title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-05 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: PLA2G16 expression predicts prognosis and gemcitabine sensitivity in patients with pancreatic cancer link: https://peerj.com/articles/19517 last-modified: 2025-05-30 description: BackgroundPancreatic cancer is highly aggressive with limited treatment options. PLA2G16 has been implicated in cancer progression, but its role in prognosis and gemcitabine sensitivity in pancreatic cancer remains poorly understood.MethodsUsing TCGA data, the study assessed the correlation between PLA2G16 expression and patient survival. The expression of PLA2G16 in gemcitabine-resistant versus sensitive pancreatic cancer cells was also compared. siRNA-mediated knockdown of PLA2G16 was performed in drug-resistant PANC-1 cells to evaluate its impact on gemcitabine sensitivity. The relationship between PLA2G16 expression, immune infiltration, and molecular pathways in pancreatic cancer was explored using CIBERSORT and DAVID tools.ResultsPLA2G16 was significantly overexpressed in pancreatic cancer tissues and associated with poorer patient survival. In PANC-1 cells, increased PLA2G16 expression correlated with gemcitabine resistance, and its knockdown improved drug sensitivity. PLA2G16 expression was linked to specific immune infiltration patterns and cancer-related molecular pathways.ConclusionsElevated PLA2G16 expression is associated with poor survival and gemcitabine resistance in pancreatic cancer, making it a potential prognostic marker and therapeutic target. creator: Xiaoyu Sun creator: Haiyang Jiang creator: Yufei Huang creator: Jing Xia creator: Jie Gu creator: Xinbing Sui creator: Xueni Sun creator: Yucheng Zhou uri: https://doi.org/10.7717/peerj.19517 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sun et al. title: Revision and validation of the Chinese version of the interpersonal reactivity index for couples for expectant couples link: https://peerj.com/articles/19505 last-modified: 2025-05-30 description: ObjectiveThis research seeks to evaluate the validity and reliability of the Interpersonal Reactivity Index for Couples (IRIC) to ensure it is culturally relevant to China, while also assessing its reliability and validity among a sample of pregnant women and their spouses.MethodsA total of 402 couples were recruited from two hospitals in Anhui Province. The English version of the IRIC was translated into Chinese in accordance with Brislin’s principles of cross-cultural translation. The reliability of the translated scale was assessed using Cronbach’s α coefficient, split-half reliability, and test-retest reliability. The structural validity of the scale was examined through exploratory factor analysis (EFA) and confirmatory factor analysis (CFA). The Perceived Partner Responsiveness Scale served as a criterion measure to evaluate its correlation with the IRIC. All data analyses were performed using SPSS 26.0 and Mplus 8.3.ResultsThe Chinese version of the IRIC comprises two dimensions and thirteen items (seven items pertaining to empathic concern and six items related to Perspective Taking). In the sample of pregnant women, the Cronbach’s α coefficient for the Chinese version of the IRIC was 0.922, with coefficients of 0.871 for Empathic Concern and 0.909 for the Perspective Taking. The split-half reliability was 0.902 and the overall test-retest reliability of the scale was 0.996. In the sample of partners of pregnant women, the Cronbach’s α coefficient was 0.938, with coefficients of 0.895 for empathic concern and 0.925 for Perspective Taking, and a split-half reliability of 0.898, while the overall test-retest reliability of the scale was 0.997. The content validity index at the scale level was 0.967, and at the item level, it ranged from 0.857 to 1.000. In the sample of pregnant women, the confirmatory factor analysis results indicated that the fit indices for the bi-factor model were satisfactory (Chi-square/degrees of freedom ($\chi^2$χ2/df) = 1.331, comparative fit index (CFI) = 0.993, Tucker-Lewis index (TLI) = 0.987, normal fit index (NFI) = 0.972, goodness of fit index (GFI) = 0.958, root mean square error of approximation (RMSEA) = 0.041, standardized root mean square residual (SRMR) = 0.038). In the sample of partners, the confirmatory factor analysis results also demonstrated satisfactory fit indices for the bi-factor model ($\chi^2$χ2/df = 1.588, CFI = 0.989, TLI = 0.976, NFI = 0.971, GFI = 0.961, RMSEA = 0.054, SRMR = 0.039). The scale successfully passed the equivalence test, with indices fitting well.ConclusionThe findings suggest that the Chinese version of the IRIC exhibits strong reliability and validity, rendering it an effective instrument for evaluating the level of empathy between pregnant women and their partners. The translated scale also facilitates the early detection of couple empathy, providing a scientific foundation for the development of early personalized intervention strategies. Overall, this scale possesses clinical relevance and practical importance in enhancing marital satisfaction. However, future research should encompass a larger and more diverse population. creator: Juju Huang creator: Tengfei Liang creator: Jinzhi Li creator: Qiankun Liu creator: Jiaxue Pang creator: Yang Xu creator: Hui Xie uri: https://doi.org/10.7717/peerj.19505 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Huang et al. title: Regulation of fruit quality formation in strawberry: from omics to biotechnology link: https://peerj.com/articles/19497 last-modified: 2025-05-30 description: Strawberry (Fragaria × ananassa Duch.), a popular fruit, is well known for its bright color, unique flavor, and high nutritional value. The quality of strawberries will greatly affect consumers’ choices, market share, and farmers’ profits. The formation of strawberry quality is a complex biological process involving the interaction of multiple genetic factors and environmental conditions. In recent years, there has been great progress on investigating strawberry quality formation and regulation in the world. In this review, we summarized the factors from internal to external that affect strawberry formation, and focused on the application of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics in the study of strawberry quality, as well as the potential of modern technologies in quality improvement. The viewpoints in this article may provide new ideas for breeders and scientists aimed to regulate and improve strawberry quality in the future. creator: Zhang-Ying Wang creator: An-Qing Shen creator: Yan-Xin Ge creator: Cheng-Ling Zhou creator: Yu-Shan Qiao creator: Ai-Sheng Xiong creator: Guang-Long Wang uri: https://doi.org/10.7717/peerj.19497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Education about pain and experience with cognitive-based interventions do not reduce healthcare professionals’ chronic pain link: https://peerj.com/articles/19448 last-modified: 2025-05-30 description: BackgroundCognitive-based interventions like pain neuroscience education (PNE), cognitive behavioral therapy (CBT), acceptance commitment therapy (ACT), and mindfulness meditation are popular for managing chronic pain. Despite their widespread adoption, evidence for their efficacy remains contradictory. Healthcare professionals (HCPs) represent a unique population to evaluate these approaches, as they possess specialized knowledge about pain mechanisms and often implement these interventions with patients. The logical premise underlying cognitive-based interventions suggests that increased knowledge and cognitive engagement with pain concepts should reduce pain intensity, making educated HCPs with chronic pain an ideal test case for this theoretical framework.PurposeTo investigate whether HCPs with chronic pain who (HCPs+CP) are familiar with these methods experience less pain and improved quality of life compared to less experienced HCPs+CP and healthy HCPs (H-HCPs).MethodsThis cross-sectional study used an anonymous online questionnaire distributed in English through closed professional social media groups internationally. Data were collected from 550 HCPs (319 healthy, 231 with chronic pain) primarily from Israel, Canada, United States, United Kingdom, and Australia. Participants were categorized by their knowledge of pain neuroscience, experience with cognitive-based interventions, and chronic pain type (primary or secondary). Pain intensity was measured using the Numerical Pain Rating Scale, and quality of life was assessed with the World Health Organization tool the WHOQOL-BREF. Statistical analyses included Spearman’s correlation tests and independent samples t-tests.ResultsPain intensity did not significantly differ between primary pain group (4.24 ± 2.21) and secondary pain group (4.37 ± 2.33) (t = −0.267, p = 0.79, Cohen’s d = −0.05). The total WHOQOL score was lower in HCPs+CP (66.81 ± 15.74) compared to healthy HCPs (71.13 ± 14.02) (t = −2.136, p = 0.035), but after removing respondents unfamiliar with interventions, no significant differences remained between groups across all WHOQOL domains (−0.09 < Cohen’s d < 0.14, p > 0.05). Among the 146 H-HCPs who had recovered from chronic pain, only 11% attributed their recovery to cognitive-based interventions, while the majority credited physical therapy (37.7%) and spontaneous recovery (32.9%).ConclusionDespite their specialized knowledge and experience with cognitive-based interventions, HCPs+CP did not report reduced pain intensity, though they maintained quality of life comparable to healthy colleagues. These findings challenge current theoretical models underlying cognitive-based pain management. creator: Asaf Weisman creator: Tomer Yona creator: Youssef Masharawi uri: https://doi.org/10.7717/peerj.19448 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Weisman et al. title: Development of a risk prediction model for postpartum stress urinary incontinence: a multicenter retrospective longitudinal study in Indonesia link: https://peerj.com/articles/19308 last-modified: 2025-05-30 description: BackgroundThe prevalence of urinary incontinence (UI) during pregnancy and the postpartum period can have significant negative impacts, including on the quality of life and economic burden for affected women.ObjectiveThe objective of this study was to develop risk-predictive models for postpartum stress urinary incontinence (SUI) among women in Indonesia.MethodsBetween January 2023 and March 2023, 430 postpartum women, aged 18 years or older, who were admitted to two study hospitals in Indonesia, were enrolled in this study. Telephone follow-up was conducted at six weeks postpartum to assess the presence of SUI. The Least Absolute Shrinkage and Selection Operator (LASSO) method was utilized to identify the relevant variables, and generalized linear models (GLM) were employed to establish predictive models for postpartum SUI. The models were internally validated using a bootstrapping method with 1,000 resamplings to assess discrimination and calibration.ResultsThe analysis included 430 participants, among whom the prevalence of postpartum SUI was found to be 21% (90 out of 430). The predictive model for postpartum SUI included pre-pregnancy body mass index (BMI), Kegel exercises, constipation, fetal weight, SUI during pregnancy, and mode of delivery. The models demonstrated satisfactory calibration, as indicated by the Hosmer-Lemeshow test (p = 0.390). The optimism-corrected C-statistic, determined through bootstrapping stepwise, was 0.763 (95% confidence interval CI [0.693–0.833]) for postpartum women.ConclusionThis study successfully developed predictive models for SUI among postpartum women in Indonesia. The implementation of this model may serve as a valuable tool for identifying high-risk individuals at post-delivery stages, aiding in the prevention and management of postpartum SUI. creator: Esti Andarini creator: Surui Liang creator: Yingying Zhang creator: Yanyan Li creator: Yan Li creator: Wenzhi Cai uri: https://doi.org/10.7717/peerj.19308 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Andarini et al. title: Hawaiian black coral (Antipatharia) complete mitochondrial genomes have limited phylogenetic signal for taxonomic resolution of species link: https://peerj.com/articles/18731 last-modified: 2025-05-30 description: Most inferences about black coral (Antipatharia) phylogenetics have relied on a handful of molecular markers from PCR-Sanger methods but recently complete mitogenomes are shedding additional light on relationships. We present the most complete survey of shallow-water to mesophotic Hawaiian black corals (‘ēkaha kū moana) to date based on complete mitogenome sequences. The phylogenetic relationships inferred from whole-mitochondrial phylogenies recover Myriopathidae as monophyletic with Myriopathes and Tanacetipathes as the outgroups to all other Hawaiian black coral taxa. Combining our data with other published mitochondrial datasets for black corals, we find that morphologically similar Cirrhipathes cf. anguina specimens are divergent and may not be conspecifics. Likewise, the genera Antipathes and Stichopathes (family Antipathidae) include species that are more divergent from one another than they are to other genera in family Aphanipathidae. Overall, data show Myriopathidae is a monophyletic family, but the families Aphanipathidae and Antipathidae are polyphyletic, and the genera Antipathes and Stichopathes live up to their reputation as a “taxonomic dumping ground”. These phylogenetic analyses underscore the need for continued research to understand the evolutionary history and phylogenetic relationships for black corals generally and ‘ēkaha kū moana specifically. creator: Van Wishingrad creator: Leah E. K. Shizuru creator: Kenji Takata creator: Anthony D. Montgomery creator: Daniel Wagner creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.18731 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wishingrad et al. title: Role of hypothalamus function in metabolic diseases and its potential mechanisms link: https://peerj.com/articles/19532 last-modified: 2025-05-29 description: The hypothalamus, a crucial neuroendocrine regulatory center, plays a significant role in the occurrence and development of metabolic diseases. Recent advances in molecular biology and imaging technology have facilitated a better understanding of the central role of the hypothalamus in the dysregulation of regulatory mechanisms. This review examines the involvement of hypothalamic nuclei in metabolic diseases, the direct effects of glucose and fat on the hypothalamus, and the influence of the hypothalamus on metabolic diseases. Furthermore, it investigates the role of the hypothalamus in the emergence and progression of metabolic disorders, including obesity and diabetes. Finally, it outlines the current research progress in treating metabolic diseases through hypothalamus regulation. This study could provide a theoretical basis for understanding the pathophysiological mechanisms of metabolic diseases and development of new treatment strategies. creator: Xinyu Zhang creator: Jie Yang creator: Yilin Li creator: Yulin Li creator: Guoqi Li uri: https://doi.org/10.7717/peerj.19532 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Longitudinal analysis of step counts in Parkinson’s disease patients: insights from a web-based application and generalized additive model link: https://peerj.com/articles/19519 last-modified: 2025-05-29 description: BackgroundParkinson’s disease (PD) is a chronic neurological disorder that affects millions of people worldwide. A common motor symptom associated with PD is gait impairment, leading to reduced step count and mobility.MethodsMonitoring and analyzing step count data can provide valuable insights into the progression of the disease and the effectiveness of various treatments. In our study, the generalized additive model (GAM) was used to identify statistically significant variables for step counts. Additionally, a web application was developed as an interactive visualization tool.ResultsThe GAM model shows that the following variables are statistically significant for daily step counts: sex (p = 0.03), handedness (p = 0.015), PD status of father (p = 0.056), COVID-19 status (Yes vs. No, p = 0.008), cohort (PD vs. Healthy, p < 0.0001), the cubic regression spline with three basis functions of age by cohorts (p < 0.0001), and the random effect of individual age trajectories (p = 0.0001).ConclusionsBased on the PPMI data, we find that sex, handedness, PD status of father, COVID-19 status, cohort, and the smoothing functions of age are all statistically significant for step counts. Additionally, a web application tailored specifically for step count analysis in PD patients was developed. This tool provides a user-friendly interface for patients, caregivers, and healthcare professionals to track and analyze step count data, facilitating personalized treatment plans and enhancing the management of PD. creator: Yuan Gu creator: Yishu Gong uri: https://doi.org/10.7717/peerj.19519 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gu and Gong title: Exploring the outcomes of non-surgical periodontal therapy in modulating periodontal parameters, renal function, and inflammatory biomarkers in chronic kidney disease patients with periodontitis link: https://peerj.com/articles/19492 last-modified: 2025-05-29 description: BackgroundThis comparative prospective cohort study investigated the outcomes of non-surgical periodontal therapy (NSPT) on periodontal parameters, renal function, and serum inflammatory markers in chronic kidney disease (CKD) patients with periodontitis.MethodsParticipants were categorised into three groups: CKD patients with periodontitis (CKD-P, n = 20), patients with periodontitis only (P, n = 20), and healthy participants (HP, n = 20). Periodontal parameters were initially evaluated for all participants. Blood samples were collected to assess renal function, including serum electrolytes, urea, creatinine and estimated glomerular filtration rate (eGFR), as well as inflammatory markers such as interleukin-6 (IL-6) and transforming growth factor-beta 1 (TGF-β1). NSPT was performed on both the CKD-P and P groups. Six weeks following treatment, periodontal parameters, renal function tests and inflammatory markers were re-evaluated to determine any modulation in these outcomes.ResultsThe CKD-P group exhibited the highest concentration of potassium, urea, and creatinine. There were no significant differences in the periodontal pocket depth (PPD) and clinical attachment loss (CAL) means between CKD-P and P groups (P > 0.05). Similarly, there was no significant difference in the gingival bleeding index (GBI) scores between CKD-P, P, and HP groups (P > 0.05). However, the CKD-P group exhibited the highest plaque score (PS) compared to the P and HP groups (P < 0.0001). Post-NSPT, both the CKD-P and P groups showed significant improvement in these periodontal parameters. The median eGFR for the CKD-P group improved significantly (P < 0.0001) after NSPT. In terms of inflammatory markers, the IL-6 levels were significantly higher in the CKD-P group compared to the P and HP groups (P < 0.001). Additionally, there were significant differences in the TGF-β1 levels across all three groups (P < 0.05). Following post-NSPT, both CKD-P (P < 0.001) and P (P < 0.0001) groups demonstrated significant reductions in IL-6. As for the TGF-β1 level, significant reduction post-NSPT was only observed in the CKD-P group (P < 0.001).ConclusionNSPT is effective in enhancing periodontal health, improving renal function, and decreasing systemic inflammation in CKD patients with periodontitis. creator: Harishini Rajaratinam creator: Nurul Aliya Abdul Rahman creator: Muhammad Hafiz Hanafi creator: Siti Lailatul Akmar Zainuddin creator: Hanim Afzan Ibrahim creator: Muhammad Imran Kamarudin creator: Wan Mohd Saifuhisam Wan Zain creator: Sirajudeen Kuttulebbai Nainamohamed Salam creator: Salbiah Isa creator: Nur Karyatee Kassim uri: https://doi.org/10.7717/peerj.19492 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Rajaratinam et al. title: Volatile organic compounds from entomopathogenic and nematophagous fungi repel banana weevil (Cosmopolites sordidus) under banana field conditions link: https://peerj.com/articles/19414 last-modified: 2025-05-29 description: Fungal volatile organic compounds (VOCs) with biological activity produced by entomopathogenic fungi (Beauveria bassiana and Metarhizium robertsii) isolated from banana fields (Canary Islands) and the nematophagous fungus Pochonia chlamydosporia, used in biocontrol of root-knot nematodes, repel the banana weevil (BW), Cosmopolites sordidus (Germar, 1824) under laboratory conditions. BW is the main pest of banana (Musa spp. (Linnaeus, 1753)). Its cryptic behavior makes it difficult to manage. Repellent VOCs alter BW behavior and can thus be used in sustainable pest management strategies. We evaluated fungal VOCs styrene (C1), benzothiazole (C2), 1,3-dimethoxybenzene (C5) and 2-cyclohepten-1-one (C7) in Canary Islands banana fields naturally infested with BW. 1,3-dimethoxybenzene (C5) significantly reduced the attraction of BW adults to sordidin (BW aggregation pheromone) in banana fields. C5 was detected in the field using GC-MS. C1 and C2 had a mild repellent effect influenced by seasonal changes. C7 VOC did not repel BW in the field. Site and season affected VOCs repellence to BW. Climate may influence VOCs evaporation and therefore their repellent efficacy. VOCs modify BW spatial ecology under field conditions. The inverse distance weighted (IDW) interpolation technique showed changes in BW infestation patterns after application of VOCs in the field. In conclusion, VOCs from biocontrol fungi reduced BW attraction to its aggregation pheromone in banana fields. These responses to experimental BW repellents were influenced by weather and BW population size. BW repellents have potential to be used in “push-pull” strategies to manage BW sustainably in banana crops. creator: Ana Lozano-Soria creator: Ana Piedra-Buena Diaz creator: Federico Lopez-Moya creator: Miguel Valverde-Urrea creator: Jose J. Zubcoff creator: Jose Emilio Martinez-Perez creator: Javier Lopez-Cepero creator: Luis V. Lopez-Llorca uri: https://doi.org/10.7717/peerj.19414 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: Effects of cadmium stress on seed germination and physiological-biochemical characteristics in okra: a comparative study of red and green varieties link: https://peerj.com/articles/19498 last-modified: 2025-05-28 description: Previous study has demonstrated that okra (Abelmoschus esculentus (L.) Moench) is capable of accumulating cadmium (Cd) in both plants and fruits. However, there is still little known about the physiological responses of different okra cultivars to Cd accumulation. This study investigated the effects of exogenous Cd application on various growth parameters and physiological aspects in two okra varieties (red and green okra). The results indicated that Cd exposure had a dose-dependent inhibitory effect on seed germination rate and potential. Addition of 50 µM Cd to the hydroponic solution led to a significant reduction in plant biomass. In the red okra variety, Cd accumulation peaked at 287.8 mg kg−1 DW in shoots and 790.3 mg kg−1 DW in roots, while in green okra, these values reached 280.8 mg kg−1 DW in shoots and 903.7 mg kg−1 DW in roots. Furthermore, the Cd treatment resulted in an increase in chloroplastic pigment content of both okra varieties. Production of superoxide anion (O2•−) and hydrogen peroxide (H2O2) significantly rose in the roots of both varieties, with O2•− levels increasing by 298.8% in red okra and 505.8% in green okra roots, and H2O2 levels increasing by 2.23-fold in red okra and 1.4-fold in green okra roots. This rise in reactive oxygen species led to elevated proline content (3.09-fold in red okra roots and 8.45-fold in green okra roots) and non-protein sulfhydryl (NPSH) levels (13.52-fold in red okra roots and 10.21-fold in green okra roots), as well as increased activities of peroxidase (POD) and superoxide dismutase (SOD). Notably, green okra exhibited a more efficient antioxidant defense system and greater tolerance to Cd-induced oxidative stress compared to red okra. This study provides a foundation for developing Cd-tolerant crop varieties and improving phytoremediation strategies. creator: Wanwan Wang creator: Lei Yu creator: Xuexia Zhang creator: Jingbo Yu creator: Zhou Jiang creator: Long Xu creator: Haiyun Rui uri: https://doi.org/10.7717/peerj.19498 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Gene expression profiling of extraocular muscles in primary inferior oblique overaction link: https://peerj.com/articles/19474 last-modified: 2025-05-28 description: BackgroundThis study investigates gene expression differences in primary inferior oblique overaction (IOOA) by performing transcriptome sequencing on extraocular muscles (EOMs) from patients with primary and secondary IOOA. Strabismus, particularly IOOA, is often associated with abnormal eye movement due to imbalanced muscle function. By using bioinformatic analyses to identify differentially expressed genes (DEGs) and enriched pathways, we aim to uncover the molecular distinctions that may underlie the unique neuromuscular characteristics of primary IOOA.MethodsTranscriptome sequencing was conducted on EOMs from ten patients with primary IOOA and ten patients with secondary IOOA. DEGs were identified using DESeq2. Gene Ontology (GO) annotations were enriched using ClusterProfiler and GlueGo, and the overall gene expression data were analyzed with Gene Set Enrichment Analysis (GSEA). The protein-protein interaction (PPI) network of DEGs was constructed using STRING.ResultsWe identified 258 DEGs, with 110 genes significantly upregulated and 148 genes downregulated in the primary IOOA group compared to the secondary IOOA group. Analysis of DEGs revealed that upregulated genes in the primary group were associated with myelination (e.g., MBP, MPZ, PRX) and ion channels (e.g., KCNA5, KCNE5). Conversely, downregulated genes were primarily related to ion channels (e.g., CACNA1B, SCN3B, SCN5A, KCNJ3), collagen fibril organization (e.g., COL11A1, COL11A2, COL22A1, COL25A1 and COL9A2). Further analysis of cellular components and molecular functions indicated that genes related to M-bands (e.g., MYOM2, MYOM3) were upregulated in the primary group. GSEA and PPI network analysis corroborated these findings, highlighting alterations in peripheral nervous system development and myelin sheath formation.ConclusionOur preliminary findings suggested that neuromuscular DEGs in primary IOOA were enriched in pathways related to myelination, ion channels, M-bands, and collagen fibril. The results indicated that multiply innervated muscle fibers were more abundant in the primary IOOA group, likely enabling slow tension generation, whereas the secondary IOOA group exhibited higher collagen fibril levels that might improve muscle stiffness. creator: Rui Hao creator: Yuchuan Wang creator: Wei Zhang uri: https://doi.org/10.7717/peerj.19474 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Hao et al. title: Traumatic spinal cord injury: identifying independent risk factors and predictive model development for symptomatic urinary tract infections link: https://peerj.com/articles/19473 last-modified: 2025-05-28 description: BackgroundTraumatic spinal cord injury (TSCI) is commonly associated with urinary tract infections (UTIs), with a reported prevalence ranging from 31.7% to 68%. Symptomatic UTIs can result in serious complications, including chronic kidney damage and recurrent infections. The objective of this study was to identify independent risk factors and develop a predictive model for symptomatic UTIs in TSCI patients, thereby providing valuable insights for prevention and management strategies.MethodsA retrospective study was conducted at the China Rehabilitation Research Center, involving 168 TSCI patients admitted between January 1, 2020, and August 1, 2024. Symptomatic UTIs were diagnosed using Delphi consensus criteria, which integrated clinical symptoms, urinalysis, and culture confirmation. Comprehensive clinical data, including demographic characteristics, injury profiles, and laboratory parameters, were systematically extracted from the hospital information system. Potential risk factors were initially screened using univariable logistic regression, with statistically significant variables subsequently analyzed in a multivariable logistic regression model to identify independent predictors. A predictive model for symptomatic UTIs was constructed using the regression coefficients. The model’s performance was evaluated using the area under the receiver operating characteristic curve (AUC), calibration with the Hosmer-Lemeshow test, and internal validation through bootstrap resampling.ResultsThe incidence of symptomatic UTIs was 57.14%, with the majority presenting with fever (65.07%) and Escherichia coli infections (44.52%). Prolonged hospitalization (OR = 1.005, 95% CI [1.001–1.010]) and cumulative antibiotic exposure (OR = 1.011, 95% CI [1.000–1.022]) were identified as independent risk factors. The predictive model, which incorporated these factors, demonstrated strong discrimination (AUC = 0.81, 95% CI [0.746–0.879]) and good calibration (P = 0.44).ConclusionsThis study presents the incidence of symptomatic UTIs in TSCI patients and identifies two critical predictive factors along with a risk score for early prediction of symptomatic UTIs. The findings provide a foundation for improved clinical practices aimed at preventing and managing symptomatic UTIs in this patient population, potentially reducing healthcare costs and improving patient outcomes. creator: Huayong Du creator: Zehui Li creator: Jinming Zhang creator: Xiaoxin Wang creator: Yingli Jing creator: Degang Yang creator: Jianjun Li uri: https://doi.org/10.7717/peerj.19473 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Du et al. title: Synchrony on the reef: how environmental factors shape coral spawning patterns in Acropora corals in the Maldives link: https://peerj.com/articles/19447 last-modified: 2025-05-28 description: Elucidating our knowledge on the reproductive phenology of scleractinian corals and the environmental drivers of reproductive synchronicity is pivotal for assessing gene flow between populations and the potential for ecosystem recovery. The timing of gamete release in sessile broadcast spawning corals is key to successful reproduction; and is dependent on a complex interaction between an organism’s genes and external environmental factors. In this study we assessed the effect of various environmental factors on the spawning timing and synchronicity of Acropora corals in the Maldives. A total of 3,026 colonies from 24 species of Acropora were recorded spawning between October 2021 and May 2024: 1,709 from 20 species in North Male Atoll and 1,317 from 18 species in Baa Atoll. Generalised linear models (GLMs) were used to estimate the effect of average daily wind speed (mph), total daily precipitation (mm), tide depth (m), and mean sea surface temperature (SST) over a 30-day period prior to spawning, on the proportion of colonies to spawn per day and the spawning day deviation to full moon. Models were run for all Acropora corals, and three species in which more than 30 days of spawning were observed enabling robust statistical models to be tested: A. secale, A. tenuis, and A. humilis, to determine the presence of species-specific relationships. Based on additional GLMs, we found that a change in SST does not determine the likelihood of Acropora spawning to occur in a given month, but does significantly predict the number of Acropora colonies to spawn per month. We also found that the relationship between SST and spawning as a predictor of probability or synchronicity on a monthly temporal scale can be species specific. We found a significant, positive correlation between daily precipitation levels and the proportion of Acropora colonies to spawn per day, however, there were some variations between species. Additionally, a higher proportion of Acropora colonies spawned closer to the full moon. Spawning events of Acropora corals closer to the full moon are significantly correlated with lower tide depths across both atolls. This knowledge will be beneficial for the management of reef systems in the Maldives following a global bleaching event, due to increased reliance on targeted conservation measures to retain diversity and re-populate degraded reefs, such as in-situ larval settlement. While our analyses of environmental factors goes someway in explaining variability in spawning patterns within the Acropora genus in the Maldives, we must also conclude there are other factors which remain unexplored, or there is a wide range of ecologically appropriate conditions for spawning. However, our results highlight the importance of considering environmental conditions, and species-specific relationships, when predicting Acropora spawning, due to the temporal and spatial deviations in timing and synchronicity observed within and between species. creator: Kate Sheridan creator: Margaux A.A. Monfared creator: Simon P. Dixon creator: Amelia J.F. Errington creator: Thomas Le Berre uri: https://doi.org/10.7717/peerj.19447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sheridan et al. title: A hundred species, mostly new—first assessment of ribbon worm diversity and distribution in Oman link: https://peerj.com/articles/19438 last-modified: 2025-05-28 description: BackgroundBiodiversity is a key characteristic of any ecosystem but remains largely undescribed for most marine animals. Ribbon worms (phylum Nemertea), a diverse but poorly sampled phylum ubiquitous in the world’s oceans, are a case in point. Aside from their function as predators in marine communities, nemerteans are biomedically relevant because they produce diverse toxins, and some impact bivalve, decapod, and glass eel fisheries. Identification of nemerteans is challenging because many species look alike. The task is further complicated by many descriptions being based on preserved specimens, and therefore lacking characters of external appearance of live specimens. Characters of internal anatomy form the basis of traditional systematics but are more recently shown to be of little use in distinguishing between closely related species. This makes DNA data essential in species descriptions, and assessments of diversity and distribution.MethodsIn a first modern survey of the phylum in Arabian waters, we collected nemerteans from a variety of habitats, focusing sampling on hard-bottom substrata, especially coral reefs. Specimens were triple-documented with photos, morphological vouchers, and DNA barcodes. Species delineation was based on morphology and Cytochrome Oxidase I sequences. Sequences and associated data are deposited in public databases, and vouchers at the Florida Museum of Natural History.ResultsWe documented 107 nemertean species in Oman, where none were previously known. This doubles the number of genetically characterized nemertean species for the entire Indo-West Pacific—a testament to how poorly sampled the phylum is in the most biodiverse marine region of the world. As many as 98% of the species were undescribed, and 93% are not documented outside Arabia. Half of the species were rare, and most—cryptic. Undescribed species were assigned unique alphanumeric temporary names for tracking in the literature and public databases. Estimates of source diversity suggest that future surveys might uncover an additional ∼200 species by including other locations and types of habitats, particularly soft bottoms, and the water column. Little overlap was observed between species found in the northern (Gulf of Oman) and southern (Sea of Arabia) regions, and many that occurred in both areas showed evidence of genetic differentiation corresponding to the major biogeographic break at R’as-al-Hadd.ConclusionsThe high diversity, novelty, and distinctiveness of this fauna underscore the importance of sampling the most biodiverse and least studied tropical marine regions of the world. The large amount of cryptic and undescribed diversity highlights the critical role of DNA barcodes and rapid approaches to species descriptions. creator: Svetlana Maslakova creator: Irina Cherneva creator: Ethan Kahn creator: Audrey Wong creator: Gustav Paulay uri: https://doi.org/10.7717/peerj.19438 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Maslakova et al. title: Alleviation of dextran sulfate sodium (DSS)-induced colitis in mice through the antioxidative effects of muscone via the MyD88/p38 MAPK signalling pathway link: https://peerj.com/articles/19397 last-modified: 2025-05-28 description: BackgroundInflammatory bowel disease (IBD) is characterized by chronic inflammation. Ulcerative colitis (UC) is a subtype of IBD. The symptoms of UC include inflammation, damage to crypts, and ulceration. UC patients frequently experience comorbid psychological disorders. Muscone has notable anti-inflammatory, antioxidative, and antidementia properties. Our study aimed to investigate the potential of muscone to alleviate colitis, the underlying mechanisms, and the signalling pathways involved.MethodsC57BL/6 mice were administered dextran sulfate sodium (DSS) to induce colitis. The SMART v3.0 (Panlab, Barcelona, Spain) was used to measure parameters in the open field test and the tail suspension test to assess depression and anxiety. Gait changes were analysed using the DigiGait™ imaging system. The severity of colitis was assessed through body weight loss, stool consistency, gross bleeding, and histopathological evaluation. Proteins related to anti-inflammatory and antioxidative effects were analysed in dissociated tissues using mouse-specific commercial enzyme-linked immunosorbent assay (ELISA) kits.ResultsMuscone treatment reduced gross bleeding and histopathological damage scores and increased the ratio of colon length to body weight. Gait analysis revealed improvements in swing time, brake time, propulsive time, stance duration, stride duration, stride length, stride frequency, and paw area with muscone treatment. However, muscone treatment did not improve the distance travelled or the time spent in the open field test, nor did it affect the immobility duration in the tail suspension test. We observed that the expression of claudin-1, occludin, and zonula occludens-1 (ZO-1) increased in response to treatment with muscone. Muscone treatment downregulated the expression of interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-17 (IL-17), interleukin-33 (IL-33), and tumour necrosis factor-α (TNF-α), while increasing the expression of interleukin-4 (IL-4) and interleukin-10 (IL-10). Muscone treatment increased the concentrations of catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), and haem oxygenase (HO-1), and suppressed the expression of myeloperoxidase (MPO), cyclooxygenase-2 (COX-2), and nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (NOX1 and NOX2). Furthermore, muscone treatment inhibited the expression of myeloid differentiation primary response 88 (MyD88) and p38 mitogen-activated protein kinase (MAPK).ConclusionMuscone effectively alleviated the symptoms of colitis, which may be due to the reduction in reactive oxygen species (ROS). The potential mechanism underlying the mitigation of colitis may involve the inhibition of the MyD88/p38 MAPK signalling pathway. Our studies suggest that muscone could be a promising target for treating IBD in clinical studies. creator: Gang Yao creator: Jian Zhang creator: Lingyan Zhang creator: Hai Zhao creator: Shuguang Wu creator: Hongmei Yang creator: Jiangwei Yu uri: https://doi.org/10.7717/peerj.19397 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yao et al. title: Unveiling the role of gasdermin B in cancer and inflammatory disease: from molecular mechanisms to therapeutic strategies link: https://peerj.com/articles/19392 last-modified: 2025-05-28 description: Gasdermin B (GSDMB) is a member of the gasdermin (GSDM) protein family, primarily known for mediating pyroptosis, an inflammatory form of programmed cell death. Recent studies have revealed the diverse molecular functions of GSDMB and its close association with various diseases, particularly cancers (e.g., breast cancer, gastric cancer, bladder cancer) and inflammatory diseases (e.g., asthma, inflammatory bowel disease). At the molecular level, GSDMB induces pyroptosis by forming pores in the cell membrane, leading to membrane rupture. This function is