title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=96 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effects of gerbil disturbance on the ecological stoichiometric characteristics and nutrient uptake and utilization of H. ammodendron link: https://peerj.com/articles/19287 last-modified: 2025-04-18 description: Rodent activity is an important factor that affects the growth and development of Haloxylon ammodendron. Studying the effect of rodent disturbance on plant ecological stoichiometric ratios helps evaluate the mechanism by which rodent disturbance affects plant growth and development. In this study, H. ammodendron, a dominant plant, and the gerbil, a typical rodent in the Gurbantunggut Desert, were selected as research objects. By measuring the biomass, root soil , and C: N: P ecostoichiometric ratios of the assimilated branches of H. ammodendron at different growth phases, the impact of great gerbil disturbance on the biomass, ecostoichiometric ratios, and nutrient uptake and use of H. ammodendron were investigated at different growth stages. The results showed that the gerbil disturbance increased the biomass of the aboveground part of the adult H. ammodendron. Gerbil disturbance also increased the soil N/P around the roots during the growth stage and the assimilation branch when the plants were middle-aged. In addition, this disturbance decreased the C/N value. The photosynthetic nitrogen use efficiency (PNUE) and photosynthetic phosphorus use efficiency (PPUE) of H. ammodendron during various growth periods decreased, and the absorption of total nitrogen (TN) in the soil decreased. However, soil total potassium (TK) absorption increased. The soil TN absorption capacity was weakened by gerbil disturbance. Meanwhile, the TK absorption capacity was enhanced, and the biomass of adult H. ammodendron increased. PNUE and PPUE of H. ammodendron were decreased by gerbil interference. In this study, the influence of gerbil disturbance on nutrient absorption by H. ammodendron and use of H. ammodendron was determined. This has provided a baseline for further studies on the coexistence mechanisms of gerbils and H. ammodendron. creator: Jinshun Shi creator: Shuyue Pang creator: Xingming Hao creator: Hongling Liu creator: Li Zhuang creator: Zhongke Wang uri: https://doi.org/10.7717/peerj.19287 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shi et al. title: Genome-wide characterization and expression analysis of the CONSTANS-like gene family of Juglans mandshurica Maxim link: https://peerj.com/articles/19169 last-modified: 2025-04-18 description: The zinc-finger proteins encoded by the CONSTANS-like (COLs) gene family in Juglans mandshurica Maxim. play a significant role in regulating photoperiod-dependent flowering time, as well as in various processes such as growth and development. In this study, 15 members of the CONSTANS-like gene family were identified based on the genomic data of Juglans mandshurica. All of these proteins possess an N-terminal zinc-finger B-box domain and a C-terminal CCT domain. Phylogenetic analysis indicates that the JmCOLs proteins can be divided into three subgroups, with gene structures and motif compositions varying among these subgroups. Chromosomal analysis reveals that the 15 JmCOLs genes are distributed across nine chromosomes. The promoters of genes in this family contain stress-related cis-acting elements, hormone-related response elements, and other elements associated with growth and development. Notably, the most prominent elements are the light-responsive elements, suggesting that genes in this family are predominantly expressed in leaves. The expression patterns of JmCOLs genes differ among the members. Specifically, JmCOL5 and JmCOL10 are expressed exclusively in flower buds (p < 0.05). Throughout the 10 stages of flower bud development, the overall expression level of JmCOL4a peaks at approximately 50 to 100 times higher than its lowest point. The expression pattern of JmCOL5, which first reaches its maximum during the physiological differentiation stage of protogynous male flower buds before declining, suggests its potential involvement in the development of heteromorphic and dichogamous flowers. creator: Jingwen Wu creator: Mengmeng Zhang creator: Yue Gao creator: Shuhan Li creator: Ruoxue Jia creator: Lijie Zhang uri: https://doi.org/10.7717/peerj.19169 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: Anesthesia videos in geriatric and elderly patients on YouTube: content, quality, reliability, and usefulness assessment link: https://peerj.com/articles/19280 last-modified: 2025-04-17 description: PurposeThis study aimed to assess the quality, reliability, content, and usefulness of YouTube videos related to anesthesia in geriatric and elderly patients.MethodsUsing Google Trends, the most popular search terms in the past five years, “geriatric anesthesia” and “anesthesia in the