title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-04 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Preoperative prediction of p16 expression in cervical cancer by amide proton transfer imaging combined with diffusion kurtosis imaging: a retrospective study link: https://peerj.com/articles/19387 last-modified: 2025-04-30 description: BackgroundImmunohistochemical p16 expression is important for the assessment of risk factors and prognosis of cervical cancer. This study evaluated the correlation between preoperative amide proton transfer imaging (APT), diffusion kurtosis imaging (DKI), and p16 expression in cervical cancer.MethodsFifty-five records of patients with cervical cancer with preoperative magnetic resonance imaging (MRI) and complete postoperative pathology were retrospectively analyzed. Uterine MRI scans were examined, and the corresponding APT values, mean kurtosis (MK), and mean diffusivity (MD) were obtained. Pathology was used to determine p16 positivity. The predictive effects of the APT- and DKI-derived parameters applied alone or in combination with p16 expression were compared.ResultsAmong the 55 cases of cervical cancer, 35 were p16 positive and 20 were p16 negative. The receiver operating characteristic curve area (AUC) of p16 was 0.809, 0.801, 0.790, 0.845, 0.866, and 0.871 when APT, MK, and MD were used individually and then jointly. The effect of APT combined with the DKI derivative parameters was more pronounced than when they were used separately.ConclusionPreoperative APT and DKI imaging are valuable in predicting the expression of p16 in cervical cancer, and the combination of the two can improve the prediction efficacy. These findings could help to guide treatment decisions and determine prognosis in cervical cancer. creator: XingChen Wu creator: Chen Xu creator: Xiaoyan Zhang creator: Qianqian Qu creator: Zhe Wang creator: Kai Deng uri: https://doi.org/10.7717/peerj.19387 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wu et al. title: Integrative bioinformatics analysis and experimental validation of key biomarkers driving the progression of cirrhotic portal hypertension link: https://peerj.com/articles/19360 last-modified: 2025-04-30 description: BackgroundPortal hypertension is a driving factor of cirrhosis complications, but the specific molecular mechanism of portal hypertension in cirrhosis remains unclear. The aim of this study was to identify hub genes for predicting persistent progression of portal hypertension in patients with liver cirrhosis.MethodsRelated microarray datasets were obtained from the Gene Expression Omnibus database. Weighted gene co-expression network analysis and differential expression genes analysis were used to identify the correlation sets of genes. In addition, protein-protein interaction networks and machine learning algorithms were conducted to screen center of candidate genes. To validate the diagnostic effect of hub genes, receiver operating characteristic curves were utilized in another dataset that is publicly accessible. Furthermore, the CIBERSORT algorithm was employed to investigate the immune infiltration levels of 22 immune cells and their connection to hub gene markers. Immunohistochemistry and reverse transcription quantitative polymerase chain reaction (RT-qPCR) were conducted to validate novel hub genes in clinical specimens.ResultsWe obtained 671 differentially expressed genes and 11 module genes related to cirrhotic portal hypertension. Two candidate genes namely oncoprotein-induced transcript 3 protein (OIT3) and lysyl oxidase like protein 1 (LOXL1) were identified as biomarkers. RT-qPCR and immunohistochemistry (IHC) verified the expression of LOXL1 and OIT3 at mRNA and protein levels in liver tissue.ConclusionsOIT3 and LOXL1 were identified as potential novel targets for the diagnosis and treatment of cirrhotic portal hypertension (CPH). creator: Meilin Li creator: Lilin Jiang creator: Yunrui Ru creator: Zhonghua Lu creator: Peng Gu uri: https://doi.org/10.7717/peerj.19360 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Li et al. title: A study of repetitive sequences in the genome of Sinopodisma qinlingensis link: https://peerj.com/articles/19358 last-modified: 2025-04-30 description: The family Acrididae characterized by a remarkable genome size and a significant proportion of repetitive sequences. In this study, we find a considerable characteristics by examining the Sinopodisma qinlingensis, which has an average genome size within the range observed in Acrididae. The genome size of S. qinlingensis was determined to be 11.37 pg for females and 10.95 pg for males using flow cytometry. The analysis of low-coverage sequencing data revealed that the total repeat content of the genome was 63.58%, with long terminal repeat (LTR) elements accounting for 17.74% of the genome contents. Phylogenetic analysis of the reverse transcriptase (RT) domains, which are found within LTR and LINE sequences with consistent conserved motifs, showed that LTR elements belong to multipl within a monophyletic branch. This finging suggests that LTR elements did not originate independently, but rather shared a common evolutionary history. Additionally, the content of Ty3-Gypsy sequences within LTR elements was found to be significantly increased. Fluorescence in situ hybridisation (FISH) showed that most satellite DNA and LTR elements exhibited an aggregated distribution pattern on the chromosome. creator: Xiongyan Yin creator: Nan Zhang creator: Xiaoyu Li creator: Lijia Gan creator: Yimeng Nie creator: Yuan Huang uri: https://doi.org/10.7717/peerj.19358 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yin et al. title: Metabolomics and proteomics analyses reveal the role of the glycerophospholipid metabolism pathway in unexplained recurrent spontaneous abortion link: https://peerj.com/articles/19317 last-modified: 2025-04-30 description: BackgroundUnexplained recurrent spontaneous abortion (URSA) is a complex pregnancy complication with a high miscarriage rate. Incomprehensive understanding of the molecular mechanism in URSA also leads to a lack of effective treatment methods. Hence, the current study aimed to explore the underlying pathogenesis of URSA applying metabonomic and bioinformatics analysis.MethodsThe decidual tissues of eight URSA samples and eight normal pregnancy (normal control, NC) samples were collected for liquid chromatography-mass spectrometry (LC-MS) analysis using the Progenesis QI metabolomics software. The orthogonal partial least squares discrimination analysis (OPLS-DA) and the Human Metabolome Database (HMDB) were employed for differential metabolite analysis and pathway enrichment analysis, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway topological analysis was performed to rank the importance of pathways involved in URSA, and differential proteins were identified based on fold change difference. Finally, a metabolic network was visualized by the Cytoscape tool.ResultsAfter LC-MS analysis and quality control, samples in the same group showed high consistency and reliability. Differential metabolites between NC and URSA groups were mainly enriched to five biological processes, with glycerophospholipid metabolism pathway containing the greatest number of differential metabolites. KEGG enrichment analysis showed significant differences in glycerophospholipid metabolism, bile secretion, and choline metabolism pathways, with glycerophospholipid metabolism showing a higher pathway importance. Proteome and metabolome analysis revealed a total of 65 overlapping pathways involved in the differential proteins and differential metabolites, and finally PLD1, CHPT1 and PLA2G2A were identified as the key genes in glycerophospholipid metabolism pathway.ConclusionLC-MS analysis revealed that glycerophospholipid metabolism pathway and its three key genes were crucially involved in URSA progression, providing novel insights into the treatment strategy of URSA. creator: Yihong Chen creator: Xiumei Zhao creator: Bei Gan creator: Leiyi Jin creator: Juanbing Wei creator: Jianying Yan uri: https://doi.org/10.7717/peerj.19317 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Inhibitory effect of carvedilol on bedaquiline metabolism in vitro and in vivo link: https://peerj.com/articles/19313 last-modified: 2025-04-30 description: Bedaquiline has recently been approved for the treatment of multidrug-resistant tuberculosis. Carvedilol is a cardiovascular medication extensively used in the treatment of heart failure and hypertension. In this study, Sprague-Dawley rats, rat liver microsomes (RLM), human liver microsomes (HLM), and recombinant human CYP3A4 were used to explore the effect of carvedilol on the metabolism of bedaquiline. Ultra-performance liquid chromatography-tandem mass spectrometry was used to facilitate the quantification of the analyte concentrations. In vitro, carvedilol did not exhibit time-dependent inhibition of bedaquiline, which aligns with the half-maximal inhibitory concentration (IC50) shift results. The IC50 values of carvedilol were 15.35 ± 0.43 µM in RLM, 7.55 ± 0.74 µM in HLM, and 0.79 ± 0.05 µM in CYP3A4. Besides, the inhibition type of carvedilol was found to be mixed, un-competitive, and mixed in RLM, HLM, and CYP3A4, respectively. In vivo, the co-administration of carvedilol with bedaquiline resulted in a significant increase in the area under the plasma concentration-time curve (AUC)(0 − t), AUC(0 − ∞), and Cmax of bedaquiline while decreasing its CLz/F. Lay summary: Carvedilol could inhibit the metabolism of bedaquiline in vitro and in vivo, with different mechanisms in different enzymatic reaction systems. Hence, caution should be exercised when combining bedaquiline with carvedilol. creator: Qingqing Li creator: Wanshu Li creator: Jie Chen creator: Hangjuan Lin creator: Cixia Zhou uri: https://doi.org/10.7717/peerj.19313 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Microbial diversity of the remote Trindade Island, Brazil: a systematic review link: https://peerj.com/articles/19305 last-modified: 2025-04-30 description: Trindade Island is a unique volcanic environment in the South Atlantic, characterized by acidic soils, rich organic matter and a high diversity of micro- and macroorganisms. Such diversity can represent a range of ecological niches and functions, potentially offering valuable ecosystem services. This systematic review aimed to synthesize the current knowledge of