common across the GSDM protein family; however, GSDMB also exhibits unique non-pyroptotic functions, such as modulating cell proliferation, migration, and immune responses. In multiple cancers, including breast cancer, gastric cancer, and cervical cancer, high expression of GSDMB correlates with poor prognosis, promoting cancer cell proliferation, invasion, and metastasis through interactions with signaling pathways such as STAT3 and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK). Additionally, GSDMB influences the immune microenvironment through its pyroptotic activity, playing a role in the initiation and regulation of inflammation. Upon activation, it can directly cleave target cells via its N-terminal domain, contributing significantly to chronic inflammatory diseases and NK cell-mediated antibacterial responses. In conclusion, as a multifunctional protein, GSDMB not only participates in pyroptosis but also regulates non-pyroptotic processes, playing an important role in cancer progression and inflammatory diseases. Further elucidating the detailed mechanisms of GSDMB may offer novel therapeutic avenues for these conditions. creator: Weixiao Yang creator: Xu Hu creator: Xiang Li uri: https://doi.org/10.7717/peerj.19392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: SK4 potentially modulates the alternative splicing profile associated with papillary thyroid cancer development in BHT101 cells link: https://peerj.com/articles/19391 last-modified: 2025-05-28 description: Papillary thyroid cancer (PTC) is an ever-increasing cancer type worldwide, and greatly decreases the life quality and affects survival time of patients during its development and progression, but the underlying mechanisms and key factors for PTC progression are not clear. Recent studies demonstrated the potassium channel protein SK4 participates in the progression of many cancers, while it lacks the molecular mechanism study for SK4 function. In this study, we performed functional and molecular explorations for SK4 by overexpressing its level in thyroid cancer BHT101 cells. Cellular proliferation and invasion experiments were performed to assess the influences of SK4 on cell behaviors. Further, whole transcriptome sequencing (RNA-seq) analysis helped us systematically investigated the targets of SK4, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs), and validated several related DEGs and RASEs by RT-qPCR experiment. In thyroid cancer patients, SK4 expression was completely lost in normal tissues and significantly increased in every stage of tumor tissues compared with normal tissues, which probably results from the low DNA methylation level at its promoter region. Consistent with previous study, SK4 overexpression (SK4-OE) promoted proliferation and invasion ability of BHT10 cells compared with negative control (NC). By analyzing the RNA-seq data, we detected dozens of DEGs and found that up DEGs were enriched in negative regulation of apoptotic progress, including VTCN1, MSX1, FATE1, TEK, and PRAMEF2. More importantly, we found SK4-OE globally changed the alternative splicing (AS) pattern and identified 1,639 RASEs. The genes of RASEs were enriched in DNA damage/repair, viral process, translation, and mRNA splicing pathways, which were tightly associated with the pathogenesis and progression of cancers. The splicing regulatory genes from regulated alternative splicing genes (RASGs) could partly explain the reason of global AS dysregulation by SK4-OE in BHT101 cells. Finally, we found the expression of VTCN1, EDN1, SLC29A4, RP11-473M20.16, and CH507-513H4.4 were validated by RT-qPCR, as well as the AS pattern of TMEM116. In summary, we highlight that SK4-regulated AS pattern probably is a novel regulatory mechanism for SK4 in PTC. The identified DEGs and RASEs, as well as SK4 itself, could be used as potential therapeutic targets for PTC treatment in future. creator: Alimujiang Wupuer creator: Xuekelaiti Kuerban creator: Gong Ye uri: https://doi.org/10.7717/peerj.19391 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wupuer et al. title: An ethogram of facial behaviour in domestic horses: evolutionary perspectives on form and function link: https://peerj.com/articles/19309 last-modified: 2025-05-28 description: Understanding cause and function of animal facial behaviour can provide key insights into the animal’s cognitive and emotional state. The Equine Facial Action Coding System (EquiFACS) has characterised a wide range of equine (Equus caballus) facial movements (Action Units (AU) and Descriptors (AD)). However, there is still a lack of systematic documentation of whether and how these AUs and ADs are combined to produce discrete configurations of facial behaviour in horses. The aim of this study was to provide a systematically derived ethogram of equine facial behaviour in the domestic horse across positive, negative and neutral social interactions. Facial behaviour was recorded during horse-horse interactions occurring during affiliative (non-play), play, agonistic and attentional contexts, based on the coding of contextual behaviour. Using EquiFACS, a bank of 805 AU/AD combinations, across 22 distinct behaviours, was created. Network analysis techniques (NetFACS) were used to establish the facial movements significantly associated with each context. Domestic horses use a wide range of distinct facial behaviours, which are defined and described in our ethogram. Interestingly, there were marked similarities between the play faces of horses and the open mouth play faces of primates and carnivores, adding weight to the hypothesis that these facial behaviours are deep rooted in mammalian biology. We also defined a new EquiFACS Action Unit, AUH21, facial tightener (platysma), which makes the underlying facial structures appear more prominent. This AU is found in humans and gibbons, but no other species studied, and its addition to EquiFACS will enhance cross-species comparisons and potentially facilitate the attribution of emotional state and assessment of pain in horses. Our equine facial behaviour ethogram will be invaluable in future work exploring equine emotion, welfare, social behaviour, and perception, as well as having direct applications for those working with and around horses. creator: Kate Lewis creator: Sebastian D. McBride creator: Jérôme Micheletta creator: Matthew O. Parker creator: Alan V. Rincon creator: Jen Wathan creator: Leanne Proops uri: https://doi.org/10.7717/peerj.19309 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lewis et al. title: A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information link: https://peerj.com/articles/19296 last-modified: 2025-05-28 description: Understanding the behavior of microbial consortia is crucial for predicting metabolite production by microorganisms. Genome-scale network reconstructions enable the computation of metabolic interactions and specific associations within microbial consortia underpinning the production of different metabolites. In the context of the human gut, butyrate is a central metabolite produced by bacteria that plays a key role within the gut microbiome impacting human health. Despite its importance, there is a lack of computational methods capable of predicting its production as a function of the consortium composition. Here, we present a novel machine-learning approach leveraging automatically generated genome-scale metabolic models to tackle this limitation. Briefly, all consortia made of two up to 13 members from a pool of 19 bacteria with known genomes, including at least one butyrate producer from a pool of three known producer species, were built and their (maximum) in silico butyrate production simulated. Using network-derived descriptors from each bacteria, butyrate production by the above consortia was used as training data for various machine learning models. The performance of the algorithms was evaluated using k-fold cross-validation and new experimental data, displaying a Pearson correlation coefficient exceeding 0.75 for the predicted and observed butyrate production in two bacteria consortia. While consortia with more than two bacteria showed generally worse predictions, the best machine-learning models still outperformed predictions from genome-scale metabolic models alone. Overall, this approach provides a valuable tool and framework for probing promising butyrate-producing consortia on a large scale, guiding experimentation, and more importantly, predicting metabolic production by consortia. creator: Claudia Silva-Andrade creator: Sergio Hernández creator: Pedro Saa creator: Ernesto Perez-Rueda creator: Daniel Garrido creator: Alberto J. Martin uri: https://doi.org/10.7717/peerj.19296 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Silva-Andrade et al. title: Biochar-mediated changes in nutrient distribution and leaching patterns: insights from a soil column study link: https://peerj.com/articles/18823 last-modified: 2025-05-28 description: BackgroundNutrient leaching threatens sustainable agriculture by depleting soil fertility and contaminating groundwater. Biochar offers a promising solution, but its effectiveness varies with feedstock, production, and application rates. Specifically, the potential of hazelnut husk biochar for nutrient retention and soil improvement has not been extensively studied, leaving a gap in understanding its practical applications and optimal usage in different soil types and crop systems.MethodsThis study investigated the influence of hazelnut husk biochar application on leachate properties, soil column characteristics, and nutrient dynamics over a 112-day period. The experiment employed a randomized split-plot design with four hazelnut husk biochar application rates (0%, 0.5%, 1%, and 2%) on sandy loam soil. Leaching events were conducted six times over 112 days of incubation period, simulating irrigation and fertilizer application for potato cultivation. Leachates were collected at each leaching event for analysis of pH, electrical conductivity (EC), and various nutrient contents. Following the experiment, soil samples were analyzed at three depths to assess nutrient content.ResultsThe study revealed significant temporal dynamics in nutrient concentrations across different leaching events, emphasizing the impact of biochar on nutrient retention. Phosphorus (P) concentrations, for instance, decreased from 0.220 mg L−1 to 0.176 mg L−1 over four leaching events in the 2.0% biochar treatment. Similarly, potassium (K) concentrations declined from 6.44 mg L−1 to 3.76 mg L−1, indicating improved nutrient retention with biochar application. These findings contrast with the control (0% biochar), where nutrient leaching was more pronounced. While biochar had little effect on nitrate leaching, its inherent P content and adsorption characteristics influenced P leaching. Higher biochar application rates resulted in significant changes in soil properties and nutrient concentrations, particularly in the surface layer (0–10 cm), such as an increase in organic matter content from 0.84% in the control to 1.20% in the 2.0% biochar treatment, suggesting improved nutrient availability for plant uptake.ConclusionThese findings underscore the potential of hazelnut husk biochar as a sustainable soil management strategy for enhancing nutrient retention, reducing leaching, and improving soil fertility. However, the study also highlights the complexity of biochar-soil interactions and the need for further research to optimize biochar application practices for specific soil and crop systems. creator: Elif Gunal uri: https://doi.org/10.7717/peerj.18823 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gunal title: Xenobiotic resistance in mosquito eggs: current understanding and data gaps link: https://peerj.com/articles/19523 last-modified: 2025-05-27 description: Of all mosquito life stages, the egg continues to be the least understood and most vulnerable relative to exposure to external environmental stressors. The propensity of mosquitoes to lay eggs in or near aquatic environments exposes them to a variety of xenobiotic compounds. Owing to their increased use, two xenobiotics, antibiotics and insecticides are increasingly being detected in aquatic ecosystems. Both antibiotics and insecticides are known for their ovicidal effects. Prior to the formation of the serosal cuticle, mosquito eggs are potentially exposed to antibiotics and insecticides due to the permeability of the egg membrane. This short review attempts to summarize the current understanding and to identify the data gaps pertaining to the exposure of mosquito eggs to xenobiotics. The role of male mosquitoes in the propagation of xenobiotic resistance, something that’s been sparsely studied, is also discussed. Additionally, we address the implications of these data gaps relative to the overall objectives of vector control and public health. creator: Uday Turaga creator: Steven T. Peper creator: Carlos J. Garcia creator: Steven M. Presley uri: https://doi.org/10.7717/peerj.19523 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Turaga et al. title: Comparative analysis of fecal microbiota of central and eastern black-necked cranes (Grus nigricollis) wintering in Yunnan Province, China link: https://peerj.com/articles/19520 last-modified: 2025-05-27 description: The black-necked crane (Grus nigricollis) is the sole crane species globally that inhabits, breeds, and flourishes in high plateau environments. There are many microbial communities in the gastrointestinal tract of birds, which play an important role in the health, nutrition, and physiology of birds. This study utilized high-throughput sequencing of the 16S rRNA gene to investigate and compare the core gut microbiota of black-necked cranes in two overwintering populations of Yunnan Province, China. A total of 34,297 operational taxonomic units were identified, belonging to 49 phyla, 130 classes, 276 orders, 365 families, and 775 genera. Alpha diversity analysis indicated significant differences in the diversity of gut microbial communities between the two wintering populations, with the central population exhibiting markedly higher diversity and richness compared to the eastern population. Principal coordinate analysis revealed a clear separation of the two populations of fecal samples, suggesting notable differences in microbial communities between the populations. The dominant phyla in the eastern population were Firmicutes, followed by Proteobacteria, whereas the central population was primarily dominated by Firmicutes, Proteobacteria, and Actinobacteria. At the genus level, Lactobacillus had the highest abundance in the intestinal microbiota of the two populations. Additionally, a variety of potential pathogenic bacteria was also found, including Enterococcus, Acinetobacter, Campylobacter, Escherichia-Shigella, and Streptococcus, which may pose a risk of transmission among local black-necked crane populations. Appropriate measures should be taken to protect the health of black-necked cranes and reduce the spread of diseases. creator: Ruimei Wang creator: Yixuan Wang creator: Lulu Deng creator: Binghui Wang creator: Mingfei Shi creator: Zeya Yang creator: Dong Hu creator: Zijiao Zhao creator: Ruiling Yuan creator: Jiuxuan Zhou uri: https://doi.org/10.7717/peerj.19520 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Wang et al. title: Epidemiology and resistant profile of bacterial pathogens in a tertiary health care hospital, Medan City: a retrospective study link: https://peerj.com/articles/19510 last-modified: 2025-05-27 description: BackgroundThe epidemiology study of bacterial isolates and their resistance patterns in clinical settings is essential due to the rising threat of antibiotic resistance, which complicates treatment options. Understanding these patterns enables healthcare providers to tailor antibiotic therapies effectively, ensuring better patient outcomes and mitigating the spread of resistant strains. This study aims to analyze the prevalence and antimicrobial resistance patterns of microbes recovered from blood, wound, sputum, and urine specimens in a tertiary healthcare hospital.MethodsIn this retrospective cross-sectional study, we analyzed the clinical microbiology laboratory data of patients of all age groups from January 2022 to December 2023. Microbial isolates were identified using the commercial system bioMérieux-Vitek 2. Antimicrobial susceptibility tests were conducted using the Vitek 2 automated susceptibility system and disk diffusion methods, following the Clinical & Laboratory Standards Institute (CLSI) guidelines.ResultsA total of 1,190 (47.58%) microbial isolates were recovered from 2,501 clinical specimens, consisting of 98/714 (13.73%), 454/655 (69.32%), 394/545 (72.29%), and 244/587 (41.57%) from blood, wound, sputum, and urine, respectively. Escherichia coli was the most prevalent isolate identified from blood [27/98 (27.55%)], wound [107/454 (23.57%)], and urine [107/244 (43.85%)]. Sputum isolates were dominated by K. pneumoniae [68/394 (17.26%)]. Coagulase-negative staphylococci (CoNS) and S. aureus were the dominant Gram positives in all specimens. Polymicrobial isolates were found in 4/98 (4.08%) blood, 41/454 (9.03%) wound, 52/394 (13.2%) sputum, and 9/244 (3.69%) urine. The predominant polymicrobial pairs were K. pneumoniae and S. aureus [6/106 (5.7%)]. Poor sensitivity against cefoxitin and oxacillin was highest among the Gram-positives, dominated by CoNS. In Gram-negatives, sensitivity against ampicillin was the lowest.ConclusionsA periodical update of the epidemiological profile of microbial isolates in hospital settings presented in this study is crucial for updating the empirical antibiotics and developing the prevention and infection control program. creator: Evita Mayasari creator: Edhie Djohan Utama uri: https://doi.org/10.7717/peerj.19510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mayasari and Utama title: Diet and prey selectivity in co-occurring eelpout fish and bythograeid crabs in a deep-sea hydrothermal vent community link: https://peerj.com/articles/19476 last-modified: 2025-05-27 description: Understanding the trophic ecology of deep-sea communities is central to assessing ecological structure and function, which is often lacking in remote oceanographic environments such as hydrothermal vents. Using stomach content analysis coupled with published stable isotope data, we assessed diet and prey selectivity in two common predators, eelpouts (Pyrolycus manusanus) and crabs (Austinograea alayseae), from a South Pacific deep-sea hydrothermal vent community. Using specimens collected during a cruise in 2007, we found that eelpouts strongly preferred alvinocarididshrimp. This observation is s upported by the Ivlev index, which measures the selection of prey in relation to their abundance or availability. Crabs exhibited a diverse diet, including polychaetes and shrimp, suggesting a scavenging or omnivorous feeding strategy. Due to the lack of intact stomach contents in the crab, we were unable to apply the Ivlev method to quantify its prey selectivity. Our results emphasize the need to combine stomach contents, stable isotope analysis, and other complementary methodologies, to elucidate the role of predators in deep-sea food webs. In sum, our study underscores the importance of direct stomach content examination in revealing trophic relationships in hydrothermal vent systems. creator: Deidric B. Davis creator: Nancy Smith uri: https://doi.org/10.7717/peerj.19476 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Davis and Smith title: Clustering and classification of early knee osteoarthritis using machine-learning analysis of step-up and down test kinematics in recreational table tennis players link: https://peerj.com/articles/19471 last-modified: 2025-05-27 description: ObjectiveEarly detection of knee osteoarthritis is crucial for improving patient outcomes. While conventional imaging methods often fail to detect early changes and require specialized expertise for interpretation, this study aimed to investigate the use of frontal plane kinematic data during step-up (SU) and step-down (SD) tests to classify and predict early osteoarthritis (EOA) using machine-learning techniques.MethodsForty-three recreational table tennis players (eighty-six legs: 42 with EOA and 44 without EOA) underwent SU and SD tests. Frontal plane kinematics was analyzed using two-dimensional video analysis with markers placed at five key anatomical landmarks. Horizontal displacement measurements were compared between groups using independent t-tests. Unsupervised learning (Louvain clustering) was used to identify distinct movement patterns, whereas supervised learning algorithms were employed to classify EOA status. The feature importance was assessed using feature permutation importance (FPI).ResultsSignificant differences were observed between EOA and non-EOA groups in frontal plane kinematics during SU and SD tests (p < 0.001 for most variables). Louvain clustering identified four distinct kinematic profiles with varying proportions of EOA (ranging from 41.2% to 70.7%). Supervised learning models achieved high performance in classifying EOA status, with Random Forest, gradient boosting, and decision tree algorithms achieving 100% classification accuracy (AUC = 1.000) on the test dataset. FPI consistently highlighted the horizontal displacements of the ankle and femur during SU and of the pelvis and femur during SD as the most influential predictors.ConclusionsMachine-learning analysis of frontal plane kinematics during SU and SD tests showed promising potential for EOA detection and classification, offering a cost-effective and accessible alternative to conventional imaging-based approaches. creator: Ui-jae Hwang creator: Kyu Sung Chung creator: Sung-min Ha uri: https://doi.org/10.7717/peerj.19471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hwang et al. title: The association between sleep latency and suboptimal self-rated health in medical students: a cross-sectional study link: https://peerj.com/articles/19459 last-modified: 2025-05-27 description: BackgroundEvidence has suggested that prolonged sleep latency was associated with negative health outcomes. Little is known about the association between sleep latency and health status in university students. This study examined the association between sleep latency and suboptimal self-rated health (SRH) in medical students.MethodsA cross-sectional study was conducted involving 1,396 medical students aged 18 years and older selected through stratified cluster random sampling from an eastern Chinese university. Standardized measures of sleep latency and SRH were administered. Sleep latency was divided into four categories: <10 min, 10–19 min, 20–29 min, and ≥30 min, with “prolonged sleep latency” defined as a latency of ≥30 min. Logistic regression was used to investigate the association between sleep latency and suboptimal SRH.ResultsOf the 1,396 participants (mean age 19.6 ± 1.2 years; 58.6% female), 599 (42.9%) reported suboptimal SRH, and 390 (27.9%) reported prolonged sleep latency. Longer sleep latency was associated with higher odds of suboptimal SRH. Comparing those with sleep latency <10 min, multivariable-adjusted ORs (95% CIs) for those with sleep latency of 10–19 min, 20–29 min, and ≥30 min were 1.48 (1.07, 2.05), 2.03 (1.39, 2.97), and 2.12 (1.52, 2.96) (P for trend <0.001), respectively. The results of the stratified and sensitivity analyses were generally consistent with the main findings.ConclusionOur study found that prolonged sleep latency was strongly linked to higher odds of suboptimal SRH in medical students, even after accounting for potential confounders. Intervention programs targeting sleep latency may potentially promote health in this population. creator: Mengjia Jin creator: Liuhong Tian creator: Jie Yu creator: Xiaodan Kuang creator: Jiaming Fang creator: Shulei Chen creator: Hongying Shi uri: https://doi.org/10.7717/peerj.19459 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Jin et al. title: Research progress and strategies for the biosynthesis of keratinocyte growth factor-2 (KGF-2) in Arabidopsis thaliana link: https://peerj.com/articles/19440 last-modified: 2025-05-27 description: This review examines the current research progress of molecular agriculture for cytokine expression, the research status of keratinocyte growth factor-2 (KGF-2) for skin care, hair growth, and the research status of plants for hair growth. KGF-2 application and use are inhibited by factors, such as the cost of production and efficacy due to low transdermal penetration potential. However, cell penetrating peptides (CPPs) are powerful transporter tools that assist the transmembrane delivery of attached biomacromolecules. Biomacromolecules such as KGF-2 have poor transdermal ability, which can be enhanced by combining with CPP such as TD1 to construct fusion proteins. Arabidopsis thaliana has many advantages, such as short growth cycle, high transformation efficiency, large biomass and hair growth promotion substances. Therefore, we also discuss the feasibility and expression strategies of using A. thaliana plant system to express fusion protein TDP1-KGF-2, which provides new idea for enhancing the transdermal ability of KGF-2 and providing new idea for plant system expression of fusion protein. This offers a promising new direction for the development of natural hair care and hair growth materials, as well as innovative possibilities for the application of molecular agriculture. creator: Chengyang Song creator: Guangdong Yu creator: Shuang Gao creator: Wengang Zhao creator: Yunpeng Wang creator: Nuo Xu uri: https://doi.org/10.7717/peerj.19440 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Song et al. title: Genome-wide identification of PP2A gene family in Camellia sinensis reveals the potential role of CsPP2A-TON2/FASS1 in abiotic stress link: https://peerj.com/articles/19431 last-modified: 2025-05-27 description: BackgroundProtein phosphatases (PP) play a crucial role in regulation of physiological response to various environmental stimuli in plants. Protein phosphatase 2A (PP2A) are a class of Ser/Thr protein phosphatases which are present widely across plant species and facilitate plant responses to biotic and abiotic stresses, and hormone treatment.MethodsUsing BLASTp, tea PP2A genes were found and their physicochemical characteristics (ExPASy), subcellular localization, and intron-exon structure (GSDS) were described. MEGA software was used to examine phylogenetic relationships, SMART online tool to analyze conserved domains, and PlantCARE tool to analyze cis-elements. The Heatmapper online tool was used to visualize expression profiles across plant tissues and stress conditions. Under controlled conditions, 2-year-old Camellia sinensis plants were exposed to methyl jasmonate (MeJA) stress treatments, cold drought, and salt stresses and qRT-PCR (2−ΔΔCt technique, CsACTIN as internal control) was used to validate the results.ResultsWe found 11 PP2A genes in C. sinensis (CsPP2A) through a genome-wide search wherein Arabidopsis thaliana was taken as the reference genome. Further, a systematic study was conducted wherein physicochemical properties, phylogeny, gene structure and gene expression were explored. Analysis of cis-elements, gene ontology, and expression patterns of CsPP2A genes under various stresses, combined with prior research on the PP2A gene family in other plants, suggests that the PP2A family plays a role in regulating phytohormone (auxin, salicylic acid, gibberellin, abscisic acid, MeJA) responses during stress in C. sinensis. The real time PCR also confirmed the potential role of (TEA018948.1) CsPP2AB9/CsPP2A-TON2/FASS1 gene in abiotic stress responses.ConclusionThis study offers potential goals for further in-depth investigation and functional analysis, alongside enhancing our understanding of the regulatory network of PP2A genes in C. sinensis. creator: Surjit Bhattacharjee creator: Abhirup Paul creator: Aradhana Jana creator: G. Meher Unnati creator: Deepak R. creator: Ye Miao creator: Honglin Lu creator: Guoxin Shen creator: Neelam Mishra uri: https://doi.org/10.7717/peerj.19431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bhattacharjee et al. title: A genetically engineered mouse model for ovarian hyperstimulation syndrome link: https://peerj.com/articles/19531 last-modified: 2025-05-26 description: Ovarian hyperstimulation syndrome (OHSS) is a common iatrogenic complication resulting from ovarian stimulation in assisted reproductive technology (ART). Excessive stimulation by follicle-stimulating hormone (FSH) has been recognized as a primary cause of OHSS. However, understanding the pathophysiological mechanisms of OHSS and developing effective drugs have been limited due to the absence of suitable animal models. In this study, we generated a FSH gene knock-in (FKI) mouse model to inducible FSH expression by the Tet-on system, that reflects the clinical manifestations of OHSS in patients. Upon administration of doxycycline (Dox), the FKI mice exhibited significantly elevated serum FSH levels compared to their wild-type (WT) littermate controls, accompanied by increased levels of estradiol (E2) and luteinizing hormone (LH), ovarian enlargement, and enhanced peritoneal permeability. Thus, the FKI mouse model is a valuable tool for studying OHSS, particularly dissecting the pathophysiological mechanism and developing potential prevention strategies. creator: Wenkai Bi creator: Xinchen Jin creator: Shanshan Wu creator: Jing Wang creator: Xinhuan Su creator: Ling Gao creator: Zhao He uri: https://doi.org/10.7717/peerj.19531 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bi et al. title: Development and validation of an in-hospital major adverse cardiovascular events risk model for young patients with acute coronary syndrome: a retrospective cohort study link: https://peerj.com/articles/19513 last-modified: 2025-05-26 description: BackgroundThe incidence of acute coronary syndrome (ACS) among young individuals is increasing, making it a leading cause of mortality in this population. This study aimed to develop and validate a risk prediction model for in-hospital major adverse cardiovascular events (MACE) in young ACS patients.MethodsA retrospective analysis was performed to predict in-hospital MACE. Patients were divided into a training set (n = 342) and a testing set (n = 171). Screening variables were optimized using least absolute shrinkage and selection operator (LASSO) regression and univariable logistic regression analysis. A predictive nomogram model was developed through multivariate logistic regression. The model’s discrimination and calibration were assessed using the receiver operating characteristic (ROC) curve, calibration plots, and Hosmer-Lemeshow goodness-of-fit tests. Clinical utility was evaluated using decision curve analysis (DCA).ResultsWhite blood cell count, Killip classification, lymphocyte count, heart rate, triglycerides, and Gensini score were identified as significant predictors. The constructed nomogram demonstrated strong predictive performance. The area under the ROC curve (AUC) was 0.9242 (95% confidence interval [CI]: [0.8841–0.9643]) for the training set and 0.8346 (95% CI [0.742–0.9272]) for the testing set, with respective cut-off values of 0.107 and 0.119. Calibration was confirmed with Hosmer-Lemeshow statistics of 12.454 (p = 0.2558) in the training set and 7.16 (p = 0.7102) in the testing set. DCA showed threshold probabilities ranging from 0% to 100% in the training set and 0% to 90% in the testing set.ConclusionsThe proposed nomogram model demonstrated robust discrimination and calibration, offering a valuable tool for predicting the risk of in-hospital MACE in young ACS patients. creator: Jia Zheng creator: Junyang Li creator: Tingting Li creator: Fang Hu creator: Degang Cheng creator: Chengzhi Lu uri: https://doi.org/10.7717/peerj.19513 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zheng et al. title: Volumetric atlas of the rat inner ear from microCT and iDISCO+ cleared temporal bones link: https://peerj.com/articles/19512 last-modified: 2025-05-26 description: BackgroundVolumetric atlases are an invaluable tool in neuroscience and otolaryngology, greatly aiding experiment planning and surgical interventions, as well as the interpretation of experimental and clinical data. The rat is a major animal model for hearing and balance studies, and a detailed volumetric atlas for the rat central auditory system (Waxholm) is available. However, the Waxholm rat atlas only contains a low-resolution inner ear featuring five structures. In the present work, we segmented and annotated 34 structures in the rat inner ear, yielding a detailed volumetric inner ear atlas which can be integrated with the Waxholm rat brain atlas.MethodsWe performed iodine-enhanced microCT and iDISCO+-based clearing and fluorescence lightsheet microscopy imaging on a sample of rat temporal bones. Image stacks were segmented in a semiautomated way, and 34 inner ear volumes were reconstructed from five samples. Using geometrical morphometry, high-resolution segmentations obtained from lightsheet and microCT stacks were registered into the coordinate system of the Waxholm rat atlas.ResultsCleared sample autofluorescence was used for the reconstruction of most inner ear structures, including fluid-filled compartments, nerves and sensory epithelia, blood vessels, and connective tissue structures. Image resolution allowed reconstruction of thin ducts (reuniting, saccular and endolymphatic), and the utriculoendolymphatic valve. The vestibulocochlear artery coursing through bone was found to be associated to the reuniting duct, and to be visible both in cleared and microCT samples, thus allowing to infer duct location from microCT scans. Cleared labyrinths showed minimal shape distortions, as shown by alignment with microCT and Waxholm labyrinths. However, membranous labyrinths could display variable collapse of the superior division, especially the roof of canal ampullae, whereas the inferior division (saccule and cochlea) was well preserved, with the exception of Reissner’s membrane that could display ruptures in the second cochlear turn. As an example of atlas use, the volumes reconstructed from segmentations were used to separate macrophage populations from the spiral ganglion, auditory neuron dendrites, and Organ of Corti.ConclusionWe have reconstructed 34 structures from the rat temporal bone, which are available as both image stacks and printable 3D objects in a shared repository for download. These can be used for teaching, localizing cells or other features within the ear, modeling auditory and vestibular sensory physiology and training of automated segmentation machine learning tools. creator: Daniele Cossellu creator: Elisa Vivado creator: Laura Batti creator: Ivana Gantar creator: Roberto Pizzala creator: Paola Perin uri: https://doi.org/10.7717/peerj.19512 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cossellu et al. title: Zero-inflated models for the evaluation of colorectal polyps in colon cancer screening studies—a value-based biostatistics practice link: https://peerj.com/articles/19504 last-modified: 2025-05-26 description: BackgroundColon cancer screening studies are needed for the early detection of colorectal polyps to reduce the risk of colorectal cancer. Unfortunately, the data generated on colon polyps are typically analyzed in their dichotomized form and sometimes with standard count models, which leads to potentially inaccurate findings in research studies. A more appropriate approach for evaluating colon polyps is zero-inflated models, considering undetected existing polyps at colonoscopy screening.MethodWe demonstrated the application of the zero-inflated and hurdle models including zero-inflated Poisson (ZIP), zero-inflated robust Poisson (ZIRP), zero-inflated negative binomial (ZINB), zero-inflated generalized Poisson (ZIGP), zero hurdle Poisson (ZHP), and zero hurdle negative binomial (ZHNB) models, and compared them with standard approaches including logistic regression (LR), Poisson regression (PR), robust Poisson (RP), and negative binomial (NB) regression for the evaluation of colorectal polyps using datasets from two randomized studies and one observational study. We also facilitated a step-by-step approach for selecting appropriate models for analyzing polyp data.ResultsAll datasets yielded a significant amount of no polyps and therefore inflated or hurdle models performed best over single distribution models. We showed that cap-assisted colonoscopy yielded significantly more colon polyps (risk ratio [RR] = 1.38; 95% confidence interval [CI] [1.05–1.81]) compared with the standard colonoscopy by using the ZIP analysis. However, these findings were missed by standard analytic methods, including LR (odds ratio [OR] = 0.90; 95% CI [0.59–1.37]), PR (RR = 1.14; 95% CI [0.93–1.41]), and NB (RR = 1.16; 95% CI [0.89–1.51]) for evaluating colon polyps. The standard approaches, such as LR, PR, RP, or NB regressions for analyzing polyp data, produced potentially inaccurate findings compared to zero-inflated models in all example datasets. Furthermore, simulation studies also confirmed the superiority of ZIRP over alternative models in a range of datasets differing from the case studies. ZIRP was found to be the optimal method for analyzing polyp data in randomized studies, while the ZINB/ZHNB model showed a better fit in an observational study.ConclusionWe suggest colonoscopy studies should jointly use the polyp detection rate and polyp counts as the quality measure. Based on theoretical, empirical, and simulation considerations, we encourage analysts to utilize zero-inflated models for evaluating colorectal polyps in colonoscopy screening studies for proper clinical interpretation of data and accurate reporting of findings. A similar approach can also be used for analyzing other types of polyp counts in colonoscopy studies. creator: Alok K. Dwivedi creator: Sherif E. Elhanafi creator: Mohamed O. Othman creator: Marc J. Zuckerman uri: https://doi.org/10.7717/peerj.19504 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dwivedi et al. title: BNC1 inhibits the development and progression of gastric cancer by regulating the CCL20/JAK-STAT axis link: https://peerj.com/articles/19477 last-modified: 2025-05-26 description: The role of basonuclin 1 (BNC1), a zinc finger protein-specific transcription factor, in gastric cancer remains unclear. In this study, BNC1 was downregulated in gastric cancer and functioned as a tumor suppressor. Through integrative analyses of transcriptome sequencing and functional assays, C-C motif chemokine ligand 20 (CCL20) was identified as a direct downstream target of BNC1. Overexpression of BNC1 inhibited the proliferation, migration, and invasion of gastric cancer cells both in vitro and in vivo. Mechanistically, BNC1 suppresses CCL20 expression by binding to its promoter, leading to reduced activation of the JAK-STAT signaling pathway and promoting apoptosis in gastric cancer cells. These findings highlight the pivotal role of BNC1 in gastric cancer progression and suggest that targeting BNC1 and its downstream pathways could serve as a potential therapeutic strategy. creator: Lixin Liu creator: Li Xiong creator: Hong Peng creator: Qin Deng creator: Kang Liu creator: Shusen Xia uri: https://doi.org/10.7717/peerj.19477 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Association between gut microbiota and allergic rhinitis: a systematic review and meta-analysis link: https://peerj.com/articles/19441 last-modified: 2025-05-26 description: BackgroundMany studies have shown that allergic rhinitis (AR) is closely related to intestinal flora, and probiotics are effective in treatment. However, the results of human observational studies on the correlation between intestinal flora and AR have been contradictory. The aim of this study was to determine the relationship between gut microbiota and allergic rhinitis and to provide a clinical reference.MethodsPubMed, Web of Science, Medline, Embase, Cochrane Library, and Cinahl databases were searched, and the literature on the correlation between allergic rhinitis and the gut microbiota reported from database establishment to December 2023 was included. Literature meeting the inclusion criteria was screened, and meta-analysis of the included literature was performed using R software (4.3.3). Literature quality underwent assessment utilizing the Newcastle-Ottawa Quality Assessment Scale. Hedge’s g standardized mean difference (SMD), confidence intervals (CIs), and heterogeneity (I2) for alpha diversity were