment that applies weaker selective effects on microbial taxa due to variability in host chemical and morphological phenotypes. Although bacterial communities did not support our prediction, fungal assemblages of the hybrid host (P. × jackii) were more phylogenetically random within (ses.MNTDab) and between assemblages (ses.βMNTDab and ses.βMPDab) then the non-hybrid (P. deltoides)—consistent with an increased role of stochastic community assembly processes and less selective host environment. Host identity had a large influence on fungal community composition (weighted UniFrac R2 = 34%), which may result from the differences in fungal selection we detected between hosts. Conversely, host identity was a weaker predictor of bacterial composition (weighted UniFrac R2 = 13%), which may reflect the more dominant role of stochasticity we detected in bacterial assembly. Our findings provide evidence that host hybridisation may alter fungal assembly processes and diversity within the woody endosphere, leading to more phylogenetically diverse associations both within and between the fungal assemblages of hybrid trees. More broadly, our results highlight how genetically diverse host populations may promote microbial biodiversity within forests and hybrid transition zones. creator: Kyle R. Grant creator: Steven W. Kembel creator: Sachin Naik creator: Selvadurai Dayanandan uri: https://doi.org/10.7717/peerj.20073 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Grant et al. title: ShinyDegSEM: an interactive application for pathway perturbation analysis in gene expression studies via structural equation modeling link: https://peerj.com/articles/20033 last-modified: 2025-10-10 description: BackgroundResearchers in biology and bioinformatics are increasingly interested in unraveling the complex mechanisms underlying phenotypic variations. A key challenge lies in identifying perturbed biological pathways and understanding how these perturbations propagate through intricate gene regulatory networks.ResultsTo address this challenge, we developed ShinyDegSEM, an interactive R Shiny application that leverages structural equation modeling (SEM) to facilitate pathway perturbation analysis in gene expression studies. ShinyDegSEM streamlines identifying differentially expressed genes (DEGs), generating pathway models based on biological knowledge, and evaluating these models to uncover perturbed pathway modules. This article is a tutorial to guide users through the analysis workflow, providing detailed explanations and examples. This feature ensures that even novice researchers can quickly grasp the concepts and apply the tool to their datasets.ConclusionsThe application integrates multiple steps, including DEG detection using significance analysis of microarray, perturbed pathway analysis with signaling pathway impact analysis, and SEM-based model refinement and comparison between experimental and control groups. The interactive interface of ShinyDegSEM allows researchers to easily upload their gene expression data, select appropriate criteria for DEG detection and pathway analysis, and visualize the results in intuitive graphs and tables. The tool provides insights into deregulated genes and modified gene-gene relationships within perturbed pathways. creator: Zhehan Jiang creator: Jihong Zhang creator: Yuanfang Liu creator: Jinying Ouyang creator: Linlin Sun creator: Hao Guo uri: https://doi.org/10.7717/peerj.20033 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jiang et al. title: DNA-based prediction of external ear morphology in the Chinese population: an exploratory study link: https://peerj.com/articles/20169 last-modified: 2025-10-09 description: BackgroundThe external human ear is a polymorphic and polygenic structure with individual uniqueness, making it a valuable target in forensic DNA phenotyping (FDP) studies. Previous genome-wide association studies have identified multiple genetic loci associated with variation in ear characteristics. However, research focused on predicting ear morphology within the context of FDP remains limited. This study aimed to develop DNA-based predictive models for external ear morphology in the Chinese population.MethodsDigital photographs of 675 volunteers were used to score 13 ear phenotypes, each categorized into three levels. Multinomial logistic regression (MLR) was applied for genetic association analysis. Five predictive models—MLR, support vector machines, random forest, AdaBoost, and k-nearest neighbors—were developed and evaluated using 10-fold cross-validation.ResultsGenetic association analysis identified several influential single-nucleotide polymorphism (SNPs) for each ear phenotype. Among the five models, AdaBoost and MLR demonstrated superior performance, achieving area under the curve (AUC) values above 0.7 for predicting absent tragus cases (level_0). To simplify classification, binary models incorporating genetic interactions were constructed for absent tragus cases. Specifically, the AdaBoost model achieved an AUC of 0.74, while the binary logistic regression (BLR) model reached an AUC of 0.72.ConclusionsThese findings highlight the potential forensic application of genetic markers in predicting ear morphology within the Chinese population, contributing to the advancement of FDP research and practice. creator: Xindi Wang creator: Zibo Zhao creator: Jingting Wu creator: Yuan Li creator: Yufei Yang creator: Bo Liu creator: Chengye Zhou creator: Chuanxu Wang creator: Xiaogang Chen creator: Feng Song uri: https://doi.org/10.7717/peerj.20169 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Impact of rainfall on root water uptake in two characteristic species of coal mining subsidence areas in Northwest China link: https://peerj.com/articles/20158 last-modified: 2025-10-09 description: Clarifying how plants utilize water in coal mining subsidence zones is essential for grasping plant-soil dynamics and guiding ecological rehabilitation. However, current knowledge on species-specific variations in water uptake and their adaptive responses to such subsidence remains limited. This research leveraged isotopic fingerprinting (δ2H, δ18O) alongside soil water content and root distribution to explore the root water uptake sources of two predominant species (Stipa bungeana Trin. and Artemisia desertorum Spreng.) in coal mining zones and their reactions to land subsidence triggered by coal extraction. The results indicated negligible differences in soil water content and soil water isotopic composition between subsidence and non-subsidence zones, irrespective of rainfall. Before rainfall, the water sources of the two species were unaffected by subsidence; however, after rainfall, discernible changes occurred. Plants in the subsidence area absorbed more water from the top 0–10 cm soil layer, indicating a more pronounced response to rainwater infiltration. Notably, A. desertorum, in contrast to S. bungeana, tapped into deeper soil water during arid conditions and swiftly switched to shallow soil water sources following rainfall, highlighting its adaptable water usage strategy and greater ecological resilience. The findings of this study cast new light on plant-water relationships in coal mining subsidence regions, providing essential guidance for ecological restoration and management efforts. creator: Ruimin He creator: Haoyan Wei creator: Mingzhe Lei creator: Jiping Niu creator: Zhenguo Xing creator: Shi Chen creator: Da Lei creator: Gang Liu creator: Min Guo creator: Yang Lei creator: Min Li uri: https://doi.org/10.7717/peerj.20158 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 He et al. title: The 6-item specific object anthropomorphism scale: a new questionnaire for children and adults link: https://peerj.com/articles/20153 last-modified: 2025-10-09 description: The attribution of human characteristics, emotions, or behaviors to nonhuman entities or objects is known as anthropomorphism. Research on anthropomorphism has been limited by abstract measures that may be difficult for both children and adults to understand. To address this issue, we developed and tested the reliability and validity of the Specific Object Anthropomorphism Scale (SOAS) across three studies involving child and adult participants. The SOAS consists of six items that ask respondents to rate the extent to which a specific object possesses anthropomorphic qualities using simple, concrete statements. Study 1 found that the measure fit a one-factor solution in adults (aged 17–72, M = 32.3). In Study 2, we confirmed the unidimensional structure in adults (aged 18–73, M = 32.2) and demonstrated excellent test-retest reliability, convergent validity, and divergent validity. Study 3 confirmed the unidimensional structure in children (aged 5–12, M = 8.3) and showed that the items were highly understandable. Taken together, these findings indicate that the SOAS is a promising measure of anthropomorphic tendencies that may be easier for both children and adults to complete, potentially leading to a better understanding of the nature of anthropomorphism. creator: Jonathan David creator: Mikaela Stowe creator: Nathan Caruana creator: Melissa M. Norberg uri: https://doi.org/10.7717/peerj.20153 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 David et al. title: Interaction and mechanisms of depression and cardiovascular disease: a mini-review link: https://peerj.com/articles/20148 last-modified: 2025-10-09 description: Cardiovascular disease (CVD) is the world’s leading cause of death and frequently comorbid with depression. Numerous clinical studies reveal a bidirectional interaction between CVD and depression, mutually exacerbating the pathological progression of both conditions. This comorbidity has emerged as a significant global health challenge, yet targeted therapeutic drugs and strategies remain underdeveloped. This article summarizes the relationship between depression and various CVD types, including coronary heart disease, atherosclerosis, myocardial infarction, and heart failure. We further analyze the underlying mechanisms through autonomic nervous system dysfunction, hypothalamic-pituitary-adrenal axis dysregulation, inflammatory responses, endothelial dysfunction, and platelet activation pathways. By integrating these insights, this review aims to provide references for the development of novel therapeutics for CVD combined with depression. creator: Ling Huang creator: Lei Zhang creator: Cuihua Liu creator: Qiang Xu creator: Kuncheng Qiu uri: https://doi.org/10.7717/peerj.20148 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Development and external validation of a multivariate model for predicting pneumonia in patients receiving maintenance hemodialysis: a retrospective study link: https://peerj.com/articles/20070 last-modified: 2025-10-09 description: BackgroundPatients receiving maintenance hemodialysis (MHD) who develop pneumonia experience substantially elevated risks of hospitalization and mortality, while also incurring significantly heightened healthcare-related financial burdens. Our goal is to establish a forecasting model to assess the individual risk of pneumonia in patients undergoing MHD.Materials and MethodsA retrospective analysis was carried out between January 2018 and November 2024, involving 405 MHD patients from two medical centers. The variables underwent adjustment through multivariate Cox regression analysis, and the forecasting model was created and verified.ResultsThe median follow-up time of the external validation set was 35 months (interquartile range: 20–43), and the median follow-up time of the modeling set was 22 months (12–24). The event happened in 101 (34.83%) out of 290 patients in the modeling set and 45 (39.13%) out of 115 patients in the external validation set. The model predictors included history of diabetes and coronary heart disease; serous effusion; white blood cell; albumin-globulin ratio; left ventricular mass index, and age. The C-index was 0.753 (0.684, 0.822) for the external validation set and 0.772 (95% CI [0.724–0.821]) for the modeling set. The model showed excellent calibration ability throughout the risk spectrum, and decision curve analysis showed that it could maximize the prognosis of patients.ConclusionThe created predictive model provided a precise, individualized evaluation of pneumonia risk in patients with MHD. It can be used to identify individuals at high risk of pulmonary infection in patients undergoing MHD and guide their treatment and prognosis follow-up. creator: Xiao Hua Yang creator: Ju Zhang creator: Xi Sheng Xie creator: Wen Wu Tang uri: https://doi.org/10.7717/peerj.20070 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: Exploring phytochemicals as potential pharmacological inhibitors for NS1 protein of Kyasanur forest disease virus using virtual screening, molecular docking, and molecular simulation approach link: https://peerj.com/articles/19954 last-modified: 2025-10-09 description: BackgroundKyasanur forest disease virus (KFDV) remains a significant public health challenge due to the limitations of existing vaccines, creating a critical need for effective antiviral treatments. KFDV is a tick-borne virus responsible for 400–500 new cases annually, with a mortality rate of 3–5%. The nonstructural protein 1 (NS1), which plays crucial roles in host cell interactions, immune evasion, and viral replication, represents a promising target for antiviral drug development.ObjectiveThis study aims to identify potential antiviral compounds that inhibit the activity of KFDV NS1 protein using a computational pharmacological drug design approach. The objectives include determining the 3D structure of the NS1 protein through homology modeling, conducting virtual screening of phytochemicals to identify potential inhibitors, and performing molecular dynamics simulations to assess the stability and binding free energies of the selected compounds.MethodsThe 3D structure of KFDV NS1 protein was predicted using homology modeling and validated using Ramachandran plot analysis. Virtual screening of phytochemicals from the Indian Medicinal Plants, Phytochemistry And Therapeutics (IMPPAT) database was performed to identify potential NS1 inhibitors. The top 15 compounds with the highest binding affinities were selected and subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Molecular dynamics simulations were conducted in duplicates for 200 ns to evaluate the stability of the ligand-NS1 complexes, and an additional independent simulation with randomized initial velocities was performed to ensure statistical robustness. Binding free energies were calculated using the molecular mechanics-generalized born surface area (MM-GBSA) method to determine the binding strength of each compound.ResultsThe 3D structure of the KFDV NS1 protein was determined using I-Tasser-MTD, Robetta, and Swiss Model servers, and a minimized model of I-Tasser, achieving an ERRAT score of 94.37, was selected. Virtual screening of 11,530 phytochemicals from the IMPPAT database identified the top 115 compounds after three screening phases. Out of the 15 screened compounds, L2, L3, and L5 demonstrated notable binding affinities of −9.34, −9.12, and −9.08 kcal/mol, respectively, compared to the FDA-approved antiviral dasabuvir, which had a binding affinity of −8.0 kcal/mol. Molecular dynamics simulations confirmed the stability of compounds L2 (IMPHY010294), L3 (IMPHY001281), L5 (IMPHY011162), and dasabuvir, with free-energy binding values of −62.97 ± 4.0, −77.22 ± 4.71, −62.07 ± 2.88, and −87.68 ± 4.31 kcal/mol, respectively.ConclusionThe computational analysis suggests that compounds L2 