title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=19 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Biomarkers of mitochondrial permeability transition-driven necrosis in the regulation of ulcerative colitis link: https://peerj.com/articles/20345 last-modified: 2025-12-05 description: BackgroundUlcerative colitis (UC) is a gastrointestinal condition characterized by chronic intestinal inflammation and damage to the mucosal barrier, with regulated cell death (RCD) playing a pivotal role in its pathogenesis. Among the various forms of RCD, mitochondrial permeability transition-driven necrosis (MPTDN) has not been thoroughly investigated in relation to UC in the current literature.ObjectiveThe objective of this study was to identify genes associated with MPTDN that are relevant to UC and to explore their potential implications in the disease process.MethodsData were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify differentially expressed MPTD-related genes (MPTDEGs). Machine learning techniques, including Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine-Recursive Feature Elimination (SVM-RFE), and Random Forest (RF), were employed to isolate key hub genes. The diagnostic potential of these genes was evaluated through receiver operating characteristic (ROC) curve analysis, and their expression was validated using an external dataset. Additionally, immunoinfiltration analysis was conducted to investigate the relationship between differentially expressed immune cells and the identified diagnostic genes. The correlation between gene expression and response to anti-TNF therapy was also assessed. Finally, the differential expression of these genes was confirmed in a mouse model of UC induced by 2.5% dextran sulfate sodium (DSS).ResultsA total of six MPTDEGs were identified. The genes CASP1 and CASP4, which were identified through machine learning algorithms, exhibited strong diagnostic performance, with area under the curve (AUC) values exceeding 0.7, indicating the effectiveness of the model. Immunoinfiltration analysis demonstrated a significant correlation between the expression of CASP1 and CASP4 and the presence of macrophages and neutrophils. Importantly, low expression levels of CASP1 were associated with a favorable response to infliximab treatment. Furthermore, the expression levels of CASP1 and CASP4 were significantly increased in UC mouse models (p < 0.05).ConclusionsThe MPTDN-related genes CASP1 and CASP4 have been identified as potential biomarkers for the diagnosis of UC and are associated with abnormal immune cell infiltration in UC patients. Additionally, CASP1 may serve as a predictor of sensitivity to infliximab therapy. creator: Manqin Sun creator: Fengjun Ni creator: Yong Yao creator: Huayuan Yang uri: https://doi.org/10.7717/peerj.20345 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Sun et al. title: The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more link: https://peerj.com/articles/20328 last-modified: 2025-12-05 description: Metatranscriptomics–the sequencing of community RNA–has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation. creator: Danilo Di Leo creator: Emelie Nilsson creator: Arianna Krinos creator: Jarone Pinhassi creator: Daniel Lundin uri: https://doi.org/10.7717/peerj.20328 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Di Leo et al. title: Association between bone marrow adipose tissue, abdominal adipose tissue distribution, and volumetric bone mineral density in the Chinese adult population: a retrospective cohort study link: https://peerj.com/articles/20446 last-modified: 2025-12-04 description: BackgroundIncreasing studies have suggested that bone closely interacts with bone marrow adipose tissue (BMAT) and abdominal adipose tissue. However, this relationship remains debated. This study aimed to explore the association among BMAT, abdominal adipose tissue, and lumbar volumetric bone mineral density (vBMD).MethodsA total of 306 Chinese adult living liver transplant donors were enrolled in this cross-sectional study. vBMD and abdominal adipose tissue in terms of total adipose tissue (TAT), visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT), were derived using quantitative computed tomography (QCT). Chemical shift encoded magnetic resonance imaging (MRI) of the lumbar spine was performed, and proton density fat fraction (PDFF) maps were calculated. Correlation analysis and multiple linear regression were used to assess the associations among BMAT, abdominal adipose tissue distribution, and vBMD.ResultsThe mean age of the participants was 38.1 ± 9.5 years (range: 19–66 years). The vBMD was significantly negatively associated with age (r = −0.508, p < 0.001), VAT (r = −0.235, p < 0.001), TAT (r = −0.127, p = 0.03), and BMAT measured by PDFF (r = −0.642, p < 0.001). After adjusting for age, gender, and