calculated. Median interquartile range (IQR) were calculated as effect statistics for the abundance of bacteria. The Egger test determined publication bias in the literature.ResultsA total of 10 observational studies in humans were conducted, identifying 550 patients with AR and 385 healthy individuals. No statistically significant differences were observed in alpha diversity between two groups, including Shannon index (SMD = −0.3938, 95% CI [−0.9847–0.1972], I2 = 94%), Simpson index (SMD = −0.16, 95% CI [−1.12–0.80], I2 = 96%) and Chao1 index (SMD = −0.00, 95% CI [−1.32–1.32], I2 = 97%). We performed a meta-analysis for the following four phyla, but found no significant differences: Firmicutes (95% CI [−0.10–0.19], I2 = 75%), Bacteroidetes (95% CI [−0.42–0.19], I2 = 95%), Proteobacteria (95% CI [−0.06–0.03], I2 = 92%), Actinobacteria (95% CI [−0.09–0.03], I2 = 83%).ConclusionsThe currently available evidence does not suggest that patients with allergic rhinitis may have similar intestinal flora imbalances. Nevertheless, further corroboration is required with larger samples and higher-quality studies. creator: Mengyao Li creator: Qian Wang creator: Ruikun Wang creator: Jian Pu creator: Yimin Zhang creator: Siyu Ye creator: Jieqiong Liang creator: Tao Li creator: Qinglong Gu uri: https://doi.org/10.7717/peerj.19441 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: TaRTLEt: Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection link: https://peerj.com/articles/19418 last-modified: 2025-05-26 description: Structured RNAs have emerged as a major component of cellular regulatory systems, but their mechanism of action is often poorly understood. Riboswitches are structured RNAs that allosterically regulate gene expression through any of several different mechanisms. In vitro approaches to characterizing this mechanism are costly, low-throughput, and must be repeated for each individual riboswitch locus of interest. Bioinformatic methods promise higher throughput; despite robust computational identification of riboswitches, however, computational classification of the riboswitch mechanism has so far been both model-bound, relying on identification of sequence motifs known to be required for specific models of riboswitch activity, and empirically untested, with predictions far outpacing biological validation. Here, we introduce TaRTLEt (Transcriptionally-active Riboswitch Tracer Leveraging Edge deTection), a new high-throughput tool that recovers in vivo patterns of riboswitch-mediated transcription termination from paired-end RNA-seq data using edge detection methods. TaRTLEt successfully extracts transcription termination signals despite numerous sources of biological and technical noise. We tested the effectiveness of TaRTLEt on riboswitches identified from a wide range of sequenced bacterial taxa by utilizing publicly available paired-end RNA-seq readsets, finding broad agreement with previously published in vitro characterization results. In addition, we use TaRTLEt to infer the in vivo regulatory mechanism of uncharacterized riboswitch loci from existing public data. TaRTLEt is available on GitHub and can be applied to paired-end RNA-seq datasets from isolates or complex communities. creator: Sachit Kshatriya creator: Sarah C. Bagby uri: https://doi.org/10.7717/peerj.19418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kshatriya and Bagby title: Unconscious information processing of table tennis athletes in a masked priming paradigm: an event-related potentials (ERP) study link: https://peerj.com/articles/19508 last-modified: 2025-05-23 description: BackgroundUnconscious information processing is enhanced among athletes for sports-specific contexts. Whether this enhancement is transferable to general contexts is unknown. This study explored unconscious information processing and brain activity in highly trained table tennis athletes and non-athletes in general contexts.MethodsTwenty table tennis athletes (six females, mean age = 20.38 ± 1.28, mean ± standard error) and 21 aged-matched college students (eight females, mean age = 19.81 ± 1.29) were recruited for this study. Each participant first performed a masked priming task. In this task, a prime stimulus (arrows pointing left or right) was presented, followed by a visual mask (arrows pointing in both directions) and then a target stimulus, the target stimulus consisted of arrows pointing in the same direction as the prime for congruent stimuli or in the opposite direction for incongruent trials, while the P3 component of the event-related potential was simultaneously recorded in the brain. As a control, participants then performed a prime identification task (the subjective threshold test and the objective threshold test) to determine whether they could consciously detect the priming arrows. Reaction times, error rates, P3 latency and P3 peak amplitude were analyzed to examine the unconscious information processing of table tennis athletes in general contexts.ResultsParticipants responded with the direction of the target arrow and were not consciously aware of the priming stimulus. Athletes responded faster in comparison of non-athletes. Athletes and non-athletes responded faster and committed fewer errors in incongruent vs. congruent conditions. In addition, the years of table tennis training were negatively correlated with the magnitude of negative compatibility effect. Both groups displayed longer P3 latencies, a measure of inhibitory control, in the incongruent vs. congruent trials. However, athletes displayed higher P3 peak amplitudes, reflecting larger attention resource input, and longer P3 latencies than non-athletes in central brain sites.ConclusionUnconscious information processing among table tennis athletes is not prominent in general contexts, but may be limited to the sports-specific context or more complex cognitive tasks. creator: Fanying Meng creator: Lijiao Chen creator: Chun Xie creator: Jiadong Zheng creator: Ning Chen creator: Fanghui Qiu creator: Jiaxian Geng uri: https://doi.org/10.7717/peerj.19508 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Meng et al. title: Early conch morphology of a gigantic Cretaceous ammonoid, Pachydesmoceras denisonianum (Desmoceratidae) link: https://peerj.com/articles/19488 last-modified: 2025-05-23 description: Gigantic ammonoids, with conch diameters exceeding 1 m, remain one of the most enigmatic groups of extinct organisms. Their paleoecology has been the subject of ongoing debate, with some uncertainties arising from preservation biases, especially of an early conch. This study focuses on an exceptionally preserved early conch of the giant Cretaceous ammonoid Pachydesmoceras denisonianum from southern India. Conch morphology and the ontogenetic trajectories of constrictions and septal spacings were examined. The results indicate that constrictions were frequently present in the early conch; based on the shell layers observed in the cross-section, these constrictions likely resulted from periods of halted or slowed growth. The common occurrence of constrictions during early ontogeny suggests that Pachydesmoceras lifespan may have been longer than previously assumed. Additionally, the ontogenetic patterns of septal spacing might not reflect these growth halts or slowdowns in the examined species. creator: Ryoji Wani uri: https://doi.org/10.7717/peerj.19488 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wani title: Regulation of plant gene expression by tsRNAs in response to abiotic stress link: https://peerj.com/articles/19487 last-modified: 2025-05-23 description: ObjectiveTransfer RNA-derived small RNAs (tsRNAs) are emerging regulators of gene expression in response to abiotic stress. This review aims to summarize recent advances in the classification, biogenesis, and biological functions of tsRNAs, with a focus on their roles in plant stress responses and the methodologies for investigating these molecules.MethodsWe conducted a comprehensive literature search across PubMed, Web of Science, and Google Scholar using keywords such as “tRNA-derived small RNAs”, “abiotic stress”, “plant gene regulation”, and “RNA sequencing”. Studies were selected based on their relevance to tsRNA biogenesis pathways, stress-responsive mechanisms, and functional validation in plant systems. Classification of tsRNAs was performed according to cleavage site specificity and nucleotide length. Bioinformatic tools and experimental approaches for tsRNA identification, target prediction, and functional validation were evaluated.ResultstsRNAs are categorized into two main types: tRNA-derived stress-induced RNAs (tiRNAs; 29–50 nt) and tRNA-derived fragments (tRFs; 14–40 nt). tiRNAs arise from anticodon loop cleavage by RNase A/T2, while tRFs are generated via Dicer-dependent or -independent pathways. These molecules regulate gene expression at transcriptional, post-transcriptional, and translational levels by interacting with AGO proteins, displacing translation initiation factors, and modulating stress granule assembly. In plants, tsRNAs respond dynamically to abiotic stresses (e.g., drought, salinity, heat), influencing stress signaling pathways and epigenetic modifications. Advanced sequencing techniques (e.g., cP-RNA-seq, RtcB sRNA-seq) and databases (PtRFdb, tRFanalyzer) have facilitated tsRNA discovery and functional annotation.ConclusionstsRNAs represent a versatile class of regulatory molecules in plant stress biology. Their ability to fine-tune gene expression underpins adaptive responses to environmental challenges. Future research should prioritize standardized methodologies for tsRNA profiling, elucidation of stress-specific biogenesis mechanisms, and exploration of their potential as biomarkers or therapeutic targets for crop improvement. Integrating tsRNA research with systems biology approaches will deepen our understanding of plant resilience mechanisms. creator: Chunmei Li creator: Jing Zhu creator: Han Jin creator: Haotian Feng creator: Haimin Zhuang creator: Zijun Du creator: Guolin Zhu creator: Haiyang He creator: Fuyang Ye creator: Zhaohui Mo creator: Qingtao Hu creator: Zhenbang Chen creator: Kai Liu creator: Xiaorong Wan uri: https://doi.org/10.7717/peerj.19487 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Comparison of lower-leg muscle activation and establishment of muscle activation patterns during single-leg stance under various instability conditions in healthy active subjects: a cross-sectional study link: https://peerj.com/articles/19461 last-modified: 2025-05-23 description: BackgroundBalance training exercises are essential for treating and preventing a variety of ankle conditions such as sprains, chronic ankle instability, and muscular weakness. This muscle activation could often be increased using unstable devices. The Blackboard is a new configurable selective instability device, that has the potential to focus directly on desired muscles without overloading others through wooden half cylinders slats joined to a board by a tape in different positions. Depending on the position where they are situated, different stability training could be performed. However, its specific muscle activation patterns remain unknown.MethodsSurface electromyography was used to measure the activation level of six lower-leg muscles (i.e., soleus, gastrocnemius medialis, gastrocnemius lateralis, tibialis anterior, peroneus longus, and peroneus brevis) in a single-leg stance on the floor and on seven Blackboard configurations. Thirty healthy active subjects participated in the study.ResultsMultiple differences in muscle activation were observed between conditions and among muscles. Notably, the tibialis anterior and the peroneus showed the greatest differences between conditions and the highest activation levels on the Blackboard. Additionally, forefoot supination and rearfoot eversion configurations induced selective activation of the tibialis anterior and peroneus longus, respectively, highlighting their usefulness for isolating specific muscle contractions. creator: Mariana Sánchez-Barbadora creator: Vicente Alepuz-Moner creator: Noemi Moreno-Segura creator: Rodrigo Martín-San Agustín uri: https://doi.org/10.7717/peerj.19461 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sánchez-Barbadora et al. title: A scoping review of tropical pioneer trees’ roles for restoration and conservation management: Harungana madagascariensis (Hypericaceae) a widespread African species as a model link: https://peerj.com/articles/19458 last-modified: 2025-05-23 description: BackgroundGlobally, biodiversity is declining rapidly, including tropical forests ecosystems in particular. To stop and reverse this trend, governments worldwide signed up to international agreements and initiatives, but success to date has been limited. In this context, reviewing pioneer trees’ ecology, particularly the most widespread species, can help gauge their pros and cons and guide their judicious use for cost-effective ecological restoration projects.ObjectivesThis study aims to review the potential of pioneer tree species for biodiversity conservation and forest restoration and identify eventual knowledge gaps, using a widespread species from Africa, Harungana madagascariensis Lam. (Hypericaceae), as a model. Our specific objective was to synthetize information on the distribution and habitat of H. madagascariensis; its documented interspecific ecological interactions; and its potential for forest restoration.MethodologyA scoping review was conducted using multiple databases to identify relevant papers, supplemented by the Global Biodiversity Information Facility database (GBIF) to extract distribution records of H. madagascariensis. Following the PRISMA screening process for scoping reviews, 398 publications and 4,379 records from GBIF (2023) were used in the final analysis out of a total of 1,159 unique articles and 5,230 records originally retrieved.ResultsWe show that H. madagascariensis, which is native to tropical Africa, Madagascar, and some islands of the Mascarenes, is a key component of young secondary forests, wetland areas, and grasslands. At least 125 species were found to interact directly with H. madagascariensis, including through commensalism, mutualism, and herbivory. It is recognized as a tool for restoration regionally, and considered as invasive in Australia where it has been introduced and, by some, in Mauritius where it is native. The benefits it provides for restoration include its capacity to improve degraded soil fertility, its ability to compete with invasive alien species mostly due to its heliophilous and fast-growing nature, and its good nurse tree potential along with its ecological interactions that support numerous species including threatened ones.ConclusionThe widespread African pioneer tree H. madagascariensis plays a critical role in vegetation dynamic and holds great potential for fostering forest restoration and biodiversity conservation in its range of nearly 13 M km2. Its greater use in restoration projects could significantly accelerate ecological restoration, decrease its costs, and increase benefits to biodiversity, leading to larger areas being restored, contributing effectively to national and international objectives. However, a number of aspects deserve further studies, such as the species’ role in multitrophic interactions and its precise interactions, and their strengths, with species in each of its specific geographical contexts and through different temporal scales. creator: François M.M.P. Baguette creator: Cláudia Baider creator: F.B. Vincent Florens uri: https://doi.org/10.7717/peerj.19458 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Baguette et al. title: Improving the cultivated rice Sakha104 (Oryza sativa L.) using gene pools of some relative wild species link: https://peerj.com/articles/19453 last-modified: 2025-05-23 description: BackgroundRice (Oryza sativa L.) is considered a staple food for one-half of the world’s population. The yield of rice must increase to keep up with the world’s population growth. Blast disease (caused by Magnaporthe oryzae) is biotic stress that threatens rice production and can result in yield losses up to 70%.MethodsThe present research attempted to widen the genetic base of Egyptian cultivated rice Sakha 104 (Oryza sativa), using gene pools from certain relative wild ancestors, in order to cope with blast infection and grain yield. Crossing Sakha 104 × O. glaberrima and Sakha 104 × O. glumaepatula resulted in selecting 20 genotypes. The produced genotypes and the Egyptian cultivar Sakha 104 were assessed for days to heading (HD), plant height (PH), number of tillers/plant (NTP), panicle weight (PW), 1,000-grain weight (TGW), grain yield/plant (GYP), spikelet fertility (SF), blast reaction (BR), hulling percentage (HP), milling percentage (MP), head rice (HR), and amylose content (AC).ResultsLine AS-AF L3 had the earliest heading date, whereas AS-AF L6 revealed the lowest and the best values in plant height. In addition, line AS-AM L9 generated the most tillers/plant and the heaviest panicle weight. For TGW, AS-AM L3 showed the uppermost value, while AS-AM L4 recorded the highest percentage in spikelet fertility and high productivity of grain yield/plant. Furthermore, all assessed genotypes presented a unity (the value of 1) across the two seasons of evaluation in blast reaction. Grain quality criteria such as hulling, milling percentages and head rice assigned to AS-AF L10 and AS-AM L3, whereas AS-AF L2 possessed the lowest values in amylose content. Moreover, genetic variance (GV), phenotypic variance (PV), genotypic and phenotypic coefficient variations (GCV and PCV) were estimated for all traits with higher PV and PCV than GV and GCV, respectively. Heritability in broad sense (h2b%) disclosed high heritability values for heading date (0.85), plant height (0.925), grain yield/plant (0.95), 1,000 grains weight (0.92), blast reaction (0.935), head rice (0.97) and amylose content (0.90), reflecting strong genetic control of these traits. Eventually, broadening the genetic background of Sakha 104 cultivar against blast infection will minimize its impact and enhance the food security in Egypt. creator: Walid H. Elgamal creator: Mostafa M. Elshenawy creator: Samah M. Abdelkhalek creator: Dayun Tao creator: Jiawu Zhou creator: Jing Li creator: Medhat Rehan uri: https://doi.org/10.7717/peerj.19453 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Elgamal et al. title: Phylogeographic analysis of long-legged bats, Macrophyllum macrophyllum, with notes on roosting behavior and natural history link: https://peerj.com/articles/19432 last-modified: 2025-05-23 description: The long-legged bat (Macrophyllum macrophyllum) is widely distributed in the continental Neotropics, but poorly known because it is not commonly caught in mist nets. Available data suggest that this species is closely associated with water where it forages for insect prey. We compiled the first comprehensive molecular dataset assembled for the species, spanning its entire distributional range to investigate if the phylogeography of this monotypic genus is associated with the hydrographic drainage, ecosystem regions, or genetic clustering in Central and South America. To survey under sampled areas, fieldwork was conducted in the Brazilian Pantanal and Cerrado targeting the search for riverine roost sites of Macrophyllum. A literature review was also done to summarize roosting information for the species. New sequences of the mitochondrial cytochrome b gene were generated for tissue samples from Brazil and in museum collections. Phylogenetic trees were constructed using both maximum likelihood and Bayesian inference methods and a haplotype network was used to analyze population structure. Our phylogenetic results identified five geographic lineages of Macrophyllum from (1) the western Cerrado, (2) eastern Cerrado and Pantanal, (3) Guianas, (4) Amazonia, and (5) Central America. However, the haplotype network in conjunction with the genetic clustering identified four populations with the eastern Cerrado and Pantanal grouping with the Guianas and the eastern part of Amazonia. The fieldwork in the Cerrado and Pantanal along with the literature review identified that about half of the roost sites for the long-legged bats were drainage culverts. There is geographic structuring in the mitochondrial data of Macrophyllum with Central America, western Cerrado, Pantanal, Guianas, and eastern Ecuador reciprocally monophyletic and well differentiated populations. However, the under sampled eastern Amazonia is poorly resolved in relation to the other areas. The long-legged bats seem to be relatively adaptable to certain levels of human disturbance and landscape development with man-made drainage culverts commonly used as roosting sites. Increased biodiversity surveys of bats in central Brazil are needed to fill in distributional gaps, such as the lower Amazon River basin, to resolve phylogeographic patterns of Macrophyllum in South America and better understand the potential of cryptic species in this monotypic genus. creator: Guilherme S.T. Garbino creator: Thiago Borges Fernandes Semedo creator: Juliane Saldanha creator: Daniela Cristina Ferreira creator: Rogerio Vieira Rossi creator: Maria Nazareth Ferreira da Silva creator: Burton K. Lim uri: https://doi.org/10.7717/peerj.19432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Garbino et al. title: Effect of hypoxia conditioning on physical fitness in middle-aged and older adults—a systematic review and meta-analysis link: https://peerj.com/articles/19348 last-modified: 2025-05-23 description: BackgroundHypoxic conditioning has emerged as a promising intervention for enhancing physiological adaptations. This systematic review and meta-analysis of randomized controlled trials aims to investigate the efficacy of hypoxic conditioning on physical fitness measures in aging populations.MethodsThe Embase, PubMed, Cochrane Library, and Web of Science were searched from inception to November 2024 (Prospero registration: CRD42023474570). The Cochrane Evaluation Tool and Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework were used for risk of bias assessment and evidence certainty evaluation. Mean differences (MD) and standardized mean differences (SMD) and 95% confidence intervals (CI) were calculated using the Review Manager software. Subgroup analysis was performed to explore possible associations between the study characteristics and the effectiveness of the intervention.ResultsA total of 13 randomized controlled trials (RCTs) with 368 subjects were included in the meta-analysis. High certainty evidence found hypoxic conditioning (HC) significantly improved peak oxygen uptake (VO2peak) (SMD = 0.31, 95% CI [0.01–0.61]; P < 0.05), while very low to moderate certainty evidence shown that hypoxic conditioning (HC) have not induced greater changes on functional outcomes (SMD = −0.21, 95% CI [−0.66–0.24]; P > 0.05), muscle strength (SMD = −0.19, 95% CI [−0.63–0.26]; P > 0.05), maximal power output (SMD = 0.29, 95% CI [−0.17–0.76]; P > 0.05), VO2max (SMD = −0.39, 95% CI [−1.12–1.90]; P > 0.05), and exercise workload (MD = −10.07, 95% CI [−34.95–14.80]; P > 0.05).ConclusionThis study suggests that hypoxia conditioning has a greater effect on enhancing VO2peak compared to equivalent normoxic training in the middle-aged and older population. More high-quality RCTs are needed in the future to explore the optimal oxygen concentration and exercise intensity during hypoxia conditioning. creator: Fanji Qiu creator: Jinfeng Li creator: Liaoyan Gan uri: https://doi.org/10.7717/peerj.19348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Qiu et al. title: Effects of a combined nature-based and audio-based virtual mindfulness intervention on stress and wellbeing of COVID-19 healthcare workers: a randomized controlled trial link: https://peerj.com/articles/19109 last-modified: 2025-05-23 description: BackgroundThe global COVID-19 pandemic and its subsequent transition to an endemic phase has highly increased psychosocial distress among healthcare workers. This chronic stress may culminate into burnout, which has been associated with impaired patient care and increased medical errors. Exposure to nature-based programs have been shown to reduce levels of perceived stress and promote well-being. However, benefits derived from nature programs can be short-lived. Mindfulness-based interventions represent a promising additive option to enhance benefit. The present study proposes to combine a nature-based program with an audio-based mindfulness intervention to address stress and promote psychosocial-spiritual wellbeing in COVID-19 healthcare workers.MethodsBetween June 2021 and October 2023, 78 healthcare workers were randomized into a Nature only group (Nature), a Combined Nature-Mindfulness group (Combined), and a control group (Control), with 19, 16, and 18 subjects completing the study, respectively (23–46 years, mean = 35, SD = 6). The nature program was a three or five-day retreat during which participants engaged in rock climbing, surfing or kayaking. The virtual audio mindfulness intervention was a 10-day program offered online and included mindful breathing, body scan, and loving-kindness meditation. Participants completed self-administered assessments at three or four time points during the study, including at baseline and following study procedures. Assessments included a measure of stress, the Perceived Stress Scale, and a measure of wellbeing, the National Institute of Health Healing Experience of All Life Stressors (NIH-HEALS).ResultsThe mean baseline Perceived Stress Scale score was 21.2 ± 3.2 in the Combined group, 22.3 ± 2.8 in the Nature group, and 23.2 ± 3.3 in the Control group. Perceived Stress Scale levels did not change following nature-based and mindfulness-based interventions. The mean baseline NIH-HEALS score was 123.1 ± 19.4 in the Combined group, 118.1 ± 17.1 in the Nature group, and 114.3 ± 17.8 in the Control groups. NIH-HEALS scores increased in both the Nature and Combined groups when compared to the Control group. At follow-up, the Combined group maintained improvements in wellbeing when compared to the Nature group.ConclusionsFindings suggest that nature-based programs can be used to improve overall wellbeing among COVID-19 healthcare workers. Additionally, integrating audio-based mindfulness practices to these programs may enhance their benefits. Notably however, these interventions may not effectively reduce perceived stress among COVID-19 healthcare workers. Due to diminished power of the present study, further research is needed to validate and refine the present findings. creator: Polycarpe Bagereka creator: Rezvan Ameli creator: Ninet Sinaii creator: Marcelli Cristine Vocci creator: Angelina Mangiardi Coulter creator: Michael Neustedter creator: Ann Berger uri: https://doi.org/10.7717/peerj.19109 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2025 Bagereka et al. title: The role of 18F-FDG PET/CT in patients with serous cavity effusion of undetermined origin: a retrospective clinical study link: https://peerj.com/articles/19495 last-modified: 2025-05-22 description: AimThe diagnostic performance of positron emission tomography with fluoro-18 fluorodeoxyglucose integrated with computed tomography (18F-FDG PET/CT) in identifying the primary cause of unknown serous effusion and malignant tumors with serous metastasis was evaluated in our study.MethodsA retrospective analysis was conducted on 134 patients with unexplained serous cavity effusion, including pericardial effusion, pleural effusion, and ascites, who underwent 18F-FDG PET/CT scans. The cohort comprised 94 cases of malignant disease and 40 cases of benign disease. Visual analysis of all 18F-FDG PET/CT images and semi-quantitative analysis by measuring maximum standardized uptake value (SUVmax) in the region of interest were performed. The diagnostic capabilities of SUVmax, Ca125, Ca199, and serum carcinoembryonic antigen were compared by plotting the areas under the receiver operating characteristic curve.ResultsThe primary disease of serous cavity effusion was diagnosed with a sensitivity of 90.1%, specificity of 78.8%, and accuracy of 85.7% using 18F-FDG PET/CT. The SUVmax of primary malignant lesions was found to be significantly higher than that of benign lesions, with values of 12.83 ± 6.64 and 4.48 ± 3.16 (P < 0.001), respectively. The detection of serous cavity metastasis by PET/CT showed a sensitivity of 84.3%, specificity of 94.0%, and accuracy of 88.3%. In receiver operating characteristic (ROC) analysis, the area under the curve of SUVmax was the largest (P < 0.01), significantly surpassing that of serum Ca125, Ca199, and CEA.Conclusion18F-FDG PET/CT was determined to be an effective imaging modality for detecting undetermined serous cavity effusion, exhibiting high diagnostic performance in the differentiation of primary disease from benign to malignant and the evaluation of serous cavity metastasis. creator: Xianwen Hu creator: Ya Li creator: Jiong Cai creator: Pan Wang uri: https://doi.org/10.7717/peerj.19495 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hu et al. title: Hydrogen sulfide protects against cisplatin-induced experimental nephrotoxicity in animal models: a systematic review and meta-analysis link: https://peerj.com/articles/19481 last-modified: 2025-05-22 description: BackgroundCisplatin-induced acute kidney injury (cis-AKI) is not rare in oncological patients clinically, but there are limited prevention and treatment methods available. The efficacy of hydrogen sulfide (H2S) in mitigating cis-AKI has been studied and determined in animal models.MethodsAccording to the pre-registered program (PROSPERO: CRD 42023463779), we searched PubMed/Medline, Embase, and Web of Science databases using the keywords: hydrogen sulfide, cisplatin, acute kidney injury, and alternatives. A total of 13 articles met the inclusion criteria were included. Standardized mean difference (SMD) and 95% confidence interval (CI) were calculated and aggregated using random effects meta-analysis.ResultsThe results showed that H2S treatment significantly improved renal function (serum creatinine SMD = −2.96, 95% CI [−3.72 to −2.19], p < 0.00001; blood urea nitrogen SMD = −2.73, 95% CI [−3.68 to −1.78], p < 0.00001), decreased oxidative stress (superoxide dismutase SMD = 2.90, 95% CI [1.36–4.43], p = 0.0002) and inflammation levels (interleukin-1β SMD = −4.41, 95% CI [−5.84 to −2.97], p < 0.00001). However, there was a high degree of heterogeneity between studies (I2 > 70%). Further subgroup analysis did not show a clear source of the heterogeneity, but various H2S donors exhibited positive renal protection in those studies.ConclusionsH2S could be a new approach for treating cis-AKI, while the differential efficacies among natural and slow-release H2S donors remain to be compared and evaluated further. This meta-analysis may shed light on establishing preclinical and clinical investigation guidelines for treating human cis-AKI with H2S donors. creator: Zhenyuan Han creator: Tianyu Deng creator: Dechao Yan creator: Yutao Jia creator: Jing Tang creator: Xiaoyan Wang uri: https://doi.org/10.7717/peerj.19481 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Han et al. title: Repeatability and reproducibility of Keratograph 5M corneal topography link: https://peerj.com/articles/19478 last-modified: 2025-05-22 description: BackgroundCorneal topography is an important diagnostic tool and highly repeatable and reproducible topographic devices are essential in eye care practice. Placido disc-based topography is one of the most widely used methods because of its high resolution and accuracy. The aim of this study was to analyse the intrasession repeatability and intersession reproducibility of measurements obtained with a Keratograph 5M in a sample of healthy subjects.MethodsThree consecutive measurements were performed with a Keratograph 5M during two sessions in 24 healthy subjects to calculate the within-subject standard deviation (Sw), repeatability and reproducibility limits, coefficient of variation (CoV), and intraclass correlation coefficient (ICC) of corneal curvature (K1, K2 and Max-K), eccentricity, corneal diameter, and corneal aberration (6-mm pupil; coma, trefoil, spherical aberration, secondary astigmatism and quadrafoil).ResultsNo statistically significant differences were found between the three measurements in either session (P ≥ 0.06). The corneal parameters that demonstrated the best repeatability were corneal curvature and corneal diameter with a CoV, and the ICCs ranged from 0.41% and 0.990 (corneal diameter) to 0.28% and 0.998 (K2). Eccentricity and corneal aberrations had lower repeatability results, with CoVs and ICCs ranging from 3.88% and 0.992 (spherical aberration) to 40.21% and 0.643 (quadrafoil), respectively. In the case of reproducibility, excellent results were obtained for corneal curvature and diameter measurements (CoV ≤ 0.36% and ICC ≥ 0.987), with moderate reproducibility for corneal eccentricity (CoV ≥ 2.03% and ICC ≤ 0.986), secondary astigmatism (CoV = 20.05% and ICC = 0.787), and quadrafoil (CoV = 23.55% and ICC = 0.696).ConclusionsThe Keratograph 5M demonstrated excellent repeatability and reproducibility in measuring corneal curvature and corneal diameter in healthy subjects. Corneal eccentricity shows moderate accuracy, whereas corneal aberrations (except coma, trefoil, and spherical aberrations) exhibit moderate measurement reliability and should be interpreted with caution in clinical practice. creator: Sara Ortiz-Toquero creator: Irene Sanchez creator: Raul Martin uri: https://doi.org/10.7717/peerj.19478 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ortiz-Toquero et al. title: Association of red blood cell distribution width-platelet ratio with mortality after coronary artery bypass grafting link: https://peerj.com/articles/19472 last-modified: 2025-05-22 description: BackgroundThis study aims to explore the association between red blood cell distribution width-platelet ratio (RPR) and mortality in patients after coronary artery bypass grafting (CABG).MethodsData on patients who underwent CABG from January 1, 2021, to July 31, 2022, were retrospectively collected. The locally weighted scatter plot smoothing (Lowess) method was utilized to display the crude association between RPR and in-hospital mortality. The areas under the receiver operating characteristic curves (AUC) were used to assess the discrimination. The cut-off value (0.107) of RPR was calculated using the Youden index method. The primary outcome was in-hospital mortality.ResultsIn total, 1,258 patients were included. The Lowess curve showed an approximate positive linear relationship between RPR and in-hospital mortality. In the multivariable logistic regression model, RPR was an independent risk factor (OR 1.493, 95% CI [1.119–1.992] per standard deviation (SD) increase, p = 0.006) for in-hospital mortality after CABG. RPR (AUC 0.716, 95% CI [0.617–0.814]) demonstrated greater discrimination than RDW (AUC 0.578, 95% CI [0.477–0.680], p = 0.002). The cut-off value (0.107) of RPR was calculated for further analysis, and groups were further divided into the high RPR group (≥ 0.107) and the low RPR group (< 0.107). In the multivariable logistic regression model, high RPR (≥ 0.107) correlated with elevated risks of in-hospital mortality (OR 6.097, 95% CI [2.308–16.104], p < 0.001) and one-year mortality (OR 6.395, 95% CI [2.610–15.666], p < 0.001) after adjusting for all included covariates. Subgroup analyses revealed that high RPR consistently had increased risks of in-hospital mortality and one-year mortality. Besides, patients with low RPR show better one-year survival than those with high RPR.ConclusionPreoperative high RPR could serve as an independent risk predictor for in-hospital mortality and one-year mortality, which can be utilized to assess the prognosis of patients and further provide guidance for the treatment in patients following CABG. creator: Bufan Zhang creator: Yize Liu creator: Jiyang Zuo creator: Tianxu Song creator: Naishi Wu uri: https://doi.org/10.7717/peerj.19472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Genomic profiling of Streptococcus agalactiae (Group B Streptococcus) isolates from pregnant women in northeastern Mexico: clonal complexes, virulence factors, and antibiotic resistance link: https://peerj.com/articles/19454 last-modified: 2025-05-22 description: BackgroundStreptococcus agalactiae (Group B Streptococcus, GBS) is an important pathogen associated with neonatal sepsis, pneumonia, and meningitis, which can be transmitted from colonized pregnant women to their newborns. This study aimed to determine the prevalence and characterize the genomic features of S. agalactiae isolates from pregnant women attending a referral hospital in Northeastern Mexico.MethodsVaginal-rectal swabs were collected from pregnant women during routine prenatal care between April 2017 and March 2020. Whole-genome sequencing was conducted to determine sequence type (ST), clonal complex (CC), capsular polysaccharide (Cps) genotype, virulence factors, and antibiotic resistance genes through comparative genome analysis.ResultsS. agalactiae colonization was detected in 51 (2.7%) of 1,924 pregnant women. The most common STs were ST8 (23.5%) and ST88 (15.7%). Cps genotyping showed high concordance between serological and molecular methods. Genes conferring resistance to tetracyclines (tetM, 60.1%) and macrolides (mreA, 100%) were identified. Key virulence factor genes, including cylE, bca, and scpB, were present in over 90% of the isolates.ConclusionAlthough GBS colonization prevalence was low, genomic analysis revealed the genetic diversity of S. agalactiae in Northeastern Mexico, emphasizing the importance of molecular techniques for epidemiological surveillance and infection control. creator: Jose Manuel Vazquez-Guillen creator: Gerardo C. Palacios-Saucedo creator: Lydia Guadalupe Rivera-Morales creator: Amilcar Caballero-Trejo creator: Aldo Sebastian Flores-Flores creator: Juan Manuel Quiroga-Garza creator: Rocio Alejandra Chavez-Santoscoy creator: Jesus Hernandez-Perez creator: Silvia Alejandra Hinojosa-Alvarez creator: Julio Antonio Hernandez-Gonzalez creator: Maurilia Rojas-Contreras creator: Ricardo Vazquez-Juarez creator: Ramon Valladares-Trujillo creator: Cesar Alejandro Alonso-Tellez creator: Joaquin Dario Treviño-Baez creator: Miguel Angel Rivera-Alvarado creator: Reyes S. Tamez-Guerra creator: Cristina Rodriguez-Padilla uri: https://doi.org/10.7717/peerj.19454 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Vazquez-Guillen et al. title: Human-elephant conflicts and attitude of the local communities toward African elephant (Loxodonta africana) conservation in Kafta Sheraro National Park, Tigray region, Ethiopia link: https://peerj.com/articles/19428 last-modified: 2025-05-22 description: Human-wildlife conflict (HWC), particularly elephant crop raiding, has been increasing over the past decade in Kafta Sheraro National Park (KSNP). The objectives of this study were to assess the degree of KSNP natural resources utilization by the local community, the existing human-elephant conflict (HEC), trends of the conflict, methods used to minimize their negative impacts, and community attitudes and socio-demographic influencing factors regarding the conservation of African elephant in rather than and KSNP. The survey was carried out from November 2018 to September 2020. A total of 395 household heads were selected systematically from seven kebeles (the lowest governmental administrative units of Ethiopia). Direct field observations, household-based questionnaire surveys, focus group discussions, and key informant interviews (i.e., administrators, professional experts, and park management staffs) were applied. The majority (74.51%) of the local communities utilized the park resources as grazing for livestock followed by fuel wood sources (46.04%), water sources (39.57%), and house construction materials (30.38%). More than 72% of the respondents suggested that crop raiding by elephants is a serious problem in the study area and increased in the past ten years. About 60.9% and 60.51% of the respondents mentioned that elephant-induced crop damage was during the wet season and at night, respectively. Crop damage was relatively high as cropland found inside and at the periphery of the park. Majorities of the respondents recommended that gun sounds/banging noisy materials (81.99%) and lighting fire/flashlight (44.95%) were the most common traditional protection methods from elephant crop damage. More than 56% of the