and L3 have strong binding affinities comparable to dasabuvir, indicating their potential as pharmacological inhibitors of the KFDV NS1 protein. Further validation through in vitro assays would complement these in silico findings. creator: Sharanappa Achappa creator: Nayef Abdulaziz Aldabaan creator: Ibrahim Ahmed Shaikh creator: Mater H. Mahnashi creator: Shivalingsarj V. Desai creator: Mufarreh Asmari creator: Mohammed Alasmary creator: Uday M. Muddapur creator: Basheerahmed Abdulaziz Mannasaheb creator: Aejaz Abdullatif Khan uri: https://doi.org/10.7717/peerj.19954 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Achappa et al. title: Scanning electron microscopy (SEM) reveals high diversity of setae on the hind tibiae and basitarsi of Peruvian Stingless Bees (Apidae: Meliponini) link: https://peerj.com/articles/19749 last-modified: 2025-10-09 description: Stingless bees belong to the group of corbiculate bees, all characterized by the presence of a corbicula, a specialized structure of the hind tibia used for pollen collection. This group exhibits significant variation in foraging behavior, from flower-visiting foragers to kleptoparasites and obligate necrophagous. So far, scanning electron microscopy (SEM) studies have been mainly focused on the hind leg setae of Apis spp. and Bombus spp. Here, we performed a comparative morphological analysis of the setae and the pollen handling structures in the hind tibiae and basitarsi of seven stingless bee species: the floral pollen collector bees Melipona cf. eburnea, Partamona testacea, Scaura cf. latitarsis, Trigonisca cf. atomaria, Trigona dallatorreana, the robber bee Lestrimelitta sp. and the obligate necrophagous Trigona cf. hypogea, collected in Peruvian forests in 2020. The setae were classified into simple and branched types, subdivided into five and seven subtypes, respectively. In addition, we described three types of penicillum, five types of rastellum, three types of pollen brush, two types of setae covering the auricular area, and show the setae forming the sericeous area of Trigona spp. Finally, seven types of keirotrichia are described. We highlight that certain types of setae show a high degree of conservation across species, while others are unique and potentially indicative of adaptive specialization. Among species that have abandoned pollen foraging on flowers, we observed a simplification in the number of setal types and the absence of pollen handling structures in Lestrimelitta sp., whereas T. cf. hypogea exhibits the highest diversity of setae and retains most of these structures. Finally, based on these two species, we reflect on the link between reduced corbicula and functional corbicula. The study highlights the importance of further exploring the mechanical and sensory roles of setae and expanding this research in Meliponini. Such investigations can improve our understanding of their adaptive functions and provide valuable insights into the functional ecology, taxonomy and phylogenetic studies of these tropical pollinators. creator: Marilena Marconi creator: Carlos Daniel Vecco-Giove creator: Javier Ormeño Luna creator: Agustín Cerna Mendoza creator: Emiliano Mancini creator: Andrea Di Giulio uri: https://doi.org/10.7717/peerj.19749 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Marconi et al. title: Retrospective study: anthropometric and metabolic characteristics of patients with metabolic syndrome–a gender-specific analysis of clinical and correlation patterns link: https://peerj.com/articles/20183 last-modified: 2025-10-08 description: BackgroundMetabolic syndrome (MetS) is a prevalent condition associated with increased cardiometabolic risk. Despite its clinical significance, the relationships between anthropometric indices and metabolic markers—particularly in a gender-specific context—remain inadequately explored.MethodsThis retrospective study included 104 patients diagnosed with MetS between 2016 and 2022. Anthropometric indices, including body roundness index (BRI), body mass index (BMI), waist-to-height ratio (WHtR), and weight-to-waist index (WWI), were analyzed for their associations with metabolic markers reflecting insulin resistance and glucose metabolism: fasting blood glucose (FBG), fasting insulin (FIns), and homeostatic model assessment of insulin resistance (HOMA-IR). These markers represent key components of MetS, although other diagnostic elements such as dyslipidemia and hypertension were beyond the scope of this analysis. Gender-specific subgroup analyses were conducted for 57 female and 47 male patients.ResultsSignificant differences in anthropometric and metabolic characteristics were observed between genders. Male patients exhibited higher BMI (40.4 [37.5, 44.2] vs. 37.2 [33.6, 40.3], p = 0.022), waist circumference (128.0 [120.2, 137.5] cm vs. 115.0 [106.0, 120.0] cm, p < 0.001), and FIns levels (22.8 [16.4, 29.5] μIU/mL vs. 17.8 [15.0, 23.4] μIU/mL, p = 0.107). Correlation analyses revealed that BMI and BRI were strongly associated with HOMA-IR and FIns in both genders, with stronger associations observed in males (e.g., BMI vs. FIns, r = 0.60, p < 0.001). WHtR was significantly correlated with metabolic markers in males but not in females. WWI showed limited correlations across both genders.DiscussionThis study highlights distinct gender-specific patterns in the relationships between anthropometric indices and metabolic markers in MetS patients. These findings underscore the importance of tailored strategies in managing MetS, particularly considering gender-based differences in clinical and metabolic profiles. creator: Yingxin Li creator: Huanhua Wu creator: Yingtong Lu creator: Jingjie Shang creator: Yong Cheng creator: Xiaozheng Cao creator: Zhiqiang Tan creator: Qijun Cai creator: Hao Xu creator: Bin Guo uri: https://doi.org/10.7717/peerj.20183 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Barriers to care and the need for dental educational materials for the Lowe syndrome community: a survey of dentists link: https://peerj.com/articles/20174 last-modified: 2025-10-08 description: BackgroundThis study aimed to assess dentists’ experience in treating individuals with Lowe syndrome (LS), reasons they may be unable to provide dental care for individuals with LS, and perceptions of the need for educational materials tailored to the LS community regarding the dental setting.MethodsA link to an electronic Qualtrics survey addressing these topics was emailed to the Tufts University School of Dental Medicine Alumni Network listserv.ResultsData from 73 respondents were analyzed. Of the 57 who answered the question about having treated a patient with LS, three (5.3%) responded affirmatively. Among the 61 who answered why they might not be able to treat an individual with LS, the most common reasons were lack of experience treating children with special needs and not accepting medical assistance such as Medicaid/Medicare (both 31.1%). Of the 58 who responded to the item regarding the need for educational materials to support patients with LS in the dental setting, 47 (81.0%) agreed or strongly agreed.ConclusionSubstantial barriers to dental care exist for individuals with LS. Educational materials about the dental setting should be developed for the LS community. creator: Adam Lowenstein creator: Matthew Finkelman creator: Jay Dalal creator: Crystal Smith creator: Glory Ogunyinka creator: David Tesini creator: Carlos Fernando Mourão uri: https://doi.org/10.7717/peerj.20174 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lowenstein et al. title: Impact of two field preservation methods on genotyping success of feces link: https://peerj.com/articles/20154 last-modified: 2025-10-08 description: Non-invasive samples, such as feces, remain an important source of DNA for genetic analyses in molecular ecology and conservation genetics, especially when working with elusive or endangered species. However, as labs transition to higher throughput and genomic-based technologies, many protocols that have been used for decades are becoming obsolete. New approaches have been developed for high-quality samples, now low-quality samples require further technical advances. Fecal samples obtained for non-invasive wildlife studies are typically of very low quality and sampling methods need to be optimized to reduce work and costs per sample. Preservation methods in the field affect the workload in the lab required to obtain genetic data, as well as the final genotype quality. Liquid preservation methods, such as nucleic acid preservation (NAP) buffer and ethanol, have been used during sampling to maintain DNA quality at room temperature until samples can reach the lab. NAP buffer is a non-hazardous, non-flammable solution (easy to send through post), and avoids having to dry the feces before DNA extraction (saving time and increasing safety). Here we compare two different liquid preservation methods (NAP buffer and 96% ethanol) for microsatellite genotyping by next generation sequencing of wolf fecal samples collected in the field and shipped at ambient temperature. Samples preserved in ethanol showed a higher rate of amplification and genotyping success than in NAP buffer, especially due to a higher rate of allelic dropout in NAP. Consequently, the number of replicates required to achieve high quality genotypes was slightly higher for fecal samples preserved in NAP buffer than for those preserved in ethanol. These results are important for the planning and optimization of projects that involve microsatellite genotyping from feces using high throughput technologies. creator: Valentina Valencia-Montoya creator: Isabel Salado creator: Ines Sanchez-Donoso creator: Alberto Fernández-Gil creator: Carles Vilà creator: Jennifer A. Leonard uri: https://doi.org/10.7717/peerj.20154 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Valencia-Montoya et al. title: Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements link: https://peerj.com/articles/20152 last-modified: 2025-10-08 description: Stable isotope analysis of skin collagen is useful for detecting short-term or seasonal diet. Preparation of skin for stable isotope analysis varies across laboratories, and this may impact the comparability of data. It is important to understand the effects of different preparatory protocols on the stable isotopic and elemental compositions of skin samples. Using a Eurovector 3,300 elemental analyzer coupled to a Nu Horizon isotope ratio mass spectrometer, we tested the impact of three treatment variants (refluxing at three temperatures to remove non-collagenous proteins, treatment with sodium hydroxide (NaOH), and chemical lipid extraction using 2:1 chloroform:methanol) on the stable isotope (δ13carbon (C) and δ15nitrogen (N)) and elemental (wt% C, and wt% N) composition of pig (Sus scrofa domesticus) skin. The refluxing step produced pig skin with higher δ13C values, lower C:NAtomic ratios, less variable C:NAtomic ratios, wt% C, and wt% N. The chemical lipid extraction also produced higher, more reliable δ13C values and lower, less variable C:NAtomic ratios. The isotopic data in the lipid-extracted and refluxed samples were more consistent in the refluxed samples than the non-refluxed and non-lipid-extracted samples, as determined by the elemental compositions. creator: Alexandra A.Y. Derian creator: Ryan Pawlowski creator: Paul Szpak uri: https://doi.org/10.7717/peerj.20152 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Derian et al. title: Quality assessment from biobank plasma and serum specimens: a systematic review link: https://peerj.com/articles/20122 last-modified: 2025-10-08 description: Accurate assessment of serum and plasma quality is essential for reliable biobanking and research. This systematic review synthesizes 46 studies and shows that current evaluation methods prioritize sample processing delays, freeze-thaw cycles, storage duration, and temperature variations, while neglecting preanalytical factors like medication and diet. Temperature critically affected stability: non-refrigerated samples (8–37 °C) showed 3.2 times more biomarker alterations than refrigerated samples after >24 h delays. Freeze-thaw cycles caused dose-dependent instability, with >10 cycles triggering severe degradation (70% altered biomarkers) and universal enzyme impairment. Even ≤5 cycles significantly altered enzymes (43% affected). Enzymes also degraded over time at <−20 °C, with alteration rates rising from 20% (1–5 years) to 55% (>10 years). The analysis consolidates stability data for enzymes, sterols, cytokines, and metabolites across conditions, providing an evidence-based foundation for quality control. Standardizing procedures to address these gaps will enhance sample integrity, research reliability, and clinical utility. Critically, this review underscores that preexisting biobank collections may have inherent limitations, necessitating careful evaluation of sample history when designing studies. creator: Xiongshun Liang creator: Wanna Xu creator: Lin Chen creator: Xiaoqian Liu creator: Wenxu Hong creator: Xuqiao Hu uri: https://doi.org/10.7717/peerj.20122 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liang et al. title: Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer link: https://peerj.com/articles/19968 last-modified: 2025-10-08 description: BackgroundTo assess the status of NEUROG1 methylation in the advanced adenoma and colorectal cancer.MethodsThe NEUROG1 methylation in tissue and stool samples from patients with colorectal cancer (CRC), advanced adenoma (AA), and non-advanced adenoma (NAA) were evaluated using methylation-specific quantitative polymerase chain reaction (PCR).ResultsIn tissue samples, the NEUROG1 methylation detection rates were 36% for CRC, 24% for NAA, and 88% for AA. In stool samples, the NEUROG1 methylation detection had a sensitivity of 63.46% for CRC with a positive predictive value (PPV) of 85.94%. The overall diagnostic specificity of the test for the NAA and the healthy control was 76.32%, with a negative predictive value (NPV) of 40.28%.ConclusionNEUROG1 methylation detection can potentially be used in the CRC and AA screening. creator: Lijin Zhang creator: Aiping Lin creator: Jie Lin creator: Juan Chen creator: Mengshi Chen creator: Xunbin Yu creator: Yijuan Wu creator: Tao Wang creator: Yan Lu creator: Zhaofen Ba creator: Xiaowei Cheng creator: Tiantian Zhang creator: Minghong Chen uri: https://doi.org/10.7717/peerj.19968 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis link: https://peerj.com/articles/19938 last-modified: 2025-10-08 description: BackgroundAcne is a common skin condition that can cause permanent scarring and profoundly affect patients’ quality of life. Despite the increasing diversity of acne scar treatments, there is a dearth of comprehensive evidence-based guidelines to help clinicians and patients make the best choices. This study aimed to comprehensively assess the efficacy and safety of existing acne scar treatments through a network meta-analysis.MethodPubMed, Embase, Cochrane Library, and Web of Science were thoroughly searched for relevant studies from database establishment to September 19, 2024. Outcome included Echelle d’evaluation clinique des cicatrices d’acne (ECCA), Goodman and Baron Scale (GBS), pain, patient satisfaction, and adverse events. Bayesian network meta-analyses were performed using the gemtc package in R. Risk of bias was assessed using Cochrane Risk of Bias (RoB 2) tool, while publication bias was assessed via funnel plots. The study protocol was registered with PROSPERO (CRD42024598780).ResultsA total of 68 randomized controlled trials were enrolled, comprising 