title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=41 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effect of circadian rhythm disruption on benign prostatic hyperplasia in rats link: https://peerj.com/articles/20173 last-modified: 2025-10-15 description: Benign prostatic hyperplasia (BPH) is a common condition in middle-aged and elderly men. Disrupted circadian rhythms (CRD) can directly influence aging, inflammation, metabolic syndrome, and hormonal changes—all of which are closely linked to BPH. This study aimed to investigate whether CRD accelerates prostatic hyperplasia in rats. Twenty male Sprague-Dawley (SD) rats were divided into two batches. A BPH model was established using mixed slow-release pellets of testosterone (T) and estradiol (E2). CRD was induced by continuous light exposure (Cle), while a 12-hour light/12-hour dark cycle defined the control (Con) group.First batchRats were divided into T+E2 and T+E2+Cle groups. Initial and final body weight, prostate weight, and prostate index (PI) were recorded. Hematoxylin and eosin (H&E) staining was performed. Serum levels of dihydrotestosterone (DHT) and estradiol (E2) were measured by ELISA, and mRNA expression of circadian rhythm genes was assessed via qRT-PCR.Second batchRats were divided into Con and Cle groups. Body weight, prostate weight, and PI were recorded. H&E staining was used for pathological analysis. Ki-67 expression was assessed by immunohistochemistry (IHC). RNA sequencing (RNA-Seq) was used to investigate gene expression in prostate tissue, validated by qRT-PCR. Differentially expressed genes (DEGs) were analyzed using bioinformatics methods.First batch resultsCRD significantly increased prostate weight, PI, and epithelial thickness; elevated serum DHT levels; and reduced E2 levels. qRT-PCR confirmed that CRD altered circadian gene expression.Second batch resultsCRD significantly increased PI and Ki-67 expression in the prostate. GO analysis revealed significant enrichment in immune response, external side of plasma membrane, and carbohydrate binding (p < 0.001). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed enrichment in cytokine-cytokine receptor interaction, viral protein interaction with cytokine and receptor, phenylalanine metabolism, and chemokine signaling pathways (p < 0.001). Gene set enrichment analysis (GSEA) indicated positive enrichment in voltage-gated calcium channel activity and type II diabetes mellitus. Protein–protein interaction (PPI) network analysis identified Itgad, Ccr7, CD27, Sell, CD69, Gzmb, IRF8, and KIrd1 as highly correlated genes.ConclusionThese findings suggest that CRD may accelerate prostate cell growth by modulating immune and inflammatory responses, contributing to the development of benign prostatic hyperplasia. creator: Xiaoxue Huang creator: Xiaohu Tang creator: Yuanzhao Xu creator: Zhiyan Liu creator: Guangheng Luo uri: https://doi.org/10.7717/peerj.20173 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles link: https://peerj.com/articles/20170 last-modified: 2025-10-15 description: As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds. creator: Yonggang Dong creator: Sitong Fan creator: Shunfu He creator: Wenxin Zhao creator: Zhuoma Lancuo creator: Kirill Sharshov creator: Ying Li creator: Wen Wang uri: https://doi.org/10.7717/peerj.20170 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dong et al. title: Detection of terrestrial mammals using environmental DNA during heavy rainfall events and associated influencing factors link: https://peerj.com/articles/20166 last-modified: 2025-10-15 description: Recent developments in environmental DNA (eDNA) analyses have facilitated non-invasive and cost-effective ecological monitoring. Based on eDNA of terrestrial species released into water upon contact, simultaneous detection of aquatic and terrestrial species is feasible. However, an efficient sampling design for terrestrial vertebrate eDNA in aquatic environments has not yet been established because DNA is rarely released into these environments. In this study, we targeted eDNA transported from land to rivers through surface runoff during rainfall in three rivers and one irrigation channel within the Kiyotake River system, Japan. We quantified the eDNA concentration of a specific terrestrial vertebrate (Bos taurus) using digital polymerase chain reaction (PCR) and examined the efficiency of using filter papers with different pore sizes (0.7 µm and 2.7 µm). We also assessed the influence of various environmental factors (e.g., rainfall characteristics described by the parameters of Gaussian distribution, water turbidity) on eDNA detection across different rainfall events. During the surveys, target DNA was detected