title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=33 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Comparing the reliability of the single leg squat test using two, three, and four category ordinal rating scales link: https://peerj.com/articles/20218 last-modified: 2025-10-15 description: BackgroundThe single-leg squat test (SLST) is supported by evidence for reliability and validity across various visual rating methods, but the optimal number of ordinal categories for assessing movement quality remains unclear. The study aims to determine the most informative and reliable number of ordinal scoring categories for visually rating the SLST.MethodsA total of 58 subjects with lower extremity injuries participated. A single therapist rated the SLST with a 1-week interval to establish intra-rater reliability. Two therapists independently rated the SLST at the same time point to establish inter-rater reliability. Two-, three-, and four-category ordinal scales were simultaneously used to evaluate SLST performance in rating the components of trunk deviation, hip adduction, and lower extremity internal rotation. Reliability was assessed using unweighted kappa (κ) values.ResultsThe overall intra-rater reliability was κ = 0.60, 0.35, and 0.20, with inter-rater reliability being κ = 0.60, 0.61, and 0.33 for the two-, three-, and four-category scales, respectively. When specifically looking at the components of trunk deviation, hip adduction, and lower extremity internal rotation, intra-rater reliability was moderate to good for two-category scales (κ = 0.47–0.65), fair to good for three-category scales (κ = 0.3–0.7), and fair to good for four-category scales (κ = 0.36–0.65). Inter-rater reliability for the three components was good to excellent (κ = 0.65–0.86) for the two-category, good to excellent (κ = 0.69–0.86) for the three-category, and fair to excellent (κ = 0.55–0.76) for the four-category.ConclusionWhen applied to specific movement components, the three-category ordinal scale demonstrated the best balance between detailed assessment and reliability for visually rating trunk deviation, hip adduction, and lower extremity internal rotation during the SLST in patients with lower extremity injuries. creator: Yongni Zhang creator: Yifan Liu creator: Zhicheng Pan creator: Hui Gao creator: RobRoy L Martin creator: Xinwei Huang uri: https://doi.org/10.7717/peerj.20218 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Evaluation of enamel integrity after clear aligner attachments removal: a risk–benefit comparison of one-step tools link: https://peerj.com/articles/20200 last-modified: 2025-10-15 description: BackgroundAt the end of clear aligner treatment, attachment removal is essential to restore natural tooth morphology while preserving enamel integrity. This study aimed to compare the effects of seven different composite removal instruments on the enamel surface using a risk–benefit model.MaterialsThe instruments assessed were: OneGloss, Enhance, SM 104, Sof-Lex disc (coarse grit), tungsten carbide bur, zirconia bur, and white stone bur. Seventy extracted premolar teeth were bonded with standardized condensable composite attachments (2 × 4 × 1 mm). Enamel integrity was quantitatively assessed by measuring surface roughness (µm) and enamel loss depth (mm), and qualitatively analyzed using scanning electron microscopy (SEM). The time required for attachment removal was recorded in seconds. A risk–benefit model was applied to compare enamel damage and time efficiency across tools.ResultsWhite stone bur exhibited higher surface roughness and greater enamel loss compared to other groups (p = 0.000). Aluminium oxide-based tools (OneGloss, Enhance, SM 104, and the Sof-Lex disc) resulted in less enamel loss than the tungsten carbide bur. The risk–benefit model indicated that OneGloss, Enhance, and SM 104 offered the best balance between enamel preservation and time efficiency. SEM analysis further confirmed that OneGloss and SM 104 produced smoother enamel surfaces compared to other instruments.ConclusionOneGloss and SM 104 demonstrated superior time efficiency and preservation of enamel integrity compared to other evaluated tools. creator: Anh Viet Nguyen creator: Trang Thi Nguyen uri: https://doi.org/10.7717/peerj.20200 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nguyen and Nguyen title: Recognizing IgA-class endomysial antibody equivalent binding patterns on monkey liver substrate through EfficientNet architectures and deep learning link: https://peerj.com/articles/20191 last-modified: 2025-10-15 description: Deep learning offers promising potential for automating the interpretation of immunoglobulin A (IgA) endomysial antibody (EMA) tests, a critical serological test for the diagnosis of celiac disease that currently requires labor-intensive and subjective human interpretation. In this study, we employ and comprehensively evaluate the performance of the EfficientNet and EfficientNetV2 architectures in binary (positive vs negative, where all weak and strong positive signals were grouped as positive), three-class (negative, weak positive, strong positive), and four-class (negative, weak positive, strong positive and gray zone) classification scenarios using immunofluorescence images of IgA EMA equivalent (EMA-eq) tests. Our experiments on 368 clinical samples show high performance, with EfficientNetV2-S achieving an accuracy of 99.37% in binary classification, 95.28% in three-class classification, and 86.98% in the complex four-class scenario that introduces gray zone cases as a distinct interpretive category. Contrary to conventional assumptions, medium-sized deep architectures consistently outperformed their larger counterparts. The superior performance of the EfficientNet-V2 models can be attributed to their architectural innovations and higher input resolution (640 × 640 pixels), which proved critical for capturing subtle immunofluorescence patterns. We also incorporate HiRes-CAM (Class Activation Mapping), a convolutional neural network oriented visual explanation tool, to better understand the decisions of the underlying trained deep learning model in an explainable artificial intelligence (AI) manner. This study demonstrates that deep learning has the potential to achieve expert-level performance in EMA-eq test interpretation, offering a path toward more standardized, efficient and objective celiac disease diagnosis while reducing the burden on specialist medical staff. creator: Mehmet Soylu creator: Ahmet Selman Bozkir uri: https://doi.org/10.7717/peerj.20191 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Soylu and Bozkir 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.