4,480 patients with acne scarring. Laser + platelet-rich plasma (PRP) ranked best in reducing ECCA scores (surface under cumulative ranking curve to the total area (SUCRA): 98.4%), laser + filler injection ranked best in reducing GBS (SUCRA: 72.1%), and laser + chemical peels ranked the best in patient satisfaction (SUCRA: 89.6%). Microneedling was ranked as the most tolerable in terms of pain (SUCRA: 72.6%). In addition, no strong evidence suggesting a treatment reduced the risk of erythema nor post-inflammatory hyperpigmentation compared to the other treatments.ConclusionsThe evidence suggests laser combined with PRP or filler injections are the best options for reducing scar severity, while laser combined with chemical peeling yields the best patient satisfaction. Laser combined with other therapies should be considered to optimize treatment of acne scarring. creator: Bingwei Wu creator: Mingju Gao creator: Yixuan Zhang creator: Xinping Bai uri: https://doi.org/10.7717/peerj.19938 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis link: https://peerj.com/articles/19937 last-modified: 2025-10-08 description: BackgroundGroundwater is a critical water resource in the Poyang Lake basin, especially given the increasing frequency of extreme drought events. However, comprehensive assessments of its chemical characteristics and associated health risks remain insufficient. This study aims to provide a comprehensive assessment of groundwater quality and associated health risks in the Poyang Lake basin, China.MethodsThis study collected 670 groundwater samples from domestic and agricultural wells across the basin during the 2022 dry season. Hydrochemical parameters, including manganese (Mn), ammonia nitrogen (NH4+), iron (Fe3+), aluminum (Al3+), chemical oxygen demand (COD), fluoride (F−), and nitrate (NO3−), were analyzed and compared against China’s Class III groundwater quality standards. Spatial variations in water quality were evaluated using the Entropically Weighted Water Quality Index (EWQI). Non-carcinogenic health risks via ingestion and dermal contact pathways were quantified through deterministic risk assessment models, with uncertainty and probability analyzed via Monte Carlo simulations (10,000 iterations). Sensitivity analysis was conducted to identify dominant factors influencing risk outcomes, ensuring a robust probabilistic interpretation of health hazards.ResultsThe results unveils pronounced spatial variability across key hydrochemical parameters: pH ranges from 3.05 to 11.09, total dissolved solids (TDS) from 25.38 to 1,635.21 mg/L, Mn from below detection limits to 19.93 mg/L, COD from below detection limits to 8.57 mg/L, and TH from 9.47 to 905.78 mg/L. A notable proportion of samples breach the Class III groundwater quality standards, with 38% for Mn, 39% for COD, and 15% for NH4+. The Piper diagram analysis categorizes the primary groundwater type as HCO3− -Ca, with a secondary Cl-Ca-Mg type. Through the EWQI assessment, while the overall water quality is deemed acceptable, we identify 56 sites with EWQI values indicative of poor to very poor quality, predominantly influenced by Mn and NH4+. The irrigation risk assessment highlights extensive areas unsuitable for irrigation, particularly within the Ganjiang River basin. Health risk assessments utilizing a deterministic model reveal significant non-carcinogenic risks from F− and NO3− in groundwater, especially for children. However, our Monte Carlo simulation indicates that the probabilities of F− and NO3− posing non-carcinogenic health risks are virtually zero, suggesting that the deterministic assessment may have overestimated the health risks. This study provides critical insights into the groundwater quality and health risks in the Poyang Lake basin and underscores the necessity for targeted water management strategies to mitigate pollution sources and safeguard public health. creator: Xiaodong Chu creator: Jingyuan He creator: Ting Chen creator: Hailin You creator: Xuhui Luo creator: Shuping Liu creator: Jinying Xu creator: Zhifei Ma uri: https://doi.org/10.7717/peerj.19937 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Chu et al. title: From lowlands to highlands: how elevation and habitat complexity drive anuran multidimensional diversity? link: https://peerj.com/articles/19561 last-modified: 2025-10-08 description: BackgroundMontane environments in Neotropical regions are known for their rich diversity of amphibians, but the ecological drivers behind this diversity along altitudinal gradients remain poorly understood. We investigated the effects of the altitudinal range and local environmental variables on the taxonomic, phylogenetic, and functional alpha and beta diversity of anuran assemblages along an altitudinal gradient in the Atlantic Forest of northeastern Brazil.MethodsWe characterized the richness, abundance, taxonomic, functional, and phylogenetic diversity of anurans in 24 transects within the interior of the forest along an altitudinal range of 200–950 m in the Private Reserve of Natural Heritage (RPPN) Serra Bonita, southern Bahia state, northeastern Brazil. For each transect, we measured the following environmental variables: altitude, leaf litter depth and cover, canopy opening, number of tank-bromeliads, number of trees, and mean air temperature.ResultsWe found 36 anuran species distributed in 10 families. Altitudinal strata plays an important role in explaining anuran abundance, with direct-developing frogs being the most abundant species. The number of tank-bromeliads was interpreted as having the most substantial support to explain the anuran abundance, lineage richness and functional diversity, whereas leaf litter depth influenced the dominant lineages. Additionally, altitude significantly influenced taxonomic and phylogenetic dissimilarity. Lastly, we found an inverse pattern of altitudinal Rapoport’s rule, in which species with optimal altitudes in the highlands exhibit a lower range-size distribution, likely due to habitat specialization or micro-endemism at higher altitudes.ConclusionAltitude significantly influenced the abundance, taxonomic composition, and phylogenetic diversity of anuran communities, with higher elevations supporting a greater number of individuals and distinct evolutionary lineages. In contrast, functional diversity did not vary with altitude, suggesting functional redundancy, where different species perform similar ecological roles, thereby maintaining community resilience. Local factors, such as the number of tank-bromeliads and leaf litter depth, were also key variables shaping community structure. Given the high species turnover and the presence of unique evolutionary lineages, especially in the highlands, conservation efforts should prioritize the protection of the entire montane habitat to sustain the ecological and evolutionary processes that support this exceptional biodiversity. Understanding how species are distributed and identifying the most important filters of anuran diversity along altitudinal gradients in the Atlantic Forest is essential for developing management plans and conservation actions in this threatened region that harbors one of the world’s most remarkable assemblages of anurans. creator: Iuri Ribeiro Dias creator: Kássio de Castro Araújo creator: Jorge Mario Herrera-Lopera creator: Caio Vinícius de Mira-Mendes creator: Tadeu Teixeira Medeiros creator: Marcos Ferreira Vila Nova creator: Marcelo Felgueiras Napoli creator: Mirco Solé uri: https://doi.org/10.7717/peerj.19561 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dias et al. title: The safety and efficacy of phosphodiesterase type 5 inhibitors in the treatment of diabetic erectile dysfunction: a systematic review and meta-analysis link: https://peerj.com/articles/20147 last-modified: 2025-10-07 description: BackgroundPrevious studies have confirmed the efficacy of phosphodiesterase type 5 inhibitors (PDE-5 inhibitors) in treating diabetic erectile dysfunction (DED), but they still have research value in terms of efficacy comparison and individualized safety. This study, while evaluating safety and efficacy, also focused on the sources of heterogeneity and innovatively explored the nonlinear relationship between therapeutic effect and age.AimThis study aimed to systematically evaluate the safety and efficacy of PDE-5 inhibitors for the treatment of DED and the related application effects and to provide a clinical basis for its treatment.MethodsBy searching PubMed, Embase, Web Of Science, Cochrane Library, China Knowledge Network (CNKI), Wipro (VIP), Wanfang, and China Biomedical Literature Database (CBM) before December 31, 2024, and reading the retrieved articles and references, PDE-5 inhibitors for diabetic erectile dysfunction in randomized controlled trials (RCTs). The literature of the included studies was evaluated using the Cochrane Literature Quality Assessment Tool. The meta-analysis was registered to PROSPERO (CRD42025637725).OutcomesThe International Index of Erectile Function (IIEF-5) overall and related evaluation questionnaires were used as the primary efficacy evaluation indicators, and adverse events were used as secondary indicators.ResultsMeta-analysis was performed using Rever Manager 5.3 and STATA18 software. A total of 10 studies were included, and random-effects model meta-analysis analyzed the post-treatment efficacy of the 10 articles with a combined RR = 2.91, 95% CI of [1.95–4.34], P < 0.001. Fixed-effects model meta-analysis investigated adverse effects with RR = 2.0, 95% CI of [1.53–2.61], P < 0.001. There was a non-linear relationship between age and PDE-5 inhibitors.ConclusionPDE-5 inhibitors can safely and effectively improve diabetic erectile dysfunction, but the degree of effectiveness of different types of drugs, the occurrence of related adverse effects, and the differences that exist between individuals still need to be taken into account during use. creator: Zexin Zhu creator: Jian Xu creator: Bo Dai creator: Minghao Lin creator: Huhu Yang creator: Shilin Liu creator: Pengjie Bao creator: Zheng Nan uri: https://doi.org/10.7717/peerj.20147 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhu et al. title: Comprehensive analysis of DNA methylation patterns in recurrent miscarriage: imprinted/non-imprinted genes and their regulation across sperm and fetal-maternal tissues link: https://peerj.com/articles/20125 last-modified: 2025-10-07 description: BackgroundEpigenetic regulation, including DNA methylation, is essential for normal embryonic development and maternal-fetal interactions. Recurrent miscarriage (RM), defined as the loss of two or more consecutive pregnancies, poses significant clinical and emotional challenges. However, the role of epigenetic alterations in RM, particularly in gametes and placental tissues, remains underexplored. This study aims to investigate global DNA methylation profiles and imprinting gene expression in the context of RM, providing insights into epigenetic mechanisms that contribute to pregnancy failure.MethodsGenome-wide DNA methylation profiling was performed on sperm and chorionic villi from RM patients and control couples undergoing artificial abortion using the Illumina HumanMethylation 450 BeadChip platform. Genes related to differentially methylated probes (DMPs) in functionally critical genomic regions, including enhancers, promoters, and DNase hypersensitive sites (DHS), were identified and submitted to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Key imprinting genes (CPA4 and PRDM16) were validated at the protein level using Western blotting.ResultsRM samples exhibited a significant increase in hypermethylated DMPs across all analyzed tissues, with villi and decidua showing the highest numbers of epigenetic changes. Enrichment analyses highlighted pathways implicated in tissue morphogenesis, immune regulation, and cell signaling, including the PI3K-Akt, TGF-beta, and Wnt signaling pathways. Among imprinting genes, CPA4 and PRDM16 showed distinct hypomethylation at enhancer regions, corresponding to elevated protein expression in RM villi tissues.ConclusionsThis study identifies profound epigenetic dysregulation in RM-associated tissues, emphasizing the contribution of imprinting gene methylation abnormalities to pregnancy loss. Future studies incorporating functional assays and animal models are essential to elucidate the causal roles of candidate genes in RM pathogenesis and maternal-fetal health. creator: Yanru Niu creator: Lanlan Yin creator: Yulan Zhou creator: Xiaoyan Pang creator: Yunqinq Li creator: Cailing Peng creator: Meihua Yao creator: Guoling Zhang creator: Kaijie Yang creator: Tianzhong Ma uri: https://doi.org/10.7717/peerj.20125 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Niu et al. title: Sucking lice in bandicoot rats with first complete description of Hoplopleura malabarica nymphs link: https://peerj.com/articles/20115 last-modified: 2025-10-07 description: BackgroundStudies of insect biodiversity and parasitism are often based on adult stages, as immature stages are poorly known and often cannot be identified to species level. However, sucking lice (Anoplura) are permanent, hematophagous parasites with single-host life cycles, making it possible to track the occurrence of all life stages. Only the complete identification of all life stages provides a full picture of parasitism, including infestation levels, parasite topography preferences on the host, and host specificity. The detection of different development stages on a host provides strong evidence that lice of a particular species are actively reproducing and completing their life cycle on that host, making full use of its resources. Conversely, the presence of adult lice alone, particularly when found sporadically, may suggest a failed or incidental attempt at host colonization rather than an established parasitic association.MethodologyThe description of the nymphal stages of Hoplopleura malabarica is based on specimens of sucking lice from the greater bandicoot rat Bandicota indica from Southeast Asia, specifically from the Vientiane area of Lao PDR. The study used morphometric analysis and scanning microscopy techniques.ResultsThis study presents the first description of the nymphal stages of Hoplopleura malabarica, an oligoxenous parasite of rodents of the genus Bandicota. In addition, a global checklist of Anoplura parasitizing rodents of the genus Bandicota was provided.ConclusionsThe detection of different life stages of lice within the host confirms that they reproduce and develop on a given host species, fully utilizing its resources. creator: Paulina Kozina creator: Joanna N. Izdebska creator: Serge Morand creator: Alexis Ribas uri: https://doi.org/10.7717/peerj.20115 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kozina et al. title: Transcriptome reveals differential expression of flavor and color in closely related strains of tomato (Solanum lycopersicum) link: https://peerj.com/articles/20113 last-modified: 2025-10-07 description: Fruit flavor and color are critical quality characteristics of tomatoes (Solanum lycopersicum). Numerous studies have demonstrated that tomato flavor is primarily linked to the sugar-acid content and its ratio, while fruit color is predominantly determined by the composition and concentration of carotenoids and flavonoids. To elucidate the regulatory mechanisms underlying the differences in sugar-acid and color formation during fruit ripening, transcriptome analysis was conducted for the first time on the breaker stage (Br) and mature fruit stage (MF) of the closely related strains yellow-fruited tomato (No. 19) and red-fruited tomato (No. 20). This analysis aimed to identify key regulatory genes and biosynthetic pathways associated with the formation of flavor and color in tomato fruits. The transcriptome analysis revealed that 1,546 differentially expressed genes (DEGs) were identified in the Br19_vs_Br20 comparison, of which 507 were up-regulated and 1,039 were down-regulated. In the MF19_vs_MF20 comparison, 2,178 DEGs were detected, with 1,235 up-regulated and 943 down-regulated. Upon further analysis of the DEGs, we identified several key genes in the sugar-acid metabolic pathway, including sucrose synthase (SUS), phosphofructokinase (PFK), fructose-bisphosphate aldolase (FBA), citrate synthase (CS), and succinate dehydrogenase (SuDH), which may significantly influence tomato flavor. Additionally, differential genes related to carotenoid and flavonoid metabolism, such as cytochrome P450 98A (CYP98A), caffeoyl-CoA3-O-methyltransferase (CCoAMT), carotenoid isomerase (CRTISO), lycopene beta cyclase (LCYB), zeaxanthin epoxidase (ZEP), violaxanthin deepoxidase (VDE), and 9-cis-epoxycarotenoid dioxygenase (NCED), as well as genes linked to ethylene synthesis, such as 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), may play a role in the color changes observed in tomatoes. The findings of this study provide insights into the underlying mechanisms of flavor and color development in tomato fruit, offering valuable information for the genetic improvement of tomatoes. creator: Chunmei Guo creator: Xiuyuan Liu creator: Yingfeng Ding creator: Zhaoyilan He creator: Songmei Shi creator: Yumei Ding creator: Hui Shen creator: Zhengan Yang uri: https://doi.org/10.7717/peerj.20113 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo et al. 