respondents had positive attitudes toward the conservation of KSNP and elephant. About 54.18% of respondents were aware of park conservation and their awareness varied with age, education level, gender, settlement condition, and distance between settlement and park. The probability that males tended to respond to awareness was 3.5 times higher than that of female respondents. Males were more likely to have awareness about the aims of KSNP conservation and related issues. Factors influencing the attitude of the local community toward KSNP and elephant conservation in the area were age, education level, the distance between settlement and park, and their awareness status. Trends and levels of crop damage by elephants negatively influenced communities’ attitudes toward elephant conservation. Significant variation (P < 0.05) of respondents was observed on HEC, trends of crop damage, mitigation measures, awareness, and their attitudes toward protected area (PA) and elephant conservation. Therefore, the smooth coexistence of KSNP and wildlife/elephants with the local communities could be maintained by establishing buffer zones in the area to ensure conservation sustainability and community livelihoods. creator: Fitsum Temesgen creator: Bikila warkineh uri: https://doi.org/10.7717/peerj.19428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Temesgen and Warkineh title: Sialyltransferase-related genes as predictive factors for therapeutic response and prognosis in cervical cancer link: https://peerj.com/articles/19422 last-modified: 2025-05-22 description: BackgroundCancer-associated hypersialylation is believed to be related to the metastatic cell phenotype and the suppression of sialyltransferases (SiaTs) has been suggested to be a potent preventive strategy against metastasis. The present research discovered SiaTs-related genes for cervical cancer (CC).MethodsThe Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were applied to obtain the relevant samples. Mutation dataset were processed using mutect2 software. The gene modules were obtained via weighted gene co-expression network analysis (WGCNA), and the enrichment analysis on the genes within the modules was implemented. Cox regression analysis and “glmnet” R package were applied to establish the relevant risk model. “MCPcounter” R package, ESTIMATE algorithm and TIMER online tools were used to depict the tumor immune microenvironment in CC. The mutation landscape was additionally plotted, and the response to immunotherapy in different cohorts were compared. Further reverse-transcription quantitative PCR and Transwell assays were performed to verify the expression and potential function of the screened key genes.ResultsMutation of 14 SiaTs was seen in CC. Subsequently, WGCNA-based identification of SiaTs-related gene modules was significantly enriched in metabolism-related pathways. The established RiskScore model manifested excellent prognostic classification efficiency. A poorer prognosis and occurrence of both immune evasion and reduced immunoreactivity may be seen in high-risk patients yet relatively higher immune cell scores were noticeable in low-risk patients. Angiogenesis and MYC target V2 may be the differentially activated pathways in high-risk patients, while those in low-risk patients were KRAS Signaling DN and Interferon alpha response. In addition, most immune checkpoint-correlated genes were identified to express higher in low-risk patients, while higher sensitivities to chemotherapy drugs was discovered in high-risk patients. Cellular assays have revealed that KCNK15, LIF, TCN2, SERPINF2, and CXCL3 were highly expressed yet PIH1D2, DTX1 and GCNT2 were low-expressed in Hela cells and that silencing CXCL3 diminished the number of migrated and invaded Hela cells.ConclusionIn this study, we systematically constructed and validated a risk scoring model based on SiaTs-related genes, which can effectively predict the prognosis and potential response to immunotherapy and chemotherapy in CC patients. This provides a new molecular basis and clinical reference for achieving individualized treatment. creator: Jia Shao creator: Can Zhang creator: Yaonan Tang creator: Aiqin He creator: Xiangyan Cheng uri: https://doi.org/10.7717/peerj.19422 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Shao et al. title: Remote sensing-based detection of brown spot needle blight: a comprehensive review, and future directions link: https://peerj.com/articles/19407 last-modified: 2025-05-22 description: Pine forests are increasingly threatened by needle diseases, including Brown Spot Needle Blight (BSNB), caused by Lecanosticta acicola. BSNB leads to needle loss, reduced growth, significant tree mortality, and disruptions in global timber production. Due to its severity, L. acicola is designated as a quarantine pathogen in several countries, requiring effective early detection and control of its spread. Remote sensing (RS) technologies provide scalable and efficient solutions for broad-scale disease surveillance. This study systematically reviews RS-based methods for detecting BSNB symptoms, assessing current research trends and potential applications. A comprehensive bibliometric analysis using the Web of Science database indicated that direct RS applications for BSNB remain scarce. However, studies on other needle diseases demonstrated the effectiveness of multisource RS techniques for symptom detection, spatial mapping, and severity assessment. Advancements in machine learning (ML) and deep learning (DL) have further improved RS capabilities for automated disease classification and predictive modeling in forest health monitoring. Climate-driven factors, such as temperature and precipitation, regulate the distribution and severity of emerging pathogens. Geospatial analyses and species distribution modeling (SDM) have been successfully applied to predict BSNB pathogen’s range expansion under changing climatic conditions. Integrating these models with RS-based monitoring enhances early detection and risk assessment. However, despite these advancements, direct RS applications for BSNB detection remain limited. This review identifies key knowledge gaps and highlights the need for further research to optimize RS-based methodologies, refine predictive models, and develop early warning systems for improved forest management. creator: Swati Singh creator: Lana L. Narine creator: Janna R. Willoughby creator: Lori G. Eckhardt uri: https://doi.org/10.7717/peerj.19407 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Singh et al. title: Description of a novel Ligia species from Nihoa, a remote island in the Papahānaumokuākea Marine National Monument link: https://peerj.com/articles/19373 last-modified: 2025-05-22 description: Isopods in the genus Ligia have been shown to harbor deeply divergent genetic lineages that have, in some instances, been recognized as cryptic species. For instance, the use of molecular taxonomic approaches to characterize coastal Ligia from the Hawaiian Islands led to the redescription of Ligia hawaiensis, the sole endemic coastal species previously recognized in the region, and to the description of seven new species endemic to the region. These species appear to be highly restricted to rift zones within single islands, single islands, or previously connected islands, suggesting these species evolved in allopatry. These findings, coupled with the poor dispersal capabilities exhibited by Ligia isopods and the geology of the Hawaiian Islands, suggest that additional cryptic species may exist in highly isolated populations yet to be studied. Studies to date have characterized Ligia from throughout the younger Hawaiian Islands (e.g., Kaua‘ i, O‘ ahu, Moloka‘ i, Maui, Lanai, and Hawai‘ i); however, no endemic Ligia populations from the older islands and more remote islands that form part of the Papahānaumokuākea Marine National Monument (PMNM) have been studied. This region represents the largest marine conservation area in the USA, and includes at least three islands where L. hawaiensis have been previously reported from. Herein, we apply molecular taxonomic approaches to characterize Ligia specimens from Nihoa, a remote island in the PMNM. Results show that Ligia from Nihoa form a highly divergent that is reciprocally monophyletic lineage with other Hawaiian Ligia species. This lineage, described as Ligia barack sp. nov., adds to the known biodiversity of the PMNM and highlights the importance of continued exploration and conservation of this remote and highly biodiverse region. creator: Carlos A. Santamaria creator: Annabelle Bork creator: Alexandra J. Larson creator: Daniel J. Link uri: https://doi.org/10.7717/peerj.19373 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2025 Santamaria et al. title: Optimizing stretch-shortening cycle performance: effects of drop height and landing strategy on lower-limb biomechanics in drop jumps link: https://peerj.com/articles/19490 last-modified: 2025-05-21 description: BackgroundThe stretch-shortening cycle (SSC) enhances performance in jumping, sprinting, and changes of direction. Drop heights and landing strategies affect its efficiency. This study investigates the effects of varying drop heights and landing strategies (hip- vs. knee-dominant) on lower-limb stretch-shortening cycle performance during drop jumps (DJs), which involve a drop followed by an immediate vertical jump.MethodsA three-dimensional (3D) motion capture system and force plate collected biomechanical data from 18 college athletes performing DJs with hip- and knee-dominant strategies at 30, 45, and 60 cm heights. A two-factor repeated measures analysis of variance (ANOVA) compared peak impact force, reactive strength index (RSI), leg stiffness (Kleg), joint stiffness (Kjoint), joint angular displacement, change in joint moment, and joint work (positive, negative, net) across heights and strategies.ResultsDrop height significantly affected biomechanical variables (p < 0.05). Peak impact force and negative joint work increased from 30 cm to 60 cm, with the highest values at 60 cm. RSI, Kleg, Kjoint, and net joint work peaked at 30 cm. Landing strategy significantly influenced outcomes (p < 0.05). The knee-dominant strategy had higher peak impact force, RSI, Kleg, knee angular displacement, change in knee moment, and ankle work, but lower net knee work, compared to the hip-dominant strategy, which showed higher hip angular displacement and hip work. A significant interaction was observed between drop height and landing strategy (p < 0.05). The knee-dominant strategy had greater RSI, Kleg, and positive ankle work at 30 cm, while the hip-dominant strategy had greater negative ankle work at 60 cm.ConclusionIn DJs, SSC performance was optimised at a 30 cm drop height, with peak efficiency observed in the knee-dominant strategy. At 45 and 60 cm, SSC efficiency declined and knee energy dissipation increased, while the hip-dominant strategy may provide greater joint protection by increasing energy dissipation at the ankle. These findings suggest the knee-dominant strategy is best suited to 30 cm, whereas the hip-dominant strategy may enhance safety at higher drop heights. creator: Qin Zhang creator: Fei Li creator: Danielle Anne Trowell creator: Muzu Hou creator: Zhenghe Qiu creator: Shiqin Chen creator: Haifeng Ma uri: https://doi.org/10.7717/peerj.19490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Short-term safety and efficacy of aspirin in patients with COVID-19: a systematic review and meta-analysis of randomized controlled trials link: https://peerj.com/articles/19466 last-modified: 2025-05-21 description: ObjectiveCoagulation activation and inflammatory derangements are key characteristics of coronavirus disease 2019 (COVID-19). Aspirin therapy in patients with COVID-19 remains uncertain due to conflicting evidence regarding its ability to balance anti-inflammatory and antithrombotic benefits against potential bleeding risks in the context of COVID-19-associated coagulopathy. This study aimed to compare the clinical safety and efficacy of aspirin in patients with COVID-19 in randomized controlled trials (RCTs).MethodsIn the present systematic review and meta-analysis, the Medline, Embase, and Cochrane Library databases were searched for RCTs from database inception to January 13, 2023. Data were independently extracted and screened by two authors using structured data collection forms based on published reports. Results were calculated using odds ratios (ORs) and 95% confidence intervals (CIs) with the Mantel-Haenszel method. Quality was assessed using the Cochrane Risk of Bias tool. The main outcomes were short-term all-cause mortality, bleeding events and any thrombosis events. This meta-analysis was registered on PROSPERO.ResultsA total of 922 studies were identified. Finally, six RCTs with low risk of bias were pooled in the analysis. The results showed that aspirin use was not associated with a reduction in all-cause mortality (OR = 0.95, 95% CI [0.88–1.03], I2 = 0%) or the risk of any thrombosis (RR 0.88, 95% CI [0.77–1.01], I2 = 0%), but aspirin use was associated with a higher risk of bleeding (OR 1.72, 95% CI [1.32–2.24], I2 = 0%). No obvious risk of bias was found among the included RCTs for the primary outcome.ConclusionRoutine low-dose aspirin use does not reduce the risk of short-term mortality and risk of any thrombosis but increases the risk of bleeding. The data does not support the use of low-dose aspirin in patients with COVID-19. creator: Liwen Xue creator: Yuhan Qi creator: Yingying Zou uri: https://doi.org/10.7717/peerj.19466 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xue et al. title: Prognostic significance of C-reactive protein (CRP) and albumin-based biomarker in patients with breast cancer receiving chemotherapy link: https://peerj.com/articles/19319 last-modified: 2025-05-21 description: BackgroundBreast cancer patients with similar clinicopathologic characteristics may experience varied outcomes. This urges an increased effort to investigate other prognostic factors. C-reactive protein (CRP)-to-albumin ratio (CAR) is an inflammatory and nutritional biomarker that has been well studied and reported to have an impact on the survival of patients with diverse types of cancer, but limitedly in breast cancer. Therefore, this study aimed to investigate the prognostic significance of CAR in local patients with breast cancer.MethodsThis study included 202 stage I–IV breast cancer patients receiving first-line chemotherapy. We calculated inflammatory and nutritional biomarkers including CAR, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), lymphocyte-to-monocyte ratio (LMR), systemic immune-inflammation index (SII), systemic inflammation response index (SIRI), pan-immune-inflammation value (PIV), and prognostic nutrition index (PNI) before treatment. The Kaplan-Meier with log-rank test and Cox proportional hazard regression were used to analyze the prognostic role of clinicopathologic factors and biomarkers on disease-free survival (DFS), progression-free survival (PFS), and overall survival (OS).ResultsThe median follow-up period was 46 months (1–77 months). The 3-year DFS and 3-year OS in patients with high CAR (CAR > 1.5) were significantly lower than those with low CAR (CAR ≤ 1.5) (47.0% vs 68.9%, P = 0.022 and 59.5% vs 78.6%, P = 0.009, respectively). Multivariate analysis showed high CAR as prognostic factors for poor DFS (HR 2.10, 95% confidence interval/CI [1.10–3.99], P = 0.023) and OS (HR 2.16, 95% CI [1.27–3.68], P = 0.005), but not for PFS (HR 1.43, 95% CI [0.73–2.80], P = 0.293). In addition, more advanced stage and HER2 positive were correlated with unfavorable DFS and OS, older age predicted poor DFS, and stage was the only prognostic factor of PFS (all P values < 0.05).ConclusionBesides age, stage, and molecular subtypes that have been widely observed to have impact on the survival of breast cancer patients, CAR was demonstrated as a promising prognostic marker in our local patients. A high CAR at diagnosis was associated with unfavorable DFS and OS, which can aid in identifying patients at risk and guide personalized treatment planning. creator: Susanna Hilda Hutajulu creator: Yufi Kartika Astari creator: Meita Ucche creator: Nyoman Kertia creator: Yanri Wijayanti Subronto creator: Dewi Kartikawati Paramita creator: Lina Choridah creator: Ericko Ekaputra creator: Irianiwati Widodo creator: Suwardjo Suwardjo creator: Mardiah Suci Hardianti creator: Kartika Widayati Taroeno-Hariadi creator: Ibnu Purwanto creator: Johan Kurnianda uri: https://doi.org/10.7717/peerj.19319 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hutajulu et al. title: Selected Alu methylation levels in the gastric carcinogenesis cascade link: https://peerj.com/articles/19485 last-modified: 2025-05-20 description: BackgroundGenome-wide hypomethylation, a common epigenetic change that occurs during cancer development, primarily affects repetitive elements, such as Alu repeats. Consequently, Alu repeats can be used as a surrogate marker of genomic hypomethylation.MethodsIn this study, we aimed to investigate the correlation between Alu methylation levels and the multistage course of gastric carcinogenesis.ResultsWe found that the Alu methylation levels in gastric cancer tissue decreased compared with those in normal gastric tissue, with the change in methylation levels and pattern being most significant between chronic gastritis and intestinal metaplasia. Moreover, Alu methylation levels were not associated with Helicobacter pylori or Epstein–Barr virus infection.ConclusionsFinally, our sensitivity and specificity analyses suggested that Alu methylation level can be used to distinguish gastric cancer tissue from normal tissue. Thus, Alu methylation level shows promise as biomarker for gastric cancer diagnosis. creator: Jiraroch Meevassana creator: Chawisa Wanda Vongsuly creator: Tanchanok Nakbua creator: Supitcha Kamolratanakul creator: Pichaya Thitiwanichpiwong creator: Fardeela Bin-Alee creator: Somboon Keelawat creator: Nakarin Kitkumthorn uri: https://doi.org/10.7717/peerj.19485 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Meevassana et al. title: Exploring the effect of the triglyceride-glucose index on bone metabolism in prepubertal children, a retrospective study: insights from traditional methods and machine-learning-based bone remodeling prediction link: https://peerj.com/articles/19483 last-modified: 2025-05-20 description: BackgroundChildhood obesity poses a significant risk to bone health, but the impact of insulin resistance (IR) on bone metabolism in prepubertal children, as assessed by the triglyceride-glucose (TyG) index, remains underexplored. Bone turnover markers (BTMs) provide a non-invasive method for evaluating bone remodeling, but their relationship to obesity-related metabolic changes requires further study.MethodsIn this retrospective study of 332 prepubertal children (163 boys and 169 girls), we used multivariate linear regression and five machine learning (ML) algorithms to explore the association between the TyG index and BTMs, including β-C-terminal telopeptide of type 1 collagen (β-CTx), total procollagen type 1 N-terminal propeptide (T-P1NP), and N-terminal mid-fragment of osteocalcin (N-MID). The categorical boosting (CatBoost) models selected based on optimal performance metrics were interpreted using SHapley Additive exPlanation (SHAP) analysis to identify key features affecting prediction.ResultsThe TyG index was negatively correlated with β-CTx, T-P1NP, and N-MID levels (P < 0.05), with a dose-response effect. The CatBoost model showed higher predictive accuracy and robustness, with the area under the receiver operating characteristic curve (AUROC) values of 0.782 (95% CI [0.68–0.885]), 0.789 (95% CI [0.691–0.874]), and 0.727 (95% CI [0.619–0.827]) for β-CTx, T-P1NP, and N-MID predictions, respectively. The SHAP analysis highlighted body mass index (BMI) and HbA1c as the key predictors.ConclusionsThe TyG index is a reliable predictor of bone metabolic disorders in prepubertal obese children, and the interpretable CatBoost model provides a cost-effective tool for early intervention. This study has important implications for prevention strategies for disorders of bone metabolism in prepubertal obese children to reduce the risk of skeletal fragility in adulthood or old age. creator: Shunshun Cao creator: Aolei Chen creator: Botian Song creator: Yangyang Hu uri: https://doi.org/10.7717/peerj.19483 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cao et al. title: Identification of bacteria on Thai banknotes and coins using MALDI-TOF mass spectrometry and their phenotypic antimicrobial susceptibility profiles link: https://peerj.com/articles/19465 last-modified: 2025-05-20 description: BackgroundThe existence and transmission of pathogenic and antibiotic-resistant bacteria through currency banknotes and coins poses a global public health risk. Banknotes and coins are handled by people in everyday life and have been identified as a universal medium for potentially microbial contamination.MethodsTo ascertain existence of medically important bacteria, a total of 300 samples including 150 banknotes and 150 coins were randomly collected at onsite retail fresh meat stores, i.e., pork and chicken, fish, and seafood stores, from nineteen fresh markets distributed across Bangkok, Thailand. An individual banknote or coin was entirely swabbed, and bacterial culture was carried out using tryptic soy agar (TSA), sheep blood agar (SBA) and MacConkey agar (Mac). A colony count was performed and bacterial species identification was conducted using matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry. Phenotypic antimicrobial susceptibility testing was carried out using the Kirby–Bauer disc diffusion methods.ResultsThe results demonstrated that the bacterial contamination rate was higher on banknotes than on coins (93.33% vs. 30.00%) in all three store types. A substantial number of colonies of >3,000 colony forming units (CFU) was predominantly found in banknotes (70.00%), especially from fish store (83.3%); meanwhile, <1,000 CFU was observed in coin sample (76.67%). MALDI-TOF mass spectrometry could identify 107 bacterial species, most of them were Staphylococcus kloosii (14.02%, 15/107), Staphylococcus saprophyticus (12.15%, 13/107), and Macrococcus caseolyticus (8.41%, 9/107). The prevalence based on genera were Staphylococcus (36.45%, 39/107), Acinetobacter (20.56%, 22/107), and Macrococcus (10.28%, 11/107). Almost all Staphylococcus isolates had low susceptibility to penicillin (21%). Notably, Staphylococcus arlettae, Staphylococcus haemolyticus and M. caseolyticus were multidrug-resistant (MDR). It is notable that none of the staphylococci and macrococci isolates exhibited inducible clindamycin resistance (D-test negative). Escherichia coli and Pseudomonas putida isolates were carbapenem-resistant, and Acinetobacter baumannii isolates were MDR with showing carbapenem resistance.ConclusionOur data demonstrated a high prevalence of medically important bacteria presented on Thai currency, which may pose a potential risk to human health and food safety. Food vendors and consumers should be educated about the possible cross-contamination of bacteria between the environment, food item, and currency. creator: Nattamon Niyomdecha creator: Suwitchaya Sungvaraporn creator: Arisa Pinmuang creator: Narissara Mungkornkaew creator: Thanchira Saita creator: Waratchaya Rodraksa creator: Achiraya Phanitmas creator: Nattapong Yamasamit creator: Pirom Noisumdaeng uri: https://doi.org/10.7717/peerj.19465 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Niyomdecha et al. title: Isolation and identification of endophytic fungi from Conyza blinii that exhibit antioxidant and antibacterial activities link: https://peerj.com/articles/19464 last-modified: 2025-05-20 description: BackgroundAs a medicinal plant, Conyza blinii is known to contain a wealth of bioactive constituents, including flavonoids, terpenes, and triterpenoid saponins, which contribute to its anti-inflammatory and anticancer properties. Endophytic fungi, which symbiotically inhabit plant tissues, are recognized for their ability to synthesize bioactive metabolites analogous to those of their hosts. However, the potential of C. blinii-associated endophytes remains underexplored. This study aims to isolate and characterize phenols-producing endophytic fungi from C. blinii, evaluate their biological activities, and analyze their chemical components to provide new insights for drug development.MethodsDuring the study, 20 endophytic fungi were isolated from C. blinii. The Folin-Ciocalteu method was used to screen for strains capable of producing phenolic compounds. To assess their bioactivity, ethyl acetate extracts of different concentrations were tested for antibacterial and antioxidant activities. Antibacterial activity was evaluated using minimum inhibitory concentration (MIC) determinations, while antioxidant activity was assessed through 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical, 2,2′-Azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical, hydroxyl radical, and superoxide anion radical scavenging assays. Additionally, liquid chromatography-mass spectrometry analysis was conducted to quantify the active components in the extracts.ResultsAmong the isolated 20 endophytic fungi, four strains successfully produced phenolic compounds, with the highest total phenolic content of 77.17 ± 1.93 mg milligrams of gallic acid equivalents per gram of extract (GAE/g). All ethyl acetate extracts from the endophytic fungi exhibited good antibacterial and antioxidant properties. Notably, Fusarium circinatum demonstrated exceptional antioxidant activity, with scavenging rates for DPPH and ABTS radicals reaching 94.28 ± 0.042% and 96.60 ± 0.017%, respectively. The ethyl acetate extract of F. foetens showed remarkable antibacterial effects against Escherichia coli and Staphylococcus aureus, with MIC values as low as 0.5 mg/mL. Furthermore, liquid chromatography-mass spectrometry (LC-MS) analysis revealed that F. foetens could produce various high-value phenolic compounds, including tyrosol (626.1884 ng/mL) and homovanillic acid (369.15486 ng/mL), which hold potential pharmaceutical value.DiscussionThis study isolated 20 endophytic fungi from C. blinii, discovering that four strains, produced phenolic compounds with strong antioxidant and antimicrobial properties. Among them, F. circinatum exhibited the highest antioxidant activity. Additionally, the fungi produced bioactive metabolites with potential applications in health care, medicine, and agriculture. These findings highlight the potential of C. blinii endophytes for sustainable bioactive compound production. creator: Yujie Jia creator: Guodong Zhang creator: Qiqi Xie creator: Jiwen Tao creator: Tongliang Bu creator: Xinyu Zhang creator: Yirong Xiao creator: Zhao Chen creator: Qingfeng Li creator: Zizhong Tang uri: https://doi.org/10.7717/peerj.19464 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Jia et al. title: Correlation of the sperm DNA fragmentation index with semen parameters and its impact on fresh embryo transfer outcomes—a retrospective study link: https://peerj.com/articles/19451 last-modified: 2025-05-20 description: PurposeTo evaluate the relationships between the sperm DNA fragmentation index (DFI) and semen parameters and its application in fresh embryos via in vitro fertilization and transfer.MethodsA retrospective propensity score matching (PSM) study was conducted on 162 cycles of in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) and fresh embryo transfer (fresh IVF/ICSI-ET) from 2020–2024.ResultsSpearman correlation analysis revealed a negative correlation between the sperm DFI and sperm motility (r = −0.44, p = 3.32e−08), forward movement of sperm (r = −0.46, p = 3.25e−09), and normal morphology of sperm (r = −0.25, p = 0.000); there was no correlation between the sperm DFI and male age (r = 0.08, p = 0.31), semen volume (r = −0.15, p = 0.05), sperm concentration (r = −0.16, p = 0.32), or male body mass index (BMI) (r = 0.02, p = 0.98). There were no significant differences in the 2PN fertilization rate (64.98% vs. 67.18%, p = 0.362), D3 high-quality embryo rate (28.34% vs. 23.91%, p = 0.107), biochemical pregnancy rate (71.60% vs. 71.60%, p = 1), clinical pregnancy rate (65.00% vs. 65.00%, p = 1), delivery rate (50.72% vs. 48.44%, p = 0.928), miscarriage rate (7.25% vs. 6.25%, p = 1), or singleton birth weight (3,350 g vs. 3,200 g, p = 0.599) between the normal DFI (DFI < 30%) group and the high DFI (DFI ≥ 30%) group.ConclusionSperm DFI is weakly associated with sperm motility, forward movement, and normal sperm morphology, and the correlations are not strong. However, there is no correlation between the sperm DFI and the clinical outcomes of fresh IVF/ICSI-ET. creator: Xiao Ju Wan creator: Meizhen Huang creator: Min Yu creator: Tao Ding creator: Zhihui Huang creator: Zhiqin Zhang creator: Xingwu Wu creator: Jun Tan uri: https://doi.org/10.7717/peerj.19451 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wan et al. title: Intrinsic factors behind long COVID: exploring the role of nucleocapsid protein in thrombosis link: https://peerj.com/articles/19429 last-modified: 2025-05-20 description: COVID-19, caused by the SARS-CoV-2, poses significant global health challenges. A key player in its pathogenesis is the nucleocapsid protein (NP), which is crucial for viral replication and assembly. While NPs from other coronaviruses, such as SARS-CoV and MERS-CoV, are known to increase inflammation and cause acute lung injury, the specific effects of the SARS-CoV-2 NP on host cells remain largely unexplored. Recent findings suggest that the NP acts as a pathogen-associated molecular pattern (PAMP) that binds to Toll-like receptor 2 (TLR2), activating NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) and MAPK (mitogen-activated protein kinase) signaling pathways. This activation is particularly pronounced in severe COVID-19 cases, leading to elevated levels of soluble ICAM-1 (intercellular adhesion molecule 1) and VCAM-1 (vascular cell adhesion molecule 1), which contribute to endothelial dysfunction and multiorgan damage. Furthermore, the NP is implicated in hyperinflammation and thrombosis—key factors in COVID-19 severity and long COVID. Its potential to bind with MASP-2 (mannan-binding lectin serine protease 2) may also be linked to persistent symptoms in long COVID patients. Understanding these mechanisms, particularly the role of the NP in thrombosis, is essential for developing targeted therapies to manage both acute and chronic effects of COVID-19 effectively. This comprehensive review aims to elucidate the multifaceted roles of the NP, highlighting its contributions to viral pathogenesis, immune evasion, and the exacerbation of thrombotic events, thereby providing insights into potential therapeutic targets for mitigating the severe and long-term impacts of COVID-19. creator: Ahmed Eltayeb creator: Muhamed Adilović creator: Maryam Golzardi creator: Altijana Hromić-Jahjefendić creator: Alberto Rubio-Casillas creator: Vladimir N. Uversky creator: Elrashdy M. Redwan uri: https://doi.org/10.7717/peerj.19429 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Eltayeb et al. title: The chronic effects of change of direction during repeated-sprint training on jumping, sprinting, and change-of-direction abilities in players: a systematic review and meta-analysis link: https://peerj.com/articles/19416 last-modified: 2025-05-20 description: ObjectivesThis systematic review and meta-analysis aimed to compare the effects of repeated sprint training with one change of direction (RS-OCOD) and multidirectional changes of direction (RS-MCOD) on players’ jumping, sprinting, and change-of-direction (COD) ability.MethodsFollowing PRISMA guidelines, 15 randomized controlled trials involving 223 players were analyzed. Standardized mean differences (SMD) and 95% confidence intervals (CI) were calculated using fixed- or random-effects models. Heterogeneity (I2 statistic), publication bias (funnel plots and Egger’s test), and sensitivity analyses were conducted. Subgroup analyses differentiated RS-OCOD and RS-MCOD outcomes.ResultsRS-COD training significantly improved countermovement jump (CMJ) (SMD = −0.68, 95% CI [−1.04 to −0.34]), 20–40 m sprinting ability (SMD = 0.70 [0.39, 1.01]), and COD ability (SMD = 0.77 [0.39, 1.16]). RS-MCOD demonstrated superior effects on 20–40 m sprinting ability (large effect: SMD = 0.97) and COD ability (large effect: SMD = 0.97), while RS-OCOD showed greater benefits for CMJ (large effect: SMD = −0.92). High heterogeneity (I2 > 70%) was observed in 5 m/10 m sprint analyses, attributed to methodological diversity and age variability. Prediction intervals indicated potential overestimation of RS-MCOD effects.ConclusionRS-OCOD can significantly enhance a player’s CMJ ability, while RS-MCOD can notably improve sprinting and COD abilities. These findings advocate for the incorporation of RS-COD into training programs to boost competitive performance. However, the effectiveness of RS-COD may vary based on the number and complexity of directional changes incorporated into the training regimen. Among them, RS-MCOD is prioritized for sports requiring frequent directional changes, whereas RS-OCOD enhances vertical jump performance in explosive sports. creator: Runzhou Kong creator: Lei Cao creator: Dongyu Li uri: https://doi.org/10.7717/peerj.19416 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kong et al. title: Interpretable noninvasive diagnosis of tuberculous pleural effusion using LGBM and SHAP: development and clinical application of a machine learning model link: https://peerj.com/articles/19411 last-modified: 2025-05-20 description: BackgroundTuberculous pleural effusion (TPE) is a prevalent tuberculosis complication, with diagnosis presenting considerable challenges. Timely and precise identification of TPE is vital for effective patient management and prognosis, yet existing diagnostic methods tend to be invasive, lengthy, and often lack sufficient accuracy. This study seeks to design and validate an interpretable machine learning model based on routine laboratory data to enable noninvasive and rapid TPE diagnosis.MethodsA multicenter prospective study was conducted across China between January 2021 and September 2024, enrolling 963 patients. The derivation cohort, comprising 763 patients, was employed for model training and internal validation, while 200 patients formed the external validation cohort. The model was built upon 18 routine laboratory parameters, including pleural fluid and serum biomarkers, with multiple machine learning (ML) algorithms evaluated. Light gradient boosting machine (LGBM) emerged as the top-performing model. Shapley Additive exPlanations (SHAP) analysis assessed feature importance and interpretability. Model performance was evaluated via area under the curve (AUC) and accuracy metrics. ResultsOf the 10 ML models compared, LGBM demonstrated superior performance. Feature importance analysis identified 11 key variables, leading to constructing a highly interpretable LGBM model. The model achieved an AUC of 0.9454 in internal validation and 0.9262 in external validation, showcasing strong robustness and generalizability. SHAP analysis enhanced interpretability by highlighting each feature’s contribution to prediction outcomes. This model has since been integrated into clinical practice for noninvasive, rapid TPE diagnosis. During external validation, the model achieved a sensitivity of 0.8600, specificity of 0.9056, positive predictive value of 0.8698, and negative predictive value of 0.8686, underscoring its accuracy across diverse patient cohorts. InterpretationThis interpretable machine learning model offers a noninvasive, accurate solution for early TPE diagnosis, significantly reducing reliance on invasive procedures. The integration of SHAP ensures the model’s clinical interpretability, mitigating concerns surrounding the “black-box” nature of many machine learning approaches. ConclusionsThis interpretable LGBM-based model provides a reliable, noninvasive tool for TPE diagnosis. It supports clinical decision-making with real-time risk assessment and promises broader applicability through future integration into clinical information systems. creator: Bihua Yao creator: Xingyu Yu creator: Liannv Qiu creator: Er-min Gu creator: Siyu Mao creator: Lei Jiang creator: Jijun Tong creator: Jianguo Wu uri: https://doi.org/10.7717/peerj.19411 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Yao et al. title: Antifungal activity and mechanism of novel peptide Glycine max antimicrobial peptide (GmAMP) against fluconazole-resistant Candida tropicalis link: https://peerj.com/articles/19372 last-modified: 2025-05-20 description: BackgroundThere is a pressing need to create innovative alternative treatment approaches considering the overuse of antifungal drugs causes the number of clinically isolated fluconazole-resistant Candida species to increase. Glycine max antimicrobial peptide (GmAMP) is a novel peptide screened by us using artificial intelligence modeling techniques, and pre-tests showed its strong antimicrobial activity against clinically fluconazole-resistant Candida tropicalis.MethodsThe study aimed to comprehensively investigate the antimicrobial activity and mechanisms of GmAMP against fluconazole-resistant C. tropicalis. The antifungal activity of GmAMP against fluconazole-resistant C. tropicalis was assessed by using broth microdilution method, growth and fungicidal kinetics, hypha transformation, and antibiofilm assay. To further uncover the potential mechanisms of action of GmAMP, we performed scanning electron microscopy, flow cytometry, cell membrane potential probe 3, 3′-Dipropylthiadicarbocyanine Iodide (DiSC3(5)), and reactive oxygen species (ROS) probe 2′, 7′-Dichlorodihydrofluorescein diacetate (DCFH-DA) detection to assess the cellular morphology and structure, membrane permeability, membrane depolarization, and ROS accumulation, respectively. At the same time, we used cytotoxicity and degree of erythrocyte hemolysis assays to assess GmAMP’s toxicity in vitro. Cytotoxicity and treatment efficacy were evaluated in vivo by utilizing the Galleria mellonella larvae infection model.ResultsGmAMP exhibited significant antifungal activity against fluconazole-resistant C. tropicalis with a minimum inhibitory concentration (MIC) of 25 µM and demonstrated fungicidal effects at 100 µM within 2 h. GmAMP prevented the transition from yeast to hypha morphology, inhibited the biofilm formation rate of 88.32%, and eradicated the mature biofilm rate of 58.28%. Additionally, GmAMP treatment at 100 µM caused cell structure damage in fluconazole-resistant C. tropicalis, whereas GmAMP treatment at concentrations ranging from 25 to 100 µM caused membrane permeability, depolarization of cell membrane potential, and intracellular ROS accumulation. Moreover, GmAMP enhanced the survival rate of 75% for G. mellonella with fluconazole-resistant C. tropicalis infection as well as reduced fungal burden in vivo by approximately 1.0 × 102 colony forming units per larva (CFU per larva).ConclusionGmAMP can disrupt the cell membrane of fluconazole-resistant C. tropicalis and also shows favorable safety and therapeutic efficacy in vivo. Accordingly, GmAMP has the potential to be an agent against drug-resistant fungi. creator: Ruxia Cai creator: Na Zhao creator: Chaoqin Sun creator: Mingjiao Huang creator: Zhenlong Jiao creator: Jian Peng creator: Jin Zhang creator: Guo Guo uri: https://doi.org/10.7717/peerj.19372 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cai et al. title: Bulk and single-cell RNA sequencing identify prognostic signatures related to FGFBP2+ NK cell in hepatocellular carcinoma link: https://peerj.com/articles/19337 last-modified: 2025-05-20 description: BackgroundHepatocellular carcinoma (HCC) is a highly aggressive malignancy. As a specific immune cell subpopulation, FGFBP2+ NK cells play a crucial part in immune surveillance of HCC progression. This study set out to identify prognostic signature related to FGFBP2+ NK cell in HCC.MethodsBulk and scRNA-seq data were derived from the public databases. The single cell atlas of HCC and heterogeneity of natural killer (NK) cells were delineated by “Seurat” package. Pseudo-time trajectory of FGFBP2+ NK cell was constructed by “Monocle2” package. Cell-cell interactions were analyzed by “CellChat” package. Prognostic signature was screened to develop a RiskScore model, and the prediction robustness was verified. Immune cell infiltration and