BMI, multiple linear regression analysis showed BMAT (β = −0.523, p < 0.001), SAT (β = 0.116, p = 0.045) and VAT (β = −0.108, p = 0.037) to be independent factors influencing vBMD.ConclusionOur results indicated a negative association between BMAT and BMD. The association between abdominal adipose tissue distribution and BMD was dual; there was a positive association between SAT and BMD and a negative association between VAT and BMD. These findings suggest that the distribution of abdominal adipose tissue, particularly visceral adipose tissue accumulation, should be prioritized over total body weight in considerations of bone health. creator: Wei Zhu creator: Wen-Min Guan creator: Bo-Xin Chen creator: Yi-Da Lu creator: Jia Li creator: Xiao-Qing Yuan creator: Wei-Hua Li creator: Feng-Xia Yu creator: Jing-Yi Liu creator: Hong-Xia Yin creator: Lin Wei creator: Zhen-Chang Wang creator: Zhi-Jun Zhu creator: Peng Zhang uri: https://doi.org/10.7717/peerj.20446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhu et al. title: Exploring the impact of visual stimuli on taste expectations and the role of pull-tab position in food packaging link: https://peerj.com/articles/20417 last-modified: 2025-12-04 description: BackgroundPreference for an image is often associated with the perceived ease of use of the depicted object.AimThis study investigated the impact of visual stimuli on taste expectations, focusing on the presentation of food in images. Specifically, it explored how the presence of a pull-tab—perceived by participants as a tool that makes the product easy to use or open—influences these expectations.MethodsA sample of 42 right-handed university students (30 women, 12 men; mean age = 20.4 years) evaluated perceived taste expectations of food presented under different conditions using a 9-point Likert scale. The conditions included images of canned food (“Can condition”) with varying pull-tab positions (0°, 90°, 180°, 270°, and Down), as well as images of actual food (“Pineapple condition”). Each participant was shown 12 images per trial in a randomized order and rated their taste expectations immediately after viewing each image. Statistical analyses were conducted using linear mixed models and ANOVA using the Kenward-Roger method.ResultsTaste expectations were significantly lower in the Can condition compared with the Pineapple condition (mean difference = 3.14, SE = 0.23, p < 0.001). Within the Can condition, pull-tab positions had a significant effect on taste expectation ratings (F = 116.94, p < 0.001). The 0° position (pull-tab facing the viewer) received the highest rating (M = 4.87, SD = 1.86), while the 180° position (pull-tab facing away) received the lowest (M = 3.95, SD = 1.73).ConclusionThese findings underscore the complex relationship between visual presentation and taste expectations, providing valuable insights for optimizing product presentation in marketing strategies. creator: Kenichi Shibuya creator: Mana Miyamoto uri: https://doi.org/10.7717/peerj.20417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shibuya and Miyamoto title: Metabolites of traffic-related volatile organic compounds in age-related macular degeneration link: https://peerj.com/articles/20405 last-modified: 2025-12-03 description: BackgroundVolatile organic compounds (VOCs), commonly emitted from vehicle exhaust and industrial activities, are prevalent air pollutants in urban environments. These compounds have been reported to cause various health effects through mechanisms such as oxidative stress and neurotoxicity. Recently, air pollution has attracted attention as a potential risk factor for age-related macular degeneration (AMD); however, the association between VOC exposure and AMD remains unclear.ObjectiveThis study aimed to assess VOC exposure levels among urban-dwelling AMD patients by quantifying urinary metabolites and investigating the association between VOCs and AMD.MethodsThis cross-sectional study included 40 untreated AMD patients (AMD group), 10 cataract patients (Cataract group), and 10 healthy controls (Healthy group). Representative urinary metabolites of VOCs—2-methylhippuric acid, 3-methylhippuric acid, mandelic acid, phenylglyoxylic acid, and trans,trans-muconic acid—were measured using gas chromatography-mass spectrometry (GC/MS), with concentrations corrected for urinary creatinine. Group comparisons were performed based on creatinine-adjusted metabolite levels.ResultsThe AMD group exhibited elevated urinary VOC metabolite levels compared to both control groups. The ratios of mean concentrations in the AMD group versus the Healthy and Cataract groups, respectively, were: 2-methylhippuric acid (201% and 181%), 3-methylhippuric acid (190% and 139%), mandelic acid (304% and 198%), phenylglyoxylic acid (118% and 90%), and trans,trans-muconic acid (214% and 92%). Among these, 2-methylhippuric