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. title: cpSNP discovery and genotyping for a Pinus taeda breeding population with targeted comparison to related conifers link: https://peerj.com/articles/20092 last-modified: 2025-10-06 description: Pinus taeda (Loblolly pine) is the most important commercial tree species in the southern United States and a significant non-native plantation species in China. Its genetic improvement program has been implemented in South China for 30 years. In this study, the chloroplast (cp) genome of P. taeda was sequenced, assembled, and compared with other available chloroplast genomes of Pin aceae using BLAST. Codon usage among 33 species of Pinaceae was analyzed using the relative synonymous codon usage (RSCU) value. The results were then visualized using the pheatmap v1.0.10 in R. The rates of nonsynonymous (Ka) and synonymous (Ks) substitutions in the chloroplast genomes among five species of Pinus were estimated using the seqinr package in R. Additionally, selected single nucleotide polymorphisms (SNPs) were used to genotype 33 individuals from the P. taeda breeding population. The P. taeda cp genome is 121,530 bp, with certain regions (e.g., ycf1 and ycf2) showing lower sequence conservation compared to other Pinaceae species. Codon usage analysis revealed that codons ending in G or C were not prevalently used, with significant differences in natural selection pressure on chloroplast genes between three species (P. taiwanensis, P. thunbergii, and P. koraiensis) and the other 30 species. Phylogenomic analysis using 36 cp genomes (representing 25 species) resolved Pinus into two subgenera, with P. taeda clustered with P. rigida within the diploxylon pines. Notably, ycf1-based phylogenetic analysis recovered a topology highly congruent (normalized RF = 0.15) with whole-plastome phylogenies. This study validates the single-copy gene ycf1 as a robust and low-cost phylogenetic marker for conifer genus-level reconstruction. The identified SNPs provide valuable molecular markers for genotyping individuals in P. taeda breeding programs, supporting germplasm characterization and management. creator: Ling Wang creator: Jipeng Mao creator: Kaibin Jiang creator: Zhengyu Wu creator: Chunxin Liu creator: Huagong Ning creator: Haibiao Zhou creator: Jiehu Chen creator: Shaowei Huang creator: Tianyi Liu uri: https://doi.org/10.7717/peerj.20092 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Eyestalk transcriptome analysis reveals sexually dimorphic host-parasite interactions: divergent molecular strategies of Polyascus sp. for reproductive and growth regulation in Eriocheir sinensis link: https://peerj.com/articles/20089 last-modified: 2025-10-06 description: BackgroundThe Chinese mitten crab (Eriocheir sinensis), an economically critical migratory species inhabiting both freshwater and marine environments, is susceptible to parasitization by the rhizocephalan barnacle Polyascus sp. in estuarine ecosystems. In this study, E. sinensis was found to be parasitized by Polyascus sp. in the freshwater waters of the Anqing section of the Yangtze River, which manifested itself as restricted growth and development, hindered gonadal development, and apparent changes in sexual characteristics.MethodsMorphological analysis, serological testing, and eyestalk transcriptome analysis were conducted on male and female parasitized and non-parasitized crabs to investigate the molecular mechanisms by which Polyascus sp. affects host growth and reproduction.ResultsThe study revealed that parasitized hosts of both sexes were significantly smaller than normal individuals and exhibited gonadal atrophy. Male hosts displayed feminization of secondary sexual characteristics, whereas females showed no significant alterations. Testosterone and ecdysterone levels decreased in male hosts, whereas estradiol levels declined in female hosts. Transcriptomic profiling revealed differentially expressed genes predominantly associated with metabolic processes, stimulus response, signal transduction, and reproduction. Thirteen key candidate genes related to parasite-induced suppression of host molting and growth, fourteen key candidate genes involved in male reproductive regulation, and ten candidate genes affecting female gonadal development were identified. Key genes involved in gonadal development—including 5-HT1B, CHH, MIH, JHE1, Dmrt family, cytochrome P450 family, Abd-A, and Antp exhibited sex-specific expression patterns. Additionally, critical growth-related genes such as Dib, HR38, and Cht3 exhibited significant alterations in hosts of both sexes. Polyascus sp. parasitism suppresses gonadal development and growth in both sexes, employing distinct regulatory strategies. It uses a “neuroendocrine disruption and reproductive gene regulation” strategy to regulate reproductive development in male hosts, while influencing female reproductive metabolism through a “Nutrient Hijacking-Hormonal Suppression” mechanism. Additionally, the parasitism disrupts host growth via “molting inhibition”. These findings elucidate the sex-specific metabolic, reproductive, and growth disruption strategies of Polyascus sp., providing new insights into host-parasite interactions in decapod crustaceans. creator: Jing Xie creator: Congping Ying creator: Zhen Tang creator: Yanping Yang creator: Kai Liu uri: https://doi.org/10.7717/peerj.20089 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Xie et al. title: Hemodynamic outcomes in patients undergoing bidirectional cavopulmonary connection with additional or antegrade pulmonary blood flow: a single-centre retrospective study link: https://peerj.com/articles/20021 last-modified: 2025-10-06 description: BackgroundThe bidirectional cavopulmonary connection (BCPC) is a pivotal stage in the surgical palliation of single-ventricle patients. However, there is ongoing debate regarding the benefits and drawbacks of BCPC with additional or antegrade pulmonary blood flow (AAPBF) in optimizing the subsequent stage—total cavopulmonary connection (TCPC).ObjectiveTo determine the influence of BCPC with AAPBF on pulmonary artery growth and hemodynamic outcomes.MethodsA retrospective review was conducted of 167 single-ventricle patients who underwent BCPC at Siriraj Hospital between 2006 and 2022. Patients were categorized into two groups based on AAPBF status: group 1 (with AAPBF, n = 44) and group 2 (without AAPBF, n = 123). Variables from pre-BCPC and pre-TCPC cardiac catheterization—including pulmonary artery growth, McGoon ratio, Nakata index, mean pulmonary arterial pressure (mPAP), ventricular end-diastolic pressure (EDP), and indexed pulmonary vascular resistance (PVRi)—were compared between groups. Pulmonary artery branch z-scores were analyzed and adjusted using analysis of covariance (ANCOVA). Survival rate, all-cause mortality, and incidence of atrioventricular valve regurgitation (AVVR) and pulmonary arteriovenous malformation (AVM) were also assessed.ResultsMedian ages at pre-BCPC assessment were 1.06 years (group 1) and 2.17 years (group 2), and at pre-TCPC assessment were 6.19 and 7.27 years, respectively. Median age at BCPC operation was similar between groups (1.58 vs. 1.51 years). Over a median follow-up of 64.33 months, group 1 showed significantly greater increases in right and left pulmonary artery size compared to group 2 (RPA: 3.27 vs. 1.6 mm (p = 0.019); LPA: 2.38 vs. 0.88 mm (p = 0.004)). The Nakata index increased in group 1 but decreased in group 2 (26.70 vs. –84.67 mm2/m2, p < 0.001). Z-scores confirmed significant growth in both pulmonary arteries when adjusted for body surface area (p < 0.001). No significant differences were found in pre-BCPC mPAP (16 vs. 15 mmHg, p = 0.38), EDP (12 vs. 12 mmHg, p = 0.584), or PVRi (1.77 vs. 2.03 WU m2, p = 0.890). Survival rates did not differ significantly between groups (p = 0.350).ConclusionsBCPC with AAPBF effectively promotes pulmonary artery growth without adversely affecting ventricular volume loading or pulmonary artery pressure. Further investigation into the development of arteriovenous malformations is recommended. creator: Kernfan Puthikitakawiwong creator: Chodchanok Vijarnsorn creator: Teerapong Tocharoenchok creator: Prakul Chanthong creator: Kritvikrom Durongpisitkul creator: Paweena Chungsomprasong creator: Supaluck Kanjanauthai creator: Ploy Thammasate creator: Thita Pacharapakornpong creator: Jarupim Soongswang creator: Kriangkrai Tantiwongkosri creator: Ekarat Nitiyarom creator: Thaworn Subtaweesin uri: https://doi.org/10.7717/peerj.20021 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Puthikitakawiwong et al. title: NT-proBNP serves as a prognostic marker for adverse outcomes in severe immune checkpoint inhibitor-associated myocarditis link: https://peerj.com/articles/20020 last-modified: 2025-10-06 description: BackgroundImmune checkpoint inhibitors (ICIs) have transformed cancer treatment but carry risks of rare, life-threatening immune-related adverse events, particularly myocarditis. Prognostic biomarkers and optimal management strategies for severe ICI-associated myocarditis remain poorly defined.MethodsThis single-center retrospective cohort study analyzed 71 patients diagnosed with ICI-associated myocarditis among 7,157 ICI-treated individuals at a tertiary center (August 2018–August 2024). Myocarditis severity was graded per American Society of Clinical Oncology (ASCO) guidelines. Cardiac biomarkers, including NT-proBNP and troponin T, were assessed. Binary logistic regression identified predictors of mortality. Treatment protocols and immunotherapy rechallenge outcomes were evaluated.ResultsSevere myocarditis (Grades 3–4) occurred in 33 patients (46.5%), with an overall mortality rate of 54.5% in this subgroup (18/33). NT-proBNP levels were significantly elevated in fatal cases versus survivors (median: 13,804 vs. 4,050 pg/mL; P < 0.001) and independently predicted mortality risk (odds ratio (OR) 4.3, 95% confidence interval (CI) [1.2–21.9]; P = 0.023). A multimodal regimen combining plasmapheresis with high-dose corticosteroids, intravenous immunoglobulin, and mycophenolate mofetil was associated with improved survival. Among nine patients rechallenged with immunotherapy, seven (77.8%) tolerated subsequent cycles without recurrent immune toxicity, while two with prior Grade 2 myocarditis experienced symptom recurrence.DiscussionElevated NT-proBNP emerges as a critical prognostic marker for risk stratification in severe ICI-associated myocarditis. Immunotherapy rechallenge appears feasible in select patients but warrants caution in those with prior moderate-grade myocarditis. These findings advocate for biomarker-guided escalation of therapies and shared decision-making frameworks to balance oncologic efficacy with cardiovascular safety. creator: Cheng He creator: Linjuan Xu creator: Zhihong Zhang creator: Jiong Wang uri: https://doi.org/10.7717/peerj.20020 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 He et al. title: Oropharyngeal microbiome dysbiosis in esophageal squamous cell carcinoma: taxonomic shifts, metabolic reprogramming, and geographic disparities in a high-incidence cohort link: https://peerj.com/articles/20009 last-modified: 2025-10-06 description: BackgroundEsophageal squamous cell carcinoma (ESCC) is a leading cause of cancer mortality globally, with pronounced geographic disparities in incidence. Emerging evidence links oral microbiome dysbiosis to ESCC pathogenesis, yet comprehensive insights into microbial diversity, taxonomic shifts, and functional alterations in high-risk populations remain limited.MethodsUsing 16S rRNA amplicon sequencing, we compared the oral microbiome of ESCC patients and healthy controls from a high-incidence region in Northwest China. Alpha and beta diversity metrics, taxonomic composition, and predicted functional pathways were analyzed to identify microbial signatures associated with ESCC.ResultsESCC patients exhibited significantly elevated microbial richness (observed amplicon sequence variants (ASVs), Chao1, ACE; p < 0.05) but comparable Shannon/Simpson diversity to controls. Unique amplicon sequence variants (ASVs) were more prevalent in ESCC samples, and principal component analysis confirmed distinct community structures (p < 0.05). Taxonomically, Streptococcus and Neisseria dominated both groups, but ESCC patients showed enrichment of Gemella (p = 0.0003) and Corynebacterium (p < 0.00001), alongside depletion of Prevotella_7 (p = 0.0002) and Moraxella (p < 0.001). Functional profiling revealed upregulated amino acid metabolism (e.g., beta-alanine and valine degradation) and downregulated carbohydrate metabolism in ESCC-associated microbiota.ConclusionThis study uncovers unique oral microbial signatures in ESCC patients from a high-incidence region, characterized by increased richness, taxon-specific shifts, and metabolic reprogramming favoring amino acid catabolism. These findings highlight the potential of microbial biomarkers for ESCC detection and provide mechanistic insights into microbiome-driven carcinogenesis. The geographic specificity of the cohort underscores the urgency of tailored interventions in high-risk populations and advances our understanding of microbial contributions to esophageal cancer. creator: Ying Liu creator: Erman Wu creator: Fang Cheng creator: Meng Zhang creator: Qian Rou creator: Zinati Nuertai creator: Maorong Xu creator: Shanshan Xu creator: Minghui Li creator: Lei Zhang creator: Aheli Nasiroula uri: https://doi.org/10.7717/peerj.20009 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: The 12-LOX/12-HETE/GPR31 metabolic pathway promotes tumor-associated macrophage M2 polarization mediated pancreatic cancer development link: https://peerj.com/articles/19963 last-modified: 2025-10-06 description: BackgroundThe 12-lipoxygenase (12-LOX)/12-hydroxyeicosatetraenoic acid (12-HETE) pathway is associated with