in 42 out of 47 samples, suggesting the feasibility of consistently detecting terrestrial mammals from stormwater runoff. Overall, compared with the glass fiber filter with larger pore size, the smaller pore size filter captured more eDNA. The generalized linear mixed model revealed that prolonged rainfall duration, turbidity, and pH had a significant positive effect on eDNA concentration, whereas the distance from the assumed point of entry into the river to the sampling point had a significant negative effect. These results suggest that the runoff and transport of eDNA from terrestrial areas to rivers are enhanced under prolonged rainfall conditions, although eDNA degrades while transported along a longer watercourse by biochemical decomposition and sedimentation. creator: Chen Xu creator: Kei Nukazawa uri: https://doi.org/10.7717/peerj.20166 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xu and Nukazawa title: Comparison of IAA and amino acid profiles of the selected rootstocks and their accumulation in grafted scion of Cucumis sativus L. link: https://peerj.com/articles/20159 last-modified: 2025-10-15 description: Finding a suitable rootstock for Cucumis sativus L. is an important area of research, as it is aimed at extending the fruiting period and increasing the yield. In such studies, it is important to evaluate various biochemical parameters in addition to morphometric data, such as amino acid and auxin content, which will reflect the effectiveness of the rootstock for scion growth. In this research, we tested 56 genotypes and lines from four species of the Cucurbitaceae family as potential candidates for grafting cucumber rootstock: Cucurbita ficifolia Bouché, Cucurbita moschata L., Cucurbita pepo L. and Cucurbita maxima Duch. The study focused on the study of morphometric parameters, amino acid and indoleacetic acid (IAA) accumulation in rootstocks at the age of 2 and 4 weeks. Based on the results of the work, the Dunganskaya otb 3 variety of C. maxima was selected as a rootstock for cucumber, since it showed the largest plant and root weight, as well as the highest content of amino acids and IAA. Further, an optimized tongue grafting method was used for grafting cucumber with the selected variety of C. maxima, which in turn contributed to the rapid healing and adaptation of the scion. Also, a significant increase in the amino acids L-valine, L-threonine, L-alanine, L-tyrosine by 28.8; 38.8; 42.5; 98%, respectively and IAA by 39% in the scions compared to the control cucumber plants were observed at the end of the fourth week after grafting. The yield of grafted cucumber plants per plant and per square meter showed an increase of 23% compared to the control. In conclusion, from the obtained data, it can be assumed that grafting of C. sativus onto C. maxima plants is the most suitable and can be recommended for production. creator: Serik Jantassov creator: Alima Shoibekova creator: Aigerim Jantassova creator: Ali Samatov creator: Bulat Kuluev creator: Yakov Mineev creator: Izat Smekenov creator: Maxat Toishimanov creator: Gabit Bari uri: https://doi.org/10.7717/peerj.20159 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jantassov et al. title: Serum proteomic profiling during the periovulatory period identifies preliminary candidate biomarkers of oocyte maturation in deslorelin-induced ovulation in dogs link: https://peerj.com/articles/20106 last-modified: 2025-10-15 description: BackgroundThe reproductive physiology of canines is unique from other mammals because oocyte maturation occurs about 48–72 hours after ovulation. This study aimed to evaluate the blood serum protein profile in canines during the periovulatory period by using shotgun proteomics to identify potential biomarkers of oocyte maturation.MethodAnestrus female dogs (n = 9) were implanted subcutaneously with 4.7 mg of deslorelin to induce estrus and ovulation. After implantation, ovariectomy was performed based on the level of progesterone and vaginal cytology evaluations conducted every 48 hours. Simultaneously, serum samples were collected for proteomic analysis. The oocytes were flushed from the oviduct, and the oocyte maturation stage was identified. Based on oocyte staging, all samples were categorized into three groups (n = 3 dogs per group): pre-ovulation, ovulation with immature oocytes, and ovulation with mature oocytes. All serum samples were analyzed in triplicate (27 independent injections) using liquid chromatography-tandem mass spectrometry to investigate the protein profile.ResultsProteomics analysis showed 11 proteins upregulated from three different groups: tubulin-specific chaperone D (TBCD); coiled-coil domain-containing protein 93 (CCDC93); WDFY family member 