acid and mandelic acid were significantly higher in the AMD group than in both controls (p < 0.001 and p = 0.042; p < 0.001, respectively). Trans,trans-muconic acid also showed a significant increase compared to the Healthy group (p < 0.001). Correlation analysis within the AMD group revealed moderate but significant associations for 2-methylhippuric acid (r = 0.29, p = 0.011), mandelic acid (r = 0.47, p < 0.001), and trans,trans-muconic acid (r = 0.27, p = 0.020). Multivariate logistic regression identified mandelic acid as an independent factor significantly associated with AMD (odds ratio = 17.20, p < 0.001). Subgroup analysis categorized the AMD group into drusenoid AMD, typical AMD (t-AMD), polypoidal choroidal vasculopathy (PCV), and retinal angiomatous proliferation (RAP). No significant differences in urinary VOC metabolite levels were observed among the four subtypes after multiple comparison adjustment.ConclusionsThese findings indicate that AMD patients are exposed to higher levels of traffic-related VOCs. While mandelic acid—a styrene metabolite—was independently associated with AMD, its role should be interpreted as a potential exposure marker rather than a definitive disease biomarker. Further longitudinal studies are warranted to clarify causal relationships between VOC exposure and AMD development. creator: Tatsuya Mimura creator: Hidetaka Noma uri: https://doi.org/10.7717/peerj.20405 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mimura et al. title: Virtual reality technology for upper and lower limb motor function, daily function, and balance in stroke patients: a meta-analysis of randomized controlled trials link: https://peerj.com/articles/20402 last-modified: 2025-12-03 description: BackgroundStroke is a common neurological disorder that often results in motor dysfunction, significantly impairing patients’ quality of life and increasing the economic burden on healthcare systems. Virtual reality (VR) technology has emerged as an innovative approach in stroke rehabilitation. This meta-analysis aimed to comprehensively evaluate the effects of VR-based interventions on motor function, daily function, and balance in stroke patients.MethodsWe systematically searched PubMed, Embase, the Cochrane Library, Web of Science, and China National Knowledge Infrastructure (CNKI) databases from inception to October 2025 for randomized controlled trials (RCTs) investigating VR technology in stroke rehabilitation. Study quality was assessed using the Cochrane Risk of Bias 2.0 tool. Data synthesis involved pooling effect sizes, conducting subgroup analyses, and assessing publication bias using Stata 17.ResultsA total of 27 RCTs involving 877 stroke patients were included in the meta-analysis. VR technology demonstrated statistically significant improvements across multiple functional domains: lower limb motor function (Cohen’s d = 0.41, 95% CI [0.25–0.57], P < 0.001), upper limb motor function (Cohen’s d = 0.25, 95% CI [0.03–0.48], P = 0.03), daily function (Cohen’s d = 0.24, 95% CI [0.07–0.42], P = 0.01), and balance (Cohen’s d = 0.31, 95% CI [0.09–0.52], P < 0.001). The effects ranged from small to moderate across domains, with lower limb function showing the most substantial improvement. Sensitivity analyses confirmed the robustness of these findings, and subgroup analyses revealed that factors such as training cycle influenced treatment effects.ConclusionVR technology demonstrates significant potential as an effective complementary intervention for improving motor function, daily function, and balance in stroke patients. The small to moderate effect sizes across domains support its integration into conventional rehabilitation protocols. Future research should focus on optimizing VR parameters, investigating different VR technology types, and evaluating long-term sustainability to further establish its efficacy in stroke rehabilitation. creator: Weixiao Zhang creator: Shanshan Lyu creator: Shuwen Zhang uri: https://doi.org/10.7717/peerj.20402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Metabolite profiling from the fermentation of marine-derived extracts by Lactobacillus acidophilus LB link: https://peerj.com/articles/20399 last-modified: 2025-12-03 description: BackgroundLactobacillus acidophilus LB is a probiotic strain with the ability to produce valuable bioactive metabolites through fermentation. Sustainable biomass sources such as Spirulina platensis, Ulva reticulata, and Caulerpa lentillifera, which can also be obtained from agricultural or aquacultural by-products, offer a promising alternative for microbial cultivation, but their effects on the metabolic profile of L. acidophilus LB are still unclear.MethodsThe study utilized L. acidophilus LB (GenBank accession OK398226) cultivated in media containing Spirulina platensis, Ulva reticulata, and Caulerpa lentillifera