elderly,” were identified. A search on YouTube using these terms initially yielded 200 of the most viewed videos for each term. After applying exclusion criteria, 87 videos were included for detailed analysis. Major themes and topics related to anesthesia in geriatric and elderly patients were identified using a pre-determined qualitative thematic analysis method. The usefulness of the videos was assessed using the specially developed Geriatric and Elderly Anesthesia Usefulness Score (GAEUS). The overall quality and reliability of the videos were evaluated using the Global Quality Scale (GQS) and the Modified DISCERN Scale (M-DISCERN), respectively. The average of the quality, reliability, and usefulness scores calculated by the researchers was used for consistency analysis.ResultsIn our study, 48.3% (42) of the videos on geriatric and elderly patients concerning anesthesia on YouTube were created by personal blogs. The quality of the videos was measured using the GQS, with a mean score of 3.34 and a median of 3 (range: 1–5), showing no significant difference according to the video source (p = 0.166). Reliability was assessed using the M-DISCERN scale, with a mean score of 3.37 and a median of 3.50 (range: 1–5), again showing no significant difference according to the video source (p = 0.097). Usefulness was measured using the GAEUS score, with a mean score of 15.30 and a median of 12.5 (range: 2–63), which showed a significant difference according to the video source (p = 0.000). The average duration of videos with low usefulness was 31.59 minutes (range: 5–44), while the average duration of moderately and highly useful videos was 59.37 minutes (range: 19.44–119.05). This duration difference was statistically significant (u = 2.569, p = 0.010).ConclusionIn our study, we examined YouTube videos covering anesthesia topics for geriatric and elderly patients. The highest usefulness scores were obtained from personal blogs; however, all sources generally showed low usefulness. The quality of the videos was assessed using the GQS, and their reliability was evaluated with the M-DISCERN. On both scales, the videos showed moderate performance across all sources. These findings indicate a need for more comprehensive and informative content on YouTube, especially for the education of healthcare professionals and patients. To better address the needs of elderly patients, the richness of content and educational value of these videos should be enhanced. creator: Turan Evran creator: Seher İlhan uri: https://doi.org/10.7717/peerj.19280 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Evran and İlhan title: Comprehensive evaluation of methods for identifying tissues or cell types of origin of the plasma cell-free transcriptome link: https://peerj.com/articles/19241 last-modified: 2025-04-17 description: Plasma cell-free RNA (cfRNA) is derived from cells in various tissues and organs throughout the body and reflects the physiological and pathological conditions. Identifying the origins of cfRNA is essential for comprehending its variations. Only a few tools are designed for cfRNA deconvolution, and most studies have relied on traditional bulk RNA methods. In this study, we employed human tissue and cell transcriptomic data as reference sets and evaluated the performance of seven deconvolution methods on cfRNA. We compared the analysis results of cell types and tissues of origin of plasma cfRNA and chose to use single-cell RNA sequencing (scRNA-seq) data as reference to conduct further evaluation of deconvolution methods. Subsequently, we assessed the accuracy and robustness of the methods by utilizing simulated cfRNA data generated from scRNA-seq. We also evaluated the methods’ accuracy on real plasma cfRNA data by analyzing the correlation between the predicted cell proportions and the corresponding clinical indicators. Moreover, we compared the methods’ effectiveness in revealing the impacts of diseases on cells and evaluated the performance of cancer classification models based on the cell origin data they provided. In summary, our study provides valuable insights into cfRNA origin analysis, enhancing its potential in biomedical research. creator: Tingyu Yang creator: Yulong Qin creator: Shuo Yan creator: Sijia Guo creator: Jinghua Sun creator: Jiayi Huang creator: Jiayi Li creator: Qing Zhou creator: Xin Jin creator: Wen-Jing Wang uri: https://doi.org/10.7717/peerj.19241 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Yang et al. title: Understanding trends in Zostera research, stressors, and response variables: a global systematic review of the seagrass genus link: https://peerj.com/articles/19209 last-modified: 2025-04-17 description: BackgroundSeagrass meadows are ecologically significant habitats that are globally threatened. Thus, there is increased interest in conservation of seagrasses as they face widespread decline. Biotic and abiotic