the island’s microbial communities, focusing on their ecological roles and biotechnological potential. Following the PRISMA guidelines, a comprehensive search of the scientific literature was conducted to identify studies that performed DNA sequencing of samples collected on Trindade Island, Brazil. The selected studies used approaches, such as shotgun metagenomics and marker gene sequencing, including samples from microcosm experiments and culture-dependent samples. A total of eight studies were selected, but only six provided detailed taxonomic information, from which more than 850 genera of Bacteria, Archaea, and Fungi were catalogued. Soil communities were dominated by Actinobacteriota, Acidobacteriota, and Ascomycota (Fungi) while marine and coral environments showed high diversity of Pseudomonadota and Cyanobacteria. Microcosm experiments revealed adaptive responses to hydrocarbon contamination, mainly for Alcanivorax and Mortierella (Fungi). Compared to other ecosystems, such as the oligotrophic Galapagos Islands and the sea-restricted Cuatro Cienegas Basin, Cyanobacteria were shown to be more adaptive. creator: Glen Jasper Yupanqui García creator: Fernanda Badotti creator: Alice Ferreira-Silva creator: Joyce da Cruz Ferraz Dutra creator: Kelmer Martins-Cunha creator: Rosimeire Floripes Gomes creator: Diogo Costa-Rezende creator: Thairine Mendes-Pereira creator: Carmen Delgado Barrera creator: Elisandro Ricardo Drechsler-Santos creator: Aristóteles Góes-Neto uri: https://doi.org/10.7717/peerj.19305 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yupanqui García et al. title: The efficacy of pre-operative oral aceclofenac and intra-ligamentary mepivacaine on the success of failed inferior alveolar nerve block in patients with symptomatic irreversible pulpitis: a prospective, randomised, double-blinded clinical trial link: https://peerj.com/articles/19293 last-modified: 2025-04-30 description: ObjectiveThis study aimed to compare the effects of oral pre-operative aceclofenac and supplemental intra-ligamentary mepivacaine and articaine injection on the anaesthetic efficacy of failed inferior alveolar nerve block (IANB) in patients with symptomatic irreversible pulpitis in mandibular molars.Materials and MethodsA total of 126 patients who fulfilled the inclusion criteria were selected for the study intervention. The study design was a prospective, randomised, double-blinded clinical trial. Pre-operative medication was administered 15 minutes before the patients received the standard IANB. Subsequently, the endodontic therapy was started. Pain felt at any time during the procedure was recorded on a 170 mm Heft–Parker visual analogue scale (VAS), and a supplemental intra-ligamentary injection was administered. Based on the pre-operative medication and the intra-ligamentary injection received, the patients were categorized into the following four groups: two groups received 4% articaine with 1:100,000 epinephrine as an intra-ligamentary injection with or without aceclofenac as the pre-operative medication (Group 1 and Group 2, respectively), and two other groups received 3% plain mepivacaine with or without aceclofenac (Group 3 and Group 4, respectively). The VAS scores were determined pre-operatively, following access preparation and/or instrumentation within the dentin, the pulpal space, and the instrumentation of canals. Data were analyzed using Pearson’s chi-square test and independent t-test. A p-value < 0.05 was considered statistically significant.ResultsConcerning the supplemental intra-ligamentary injection, 4% articaine with 1:100,000 epinephrine showed a higher success rate than 3% plain mepivacaine, irrespective of the pre-operative medication used, and the difference was statistically significant (p < 0.05). In addition, if the supplemental intra-ligamentary injection was complemented with pre-operative medication such as aceclofenac 100 mg, the anaesthetic efficacy improved compared to groups receiving a placebo as pre-operative medication (p > 0.05). The anesthetic efficacies of the four groups were as follows: Group 1 (87.1%) > Group 2 (66.7%) > Group 3 (60.6%) > Group 4 (53.1%).ConclusionsIn patients with symptomatic irreversible pulpitis of mandibular molars, an intraligamentary injection of 4% articaine combined with 1:100,000 epinephrine can significantly aid in achieving anesthesia in situations where primary IANB is unsuccessful.Clinical RelevanceMandibular molars with symptomatic irreversible pulpitis are associated with a high anaesthetic failure rate of a single primary IANB injection during endodontic treatment. Adding an oral pre-operative aceclofenac medication and a supplemental intra-ligamentary injection, augments the anaesthetic efficacy in such cases. creator: Susmita Ghosh creator: Paras Mull Gehlot creator: Ganesh Jadhav creator: Annapoorna Ballagere Mariswamy creator: Karkala Venkappa Kishan creator: Ahmed Al Malwi creator: Shahabe Saquib Abullais uri: https://doi.org/10.7717/peerj.19293 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ghosh et al. title: Establishing isotopic turnover rates and trophic discrimination factors in tiger beetle (Coleoptera: Cicindelidae) larvae through a diet switch experiment link: https://peerj.com/articles/19279 last-modified: 2025-04-30 description: Stable isotope ratios give insight into food web interactions, but interpretation can be clouded by the timing of isotopic change associated with changes in diet and the difference in isotope ratios between consumers and their diets at equilibrium. The 15N/14N, deemed δ15N, increases with each trophic transfer as 15N becomes enriched, whereas the 13C/12C ratio, denoted as δ13C, remains relatively constant with each trophic transfer but can be influenced by lipid content. This study reports the trophic discrimination factors and isotopic half-lives in tiger beetles (Coleoptera: Cicindelidae). Wild-caught tiger beetle larvae were reared in a laboratory setting, subjected to a diet switch experiment, and sampled over time. Quadratic plateau models were used to characterize the change in δ15N, δ13C, and δ13Ccorr over time. Trophic discrimination factors were calculated by subtracting the mean prey δ15N, δ13C, and δ13Ccorr from that of the tiger beetle asymptotic δ15N, δ13C and δ13Ccorr values, respectively. The tiger beetle trophic discrimination factor for δ15N was 1.7 ± 0.2‰ with a half-life of 11.4 days. For δ13C, the trophic discrimination factor and half-life were –0.6 ± 0.2‰ and 3.9 days, respectively. After correcting for lipids (δ13Ccorr), the trophic discrimination factor was –0.2 ± 0.2‰ with a half-life of 4.7 days. Isotopic turnover was fast with short half-lives, but factors that influence metabolic rates, such as ambient temperatures and life stage, should be considered when applying these estimates to wild tiger beetles. Despite this, the trophic discrimination factors and turnover rates calculated in this article are suitable estimates which can be applied to future studies. creator: Lesa S. Giesbrecht creator: Aaron J. Bell creator: Timothy D. Jardine creator: Sean M. Prager creator: Iain D. Phillips uri: https://doi.org/10.7717/peerj.19279 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Giesbrecht et al. title: Nutritional value of ensiled Guizotia abyssinica (L. f.) Cass. (Noug: Niger) treated with salt, molasses, urea or barley link: https://peerj.com/articles/19267 last-modified: 2025-04-30 description: The research aimed to assess the nutritional value of ensiled Guizotia abyssinica (L. f.) Cass. (GA), also known as Noug or Niger, when treated with various additives, including urea, salt, molasses, and barley. The eight treatment groups were as follows: (I) GA forage without any supplementation (control), GA with supplement (II) 1% salt, (III) 2.5% molasses, (IV) 2.5% urea, (V) 5% barley, (VI) 2.5% molasses + 1% salt, (VII) 2.5% urea + 1% salt, (VIII) 5% barley + 1% salt supplement with GA. Silage samples were analyzed using physical, chemical, and microbiological methods to determine their nutritional composition, sensory characteristics, and microbial content. The objective of this analysis was to provide a comprehensive and objective evaluation of the silage samples. Based on the assessment of relative feed value (RFV) and relative forage quality (RFQ), it was determined that GA forage supplemented with 2.5% urea produced the highest-quality silage. The findings suggest that GA forage has the potential to serve as a high-quality silage. It is recommended that GA forage be ensiled with various additives at different inclusion rates. Further research is required to establish its in vitro digestibility and assess animal preference in vivo. creator: Ayşe Gül Filik uri: https://doi.org/10.7717/peerj.19267 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Filik title: Acute effect of three functional fitness training designs with equalized load on inexperienced and experienced athletes link: https://peerj.com/articles/19265 last-modified: 2025-04-30 description: BackgroundIn the realm of functional fitness training (FFT), three common circuits—as many repetitions or round as possible (AMRAP), for time (FT), and every minute on a minute (EMOM)—are prevalent. We aimed to elucidate the immediate impacts on athletes, considering the experience, when performing three workout modalities with matched training loads.MethodsTwenty-five healthy men and women, with at least three months of experience in FFT, were allocated into the Inexperienced group (IG) and Experienced group (EG). The cut point for allocating participant in each group was set at 24 months. All of them participated in three workouts (AMRAP, FT and EMOM) with three days of rest. A double comparison was performed between level of experience (IG and EG) and among kinds of training in rating of perceived exertion (RPE), lactate concentration (LAC), countermovement jump (CMJ), heart rate (HR) and heart rate variability (HRV) using ANOVA and post-hoc Bonferroni tests.ResultsSex was initially analyzed but had no influence, leading to combined group analyses. The workout type significantly impacted performance, with AMRAP showing differences between expertise levels (ES = 0.81, p = .044). RPE varied by workout type (F(2,46) = 11.003; p < .001), with EG reporting FT as the most and EMOM as the least demanding. Lactate levels increased across all workouts, with FT showing the highest and EMOM the lowest levels (ES = 1.05, p < .001). CMJ performance declined post-AMRAP and FT in both groups, but not after EMOM. No expertise-level differences were found in HRmean or HRmax, but HRV changes were influenced by workout type (F(2,46) = 7.381; p < .01) and expertise (F(1,23) = 4.657; p = .034), with significant decreases in HRV after AMRAP and FT for IG.ConclusionThe study demonstrates that FT produced greater LAC and RPE as compared to an AMRAP, whereas EMOM generated less neuromuscular fatigue and Lac, particularly in EG. These results underscore the importance of individualizing workout selection to expertise level to optimize performance. Future research should explore longitudinal adaptation to different workout types across diverse populations. creator: Alejandro Oliver-López creator: Adrián García-Valverde creator: Rafael Sabido uri: https://doi.org/10.7717/peerj.19265 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Oliver-López et al. title: The effect of transcutaneous electrical nerve stimulation on fatigue recovery in recreational rowers link: https://peerj.com/articles/19388 last-modified: 2025-04-29 description: BackgroundThe quadriceps muscle group plays an important role in rowing performance but is also susceptible to fatigue. Transcutaneous electrical nerve stimulation (TENS) has been shown to be effective in delaying the onset of fatigue, suggesting it may play a role in fatigue recovery after exercise. This study aimed to assess the effects of TENS on quadriceps recovery following a 2000-m rowing ergometer exercise.MethodsTwenty-eight recreational rowers were randomly allocated in a TENS group and a sham-TENS group. Following a 2000-m rowing ergometer exercise, the TENS group immediately received a 20-min TENS intervention, while the sham-TENS group received a placebo TENS. Ratings of perceived exertion, blood lactate (BLa), heart rate, the peak torque of knee extensors, and the surface electromyography (sEMG) activity (vastus lateralis and rectus femoris) of both limbs were recorded before and immediately after the exercise, and after the intervention.ResultsThe TENS group showed a superior recovery in muscle strength (increased 20.76% vs 9.44%, F(2, 106) = 11.549, p < 0.001, η2p = 0.179) and BLa (reduced 7.93 vs. 6.34 mmol/L, F(1, 26) = 6.768, p = 0.015, η2p = 0.207) when compared to sham-TENS. However, no time by group interaction was observed in EMG responses in both time (F(2, 214) = 1.268, p = 0.268, η2p = 0.012) and frequency (F(2,214) = 0.997, p = 0.371, η2p =0.009) domains.ConclusionA TENS intervention may be effective in facilitating recovery from quadriceps muscle fatigue in recreational rowers. Thus, it could serve as an alternative recovery treatment to enhance fatigue recovery in recreational rowers. creator: Yinan Zhou creator: Xinyu Mao creator: Wen Luo creator: Kaiyuan Qu creator: Anqi Lu creator: Jiayu Zang creator: Yu Chen creator: Rui Wu creator: Dan Wang uri: https://doi.org/10.7717/peerj.19388 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhou et al. title: Prognostic impact of serum interleukin-6 and 17 level in patients with bladder cancer: a systematic review and meta-analysis link: https://peerj.com/articles/19385 last-modified: 2025-04-29 description: BackgroundInterleukin, a noninvasive biomarker, holds huge potential for providing valuable insights into the management of inflammatory conditions and tumor diseases. This systematic review and meta-analysis aimed to evaluate the prognostic role of interleukin in bladder cancer (BCa) patients.MethodsA comprehensive search of six English and Chinese databases (PubMed, Embase, Web of Science, Chinese National Knowledge Infrastructure (CNKI), Wanfang, and Chinese Biomedical Literature Service System) was conducted from inception to July 10, 2024. Studies investigating the association between serum interleukin levels and BCa were included. Outcome measures encompassed disease-free survival (DFS), overall survival (OS), and disease-specific survival (DSS). Statistical analyses were performed using RevMan 5.4.1, employing random or fixed-effects models as appropriate. Sensitivity, subgroup, and descriptive analyses were also conducted.ResultsA total of seven studies involving 1,505 patients were included. Four studies reported the association between serum interleukin-6/17 (IL-6/17) and OS in BCa. Patients with elevated serum IL levels exhibited a worse OS (HR = 2.28; 95% CI [1.03–5.05]; P = 0.04); however, subgroup analysis revealed that only high serum IL-17 levels were significantly associated with shorter OS, while IL-6 levels showed no association with OS. Six studies examined the relationship between serum IL-6/17 and DFS in BCa. Patients with elevated serum IL levels were associated with poorer DFS (HR = 2.57; 95% CI [1.55–4.26]; P < 0.001). This association remained consistent across subgroup analyses based on interleukin type, publication country, and surgical methods. Only two studies investigated the relationship between serum IL-6/17 and DSS in BCa, with no significant association found (HR = 1.58; 95% CI [1.00-2.51]; P = 0.05).ConclusionThis meta-analysis demonstrates a strong association between serum interleukin levels and survival outcomes in BCa, suggesting that serum interleukin testing may be a valuable clinical tool for predicting patient outcomes and guiding treatment decisions. creator: Liang Liu creator: Jun-Hui He creator: Yu Xiao creator: Dong Wei uri: https://doi.org/10.7717/peerj.19385 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Clinical significance of platelet-to-white blood cell ratio in patients with Wilson disease: a retrospective cohort study link: https://peerj.com/articles/19379 last-modified: 2025-04-29 description: ObjectiveTo assess the correlation between the platelet-to-white blood cell ratio (PWR) and the severity of liver dysfunction, hepatic complications, and prognosis in Wilson disease (WD) patients.MethodsA retrospective analysis was conducted on medical records from January 1, 2016, to March 30, 2022. Both univariate and multivariate analyses were performed to examine the impact of a low PWR (<26.3) on WD severity, liver complications, and disease progression. Additionally, the effect of splenectomy on PWR was evaluated.ResultsThe study included 315 patients with WD, among whom 105 had a low PWR and 210 had a high PWR. Those with low PWR exhibited significantly elevated levels of bilirubin, international normalized ratio, prothrombin time, procollagen type-III N-terminal propeptide, type IV collagen, hyaluronic acid, and portal vein diameter. Conversely, they had lower levels of albumin, total cholesterol, low-density lipoprotein cholesterol, and triglycerides (all P < 0.05). A low PWR correlated with a greater incidence of splenomegaly/hypersplenism, esophagogastric varices, and ascites (all P < 0.05). Furthermore, low PWR independently predicted hepatic decompensation (P < 0.05), and splenectomy led to a marked increase in PWR among WD patients (P < 0.001).ConclusionA low PWR in WD patients is linked to heightened disease severity, increased risk of liver complications, and rapid progression to decompensation. The results imply that splenectomy, by enhancing PWR, may serve as a viable strategy to slow WD progression. creator: Hao-Jie Zhong creator: Jun-Yi Chen creator: Wei-Ming Wu creator: Xing-Xiang He creator: Yong-Qiang Zhan uri: https://doi.org/10.7717/peerj.19379 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhong et al. title: A prognostic glycolysis-related gene signature in osteosarcoma: implications for metabolic programming, immune microenvironment, and drug response link: https://peerj.com/articles/19369 last-modified: 2025-04-29 description: Background/AimsOsteosarcoma (OS), a malignant tumor originating in the bone or cartilage, primarily affects children and adolescents. Notably, glycolysis is the main target for metabolic programming to ensuring the energy supply for cancer. This study aimed to establish a glycolysis-related gene (GRG) risk signature in OS to comprehensively assessing the pathogenic, prognosis, and their application in predicting drug response.MethodsmRNA expression profiles were acquired from the Gene Expression Omnibus (GEO, GSE16091, GSE39058, and GSE21257). Using the non-negative matrix factorization (NMF) algorithm, patients with OS were stratified into distinct subgroups based on 288 GRGs identified through univariable Cox analysis. Univariate Cox regression analysis of differentially expressed genes (DEGs) between the molecular clusters was conducted to establish a risk signature comprising GRGs in OS. The prognostic efficacy of this risk signature was assessed via Kaplan–Meier curve analysis and Cox regression, evaluating its independence as a prognostic indicator. Additionally, the predictive potential of the risk model for drug response was evaluated using the “OncoPredict” package. Furthermore, the distribution of immune cell types in single-cell RNA sequencing (scRNA-seq) data was examined in correlation with the four identified GRGs risk signatures, followed by validation of expression levels in vitro using RT-PCR.ResultsPatients diagnosed with OS were categorized into two distinct molecular subgroups, exhibiting notable variations in prognosis and tumor microenvironment. Univaria te Cox regression analysis was employed to identify four GRGs, namely chondroitin sulfate glucuronyltransferase (CHPF), Ras-related GTP-binding protein D (RRAGD), nucleoprotein TPR (TPR), and versican core protein (VCAN), which constitute a prognostic signature for patients with OS. This signature demonstrated robust prognostic value, as corroborated by Kaplan–Meier, univariate, and multivariate Cox regression analyses. Significant differences in tumor microenvironment immune infiltration (such as B cells, monocytes) were observed between molecular subgroups. Moreover, a significant disparity in drug sensitivity to AZD8055, paclitaxel, and PD0325901 was noted between the high-risk and low-risk cohorts, and the established four-gene risk signature served as dependable prognostic indicators in the validation cohort, confirmed at the cellular level through external dataset validation and reverse transcription quantitative PCR (RT-qPCR) experiments.ConclusionA risk signature based on GRGs was established for OS, exhibiting robust predictive efficacy for prognostic assessment, and offering significant clinical utility for the prognosis of OS. creator: Naiqiang Zhu