immunotherapy response were assessed between different risk groups. Drug sensitivity was predicted by “oncoPredict” package. The expressions of the prognosis gene signature were detected by in vitro test utilizing HCC cells. The effects of key genes on the proliferative, migratory and invasive capacity of HCC cells were assessed by EdU assay, wound healing and Transwell assay.ResultsThe proportion of NK cell in HCC samples was markedly decreased than that in healthy samples. NK cell was further divided into three cell subpopulations, and FGFBP2+ NK cell was associated with the prognosis of HCC patients. Pseudo-time trajectory analysis of FGFBP2+ NK cell revealed two differential expression gene clusters. FGFBP2+ NK cell exhibited extensive intercellular communication in HCC. Further, eight prognostic signatures were identified, including six “risk” genes (UBE2F, AHSA1, PTP4A2, CDKN2D, FTL, RGS2) and two “protective” genes (KLF2, GZMH). RiskScore model was established with good prognostic prediction performance. In comparison to low-risk group, high-risk group had poorer prognosis, lower immune cell infiltration, and higher TIDE score. Moreover, 16 drugs showed significant correlation with RiskScore. Additionally, the expressions of GZMH was downregulated while FTL, PTP4A2, UBE2F, CDKN2D, RGS2, and AHSA1 were up-regulated in HCC cells. FTL and PTP4A2 silencing could suppress the proliferation, migration and invasion abilities of HCC cells.ConclusionThis study identified eight prognostic gene signatures related to FGFBP2+ NK cell in HCC, which may serve as potential therapeutic targets for HCC. creator: Yinbing Wu creator: Huanjun Peng creator: Guangkang Chen creator: Yinuo Tu creator: Xinpei Yu uri: https://doi.org/10.7717/peerj.19337 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: Exploring the potential of online social listening for noncommunicable disease monitoring link: https://peerj.com/articles/19311 last-modified: 2025-05-20 description: Noncommunicable diseases (NCDs) are a significant global health challenge, claiming about 41 million lives annually. Early establishment of healthy habits is vital as childhood behaviors often persist into adulthood, affecting long-term well-being. However, pervasive health misinformation on social media exacerbates the challenge of addressing NCDs. The vast online information exposes individuals to misinformation, leading to uninformed health decisions. Countering this misinformation is crucial to promote accurate understanding and preventive strategies for NCDs, improving public health outcomes. To address this, the study proposes a system using online social listening (OSL) to collect and analyze social media data, focusing on children’s nutrition, physical exercise, sleep patterns, and related NCD risk factors. This platform aids healthcare professionals in recognizing and responding to online misinformation, facilitating informed decision-making. Collaboration with parents, teachers, and healthcare providers aims to instill healthy habits in children from an early age. Utilizing the Twitter Application Programming Interface (API), the study collected data on NCDs, their risk factors, and their impact on children. Despite challenges from recent Twitter API policy changes, the methodology remains adaptable. Additionally, the study integrates diverse data sources, including traditional news outlets like PressReader, providing comprehensive coverage of health issues. Analysis comparing data from PressReader and Twitter underscores differences in discussion frequency and nature, emphasizing the need to leverage insights from various sources. The results highlight the effectiveness of the OSL system in identifying prevalent health topics, benefiting healthcare professionals. This collaborative approach positions the system as a valuable tool for addressing NCDs and promoting well-being. The study lays a foundation for future research, suggesting expansions to include additional platforms and languages, as well as advanced features like sentiment analysis. creator: Diana Braga creator: Inês Silva creator: Rafaela Rosário creator: Paulo Novais creator: Hugo Peixoto creator: José Machado uri: https://doi.org/10.7717/peerj.19311 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Braga et al. title: Support for the intermittent upwelling hypothesis using 10 years of barnacle recruitment data from a western ocean boundary in Atlantic Canada link: https://peerj.com/articles/19470 last-modified: 2025-05-19 description: Recruitment is a key demographic step for the persistence of populations, so understanding its drivers has traditionally been a relevant goal of ecology. On marine rocky shores, coastal oceanography is an important driver of the recruitment of intertidal invertebrates that reproduce through pelagic larvae by affecting larval transport and delivery. The intermittent upwelling hypothesis (IUH) posits that coastal pelagic larvae are driven offshore under intense upwelling or to depths under intense downwelling, while weak upwelling allows larvae to stay near the shore, thereby facilitating intertidal recruitment. The IUH thus predicts a unimodal relationship between Bakun’s upwelling index (BUI) and intertidal recruitment. The IUH has been supported by studies that plotted simultaneously single average values of recruitment and BUI for various coastal locations that collectively span downwelling to upwelling conditions. Based on its theoretical foundations, the IUH should also hold for a target location analyzed over the years provided enough interannual variation in BUI. On the Atlantic Canadian coast in Nova Scotia, upwelling varies interannually depending on wind patterns. Therefore, for a location that is representative of the abiotic and biotic conditions on this coast (Western Head), we tested the IUH by measuring annual intertidal barnacle recruitment and BUI for the pelagic larval season of barnacles for a period of 10 years (2014–2024). On this coast, BUI averaged for the barnacle larval season varied among years from mild downwelling to clear upwelling. Generalized additive modelling revealed a unimodal relationship between intertidal barnacle recruitment and BUI, thereby supporting the IUH. These results add this western ocean boundary to the known list of coastal systems where upwelling may influence intertidal invertebrate recruitment. creator: Ricardo A. Scrosati creator: Julius A. Ellrich uri: https://doi.org/10.7717/peerj.19470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Scrosati and Ellrich title: Investigating the “off-hour effect” on outcomes of neonates undergoing emergency gastrointestinal surgery link: https://peerj.com/articles/19468 last-modified: 2025-05-19 description: BackgroundEvidence regarding the off-hour effect on outcomes in neonates with gastrointestinal disease who received urgent surgical intervention is unknown. Because of the workforce shortage, insufficient experience of surgeons, and delayed radiography examination during off-hours, we hypothesized that emergency surgeries performed during off-hours were associated with worse outcomes. This study aims to analyze the association between the “off-hour effect” and adverse events of neonates undergoing emergency gastrointestinal surgery.MethodsWe extracted patient data from the electronic medical record system at our institution for all neonates undergoing emergency gastrointestinal surgery between July 2018 and October 2021. The primary outcomes were 24-hour and in-hospital mortality. The secondary outcomes were actual postoperative length of stay (PLOS) and the incidence of unplanned re-operation.ResultsA total of 275 neonates were identified, and 207 (75.3%) were treated during off-hours. The “off-hour effect” was not associated with increased 24-hour mortality, in-hospital mortality, PLOS, and unplanned re-operation. After propensity score matching, 68 off-hours were matched to the nearest 68 on-hours based on their age, weight, gestation weeks, and American Society of Anesthesiologists (ASA) status. No differences were detected in the primary and secondary outcomes.ConclusionIn this retrospective study with neonates who underwent emergency gastrointestinal surgery, after controlling for age, weight, gestation weeks, and ASA status, surgical and medical outcomes were not different in those undergoing off-hours surgery, which can be considered a surrogate for similar quality of care. However, in the future, a multi-center, prospective study is needed to confirm the results, to overcome the bias related to the presence of only one surgical team. creator: Yu Cui uri: https://doi.org/10.7717/peerj.19468 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cui title: Longitudinal effects of aerobic training programme on body composition in non-elite adolescent female swimmers link: https://peerj.com/articles/19456 last-modified: 2025-05-19 description: IntroductionThe aim of this study was to assess the impact of a 3-year swimming training programme on body fat measurements in adolescent girls, without prior selection.MethodTwo groups of 10-year-old girls were analysed at the beginning of the study (4th grade in primary school). The experimental group consisted of 14 swimmers (body mass: 34.99 ± 2.77 kg; height: 146.00 ± 3.05 cm). The control group consisted of 14 girls (body mass: 37.93 ± 6.02 kg; height: 145.55 ± 3.88 cm) who only participated in mandatory physical education classes. The study was conducted over a period of 3 years, with measurements taken every 6 months. Body fat was measured through the thickness of skinfolds at four anatomical locations: above the biceps; above the triceps; below the lower angle of the scapula; and above the superior iliac crest. Based on these measurements, the percentage of body fat was calculated.ResultsStatistical analysis revealed that despite the lack of initial selection, there was no significant difference in the percentage of body fat between the experimental and control groups at the start of the study—18.62% vs 24.85%. This difference persisted until the final measurement after 3 years, at which point it became statistically significant—17.31% vs 27.14% (F = 37.44, p < 0.05).DiscussionOur findings indicate that 3 years of swimming training in adolescent girls resulted in a reduction in fat tissue growth across all four measurement sites. Initially, body fat percentage had a strong negative impact on VO2 max, particularly in the experimental group. However, this effect diminished in both groups over the course of the study.ConclusionSwimming may be an effective means of preventing obesity. Coaches should consider a slim physique in swimming candidates. creator: Mariusz Kuberski creator: Agnieszka Musial creator: Maciej Choroszucho creator: Jan M. Konarski creator: Jacek Wąsik uri: https://doi.org/10.7717/peerj.19456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kuberski et al. title: Association between non-alcoholic fatty liver disease and arterial stiffness measured by brachial-ankle pulse wave velocity: a cross-sectional population study link: https://peerj.com/articles/19405 last-modified: 2025-05-19 description: BackgroundNon-alcoholic fatty liver disease (NAFLD) is strongly linked with metabolic syndrome and atherosclerotic cardiovascular diseases (ASCVDs). This study aimed to assess the feasibility of using brachial-ankle pulse wave velocity (baPWV), a non-invasive technique, to monitor atherosclerosis (AS) in NAFLD patients and to evaluate the AS risk in various sub-populations of NAFLD patients.Materials and methodsA cross-sectional study was conducted with 4,844 participants, enrolled from January 1, 2019, to December 31, 2021, at the Physical Examination Center of Zhongnan Hospital of Wuhan University. Participants were aged 18 to 88 years. According to the main points of the ultrasonic diagnosis of NAFLD, the ultrasonic image report was made for the subjects. AS is defined as baPWV ≥ 1,400 cm/s. We used multiple logistic regression analysis to explore the relationship between NAFLD and AS, and multiple linear regression analysis to explore the correlation between NAFLD and baPWV by modeling. Subgroup analysis was performed based on age and gender to adjust for confounding bias and complete sensitivity analysis.ResultsThe prevalence of NAFLD was 38.3% in all participants, with 45.4% in men and 25.1% in women. Among the overall NAFLD population and male NAFLD patients, baPWV exceeded the diagnostic threshold for AS (1,419.70 ± 205.51, 1,429.71 ± 196.13) starting from the 45–55 age group. Through the analysis of the age-baPWV scatter plots and fitted lines, along with sensitivity analysis, it is recommended that male patients should start monitoring at 46 years old for AS using baPWV, while female patients should begin at 51 years old. NAFLD was associated with increased odds of AS (OR: 1.206, 95% CI [1.021–1.423], P = 0.027) after adjusting for confounders. NAFLD was independently positively correlated with baPWV (Model 2: β = 0.086, ΔR2 = 0.006, P < 0.001; Model 3: β = 0.05, P < 0.001). This positive correlation was also observed in both males and females (male: Model 2: β = 0.081, ΔR2 = 0.005, P < 0.001; Model 3: β = 0.052, P = 0.001; female: Model 2: β = 0.088, ΔR2 = 0.006, P < 0.001; Model 3: β = 0.042, P = 0.02).ConclusionNAFLD demonstrated an independent association with AS assessed via baPWV, an accessible non-invasive tool for early AS evaluation. Regular baPWV monitoring is recommended for NAFLD patients > 45 years, with males and females initiating surveillance at 46 and 51 years, respectively. Study limitations, including potential biases in NAFLD diagnosis, gender distribution imbalances, and confounding variable interdependencies, necessitate further stratified population analyses. creator: Yujie Wang creator: Zhicheng Fang creator: Qiuyue Fu creator: Dongai Yao creator: Xiaoqing Jin uri: https://doi.org/10.7717/peerj.19405 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Stochastic processes dominate the community assembly of ectomycorrhizal fungi associated with Betula platyphylla in Inner Mongolia, China link: https://peerj.com/articles/19364 last-modified: 2025-05-19 description: The maintenance and driving mechanisms of microbial community structure have become important research focuses in microbial ecology. Therefore, clarifying the assembly of ectomycorrhizal (EM) fungal communities can provide a relevant basis for studying forest diversity, ecological diversity, and ecological evolution. Betula platyphylla is a typical EM dependent tree species with characteristics such as renewal ability and strong competitive adaptability, and it plays a crucial ecological function in Inner Mongolia. However, the research on EM fungi’s diversity and community assembly is very limited. We investigated EM fungal communities associated with B. platyphylla from 15 rhizosphere soil samples across five sites in Inner Mongolia. The fungal rDNA ITS2 region was sequenced using Illumina Miseq sequencing. A total of 295 EM fungal OTUs belonging to two phyla, three classes, nine orders, 20 families, and 31 genera were identified, of which Russula, Cortinarius, and Sebacina were the most dominant taxa. Significant differences existed in the composition of dominant genera of EM fungi across the five sites, and the relative abundances of dominant genera also showed significant differences among the sites. The β NTI and NCM fitting analyses suggest that stochastic processes mainly determine the EM fungal community assembly. Our study indicates that B. platyphylla harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with B. platyphylla in north China. creator: Min Li creator: Zhaoyun Meng creator: Jinyan Li creator: Xuan Zhang creator: Yonglong Wang creator: Xinyu Li creator: Yuze Yang creator: Yue Li creator: Xunjue Yang creator: Xiuli Chen creator: Yongjun Fan uri: https://doi.org/10.7717/peerj.19364 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Adult picky eating and associations with childhood picky eating, maternal feeding, aversive sensory responsiveness, disgust and obsessive-compulsive symptoms link: https://peerj.com/articles/19444 last-modified: 2025-05-16 description: BackgroundAdult picky eating (PE) can cause distress, malfunction, and malnutrition. The purpose of this study was to examine adult PE, its relationship to childhood PE and to symptoms of obsessive-compulsive disorder (OCD), sensory processing disorder, food and general disgust, and maternal child feeding practices.MethodsAdult participants (N = 772; 636 women) self-reported on measures of adult PE (Adult Picky Eating Questionnaire (APEQ)), obsessive-compulsive symptoms (Obsessive-Compulsive Inventory–Revised (OCI-R)), sensory processing difficulties (Sensory Responsiveness Questionnaire–Intensity Scale (SRQ-IS)), general disgust propensity (Disgust Propensity and Sensitivity Scale-12 (DPSS-12)), food disgust (Food Disgust Scale–short (FDS-S)), and three maternal feeding practices (Retrospective Child Feeding Questionnaire (RCFQ)).ResultsChildhood PE and current adult PE were strongly associated. Adults with PE who scored in the top 25 percentile on the APEQ were at risk for OCD and sensory processing disorder; most reported having been picky eaters in childhood. Structural equation modelling with good fit indices confirmed a developmental model in which general disgust, food disgust and sensory processing difficulties contributed to childhood PE and maternal feeding practices (pressure to eat, restriction), which in turn contributed to OCD symptoms. In addition, pressure to eat, restriction and OCD symptoms contributed directly to adult PE.ConclusionsSevere adult PE is related to childhood PE and disgust sensitiviy, OCD and sensory processing disorder. Adults with severe PE may meet criteria for adult avoidant restrictive feeding or eating disorders. For adults with extreme PE clinical intervention may be warranted. creator: Ada H. Zohar creator: Dorin Barhum Shapira creator: Lilac Lev-Ari creator: Rachel Bachner-Melman uri: https://doi.org/10.7717/peerj.19444 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zohar et al. title: Genetic variability and trait associations for physiological and agronomic characteristics in bread wheat genotypes under drought stress and well-watered conditions link: https://peerj.com/articles/19341 last-modified: 2025-05-16 description: Drought is a critical abiotic stress significantly reducing global wheat production, especially under climate fluctuations. Investigating wheat genetic variability using physiological and agronomic characteristics is essential for advancing breeding to enhance drought resilience and ensure sustainable production in light of global population growth. The genetic diversity and associations among traits of fourteen diverse genotypes of bread wheat in drought-stressed and well-watered conditions were studied, focusing on physiological and agronomic responses. Significant variations were detected among irrigation regimes, genotypes, and their interactions for all assessed characteristics. Drought stress substantially declined chlorophyll a (Chl a) and b (Chl b), net photosynthetic rate (NPR), transpiration rate (Tr), stomatal conductance (gs), membrane stability index (MSI), relative water content (RWC), plant height (PH), yield-related attributes, and grain yield. Conversely, it significantly increased malondialdehyde content, proline content (ProC), and activities of antioxidant enzymes, including catalase (CAT), ascorbate peroxidase (APX) and superoxide dismutase (SOD). The genotypes, G3 (L-1117), G8 (L-120), and G12 (L-1142) exhibited superior drought tolerance, maintaining high photosynthetic efficiency, RWC, antioxidant enzyme activity, and grain yield. Under drought conditions, these genotypes achieved grain yields of 6.32 t/ha (G8), 5.97 t/ha (G12), and 5.84 t/ha (G3), significantly surpassing the other genotypes. Genotypic classification and drought tolerance indices confirmed the superiority of G3, G8, and G12 as drought-resilient candidates, while G2, G5, G7, and G14 exhibited lower adaptability. Genotypic stability analysis (additive main effects and multiplicative interaction (AMMI) and ranking biplot) indicated that G3, G8, G6, and G12 were highly stable across diverse environments, making them promising candidates for wheat breeding programs. Agronomic traits such as PH, number of grains per spike (NGPS), and thousand kernel weight (TKW) were positively associated with drought tolerance. Furthermore, the multivariate analyses, including principal component analysis (PCA), correlation, and path analysis, highlighted the significance of RWC, MSI, chlorophyll content, and antioxidant enzymes in sustaining yield under drought stress. Broad-sense heritability estimates were high for key drought-related traits, particularly APX, SOD, and NGPS, indicating strong genetic potential for selection. These findings indicated the importance of integrating physiological and biochemical markers into breeding programs to develop high-yielding drought-tolerant wheat varieties, contributing to sustainable wheat production under water-limited conditions. creator: Mohammed O. Alshaharni creator: Fatmah A. Safhi creator: Nora M. Al Aboud creator: Dmitry E. Kucher creator: Eman Fayad creator: Mohammed Alqurashi creator: Rahmah N. Al-Qthanin creator: Ibtesam S.M. Almami creator: Heba I. Ghamry creator: Diaa Abd El-Moneim creator: Mohamed M. Kamara creator: Abdelraouf M. Ali uri: https://doi.org/10.7717/peerj.19341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alshaharni et al. title: Effect of whole-body vibration training on bone mineral density in older adults: a systematic review and meta-analysis link: https://peerj.com/articles/19230 last-modified: 2025-05-16 description: BackgroundWhole-body vibration (WBV) aims to increase bone mineral density (BMD) using vertical mechanical accelerations from the plantar surface of the feet through the muscles and bones. A vibration platform is used for this purpose. This systematic review (PROSPERO—CRD 42023395390) analysed the effects of WBV training on BMD at anatomical sites most affected by osteoporotic fractures in older adults.MethodologySystematic searches were conducted in the databases. Randomized controlled studies quantifying aerial BMD (aBMD) using the dual-energy X-ray absorptiometry method before and after WBV training in adults aged 55 and older were included. Independent reviewers performed methodological quality analysis (TESTEX) and assessed the risk of bias, and the GRADE scale determined the certainty of evidence in the results of the selected studies. The aBMD values from anatomical sites in the femoral neck, total proximal femur, and lumbar spine from WBV training protocols were included in the meta-analysis. The forest plot was generated using the random-effects model, and the effect size was measured by Hedges’ g.ResultsSeven studies involving 202 participants were included, with TESTEX = 12.6 (excellent quality) and risk of bias (43% low risk, and 57% some concerns), demonstrating with low heterogeneity, a significant effect of WBV training on total femur aBMD (g = 0.28 (small), p = 0.04). However, in spite of the low heterogeneity, the femoral neck (g = 0.15 (trivial), p = 0.19) and lumbar spine (g = 0.13 (trivial), p = 0.31) regions did not show a significant effect with WBV training.ConclusionsThe results showed with low certainly evidence that WBV training had a statistically significant effect on total femur aBMD but not on femoral neck and lumbar spine. creator: Danilo A. Massini creator: Tiago A. F. Almeida creator: Anderson G. Macedo creator: André B. Peres creator: Víctor Hernández-Beltrán creator: José M. Gamonales creator: Mário C. Espada creator: Cassiano M. Neiva creator: Dalton M. Pessôa Filho uri: https://doi.org/10.7717/peerj.19230 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Massini et al. title: HD-6mAPred: a hybrid deep learning approach for accurate prediction of N6-methyladenine sites in plant species link: https://peerj.com/articles/19463 last-modified: 2025-05-15 description: BackgroundN6-methyladenine (6mA) is an important DNA methylation modification that serves a crucial function in various biological activities. Accurate prediction of 6mA sites is essential for elucidating its biological function and underlying mechanism. Although existing methods have achieved great success, there remains a pressing need for improved prediction accuracy and generalization cap ability across diverse species. This study aimed to develop a robust method to address these challenges.MethodsWe proposed HD-6mAPred, a hybrid deep learning model that combines bidirectional gated recurrent unit (BiGRU), convolutional neural network (CNN) and attention mechanism, along with various DNA sequence coding schemes. Firstly, DNA sequences were encoded using four different ways: one-hot encoding, electron-ion interaction pseudo-potential (EIIP), enhanced nucleic acid composition (ENAC) and nucleotide chemical properties (NCP). Secondly, a hold-out search strategy was employed to identify the optimal features or feature combinations for both BiGRU and CNN. Finally, the attention mechanism was introduced to weigh the importance of features derived from the BiGRU and CNN.ResultsA series of experiments on the Rosaceae, rice and Arabidopsis datasets were conducted to demonstrate the superiority of HD-6mAPred. In Rosaceae, the HD-6mAPred model achieved excellent performance: accuracy (ACC) of 0.996, Matthew correlation coefficient (MCC) of 0.993, sensitivity (SN) and specificity (SP) of 0.995 and 0.998, respectively. In rice, the evaluation metrics are 0.952 (ACC), 0.905 (MCC), 0.955 (SN), and 0.949 (SP). In Arabidopsis, the corresponding metrics are 0.937 (ACC), 0.875 (MCC), 0.927 (SN), and 0.948 (SP). Compared to existing methods, these results demonstrate that HD-6mAPred achieves state-of-the-art performance in predicting 6mA sites across three plant species. Furthermore, HD-6mAPred not only improves the accuracy of 6mA site prediction, but also shows excellent generalization capability across species. The source code utilized in this study is publicly accessible at https://doi.org/10.5281/zenodo.15355131. creator: Huimin Li creator: Wei Gao creator: Yi Tang creator: Xiaotian Guo uri: https://doi.org/10.7717/peerj.19463 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Expected mortality risk for coho salmon landed in recreational troll fisheries using 1/0 and 6/0 hooks in the marine waters of Washington state link: https://peerj.com/articles/19434 last-modified: 2025-05-15 description: Recreational salmon fisheries in the state of Washington are managed with size-selective and mark-selective rules to promote the release of wild and undersized salmon. In order for this management approach to be effective, the fishery must have low mortality of hooked and released salmon. In this study, we directly compared the fishing performance of small (1/0, 14.36 mm gap) and large (6/0, 17.20 mm gap) hooks in recreational salmon troll fisheries with the goal of evaluating differences in drop-off rates, size of salmon caught, and the probability a fish would be hooked in a region documented to have low, intermediary, or high risk of mortality. We found strong evidence that hook size affects the probability that an angler can land a fish with drop-off rates of 48.9% for fish hooked on small (1/0) hooks and 34.0% for fish hooked on large (6/0) hooks. There were no significant differences in the average length of pink, coho, or Chinook salmon caught on small (1/0) or large (6/0) hooks. Likewise, we found no significant differences in the proportion of coho and Chinook catch that were longer or shorter than their respective legal-size limits. Hook size did significantly affect the expected mortality risk of coho salmon with large (6/0) hooks being 1.82 times more likely to hook a salmon in body regions associated with high or intermediary risk of mortality than small (1/0) hooks. No significant differences were observed in the hooking rates of Chinook and pink salmon in body regions with high, intermediary, or low expected mortality risk, however our confidence in this finding is limited due to sample size. It is important to carefully assess whether these results support restrictions on hook sizes used in recreational coho salmon troll fisheries. The observation of reduced expected mortality risk of coho salmon landed using small (1/0) hooks as compared to when using large (6/0) hooks highlights the importance of evaluating the effect of hook size during recreational salmon troll fisheries on post-release survival and will hopefully stimulate more research on the effects of hook size and modeling on whether hook size regulations can improve salmon conservation. creator: Jonathan J. Scordino creator: Ryan P. Walsh creator: William Jasper creator: Deon J. Roche creator: William Tyler uri: https://doi.org/10.7717/peerj.19434 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Scordino et al. title: Emodin, a rising star in the treatment of glycolipid metabolism disorders: a preclinical systematic review and meta-analysis link: https://peerj.com/articles/19221 last-modified: 2025-05-15 description: BackgroundRhubarb has a remarkable effect on lowering blood lipid and glucose levels, and its main component, emodin, is an anthraquinone derivative. To elucidate the role and mechanism of emodin in the treatment of type 2 diabetes mellitus (T2DM) and to provide robust evidence for its clinical application, we conducted a systematic review and meta-analysis to assess the influence of emodin on T2DM animal models and the overall therapeutic effect, and further to evaluate its benefits and risks in the management of T2DM.MethodsEight databases were searched from inception to May 2023. Two reviewers extracted the data independently. SYRCLE’s risk of bias tool for animal studies was used to assess the quality of articles. RevMan V.5.4 software and STATA 15.1 software were applied for data analyses. Body weight, serum insulin level (INS), fasting blood glucose (FBG), 2-hour postprandial blood glucose (2hPG, IPGTT/OGTT), insulin tolerance test (IPITT) indicators, total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL-c), and low-density lipoprotein cholesterol (LDL-c) were used as outcome measures. Data for outcome messures presented in graphical form were extracted using GetData graphic digitizer software (version 2.26). For outcome indicators with a small number of included studies, we will conduct descriptive analyses.ResultsTwelve existing studies were included in this meta-analysis, and all of the studies included in this review had a low to moderate risk of bias. The results showed that emodin significantly reduced the glucose and lipid metabolism indicators and effectively lowered body weight and serum insulin levels (FBG, 2hPG(IPGTT/OGTT), IPITT, TG, TC, LDL-c, HDL-c) (P < 0.05).ConclusionEmodin demonstrates significant potential in treating T2DM by reducing FBG, 2hPG (IPGTT/OGTT), IPITT, TC, TG, INS, and body weight in animal models. The therapeutic mechanisms of emodin include enhancing glucose utilization in peripheral tissues, inhibiting glucosidase absorption, alleviating insulin resistance, and strengthening L-type calcium channels. Additionally, emodin shares characteristics with first-line antidiabetic drugs such as metformin, acarbose, and repaglinide, promoting insulin secretion and enhancing cellular sensitivity to insulin. Furthermore, emodin exhibits actions similar to glucagon-likepeptide-1(GLP-1) receptor agonists, suggesting its potential for protecting target organs. Therefore, emodin is a highly promising drug with substantial research and clinical value. However, caution should be exercised due to significant heterogeneity among the studies, and results may evolve with additional research. creator: Yang Xiao creator: Zhixuan Zhao creator: Binqin Chen creator: Jian Sun creator: Li Wang creator: Yu Wang creator: Zheng Nan creator: Qi Zhang uri: https://doi.org/10.7717/peerj.19221 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xiao et al. title: Construction and validation of a prognostic model for colorectal cancer based on migrasome-related long non-coding RNAs link: https://peerj.com/articles/19443 last-modified: 2025-05-14 description: BackgroundColon adenocarcinoma (COAD) is a globally prevalent and deadly malignancy of the digestive system. Recently, migrasomes have gained significant attention as important regulators of tumor cell migration and metastasis. The current research developed a highly accurate prognostic model using migrasome-related long non-coding RNAs (lncRNAs) in COAD, providing new insights for prognostic assessment and immunotherapy of COAD patients.MethodsRNA sequencing data from COAD patients were acquired from The Cancer Genome Atlas Program (TCGA) database to construct a prognostic lncRNA model based on known migrasome-related genes (MRGs). The model’s predictive accuracy was then assessed using concordance index (C-index) analysis, nomograms, principal component analysis, and receiver operating characteristic curves. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to identify significant differences in biological functions and signaling pathways associated with differentially expressed genes in the high-risk subgroup. A comprehensive evaluation of the model incorporated clinical-pathological features, tumor microenvironment, and chemotherapy sensitivity. The expression levels of prognostic genes in COAD patients were validated via quantitative reverse transcription polymerase chain reaction (RT-qPCR). Furthermore, the role of LCMT1-AS1 in colorectal cancer was examined through CCK-8 assays, colony formation assays, and Transwell experiments.ResultsMigrasome-related lncRNAs were identified as robust prognostic predictors for COAD. Multivariate analysis revealed that the risk score derived from these lncRNAs is an independent prognostic factor for COAD. Patients in the low-risk group exhibited significantly longer overall survival (OS) compared to those in the high-risk group. Accordingly, the nomogram prediction model we developed, which integrates clinical features and risk scores, demonstrated excellent prognostic performance. In vitro experiments further showed that LCMT1-AS1 promotes the proliferation and migration of COAD cells. creator: Qiang Lv creator: Qingzhu Yang creator: Hongsheng Chen creator: Yang Wang creator: Yuliuming Wang creator: Xu Hu creator: Ming Liu uri: https://doi.org/10.7717/peerj.19443 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Lv et al. title: Impact of forest fragmentation on river water quality: an example from a typical subtropical hilly basin link: https://peerj.com/articles/19435 last-modified: 2025-05-14 description: BackgroundForest fragmentation, driven by natural and human activities, is increasing. However, the impact of forest fragmentation on river water quality remains ambiguous.MethodsIn this study, water quality data were collected from 15 monitoring sites in the upper Ganjiang River basin in winter and summer, and the forest landscape fragmentation metrics in the sub-basin was calculated to assess its seasonal impact on river water quality.ResultsThe results indicated that water quality in the area is generally satisfactory, with total nitrogen (TN) as the main pollutant. Redundancy analysis (RDA) showed that the explanation rate of the six forest landscape fragmentation metrics to the water quality change in summer was 41.21%, and in winter, their explanation rate of water quality change increased by 14.26%. Among them, the effective mesh size (MESH) was negatively correlated with most river water quality indicators, with a contribution rate of 20.9%. While the interspersion and juxtaposition index (IJI) was positively correlated with most water quality indicators in winter, with a contribution rate of 44.9%. It is worth noting that the thresholds for IJI and MESH of forest were the same in winter and summer, 28.1% and 7.89e+0.5ha, respectively, when the probability of an abrupt change in TN concentration reached 100%. This is implied that when the adjacency of forest patches is less than 28.1% and the connectivity of forest patches is more than 7.89e+0.5ha, it may contribute to the reduction of TN concentration in rivers. These findings provide valuable insights into how varying degrees of forest fragmentation can lead to deterioration in river water quality, and allow for further planning of forest structure based on forest fragmentation thresholds to improve regional water quality. creator: Biao Li creator: Xiaolei Huang creator: Qiang Zhong creator: Xiuxiu Wu uri: https://doi.org/10.7717/peerj.19435 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Li et al. title: Elevated albumin-bilirubin score as a predictor of kidney stones in adults with type 2 diabetes mellitus: evidence from a cross-sectional study link: https://peerj.com/articles/19419 last-modified: 2025-05-14 description: The presence of kidney stones in individuals with type 2 diabetes mellitus (T2DM) poses a significant challenge and burden, yet the underlying pathogenesis remains elusive. This study aimed to reveal the relationship between the albumin-bilirubin (ALBI) score and kidney stones in adult patients with T2DM. This cross-sectional study was conducted using data from 9,511 eligible patients. The main outcome of interest was the incidence of kidney stones, with the ALBI score serving as the primary exposure factor. Logistic regression analysis was performed to calculate the odds ratios and 95% confidence intervals for the association between ALBI score and kidney stones. Our study found that a higher ALBI score was independently related to the presence of kidney stones in adult patients with T2DM. When the ALBI score was stratified into tertiles, compared to patients with an ALBI score in the T1 category, those with ALBI scores in the T2 and T3 categories exhibited a significantly higher prevalence of kidney stones after adjusting for multiple potential confounding factors. Additionally, our results revealed a non-linear relationship between ALBI score and the presence of kidney stones, which was further supported by subgroup and interaction analyses. These findings offer preliminary insights that could potentially inform future approaches to understanding kidney stone risk in adults with T2DM. Additional studies are needed to validate our conclusions. creator: Wenya Mo creator: Tao Zhou creator: Qifei Dong creator: Yuhan Chen creator: Xuechun Hu creator: Jun Xiao creator: Changming Wang creator: Ping Xiang uri: https://doi.org/10.7717/peerj.19419 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mo et al. title: Experimental study on the impact of Speed-Agility-Quickness Training method on the agility performance of collegiate sanda specialty students link: https://peerj.com/articles/19406 last-modified: 2025-05-14 description: Research objectiveThis study investigates the effects of Speed, Agility, and Quickness (SAQ) training on the agility of collegiate sanda athletes at Henan Normal University.Research methodsThe experimental group (EG) (n = 12, Age: 19.58 ± 1.165, height: 176.592 ± 3.181 cm, weight: 71.38 ± 15.84 kg, training years: 2.92 ± 0.793) was trained by the SAQ training method, and the control group (CG) (n = 12, Age: 19.92 ± 1.084, 177.308 ± 2.171 cm, 71.63 ± 16.80 kg, training years: 2.75 ± 0.754) was trained by traditional agility. The data of the CG group and the EG group were compared by repeated measures of analysis of variance (ANOVA) in different periods of the test indexes (pro agility run, Illinois agility run, compass pointer run, cross quadrant jump, 15s repeated ring jump, and punch-kick combination test) in the CG group and EG group.Research resultsPost-experiment, the EG group showed significant differences in all six agility test indicators after adopting SAQ training. There were no significant differences in the Pro Agility Test, the Compass Pointer Test, and the 15s Repeated Ring Jump after the CG group used traditional agility performance training (P > 0.05). There were significant differences in the Illinois agility test (effect size D = 0.626), the cross quadrant jump test (effect size D = 0.558), and the punch-kick combination test (effect size D = 0.519) in the CG group after the experiment (P < 0.001). Similarly, the EG group showed significant differences in the Illinois agility test (effect size D = 0.894), the cross quadrant jump test (effect size D = 0.852), and the punch-kick combination test (effect size D = 0.896).Research conclusionSAQ training significantly enhances the