4 (WDFY4); calcium and integrin-binding protein 1 (CIB1); IQ motif containing E (IQCE); large ribosomal subunit protein uL23 N-terminal domain-containing protein (RPL23A); neuraminidase 4 (NEU4); G protein-coupled receptor kinase (GRK3); NF-keppaB inhibitor delta (NFKBID); leucine rich repeat containing 4B (LRRC4B); and Rho family-interacting cell polarization regulator 2 (RIPOR2). Among these proteins, NFKDIB, which are oocyte maturation markers in other mammalian species, was upregulated in the ovulation with mature oocyte group (P < 0.01). Therefore, NFKBID is a possible to be an oocyte maturation marker in canines, but further studies on larger populations are needed to confirm its potential. creator: Larindhorn Udomthanaisit creator: Sittiruk Roytrakul creator: Wirakan Kallayanathum creator: Sawanya Charoenlappanit creator: Theerawat Tharasanit uri: https://doi.org/10.7717/peerj.20106 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Udomthanaisit et al. title: Hyperhomocysteinemia and its association with decreased glomerular filtration rate in patients with chronic kidney disease: a comprehensive meta-analysis link: https://peerj.com/articles/20064 last-modified: 2025-10-15 description: BackgroundHyperhomocysteinemia (elevated homocysteine, Hcy) is common in chronic kidney disease (CKD) patients, but its effect on glomerular filtration rate (GFR), a key renal function indicator, is unclear.ObjectiveThis meta-analysis aimed to clarify the association between hyperhomocysteinemia (HHcy, defined as Hcy > 15 µmol/L) and reduced glomerular filtration rate (GFR) in chronic kidney disease (CKD) patients, hypothesizing that HHcy is associated with a more significant GFR reduction. To test this hypothesis, a comprehensive search was conducted in PubMed, Embase, Cochrane databases, and reference lists. The primary outcome of interest was the relationship between HHcy and GFR decline in CKD. Methods For this meta-analysis, we established clear inclusion and exclusion criteria to identify eligible studies. Studies were included if they involved patients with chronic kidney disease (CKD), employed randomized controlled, cross-sectional, or cohort study designs, included participants aged 14 years or older, and reported or permitted the calculation of glomerular filtration rate (GFR) and homocysteine (Hcy) levels. We excluded studies that were not in English, focused on acute kidney injury, end-stage kidney disease, or dialysis patients, lacked clear group definitions, were based on animal models, or used non-standard CKD definitions. A comprehensive search strategy was employed to identify relevant studies. We combined MeSH terms (e.g., “homocysteine [MeSH]” and “renal insufficiency, chronic [MeSH]”) with free-text keywords in major databases, including PubMed, Embase, and Web of Science. Additionally, we utilized the “related items” function and applied Boolean operators to refine search results. Data were synthesized through meta-analysis, and the mean ± SD of GFR in CKD patients according to Hcy levels were calculated for comparison. All databases were searched from their inception dates to June 2024.ResultsCKD patients with hyperhomocysteinemia had a lower GFR (SMD = 2.26, 95% CI [1.37–3.15]). However, significant inter-study heterogeneity (P < 0.01, I2 = 99.5%) was found. Five articles (Z 2016, Ye, Z 2017, Zhang, Y 2020, Shen, Z 2022, Wu, and J 2022) contributed to it (P = 0.015 < 0.05). Subgrouping them eliminated heterogeneity (P = 0.52, I2 = 0.00%). Sensitivity analysis showed individual article exclusion had little effect on the result. But Egger tests showed publication bias (P < 0.05), while scissors graph analysis supported result stability (P < 0.01).ConclusionsIn CKD, elevated Hcy is related to kidney function decline. creator: Wei Chen creator: Xueming Liang creator: Gao Liang creator: Xueli Zhao creator: Jie Wang creator: Qinhe Jiang uri: https://doi.org/10.7717/peerj.20064 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Chen et al. title: Sleep and geriatric syndromes in elderly emergency patients in China: a cross-sectional survey link: https://peerj.com/articles/20194 last-modified: 2025-10-14 description: This study aims to assess the prevalence of abnormal sleep conditions and geriatric syndromes in elderly emergency patients in China and to explore the relationship between them. The convenience sampling method was used to recruit elderly patients in the Emergency Department of Yueyang Central Hospital in Hunan Province from July to November 2023. A total of 205 elderly emergency patients were included. Sleep conditions and four geriatric syndromes (frailty, sarcopenia, malnutrition, and cognitive impairment) were investigated. Logistic