creator: Jingyi Hou creator: Yu Zhang creator: Ning Yang creator: KaiKai Ding creator: Chengbing Chang creator: Yanqi Liu creator: Haipeng Gu creator: Bin Chen creator: Xu Wei creator: Liguo Zhu uri: https://doi.org/10.7717/peerj.19369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhu et al. title: Heart rate variability over the decades: a scoping review link: https://peerj.com/articles/19347 last-modified: 2025-04-29 description: Heart rate variability (HRV) measures the variation in the time interval between successive heartbeats, reflecting the influence of the autonomic nervous system (ANS) on heart rate (HR) changes. This review provides an extensive overview of HRV measurement techniques, their applications, and their limitations in healthcare, exploring their potential for prognosis and condition assessment. A scoping review was conducted, gathering literature reviews on HRV spanning the past fifty years using PubMed, Scopus, and Web of Science databases. Our findings identified significant research gaps, including contradictions in the literature and the absence of standardized protocols for HRV measurements, which complicate the establishment of consistent baseline values. Additionally, the lack of protocols for pulse rate variability (PRV) in the context of advanced sensor technology hinders progress in HRV research. Despite these challenges, HRV remains significant in assessing cardiac autonomic function and its potential clinical applications. However, barriers such as device unfamiliarity, data accuracy concerns, and a lack of clinical trials limit its adoption. Further research is required to elucidate the relationship between abnormal HRV and health problems and to establish consistent baseline values for advancing HRV applications. creator: Amina Sundas creator: Ivan Contreras creator: Judith Navarro-Otano creator: Júlia Soler creator: Aleix Beneyto creator: Josep Vehi uri: https://doi.org/10.7717/peerj.19347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sundas et al. title: Evaluation of the effect of the application of Quercus cerris extract and the use of fluoride bonding material on the bonding strength of orthodontic brackets after tooth bleaching with hydrogen peroxide link: https://peerj.com/articles/19335 last-modified: 2025-04-29 description: The aim of this study was to evaluate the effect of natural antioxidant activity obtained from Q. cerris (Quercus cerris) extract and fluoride-releasing sealant on the shear bond strength (SBS) of orthodontic brackets in teeth after bleaching with hydrogen peroxide (HP). In this research, 200 teeth were divided into two groups, the TT (n = 100) and the OT (n = 100). Each group was further divided into five subgroups (n = 20): TT1 and OT1 = no bleaching; TT2 and OT2 = bleaching; TT3 and OT3 = bleaching+two weeks delayed bonding; TT4 and OT4 = bleaching+10% sodium ascorbate (SA) TT5 and OT5 = bleaching+10% Q. cerris extract. The TT groups were bonded with Transbond sealent + Transbond XT (TT; 3M/Unitek), and the OT groups were bonded with Opal Seal primer (Reliance Orthodontic Products Itasca, IL, USA)+ Transbond XT. Samples were assessed by SBS testing and adhesive remnant index (ARI) scoring. Two-way ANOVA variance analysis, Tukey multiple comparison test and the Chi-square test were used for statistical evaluation. The highest SBS values were obtained in the TT1 (3.17 ± 1.1 MPa) and OT1 (12.58 ± 1.47 MPa) groups, and the lowest SBS values were obtained in the TT2 (4.40 ± 1.11 MPa) and OT2 groups (4.19 ± 1.02 MPa) (p = 0.0001). The mean value of SBS of TT5 was statistically significantly lower than the mean SBS value of TT3 and TT4 (p = 0.042, p = 0.047). No statistically significant difference was observed in the ARI score distribution in the OT groups (p = 0.062), while a significant difference was noticed in the TT groups (p = 0.006). The results indicated that Q. cerris can be safely used to enhance SBS in bleached teeth, based on the dose, duration, and application procedure parameters utilized in this study. In addition, the fluoride-releasing sealant provides clinically sufficient SBS. creator: Ezgi Ay creator: Derya Dursun uri: https://doi.org/10.7717/peerj.19335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ay and Dursun title: Advancements in understanding and treating psoriasis: a comprehensive review of pathophysiology, diagnosis, and therapeutic approaches link: https://peerj.com/articles/19325 last-modified: 2025-04-29 description: Psoriasis is a chronic autoimmune disease affecting millions worldwide. This condition is characterized by scaly, red patches of skin that can be painful, itchy, and disfiguring. This non-contagious illness forms plaques and accelerates the dermal cell’s life cycle. This review provides a comprehensive overview of the current knowledge on psoriasis, covering its definition, prevalence, causes, pathogenesis, clinical features, diagnosis, and treatment options. The psychosocial impact of psoriasis on patients and their coping mechanisms is also explored. Biologic agents, which target specific cytokines involved in psoriasis pathogenesis, have revolutionized psoriasis treatment and have significantly improved patient outcomes. However, effective and safe treatments for moderate to severe psoriasis are still needed. Future research directions include the development of biomarkers for predicting disease severity and treatment response, investigating new therapeutic targets like the microbiome and epigenetics, and leveraging advancements in technology and genomics for deeper insights into psoriasis pathogenesis and treatment. This study summarizes the key aspects of psoriasis, including its epidemiology, pathophysiology, clinical traits, disease burden, and management. However, further research is needed to improve treatment outcomes and enhance the quality of life for patients affected by this complex condition. creator: Sai Chakith M. R. creator: Sushma Pradeep creator: Manu Gangadhar creator: Chaithra Maheshwari N. creator: Shuaib Pasha creator: Shiva Prasad Kollur creator: Nagashree S. creator: Chandan Shivamallu creator: Satish Allur Mallanna uri: https://doi.org/10.7717/peerj.19325 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chakith M R et al. title: Urban ecosystem quality assessment based on the improved remote sensing ecological index link: https://peerj.com/articles/19297 last-modified: 2025-04-29 description: The remote sensing ecological index (RSEI) is an important tool for assessing ecosystem quality. However, its land surface temperature (LST) component poses challenges due to complex calculations and mismatched spatial resolution with other indicators. This study proposed an improved remote sensing ecological index (DRSEI). By replacing the LST component in RSEI with the difference index (DI) (representing PM2.5 concentration), the new index better reflects air pollution’s impact on ecosystem quality. The results demonstrated that DRSEI outperformed the RSEI in assessing ecosystem quality in Chongqing’s urban area. It exhibited three advantages: stronger correlation with the ecological index (EI), standard deviation values closer to EI’s baseline, and lower root mean square error. The applicability of the DRSEI and RSEI varied across different regions: the DRSEI proved to be more suitable for highly urbanized areas, whereas the RSEI performed better in suburban regions. Further analysis revealed that the spatial variability of indicators influenced their loadings in principal component analysis, thereby affecting ecosystem quality assessment results. This study emphasizes the importance of considering the spatial distribution of indicators when constructing ecological indices. The findings suggest DRSEI could effectively assess ecosystem quality in urbanized areas. This approach provides new insights for urban ecological monitoring and environmental management. creator: Guolin Zhang creator: Honghai Kuang uri: https://doi.org/10.7717/peerj.19297 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang and Kuang title: Spatial planning model for optimizing conservation priorities for local community utilization on Arefi Island in the Raja Ampat Marine Protected Area (MPA) Southwest Papua, Indonesia link: https://peerj.com/articles/19292 last-modified: 2025-04-29 description: This study investigates the application of remote sensing technologies to identify the biophysical characteristics of marine ecosystems for spatial planning, focusing on optimal conservation scenarios within the Raja Ampat Marine Protected Area (MPA) on Arefi Island, Southwest Papua, Indonesia. Indigenous communities manage this area. WorldView-3 satellite imagery, combined with an object-based image analysis (OBIA) approach, was used to classify and map coastal ecosystems. A Marine Reserve Design using the Spatially Explicit Annealing (Marxan) model was applied to delineate conservation areas and propose zoning strategies. Based on ecological values (EV), three scenarios were tested to prioritize conservation features while ensuring sustainable ecosystem use. Image analysis revealed that Arefi Island’s coastal ecosystems cover 64.78 hectares, consisting of seagrass beds (45.41%), coral reefs (36.35%), and mangroves (18.24%), with a kappa accuracy of 0.82. Results indicate that EV3 selects the highest number of planning units, ensuring broader conservation coverage, while EV1 selects the fewest. EV2 is the most budget-friendly option with the lowest cost, whereas EV3 is the most expensive. Ecological Scenario II provided a balanced approach, allocating larger areas for local community use while preserving conservation integrity. Moreover, sensitivity analysis confirmed that a conservation objective targeting 40% of the total area (EV II) is the most effective model for Arefi Island. The zoning breakdown under this scenario includes a core zone of 19.53 hectares, a utilization zone of 15.96 hectares, a sustainable fisheries zone of 15.67 hectares, and other zones covering 92.89 hectares. This study highlights the effectiveness of remote sensing and spatial planning tools, such as Marxan, in marine conservation within indigenously managed areas, emphasizing the importance of balancing conservation efforts with sustainable community use for future planning. creator: Mulyanto Darmawan creator: Debora Christi Simamora creator: Irmadi Nahib creator: Fadhlullah Ramadhani creator: Dewayany Sutrisno creator: Fahmi Amhar