factors that influence seagrass can be classified as stressors, such as rising temperature and eutrophication. Our study met an imminent need to consolidate data from previous studies to discern knowledge gaps and identify trends in studies, stressors, species, and geographic origination of research for the genus Zostera. For our systematic review, the objectives were to (A) qualitatively assess and summarize the current state of literature focused on seagrass species within the Zostera genus and their stressors; (B) utilize data extracted from full-text articles to identify trends and knowledge gaps for the study of stressors, response variable measurements, species, geography, and study designs; and (C) map the distribution, type, and number of these studies globally.MethodologyWe included articles that focused on stressors associated with Zostera seagrass species, and excluded studies of other seagrasses and non-stressor related articles. We conducted a Web of Science search of all databases, concluding in January of 2021, followed by a standardized review and data extraction protocol using Colandr (colandrapp.com) as our article screening tool. All 15 review participants were trained on the same set of practice articles and decision trees to minimize variation between individuals. After full text extraction, we analyzed our data by frequency and association between species, stressors, and geographic locations studied.ResultsWe screened 7,331 titles and abstracts and extracted data from 1,098 full-text articles. We found nutrients, temperature, and light were the most studied stressors. The United States of America produced the most articles in our review, followed by Australia. Zostera marina was most frequently studied, and our review found no stressor studies for five species in the genus. Studies most frequently measured response variables across multiple levels of ecological organization, including the individual plant, biotic community, and environmental conditions. As a part of our review, we made all extracted data publicly available as an interactive map.ConclusionUndertaking a review of global studies allowed us to assess more seagrass articles for a single genus than any prior systematic review, summarizing a breadth of stressor studies related to the Zostera genus. A team effort and standardized training minimized bias during screening and data extraction. Evidence limitations may exist due to the single database used in our search protocol, as well as species, geographic, and stressor biases in included studies. Our review creates a centralized knowledge base that serves as a foundational information source for Zostera research, while highlighting existing knowledge gaps in the literature. creator: Hannah R. Lyford creator: Emma Guerrini Romano creator: Shayna A. Sura creator: Sarah Joy Bittick uri: https://doi.org/10.7717/peerj.19209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lyford et al. title: Risk factors and predictive model for renal outcomes in autoimmune membranous nephropathy with and without acute kidney injury: a retrospective cohort study link: https://peerj.com/articles/19331 last-modified: 2025-04-16 description: ObjectiveThis study aimed to delineate the risk factors affecting renal outcomes in autoimmune membranous nephropathy (aMN) with or without acute kidney injury (AKI) and develop a predictive model.MethodsThis retrospective cohort study included 441 patients with biopsy-confirmed aMN from the First Affiliated Hospital of Fujian Medical University (January 2010 to March 2023). Patients were grouped based on the presence of AKI and followed up until a renal endpoint event (progression to end-stage renal disease, initiation of dialysis, or either a >40% decline in estimated glomerular filtration rate from baseline or a doubling of serum creatinine levels from baseline, both sustained for ≥3 months) or study endpoint (March 2024). Clinicopathological and renal outcomes were collected and analyzed. Risk factors for renal endpoints were identified via Cox regression analyses, and a nomogram was constructed. Model performance was evaluated using the C-index, time-dependent receiver operating characteristic (Time-ROC) curves, calibration curves, and decision curve analysis (DCA). Kaplan–Meier survival curves compared renal survival between AKI subgroups.ResultsAmong 441 patients, 109 (24.72%) experienced AKI. Renal endpoint events occurred in 40.4% of the AKI group and 4.5% of the non-AKI group. Multivariate Cox regression identified AKI (HR = 7.298, P < 0.001), triglycerides (HR = 1.140, P = 0.002), serum creatinine (HR = 1.008, P = 0.012), hematuria (HR = 2.246, P = 0.040), and kidney anti-M-type phospholipase A2 receptor staining 4+ (HR = 2.473, P = 0.003) as independent risk factors, while serum C3 (HR = 0.082, P < 0.001) was an independent protective factor. The nomogram had a C-index of 0.845 (P < 