extracts. High-resolution mass spectrometry (liquid chromatography-high resolution mass spectrometry-quadrupole-time-of-flight, LC-HRMS QTOF) was employed for compound profiling. Principal component analysis (PCA) and Pearson correlation were used to analyze metabolic variations across different culture conditions. The Kruskal-Wallis test assessed statistical differences in metabolite concentrations.ResultsMethyl lucidenate Q and 6-Gingerol were the most abundant bioactive compounds detected across samples. PCA revealed that L. acidophilus LB in media supplemented with different preparations of Spirulina platensis, Ulva reticulata, and Caulerpa lentillifera was associated with distinct differences in metabolite profiles, leading to clustering patterns. K-means clustering identified three metabolomic groups, with the pellet obtained from L. acidophilus LB cultured in medium supplemented with U. reticulata seaweed showing a unique chemical profile. Pearson correlation analysis suggested possible biochemical interactions among metabolites, with Auraptenol and Daturametelin B exhibiting a strong positive correlation (r = 0.99). The absence of Methyl lucidenate Q in this sample indicates potential enzymatic degradation or metabolic inhibition.ConclusionThis study highlights the impact of L. acidophilus LB on metabolite diversity in substrate-driven fermentation systems. The findings suggest microbial interactions modulate metabolite patterns in the fermented supernatants, potentially enhancing pharmacological properties. Future research should focus on optimizing culture conditions to maximize yield and functional validation of identified compounds for therapeutic applications. These insights contribute to the broader field of natural product discovery and marine biotechnology. creator: Ha Phuong Hoang creator: Thi Minh Nguyen creator: Tuyet Thi Anh Le creator: Huong Giang Bui creator: Ngoc Anh Ho creator: Thu Ngo Thi Hoai creator: Nhat Huy Chu uri: https://doi.org/10.7717/peerj.20399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hoang et al. title: Athletic participation and its impact on self-concept, body image, and physical fitness in Saudi female adolescents: a cross-sectional comparison between athletes and non-athletes link: https://peerj.com/articles/20353 last-modified: 2025-12-03 description: BackgroundAdolescence is a critical developmental period marked by significant physical and psychosocial changes that shape adult behavior and personality. In Saudi Arabia, where female sports participation is newly encouraged, this study therefore aimed to explore how athletic participation influences body image perception, including potential discrepancies between self-perception and fitness outcomes, in a context where female participation in structured physical activity has historically been limited but is now being promoted under Vision 2030.MethodsA cross-sectional study was conducted in Riyadh province from October 2024 to February 2025, involving 439 female students aged 12–18. Participants were recruited from schools in Al Majma’ah city and were categorized as athletes (school sports participants, n = 252) or non-athletes (n = 241). Outcomes were assessed using the Physical Self-Inventory-Short (PSI-S) for self-perception, the Stunkard Scale for body image, and physical performance tests (Shuttle Run, V Sit-and-Reach, and Wall Sit Test).ResultsOur findings revealed that athletes reported significantly higher self-perception on the PSI-S compared to non-athletes (53.17% vs. 37.34% high self-perception; p = 0.002). After body mass index (BMI) adjustment, athletes scored higher on the Stunkard Scale (5.83 vs. 4.31; p < 0.001). Athletes demonstrated a tendency to perceive their bodies as moderately larger than their actual BMI-adjusted size, a disparity not observed in non-athletes. This self-perception coexisted with superior physical performance, suggesting that athletic training may decouple size perception from functional capability. Athletes outperformed non-athletes in cardiorespiratory fitness (Shuttle Run: 9.96 vs. 8.01; p < 0.001), flexibility (V Sit-and-Reach: 14.50 vs. 13.02; p = 0.012), and muscular endurance (Wall Sit Test: 63.17 vs. 58.30; p = 0.024). No significant differences in self-perception were observed across BMI categories, suggesting athletic participation’s benefits transcend weight status.ConclusionThe findings align with global research linking physical activity to enhanced body satisfaction and self-worth. However, athletes’ self-perception of larger body figures may reflect societal pressures toward thinness, highlighting the complex interplay of cultural ideals and body image. The study underscores the role of sports in promoting physical fitness and psychological well-being among Saudi adolescent females, supporting national efforts to encourage female