creator: Muhammad Ramdhan creator: Sitarani Safitri creator: Bayu Sutejo creator: Samsul Arifin creator: Syamsul Bahri Agus uri: https://doi.org/10.7717/peerj.19292 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Darmawan et al. title: Comparative transcriptome analysis of emerging young and mature leaves of Bienertia sinuspersici, a single-cell C4 plant link: https://peerj.com/articles/19282 last-modified: 2025-04-29 description: BackgroundEfficient carbon capture by plants is crucial to meet the increasing demands for food, fiber, feed, and fuel worldwide. One potential strategy to improve the photosynthetic performance of plants is the conversion of C3-type crops to C4-type crops, enabling them to perform photosynthesis at higher temperatures and with less water. C4-type crops, such as corn, possess a distinct Kranz anatomy, where photosynthesis occurs in two distinct cell types. Remarkably, Bienertia sinuspersici is one of the four known land plant species that perform C4 photosynthesis within a single cell. This unique single-cell C4 (SCC4) anatomy is characterized by dimorphic chloroplasts and corresponding intracellular biochemistry. Because young, emergent Bienertia leaves first exhibit C3anatomy and then differentiate into the C4 anatomy as the leaves mature, Bienertia represents an excellent system to explore the basis for a C3 to C4 transition.MethodsTo gain insight into the genes and pathways associated with the C3 to C4 transition between emerging young and mature Bienertia sinuspersici leaves, a comparative transcriptome analysis was conducted in which global gene expression and gene ontologies were compared between the two stages.ResultsIn the emergent leaf, differentially expressed genes and enrichment of ontologies associated with the cell cycle and cytoskeletal dynamics were observed, while the mature leaf displayed enrichment of processes associated with photosynthesis and cellular energetics. Additionally, numerous transcription factors (TFs) associated with metabolic homeostasis, hormone and stress signaling, and developmental regulation were expressed throughout development, with unique TF expression profiles at each stage. These data expand our insights into the molecular basis of Binertia’s unique cellular compartmentalization, chloroplast dimorphism, and single-cell C4 biochemistry and provide information that will be useful in the ongoing efforts to transform C3-type crops into C4 type. creator: Richard M. Sharpe creator: Seanna Hewitt creator: Gerald Edwards creator: Amit Dhingra uri: https://doi.org/10.7717/peerj.19282 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sharpe et al. title: Extraordinarily corrupt or statistically commonplace? Reproducibility crises may stem from a lack of understanding of outcome probabilities link: https://peerj.com/articles/18972 last-modified: 2025-04-29 description: Reports of crises of reproducibility have abounded in the scientific and popular press, and are often attributed to questionable research practices, lack of rigor in protocols, or fraud. On the other hand, it is a known fact that—just like observations in a single biological experiment—outcomes of biological replicates will vary; nevertheless, that variability is rarely assessed formally. Here I argue that some instances of failure to replicate experiments are in fact failures to properly describe the structure of variance. I formalize a hierarchy of distributions that represent the system-level and experiment-level effects, and correctly account for the between-and within-experiment variances, respectively. I also show that this formulation is straightforward to implement and generalize through Bayesian hierarchical models, although it doesn’t preclude the use of Frequentist models. One of the main results of this approach is that a set of repetitions of an experiment, instead of being described by irreconcilable string of significant/nonsignificant results, are described and consolidated as a system-level distribution. As a corollary, stronger statements about a system can only be made by analyzing a number of replicates, so I argue that scientists should refrain from making them based on individual experiments. creator: Caetano Souto-Maior uri: https://doi.org/10.7717/peerj.18972 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Response of soil pH to biochar application in farmland across China: a meta-analysis link: https://peerj.com/articles/19400 last-modified: 2025-04-28 description: BackgroundBiochar, an alkaline material derived from agricultural and forestry waste, can ameliorate soil quality by adjusting soil pH. However, various types of biochar have distinct effects on soil pH due to diversity in feedstock type, pyrolysis temperature, and application rate.MethodTherefore, a meta-analysis was conducted with 598 paired comparisons obtained from 104 published studies (January 2010–July 2022) to comprehensively depict the response of soil pH to biochar in farmland systems across China.ResultThe results showed that adding biochar significantly increased the acid soils’ pH. Still, its effects on neutral and alkaline soils varied depending on the biochar’s pH and the soil’s initial pH. The pH of acid and neutral soils was raised by 5–10% straw biochar (600–800 °C and 400–600 °C, respectively). In alkaline soils, 5–10% other biochar (200–400 °C) raised pH, while 1–5% straw biochar (200–400 °C) reduced it. The findings underscore the importance of biochar pH and initial soil pH in the divergent consequences of biochar application in farmland systems, and both factors should be considered to choose the optimal biochar type for acid, neutral, and alkaline soils. creator: Jia Yao creator: Xueren Wang creator: Mei Hong creator: Hui Gao creator: Shixiang Zhao uri: https://doi.org/10.7717/peerj.19400 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yao et al. title: Association between fetal sex and metabolic syndrome in women aged 40 years and older: the REACTION study link: https://peerj.com/articles/19380 last-modified: 2025-04-28 description: IntroductionThis study aimed to investigate whether fetal sex influences the risk of metabolic syndrome (MetS) in women in China.Materials and MethodsA cohort of 3,758 Chinese women, each having given birth to only one child and aged 40 years or older, was included in the study. Registry data on all pregnancies and miscarriages were collected for each participant. This retrospective cohort study aimed to determine whether fetal sex was associated with metabolic syndrome. MetS was defined as meeting at least three of the following five criteria: impaired insulin metabolism, reduced glucose tolerance, hypertension, dyslipidemia, and large waist circumference.ResultsAmong the 3,758 women aged 40 years and older in Luzhou City, 1,018 (27.1%) developed MetS. Mothers who had carried a male fetus had higher triglyceride (TG) and total cholesterol (TC) levels and a greater prevalence of diabetes than those who had carried a female fetus (P < 0.05). Although the incidence of MetS was higher in women who had carried a male fetus than in those who had carried a female fetus, the difference was not statistically significant (P > 0.05). Notably, MetS was significantly less prevalent in premenopausal women than in postmenopausal women, irrespective of fetal sex (P < 0.05). In the postmenopausal subgroup, the incidence of MetS was significantly higher in women who had carried a male fetus compared to those who had carried a female fetus (P < 0.05).ConclusionsOur study found no significant association between fetal sex and MetS in Chinese women aged 40 years and older. However, among postmenopausal women, the incidence of MetS was significantly higher in those who had carried a male fetus. Greater attention should be given to postmenopausal women with a history of carrying a male fetus, and early preventive measures should be implemented to reduce the risk of related chronic diseases. creator: Qian Xie creator: Ruoqing Li creator: Qin Wan creator: Nanwei Tong uri: https://doi.org/10.7717/peerj.19380 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al. title: Robust phylogenetic profile clustering for Saccharomyces cerevisiae proteins link: https://peerj.com/articles/19370 last-modified: 2025-04-28 description: BackgroundGenes are continually formed and lost as a genome evolves. However, new genes may tend to appear during specific evolutionary epochs rather than others, or disappear together in a more recent organismal clade. Methods to identify gene origination might simply use the last common ancestor to contain an ortholog as the putative gene origination point, or use a heuristic threshold that allows for a certain amount of missing orthologs in the cohort of species examined. Here, to avoid such issues, an alternative approach based on the clustering of phylogenetic profiles is applied, and the results are examined for any evidence of epochal trends in gene origination, and associated trends in specific sequence traits or functional associations.MethodsA phylogenetic profile is simply an array indicating the presence or absence of a gene in a list of species. These profiles were compared and clustered to discern patterns in gene occurrences across >800 fungal species, centering the analysis on the budding yeast Saccharomyces cerevisiae.ResultsClear epochs of gene origination were observed linked to the last common ancestors of Saccharomycetaceae and Saccharomycetes, and also to Fungi and earlier ancestors. These trends are independent of the proteome and genome-assembly quality of the underlying data. Clusters of phylogenetic profiles demonstrated some significant functional associations, such as to cellular spore formation and chromosome segregation in genes originating in Saccharomycetaceae. The phylogenetic profile clustering analysis enabled detection of parameter-independent trends in intrinsic disorder, prion-like composition and gene uniqueness as a function of epochal gene age. For example: new proteins with prion-like domains have arisen at a similar rate for most of fungal evolution centred on S. cerevisiae; the most proteins with mild intrinsic disorder have appeared during the early Saccharomycetaceae epoch rather than more recently, and very recently formed genes are the least likely to be single-copy (i.e., ‘unique’ yeast proteins).ConclusionsFor individual proteins, the profile cluster data generated here are useful for