various tumors. M2 macrophages in the tumor microenvironment promote tumorigenesis and progression. However, the role of the 12-LOX/12-HETE/G protein-coupled receptor 31 (GPR31) metabolic pathway and its relationship with M2 macrophages remains unclear in pancreatic cancer (PC).MethodsThe expression levels of 12-LOX, GPR31, and 12-HETE were detected in PC and mouse PC models using western blot and enzyme-linked immunosorbent assays (ELISA). In vivo and in vitro experiments were conducted using the 12-LOX inhibitor ML355 to investigate the role of the 12-LOX/12-HETE/GPR31 metabolic pathway in M2 macrophage polarization and tumor progression through flow cytometry, reverse transcription polymerase chain reaction (RT-PCR), 5-Ethynyl-20-deoxyuridine (EdU) assays, and Transwell experiments.ResultsThe 12-LOX/12-HETE/GPR31 metabolic pathway is expressed actively in PC. Inhibition of 12-LOX in a mouse model of pancreatic cancer suppressed the expression of this metabolic pathway, retarded tumor growth, and reduced the polarization of macrophages towards the M2 type. In vitro, co-culturing PC cell line PANC-1 with macrophages and selectively inhibiting 12-LOX influenced the proliferation, migration, and invasion of PC cells. Inhibiting 12-LOX did not suppress the function of individual PC cells, but it inhibited the development of PC cells co-cultured with macrophages. Moreover, inhibiting 12-LOX reduced the co-cultured M2 macrophages.ConclusionThis study, through in vivo and in vitro experiments, reveals that the 12-LOX/12-HETE/GPR31 metabolic pathway affects the growth, migration, and invasion of PC by modulating M2 macrophage polarization patterns. creator: Ying Yang creator: Yuanzhen Wang creator: Jia Wu creator: Chunxiu Tan creator: Liya Huang uri: https://doi.org/10.7717/peerj.19963 license: https://creativecommons.org/licenses/by-nc/4.0/ rights: ©2025 Yang et al. title: The BAF53A-BACH1-GCLM axis regulates glutathione metabolism and enhances ferroptosis resistance in esophageal squamous cell carcinoma link: https://peerj.com/articles/20156 last-modified: 2025-10-03 description: ObjectiveEsophageal squamous cell carcinoma (ESCC), a highly lethal malignancy, exhibits poor survival rates and limited treatment options. Ferroptosis, a regulated form of cell death driven by lipid peroxidation, emerges as a potential therapeutic target. However, the mechanisms suppressing ferroptosis in ESCC remain poorly understood.MethodsShort hairpin RNA (shRNA) was employed to knock down BAF53A and BACH1 in ESCC cell lines, followed by assessments of cell proliferation, colony formation, and ferroptosis sensitivity. Glutathione (GSH) metabolism was evaluated by measuring GSH/GSSG and NADP+/NADPH ratios, reactive oxygen species (ROS) levels, and lipid peroxidation through flow cytometry and fluorescence imaging. Molecular interactions were evaluated using co-immunoprecipitation and chromatin immunoprecipitation sequencing (ChIP-seq) to identify transcriptional targets of the BAF53A-BACH1 complex.ResultsBAF53A was elevated in ESCC, and its depletion impaired cell proliferation and colony formation ability of cells. Knockdown of BAF53A disrupted GSH metabolism, leading to increased ROS levels, reduced GSH/GSSG and NADP+/NADPH ratios, and enhanced ferroptosis sensitivity. Mechanistically, BAF53A collaborated with BACH1 to transcriptionally activate glutamate-cysteine ligase modifier subunit (GCLM), a key enzyme in GSH biosynthesis. Overexpression of GCLM restored redox balance and cell viability in BAF53A- or BACH1-silenced cells.ConclusionsThe BAF53A-BACH1-GCLM axis constitutes a novel egulatory pathway that integrates chromatin remodeling, transcriptional regulatione, and ferroptosis resistance in ESCC. Targeting this axis may offer a promising approach to exploit metabolic vulnerabilities and enhance ferroptosis sensitivity in ESCC treatment. creator: Weijuan Jiang creator: Jie Zhang creator: Canjuan Chen creator: Jiangwei Shi creator: Lihua Fan uri: https://doi.org/10.7717/peerj.20156 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Jiang et al. title: The association between ADIPOQ gene variants (rs266729, rs2241766, rs1501299) and acute myocardial infarction in Vietnamese patients with type 2 diabetes mellitus link: https://peerj.com/articles/20145 last-modified: 2025-10-03 description: BackgroundType 2 diabetes mellitus (T2DM) significantly increases the risk of acute myocardial infarction (AMI). Polymorphisms in the ADIPOQ gene, which encodes the adiponectin hormone, are believed to influence cardiovascular disease risk. This study aims to evaluate the association between three ADIPOQ gene variants—rs266729, rs2241766, and rs1501299—and the risk of AMI in Vietnamese patients with T2DM.MethodsA case–control study was conducted from January 2023 to June 2024 at the University Medical Center, Ho Chi Minh City. The study included 275 T2DM patients with a history of AMI (case group) and 275 T2DM patients without AMI (control group). Participants were matched by age, gender, smoking status, and duration of T2DM to control for potential confounding factors. DNA was extracted from peripheral blood samples, and the three polymorphisms were genotyped using Sanger sequencing.ResultsSignificant associations were found between ADIPOQ gene polymorphisms and AMI risk. The G/G genotype of rs266729 and the T/T genotype of rs1501299 were associated with a reduced risk of AMI (OR = 0.45, 95% CI [0.23–0.89], p = 0.021; OR = 0.45, 95% CI [0.22–0.90], p = 0.025, respectively). In contrast, the T/G genotype of rs2241766 was significantly associated with an increased risk of AMI (OR = 2.07, 95% CI [1.44–2.97], p < 0.001).ConclusionThis study suggests that rs266729 and rs1501299 may have protective effects, while rs2241766 may increase the risk of AMI in Vietnamese patients with T2DM. These findings highlight the importance of further research into adiponectin levels and long-term monitoring, and support the potential use of genetic variants in personalized cardiovascular risk management for patients with T2DM. creator: Bao Hoang Le creator: Khanh Quang Tran creator: Nhu Nhat Quynh Nguyen creator: Truc Thanh Thai uri: https://doi.org/10.7717/peerj.20145 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Le et al. title: Optimizing legume green manure applications for enhanced forage sorghum-sudangrass performance and soil property improvements link: https://peerj.com/articles/20137 last-modified: 2025-10-03 description: BackgroundLegume-based green manuring is an environmentally sustainable and economically viable approach that enhances soil fertility by improving organic matter content, facilitating biological nitrogen fixation, and stimulating microbial activity. These benefits collectively reduce reliance on mineral fertilizers, which are associated with environmental degradation. While the soil-enhancing properties of legumes are well-established, limited information is available regarding how the timing of green manure incorporation affects the growth performance and forage quality of subsequent crops. This study aimed to assess the effects of incorporating different legume species at various phenological stages on the growth, yield, and forage quality of sorghum × sudangrass under Mediterranean climatic conditions.MethodsA field experiment was conducted from 2022 to 2024 at Aydın Adnan Menderes University, Türkiye, using a randomized complete block design with three replicates. Eleven treatments were implemented, consisting of three legume species (common vetch, narbon vetch, and forage pea) incorporated at three distinct phenological stages (pre-flowering, 10% flowering, and full flowering), along with unfertilized and fertilized controls. Following incorporation, sorghum × sudangrass was sown without additional fertilization, except in the fertilized control. Key response variables included fresh forage yield (FFY), hay yield (HY), plant height, leaf number, leaf area index (LAI), chlorophyll content (SPAD), and crude protein yield (CPY). Soil organic matter and total nitrogen levels were also measured before and after treatments.ResultsGreen manure application significantly enhanced the growth, biomass accumulation, and forage quality of sorghum × sudangrass. The incorporation of common vetch and narbon vetch at the 10% flowering stage led to up to a 50% increase in fresh forage yield compared to the unfertilized control. Forage pea maintained consistent yield performance across all incorporation stages. Improvements in soil organic matter and nitrogen content were particularly notable in legume-amended plots. Furthermore, the highest SPAD and LAI values were recorded at early flowering stages, suggesting enhanced photosynthetic efficiency. These findings underscore the effectiveness of legume green manuring, particularly with optimal incorporation timing, as a sustainable strategy to improve soil health, forage productivity, and resource-use efficiency in Mediterranean agroecosystems. creator: Emre Kara uri: https://doi.org/10.7717/peerj.20137 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kara title: Reconstruction of masked sequences via inverse mapping of incomplete information natural vectors link: https://peerj.com/articles/20126 last-modified: 2025-10-03 description: Alignment-free embedding methods, which map biological sequences into a fixed-dimensional space using mathematical techniques, hold significant value in biology. A key challenge in this field is constructing an inverse mapping to recover sequences from embedded vectors. The natural vector approach uniquely provides a theoretical one-to-one correspondence between sequences and high-order natural vectors, but reconstructing sequences from lower-order vectors remains unsolved. Moreover, when sequences contain masked regions, extracting features and constructing the inverse mapping to restore the original sequence, including the masked parts, becomes even more challenging. In this article, we define incomplete information natural vectors for masked sequences and develop a long short-term memory model that achieves over 99.9% accuracy in reconstructing unmasked positions in original sequences on SARS-CoV-2 and HIV-1 datasets, while also providing predictions for masked sites that significantly outperform random prediction. Our model can robustly handle sequences with varying masked nucleotides. Overall, our approach expands the scope of alignment-free embedding methods by enabling bidirectional conversion and addressing challenges posed by incomplete information. creator: Patrick Ding creator: Guoqing Hu creator: Hongyu Yu creator: Stephen S.-T. Yau uri: https://doi.org/10.7717/peerj.20126 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ding et al. title: Proteomic landscape of porcine induced neural stem cell reprogramming and differentiation link: https://peerj.com/articles/20120 last-modified: 2025-10-03 description: BackgroundDirect reprogramming of somatic cells into induced neural stem cells (iNSCs) holds strong potential for regenerative medicine, especially in large animal models like pigs, which are crucial for translational and preclinical research. However, the molecular mechanisms underlying porcine fibroblast-to-iNSC reprogramming and subsequent differentiation remain poorly understood at the proteomic level.MethodsTo map the proteomic landscapes associated with reprogramming and differentiation, we performed unbiased label-free discovery proteomics (nano-LC-MS/MS) and targeted SWATH-MS quantification. Proteomes of porcine tail fibroblasts (PTFs; passage 3), two porcine iNSC lines (piNSCs; VSMUi002-B and VSMUi002-E, passage 20), and their differentiated progeny (piNSCs-NGs; VSMUi002-B-NGs and VSMUi002-E-NGs, representing piNSCs at passage 20 cultured for an additional 14 days under differentiation conditions) were compared. Two previously established piNSC lines (VSMUi002-B and VSMUi002-E), generated via Sendai virus-mediated reprogramming, were used as the cellular models.ResultsThe piNSC lines displayed hallmark neural stem cell (NSC) morphology and expressed canonical markers (PAX6+, SOX2+, NES+, VIM+, OCT4−). Upon differentiation, they generated neuronal and glial cells expressing TUJ1, MAP2, SYP, TH, and GFAP, confirming their multipotency. A total of 4,094 proteins were identified across the three cell states. Multivariate analysis revealed distinct proteomic signatures separating fibroblasts, iNSCs, and their neuronal/glial progeny. The proteomic shift from the fibroblast to the piNSC state was marked by increased expression of stathmin 1 (STMN1), neurofilament light polypeptide (NEFL), aconitate hydratase (ACO2), electron transfer flavoprotein subunit beta (ETFB), fructose-bisphosphate aldolase B (ALDOB), and transketolase (TKT), alongside suppression of actin-related protein 2/3 complex subunit 5 (ARPC5) and LIM domain and actin-binding protein 1 (LIMA1). These shifts indicate a dismantling of the fibroblast cytoskeleton and a broad upregulation of cellular energy and biosynthetic metabolism, reflecting a loss of fibroblast identity and the acquisition of an NSC state. Upon differentiation into piNSCs-NGs, 19 proteins were consistently upregulated. These included neuronal structural proteins (INA, STMN1), cytoskeletal regulators (PFN1), signaling modulators (MBIP), and proteins involved in lysosomal function (NCOA7), cell adhesion (CDHR2), and calcium signaling (ANXA4). Pathway and network analyses highlighted post-transcriptional regulation—particularly involving RNA processing and the RNA exosome complex (e.g., EXOSC3)—as a key feature of differentiation.ConclusionThis study provides the first comprehensive proteomic map of piNSC reprogramming and differentiation in a large animal model. Our findings uncover critical regulatory proteins and pathways governing cytoskeletal organization, metabolism, and RNA processing, offering valuable insights into neural fate states. This resource advances the understanding of neural reprogramming in translational models and supports future regenerative and comparative neuroscience efforts. creator: Sekkarin Ploypetch creator: Sataporn Phochantachinda creator: Warunya Chakritbudsabong creator: Walasinee Sakcamduang creator: Nattarun Chaisilp creator: Somjit Chaiwattanarungruengpaisan creator: Supitcha Pannengpetch creator: Piyada Na Nakorn creator: Tharathip Muangthong creator: Sasitorn Rungarunlert uri: https://doi.org/10.7717/peerj.20120 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ploypetch et al. title: Exploration of nitrogen use efficiency and root-shoot-soil variation on the stoichiometric characteristics of carbon, nitrogen, phosphorous and potassium for winter wheat under various nitrogen treatments link: https://peerj.com/articles/20101 last-modified: 2025-10-03 description: BackgroundNitrogen (N) addition has significant effects on grain yield and nutrient use efficiency (NUE) in farmland ecosystems, and the total carbon: nitrogen: phosphorus: potassium (TC:TN:TP:TK) stoichiometry in plants and soil is of great significance for improving plant productivity and nutrition. However, there is still uncertainty regarding the effects of N fertilizers on the stoichiometric characteristics of different root-shoot parts of winter wheat during growth progression.Methods‘Fengdecunmai5’ wheat was selected as the material for the positioning test field. Three N application treatments (0, 180 and 300 kg ha−1, designated N0, N180 and N300) were designed to study the yield, NUE, and stoichiometric characteristics of TC, TN, TP and TK in each organ at different stages, and to analyze the relationships among them.ResultsThe N180 