regression analysis was used to assess the relationship between sleep and the four geriatric syndromes. After adjusting for age, gender, marital status, education level, and number of comorbidities, it was found that patients with mild and significant daytime sleepiness were more likely to have frailty than those with no daytime sleepiness (OR = 2.509, p = 0.018; OR = 4.395, p = 0.048). Patients with mild and significant dissatisfaction with sleep quality were more likely to have sarcopenia than those with good sleep quality (OR = 4.153, p = 0.006; OR = 5.955, p = 0.013). Additionally, patients with normal sleep duration had a lower risk of malnutrition than those with insufficient sleep duration (OR = 0.353, p = 0.043), and patients with slight daytime sleepiness had a higher risk of malnutrition than those with no daytime sleepiness (OR = 3.414, p = 0.004). Finally, patients with mild daytime sleepiness were more likely to have cognitive impairment than those without daytime sleepiness (OR = 2.564, p = 0.026). This study indicates that improving sleep may be a favorable factor for controlling geriatric syndromes. However, as the single-center design and convenience sampling restrict generalizability, the results should be validated in multi-center studies using probability sampling. creator: Qiong Zhang creator: Peng Li creator: Lingyun Lu creator: Cheng He creator: Dan Chen creator: Fen Xiang creator: Can Huang creator: Xingliang Gan creator: Feng Yi uri: https://doi.org/10.7717/peerj.20194 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: 24-epibrassinosteroid and jasmine oil improve vegetative growth and productivity of Flame Seedless grapevines under abiotic stresses link: https://peerj.com/articles/20181 last-modified: 2025-10-14 description: Abiotic stresses such as high temperature, humidity fluctuations, and excessive light negatively impact grapevine physiological functions, resulting in irregular vegetative growth and reduced productivity. Natural plant growth regulators and essential oils offer potential eco-friendly strategies to mitigate these adverse effects. This study investigated the effects of foliar applications of 24-epibrassinosteroid (Br) at concentrations of 1, 2, and 3 mg/L and jasmine oil (JO) at 500, 1,000, and 1,500 µL/L on Flame Seedless grapevines exposed to abiotic stress. The treatments aimed to enhance vegetative development, nutrient uptake, biochemical attributes, and yield. Results showed that all treatments successfully improved the vegetative growth of Flame Seedless grapevines by increasing leaf area, shoot length, diameter, number of leaves/shoots, pruning wood weight, internode length, and coefficient of wood ripening. They also improved the mineral content in leaf petioles, total carbohydrates in canes, chlorophyll contents in leaves, and yield per vine. In addition, the quality of the Flame Seedless grapevine was improved by increasing cluster weight, length, width, berry firmness, length, width, soluble solids content (SSC), titratable acidity (TA), SSC/TA ratio, total sugars, phenols, anthocyanin, and flavonoids, activities of peroxidase (POX), phenylalanine ammonialyase (PAL), polyphenoloxidase (PPO) and catalase (CAT) enzyme in berry. Application of Br at 3 mg/L yielded the highest significant values for vegetative growth parameters, yield, and physical characteristics. While JO at a rate of 1,500 µL/L increased the total phenols, flavonoids, and anthocyanin, as well as PPO, PAL, POX activity, and CAT in the berry. Foliar application of Br and JO effectively mitigated the adverse effects of abiotic stress in Flame Seedless grapevines. creator: Abdullah Alebidi creator: Ahmed A. Elaidy creator: Ahmed F. Abd El-Khalek creator: Magda M. Abd Elmaksoud creator: Hayam M. Elmenofy creator: Ahmed M. Elzainy creator: Hail Z. Rihan creator: Mahmoud Abdel-Sattar uri: https://doi.org/10.7717/peerj.20181 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alebidi et al. title: Prediction of pathological complete response to neoadjuvant chemotherapy for invasive breast cancers based on longitudinal ultrasound and superb microvascular imaging: a single-center retrospective study link: https://peerj.com/articles/20171 last-modified: 2025-10-14 description: PurposeTo examine whether dynamic alterations in conventional ultrasound (US) and superb microvascular imaging (SMI) can act as predictors of pathological complete response (pCR) following neoadjuvant chemotherapy (NAC) in breast cancer (BC).MethodsThis single-center, retrospective study included women with invasive BC who underwent NAC between January 2022 and December 2024. The features of conventional US and SMI characteristics of BC were analyzed before NAC and the change (Δ) after two cycles. Multivariate logistic regression analysis (Forward, Wald, α = 0.05) was used to screen factors independently associated with pCR. Area under the receiver operating characteristic curve (AUC) analysis was performed to confirm the predictive effectiveness and evaluate the internal validity through bootstrap resampling. A nomogram was created to graphically represent the predictive power of the various factors for pCR.ResultsBefore NAC, the pCR group exhibited significantly higher negative rates for the estrogen receptor (ER) and progesterone receptor (PR). (P < 0.001 and P = 0.005, respectively) and significantly higher positive rates of human epidermal growth factor receptor 2 (HER2) and echogenic rinds (P < 0.001 and P = 0.029, respectively). Additionally, they exhibited significantly shorter largest diameters (LD) and shortest diameters (SD) (P = 0.001 and P = 0.003). After two cycles of NAC, patients who achieved pCR exhibited a significantly higher proportion of monochrome superb microvascular imaging (mSMI) that had not expanded, as well as disappearance of the echogenic rind (P < 0.001 and P = 0.002). Regarding the rate of change in LD, SD, and vascular index (VI), patients in the pCR group showed significantly higher values than those in the non-pCR group (all P < 0.001). The multivariate logistic regression model identified ΔVI (%), ΔSD (%), and SD to have the strongest association with pCR. The overall multivariate model demonstrated the best AUC (0.963), which was significantly higher than that of any single factor. Bootstrap resampling, calibration plots, and decision curve analysis (DCA) all demonstrated strong performance in both discrimination and calibration.ConclusionThe baseline status of US and SMI, as well as the longitudinal changes, demonstrated good predictive performance for pCR in BC following NAC. creator: Yanling Zuo creator: Yongtao Zhan creator: Jie Zhou creator: Haoming Xia creator: Tao Li creator: Fan Zhou creator: Chunyue Luo creator: Huafeng Zeng creator: Yingjia Li uri: https://doi.org/10.7717/peerj.20171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zuo et al. title: Unraveling the role of regulatory cell death in sepsis: an integrated analysis of bulk and single-cell sequencing data link: https://peerj.com/articles/20167 last-modified: 2025-10-14 description: BackgroundSepsis is a life-threatening condition characterized by systemic inflammation and dysfunction of multiple organs. Recently, regulatory cell death (RCD) has emerged as a distinct pathological feature and serve as a potential source of biomarkers or therapeutic targets in sepsis.MethodsComprehensive transcriptomic datasets of sepsis were accessed from the Gene Expression Omnibus (GEO) database. Genes involved in 18 RCD pathways were compiled from databases and published literature. The limma package was utilized to identify differentially expressed genes (DEGs). The Gene Set Variation Analysis (GSVA), CIBERSORT, Weighted Gene Co-expression Network Analysis (WGCNA), and receiver operating characteristic (ROC) analyses were combined to identify key RCDs pathways. Core RCD-related DEGs (RRDs) were selected using Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine (SVM), and Random Forest (RF) machine learning methods. The expression patterns and diagnostic performance of the core RRDs were validated across multiple datasets and further confirmed through meta-analysis. Immune localization of RRDs was examined using single-cell transcriptomic data. Prognostic significance was evaluated using multivariate Cox analysis. Finally, the mRNA expression level was validated using quantitative real-time polymerase chain reaction (qRT-PCR).ResultsZinc Finger DHHC-Type Containing 3 (ZDHHC3), Chloride Intracellular Channel 1 (CLIC1), Glutathione S-Transferase Omega 1 (GSTO1), Biogenesis of Lysosomal Organelles Complex 1 Subunit 1 (BLOC1S1), and Toll-Like Receptor 5 (TLR5) were considered as core RRDs, with monocytes and neutrophils serving as the principal cell types responsible for their overexpression and likely contributing critically to their downstream biological effects. Among them, ZDHHC3 and TLR5 were identified as independent risk factors for sepsis. Their significantly elevated mRNA expression in septic mice was confirmed by qRT-PCR.ConclusionFindings from this study underscored the crucial role of RCD pathways in the development of sepsis. Notably, ZDHHC3 and TLR5 were identified as novel and robust biomarkers for sepsis. creator: Susu Cao creator: Wenyan Xiao creator: Sinong Pan creator: Siying Liu creator: Tianfeng Hua creator: Min Yang uri: https://doi.org/10.7717/peerj.20167 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Cao et al.