investigating experimental hypotheses, since they provide evidence for functional linkages that have yet to be discerned. creator: Paul M. Harrison uri: https://doi.org/10.7717/peerj.19370 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Harrison title: Genetic variations of the SHFL gene associated with hepatitis C virus (HCV) infection in Yunnan population link: https://peerj.com/articles/19367 last-modified: 2025-04-28 description: Hepatitis C virus (HCV) infection led to hepatitis C, and even cirrhosis and hepatocellular carcinoma. The SHFL gene belonged to interferon (IFN)-stimulated genes (ISGs) and was identified to inhibit different viruses, including HCV. Whether genetic variations of the SHFL gene was associated with HCV infection was unclear. We collected 347 HCV patients and 448 general controls to genotype three SNPs in the SHFL gene, and analyzed the association between genotypes of SNPs and HCV infection, biochemical indices and disease progression of HCV patients. The results showed that genotype AT of rs77076061 (P = 0.033, OR = 1.515), AG of rs1979262 (P = 0.001, OR = 2.076), and CT of rs12611087 (P = 0.0002, OR = 1.844) were risk factors for HCV infection in Yunnan population. However, genotype TT of rs77076061 (78.1%), GG of rs1979262 (83.9%), and CC of rs12611087 (67.7%) showed statistically lower frequencies in HCV patients than that in controls. No association was found between genotypes of SNPs and biochemical indices or disease progression of patients. Functional prediction and structure alteration of RNA regions contained each single nucleotide polymorphism (SNP) suggested that these genetic variations might influence HCV infection by changing RNA structure. This study firstly investigated the association between genetic variants in the SHFL gene and HCV infection. creator: Mengren Cun creator: Xingcui Gao creator: Shuwei Dong creator: A-Mei Zhang uri: https://doi.org/10.7717/peerj.19367 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cun et al. title: Construction of a novel five programmed cell death-related gene signature as a promising prognostic model for triple negative breast cancer link: https://peerj.com/articles/19359 last-modified: 2025-04-28 description: BackgroundTriple negative breast cancer (TNBC) is a more aggressive subtype of breast cancer that usually progresses rapidly, develops drug resistance, metastasis, and relapses, and remains a challenge for clinicians to treat. Programmed cell death (PCD), a conserved mechanism of cell suicide controlled by various pathways, contributed to carcinogenesis and cancer progression. Nevertheless, the prognostic significance of PCD-related genes in TNBC remains largely unclear, and more accurate prognostic models are urgently needed.MethodsGene expression profiles and clinical information of TNBC patients were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. Least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis were used to establish the PCD-related gene signature. Kaplan-Meier plotter, receiver operating characteristic curves, and nomogram were applied to validate the prognostic value of the gene signature. Gene set enrichment analysis was carried out to investigate the pathways and molecular functions.ResultsFive PCD-related genes including SEPTIN3, SCARB1, CHML, SYNM, and COL5A3 were identified to establish the PCD-related risk score for TNBC patients. Patients stratified into high-risk or low-risk group showed significantly different survival outcome, immune infiltration, and drug susceptibility. Kaplan-Meier and receiver operating characteristic curves showed a good performance for survival prediction in different cohorts. Gene set enrichment analysis revealed that the five-gene signature was associated with tumor metabolism, cancer cell proliferation, invasion and metastasis, and tumor microenvironment. Nomogram including the five-gene signature was established.ConclusionA novel five PCD-related gene signature and nomogram could be used for prognostic prediction in TNBC. The present work might offer useful insights in digging sensitive and effective biomarkers for TNBC prognosis prediction and establishing accurate prognostic model in clinical management. creator: Quanfeng Shao creator: Hai-yan Gao creator: Zi-ying Wang creator: Yu-ling Qian creator: Wei-xian Chen uri: https://doi.org/10.7717/peerj.19359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shao et al. title: Simulation of electroporation threshold based on the evolution of transmembrane potential and pore density link: https://peerj.com/articles/19356 last-modified: 2025-04-28 description: To study the electric field threshold of electroporation of real cell membrane structures under the action of the pulsed electric field, in this article, a finite element model of the real cell containing endoplasmic reticulum and nucleus was constructed in real cell staining images by cluster segmentation and edge extraction techniques. The electroporation equation was introduced into the real cell model to calculate the threshold value of different membrane structures for electroporation under a pulsed electric field. The results showed that the transmembrane potentials of the cell membrane, endoplasmic reticulum membrane, and nuclear membrane reached the electroporation thresholds at 1.2, 2.6, and 2.9 kV/cm, while the pore density thresholds were 1.7 × 1014/m2, 3.2 × 1014/m2, and 3.5 × 1014/m2, respectively. Under a single pulse with a pulse width of 100 μs and rise and fall times of 10 μs, the pore density reaches the electroporation threshold at 1.7, 3.2 and 3.5 kV/cm, respectively. creator: Yu Zhang creator: Zhijun Luo creator: Fei Guo uri: https://doi.org/10.7717/peerj.19356 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Comparison of two benthic assemblage sampling gears for use on intertidal oyster reefs in Louisiana link: https://peerj.com/articles/19346 last-modified: 2025-04-28 description: BackgroundEstuarine biodiversity plays a vital role in supporting ecosystem functions yet remains threatened by climate change and anthropogenic activity. Tracking and identifying estuarine biodiversity trends helps management ensure long-term provisions of human and environmental benefits by contributing to the estimation of habitat loss and the monitoring of restoration and conservation progress. However, results obtained using different sampling gears and different biodiversity metrics may lead researchers to reach different conclusions, which can lead to uncertainty in the actual state of the ecosystem-level biodiversity. Sampling benthic biodiversity in complex estuarine habitats, such as oyster reefs, is particularly challenging because no one gear type captures entire target assemblages, and differences in gear efficiency on these complex habitats make comparisons across gear types challenging.MethodsWe investigated how estimates of oyster reef-associated benthic taxa abundance, richness, Pielou’s evenness, and Shannon-Wiener diversity differed across three Crassostrea virginica reefs in Louisiana between suction sampler and substrate tray sampling gears (n = 6), and how gear influenced comparisons across reefs (3 reefs × 6 replicates × 2 gears).ResultsAbundance and richness were higher, and Pielou’s evenness was lower, in trays compared to suction samples at all reefs. Shannon-Wiener diversity was similar in suction samples and trays at two out of three reefs. Amphipod taxa were numerically dominant in trays, skewing the distribution of abundances and driving the reef assemblage differences between gears. Abundance and Shannon-Wiener diversity were similar across reefs within each gear. However, there were significant differences in richness across reefs in tray samples only, while evenness differed across reefs only in suction samples. Our results highlight that gear choices, along with biodiversity metrics tracked, can result in different conclusions in biodiversity trends, ultimately affecting conservation decisions and management. creator: Finella M. Campanino creator: Stephanie K. Archer creator: Jillian C. Tupitza creator: Cassandra N. Glaspie creator: Megan K. La Peyre uri: https://doi.org/10.7717/peerj.19346 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: Subclinical hypothyroidism during pregnancy and the impact of levothyroxine therapy on pregnancy outcomes in women link: https://peerj.com/articles/19343 last-modified: 2025-04-28 description: AimsThe purpose of this study is to investigate the impact of subclinical hypothyroidism (SCH) during pregnancy and levothyroxine (LT4) therapy on pregnancy outcomes.MethodsAmong 6,510 pregnant women who came to The Fourth Hospital of Shijiazhuang for pregnancy examination and delivery, 266 pregnant women with SCH and treated with LT4 were selected as the SCH group and 672 pregnant women without SCH were selected as the non-SCH group, and the incidence rates of adverse pregnancy outcomes in pregnant women and newborns of the two groups were compared using Chi-square test and logistic regression. According to the therapeutic effect, pregnant women treated with LT4 were categorized into sustained euthyroid status (SES) and suboptimal thyroid status (STS) groups and compared with the non-SCH group using chi-square test. The correlation of thyroid stimulating hormone (TSH) levels at different stages of pregnancy was explored using Spearman’s rank test.ResultsThe incidence of hypertensive disorders of pregnancy (HDP), premature rupture of membranes (PROM), and neonatal outcomes were ventricular or atrial septal defect (V/ASD), hyperbilirubinemia, and pneumonia were higher in the SCH group (SCH pregnant women) than in the non-SCH group (non-SCH pregnant women) (p < 0.05). The incidence of multiple maternal and neonatal complications was higher in the SCH-STS group (SCH in two or three gestational trimesters) compared to the SCH group. With a tendency for TSH levels to increase as the pregnancy progressed.ConclusionSCH during pregnancy is associated with a high incidence of various pregnancy complications, and LT4 therapy that controls serum TSH levels at normal levels throughout pregnancy can reduce these risks. creator: Yutian Zhou creator: Yi Wang creator: Tianxiao Yu creator: Yuan Li creator: Meiyan Mi creator: Jianqiang Su creator: Jun Ge uri: https://doi.org/10.7717/peerj.19343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhou et al. title: A study of female tennis players: Speedcourt training