treatment increased the total nitrogen (TN) content in roots, stems plus leaves and grain at each stage. The TN and TP content in stems plus leaves gradually decreased from jointing to maturity stages, whereas the TN content in grain gradually increased from filling to maturity stages. Under the N180 treatment, TN:TP values significantly increased, by 20.3%, 27.9% and 26.3% compared with N0 treatment, respectively. Moreover, the farmland ecosystem was mainly limited by the TN content. TK content in roots and TC:TN in stems plus leaves was significantly positively correlated with NUE. TN:TK and TN: TP in stems plus leaves were positively correlated with yield, and TN and TK content in stems plus leaves considerably influenced the yield.ConclusionsUnder N180 treatment, compared with N0 and N300 treatments, wheat plants achieved higher nutrient uptake, and greater yield and NUE. This study contributes to the assessment of plant productivity and the precise optimization of ecosystem stoichiometry in the context of green sustainable agricultural development. creator: Tianyu Lv creator: Shijie Liu creator: Suhao Lu creator: Chenyang Wang creator: Dongyun Ma creator: Guozhang Kang creator: Yingxin Xie creator: Jiaming Wu creator: Jutao Sun creator: Li-fang Wang uri: https://doi.org/10.7717/peerj.20101 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lv et al. title: Influence of organic, synthetic and biofertilizers on the diversity of cassava rhizosphere microbiome in Northeastern Thailand link: https://peerj.com/articles/20085 last-modified: 2025-10-03 description: Cassava, one of Thailand’s main economic crops, is capable of growing in nearly all soil types. However, continuous monocropping depletes soil nutrients over time. Adopting good agricultural practices can help farmers reduce costs while improving soil fertility. The aim of this study was to compare cassava rhizosphere microbial communities resulting from cultivation under eight different fertilizer treatments, including synthetic, organic, and biological fertilizers, and to identify beneficial microbes that promote cassava growth and yield. The study was conducted at two sites in Northeastern Thailand. Results show that bacterial abundance and species richness (alpha diversity) peaked at 5 months after planting (MAP), showing a significant increase compared to 2 MAP. However, by 10 MAP, alpha diversity began to decline at both sites, Nampong and Seungsang. Among the treatments, the most notable differences in alpha diversity were observed at 5 MAP. At the Nampong site, experimental treatments with chicken manure (T3) and chicken manure combined with other fertilizers (T5, T6, and T8) exhibited significantly higher alpha diversity than did the control (without fertilizer, T1). At the Seungsang site, sole treatment with the full recommended rate of chicken manure (T3), and half of the recommended dose of synthetic fertilizer combined with half the recommended dose of chicken manure (T6) resulted in greater alpha diversity than did swine manure extract application (T4), half of the recommended dose of synthetic fertilizer combined with half of the recommended dose of swine manure extract (T7), and chicken manure application combined with stalk inoculation with plant growth-promoting rhizobacteria (PGPRs) (T8). Since T3 and T8 had the most significant impact on microbial abundance and diversity, as well as cassava growth and yield, the predominant bacteria in these treatments were identified as key targets. A total of eight target bacterial genera were identified: Pseudomonas, Tumebacillus, Lysinibacillus, Paenibacillus, Dongia, Acidibacter, Sphingomonas, and Bacillus. Among them, Tumebacillus was the most notable, as it showed a significant correlation with fresh tuber yield. These beneficial bacteria may serve as key candidates for future biofertilizer production. creator: Suthasinee Somyong creator: Wuttichai Mhuantong creator: Phakamas Phetchawang creator: Derrick Keith Thompson creator: Ornprapa Thepsilvisut creator: Wirulda Pootakham uri: https://doi.org/10.7717/peerj.20085 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Somyong et al. title: Immune-related hub genes in intrauterine adhesions: a bioinformatics approach link: https://peerj.com/articles/20035 last-modified: 2025-10-03 description: BackgroundIntrauterine adhesions (IUA) are a leading cause of acquired female infertility that predominantly arises following surgical intrauterine interventions. Clinical strategies are available for managing IUA, however, the molecular pathogenesis of IUA, particularly the role of immune dysregulation in endometrial repair processes, has not been fully characterized, necessitating comprehensive mechanistic studies.MethodsWe used computational biology methods to determine the molecular pathogenesis of IUA, the results of which were experimentally validated. (i) We systematically reanalyzed GSE224093, a publicly available endometrial transcriptomic dataset, using GEO2R. Differential gene expression was analyzed with stringent statistical thresholds; the results were immunologically contextualized via intersection with the ImmPort database. (ii) Multilayer functional annotation was conducted using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway topology analyses. (iii) Weighted gene co-expression network analysis and scale-free topology optimization were used to identify conserved coexpression modules. (iv) Seven hub genes underwent quantitative real-time polymerase chain reaction (qPCR) validation in human and murine models, with four verified using immunohistochemistry (IHC).ResultsOur integrated multiomics analysis identified seven hub genes associated with IUA pathogenesis through GO, KEGG, and GSEA enrichment analyses. The expression levels TUBB3, WNT5A, GDF7, IGF1, and BIRC5 were downregulated, and those of PTGDS and CCL14 were upregulated. The qPCR results confirmed these expression patterns in human and murine endometria (p < 0.05), with TUBB3 and PTGDS species-specifically diverging from the computational predictions. The IHC results provided the corresponding protein expression changes for IGF1, WNT5A, BIRC5, and GDF7 in IUA (p < 0.01). CCL14 could not be amplified in murine models due to technical constraints.DiscussionWe identified seven immune-related gene signatures through integrative bioinformatics. We experimentally validated three genes (TUBB3, PTGDS, and CCL14) demonstrating species-specific expression patterns. We proposed four mechanistically plausible biomarkers (WNT5A, IGF1, BIRC5, and GDF7) for developing IUA diagnostic tools. The conserved dysregulation of WNT5A- and TGF-β-associated genes (GDF7 and IGF1) suggest therapeutic targets for preventing adhesion recurrence. This study advances our understanding of IUA pathogenesis. Single-cell transcriptomics should be examined in future studies to determine the cellular-subtype-specific contributions to IUA. creator: Fengqing Lv creator: Sang Luo creator: Fengjuan Xu creator: Yue Du creator: Yiyun Bai creator: Jingyi Zhang creator: Xiaojie Zou creator: Dan Liu uri: https://doi.org/10.7717/peerj.20035 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lv et al. title: Genome-wide identification and expression analysis of the HSP70 gene family in Artemisia annua L. under heat stress link: https://peerj.com/articles/19866 last-modified: 2025-10-03 description: Artemisia annua L., a well-known traditional Chinese medicine, is the main source for production of artemisinin, an anti-malaria drug. Heat shock protein 70 (HSP70) plays an important role in plant growth and development as well as in response to biotic and abiotic stresses. While the HSP70 gene family has been characterized in many species, its role in A. annua remains unclear. To investigate the evolutionary relationships, functions, and expression patterns of the A. annua HSP70 (AaHSP70) gene family, we conducted a comprehensive bioinformatics analysis of the HSP70 gene family in the LQ-9 haplotype 0 genome of A. annua. In this study, 47 AaHSP70 genes containing the HSP70 protein structural domain were identified and were unevenly distributed on seven chromosomes, among which, 39 AaHSP70 genes contained 10 identical conserved motifs and eight genes contained varying numbers of seven to nine motifs. Genome collinearity analysis showed that two pairs of genes were duplicated in genome and duplicated segmental duplication (DSD) was the major mode of amplification for this gene family. Cis-acting elements analysis indicated that AaHSP70 was involved in responding to various biotic and abiotic stresses, such as abscisic acid-responsive and defense and stress responsiveness. Gene expression profiling showed that 45 differentially expressed genes (DEGs) of AaHSP70 genes responded differently to heat treatment, of which 12 genes were up-regulated and two genes were up-regulated and then down-regulated. Gene ontology (GO) enrichment showed that two AaHSP70 genes were enriched in the pathway related to reactive oxygen species (ROS). Furthermore, reverse transcription-qPCR (RT-qPCR) experiments confirmed the expression levels of 10 up-regulated genes. This study provides a comprehensive characterization of the HSP70 gene family in A. annua and systematically identifies AaHSP70 genes that were responsive to heat stress, laying the groundwork for further research into the role of the HSP70 gene family in the response of A. annua to abiotic stress. creator: Shan Zhong creator: Hengyu Pan creator: Chaoxue Ma creator: Haojia Xu creator: Xiaoxia Ding creator: Shengye Bao creator: Siyu Zhao creator: Peiqi Shi creator: Baosheng Liao creator: Xianchun Zong uri: https://doi.org/10.7717/peerj.19866 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhong et al. title: Exploring the use of mobile health among patients with cardiometabolic and respiratory chronic diseases in primary care nursing: a cross-sectional study link: https://peerj.com/articles/20130 last-modified: 2025-10-02 description: BackgroundChronic diseases, such as cardiometabolic and respiratory conditions, are major contributors to global morbidity and mortality. These conditions place a considerable burden on primary care due to rising healthcare costs and increasing patient dependency in daily life. Digital tools, such as mobile health (mHealth), have emerged as promising resources to support chronic disease management in this setting. However, patient adoption of mHealth remains limited, and few studies have specifically examined its use among individuals with multiple chronic conditions. This study aims to examine the overall use and implementation of mHealth technologies among patients with chronic cardiometabolic and/or respiratory diseases receiving care from primary care nursing services.MethodsA descriptive cross-sectional observational study was conducted from December 2022 to October 2023 in the primary care services of the Denia Health Department, Alicante, Spain. A non-probability purposive-consecutive sampling method was used. Participants were adult patients attending chronic care nursing consultations with one or more of the following diagnoses: hypertension, type 2 diabetes mellitus, chronic obstructive pulmonary disease, dyslipidemia, or obesity. Sociodemographic and clinical variables were assessed, and participants completed an ad hoc questionnaire on mobile phone use, health app usage, and online health information-seeking behaviors. Statistical analysis was performed using RStudio for macOS®. Descriptive statistics, chi-square tests, and t-tests were applied.ResultsA total of 523 participants were included (mean age: 71.65 years; SD = 11.91; range: 21–99 years; 50.9% male). Mobile phone and health app usage were significantly higher among men (P = 0.0017) and younger patients, who also demonstrated greater digital proficiency and experience (P < 0.001). Patients with diabetes were the most frequent users of these tools. Those willing to use mHealth for monitoring were also younger and more digitally skilled (P < 0.001). Most participants searched for health information online using search engines (81.8%), and among those who consulted official sources, 69.2% had secondary or higher education.ConclusionsThe use of mHealth technologies in primary care is more common among younger patients, those with higher education levels, and individuals with greater digital skills, suggesting a digital divide. Patients with diabetes were the most frequent users. These findings highlight the importance of promoting digital literacy and designing accessible, user-friendly tools tailored to patients’ individual needs. It is also crucial to consider the preference for face-to-face care, particularly among older adults. Effective implementation of digital health solutions requires inclusive strategies that account for technological, socioeconomic, and contextual differences. creator: Daniel Monasor Ortola creator: José Joaquín Mira creator: Antonio Esteve Ríos creator: Virginia García Ferrer uri: https://doi.org/10.7717/peerj.20130 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Monasor Ortola et al. title: Unlocking the potential of endothelial progenitor cells: a comprehensive review of definitions, applications, and future directions link: https://peerj.com/articles/20128 last-modified: 2025-10-02 description: Endothelial progenitor cells (EPCs) are undifferentiated cells with the capacity to mature into endothelial cells (ECs). EPCs have garnered considerable attention in the fields of regenerative medicine and cardiovascular therapy, owing to their pivotal role in neovascularization and vascular repair. Nonetheless, numerous challenges and questions persist regarding the translational research and practical application of EPCs. This review aims to examine the varying definitions of EPCs, their classification, extraction methods, and sources. It will also address the optimization of cultivation techniques for EPCs and the reprogramming of EPCs into induced pluripotent stem cells (iPSCs). Furthermore, the review will delve into the role of EPCs in cardiovascular diseases (CVD), septic shock, and rheumatic immune conditions, as well as their implications in connective tissue diseases (CTDs) and skin soft tissue regeneration. Finally, the article will discuss future research prospects for EPCs, aiming to engage and inspire readers. creator: Gongjie Ye creator: Yongfei Song creator: Yiru Weng creator: Jiangfang Lian creator: Jianqing Zhou creator: Zhouzhou Dong uri: https://doi.org/10.7717/peerj.20128 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ye et al. title: Development and application of a CRISPR/Cas12a-based reverse transcription–recombinase polymerase amplification assay with lateral flow dipstick and fluorescence detection for Getah virus link: https://peerj.com/articles/20119 last-modified: 2025-10-02 description: Getah virus (GETV), a mosquito-borne alphavirus classified as a zoonotic disease, primarily infects livestock, particularly pigs and horses. In recent years, it has re-emerged in multiple Asian countries, posing a potential threat to animal husbandry and public health. In this study, we developed a rapid and sensitive GETV detection method based on reverse transcription-recombinase polymerase amplification (RT-RPA) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system combined with a lateral flow dipstick (LFD) for visual readout. By leveraging sequence conservation in the GETV E2 envelope protein-coding regions, we engineered matched crRNA guides and amplification primers to develop a rapid CRISPR-Cas12a diagnostic workflow. The optimized platform combines RT-RPA (42 °C/20 min) with Cas12a’s trans-nuclease activity, permitting multiplex detection via real-time fluorescence quantification or immunochromatographic strip visualization. Analytical evaluation demonstrated a detection capability of 10 copies/µL and exclusive specificity against four pathogen controls, including Japanese encephalitis virus and pseudorabies virus. Validation performed using simulated clinical samples revealed 100% concordance between the results of RT–RPA–CRISPR/Cas12a–LFD and quantitative polymerase chain reaction (PCR), while reducing the total detection time to 50 minutes. This approach eliminated the need for advanced instrumentation owing to its simplified operational design, enabling field-deployable rapid detection capabilities that establish essential technical infrastructure for initiating timely GETV containment measures. This approach has broad application potential in the fields of food safety, clinical diagnostics, and environmental science. creator: Boyang Xia creator: Ziyan Wang creator: Tiantian Fei creator: Yueyu Ma creator: Yaxi Guo creator: Dongliang Fei creator: Xiuwei Shu creator: Gang Zhao creator: Mingxiao Ma creator: Hongxia Yuan uri: https://doi.org/10.7717/peerj.20119 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xia et al. title: Mauritian snail shells show evidence of extinct predators link: https://peerj.com/articles/20112 last-modified: 2025-10-02 description: Shells of several species of Tropidophora land snails of the volcanic island of Mauritius (Mascarenes, SW Indian Ocean), all dated between ~1426BCE and ~1090 CE predating the earliest confirmed human discovery (1519) and settlement (1638) of the island, have been found with characteristic predatory holes. These are either large, irregular holes on the underside of T. carinata, or circular holes 0–9–3.3 mm in diameter, in almost the exact same place in T. ligata, T. icterica and T. michaudi. The former have been suggested to be evidence of predation by the extinct red rail Aphanapteryx bonasia, which we consider to be probable. The circular holes have not been reported previously. Examination of these shows them to be very regular in shape and size, to be in the centre of a shallow depression marked by two sets of fine grooves at right angles to one another. These holes were compared to damage caused by predators reported to have ‘bored’ into shells: Drillus elaterid beetles, Poiretia spiraxid snails and rathouisiid slugs. The damage is most similar to that caused by rathouisiids and we postulate that the holes were caused by a now extinct predator of that family. The only extant members of the family in the Mascarene islands are too small to be the predators. There is no evidence of such predation in recent shells; this is an extinct interaction between an extirpated predator and its prey. creator: Justin Gerlach creator: F. B. Vincent Florens creator: Owen L. Griffiths uri: https://doi.org/10.7717/peerj.20112 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gerlach et al. title: Predictive performance of clinical scores and survival outcomes in critically ill patients with sepsis: a prospective longitudinal study at a tertiary medical centre in Ethiopia link: https://peerj.com/articles/20109 last-modified: 2025-10-02 description: BackgroundClinical scores such as quick sequential organ failure assessment (qSOFA), early warning score (EWS), and universal vital assessment (UVA) are commonly used as screening and prognostic tools in sepsis. However, consistent findings across different regions and hospital settings remain limited. This study aims to evaluate the performance of these clinical scores and identify predictors of survival in septic adults admitted to the ICU.MethodsA prospective longitudinal study was conducted from October 10, 2023, to October 9, 2024, involving adults admitted to the intensive care unit (ICU). Clinical scores were calculated on the first, third, and fifth days of admission. Their performance in detecting sepsis, identifying culture-positive cases, and predicting mortality was assessed using receiver operating characteristic (ROC) curves. Kaplan–Meier survival analysis was used to estimate survival probabilities, and a Cox proportional hazards model was applied to identify predictors of survival in sepsis patients.ResultsOf the ICU-admitted patients, 148 (51.9%) were septic, and 54 (36.5%) of them died in the ICU. The modified early warning score (MEWS) showed good performance in identifying sepsis (area under the curve (AUC) = 0.67; 95% confidence interval (CI) [0.61–0.73]) and culture-positive cases (AUC = 0.65; 95% CI [0.50–0.80]) on the day of admission. MEWS also performed better in predicting mortality on day five (AUC = 0.75; 95% CI [0.57–0.93]). Patients with sepsis had significantly lower survival probabilities than those without sepsis (log-rank test, p < 0.001). Each additional point in the Glasgow Coma Scale (GCS) score reduced the hazard of death by 10% (HR = 0.90; 95% CI [0.84–0.97]; p = 0.005).ConclusionThe MEWS score outperformed other clinical scores in identifying sepsis, detecting culture-positive cases, and predicting mortality. Sepsis was associated with higher mortality, which decreased with increasing GCS scores. MEWS may support early identification of sepsis and mortality risk, and its use could help improve ICU survival through timely intervention. creator: Girum Tesfaye Kiya creator: Zeleke Mekonnen creator: Elsah Tegene Asefa creator: Edosa Kejela creator: Edosa Tadasa creator: Esayas Kebede Gudina creator: Tilahun Yemane creator: Gemeda Abebe uri: https://doi.org/10.7717/peerj.20109 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kiya et al. title: Barriers to cervical cancer prevention and triage strategies: a study of knowledge, attitudes, and p16/Ki-67 dual-staining utility among high-risk women in Tuoli and Fuyun counties, Xinjiang link: https://peerj.com/articles/20100 last-modified: 2025-10-02 description: ObjectiveTo investigate cervical cancer screening knowledge, attitudes, and practices among high-risk women in remote western China, and to identify socioeconomic and systemic barriers influencing screening participation. Additionally, to evaluate the comparative effectiveness of p16 staining versus p16/Ki-67 dual-staining immunocytochemistry in triaging women with cytological abnormalities or HPV-positive results, aiming to reduce unnecessary colposcopy referrals in resource-limited settings.MethodsThis cross-sectional study enrolled 260 women (aged 20–65 years) with cytological abnormalities or HPV-positive results from two remote counties in Xinjiang Province (January–December 2023). Participants completed structured questionnaires assessing cervical cancer knowledge, screening attitudes, and healthcare access. Cervical specimens collected via liquid-based cytology underwent parallel testing: conventional cytology, p16 staining, and p16/Ki-67 dual-staining, with all analyses performed by blinded pathologists.ResultsAmong 260 high-risk women in Xinjiang, cervical cancer awareness (67.31%, 95% CI [61.50–72.90]) and screening rates (56.15%, 95% CI [50.23–62.17]) remained suboptimal. Multivariable analyses revealed significant disparities: college-educated women had 7.58-fold higher odds of awareness (95% CI [2.32–24.75]) compared to those with primary education, while public servants showed the strongest employment-based association (aOR = 11.23, 95% CI [2.64–47.83]). Mediation analysis demonstrated that health awareness fully mediated the effect of education (128.8% mediation) and nearly fully mediated the effect of employment (93.8%). Notably, 93.98% (95% CI [90.85–96.27]) expressed willingness to rescreen, and 82.95% (95% CI [78.33–86.84]) supported HPV vaccination. Biomarker analysis showed that p16/Ki-67 dual-staining positivity increased progressively with lesion severity (P < 0.001).ConclusionThis study reveals suboptimal cervical cancer knowledge and screening rates among women in Xinjiang, with socioeconomic disparities—particularly in education and employment—primarily mediated through health awareness. The findings support integrated interventions, including physician-led education, digital health communication for media-dependent populations, simplified visual materials for less-educated women, and active linkage to national screening programs for unemployed populations. High rescreening willingness and parental acceptance of HPV vaccination indicate strong potential for intervention. p16 staining and p16/Ki-67 dual-staining show promise for triage in resource-limited settings. These findings highlight the need for tailored strategies to enhance cervical cancer prevention in western China, with further research needed to address current limitations. creator: Hayuehashi Tali creator: Kunayimu Yeerjiang creator: Bei bei Zeng creator: Tang Rui creator: Buajier Musha creator: Yan Wang uri: https://doi.org/10.7717/peerj.20100 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tali et al. title: Two new free-living marine species of Desmodorella (Nematoda: Desmodoridae) from the continental shelf of northeastern Brazil, with an emended generic diagnosis and a dichotomous key to the species link: https://peerj.com/articles/20094 last-modified: 2025-10-02 description: Two new species of Desmodorella are described from sediment samples collected on the continental shelf of northeastern Brazil. Although the occurrence of the genus has been previously reported in this region, the present study provides the first formal descriptions of Desmodorella species based on material collected from the Brazilian coast. Desmodorella cornuta sp. nov. is characterized by a protuberant horn-shaped cuticular projection positioned dorsally in the pharyngeal region, a unique characteristic among species of the genus. Desmodorella parabalteata sp. nov. is distinguished from other species by the presence of a cephalic capsule and cuticle ornamented with vacuoles, multispiral amphidial fovea, longitudinal rows of ridges that are often indistinct under light microscopy, two pairs of lateral rows of spines that are more prominent than the remaining rows, and thin, nearly straight spicules with a slightly swollen proximal end and lacking a capitulum. An emended diagnosis of the genus and a dichotomous key to species are provided. creator: Alex Manoel creator: Patricia F. Neres creator: André M. Esteves uri: https://doi.org/10.7717/peerj.20094 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Manoel et al. title: Novel monoclonal antibodies for immunodetection of AmpC β-lactamases link: https://peerj.com/articles/20036 last-modified: 2025-10-02 description: BackgroundAccurate and easy-to-perform assays for the detection of antibiotic-resistant bacterial isolates producing AmpC β-lactamases are epidemiologically relevant, leading to more effective use of antibiotics and a comprehensive understanding of β-lactamase prevalence. We describe novel monoclonal antibodies (MAbs) against CMY β-lactamases and their application in immunoassays for the detection of CMY-producing bacterial isolates.MethodsRecombinant CMY-34 was expressed in Escherichia coli and used as an immunogen for MAb generation by hybridoma technology. Selected CMY-34-specific MAbs were comprehensively characterized by various immunoassays, computational analysis, and sequencing of their variable domains. To prove MAb reactivity with CMY β-lactamases, the antibodies were tested with CMY-producing bacterial isolates. For this purpose, the MAbs were applied in sandwich-type assays, such as sandwich enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), and two-photon excitation (TPX) assay for immunodetection of CMY enzymes.ResultsTwo high-affinity MAbs raised against recombinant CMY-34 were characterized in detail. Both MAbs recognized CMY-34 β-lactamase in the Citrobacter portucalensis isolate. The analysis of MAb epitopes revealed their sequence homology among the members of the CMY family, suggesting their potential broad reactivity. Comprehensively characterized MAbs were successfully applied in sandwich ELISA and two rapid immunoassay formats that were tested with CMY-positive bacterial isolates. MAb-based immunoassays detected all analyzed CMY-positive isolates producing CMY-2, CMY-4, CMY-6, CMY-16, and CMY-34 β-lactamases.ConclusionNovel MAbs raised against CMY-34 recognize common epitopes of CMY β-lactamases and can be applied for immunodetection of CMY β-lactamases in bacterial isolates. creator: Karolina Bielskė creator: Martynas Simanavičius creator: Julie Nuttens creator: Julija Armalytė creator: Justas Dapkūnas creator: Lukas Valančauskas creator: Aurelija Žvirblienė uri: https://doi.org/10.7717/peerj.20036 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bielskė et al. title: Aquatic sloths (Thalassocnus) from the Miocene of Chile and the evolution of marine mammal herbivory in the Pacific Ocean link: https://peerj.com/articles/19897 last-modified: 2025-10-02 description: The evolution of marine mammals in South America includes unique and extinct lineages found nowhere else in the world, such as the walrus-convergent whale Odobenocetops and multiple aquatic sloth species belonging to the genus Thalassocnus. Aquatic sloths have been collected from Mio-Pliocene marine deposits in Peru and Chile, and terrestrial deposits in Argentina. In Chile, these occurrences range over 800 km across several basins from the Bahía Inglesa, Coquimbo, and Horcón formations. Here we report aquatic sloth material belonging to the species Thalassocnus natans from a new locality, Norte Bahía Caldera from the Bahía Inglesa Formation in the Atacama Region. We find multiple lines of evidence to support a late Miocene age for this material, which consists of a nearly complete skeleton, including cranial and postcranial remains and associated mandible and postcranial elements that represent the most complete Thalassocnus specimens reported yet from Chile. Based on this finding, we review the stratigraphic origin and geologic age of Thalassocnus species from the western coast of South America and determine that remains from the Upper Pliocene of central Chile represent the youngest known record of this genus to date. Our review also suggests that overlapping stratigraphic ranges for type material of T. antiquus with both T. natans and T. littoralis weakens the proposed argument for Thalassocnus evolution through anagenesis succession. Finally, in the context of Thalassocnus material from Chile and Peru, including other marine mammal herbivores (e.g., sirenians), we demonstrate that one of the most unusual features of this guild is that South American marine mammal herbivores did not reach the body sizes of their analogous counterparts (i.e., desmostylians and sirenians) in the North Pacific. This observation builds on other paleontological evidence about the unusual features of the Peruvian biotic province during the Neogene. creator: Ana M. Valenzuela-Toro creator: Nicholas D. Pyenson creator: Jorge Velez-Juarbe creator: Mario E. Suárez uri: https://doi.org/10.7717/peerj.19897 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Valenzuela-Toro et al. title: Effects of shading stress on endogenous hormone levels in Eleutherococcus giraldii: hormonal dynamics and growth strategy analysis link: https://peerj.com/articles/20135 last-modified: 2025-10-01 description: BackgroundEleutherococcus giraldii (E. giraldii) is a quintessential traditional Chinese medicinal plant with significant developmental potential. Its growth and development are highly responsive to environmental factors, particularly light conditions. However, the endogenous