agility performance of collegiate sanda specialty students. The effects of improving agility performance through SAQ training are superior to those achieved with traditional agility training methods. creator: Xingwei Si creator: Yaojia Liu creator: Xia Feng creator: Shuyu Feng uri: https://doi.org/10.7717/peerj.19406 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Si et al. title: Gaze behavior and decision-making among handball referees: exploring gender and expertise differences link: https://peerj.com/articles/19401 last-modified: 2025-05-14 description: BackgroundGaze behavior has been extensively studied in various sports, yet research on handball referees remains limited. Understanding gaze behavior in handball officiating is crucial for enhancing training programs, particularly for novice referees. This study investigates gaze behavior and decision-making processes among male and female handball referees of varying expertise levels.MethodsA total of 51 handball referees (aged 30.25 ± 7.61 years), including 11 females and 40 males from the Polish Handball Federation, participated in the study. The sample comprised 31 higher-level referees (Super League and First League) and 20 lower-level referees (Second and Regional League). Participants wore head-mounted mobile eye-trackers to assess fixations and saccades while watching video clips of handball match scenarios. After each scene, referees made decisions based on the handball rules.ResultsHigher-level referees demonstrated significantly greater decision-making accuracy compared to lower-level referees (p < 0.05; Cohen’s d = 0.678), particularly in “punishment” scenarios (p < 0.001; Cohen’s d = 1.407). Although no significant differences in gaze behavior (e.g., number and duration of fixations and saccades) were observed concerning gender or expertise level, specific differences in decision-making accuracy emerged, particularly regarding expertise and free-throw scenarios.ConclusionThe findings indicate that differences in decision-making accuracy among handball referees are likely influenced by factors such as experience and cognitive processing rather than gaze behavior. The absence of gender differences in gaze patterns challenges prior research suggesting systematic visual search disparities. Future studies in real-game settings are needed to explore the impact of physical and psychological demands on referees’ performance, providing practical insights for training programs. creator: Jacek Świdwa creator: Stefanie Klatt creator: Adam Kantanista uri: https://doi.org/10.7717/peerj.19401 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Świdwa et al. title: Comparative efficacy of targeted therapy, chemotherapy and their combination for advanced cholangiocarcinoma: a systematic review and network meta-analysis link: https://peerj.com/articles/19386 last-modified: 2025-05-14 description: BackgroundCholangiocarcinoma is a malignant tumor with a poor prognosis. Multiple randomized controlled trial (RCT) have shown conflicting benefits of different therapies. The study was to assess the effectiveness of chemotherapy (CT), targeted therapy (TT) and both of them (targeted therapy + chemotherapy; TT+CT) for advanced cholangiocarcinoma by a systematic review and network meta-analysis.MethodsPubMed, EmBase, Medline, Cochrane were searched. Two reviewers independently selected published reports of RCT comparing any targeted therapy, chemotherapy and targeted therapy combined with chemotherapy vs. placebo. The outcomes were overall survival (OS) and progression-free survival (PFS) on the hazard ratio-scale (HR) and mean differences-scale (MD).ResultsWe included 13 RCT involving 1,914 patients. We revealed a differential reporting of outcomes. All three treatments significantly reduced the HR in OS and PFS when compared with the placebo. HR and MD values of OS and PFS in TT+CT group were significantly better than those in the other two groups. Only targeted therapy can significantly improve PFS in patients.Conclusions1) All treatments significantly reduced the hazard ratio in OS and PFS when compared with the placebo; 2) HR and MD values of OS and PFS in TT+CT group were significantly better; 3) Only targeted therapy alone significantly increased the PFS of patients, thereby improving the quality of life of patients. creator: Zhoujun Liao creator: Zhuoyue Yao creator: Zhiqing Yang creator: Shaohua Yang creator: Wenjuan Gu creator: Huijie Wang creator: Lingyan Deng uri: https://doi.org/10.7717/peerj.19386 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liao et al. title: Enhancing effect of 5-azacytidine on saline–alkaline resistance of Akebia trifoliata and underlying physiological and transcriptomic mechanisms link: https://peerj.com/articles/19285 last-modified: 2025-05-14 description: Saline-alkaline stress is a common problem in Akebia trifoliata cultivation. In this study, the enhancing effects of 5-azacytidine (5-AzaC) on the resistance of A. trifoliata to saline–alkaline stress and the underlying mechanisms were investigated. Plant height, stem diameter, biomass, root length, fresh weight of root, and root/shoot ratio of 6-month-old A. trifoliata seedlings were measured after saline–alkaline stress with or without 5-AzaC treatment. Moreover, the contents of photosynthetic pigments, malondialdehyde (MDA), H2O2, sodium, soluble sugar, and proline; activities of superoxide dismutase, peroxidase (POD), and catalase (CAT); and anatomical structures of root, stem, and leaf were assessed. Furthermore, comparative transcriptome sequencing was performed. The results demonstrated that growth and development of A. trifoliata were severely inhibited under saline–alkaline stress, suggesting that the seedlings were exposed to severe oxidative and osmotic stresses. Treatment with exogenous 5-AzaC could significantly relieve the symptoms of saline–alkaline stress in A. trifoliata. Under saline–alkaline stress, 5-AzaC could increase the stem diameter, biomass, root length, fresh weight of root, and root/shoot ratio and minimize damages to the anatomical structure. Moreover, absorption of Na+ was reduced; ionic balance was maintained; POD and CAT activities were significantly improved; proline and soluble sugar contents increased, and H2O2 and MDA contents decreased. Transcriptome analysis revealed that 5-AzaC functioned via regulating KEGG pathways such as plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, amino sugar and nucleotide sugar metabolism, and glutathione metabolism under saline–alkaline stress. Particularly, enhanced expression of genes from the auxin pathway in plant hormone signal transduction; the lignin synthetic pathway in phenylpropanoid biosynthesis; and photosystem II, photosystem I, photosynthetic electron transport, and F-type ATP pathway in photosynthesis may be related to 5-AzaC-induced saline–alkaline resistance. The results provided theoretical references for A. trifoliata cultivation in saline–alkaline soil and application of 5-AzaC to improve saline–alkaline tolerance in plants. creator: Xiao Xu Bi creator: Kai Wang creator: Xiaoqin Li creator: Jiao Chen creator: Jin Yang creator: Jin Yan creator: Guijiao Wang creator: Yongfu Zhang uri: https://doi.org/10.7717/peerj.19285 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bi et al. title: Associations of obesity-related indices with mild cognitive impairment in adults 60 years and older with type 2 diabetes: a retrospective study link: https://peerj.com/articles/19442 last-modified: 2025-05-13 description: ObjectiveTo investigate the relation between obesity-related indices and mild cognitive impairment (MCI) in elderly patients with type 2 diabetes (T2D).MethodsA total of 597 eligible elderly patients with T2D were included in this retrospective study. All patients were divided into MCI group and normal cognitive group based on neuropsychological assessment. Twelve obesity-related indices were calculated, including body mass index (BMI), waist-hip ratio (WHR), waist-to-height ratio (WHtR), lipid accumulation product (LAP), body roundness index (BRI), conicity index (CI), visceral adiposity index (VAI), body adiposity index (BAI), abdominal volume index (AVI), a body shape index (ABSI), triglyceride glucose (TyG) index and cardiometabolic index (CMI). Multivariate logistic regression analysis, tests for trend and restricted cubic splines were used to assess the relationships between the tests for trend and MCI in elderly patients with T2D. Receiver operating characteristic (ROC) curves and areas under the curves (AUC) were used to assess the performance and predictive ability of the obesity-related indices for identifying MCI in elderly patients with T2D.ResultsMultivariate logistic regression showed that elevated BMI, WHR, WHtR, LAP, BRI, CI, VAI, AVI, TyG index, and CMI were associated with an increased risk of MCI in elderly T2D patients after adjusting for potential confounders (all P < 0.05). In addition, TyG index, LAP, CMI, VAI, AVI, WHR, WHtR, BRI, and CI had negative correlations with Montreal Cognitive Assessment (MoCA) scores (all P < 0.05). There was a significant linear trend between the levels of BMI (P for trend = 0.004, P for non-linearity = 0.637), WHR (P for trend = 0.006, P for non-linearity = 0.430), WHtR (P for trend < 0.001, P for non-linearity = 0.452), BRI (P for trend < 0.001, P for non-linearity = 0.252), AVI ( P for trend < 0.001, P for non-linearity = 0.944), and TyG index (P for trend < 0.001, P for non-linearity = 0.514) and risk of MCI in elderly patients with T2D after adjusting for potential confounders. There was a nonlinear association between LAP, VAI or CMI and risk of MCI in elderly patients with T2D (all P for non-linearity < 0.001). CMI had the greatest AUC (AUC = 0.682), followed by VAI (AUC = 0.679), TyG index (AUC = 0.673), LAP (AUC = 0.669), AVI (AUC = 0.580), WHtR and BRI (AUC = 0.575), BMI (AUC = 0.560), CI (AUC = 0.556), WHR (AUC = 0.554), BAI (AUC = 0.547), and ABSI (AUC = 0.536).ConclusionElevated obesity-related indices, particularly CMI, VAI, TyG index and LAP, which displayed the higher predictive power, were instrumental in forecasting and evaluating MCI in elderly T2D patients. These findings may provide clues for future studies exploring early diagnostic biomarkers and treatment of MCI in elderly T2D patients. creator: Jing Feng creator: Zhenjie Teng creator: Shuchun Chen uri: https://doi.org/10.7717/peerj.19442 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Feng et al. title: Fitts’ law-based identification of motor development stages for the upper limb: proof of concept in three age groups link: https://peerj.com/articles/19433 last-modified: 2025-05-13 description: BackgroundPsychomotor development, including fine motor skills, progresses throughout childhood and stabilizes in adulthood. This process is closely tied to neurological maturation, with “reaching and pointing tasks” considered fundamental upper limb functions. According to Fitts’ law, movement time (MT) depends on the task’s index of difficulty (ID). From an Information Theory perspective, throughput (TP) reflects processing speed in reaching tasks, while error rate (ER) quantifies incorrect selections. As motor control improves, TP is expected to increase and ER to decrease, indicating greater efficiency and coordination. This study aimed to compare TP and ER across three age groups to assess motor control evolution.MethodsSixty participants were divided into three groups: children (5–6 years), adolescents (14–15 years), and adults (21–24 years). All participants performed a 2D reaching task on a tablet using their dominant hand, in accordance with the International Organization for Standardization (ISO) 9241-411 standard. Each participant completed 23 trials under four IDs, varying target size and distance. TP and ER were calculated and the data were statistically analyzed using an analysis of variance (ANOVA) and post-hoc tests to identify differences between groups.ResultsTP and ER showed significant differences across age groups. Children (5–6 years) had the lowest TP (3.84 ± 0.95 bits/s) and the highest ER (17.07 ± 8.15%). Adolescents (14–15 years) demonstrated higher TP (5.88 ± 0.64 bits/s) and lower ER (5.06 ± 3.13%), while adults (21–24 years) exhibited the highest TP (6.46 ± 1.05 bits/s) and a slightly higher ER (6.81 ± 5.07%) than adolescents. A one-way ANOVA confirmed a significant effect of age on TP (F2,57 = 47.18, p < 0.001, ${\rm \eta_p^2}$ηp2 = 0.623) and ER (F2,57 = 22.1, p < 0.001, ${\rm \eta_p^2}$ηp2 = 0.437). Post-hoc comparisons revealed that children had significantly lower TP and higher ER than both adolescents and adults (p < 0.001). Additionally, adolescents showed significantly lower TP than adults (p < 0.05). However, no significant differences in ER were found between adolescents and adults.ConclusionsThe results indicate that TP and ER, derived from Fitts’ law, effectively capture age-related differences in motor control across different developmental stages. These findings align with typical neuromotor development. Children show the lowest performance in both speed and accuracy, with adults outperforming both children and adolescents in processing speed, and adolescents demonstrating similar accuracy compared to adults. These metrics show potential for clinical and research applications, particularly in evaluating motor impairments or tracking rehabilitation progress in neurological conditions and advancing motor development research. Future studies should explore its use in clinical populations and across various age ranges to enhance assessment and intervention strategies. creator: Cristina Sanchez creator: Eloy Urendes creator: Alejandra Aceves creator: María Martínez-Olagüe creator: Rafael Raya uri: https://doi.org/10.7717/peerj.19433 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sanchez et al. title: Husbands’ knowledge and attitudes regarding postpartum depression link: https://peerj.com/articles/19426 last-modified: 2025-05-13 description: BackgroundPostpartum depression (PPD) is a prevalent mental health disorder that can occur anytime within the first year after childbirth. PPD has negative health consequences for mothers, infants, and other family members. Early detection and treatment are essential in mitigating these effects. This study aims to assess husbands’ knowledge and attitudes toward PPD among men aged 20 years and older residing in Saudi Arabia.MethodsThis study employed a cross-sectional design. Participants were recruited through social media and face-to-face methods using a convenience sampling approach. A total of 401 husbands were included in the study. The data were analyzed using descriptive statistics and Pearson’s simple correlation analysis.ResultsIn this study, the majority of participants (89.5%, n = 359) were Saudi nationals. Approximately half of the husbands (48.4%, n = 194) were between the ages of 30 and 39, whereas only 10% (n = 40) were 50 or older. Nearly half of the participants (45.4%) demonstrated a high level of knowledge about PPD. Additionally, 66.1% of the husbands had a positive attitude toward PPD and had received prior information about the condition. Family and friends were the most commonly cited sources of PPD knowledge. A positive correlation was found between husbands’ knowledge and attitudes toward PPD (r = 0.117, P < 0.005). Furthermore, significant associations were observed between husband’s knowledge and attitude and several sociodemographic characteristics, including nationality, educational level, occupation, monthly income, and years of marriage (P < 0.05).ConclusionThe husbands demonstrated a good level of knowledge and a positive attitude toward PPD. However, further research is needed to enhance their understanding and attitudes, particularly in addressing the negative beliefs about PPD identified in this study. creator: Aisha M. Aqeeli creator: Hanan A. Badr creator: Salmah A. Alghamdi uri: https://doi.org/10.7717/peerj.19426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Aqeeli et al. title: Multiplex polymerase chain reaction (PCR) with Nanopore sequencing for sequence-based detection of four tilapia pathogens link: https://peerj.com/articles/19425 last-modified: 2025-05-13 description: BackgroundTilapia aquaculture faces significant threats posed by four prominent pathogens: tilapia lake virus (TiLV), infectious spleen and kidney necrosis virus (ISKNV), Francisella orientalis, and Streptococcus agalactiae. Currently, employed molecular diagnostic methods for these pathogens rely on multiple singleplex polymerase chain reactions (PCR), which are time-consuming and expensive.MethodsIn this study, we present an approach utilizing a multiplex PCR (mPCR) assay, coupled with rapid Nanopore sequencing, enabling the one-tube simultaneous detection and one-reaction Nanopore sequencing-based validation of four pathogens.ResultsOur one-tube multiplex assay exhibits a detection limit of 1,000 copies per reaction for TiLV, ISKNV, and S. agalactiae, while for F. orientalis, the detection limit is 10,000 copies per reaction. This sensitivity is sufficient for diagnosing infections and co-infections in clinical samples from sick fish, enabling rapid confirmation of the presence of pathogens. Integrating multiplex PCR and Nanopore sequencing provides an alternative approach platform for fast and precise diagnostics of major tilapia pathogens in clinically sick animals, adding to the available toolbox for disease diagnostics. creator: Jérôme Delamare-Deboutteville creator: Watcharachai Meemetta creator: Khaettareeya Pimsannil creator: Han Ming Gan creator: Laura Khor creator: Mohan Chadag creator: Ha Thanh Dong creator: Saengchan Senapin uri: https://doi.org/10.7717/peerj.19425 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Delamare-Deboutteville et al. title: Susceptibility and resistance profiles of field and laboratory strains of Trogoderma granarium Everts to pirimiphos-methyl, alpha-cypermethrin and spinetoram link: https://peerj.com/articles/19423 last-modified: 2025-05-13 description: The khapra beetle, Trogoderma granarium Everts, 1898, is a significant pest of stored commodities worldwide. Insecticides are heavily relied upon to manage T. granarium. However, the long-term usage of insecticides has led to the development of resistance to insecticides, reducing their effectiveness against T. granarium. This study investigated variations in susceptibility to pirimiphos-methyl, alpha-cypermethrin and spinetoram in a laboratory and seven field strains of T. granarium, using dose-mortality bioassays. Metabolic resistance mechanisms were investigated through synergism studies using piperonyl butoxide (PBO) and S,S,S-tributyl phosphorotrithioate (DEF). Susceptibility of the laboratory strain was the highest to all insecticides compared to the field strains. For field strains, the LD50 values ranged from 25.9 to 49.6 mg/kg grain for pirimiphos-methyl, 15.0 to 40.5 mg/kg grain for alpha-cypermethrin, and 2.2 to 6.0 mg/kg grain for spinetoram. Compared to the laboratory strain, field strains of T. granarium exhibited significant resistance ratios ranging from: 19.9 to 38.1 fold against pirimiphos-methyl, 12.3 to 45.0 fold against alpha-cypermethrin, and 7.3 to 20.0 against spinetoram. In synergism bioassays, there was a significant effect of enzyme inhibitors on enhancing suceptibility to pirimiphos-methyl only in field strains, suggesting P450 monooxygenase and esterases may contribute to pirimiphos-methyl resistance. In conclusion, variable susceptibility to insecticides was observed across different strains of T. granarium. Reduced susceptibility to insecticides in field strains compared to the laboratory strain poses challenges for effective control of T. granarium. creator: Muhammad Bukhari creator: Hafiz Azhar Ali Khan uri: https://doi.org/10.7717/peerj.19423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bukhari and Khan title: Preventive behaviors of COVID-19 during the COVID-19 pandemic among community-dwelling older adults in Thailand link: https://peerj.com/articles/19412 last-modified: 2025-05-13 description: BackgroundThe COVID-19 pandemic was a major public health crisis, especially among older people. This study aimed to examine factors affecting preventive behaviors among community-dwelling older adults across all regions of Thailand during the COVID-19 pandemic using the health belief model (HBM).MethodsThis cross-sectional study included 910 participants from Thailand in July and August 2021. A multistage stratified random sampling technique was used to select participants. Data were collected through a structured interview process. Data analysis was conducted using multiple linear regression.ResultsThe participants’ mean age was 66.5 ± 4.64 years, with the majority being female (61.8%) and residing in the central region (26.5%). The results indicated that all participants (100.0%) agreed that COVID-19 can be prevented by personal protective equipment, such as masks and disposable gloves. Furthermore, the participants’ adherence to COVID-19 preventive measures was evaluated, revealing that the majority (55.8%) always practiced hand hygiene by washing hands with alcohol gel or soap and cleaning them with water before eating. Regression analysis indicated that COVID-19 preventive behaviors were significantly associated with knowledge (b = 0.091), perceived susceptibility (b = 0.066), perceived benefits (b = 0.111), perceived barriers (b = −0.040), and cues to action (b = 0.110) with p < 0.01.ConclusionsIncreased knowledge, perceived susceptibility, perceived benefits, cues to action, and decreased perceived barriers scores were associated with higher practice scores among community-dwelling older adults during the COVID-19 pandemic in Thailand. To improve practices, health information campaigns should focus on highlighting the advantages of preventive behaviors, offering tips and advice to overcome barriers, providing cues to action through various reminders on social media, and increasing awareness about disease prevention and control in future pandemics or new disease outbreaks. creator: Kanchana Piboon creator: Jarinthip Chomchaipon creator: Dhammawat Ouppawongsapat creator: Wanlop Jaidee creator: Patchana Hengboriboonpong Jaidee creator: Paiboon Pongsaengpan creator: Wiriya Mahikul uri: https://doi.org/10.7717/peerj.19412 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Piboon et al. title: Has_circRNA_0122683 (circ-PRKCI) relieves ferroptosis of HPAEpiCs in sepsis-induced acute lung injury by sponging miR-382-5p link: https://peerj.com/articles/19404 last-modified: 2025-05-13 description: Circular ribonucleic acid (RNA) protein kinase C iota (circ-PRKCI, hsa_circRNA_0122683) has been previously reported to be involved in the development of sepsis. However, the knowledge regarding the potential role and mechanism of circ-PRKCI in sepsis-induced acute lung injury (ALI) is unclear. An in vitro cellular model of sepsis-ALI was simulated by the treatment of lipopolysaccharide (LPS) in human pulmonary alveolar epithelial cells (HPAEpiCs). The expression of circ-PRKCI in plasma samples from sepsis patients with or without ALI as well as sepsis-ALI cell model was determined by quantitative real-time PCR (qRT-PCR). The diagnostic utility of circ-PRKCI was analyzed using receiver operating characteristic (ROC) curves. The levels of iron content (Fe2+), glutathione (GSH), malondialdehyde (MDA), and reactive oxygen species (ROS) were detected using corresponding commercial kits. The assessment of cell viability and production of pro-infammatory cytokines (IL-6, IL-1β and TNF-α) was measured using Cell Counting Kit-8 (CCK-8) and enzyme-linked immunosorbent assay (ELISA). The targeting relationship between circ-PRKCI and miR-382-5p was predicted by bioinformatics analysis, and subsequently confirmed by luciferase reporter and RNA immunoprecipitation (RIP) assays. Results shows that decreased circ-PRKCI expression but increased miR-382-5p expression was observed in sepsis patients with ALI and sepsis-induced ALI cell model. The area under the curve values of ROC curves for circ-PRKCI in differentiating septic ALI patients from healthy individuals and septic non-ALI patients were 0.996 and 0.999, respectively. Functional in vitro assays revealed that enforced expression of circ-PRKCI alleviated LPS-induced ferroptosis and inflammatory response of HPAEpiCs, which were reversed by Erastin or FIN56 administration. Mechanistically, circ-PRKCI was identified as a sponge of miR-382-5p and negatively regulated miR-382-5p expression. Further rescue experiments showed that miR-382-5p overexpression could compromise the anti-ferroptosis and anti-inflammatory response effects of circ-PRKCI on LPS-induced injury of HPAEpiCs. Our study demonstrated that circ-PRKCI may be a promising biomarker for septic ALI diagnosis. circ-PRKCI inhibits ferroptosis and inflammatory response in sepsis-induced ALI by sponging miR-382-5p, indicating that the circ-PRKCI/miR-382-5p axis might be a novel therapeutic target for the treatment of sepsis-induced ALI. creator: Limei Yan creator: Xiajun Lu creator: Ning Wang creator: Peng Jia uri: https://doi.org/10.7717/peerj.19404 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Yan et al. title: Antarctic macroalgal-associated amphipod assemblages exhibit long-term resistance to ocean acidification link: https://peerj.com/articles/19368 last-modified: 2025-05-13 description: The pH of the world’s oceans has decreased since the Industrial Revolution due to the oceanic uptake of increased atmospheric CO2 in a process called ocean acidification. Low pH has been linked to negative impacts on the calcification, growth, and survival of calcifying invertebrates. Along the Western Antarctic Peninsula, dominant brown macroalgae often shelter large numbers of diverse invertebrate mesograzers, many of which are calcified. Mesograzer assemblages in this region are often composed of large numbers of amphipods which have key roles in Antarctic macroalgal communities. Understanding the impacts of acidification on amphipods is vital for understanding how these communities will be impacted by climate change. To assess how long-term acidification may influence the survival of different members in these assemblages, mesograzers, particularly amphipods, associated with the brown alga Desmarestia menziesii were collected from the immediate vicinity of Palmer Station, Antarctica (S64°46′, W64°03′) in January 2020 and maintained under three different pH treatments simulating ambient conditions (approximately pH 8.1), near-future conditions for 2100 (pH 7.7), and distant future conditions (pH 7.3) for 52 days then enumerated. Total assemblage number and the relative proportion of each species in the assemblage were found to be similar across the pH treatments. These results suggest that amphipod assemblages associated with D. menziesii may be resistant to long-term exposure to decreased pH. creator: Hannah E. Oswalt creator: Julie B. Schram creator: Margaret O. Amsler creator: Charles D. Amsler creator: James B. McClintock uri: https://doi.org/10.7717/peerj.19368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Oswalt et al. title: Effects of perioperative massive transfusion on postoperative outcomes of children undergoing brain tumor removal: a retrospective cohort study link: https://peerj.com/articles/19350 last-modified: 2025-05-13 description: ObjectiveTo examine the influence of massive perioperative transfusion on both short-term and long-term outcomes in children undergoing brain tumor resection.MethodsThis retrospective cohort study analyzed pediatric patients who underwent brain tumor surgeries at the Women and Children’s Medical Center, Guangzhou Medical University, between October 2014 and March 2022. Massive transfusion was characterized as the transfusion of red blood cells equivalent to or exceeding the estimated preoperative blood volume within 48 h after surgery. To evaluate the relationship between massive transfusion and patient outcomes, logistic regression models were utilized. Survival curves were constructed to compare the long-term outcomes of patients who received massive transfusion with those who did not. The primary outcomes assessed were 30-day all-cause mortality (short-term outcomes) and 1-year survival rates (short-term outcomes).ResultsAmong the 306 patients included in the analysis, 78 were categorized as part of the massive transfusion group, while 228 were in the non-massive transfusion group. Multivariable regression analysis indicated that perioperative massive transfusion was significantly linked to an increased risk of 30-day mortality (odds ratio (OR): 0.137, 95% confidence interval (CI) [0.036–0.528], p = 0.004). Additionally, patients in the massive transfusion group exhibited higher incidences of postoperative intracranial hypertension (OR: 4.788, 95% CI [1.547–14.824], p = 0.007), extended mechanical ventilation duration (OR: 0.247, 95% CI [58.739–147.895], p < 0.001), and prolonged intensive care unit (ICU) stays (ß = 0.184, 95% CI [3.874–15.077], p = 0.001).ConclusionsMassive transfusion has a pronounced impact on short-term outcomes, particularly increasing perioperative mortality and complication risks in children undergoing brain tumor surgery. Careful consideration of the risks and benefits of transfusion is crucial in managing these cases. creator: Yingyi Xu creator: Na Zhang creator: Xinxu Ou creator: Yuyin Ye creator: Jianhua Liu creator: Siyi Zhang creator: Xinke Xu creator: Yu Gao creator: Wenchu Chen creator: Xingrong Song uri: https://doi.org/10.7717/peerj.19350 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xu et al. title: Mechanical loading regulates osteogenic differentiation and bone formation by modulating non-coding RNAs link: https://peerj.com/articles/19310 last-modified: 2025-05-13 description: Bone tissue is highly responsive to mechanical stimuli, with mechanical loading serving as a crucial regulator of bone formation and resorption. The cellular transduction of mechanical loading involves intricate mechanisms, prominently featuring non-coding RNAs (ncRNAs). Various ncRNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), collaboratively regulate pathways involved in bone formation under mechanical loading. This article elucidates the mechanisms by which mechanical loading influences bone formation through ncRNAs, summarizing key ncRNAs and their regulatory pathways. Aimed at researchers and clinicians in molecular biology, orthopedics, and regenerative medicine, this study provides a theoretical foundation for the future application of mechanical loading to regulate osteogenic differentiation and offers insights into treating diseases associated with abnormal bone formation. creator: Huili Deng creator: Dongfeng Wan uri: https://doi.org/10.7717/peerj.19310 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Deng and Wan title: Efficacy of high-frequency sonic irrigation on removing debris from root canal isthmus: an in vitro study based on simulated root canals link: https://peerj.com/articles/19445 last-modified: 2025-05-12 description: BackgroundInfection control is important in root canal treatment. Effective cleaning and shaping are challenging due to complex anatomy, particularly in the isthmus—narrow connections between canals that can harbor bacteria. Conventional needle irrigation (CNI) is inadequate in this region, prompting the use of passive ultrasonic irrigation (PUI) and high-frequency acoustic instruments like EDDY. This study evaluates the cleaning effects of four irrigation protocols using 3D-printed isthmus models.MethodsSixty digital root canal models with isthmuses in the coronal, middle, and apical thirds were designed using Ansys 19.0 and 3D printer (20 specimens per isthmus location). Specimens were prepared to 30#, 0.04 without irrigation. Debris accumulation in the isthmus was photographed and analyzed using Image J to calculate the initial debris area (S1). Specimens were then irrigated using CNI, low-frequency sonic irrigation (EndoActivator, EA; Dentsply, Charlotte, NC, USA), PUI, or high-frequency sonic irrigation (EDDY), followed by re-imaging to calculate remaining debris area (S2). Debris reduction percentage was determined using the formula: (S1–S2)/S1 × 100%.ResultsDebris reduction varied with isthmus position. In the coronal third, EDDY achieved the highest debris reduction (86.18 ± 2.25%), followed by PUI, EA, and CNI, with significant differences among groups (P < 0.05). The same trend was observed in the middle third, with EDDY showing the highest efficacy (73.96 ± 6.75%). In the apical third, debris reduction was lower overall, with no significant difference between EDDY and PUI, but both outperformed EA and CNI.DiscussionOur results showed that EDDY demonstrated superior debris removal in the coronal and middle thirds, but all irrigation protocols showed limited efficacy in the apical third. creator: Chun-Hui Liu creator: Qiang Li creator: Xiao-Ying Zou creator: Lin Yue uri: https://doi.org/10.7717/peerj.19445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: A cross-sectional study evaluating insulin injection techniques and the impact of instructions from various healthcare professionals on insulin users in the southern region of Saudi Arabia link: https://peerj.com/articles/19394 last-modified: 2025-05-12 description: BackgroundIt is evident that proper use of the insulin injection technique (IIT) is important for optimizing the efficacy of the therapy. Despite the readily available manufacturers’ instructions, healthcare professionals (HCPs) play a major role in educating patients. This study aims to investigate the knowledge, practices, and challenges faced by insulin users regarding IIT, as well as the impact of healthcare professionals’ education on it.MethodsWe conducted a questionnaire-based cross-sectional study using a validated online questionnaire to gather demographic and clinical data, as well as the participants’ knowledge, practices, and challenges related to insulin therapy.ResultsThe mean age of the participants was 38.25 ± 15.58 (mean ± SD) years, with a nearly equal distribution of genders. Thirty-six percent of the participants educated by the diabetes educators demonstrated an appropriate IIT, such as storage, priming the insulin pen (54%), skin folding (63%), injection hold time, and “use-by” date. Furthermore, the absence of diabetes education specialist training increases the likelihood of errors, potentially leading to a loss of glycemic control. Patients reported carrying insulin when traveling as one of the major challenges (27.9%), followed by timely injections (23.7%), priming (21.6%), and adjusting the insulin dose (16.8%). Forgetfulness (47.7%), traveling or altering the regular routine (15.5%), missing a meal (15.5%), and being overly busy (13.5%) were among the reasons for missing the insulin dose; all of which are easily manageable with proper education.ConclusionConsistent education and re-education are necessary for the insulin users to resolve the issues associated with suboptimal IIT. The inclusion of all stakeholders in insulin therapy, particularly the diabetes education specialists, is essential. Therefore, the Ministry of Health in Saudi Arabia should take the initiative to ensure that appropriately trained diabetes education specialists, pharmacists, nurses and other HCPs assess and follow up on patients. creator: Sirajudeen Shaik Alavudeen creator: Md Sayeed Akhtar creator: Sultan Mohammed Alshahrani creator: Vigneshwaran Easwaran creator: Asif Ansari Shaik Mohammad creator: Noohu Abdulla Khan creator: Abubakr Taha Hussein creator: Salem Salman Almujri creator: Abdulrahman Saeed Alshaiban creator: Khalid Orayj uri: https://doi.org/10.7717/peerj.19394 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shaik Alavudeen et al. title: The effect of patellar taping combined with isometric strength training on pain, muscle strength, and functional performance in patients with patellofemoral pain syndrome: a randomized comparative study link: https://peerj.com/articles/19381 last-modified: 2025-05-12 description: BackgroundPatellar taping and quadriceps strengthening exercises are commonly used in physiotherapy to manage patellofemoral pain syndrome (PFPS). However, previous research has reported inconsistent findings regarding quadriceps strength gains at specific knee angles during strength training in individuals with PFPS.ObjectivesThis study investigated the efficacy of patellar taping and quadriceps isometric strength training (quadriceps-IST) at 60° knee flexion on quadriceps strength, pain, and functional performance in female patients with PFPS.MethodsA two-arm, parallel-group, randomized comparative design was employed. Sixty adult females with PFPS were randomly assigned to either the experimental group (n = 30), which received patellar taping combined with quadriceps strength training at 60°, or the control group (n = 30), which received placebo taping with the same training. Both interventions lasted six weeks. Pain intensity, quadriceps muscle strength, and functional performance were assessed using the numeric pain rating scale (NPRS), maximum voluntary isometric contraction (MVIC) at 60° knee flexion, single leg triple hop (SLTH) test, and anterior knee pain scale (AKPS). For within and between groups comparison, a Wilcoxon signed-rank test and a Mann–Whitney U tests was employed, with confidence interval (α) set at 95%.ResultsWithin-group analysis showed significant improvements in NPRS and MVIC at 60° knee flexion, SLTH, and AKPS scores post-intervention (p < 0.05). Between-group comparisons revealed that the experimental group had significantly greater improvements in all outcomes at six weeks post-intervention. Additionally, the pre-to-post changes (i.e., mean difference scores) were larger in the experimental group compared to the control group, which confirmed the superiority of the experimental group over the control group.ConclusionsThe study demonstrates that patellar taping combined with quadriceps -IST at a 60° knee flexion improves pain, muscle strength, and functional performance compared to placebo taping combined with quadriceps-IST. These findings suggest that incorporating this combined approach may enhance rehabilitation outcomes for patients with PFPS, providing a valuable addition to clinical practice.Trial registrationThis study was registered prospectively in the ClinicalTrials.gov PRS under a trial identifier NCT05168332 and last updated date 15/03/2024. creator: Shahnaz Hasan uri: https://doi.org/10.7717/peerj.19381 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hasan title: Risk assessment of heavy metal toxicity induced by platinum accumulation in tumor patients link: https://peerj.com/articles/19375 last-modified: 2025-05-12 description: BackgroundMany studies have focused on adverse reactions caused by platinum drugs but neglected subsequent toxicities and the mechanisms during patient recovery after chemotherapy with different platinum drugs, which need attention because of the heavy metal platinum.ObjectivesWe aimed to explore the correlations between platinum accumulation, hematological indices, and clinical toxicity in patients after a metabolism period following platinum drug chemotherapy, to better understand real-world clinical toxicity caused by platinum accumulation.MethodsWe enrolled patients receiving platinum chemotherapy, specifically cisplatin, oxaliplatin, or carboplatin. On the 25th day post-chemotherapy, we measured serum platinum concentrations and hematological indices, documented clinical toxicities, and subsequently performed correlation analyses.ResultsThe serum platinum concentrations in oxaliplatin-, cisplatin-, and carboplatin-treated patients were 208.60, 349.15 and 211.30 µg/L (χ2 = 51.755, p < 0.001), respectively. Mediation effect analysis showed that decreased erythrocyte, hemoglobin and glutamic-pyruvic transaminase individually mediated 21.39, 12.0 and 10.94%, respectively, of the platinum positive effect on fatigue. Decreased erythrocyte counts mediated 5.89%, while increased creatinine mediated 5.2% of the platinum positive effect on adverse reactions. The cutoff values of hematological indices, the risk of adverse reactions and fatigue were also obtained in this research which will be applied in clinical practice.Discussion and ConclusionsPlatinum accumulation, by disrupting the red blood cell system and liver and kidney function, influences fatigue severity and common adverse reactions in patients during the post-chemotherapy recovery period. creator: Yuling Zhang creator: Pi Guo creator: Xiaoting Huang creator: Yi-Wei Xu creator: Zhiwei Zheng creator: Ling Fang uri: https://doi.org/10.7717/peerj.19375 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhang et al. title: Perceived fear and exercise difficulty in patients with migraine and their association with psychosocial factors: a cross-sectional study link: https://peerj.com/articles/19342 last-modified: 2025-05-12 description: PurposeAlthough pharmacological treatments for migraine have advanced, non-pharmacological approaches, such as exercise, offer additional benefits. However, many patients avoid physical activity due to fear of symptom exacerbation. This study aims to identify the most threatening and difficult exercises for patients with migraine and examine the relationship between exercise perceptions and factors such as physical activity levels, kinesiophobia, catastrophizing, and self-efficacy.MethodsThis cross-sectional study explored the perceived fear and difficulty of nine exercises shown via video demonstrations, and their association with psychological variables in patients with migraine. Participants aged 18–65 with physician-diagnosed migraines completed self-report measures of physical activity, kinesiophobia, catastrophizing, fear-avoidance beliefs, headache impact, neck disability, and self-efficacy.ResultsA total of 110 patients with migraine participated (88% women), with a mean age of 36 years. Chronic migraine was reported by 53% of participants. Significant differences in perceived fear and difficulty were observed across the nine exercises (p < 0.001), with jumping and spine extension rated as the most fear-inducing and difficult exercises, respectively. Beta regression models showed that the physical activity level, measured by the short form of the International Physical Activity Questionnaire (IPAQ-SF), was negatively associated with fear of jumping and difficulty of spine extension, whereas fear-avoidance beliefs were positively associated with both. A correlation analysis revealed a moderately significant negative association between the IPAQ-SF score and perceived fear of running.ConclusionJumping, running, and spine extension were perceived as the most aversive exercises. Perceived fear and difficulty levels were associated with physical activity levels and fear avoidance beliefs, emphasizing the need to assess these factors before implementing therapeutic exercise interventions. creator: Álvaro Reina-Varona creator: Beatriz Madroñero-Miguel creator: Alba Paris-Alemany creator: Roy La Touche uri: https://doi.org/10.7717/peerj.19342 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Reina-Varona et al. title: The acute effects of simulated hypoxic training at different altitudes on oxidative stress and muscle damage in elite long-distance runners link: https://peerj.com/articles/19338 last-modified: 2025-05-12 description: BackgroundUnderstanding the impact of altitude on muscle damage and oxidative stress is essential for optimizing training and recovery strategies for athletes exposed to high-altitude conditions. Therefore, this study aimed to investigate the effects of acute exercise at different altitudes on oxidative stress and muscle damage.MethodsA total of twelve elite long-distance runners (mean age: 20.3 ± 1.5 years) from different branches participated in the study. The exercise protocol was the Bruce submaximal treadmill exercise test, which was conducted under three simulated hypoxic conditions (at 1,700 m, 2,450 m, and 3,200 m) and one normoxic condition (sea level). All measurements took place at the same time of the day. After the exercise protocol, 5 ml venous blood samples were taken from the participants, while heart rate and oxygen saturation were monitored at the 3rd, 6th, 9th, and 12th minutes during the exercise.ResultsSignificant altitude-dependent variations were observed in oxidative stress markers, with total oxidant status (TOS) (p = 0.017) and malondialdehyde (MDA) (p < 0.001) levels increasing at higher altitudes, while total antioxidant status (TAS) (p < 0.001) exhibited an elevation and oxidative stress index (OSI) (p < 0.001) demonstrated a decline as altitude increased. However, no significant difference was found in creatine kinase (CK, p = 0.059) levels. Additionally, there were significant differences in the oxygen saturation measurement taken at the 3rd (p < 0.001), 6th (p < 0.001), 9th (p < 0.001), and 12th (p < 0.001), minutes following the exercise session. There was no difference in the pulse measurement taken at the 3rd and 12th minutes, but a difference was observed at the 6th and 9th minutes post-exercise (p < 0.01).ConclusionsIn conclusion, the study determined that endurance exercises performed under simulated normobaric hypoxia at different altitudes increased TAS and reduced OSI in elite long-distance runners. The increase in TAS and the reduction in OSI were more pronounced at higher altitudes, particularly at 2,450 m and 3,200 m, compared to sea level. These findings highlight the need for altitude-specific training and recovery strategies to minimize oxidative stress and muscle damage in athletes. creator: Mücahit Sarikaya creator: Beyza Öğe creator: Nuri Mert Embiyaoğlu creator: Muzaffer Selçuk creator: Vedat Çınar creator: Salih Öner creator: Yıldırım Gökhan Gencer creator: Mehdi Aslan creator: Mustafa Sencer Ulema creator: Yunus Emre Yarayan creator: Kadir Keskin creator: Nouf H. Alkhamees creator: Bodor Bin Sheeha creator: Gerasimos V. Grivas creator: Sameer Badri AL-Mhanna creator: Alexios Batrakoulis uri: https://doi.org/10.7717/peerj.19338 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sarikaya et al. title: Establishment and validation of systemic inflammatory index model and risk assessment of PVT in cirrhosis after splenectomy—a retrospective study link: https://peerj.com/articles/19254 last-modified: 2025-05-12 description: ObjectiveThe study aimed to create and validate a straightforward nomogram to predict portal vein thrombosis (PVT) in cirrhotic patient post-splenectomy, and investigate the predictive potential of systemic inflammation markers. One objective of the study was to develop a predictive model utilizing these markers to detect high-risk individuals early on.MethodsA retrospective analysis was conducted on 184 cases of patients with cirrhosis who underwent splenectomy at The First Affiliated Hospital of University of South China from January 2015 to September 2023. The cohort was randomly divided into training (n = 130) and validation (n = 54) groups. Univariate and multivariate logistic regression analysis was employed to construct the prediction model. The performance of the nomogram was evaluated based on its ability to discriminate, calibrate, and demonstrate clinical utility.ResultsAccording to univariate and multivariate logistic regression analysis, we found six prediction indexes of PVT in patients with cirrhosis after splenectomy: postoperative neutrophil-to-lymphocyte ratio (NLR), postoperative derived NLR (dNLR), C-reactive protein to albumin ratio (CAR), portal vein diameter (DPV), platelet change value (PVB), and D-dimer (p-value < 0.05). Our clinical prediction model was created based on the aforementioned risk factors and demonstrated superior predictive power in both the primary cohort (AUC = 0.876) and validation cohort (AUC = 0.817). The calibration curve demonstrated satisfactory agreement between model predictions and actual observations, and the decision curve analysis (DCA) curve indicated high clinical net benefit.ConclusionPostoperative NLR, dNLR, CAR, PVB, DPV, and D-dimer were identified as the independent risk factors of PVT in cirrhotic patients post splenectomy. We had successfully established and validated a novel predictive model with good performance, based on systemic inflammatory indices in predicting PVT in cirrhosis after splenectomy. creator: Xin Deng creator: Wenyan Liao creator: Xinmiao Jiang creator: Shun Tu creator: Xiangmin Xie creator: Yuji Xiao creator: Wuyao Chen creator: Huan Zeng creator: Chengming Ding uri: https://doi.org/10.7717/peerj.19254 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Deng et al. title: In vitro feasibility of bovine and canine whole blood and commercially prepared canine packed red blood cells as a source of xenotransfusion in swine (Sus scrofa domestica) link: https://peerj.com/articles/19436 last-modified: 2025-05-09 description: Background: Since sourcing porcine blood donors for emergent transfusions to porcine patients is difficult, bovine or canine blood donors might represent alternative sources. The primary objective of this study was to determine the frequency of incompatible major (CMMa) and minor (CMMi) crossmatches by the standard saline agglutination tube method (SSA) between bovine whole blood (bWB) and whole blood from commercial pigs (pWB), and canine universal donor whole blood or commercially-prepared packed red blood cells (pRBCs) with whole blood from companion pigs. A secondary objective was determining the agreement between the reference method (SSA) and a quick slide (QS) method.Methods: Blood was collected from 12 heifers, seven companion pigs, and eight commercial-cross pigs. A0 blood typing was performed for all porcine samples. Bovine blood was pooled into eight bags each containing three crossmatch-compatible individuals. Canine blood included whole blood from three canine blood donors (DEA 1.1, 5, 7 negative, and DEA 4 positive), and three bags each of DEA 1.1 negative and DEA 1.1 positive pRBCs. Crossmatch pairs were performed for bovine-to-porcine (n = 64) and canine-to-porcine (n = 63) samples. Incompatibility was defined as any agglutination or hemolysis on either CMMa and CMMi and reported separately. Complete incompatibility was defined as incompatibility of both CMMa and CMMi on the same pair. Kappa statistics tested the agreement between SSA and QS (significance at P < 0.05).Results: For bWB and pWB, agglutination was observed in 9.4% of CMMa and 100% of CMMi via SSA. Incompatibility on CMMa of bWB was more frequent with porcine blood type “0” (P = 0.0107) than with type “A”, whereas porcine blood group had no effect on CMMi results. All canine-to-porcine CMMa were incompatible with SSA and showed hemolysis severe enough to prevent evaluation of agglutination. The accuracy of QS at detecting incompatibilities was 87.5% in CMMa and 98.4% in CMMi in bovine-to-porcine samples. Agreement between SSA and QS methods was fair (k = 0.36) for bovine-to-porcine CMMa but could not be calculated for CMMi due to lack of compatible matches. Because all canine-to-porcine CMMa were incompatible, the effects of the porcine blood group on incompatibility, accuracy of QS, and agreement between SSA and QS could not be calculated for CMMa. For CMMi, the agreement between tests was poor (k = 0).Discussion: When a xenotransfusion to a pig is indicated, bWB appears to be suitable based on in vitro CMMa testing, whereas canine blood products are contraindicated for in vivo administration to swine based on absolute CMMa incompatibility and incidence of hemolysis. In vivo studies are needed to elucidate the clinical significance of CMMi incompatibilities. Based on these results, QS cannot be accurately used as a surrogate of SSA in pretransfusion testing for porcine patients due to the increased risk of false compatible results as QS can only be identified as agglutination, not hemolysis. creator: Victoria Diaz creator: Deanna M. W. Schaefer creator: Pierre-Yves Mulon creator: Xiaojuan Zhu creator: Joe Smith creator: Luca Giori creator: Chiara Hampton uri: https://doi.org/10.7717/peerj.19436 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Diaz et al. title: Past agricultural practices explain old field biodiversity and community composition in annually mowed grasslands: a case study of grazing and cultivation legacies in the northeastern United States link: https://peerj.com/articles/19420 last-modified: 2025-05-09 description: The northeastern United States experienced extensive deforestation for agriculture expansion and nearly equal passive reforestation following agriculture abandonment across the region over the past century. Old fields provide critical habitat as grasslands in the Northeast but tend to return to forests without intervention unless land managers implement disturbance regimes to maintain grassland states in the region. The relative importance of past and present disturbances in old field plant communities remains poorly resolved, partly because management varies widely in these systems. This motivated the present case study, which compares two proximate old fields that benefit from long and consistent management practices both before and after agriculture was abandoned in Hanover, NH. One field experienced agricultural disturbances associated with grazing while the other experienced cultivation each for 116 years followed by 50 years of the same annual mowing disturbances after agriculture was abandoned. Diversity was higher, communities more convergent across sub-plots, and woody individuals three times more numerous in the grazed site, while soil texture, type, elevation, and drainage had no discernible impact. The study helps to clarify the different legacies of grazing and cultivation on old field plant community diversity and composition. Despite undergoing 50 years of mowing following agriculture abandonment, the two old fields have divergent communities that are more consistent with the intensity of historic agricultural practices at each site than with any differences in measured soil characteristics. Understanding how agricultural legacies combine with contemporary disturbance regimes to shape successional communities may improve conservation and restoration efforts of grassland habitats and other ecosystems undergoing rapid environmental change, with implications for biodiversity, ecosystem services, and resilience. creator: Alana M. Danieu creator: Theresa W. Ong uri: https://doi.org/10.7717/peerj.19420 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Danieu and Ong title: Deep learning-based fine-grained assessment of aneurysm wall characteristics using 4D-CT angiography link: https://peerj.com/articles/19393 last-modified: 2025-05-09 description: PurposeThis study proposes a novel deep learning-based approach for aneurysm wall characteristics, including thin-walled (TW) and hyperplastic-remodeling (HR) regions.Materials and MethodsWe analyzed fifty-two unruptured cerebral aneurysms employing 4D-computed tomography angiography (4D-CTA) and intraoperative recordings. The TW and HR regions were identified in intraoperative images. The 3D trajectories of observation points on aneurysm walls were processed to compute a time series of 3D speed, acceleration, and smoothness of motion, aiming to evaluate the aneurysm wall characteristics. To facilitate point-level risk evaluation using the time-series data, we developed a convolutional neural network (CNN)—long- short-term memory (LSTM)-based regression model enriched with attention layers. In order to accommodate patient heterogeneity, a patient-independent feature extraction mechanism was introduced. Furthermore, unlabeled data were incorporated to enhance the data-intensive deep model.ResultsThe proposed method achieved an average diagnostic accuracy of 92%, significantly outperforming a simpler model lacking attention. These results underscore the significance of patient-independent feature extraction and the use of unlabeled data.ConclusionThis study demonstrates the efficacy of a fine-grained deep learning approach in predicting aneurysm wall characteristics using 4D-CTA. Notably, incorporating an attention-based network structure proved to be particularly effective, contributing to enhanced performance. creator: Teerawat Kumrai creator: Takuya Maekawa creator: Yixuan Chen creator: Yoshie Sugiyama creator: Masatoshi Takagaki creator: Shigeo Yamashiro creator: Katsumi Takizawa creator: Tsutomu Ichinose creator: Fujimaro Ishida creator: Haruhiko Kishima uri: https://doi.org/10.7717/peerj.19393 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kumrai et al. title: Endophytic fungal community composition and function response to strawberry genotype and disease resistance link: https://peerj.com/articles/19383 last-modified: 2025-05-09 description: BackgroundUtilizating the plant endophytic microbiomes to enhance pathogen resistance in crop production is an emerging alternative method to chemical pesticides. However, research on the composition and role of microbial communities related to perennial fruit plants, such as the strawberry, is still limited.MethodsWe provide a comprehensive description of the composition and diversity of fungal communities in three niches (root, stem, and leaf) of three strawberry cultivars (‘White Elves’, ‘Tokun’, and ‘Akihime’) using internal transcribed spacer (ITS) rRNA amplicon sequencing and isolation culture methods. In addition, we also evaluated the disease tolerance ability of three strawberry cultivars to Colletotrichum gloeosporioides and Alternaria alternata through pathogenicity testing.Results‘White Elves’ has stronger resistance to Colletotrichum gloeosporioides, and Alternaria alternata, followed by ‘Tokun’, while ‘Akihime’ has relatively weaker resistance to these pathogens. A total of 258 fungal strains were isolated from healthy strawberry plants and assigned to 34 fungal genera based on morphological and molecular characteristics analysis. Beneficial fungal genera such as Trichoderma and Talaromyces were more prevalent in ‘White Elves’, whereas common pathogenic fungi in strawberry, such as Colletotrichum, Alternaria, and Fusarium, were more prevalent in ‘Akihime’. The composition and diversity of microbial communities vary among genotypes, and resistance to pathogens may play dominant roles in determining the microbial community structure. This study’s results aid the biological control of strawberry fungal diseases and are useful for plant microbiome engineering in strawberry cultivation. creator: Hongjun Yang creator: Xu Zhang creator: Rui Wang creator: Quanzhi Wang creator: Yuanhua Wang creator: Geng Zhang creator: Pengpeng Sun creator: Bei Lu creator: Meiling Wu creator: Zhiming Yan uri: https://doi.org/10.7717/peerj.19383 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Yang et al. title: Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes link: https://peerj.com/articles/19376 last-modified: 2025-05-09 description: BackgroundTropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.MethodsWe used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.ResultsThe bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.ConclusionsOur data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank. creator: Rodolfo Martínez-Mota creator: Antonio Acini Vásquez-Aguilar creator: Dolores Hernández-Rodríguez creator: Emilio A. Suárez-Domínguez creator: Thorsten Krömer uri: https://doi.org/10.7717/peerj.19376 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Martínez-Mota et al. title: Response surface optimization and flavor determination of fermentation processes of orange peel tea wine link: https://peerj.com/articles/19357 last-modified: 2025-05-09 description: BackgroundIn this study, Xinyang Maojian tea and orange peel were used as raw materials to brew health wine with orange and tea flavors.MethodsBased on a single factor, the response surface method was used to optimize the fermentation of orange peel tea wine. Material volume ratio, yeast addition, fermentation temperature, fermentation time, and sucrose addition were used as the single-factor variables. The fermentation conditions of orange peel tea wine obtained by this method provide a theoretical basis for the development and utilization of tea wine and orange peel, which can promote the development of the tea wine market.ResultsThe results showed that the material volume ratio of orange peel juice to tea juice was 1:3, the yeast addition amount was 4.9%, the fermentation temperature was 29 °C, the fermentation time was 7 d, and the sucrose addition amount was 29%. The main change indexes in the fermentation process of orange peel tea wine were determined, and the results were consistent with the fermentation law of orange peel tea wine. The contents of total flavonoids and total phenols in orange peel tea wine were 0.48 and 2.32 mg/mL, respectively, and were obtained using spectrophotometry and the Folin–Ciocalteu (F–C) method. The scavenging rate of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals was 90.8%, and the scavenging rate of ·OH radicals was 77.3%. A total of 26 flavor compounds were detected by gas chromatography-mass spectrometry (GC-MS). The main aroma compounds were ethanol, 3-methyl-1-butanol, 2-methyl-1-propanol, phenylethyl alcohol, acetic acid, n-hexadecanoic acid, 2,4-di-tert-butylphenol, and other compounds.ConclusionThe resulting orange peel tea wine was transparent, yellow in color, harmonious in flavor, and had certain health benefits, including strong antioxidant properties. The results of this study provide the theoretical basis for the research and development of tea wine. creator: Yanbo Liu creator: Liu Mengge creator: Pengpeng Zhang creator: Wenxi Liu creator: Chong Yang creator: Jiayi Cui creator: Haideng Li creator: Chunmei Pan uri: https://doi.org/10.7717/peerj.19357 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Taxonomic and ecologic transitions in Triassic marine bivalve communities link: https://peerj.com/articles/19237 last-modified: 2025-05-09 description: The Permian–Triassic mass extinction was a pivotal event in shaping marine benthic ecosystems, leading to the rise of mollusks such as bivalves and gastropods as representatives of the Modern Evolutionary Fauna. However, the detailed changes in the ecological structure of marine benthic communities throughout the Triassic remain underexplored, particularly the interrelationship between taxonomic and ecological diversities. Here, we present a study on the Triassic bivalve communities from the typical shallow marine facies in South China to document regional evolutionary patterns and explore how these patterns connect to the global trends. Broad congruence in the timing of taxonomic and ecological changes was observed through the Triassic in South China. However, both the South China materials and global data revealed a decoupling of taxonomic and ecological diversities. Substantial variability in taxonomic richness was observed alongside stable ecological diversity. Taxonomic recovery occurred early in the Early Triassic, whereas ecological diversity fully recovered only in the Middle Triassic. The Carnian stage represents a significant transition in ecosystem structure, characterized by a shift towards infaunal dominance and the expansion of habitat depth. creator: Xue Miao creator: Jinnan Tong creator: Yunfei Huang creator: Shiyan Zhang creator: Peishan Li creator: Yiran Cao creator: Daoliang Chu creator: Wolfgang Kiessling uri: https://doi.org/10.7717/peerj.19237 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Miao et al. title: Effects of 12-week integrative neuromuscular training on muscular fitness and sex differences in response to intervention in five- to six-year-old preschoolers link: https://peerj.com/articles/19417 last-modified: 2025-05-08 description: ObjectivesThis study examined the effects of a 12-week integrative neuromuscular training (INT) program on muscular fitness in male and female five- to six-year-old preschoolers.MethodsThirty preschoolers were randomly assigned to either an experimental group (EG; n = 15; age = 5.3 ± 0.5 years, body height = 115.3 ± 5.2 cm, body mass = 20.7 ± 2.6 kg) or a control group (CG; n = 15; age = 5.2 ± 0.4 years, body height = 118.5 ± 4.9 cm, body mass = 22.6 ± 2.7 kg) participating in a 12-week INT program and regular physical education classes three times per week, respectively. Upper extremity maximal strength (grip strength test) and power (tennis ball throwing test), core endurance strength (one-minute sit-up test), and lower extremity power (standing long jump test) were assessed at the baseline (T0), Week 6 (T6), and Week 12 (T12). Data were analyzed using an independent samples T-test and a two-way repeated-measures ANOVA.ResultsSignificant interaction effects between the EG and CG were observed for grip strength, tennis ball throws, one-minute sit-ups, and standing long jumps (p < 0.001). Relative to the CG, the EG demonstrated significant improvements in all muscular fitness at T6 and T12 (p < 0.05). However, no significant interaction was found between the time and the sex (p > 0.05).ConclusionsThese findings suggested that a 12-week INT program can more effectively enhance the muscular fitness of 5–6-year-old preschoolers compared to regular physical education classes, serving as an effective and efficient supplement to physical education for this age group. Furthermore, there is no evidence of sex -specific differences in the development of muscular fitness among 5–6-year-old preschoolers under the INT program. creator: Zhihai Wang creator: Jiayu Zang creator: Zhaohong Wang creator: Daniel T.P. Fong creator: Dan Wang uri: https://doi.org/10.7717/peerj.19417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Screen time exposure and academic performance, anxiety, and behavioral problems among school children link: https://peerj.com/articles/19409 last-modified: 2025-05-08 description: BackgroundThe growth of the digital landscape has surely outpaced research on the effects of screen media on the health, learning, and development of children. The potential risk-to-benefit ratio of screen media exposure for education and entertainment purposes warrants further exploration. Therefore, we aimed to investigate the relationships between screen time and academic performance, anxiety, and outdoor playing among school children in India.MethodsA total of 537 parents responded to this online survey and reported approximately 537 Indian school children (mean age 10.9 years) from five schools. Data was collected using an e-questionnaire which consisted of a socio-demographic domain, recreational activities, self-reported physical measures, academic performance, information related to children’s screen time, the Spence Children Anxiety Scale (SCAS), and the Pediatric Symptom Checklist (parent version) instruments. We employed multivariate linear regression models to estimate the association between children’s screen time and the predictor variables with 0.05 alpha as level of significance.ResultsThe mean screen time was 3.06 ± 1.22 h/day, the average duration of outdoor play per week was 11.23 ± 4.1 h, and the mean body mass index (BMI) was 18.2 ± 3.2. Screen time (h) in a typical week was positively correlated with BMI, the SCAS anxiety score, and behavioral problems and negatively correlated with academic performance. School children’s screen time was a predictor of their BMI, behavioral symptoms, and academic performance according to the linear regression analysis.ConclusionOur findings pointed out that screen time was associated with increased BMI, behavioral problems and poor academic performance. These insights shall be used for development of targeted tailored interventions and strategies to reduce childhood obesity related to screen time. Further research is necessary to rule out the influence of other intricate factors, such as sleep, parental practices, family connectedness, and supervision of parents. The careful use of digital media must serve as a positive force in children’s educational and developmental trajectories. creator: Mohammad Sidiq creator: Balamurugan Janakiraman creator: Faizan Kashoo creator: Rayan Jastania creator: Abdullah Ibrahim Alhusayni creator: Abdullah Alzahrani creator: Aksh Chahal creator: Alagappan Thiyagarajan creator: Imran Khan creator: Chandan Kumar creator: Rajkumar Krishnan Vasanthi creator: Fahad Alanazi creator: Mehrunnisha Ahmad creator: Chhavi Arora Sehgal creator: Shabnam Khan creator: Mshari Alghadier uri: https://doi.org/10.7717/peerj.19409 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sidiq et al. title: Host specificity of gastrointestinal parasites in free-ranging sloths from Costa Rica link: https://peerj.com/articles/19408 last-modified: 2025-05-08 description: The diversity and host specificity of gastrointestinal parasites infecting free-ranging sloths is poorly known. We compared gastrointestinal parasites of two sloth species from Costa Rica—three-fingered sloths (Bradypus variegatus) and two-fingered sloths (Choloepus hoffmanni)—for the first time in both a primary forest and an urban habitat. We asked whether host-parasite interactions were predominantly structured by host identity, the habitats in which hosts occurred, or both. Coproparasitology revealed protozoa and nematode eggs from both host species, but cestode eggs were recorded only in C. hoffmanni. We found eight parasitic morphotypes in 38 samples, which matches the total number of these parasites described in sloths over the past 100 years. We found no significant difference in overall parasite richness between sloth species or habitats, but the parasite richness of C. hoffmanni was 2-fold greater in the primary forest vs. urban habitat. As no parasite sharing was observed between sloth species, we found strong and significant differences in parasite composition between host species regardless of habitat. In B. variegatus, we observed eggs of four nematode taxa (Spirocercidae, Subuluroidea, Spirurida, Ascaridida) and cysts of Eimeriidae (Apicomplexa). By contrast, in C. hoffmanni, we observed cestodes (Anoplocephalidae), a different nematode from the family Spirocercidae, and also different cysts of Eimeriidae (Apicomplexa). Many rare taxa were recorded only in samples from the primary forest, and these did not match any sloth parasites that had been previously described in the literature, suggesting that at least some could be undescribed species. Together, these results highlight the paucity of comparative parasitology involving tropical wildlife, the importance of characterizing host-parasite transmission networks, and the potential relevance of intermediate hosts that may be relevant to sloth health. creator: Ezequiel A. Vanderhoeven creator: Madeleine Florida creator: Rebecca N. Cliffe creator: José Guzmán creator: Juliana Notarnicola creator: Tyler R. Kartzinel uri: https://doi.org/10.7717/peerj.19408 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Vanderhoeven et al. title: Allelopathic effects and composition of aqueous extracts from different parts of Galinsoga parviflora Cav. on Medicago sativa L. and Avena sativa L link: https://peerj.com/articles/19378 last-modified: 2025-05-08 description: BackgroundGalinsoga parviflora Cav. is a high-risk invasive plant that seriously threatens the development of grasslands in southern China. However, the allelopathic effects on Medicago sativa L. and Avena sativa L., which are widely cultivated forages around the world, have not been reported.MethodsTo explore the allelopathic mechanism of G. parviflora, the allelopathic effects of aqueous extracts from different parts of G. parviflora on M. sativa and A. sativa were investigated. The germination rate (GR), germination potential (GP), seedling height, fresh weight, and chlorophyll content of M. sativa and A. sativa seedlings were measured to elucidate the allelopathy of G. parviflora on the two forages. Based on the five indicators, synthetical allelopathic effects (SAE) of extracts was also calculated. In addition, the allelopathic components of the extracts in G. parviflora were quantitatively revealed by untargeted metabolomics detection. Furthermore, two key allelopathic substances, 1,4-cyclohexanedicarboxylic acid (CHDA) and trehalose, were selected to explore the inhibitory effect on two notorious weed species in China, such as gramineous Digitaria sanguinalis L. and broad-leaved Amaranthus retroflexus L.Result(1) The inhibitory effects of aqueous extracts from different parts of G. parviflora on recipient plants were different, the root was the weakest, and the whole plants was the strongest, with the values of synthetical allelopathic effects (SAE) on M. sativa at the highest concentration being −0.12 and −0.40, respectively. (2) Compared with A. sativa, M. sativa was generally more susceptible to the extracts. (3) The differences in the content of CHDA or trehalose might be a reason why extracts from different parts of G. parviflora exhibited different allelopathic effects. (4) The herbicidal activity test of key allelopathic substances found that CHDA has a strong inhibitory effect on the germination of D. sanguinalis and almost does not affect M. sativa and A. sativa. Thus, this discovery not only revealed allelopathic effects and components in different parts of G. parviflora, but provided scientific evidence for weed control based on natural plant extracts in the future. creator: Shipu Cheng creator: Fanru Xu creator: Zhiyong Lu creator: Huairui Xu creator: Mengqi Cai creator: Juan Sun creator: Yufang Xu uri: https://doi.org/10.7717/peerj.19378 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Cheng et al. title: Oral health status, oral hygiene behaviors, and caries risk assessment of individuals with special needs: a comparative study of Pakistan and Saudi Arabia link: https://peerj.com/articles/19286 last-modified: 2025-05-08 description: BackgroundIndividuals with disabilities often experience greater challenges in managing oral diseases, including dental caries and periodontal conditions, due to functional limitations. This study aims to: (1) assess the oral health status of disabled individuals in Pakistan and Saudi Arabia, (2) evaluate their oral hygiene knowledge and behaviors, and (3) determine their caries risk using the Caries Management by Risk Assessment (CAMBRA) protocol.MethodsA cross-sectional study was conducted on 189 participants aged 13 years and older, including both young people and adults with hearing, visual, or intellectual disabilities from Pakistan and Saudi Arabia between September 2023 and April 2024. The participants were recruited from the Institute of Special Education, Pakistan, and the Saudi Institute of Rehabilitation Medicine, Saudi Arabia. Intraoral examinations and bitewing radiographs assessed oral health, including Decayed, Missing, and Filled Teeth (DMFT) index, Gingival Index, visible plaque, and molar alignment. A self-administered questionnaire gathered sociodemographic data and evaluated oral hygiene knowledge and behaviors. Caries risk was analyzed using the CAMBRA tool. Data were analyzed using descriptive statistics, Chi-square tests, and binary logistic regression.ResultsThe mean DMFT score was 6.30 (SD = 1.83), with a statistically significant difference between Pakistan and Saudi Arabia (p = 0.007). Gingival health was fair to poor in 47% of participants, while 43.4% exhibited bleeding on probing and 34.9% had visible plaque. Class III malocclusion affected approximately 30% of participants in both countries. Tooth brushing frequency showed a significant difference between the two groups (p = 0.005). Most participants (76% in Pakistan, 62% in Saudi Arabia) were classified as high caries risk. Deep pits and fissures (69.4%) and frequent snacking (63.8%) were the main risk factors in Pakistan, while frequent snacking (71.6%) and heavy plaque (60.4%) were prevalent in Saudi Arabia. Saudi participants had a significantly higher likelihood of being in the high-risk group for caries (OR = 1.86, 95% CI [0.95–3.65], p = 0.04).ConclusionThe disabled individuals in both countries face significant oral health challenges, with high caries risk and poor oral hygiene practices. Targeted preventive measures and improved dental care access are essential to addressing these disparities. creator: Osama Khattak creator: Farooq Ahmad Chaudhary creator: Shahzad Ahmad creator: Muhammad Amber Fareed creator: Shazia Iqbal creator: Asma Shakoor creator: Mohammed Nadeem Baig creator: Haifa Ali Almutairi creator: Rakhi Issrani creator: Azhar Iqbal uri: https://doi.org/10.7717/peerj.19286 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Khattak et al. title: Development of an immune-related gene signature applying Ridge method for improving immunotherapy responses and clinical outcomes in lung adenocarcinoma link: https://peerj.com/articles/19121 last-modified: 2025-05-08 description: BackgroundLung adenocarcinoma (LUAD) is a major cause of cancer mortality. Considering the critical role of tumor infiltrating lymphocytes in effective immunotherapy, this study was designed to screen molecular markers related to tumor infiltrating cells in LUAD, aiming to improve immunotherapy response during LUAD therapy.MethodsThe ConsensusClusterPlus method was used for clustering immune molecular subtypes of LUAD. Immune cell infiltration and immunotherapeutic potential in each subtype was evaluated employing single-sample gene set enrichment analysis (ssGSEA), Tumor Immune Dysfunction and Exclusion (TIDE), and Immunophenoscore (IPS). Immune-related co-expression modules were classified by weighted gene co-expression network analysis (WGCNA) analysis. The sequencing data of immune-related genes were comprehensively analyzed by introducing a new computational framework and 10 machine learning algorithms (a total of 101 combinations) to determine the prognostic genes, which were further combined to develop an immune prognostic signature (IMMPS) using the stepCox and Ridge methods. The expression of the signature genes was validated by quantitative real-time PCR (qRT-PCR).ResultsSamples from The Cancer Genome Atlas dataset (TCGA-LUAD) were divided into two subtypes (immunosuppressive subgroup C1 and immune-activated subgroup C2); notably, the C2 subgroup was more likely to benefit from immunotherapy (p < 0.05). An IMMPS developed based on seven immune infiltrating cell-related genes (SEMA7A, EFHD2, CHST11, SLC24A4, MAL, JCHAIN, and SCARF1) could accurately predict the overall survival of LUAD in five LUAD cohorts, with an average C-index higher than 0.69. LUAD patients with a low IMMPS value had a higher immune cell infiltration (p < 0.05). In addition, the IMMPS exhibited better prediction performance in comparison to 154 published gene signatures, suggesting that the IMMPS was an independent prognostic risk factor for evaluating the overall survival of LUAD patients. Since BTNL9 was the most relevant immune checkpoint gene, in vitro experiment showed that the expression of the seven key genes (SEMA7A, EFHD2, CHST11, SLC24A4, MAL, JCHAIN, and SCARF1) in LUAD cell lines was consistent with that in normal lung epithelial cells after inhibiting BTNL9 expression (p < 0.05).ConclusionsOur results contributed to a better understanding of immunological characteristics of LUAD. The IMMPS could serve as a promising tool for improving the clinical outcome of patients suffering from LUAD. creator: Zhen Chen creator: Yongjun Zhang uri: https://doi.org/10.7717/peerj.19121 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chen and Zhang title: Genotypic and phenotypic characterization of thermo-sensitive genic male sterile (TGMS) rice lines using simple sequence repeat (SSR) markers and population structure analysis link: https://peerj.com/articles/18975 last-modified: 2025-05-08 description: Thermo-sensitive genic male sterile (TGMS) lines in rice are crucial for hybrid breeding, enhancing genetic diversity by eliminating the need for manual emasculation and restorer genes. These lines induce sterility at high temperatures and restore fertility at low temperatures, in contrast to cytoplasmic male sterility (CMS) systems that require specific restorative genes. This temperature-sensitive mechanism allows for greater flexibility in pairing parent lines, increasing genetic diversity and enabling recombination of beneficial traits in hybrids. A randomized block design (RBD) with three replications was employed for the evaluation of these TGMS rice lines. This study investigates the molecular diversity and genetic variability among TGMS rice lines. Traits such as single plant yield, grains per panicle, glume angle, and pollen fertility showed significant phenotypic and genotypic variation, indicated by high coefficients of variation (PCV and GCV), heritability estimates, and genetic advance as a percentage of mean (GAM). These results highlight substantial genetic variation and selection potential. Euclidean distance matrix analysis of morphological data revealed notable genetic differences. TNAU 137S 1 and TNAU 137S 2 were the most genetically similar, while TNAU 112S and TNAU 114S showed the greatest divergence. Principal component