0.001), with Time-ROC AUCs of 0.92, 0.81, 0.83, and 0.87 for 3 to 6 years, respectively. Calibration plots revealed good consistency between the predicted and actual probabilities. DCA indicated that the nomogram had potential clinical utility. Kaplan–Meier analysis showed lower cumulative renal survival in patients with AKI (P < 0.001).ConclusionsThe risk factor model suggests that renal outcomes in patients with aMN can be predicted. Early assessment and management targeting these identified risk factors could help delay renal function decline in these patients. creator: Zhenzhou Li creator: Liyan Yang creator: Linxia Wei creator: Mengjie Weng creator: Jiaqun Lin creator: Yi Chen creator: Binbin Fu creator: Guifen Li creator: Caiming Chen creator: Yanfang Xu creator: Jianxin Wan creator: Jiong Cui uri: https://doi.org/10.7717/peerj.19331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Circular RNAs in endometriosis analyzed through RNA sequencing and bioinformatics for expression profile link: https://peerj.com/articles/19298 last-modified: 2025-04-16 description: BackgroundEndometriosis severely affects women’s physical and mental health; it is particularly important to find targets for the treatment and diagnosis of endometriosis.MethodThis research aimed to investigate the circRNA expression pattern in endometriosis, a type of non-coding RNA that can modulate parental gene expression by acting as miRNA sponges. Through high-throughput sequencing, we analyzed the circRNA expression profile in endometriosis patients in comparison to individuals without the condition.ResultsWe detected 371 circular RNAs (circRNAs) showing increased expression and 308 circRNAs displaying decreased expression levels. To validate these findings, we employed quantitative real-time PCR (qRT-PCR) to confirm the expression of the top three differential expressed circRNAs listed in circBase. We inferred potential roles of these differentially expressed circRNAs in endometriosis development by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Moreover, by examining the circRNA-microRNA-target gene network, we uncovered a plausible mechanism. Specifically, interactions involving the markedly upregulated hsa_circ_000005 and significantly downregulated hsa_circ_000011 with miR-5787 may influence downstream targets, potentially contributing to the pathogenesis of endometriosis. Our study offers a foundational and crucial circRNA expression profile within the framework of endometriosis. creator: Yan Yue creator: Jing Qian creator: Dandan Gui creator: Bin Lu uri: https://doi.org/10.7717/peerj.19298 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Yue et al. title: Effects of low-frequency vibration training on walking ability and body composition among older adults: a randomized controlled trial link: https://peerj.com/articles/19263 last-modified: 2025-04-16 description: BackgroundAs life expectancy rises, age-related decline in mobility and physical function poses challenges for older adults. While traditional exercise can help, limitations and injury risks persist. This study explores low-frequency vibration training as a potential alternative to improve walking ability and body composition in older adults.MethodsA lottery was used to randomly assign 50 participants (mean age 80.08 years) to either a vibration group (n = 25, 10 males, 15 females) or a control group (n = 25, 11 males, 14 females). While the control group continued their regular daily schedule, the vibration group completed 8 weeks of low-frequency vibration training (frequency: 4–13 Hz; amplitude: two mm), three sessions per week, with each session lasting 20–30 minutes. The walk ability was assessed using the 30-second Chair Stand Test (30-s CST), Timed Up and Go (TUG), and six-meter (six m) walk speed, while body composition was measured via body mass index (BMI), body fat percentage, and waist circumference (WC), hip circumference (HC), and waist-to-hip ratio (WHR).ResultsLow-frequency vibration training significantly increased walking speed in the six m walk speed (F(1,36) = 4.50, p = 0.04, ηp2 = 0.11) and TUG (z =  − 2.72, p = 0.007), compared with the control group. Observed improvements on the 30-s CST were not statistically significant (F(1,36) = 0.05, p = 0.81, ηp2 = 0.002). In the WC, the effect of time (F(1,36) = 7.19, p = 0.01, ηp2 = 0.16) was significant. The main effect of the group for HC (F(1,36) = 0.06, p = 0.80, ηp2 = 0.002) and WHR (F(1,36) = 2.00, p = 0.16, ηp2 = 0.05) were not significant, but the interaction effects for HC (F(1,36) = 6.37, p = 0.01, ηp2 = 0.15) and WHR (F(1,36) = 9.08, p = 0.005, ηp2 = 0.20) were significant. However, the intervention showed no statistically significant effects on BMI and body fat percentage.ConclusionLow-frequency vibration training significantly enhanced walking speed and WHR in older adults. This low-intensity intervention is especially