athletic participation. creator: Asma Alonazi creator: Deem Almutairi creator: Taif Alyousef creator: Afnan Alkhateeb uri: https://doi.org/10.7717/peerj.20353 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alonazi et al. title: Bornean orangutan nest identification using computer vision and deep learning models to improve conservation strategies link: https://peerj.com/articles/20333 last-modified: 2025-12-03 description: BackgroundRegular population surveys are crucial for the evaluation of conservation measures and the management of critically endangered species such as the Bornean orangutans. Uncrewed aerial vehicles (UAV) are useful for monitoring orangutans by capturing images of the canopy, including nests, to monitor their population. However, manually detecting and counting nests from UAV imagery is time-consuming and requires trained experts. Computer vision and deep learning (DL) models for image classification offer an excellent alternative for orangutan nest identification.MethodsThis study investigated DL for nest recognition from UAV imagery. A binary dataset (“with nest” and “without nest”) was created from UAV imagery from Sabah, Malaysian Borneo. The images were captured using a fixed-wing UAV with a complementary metal-oxide semiconductor camera. After image augmentation, 1,624 images were used for the dataset and further split into 70% training, 15% testing and 15% validation for model performance evaluation, i.e., accuracy, precision, recall and F1-score. Four DL models (InceptionV3, MobileNetV2, VGG19 and Xception) were trained to learn from the labeled dataset and predict the presence of nests in new images.ResultsThe results show that out of four DL models, Inception V3 has the best model performance with more than 99% accuracy and precision, while VGG19 has the lowest performance. In addition, gradient-weighted class activation maps were used to interpret the results, allowing visualization of the regions used by InceptionV3 and VGG19 for classification. This study shows the potential of integrating DL into orangutan conservation, particularly in monitoring the orangutan population in the protected environment. Future research should focus on the automatic detection of nests to improve UAV-based monitoring of orangutans. creator: Donna Simon creator: Keeyen Pang creator: Rayner Bili creator: Song-Quan Ong creator: Henry Bernard uri: https://doi.org/10.7717/peerj.20333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Simon et al. title: Identification of candidate long non-coding RNAs and mRNAs associated with heart aging in mice link: https://peerj.com/articles/20433 last-modified: 2025-12-02 description: BackgroundUnderstanding the molecular mechanisms underlying cardiac aging may uncover novel therapeutic targets for age-related cardiovascular disease. Long non-coding RNAs (lncRNA), which regulate cell differentiation and disease progression, are emerging as promising diagnostic biomarkers and therapeutic candidates. However, their expression profiles and functional roles in the aging heart remain poorly characterized.MethodsMale C57BL/6 wild type mice aged 20 months (aged group) and 3 months (young group) underwent transthoracic echocardiography to evaluate cardiac function. Myocardial aging phenotypes were assessed using hematoxylin-eosin, Masson’s trichrome, terminal deoxynucleotide transferase dUTP nick end labeling (TUNEL), and senescence-associated β-galactosidase staining. Transcriptomic profiling was performed using a lncRNA-focused microarray platform to identify differentially expressed lncRNAs and mRNAs in heart tissues.ResultsAged mice showed increased heart weight/body weight and heart weight/tibia length ratios. Both interventricular septum in systole and left ventricular posterior wall in diastole were elevated, while ejection fraction and fractional shortening remained unchanged. The Tei index was significantly higher, suggesting impaired myocardial performance. Histological staining revealed enlarged cardiomyocytes, increased myocardial fibrosis, enhanced apoptosis, and greater senescence-associated β-galactosidase activity. Microarray analysis identified distinct age-related expression patterns of lncRNAs and mRNAs in the heart.ConclusionsCardiac aging is characterized by structural and functional remodeling, accompanied by transcriptional reprogramming involving both lncRNAs and mRNAs. These changes offer insights into potential molecular mechanisms and provide candidate regulatory targets for diagnosis and intervention in age-related heart disease. creator: Zheng Kuai creator: Zheng Li creator: Jianguo Jia creator: Yongle Chen creator: Xiaoyi Zhang creator: Jianhui Zhang creator: Yangli Ye creator: Lihong Gao creator: Ling Li creator: Yu Hu uri: https://doi.org/10.7717/peerj.20433 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kuai et al.