analysis (PCA) revealed distinct genetic profiles among lines such as TNAU 136S, TNAU 113S, TNAU 142S, and TNAU 126S, important for hybrid development. Molecular diversity analysis using simple sequence repeat (SSR) markers identified 90 alleles and eight genetic clusters. Bayesian analysis further confirmed two major subpopulations with significant genetic divergence. These findings support the selective use of parent lines for hybrid rice breeding. creator: B Nagendra Naidu creator: Manonmani Swaminathan creator: Pushpam Ramamoorthy creator: Kumaresan Dharmalingam creator: Raveendran Muthurajan creator: Selvi Duraisamy creator: Nivedha Rakkimuthu creator: Abirami Subramanian creator: Rithesh Natarajan creator: Bonipas Antony John uri: https://doi.org/10.7717/peerj.18975 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nagendra Naidu et al. title: Unveiling the immune and vitamin profiles of blood: the potential biomarkers for alopecia areata link: https://peerj.com/articles/19430 last-modified: 2025-05-07 description: BackgroundAlopecia areata is a hair follicle disorder characterized by the development of multiple circular bald patches on the scalp, often accompanied by elevated cytokine production and immune cell infiltration around hair follicles. Our aspiration is to explore whether blood analysis can reveal additional factors that contribute to the disparities between individuals with alopecia areata and those who are healthy. Such research could potentially establish a robust foundation for the advancement of future therapeutic strategies.MethodsIn Fujian, China, we have collected blood samples from a cohort of 28 alopecia areata patients and a control group of 28 healthy individuals for comparative analysis. A detailed assessment of cytokines, eosinophil counts, vitamin levels, and immunoglobulin profiles within these samples was conducted. Subsequently, statistical analysis was applied to elucidate the differences between the two groups.ResultsWhile the blood analysis revealed higher average levels of IL-4, IL-10, and TNF-α in alopecia areata patients compared to healthy individuals, these differences were not statistically significant. Similarly, vitamin levels showed no significant variation between the patient and healthy groups. However, the Wilcoxon rank sum test identified a significant increase in IFN-γ and a significant decrease in immunoglobulin IgG4 levels among alopecia areata patients, pointing to a possible role in the disease’s pathogenesis. Receiver operating characteristic (ROC) curve analysis had demonstrated that the area under the ROC curve (AUC) for IFN-γ and IgG4 was 0.656 and 0.704, respectively, suggesting that IFN-γ and IgG4 had a certain discrimination effect on alopecia areata. Utilizing the Youden index to optimize specificity, we propose that IgG4 levels below 824.85 mg/L and IFN-γ levels above 0.565 pg/mL could serve as biomarkers for assessing the risk of alopecia areata.ConclusionsThese findings highlight the need for further exploration of the link among alopecia areata, IgG4- and IFN-γ-related mechanisms, potentially uncovering novel therapeutic targets for managing this condition. creator: Jincheng Ke creator: Fangfang Chen creator: Yu-Pei Chen creator: Mingli Zhang creator: Li Ma uri: https://doi.org/10.7717/peerj.19430 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ke et al. title: Retrospective study on the correlation between CXCL13, immune infiltration, and tertiary lymphoid structures in cutaneous squamous cell carcinoma link: https://peerj.com/articles/19398 last-modified: 2025-05-07 description: BackgroundC-X-C motif chemokine ligand 13 (CXCL13) is a crucial chemokine for the recruitment of immune cells and the formation of tertiary lymphoid structure (TLS) in the tumor microenvironment. However, the relationship between CXCL13 and immune infiltration in cutaneous squamous cell carcinoma (cSCC) remains unclear.ObjectiveWe aimed to investigate the expression of CXCL13 and explore its association with immune activation and TLS in cSCC.MethodsA total of 63 cSCC patients were involved in the present study. Hematoxylin and eosin staining was used for pathological examination of cSCC. Bioinformatics analyses and immunohistochemical staining were employed to access the expression of CXCL13 and TLS states. Public single cell RNA-sequencing atlas of skin disorders and multiplex immunofluorescence were used to explore CXCL13-producing cells.ResultsUtilizing the public database and our clinical cohort, we observed robust CXCL13 expression in cSCC tissues and a significant correlation with immune activation. Higher expression levels of CXCL13 were associated with lower histopathological grades and increased TLS formation. Furthermore, we confirmed that T cells and fibroblasts were the predominant cell types of CXCL13 secretion in cSCC.ConclusionsCXCL13 is up-regulated in cSCC, which shows a significant positive correlation with immune infiltration and TLS formation. Our results underscore the role of CXCL13 in shaping the cSCC microenvironment, highlighting its potential as a therapeutic target. creator: Yulu Chen creator: Yuhao Wu creator: Zijun Zhao creator: Long Wen creator: Mingshun Wu creator: Dekun Song creator: Qingyu Zeng creator: Yeqiang Liu creator: Guorong Yan creator: Guolong Zhang uri: https://doi.org/10.7717/peerj.19398 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Sterile seed germination and seedling cultivation of Idesia polycarpa link: https://peerj.com/articles/19395 last-modified: 2025-05-07 description: BackgroundIdesia polycarpa Maxim. is a high-quality, high-yield, edible oil tree species native to eastern Asia, where it plays important roles in ensuring national food and oil security, promoting ecological development, and facilitating rural revitalization. However, the commercial development of I. polycarpa has been hampered by the fact that it is primarily propagated by seeds, the required dormancy of which leads to low natural germination rates. Tissue culture technology offers the advantages of rapid propagation, high multiplication rates, and independence from seasonal factors, enabling the rapid production of large quantities of high-quality seedlings. The aim of this study was to establish an efficient aseptic germination system for I. polycarpa seeds.MethodsThis study utilized I. polycarpa seeds as the experimental material to investigate the effects of different disinfection times, basic medium variations, activated carbon (AC) concentrations, and the types and concentrations of plant growth regulators (PGRs) on aseptic germination. Subsequently, sterile seedlings were used as explants to screen for the effects of sucrose concentration and the types and concentrations of PGRs on rooting. The study also investigated how different substrate ratios and container types influenced the post-transplant survival rate of tissue-cultured I. polycarpa seedlings.ResultsThe results showed that the optimal time was 10 min for I. polycarpa seed disinfection with 0.1% HgCl2. The most suitable medium for I. polycarpa seed germination was 1/2 MS medium supplemented with GA3 (1.0 mg·L−1) and AC (1.0 g·L−1), achieving a germination rate of 96.0%. A sucrose concentration of 10.0 g·L−1 was most beneficial for rooting. When using a single plant growth regulator, indole-3-butyric acid (IBA) had the most significant effect on I . polycarpa root induction. The optimal medium for root development was Murashige and Skoog (MS) medium supplemented with IBA (0.3 mg·L−1) and α-naphthyl acetic acid (NAA) (0.5 mg·L−1), resulting in a 100% rooting rate and an average of 22.17 roots. These roots had an average length of 3.4 cm and were abundant and vigorous. Tissue-cultured seedlings were transplanted into transparent plastic cups containing a mixed substrate of organic nutrient soil (BALTIC PEAT), perlite, and vermiculite in a ratio of 2:1:1 (V/V/V). They grew vigorously, with a survival rate as high as 96.67%. The findings of this study can provide technical support for the factory breeding of I. polycarpa seedlings. creator: Zhangtai Niu creator: Juan Xiao creator: Chuxi Hu creator: Yunchen Yang creator: Sijing Shi creator: Xiaoyu Lu creator: Yian Yin creator: Ze Li creator: Lingli Wu uri: https://doi.org/10.7717/peerj.19395 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Niu et al. title: Integrin signaling in tumor biology: mechanisms of intercellular crosstalk and emerging targeted therapies link: https://peerj.com/articles/19328 last-modified: 2025-05-07 description: Integrins, a family of transmembrane cell adhesion receptors, mediate intercellular and cell–extracellular matrix crosstalk via outside-in and inside-out signaling pathways. Integrins, categorized into 24 distinct combinations of α and β subunits, exhibit tissue-specific expression and perform unique or overlapping roles in physiological and pathophysiological processes. These roles encompass embryonic angiogenesis, tissue repair, and the modulation of tumor cell angiogenesis, progression, invasion, and metastasis. Notably, integrins are significant contributors to tumor development, offering valuable insights into the potential of integrin-targeted diagnostics and therapeutics. Currently, there are various preclinical and clinical trials aiming to harness integrin antagonists that are safe, efficacious, and exhibit low toxicity. Owing to the functional redundancy across integrin types and the complexity of the mechanisms of integrin-mediated multiple key processes associated with tumor biology, challenges exist that impede advancements in integrin-targeted therapy. Nevertheless, innovative strategies focused on integrin modulation represent significant breakthroughs for improving patient care and promoting comprehensive insights into the underlying mechanisms of tumor biology. This review elucidates the impact of integrins on three distinct cell types in multiple key processes associated with tumor biology and explores the emerging integrin-targeted therapeutic approaches for the treatment of tumors, which will provide ideas for optimal therapeutic approaches in the future. creator: Yifan Li creator: Shantong Peng creator: Jiatong Xu creator: Wenjie Liu creator: Qi Luo uri: https://doi.org/10.7717/peerj.19328 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Establishment and validation of a method for determining anti-Xa factor potency of enoxaparin sodium link: https://peerj.com/articles/19437 last-modified: 2025-05-06 description: This study successfully established and validated an efficient, reliable, and user-friendly method for determining the anti-Xa factor potency of enoxaparin sodium. Comprehensive validation experiments demonstrated the method’s excellent performance in terms of specificity, linearity, precision, accuracy, and robustness. The method exhibited a linear detection range of 0.054–0.192 IU/mL with a strong correlation coefficient, and its precision, robustness, and consistency with the European Pharmacopoeia method were all within 2.0% relative standard deviation (RSD). These results indicate high reproducibility and strong applicability, making the method suitable for seamless transfer between laboratories. Accuracy experiments revealed recovery rates ranging from 98.0% to 102.0%, confirming the reliability of the results. The validation design and performance of this method comply with the requirements of ICH guidelines and the Chinese Pharmacopoeia. Compared with traditional methods, this approach significantly reduces sample and reagent consumption, lowers experimental costs, and optimizes operational procedures, offering a low-cost, high-efficiency tool for quality control. These findings provide essential technical support for the production and quality monitoring of enoxaparin sodium and serve as valuable references for the development and validation of quality standards for similar biological products. creator: En Zhang creator: Hanyan Zou creator: Yandong Dong creator: Bing Liu creator: Xiaorong Yang uri: https://doi.org/10.7717/peerj.19437 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Isolation and characterization of a novel lytic bacteriophage Pv27 with biocontrol potential against Vibrio parahaemolyticus infections in shrimp link: https://peerj.com/articles/19421 last-modified: 2025-05-06 description: BackgroundVibrio parahaemolyticus is a major disease-causing species of Vibrio that is pathogenic to both farmed shrimp and humans. With the increasing spread of antibiotic-resistant V. parahaemolyticus strains, bacteriophages (or phages) are considered potential agents for biocontrol as an alternative to antibiotics. In this study, a bacteriophage capable of lysing V. parahaemolyticus, named Pv27, was isolated, characterized, and evaluated for its potential to control Vibrio infections as a natural therapy.MethodsPhage Pv27 was isolated using the double-layer agar technique and its morphology was characterized by transmission electron microscopy (TEM). We further assessed the host range specificity, optimal multiplicity of infection (MOI), one-step growth kinetics, and environmental stability of Pv27 under various pH and temperature conditions. The inhibitory activity of Pv27 against V. parahaemolyticus was evaluated in vitro. Finally, genomic analysis of Pv27 was conducted through whole-genome sequencing, followed by functional annotation of open reading frames (ORFs) and phylogenetic analysis.ResultsPhage Pv27 exhibited a Myovirus-like morphology, characterized by an icosahedral head (92.7 ± 2 nm) and a contractile tail (103 ± 11 nm), and belongs to the class Caudoviricetes. Pv27 demonstrated high lytic activity against its host cells, with a short latent period of approximately 25 minutes and a large burst size of 112 plaque-forming units (PFU) per infected cell. The phage displayed significant tolerance to a wide pH range (from 3 to 11) and remained heat-stable at temperatures up to 60 °C for 90 min. Genetically, Pv27 possesses a circular double-stranded DNA genome spanning 191,395 base pairs, with a G + C content of 35% and comprising 355 open reading frames (ORFs). Remarkably, up to 23 tRNA genes were identified in its genome, while no genes associated with antibiotic resistance, virulence, or lysogeny were detected, suggesting its potential as a valuable biocontrol agent. Results from the VIRIDIC, Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses revealed that Pv27 is closely related to the two known Vibrio phages, phiKT1024 and phiTY18. Several genes associated with enhanced environmental competitiveness were also identified in the Pv27 genome, including those encoding a PhoH-like phosphate starvation-inducible protein and endolysin. Phage Pv27 effectively lyses V. parahaemolyticus highlighting its potential as a biocontrol agent. creator: Vu Thi Hien creator: Pham Thi Lanh creator: Thao Thi Phuong Pham creator: Khang Nam Tran creator: Nguyen Dinh Duy creator: Nguyen Thi Hoa creator: Nguyen Xuan Canh creator: Quang Huy Nguyen creator: Seil Kim creator: Dong Van Quyen uri: https://doi.org/10.7717/peerj.19421 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hien et al. title: Polymicrobial detection and salivary metabolomics of children with early childhood caries link: https://peerj.com/articles/19399 last-modified: 2025-05-06 description: BackgroundEarly childhood caries (ECC) has been proposed to be associated with various microorganisms and metabolites. This study aims to compare the prevalence of specific microbial species and salivary metabolomics profile in children with and without ECC, and to explore the correlation between salivary metabolites and targeted microbes.MethodFive ml of unstimulated saliva was collected from 32 ECC and 22 caries-free children. Clinical indexed were recorded and questionnaires regarding oral health and dietary habits were obtained from the guardians. The presence of eight specific microbial species were examined using species-specific quantitative PCR (qPCR). Untargeted metabolomics was analyzed to identify key differential metabolites and pathways. Correlations among clinical, microbial, and metabolomic data were further explored.ResultsThe prevalence of Scardovia wiggsiae (90.6%, P < 0.001), Streptococcus mutans (43.8%, P = 0.006), Streptococcus sobrinus (62.5%, P < 0.001), Ligilactobacillus salivarius (93.6%, P = 0.01) and Candida albicans (56.3%, P < 0.001) were significantly higher in the ECC group. The prevalence of ECC was higher in children with two targeted species present compared with children with one targeted species. Histidine metabolism and branched-chain amino acids degradation were activated in ECC group, while glyoxylate and dicarboxylate metabolism, purine and pyrimidine metabolism were inhibited. Histidine and glutathione metabolism was activated with enrichment of targeted microbial species, while linoleic acid metabolism and biotin metabolism was inhibited. The duration of each toothbrushing was a significant risk factor for ECC experience.ConclusionThe prevalence of Scardovia wiggsiae, Streptococcus mutans, Streptococcus sobrinus and Candida albicans is higher in ECC children compared to caries-free children. Oral habits and salivary metabolites also vary between ECC and caries-free children. creator: Ting Pan creator: YuJia Ren creator: JingYi Li creator: Ying Liao creator: XiangHui Xing uri: https://doi.org/10.7717/peerj.19399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pan et al. title: Enhancing bullfrog farming sustainability: circular water management through effluent treatment link: https://peerj.com/articles/19390 last-modified: 2025-05-06 description: Ensuring effective wastewater treatment is crucial for promoting sustainable water use and reducing environmental pollution in intensive bullfrog aquaculture. This study presents the design and implementation of an integrated treatment system, composed of a flotation tank, a biochemical tank, and constructed wetlands, aimed at facilitating the reuse of treated effluent. The system, operated under optimal conditions—at a flow rate of 250 m3/h, hydraulic retention time of 6 h, and aeration intensity of 2,000 m3/h—demonstrated significant removal efficiencies. Specifically, the biochemical tank reduced chemical oxygen demand (CODCr), ammoniacal nitrogen, and total phosphorus by 70%, 43%, and 42%, respectively. After a month of continuous operation, the system achieved higher removal rates of 71.7% for CODCr, 83% for ammoniacal nitrogen, and 86.7% for reactive phosphorus, rendering the treated water suitable for reuse in bullfrog farming. However, total nitrogen removal remained relatively low, and reactive phosphorus slightly exceeded discharge standards, indicating areas for further optimization. Despite these limitations, this innovative system enhances water recycling, supports circular water management strategies, and provides a practical solution for reducing water consumption and minimizing aquaculture’s environmental footprint. creator: Dandan Xie creator: Jiehua Hu creator: Liru Lin creator: Xiaomei Huang creator: Changsheng Xie creator: Haibin He uri: https://doi.org/10.7717/peerj.19390 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al. title: Oral history as a citizen science tool to understand biodiversity loss and environmental changes: on firefly extirpation in Morelia, Michoacán, Mexico link: https://peerj.com/articles/19413 last-modified: 2025-05-05 description: BackgroundNocturnal fireflies are insects easily recognizable by their notable bioluminescence. They are also bioindicators of ecosystem health due to their sensitivity to environmental changes. In this study we employ oral history regarding fireflies and their habitats to compile the collective memory of the inhabitants of Morelia, in central-western Mexico, to analyze changes in biodiversity associated with urbanization.MethodsThe main tools we used were interviews and surveys, in addition to data from scientific literature, entomological collections and citizen science platforms. We explored fireflies as useful elements both to collect oral histories from volunteers (experts or non-experts on the topic) and to serve as a source of biological data (e.g., current and past distribution of fireflies in the city, estimates of biodiversity loss, and threat factors), and even to analyze the potential loss of local ecological knowledge among human generations.ResultsA total of 112 surveys and interviews were conducted with people of three different generations and from different parts of Morelia to collect human demographic data, and spatial, temporal, abundance, and perception data on fireflies. We found local recognition of fireflies by most Morelians, as well as reports of a decrease in both the frequency and abundance of fireflies, and even identified sites of extirpation, i.e., the disappearance of these insects from the environments where people used to see them. Morelians associated these phenomena with increased anthropogenic activities in the city, such as urban growth and a notable increase in pollution and deforestation. Most Morelians believe that the current conditions of the city are unsuitable for the existence of fireflies, and that it is important to conserve these insects because they play an important role in ecosystems and are of high environmental and aesthetic value. In contrast, the younger generation of Morelians showed lower interaction and recognition of these insects in nature, which could be related to the loss of collective memory over generations and the shifting baseline syndrome.ConclusionsIn contexts where historical scientific data are not available, we suggest that fireflies can be used to assess the history of natural environments and changes in the populations of these insects. Moreover, fireflies can be beneficial in terms of engaging people in conservation strategies, citizen science, and science communication. creator: Danna Betsabe Rivera Ramírez creator: Cisteil X. Pérez-Hernández creator: Yaayé Arellanes-Cancino creator: Luis Mendoza-Cuenca uri: https://doi.org/10.7717/peerj.19413 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Rivera Ramírez et al. title: From grit to flourishing: physical literacy’s mediating role in enhancing well-being among college students with obesity link: https://peerj.com/articles/19382 last-modified: 2025-05-05 description: ObjectiveTo investigate whether physical literacy mediates the relationship between grit and well-being among college students with obesity.MethodsA total of 385 students with obesity were recruited. Participants completed validated questionnaires measuring grit, physical literacy, and well-being. Mediation analyses were performed to estimate indirect effects and generate bias-corrected 95% confidence intervals (CI).ResultsGrit was positively associated with physical literacy, and physical literacy was positively associated with well-being. Physical literacy partially mediated the relationship between grit and well-being, with the indirect effect accounting for 26.32% of the total effect (indirect effect = 0.20, 95% CI [0.09–0.31]). In a parallel mediation model analyzing the subdimensions of physical literacy, the “interaction with the environment” emerged as the strongest mediator (indirect effect = 0.15, 95% CI [0.10–0.21]), accounting for 19.74% of the total effect. The indirect effects through “motivation” and “confidence and physical competence” were also significant but accounted for smaller proportions of the total effect (6.58% and 5.26%, respectively).ConclusionsThese findings serve as an initial step in understanding how physical literacy, particularly the ability to interact with the environment, partially mediates the relationship between grit and well-being among college students with obesity. Future interventional research aiming to enhance physical literacy—especially environmental engagement—is needed to confirm whether it can amplify the positive impact of grit on well-being. A multifaceted approach that fosters both psychological traits and physical competencies may prove beneficial in improving the psychological and physical health of this population. creator: Xingyu Liu creator: Zidong Li creator: Wanru Cheng creator: Jian Zhang creator: Xiaoyu Ma creator: Di Tang creator: Jinde Liu creator: Tianyu Gao creator: Ting Liu creator: Tao Chen creator: Ruisi Ma uri: https://doi.org/10.7717/peerj.19382 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: In vitro fermentation characteristics of polysaccharide from Scrophularia ningpoensis and its effects on type 2 diabetes mellitus gut microbiota link: https://peerj.com/articles/19374 last-modified: 2025-05-05 description: BackgroundIncreasing evidence has shown a close relation between the pathogenesis of type 2 diabetes mellitus (T2DM), which is a global health problem with multifactorial etiopathogenesis, and gut microbiota.MethodsDuring in-vitro fermentation of Scrophularia ningpoensis (known as Xuanshen) polysaccharide (SNP) by T2DM gut microbiota, effects of SNP on the gas content, production of short-chain fatty acids (SCFAs), metabolite profile and microbiota composition were studied.ResultsAnalysis of chemical compositions indicates that the total sugar content of SNP was found to be as high as 87.35 ± 0.13% (w/w). SNP treatment significantly improved the gas volume and composition in T2DM fecal matter. Moreover, intestinal flora degraded SNP to produce SCFAs, thus regulating SCFA production and composition. Metabolomic analysis implied that SNP shows potential to regulate the five gut metabolites (L-valine, L-leucine, L-isoleucine, L-alanine, and xylitol) in T2DM fecal matter. Furthermore, dysbiosis of gut microbiota induced by T2DM was reversed by SNP. The evidence includes decreasing Firmicutes/Bacteroidota ratio at phylum level promoting proliferation of the bacterial abundance of Dorea, Parabacteroides, Faecalibacterium, and Lachnospira and decreased bacterial abundance of Escherichia—Shigella. Based on these findings, the action mechanism of SNP against T2DM was clarified by reshaping microbiota and regulating intestinal metabolites, and a novel target was provided for interventions of T2DM. creator: Yang Zhao creator: Juwei Wen creator: Yu Yang creator: Lina Jia creator: Qian Ma creator: Weiguo Jia creator: Wei Qi uri: https://doi.org/10.7717/peerj.19374 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhao et al. title: Impact of seasonal flooding and hydrological connectivity loss on microbial community dynamics in mangrove sediments of the southern Gulf of Mexico link: https://peerj.com/articles/19371 last-modified: 2025-05-05 description: BackgroundMangrove ecosystems play essential roles in coastal resilience, carbon sequestration, and biodiversity but are under increasing threat from anthropogenic pressures. This study explores the impact of hydrological variability on microbial communities in mangrove sediments of the southern Gulf of Mexico.MethodsWe employed 16S rRNA sequencing to assess microbial diversity and function across different hydrological zones, seasons, and sediment depths at Estero Pargo.ResultsOur results show that microbial community composition is significantly influenced by hydrological conditions, with distinct microbial assemblages observed across the fringe, basin, and impaired zones. Seasonal variations were particularly pronounced, with higher microbial diversity during the flood season compared to the dry season. Depth also played a critical role, with surface layers (5 cm) predominantly featuring aerobic microbial communities, while deeper layers (20–40 cm) harbored anaerobic taxa such as Bathyarchaeota and Thermococcaceae. Notably, the impaired zone showed enrichment in genes related to denitrification and sulfur oxidation pathways, indicating strong microbial adaptation to reduced environments. These findings highlight the intricate interactions between microbial dynamics and environmental factors in mangrove ecosystems. Understanding these relationships is crucial for developing effective conservation and management strategies that enhance mangrove resilience in the face of global environmental changes. creator: Mirna Vázquez-Rosas-Landa creator: Rosela Pérez-Ceballos creator: Arturo Zaldívar-Jiménez creator: Stephanie Hereira creator: Leonardo Pérez González creator: Alejandra Prieto-Davó creator: Omar Celis-Hernández creator: Julio Cesar Canales-Delgadillo uri: https://doi.org/10.7717/peerj.19371 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vázquez-Rosas-Landa et al. title: Flood analysis comparison with probability density functions and a stochastic weather generator link: https://peerj.com/articles/19333 last-modified: 2025-05-05 description: Flood prediction has become essential to hydrology and natural disaster management due to the increasing frequency and severity of extreme hydrological events driven by climate change. This study compares two methodologies for predicting flood events in Morelia, Mexico: theoretical distribution functions and stochastic weather generators. The methodology integrates maximum runoff results for different return periods into a drainage network hydraulic model, using the Soil Conservation Service Curve Number (SCS-CN) method and a multivariate stochastic model (MASVC). Hydrodynamic modeling with HEC-RAS, incorporating two-dimensional shallow water equations, was used to simulate flood inundation areas. The study reveals that while both modeling approaches similarly replicate the system’s behavior, they produce different water levels due to variations in maximum flow values. The stochastic model tends to generate higher maximum water levels. High-resolution digital elevation models (DEMs) with a pixel size of five m in urban areas and 0.5 m in drainage network zones, and land use data were crucial in improving the accuracy of the hydraulic simulations. Findings indicate that unregulated urban growth in flood-prone areas significantly exacerbates the impact of flooding. The generated hazard maps and flood simulations provide valuable tools for urban planning and decision-making, highlighting the need for strategic interventions to mitigate flood risks. This research underscores the importance of integrating advanced modeling techniques in flood risk management to enhance the precision and reliability of flood predictions. creator: Israel García-Ledesma creator: Jaime Madrigal creator: Jesús Pardo-Loaiza creator: Joel Hernández-Bedolla creator: Constantino Domínguez-Sánchez creator: Sonia Tatiana Sánchez-Quispe uri: https://doi.org/10.7717/peerj.19333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 García-Ledesma et al. title: Alleles of CYP3A5 and their association with renal function in chronic kidney disease link: https://peerj.com/articles/19424 last-modified: 2025-05-02 description: BackgroundThe cytochrome P450 family 3 subfamily A polypeptide 5 (CYP3A5) gene plays an important role in renal function through its product’s involvement in metabolizing endogenous substances and drugs, including immunosuppressants used following kidney transplantation. A single-nucleotide polymorphism, CYP3A5*3 (rs776746), produces a non-functional variant that may influence progression of chronic kidney disease (CKD) by impairing renal filtration. However, the frequency of the CYP3A5*3 allele in the Thai population and its association with renal parameters remain underexplored. This study aimed to determine the prevalence of CYP3A5 polymorphisms and their association with renal function.MethodsWe investigated the distribution of CYP3A5 polymorphisms in 329 northeastern Thai participants, including 205 CKD patients and 124 healthy controls. Genotyping was performed using the TaqMan allelic discrimination assay. Renal function parameters were assessed and compared between CYP3A5*1 and CYP3A5*3 allele carriers.ResultsIn the entire cohort, the allele frequency of CYP3A5*3 was 63.2%, with genotype frequencies of CYP3A5*1/*1 (16.7%), CYP3A5*1/*3 (40.1%), and CYP3A5*3/*3 (43.2%). There was no significant difference in the CYP3A5 allele frequencies between CKD and control groups. CYP3A5*3 carriers exhibited significantly lower eGFR, urine creatinine and serum creatinine clearance and higher UACR compared to CYP3A5*1 carriers. After adjusting for confounders, CYP3A5*3 remained significantly associated with reduced urine creatinine.ConclusionThis study highlights a high prevalence of CYP3A5 polymorphisms in the northeastern Thai population. The association of the CYP3A5*3 allele with renal function parameters underscores the need for further research into the mechanisms by which CYP3A5 affects kidney function, which could inform personalized CKD management strategies. creator: Onnapa Kongphan creator: Worachart Lert-itthiporn creator: Ubon Cha’on creator: Sirirat Anutrakulchai creator: Kanokwan Nahok creator: Nadthanicha Artkaew creator: Chanpen Sriphan creator: Apinya Jusakul uri: https://doi.org/10.7717/peerj.19424 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kongphan et al. title: Phase separation in DNA repair: orchestrating the cellular response to genomic stability link: https://peerj.com/articles/19402 last-modified: 2025-05-02 description: DNA repair is a hierarchically organized, spatially and temporally regulated process involving numerous repair factors that respond to various types of damage. Despite decades of research, the mechanisms by which these factors are recruited to and depart from repair sites have been a subject of intrigue. Recent advancements in the field have increasingly highlighted the role of phase separation as a critical facilitator of the efficiency of DNA repair. This review emphasizes how phase separation enhances the concentration and coordination of repair factors at damage sites, optimizing repair efficiency. Understanding how dysregulation of phase separation can impair DNA repair and alter nuclear organization, potentially leading to diseases such as cancer and neurodegenerative disorders, is crucial. This manuscript provides a comprehensive understanding of the pivotal role of phase separation in DNA repair, sheds light on the current research, and suggests potential future directions for research and therapeutic interventions. creator: Juxin Deng creator: Zhaoyang Du creator: Lei Li creator: Min Zhu creator: Hongchang Zhao uri: https://doi.org/10.7717/peerj.19402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Deng et al. title: A comprehensive analysis identified an autophagy-related risk model for predicting recurrence and immunotherapy response in stage I lung adenocarcinoma link: https://peerj.com/articles/19366 last-modified: 2025-05-02 description: BackgroundLung adenocarcinoma (LUAD) is characterized by early recurrence and poor prognosis. Autophagy is a double-edged sword in tumor development and anti-tumor therapy resistance. However, the prediction of relapse and therapeutic response in LUAD patients with stage I based on the signature of autophagy remains unclear.MethodsGene expression data were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. Autophagy-associated genes were extracted from the Human Autophagy Moderator Database. The autophagy score was established by Least Absolute Shrinkage and Selection Operator (LASSO) regression. Real-time PCR was used to detect gene expression of hub genes in LUAD patients. Protein-protein interaction (PPI) was analyzed to identify crucial genes. Gene set enrichment analysis (GSEA) was used to reveal the molecular features of patients. ESTIMATE algorithm was applied to estimate the tumor immune infiltration. TIDE score and Genomics of Drug Sensitivity in Cancer (GDSC) database were used to assess therapeutic response.ResultsWe established an autophagy score based on 19 autophagy genes. Among these genes, MAP1LC3B played a crucial role in PPI network and was down-regulated in tumor tissues both in TCGA and local cohort. Receiver operating characteristic (ROC) curve showed that the risk model effectively predict RFS of stage I LUAD (area under the curve (AUC) at 1, 2, 3 years = 0.701, 0.836, and 0.818, respectively). Multivariate regression analysis indicated that the autophagy score was an independent predictor for relapse (P < 0.001, HR = 4.8, 95% CI [3.25–7.2]). The autophagy score also showed great predictive efficacy in the external validation GEO cohorts. GSEA revealed gene sets significantly enriched in immunity, cell cycle, and adhesion, etc. Meanwhile, we found the autophagy score was negatively related to KRAS mutation (P = 0.017) but positively associated with TP53 mutation (P = 6.4e−11). The autophagy score had a negative relationship with CD8+, CD4+ T cell, and dendritic cell, and positively correlated with immune checkpoint molecule CD276. Patients with a high autophagy score were sensitive to chemotherapy and targeted therapy, while resistant to immune checkpoint inhibitors.ConclusionWe constructed an effective recurrence risk predictive model for stage I LUAD patients based on autophagy related genes. High autophagy score predicted a higher recurrence risk and suppressing tumor immune microenvironment. creator: Hongmei Zheng creator: Songqing Fan creator: Hongjing Zang creator: Jiadi Luo creator: Long Shu creator: Jinwu Peng uri: https://doi.org/10.7717/peerj.19366 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zheng et al. title: Trends in dyslipidemia prevalence among Uyghur adults of different genders in China: a retrospective cohort study link: https://peerj.com/articles/19344 last-modified: 2025-05-02 description: BackgroundTo analyze the prevalence and epidemiological characteristics of dyslipidemia among adults of different genders in Xinjiang, China, providing a basis for promoting ideal lipid management among the Uyghur population.MethodsIn this retrospective study, we included 7,646 Uyghur adults from the 2021 physical examination data in Hotan, Xinjiang, and followed up with all participants in 2023 for analysis. Participants completed lifestyle and medical history questionnaires and underwent lipid profiling. Dyslipidemia was defined according to the 2023 Chinese guidelines for lipid management. Group differences were analyzed using t-tests, ANOVA, and chi-square tests, the trend test for ordered categorical variables was conducted using univariate linear regression, and multivariable logistic regression was performed to explore risk factors for dyslipidemia.ResultsIn 2023, the average levels of waist circumference, fasting glucose, total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and non-HDL-C among Uyghur men and women, as well as the prevalence of diabetes, increased compared to 2021, with significant statistical differences within the same gender groups (P < 0.001). The primary types of dyslipidemia among Uyghur adults were low HDL-C. After age and gender standardization, the overall standardized prevalence of high low-density lipoprotein cholesterol (LDL-C), hypertriglyceridemia, and low HDL-C showed a downward trend, with a more pronounced decrease among men. The prevalence of hypercholesterolemia and high non-HDL-C increased from 2021, with a greater increase among women. In 2023, the standardized prevalence rates of hypercholesterolemia, high LDL-C, low HDL-C, hypertriglyceridemia, and high non-HDL-C were higher in women than in men. Multivariable logistic regression adjusted for multiple factors indicated that higher educational attainment (OR 1.992; 95% CI [1.042–3.808]; P = 0.037), overweight (OR 1.303; 95% CI [1.085–1.566]; P = 0.005), obesity (OR 1.520; 95% CI [1.226–1.886]; P = 0.000), and central obesity (OR 1.013; 95% CI [1.006–1.021]; P = 0.001) were associated with dyslipidemia in Uyghur men, while in Uyghur women, dyslipidemia prevalence was mainly related to obesity (OR 1.549; 95% CI [1.261–1.902]; P = 0.000) and central obesity (OR 1.009; 95% CI [1.002–1.016]; P = 0.01).ConclusionThe primary forms of dyslipidemia among Uyghur adults include low HDL-C levels. The prevalence of high LDL-C, hypertriglyceridemia, and low HDL-C is showing a declining trend, particularly among men. In contrast, the prevalence of hypercholesterolemia and high non-HDL-C is increasing more significantly among women. In men, risk factors for dyslipidemia include higher educational attainment, being overweight, obesity, and central obesity. In women, the prevalence of dyslipidemia is mainly associated with obesity and central obesity. creator: Gulinigaer Maimaitituersun creator: Subinuer Jureti creator: Ziyu Yi creator: Yaqi Zhou creator: Meng Li creator: Mengwei Wei creator: Ziyang Liu creator: Menglong Jin creator: Zhenyan Fu uri: https://doi.org/10.7717/peerj.19344 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Maimaitituersun et al.