hormonal changes in E. giraldii under shading stress remain unclear, and its adaptive growth strategies require further investigation.MethodsExperimental groups with varying light transmittance (29.12%, 39.68%, and 100%) were established using shade nets, comprising moderate shading, light shading, and control groups. The endogenous hormone contents in apical and lateral leaves of E. giraldii were quantified using the enzyme-linked immunosorbent assay (ELISA). Statistical analysis and graphical presentations were performed using IBM SPSS Statistics 27 and Origin 2022 software.ResultsShading treatment consistently promoted the accumulation of isopentenyl adenine nucleoside (iPA), zeatin riboside (ZR), gibberellic acid 3 (GA3), and abscisic acid (ABA) in both apical and lateral leaves of E. giraldii, while exhibiting differential effects on indoleacetic acid (IAA)-enhancing its content in lateral leaves but reducing it in apical leaves. Quantitative analysis revealed that moderate shading induced: (1) maximal increases in iPA, ZR, and GA3 levels in apical leaves (P < 0.05); (2) maximal increases in ABA, iPA, ZR, and GA3 concentrations as well as the ABA/ZR ratio in lateral leaves; (3) maximal reductions in the ABA/iPA and ABA/GA3 ratios in apical leaves along with the ABA/GA3 ratio in lateral leaves; (4) decreased ABA/IAA and ABA/ZR in apical leaves coupled with increased ABA/iPA in lateral leaves. Under light shading conditions, the most substantial changes included: (1) greatest ABA enhancement in apical leaves and IAA accumulation in lateral leaves; (2) most pronounced declines in IAA content (apical leaves) and ABA/IAA ratio (lateral leaves); (3) elevated ABA/IAA and ABA/ZR ratios in apical leaves with concurrent reduction of ABA/iPA in lateral leaves. Importantly, comprehensive correlation analysis demonstrated positive correlations among all examined hormones (ABA, IAA, iPA, ZR, and GA3) in both leaf types, indicating systemic hormonal coordination during shade adaptation.ConclusionShading stress significantly restructured endogenous hormone profiles and their homeostasis in E. giraldii. Under moderate shading conditions, E. giraldii likely adopted a conservative strategy characterized by “apical leaf growth promotion coupled with lateral leaf growth restriction”, whereas mild shading induced an expansive strategy featuring “apical leaf growth inhibition coordinated with moderate lateral leaf expansion”. These findings provide a theoretical foundation for optimizing cultivation protocols and offer new insights into phytohormonal dynamics in shrubs under light limitation. creator: Xu Feng Huang creator: Rui Gu creator: Guo Peng Chen creator: Rong Ding uri: https://doi.org/10.7717/peerj.20135 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Huang et al. title: Electroantennogram and Olfactory behavioral responses of Trabala vishnou gigantina (Lepidoptera: Lasiocampidae) to herbivore induced Hippophae rhamnoides leaf volatiles link: https://peerj.com/articles/20124 last-modified: 2025-10-01 description: The moth Trabala vishnou gigantina Yang, 1978 (Lepidoptera: Lasiocampidae), a leaf-eating pest, had a severe outbreak in the sea buckthorn, Hippophae rhamnoides L. (Elaeagnaceae) plantation in North China. This study aims to investigate the influence of volatiles emitted by T. vishnou gigantina-infested H. rhamnoides on the behavioral responses of T. vishnou gigantina, laying a basis for the development of plant-based elicitors. The chemical basis of herbivore insect host dynamics between these species were investigated, providing information for herbivore insect control methods. After identifying the compounds produced by the differences between healthy and infested plants, six critical volatile compounds were identified to explore their attractions to T. vishnou gigantina imagoes by using electroantennogram (EAG) and olfactory behavioral response experiments. The results showed that the EAG responses of T. vishnou gigantina imagoes did not only vary in these six different herbivore-infested volatiles, but also between different concentrations of the same volatile. The EAG responses to the herbivore-infested volatiles peaked at a stimulus concentration of 100 µg/µL, with Hexyl 2-methyl butyrate having the highest EAG response. The test results of olfactory behavioral responses had significant differences in the olfactory behavioral responses of female and male imagoes to the six herbivore-infested volatiles. Hexyl 2-methyl butyrate had the strongest attraction to female and male imagoes, followed by 2-ethylhexanol and longifolene. 2-ethylhexanol had a significant attraction to female imagoes, while there was no significant attraction to males. creator: Yonghua Liu creator: Kexu An creator: Shuo Tang creator: Jiangshuai Feng creator: Xiongfei Yan uri: https://doi.org/10.7717/peerj.20124 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Establishment and evaluation of a circAdpgk-0001 knockdown method using CRISPR–Cas13d RNA-targeting technology link: https://peerj.com/articles/20123 last-modified: 2025-10-01 description: BackgroundThe small interfering RNA (siRNA) method has been used to knock down circular RNAs (circRNAs). However, issues such as low efficiency and off-target effects have become increasingly recognized. Recent studies have demonstrated that CRISPR-Cas13 can specifically target and cleave RNA. In this study, we established a CRISPR-Cas13d-based RNA-targeting method to specifically knock down circRNAs, such as circAdpgk-0001, and compared its performance with the siRNA method.MethodsFour clustered regularly interspaced short palindromic repeats (CRISPR) RNAs (crRNAs) of different nucleotide lengths spanning the back-splicing junction (BSJ) of circAdpgk-0001 were designed. A CRISPR-RfxCas13d plasmid capable of specifically cleaving circAdpgk-0001 was constructed and transfected into the JS-1 cell line. Knockdown efficiency was assessed using quantitative real-time PCR (qRT-PCR) and compared with that of the siRNA method. The expression of activation-related factors alpha-smooth muscle actin (α-SMA) and collagen I in JS-1 cells was further evaluated using qRT-PCR and Western blot.ResultsCRISPR-Cas13d with a 24-nucleotide crRNA showed the highest knockdown efficiency (∼50%). After further optimization, the knockdown efficiency of CRISPR-Cas13d reached 70%, significantly higher than that of the siRNA method (40%). Knockdown of circAdpgk-0001 using Cas13d reduced the expression of collagen I and α-SMA by approximately 40%, which was greater than the reduction achieved by siRNA-mediated knockdown.ConclusionCRISPR-Cas13d demonstrated higher efficiency than the siRNA method in knocking down circRNAs, providing a promising tool for investigating circRNA functions. creator: Sijia Huang creator: Hailan Qin creator: Bingxin Dai creator: Miao Liu creator: Jijia Shen uri: https://doi.org/10.7717/peerj.20123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Licinophilus depressus n. gen., sp. n. (Eugregarinida: Stenophoridae) from Licinus depressus (Coleoptera: Carabidae) link: https://peerj.com/articles/20099 last-modified: 2025-10-01 description: The paper focuses on a new species of gregarines—Licinophilus depressus n. gen. sp. n., which was found in Licinus depressus (Paykull, 1790) (Coleoptera, Carabidae). The individuals of L. depressus ground beetle were collected on the bank of the Dnipro River, Ukraine and examined for the presence of gregarines in the guts. In the parasites discovered in the midguts, we measured the morphological parameters and their ratios, analyzing how they change in relation to the age of the specimens. According to our measurements, the species turned out to be incomparable to any of the ones described in the scientific literature. Because the gregarine specimens formed syzygies at late stages, were observed to have monogenous life cycle and a septum between the protomerite and deutomerite at all stages of development, and also rudimentary epimerite, they were classified to the Septatorina suborder, Stenophoricae superfamily, Stenophoridae family, and distinguished into a new genus due to the fluctuating septum between the protomerite and deutomerite.With age, the width of the segments does not change, while the gregarine increases in size due to significant elongation of the deutomerite. The most varying parameters of this species of gregarines were the deutomerite length (DL), the deutomerite length axis (DLA), and the total length of gregarine (TL) for which the coefficient of variation exceeded 30%. All the studied morphometric indices, except for the ratio of the deutomerite length to the deutomerite width (DL/DW), exhibited weak association with the age and sizes of gregarines. The indices such as the ratios of the epimerite length to the length of the protomerite-epimerite complex (EL/PECL), the protomerite length to the protomerite-epimerite complex (PL/PECL), the epimerite length to the epimerite width (EL/EW), the protomerite length to the protomerite width (PL/PW), the protomerite width to the septum width (PW/SW), the deutomerite width to the protomerite width (DW/PW), the nucleus length to nucleus width (NL/NW), and also DLA remained constant in this gregarine during growth, and therefore they can be used as constant diagnostic features. creator: Viktoriia Lazurska creator: Viktor V. Brygadyrenko uri: https://doi.org/10.7717/peerj.20099 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lazurska and Brygadyrenko title: Response of soil nematode community structure, diversity, and ecological network to elevation gradients in wild fruit forest of Tianshan Mountain, China link: https://peerj.com/articles/20090 last-modified: 2025-10-01 description: BackgroundThe Tianshan wild fruit forest is a special deciduous broad-leaved forest located in the mountains of central Asia.MethodsTo reveal how the Tianshan wild fruit forest ecosystem responds to environmental changes along an elevation gradient, we used the soil nematode index, which is widely recognized as a key indicator of soil health. This study focused on the nematode communities beneath Juglans cathayensis and Malus sieversii, two typical constructive species in the Tianshan wild fruit forest. Six elevation levels (1,480, 1,401, 1,351, 1,305, 1,252, and 1,207 m) were selected, and a nematode co-occurrence network was constructed for each elevation. We analyzed the abundance, diversity, ecological indices, and network complexity of soil nematode communities across different elevation gradients. In addition, we explored the relationships among environmental factors, soil multifunctionality, and nematode community characteristics.ResultsOur results showed that: (1) a total of 60,795 nematodes, representing 80 genera were collected. Total abundance, trophic group abundance, and diversity of nematodes peaked at middle elevations. However, in M. sieversii, nematode diversity increased with elevation. (2) The soil food web in the wild fruit forest exhibited a relatively high metabolic rate (nematode channel ratio > 0.5). (3) In J. cathayensis, the nematode ecological network was more complex and tightly interconnected at low elevations. whereas in M. sieversii, greater network complexity was observed at high elevations. (4) Environmental factors (organic matter, pH, total phosphorus, available potassium, total potassium) significantly affected the composition of nematode trophic groups (p < 0.05). Moreover, network complexity was a key factor influencing soil multifunctionality. This study provides a theoretical foundation for long-term monitoring of soil health in Tianshan wild fruit forest. creator: Yulu Zhang creator: Mengyu Yang creator: Wenxin Liu creator: Zhicheng Jiang creator: Yang Zhao creator: Gaofeng Li creator: Jing Cao creator: Minru Zhang creator: Haijun Yang creator: Dong Cui uri: https://doi.org/10.7717/peerj.20090 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Rhodelphis edaphicus sp. nov.—a new lineage of predatory archaeplastids from agricultural soil link: https://peerj.com/articles/20071 last-modified: 2025-10-01 description: Predatory flagellated protists remain extremely poorly studied but often represent the most important deep-branching lineages of eukaryotic evolution. One of the most enigmatic and poorly studied predatory protist groups is Rhodelphidia. These are heterotrophic flagellates, yet belong to the primarily photosynthetic supergroup Archaeplastida and are related to red algae in particular. Here, we describe a new rhodelphid species and the first known soil representative of this group, Rhodelphis edaphicus sp. nov., which was isolated into a clonal culture from agricultural soil. The novel species actively phagocytoses the cells of other protists and bacteria. Using light and electron microscopy, we examined its morphology and identified several novel features, including complex tripartite mastigonemes—not previously reported for this taxon—which link rhodelphids with Cryptista. We expanded a previous 18S rRNA dataset for rhodelphids with environmental sequences and revealed the presence of a soil clade to which the new species belongs. A search of soil metabarcoding data yielded several unknown rhodelphid lineages. Analysis of the distribution of known species and environmental DNA data revealed that rhodelphids inhabit diverse geographic locations worldwide and are found in a variety of habitats, including marine and fresh waters, soils, and, most likely, anaerobic bottom sediments near fumaroles. The diversity of modern rhodelphid habitats, including soil ecosystems, highlights the different environments in which early stages of Archaeplastida evolution may have occurred. The identification and comprehensive study of new lineages of basal archaeplastids provides new insights into the complex evolutionary processes associated with early eukaryotic radiation, the emergence of photosynthesis and plastid evolution that gave rise to the diversification of numerous forms of algae and land plants. creator: Artem O. Belyaev creator: Dmitry G. Zagumyonnyi creator: Elena A. Gerasimova creator: German A. Sozonov creator: Denis V. Tikhonenkov uri: https://doi.org/10.7717/peerj.20071 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Belyaev et al. title: The first leech body fossil predates estimated hirudinidan origins by 200 million years link: https://peerj.com/articles/19962 last-modified: 2025-10-01 description: Clitellata is a major annelid clade comprising oligochaetes (e.g., earthworms) and hirudineans (e.g., leeches). Due to their scant fossil record, the origins of clitellates, particularly Hirudinea, are poorly known. Here, we describe the first leech body fossil, Macromyzon siluricus, gen. et sp. nov., from the Brandon Bridge Formation (Waukesha Lagerstätte). This fossil, which is preserved in exceptional detail, possesses several hirudinean soft-tissue synapomorphies–including a large sucker at the posterior end and sub-divided segments–and phylogenetic analyses resolve Macromyzon siluricus as a stem leech. Its age, 437.5–436.5 Ma, is consistent with early age estimates for the origin of clitellates, and predates molecular-clock-based estimates of hirudinidan origins by at least 200 million years. These findings suggest that the earliest true leeches were marine and that, contrary to prevailing hypotheses, were unlikely to have fed on vertebrate blood. creator: Danielle de Carle creator: Rafael Eiji Iwama creator: Andrew J. Wendruff creator: Loren E. Babcock creator: Karma Nanglu uri: https://doi.org/10.7717/peerj.19962 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 de Carle et al.