beneficial for those with exercise limitations or a high risk of injury. Although its effects on BMI and body fat percentage were limited, the study offers valuable insights for developing personalized vibration training programs. creator: Xiaohuan Tan creator: Guiping Jiang creator: Lei Zhang creator: Dandan Wang creator: Xueping Wu uri: https://doi.org/10.7717/peerj.19263 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tan et al. title: Biomarkers associated with cell-in-cell structure in kidney renal clear cell carcinoma based on transcriptome sequencing link: https://peerj.com/articles/19246 last-modified: 2025-04-16 description: BackgroundKidney renal clear cell carcinoma (KIRC), the main histological subtype of renal cell carcinoma, has a high incidence globally. Cell-in-cell structures (CICs), as a cellular biological phenomenon, play pivotal roles in cell competition, immune evasion and tumor progression in the context of KIRC.MethodsData for this study were sourced from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases. Differentially expressed genes (DEGs) were identified using the limma package. Enrichment analyses were performed using the clusterProfiler package. Support vector machine-recursive feature elimination (SVM-RFE) and Least Absolute Shrinkage and Selection Operator (LASSO) regression, implemented via the caret and glmnet packages in R, were used to select biomarkers. The accuracy of these biomarkers was verified by using the receiver operating characteristic (ROC) curve as well as in vitro experiments (CCK-8 assay, wound healing assay, Transwell assay, and quantitative real-time PCR). The CIBERSORT algorithm was applied to explore the association between immune infiltration and the biomarkers. Further analysis explored the association between these biomarkers and clinicopathological characteristics of KIRC. For single-cell data, the Seurat package is used to read the sample data, and the SCTransform function is employed for normalization.ResultsThis study identified 1,256 DEGs which enriched in T-cell immune system regulation processes. Five hub genes (CDKN2A, VIM, TGFB1, CTSS, and CDC20) were biomarkers with area under the curve (AUC) values > 0.8, indicating high predictive performance. In vitro validation experiments demonstrated that the expressions of all five biomarkers in KIRC cells were elevated, and the knockdown of CTSS could inhibit the migration and invasion of KIRC cells. Immune infiltration analysis showed higher proportions of T-cells and macrophages in tumor tissues. CDKN2A and CDC20 expressions correlated significantly with stage and grade, while TGFB1, CDKN2A, and CDC20 were highly expressed in proliferative tumor cells.ConclusionThis study provides new biomarkers for KIRC, offering valuable insights into its developmental mechanisms for the research of CIC in this disease. creator: Zehua Wang creator: Zhongxiao Zhang uri: https://doi.org/10.7717/peerj.19246 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang and Zhang title: Weight loss effects of non-pharmacological interventions in women with polycystic ovary syndrome: a systematic review and network meta-analysis link: https://peerj.com/articles/19238 last-modified: 2025-04-16 description: ObjectiveTo compare the effectiveness of non-pharmacologic interventions in improving weight loss management in overweight patients with polycystic ovary syndrome (PCOS).MethodsFive databases, PubMed, Embase, Cochrane, Web of Science and China Knowledge, were searched for this study. The Cochrane risk of bias tool was used to assess the risk of bias of eligible studies. The included randomized controlled trials were subjected to traditional meta-analysis (TMA) and network meta-analysis (NMA), and the cumulative number of surfaces under the ranking curve (SUCRA) was calculated for each intervention to derive the optimal intervention.ResultsThe study ultimately included 29 articles involving 22 different interventions and 1,565 patients. The results of the NMA showed that the optimal intervention for the four outcome measures (body weight, body mass index (BMI), waist circumference (WC), waist-hip ratio (WHR)) was nutritional supplement + low-calorie diet, Taichi, continuous aerobic exercise and Taichi.ConclusionCurrent evidence suggests that nutritional supplements + hypocaloric diet; Taichi; continuous aerobic exercise have the greatest clinical advantage in weight loss and deserve to be promoted in the clinic. One of the best interventions for both outcome indicators, Taichi, suggests that it may be a common misconception that simply increasing the intensity of exercise is not the only way to lose weight and improve health. creator: Rong Hu creator: Lihong Zhang creator: Jingjing Zhu creator: Sihua Zhao creator: Lixue Yin creator: Junping Hu uri: https://doi.org/10.7717/peerj.19238 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hu et al.