is effective on improving agility and change-of-direction link: https://peerj.com/articles/19339 last-modified: 2025-04-28 description: ObjectiveThe aim of the present paper was to determine the impact of Speedcourt training on agility and change-of-direction (COD) in female tennis players, and to research the relevance between agility and lower limbs unilateral explosive power (UEP). Despite extensive research on agility training, limited studies have explored these effects specifically in female athletes and the number of exercises such as Speedcourt is also small, necessitating this investigation.MethodTwenty-two female tennis players underwent SpeedCourt training for 6 weeks, respectively executed random sequence shuttle run training (RS group, N = 11, age: 22.36 ±  1.21 years) and fixed sequence shuttle run training (FS group, N = 11, age: 22.27 ± 1.27 years). The spider run, T-drill, reactive agility (RA) and triple crossover hop (TCH) before and after intervention were measured. And the TCH tested the left and right legs separately to detect the subject’s UEP.ResultsThe two-way repeated measures analysis of variance showed significant improvements in spider run (p < 0.001, partial η2 = 0.95), T-drill (p < 0.001, partial η2 = 0.94) and RA (p < 0.001, partial η2 = 0.96). The RS group demonstrated significantly greater improvements in RA compared to the FS group, with statistical significance (p < 0.05, partial η2 = 0.184). And agility related tests showed moderate to strong correlations with unilateral explosive power.ConclusionSix-week Speedcourt training can effectively enhance the agility and change-of-direction of female tennis players. Incorporating lower limb explosive exercises into agility-specific training may further enhance agility improvements in female tennis players. creator: Zhihui Zhou creator: Jiawei Wang creator: Hao Wang creator: Guo Ru creator: Fanhui Kong uri: https://doi.org/10.7717/peerj.19339 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhou et al. title: Comparison of blood viscosity models in different degrees of carotid artery stenosis link: https://peerj.com/articles/19336 last-modified: 2025-04-28 description: BackgroundCarotid atherosclerotic vascular disease significantly contributes to strokes, presenting a heightened risk of early recurrent ischemia. Computational fluid dynamics (CFD) has shown potential in predicting subsequent stroke recurrence in patients with carotid stenosis.ObjectiveThis study aims to investigate the differences in computational time and accuracy of four key hemodynamic indices—wall shear stress (WSS), time-averaged wall shear stress (TAWSS), Oscillatory Shear Index (OSI), and relative residence time (RRT)—across different viscosity models, thereby providing optimal model selection for clinical cases and offering guidance for clinicians’ decision-making.MethodsA three-dimensional vessel model was established using computed tomography angiography (CTA), followed by CFD simulations to calculate WSS, TAWSS, OSI, and RRT. The accuracy of the simulations was validated by comparing the results with those from Razavi et al. (10.1016/j.jbiomech.2011.04.023). Numerical errors in different parameters under varying stenosis levels and viscosity models were analyzed.ResultsIn the transient state, when degree of stenosis is 38%, 72%–84%, the performance difference between the two is less than 6%. For TAWSS, the difference is 0% when degree of stenosis is 12%, 18%, 26%, 54%, and 76%. For OSI, the difference is 0% when stenosis is 16%, 18%, 26%. For RRT, the difference between the two is 0% when degree of stenosis is 18% and 84%. WSS exhibited an increasing trend with higher degrees of stenosis. TAWSS demonstrated significant variation in moderate to severe stenosis, while OSI increased markedly in cases of moderate to severe stenosis. High RRT values in severely stenotic regions indicated a propensity for atherosclerotic lesion development.ConclusionThis study systematically quantified the discrepancies between Newtonian and non-Newtonian blood viscosity models in predicting hemodynamic parameters across different degrees of carotid artery stenosis. Statistical analyses revealed significant differences between the two models in WSS, TAWSS, OSI, and RRT (p < 0.001 for all parameters). Newtonian models, while computationally efficient, overestimated TAWSS, OSI, and RRT while underestimating WSS, particularly in moderate to severe stenosis. In contrast, non-Newtonian models provided more physiologically accurate predictions, especially in regions with high shear stress variations. The results emphasize the importance of selecting appropriate viscosity models for CFD-based patient-specific risk assessment, particularly in stroke prediction, plaque evaluation, and surgical planning. Non-Newtonian models should be prioritized in high-risk patients where flow disturbances are more pronounced, whereas Newtonian models remain suitable for early screening and rapid assessments. creator: Siyu Liu creator: Sai Wang creator: Hongan Tian creator: Junzhen Xue creator: Yuxin Guo creator: Jingxi Yang creator: Haobin Jiang creator: Jian bao Yang creator: Yang Zhang uri: https://doi.org/10.7717/peerj.19336 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Metagenomic investigation of bacterial laccases in a straw-amended soil link: https://peerj.com/articles/19327 last-modified: 2025-04-28 description: BackgroundBacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases.MethodsMetagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization.ResultsA total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications.ImplicationsThese findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering. creator: Dali Yu creator: Ying Liu creator: Hongying Cai creator: Wanqiu Huang creator: Huijun Wu creator: Peilong Yang uri: https://doi.org/10.7717/peerj.19327 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yu et al. title: Natural products as promising therapeutics for fine particulate matter–induced skin damage: a review of pre-clinical studies on skin inflammation and barrier dysfunction link: https://peerj.com/articles/19316 last-modified: 2025-04-28 description: BackgroundParticulate matter less than 2.5 µm (PM2.5) is a significant air pollutant and is linked to an increased risk of health conditions, including skin diseases. The skin, as the first barrier and the largest organ, is primarily damaged by PM2.5 through different pathways. Several studies have shown that PM2.5 upregulates inflammatory responses through the excessive production of reactive oxygen species (ROS) and several inflammatory cytokines, leading to PM2.5-induced skin damage. The ROS/mitogen-activated protein kinase (MAPK) and Cyclooxygenase-2-Prostaglandin E2 (COX2/PGE2) inflammatory pathways are activated by free radical scavenging and phase II detoxification. Natural products have been suggested as therapeutic agents for mitigating PM2.5-induced skin damage.ObjectivesWe elaborate on the mechanisms of action of natural products and their functions as protectants against environmental skin diseases. This review highlights the optimal doses of natural products for clinical study, which may benefit dermatologists, molecular biologists, clinicians, and healthcare professionals in preventive and alternative medicine.MethodologyThe available scientific literature published between 1999 and 2024 was searched using PubMed and Google Scholar. Multiple keywords related to the topic were used. Only 41 of the screened articles were chosen for this review, as they were the most relevant publications on the topic of the preventive advantages of natural products and specific pathways targeting PM2.5-induced skin injury. All relevant articles meeting the criteria of being original full articles and written in English were included.ResultsThis review summarized the natural products, including phenolic/polyphenolic compounds and flavonoids, that can act as anti-inflammatory and antioxidant agents by protecting the skin against oxidative stress, inhibiting enzymes that promote free radical formation, enhancing antioxidant enzyme activity, and reducing overall ROS formation. Several natural products have demonstrated efficacy in alleviating intracellular ROS, oxidative stress, mitochondrial dysfunction, autophagy, and apoptosis caused by PM2.5. In addition, phytochemical agents support the restoration of the skin wound healing process and muscle contraction impaired by environmental pollutants, such as PM2.5 and UV rays.ConclusionThis review highlights promising natural agents that can protect against environment-mediated health problems by focusing on their mechanisms of action. Particular emphasis is placed on antioxidant and anti-inflammatory compounds, including sulforaphane, hesperidin, quercetin, catechin, diphloroethohydroxycarmalol, resveratrol, and ginsenoside, which have become interesting candidates as nutraceuticals due to their potential to reduce reliance on conventional medicines. However, the low stability and bioavailability of natural products remain significant challenges to their clinical use; therefore, further research and development are warranted. creator: Saowanee Jeayeng creator: Jaturon Kwanthongdee creator: Ratima Jittreeprasert creator: Kankanich Runganantchai creator: Kalayaporn Naksavasdi creator: Rosarin Rirkkrai creator: Varisara Wongcharoenthavorn creator: Wiriya Mahikul creator: Anyamanee Chatsirisupachai uri: https://doi.org/10.7717/peerj.19316 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jeayeng et al. title: Cryptocurrency trading and its relationship with other addictions among healthcare professionals in Türkiye link: https://peerj.com/articles/19314 last-modified: 2025-04-28 description: IntroductionThere is a continuum between gambling and investing behaviors, with speculative investment instruments positioned in the middle. Cryptocurrencies, being significantly more volatile than traditional investment tools, have increasingly been linked to gambling disorder (GD). This study aims to examine the relationship between cryptocurrency trading behavior and GD, high-risk substance use, high-risk alcohol use, and tobacco dependence among healthcare professionals in Türkiye.MethodsA total of 192 healthcare professionals were assessed using the Problematic Cryptocurrency Trading Scale (PCTS), Gambling Disorder Screening Test (GDST), and the Addiction Profile Index Risk Screening Form (APIRS) (Alcohol and Drug Scales). Categorical data comparisons between two independent groups were conducted using Chi-square or Fisher’s Exact tests. Spearman correlation coefficients were used to examine relationships between PCTS scores and APIRS/GDST scores. Additionally, linear regression models assessed the predictive relationships between PCTS scores and APIRS/GDST scores.ResultsAmong the participants, 25.5% reported engaging in cryptocurrency trading, 41.7% had tobacco dependence, 15.1% reported high-risk alcohol use, 5.7% had high-risk substance use, and 8.9% met the criteria for GD. Cryptocurrency traders demonstrated higher rates of substance use (p = 0.033), tobacco dependence (p < 0.001), and GD (p = 0.043). Additionally, the severity of problematic cryptocurrency trading behavior was positively correlated with the severity of substance use (r = 0.172, p = 0.017) and GD (r = 0.455, p < 0.001).ConclusionThe findings indicate a significant relationship between cryptocurrency trading behavior and addiction. Further research with clinical interviews and larger sample sizes is required to validate these findings. The high rates of alcohol, substance, tobacco, and gambling addictions observed among healthcare professionals underscore the need for targeted preventive measures and interventions in this population. creator: Ece Mumcu creator: Osman Hasan Tahsin Kılıç creator: Aysel Başer uri: https://doi.org/10.7717/peerj.19314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mumcu et al. title: Evaluating soil salinity dynamics under drip irrigation in the Manas River Basin, Xinjiang: a long-term analysis (1996–2019) link: https://peerj.com/articles/19295 last-modified: 2025-04-28 description: The Manas River Basin, located in Xinjiang, China, is one of the province’s four major agricultural irrigation regions and the first in the country to implement large-scale drip irrigation. While drip irrigation has enhanced water use efficiency, it has also contributed to soil salinization, negatively impacting crop yields and soil health. This study examines the spatial and temporal evolution of soil salinity in the oasis area of the basin from 1996 to 2019. The study evaluates salinization dynamics under long-term irrigation practices using soil salinity inversion models, regression analysis, water-salt balance calculations, geostatistical techniques, and ArcGIS. The results reveal significant improvements in soil salinity conditions, with 78.02% of the region experiencing reduced salinity and 10.09% exhibiting deterioration. From 1996 to 2019, non-salinized soil increased by 1,403.46 km2, mildly salinized soil expanded by 3,702.28 km2, while saline soils decreased by 7,685.6 km2. Statistical analysis indicates that soil salinity followed normal or logarithmic-normal distributions, with higher variability observed in 2016 and 2019. Despite these positive trends, challenges remain, particularly in the Shihezi, Manas, and Mosuowan irrigation zones, which still exhibit moderate to severe salinity. This study highlights the effectiveness of drip irrigation combined with improved management practices in mitigating soil salinity and enhancing soil quality. However, it emphasizes the need for targeted strategies to address residual salinization risks, ensuring sustainable agricultural development and ecological balance in arid regions. creator: Jianrong Shao creator: Shuaihao Li creator: Xiaohu Yang creator: Fenghua Zhang creator: Haichang Yang creator: Zicheng Peng creator: Tayyaba Zulfiqar uri: https://doi.org/10.7717/peerj.19295 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shao et al. title: Predicting the potential distribution of Phacellanthus tubiflorus (Orobanchaceae): a modeling approach using MaxEnt and ArcGIS link: https://peerj.com/articles/19291 last-modified: 2025-04-28 description: Phacellanthus tubiflorus Sieb. et Zucc, a vascular plant species, is believed to possess pharmacological properties including anti-fatigue and immunoenhancement. However, its distribution data is limited. Owing to the prospective medicinal relevance of this species, we proposed a comprehensive investigation for conservation and utilization. In this study, we aimed to scrutinize the plant holistically, ranging from the macroscopic to microscopic level. Specifically, we developed an ecological model using 51 records of P. tubiflorus subjected to seven environmental conditions. This model attained an exceptional area under curve (AUC ) value of 0.990 with a standard deviation of 0.004, and true skill statistic (TSS) value of 0.989, indicating a potently predictive capacity. Through the MaxEnt model, we completed a systematic depiction of the ecological niche of P. tubiflorus, revealing its primary global distribution. We carried out field surveys in the Changbai Mountain region to validate the model’s accuracy and conducted observations focusing on the phenological attributes of P. tubiflorus, highlighting its largely subterranean existence. Factors such as seasonality of precipitation and temperature were found to sway its distribution, engendering comparably stable acclimation habitats. This research contributes to the data repository for facilitating subsequent studies on this species. Integrating botanical and ecological approaches, we proposed a more profound comprehension and evaluation of a species’ behavior, survival strategies, and associations with other populations within specific habitats. Furthermore, this inclusive approach would assist in addressing pivotal environmental issues related to species conservation, biodiversity, and land development. creator: Cheng Chang creator: Fengkun Cai creator: Lu Shen creator: Xiang Jia creator: Zhiguo Liu creator: Chenlu Wang creator: Yujie Fu creator: Yumei Luo uri: https://doi.org/10.7717/peerj.19291 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Chang et al. title: Effects of bortezomib on intracellular antioxidant and apoptosis in HepG2cells link: https://peerj.com/articles/19235 last-modified: 2025-04-28 description: Bortezomib, as a proteasome inhibitor, is used in clinical trials related to solid cancers. However, its use is not always associated with a good response to treatment. Taking into account the above, we decided to analyze the effect of the time-dependency (24 vs. 48 h) and the dose-dependency of bortezomib (2, 4, 8 and 16 nM) on apoptosis and activities of antioxidant enzymes such as catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GR), glutathione peroxidase (GPx) and glutathione transferase (GST), as well as concentrations of reduced glutathione (GSH) and malondialdehyde (MDA) in hepatoblastoma cell line (HepG2) cells. We have shown that increasing concentrations of bortezomib caused (I) a gradual decrease in the levels of GSH; (II) changes in MDA concentrations and antioxidant enzymes activities; (III) increase in apoptosis levels in HepG2 cells. We did not find significant association between antioxidant parameters and number of apoptotic cells. Our study showed that the analyzed parameters (such as: CAT, SOD, GR, GPx, GST, GSH, MDA) changed after bortezomib treatment. It is important to search for new anti-cancer therapies based on next-generation proteasome inhibitors. It is possible that the use of proteins associated with oxidative stress will help enhance the action of these inhibitors and will provide a better treatment effect. creator: Grażyna Świderska-Kołacz creator: Magdalena Madej creator: Szymon Zmorzynski creator: Wojciech Styk creator: Iwona Surowiec creator: Bożena Witek creator: Anna Wojciechowska creator: Joanna Czerwik-Marcinkowska creator: Anna Nowakowska uri: https://doi.org/10.7717/peerj.19235 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Świderska-Kołacz et al. title: Genetic diversity and population structure of parasite infrapopulations within and across hosts for two trophically transmitted trematode parasites link: https://peerj.com/articles/19178 last-modified: 2025-04-28 description: Complex parasite life cycles frequently require trophic transfer of parasites from an intermediate host prey to a definitive host predator. This results in aggregated distributions of parasites in predator host populations, which are subsequently expected to host more genetically diverse parasite infrapopulations than lower trophic level hosts. Host dispersal and seasonal population dynamics, particularly in the case of first-intermediate hosts, are also expected to drive population genetic patterns within and across populations. To examine how parasite life history and host ecology influence parasite genetic patterns, we characterized the genetic diversity of within-host infrapopulations, as well as overall population genetic structure, of sympatric tongueworm (Halipegus occidualis) and lungworm (Haematoloechus complexus) freshwater trematode parasite populations. Parasites were collected across three host stages (snail, odonate insect, and frog) and sequenced at the cytochrome oxidase I (COI) mitochondrial region (519 bp for lungworms; 526 bp for tongueworms) to characterize genetic variation within and across hosts. Infection abundance per host and genetic diversity of within-host parasite infrapopulations generally increased with host trophic level, as expected. Additionally, tongueworm assemblages in odonate hosts were essentially equally as genetically diverse (depending on the index used) as those in definitive host frogs; tongueworms have an additional trophic transfer in their life cycle before the odonate stage, which highlights how trophic transmission and multi-host life cycle structure can benefit parasites by increasing genetic diversity of sexually reproducing adult assemblages. We also found that tongueworm populations, which infect a long-lived snail as a first-intermediate host, had higher population genetic diversity than lungworms, which infect a much shorter-lived snail with highly unstable population dynamics. Thus, we expect that first-intermediate host dynamics and dispersal ability played a large role in predicting population-level parasite genetic diversity and genetic structure in this system. This study investigates the effects of small- and large-scale processes on parasite genetic population structure and diversity and provides critical genetic data for future studies on these genera. creator: Sarah R. Goodnight creator: April M.H. Blakeslee creator: Michael W. McCoy uri: https://doi.org/10.7717/peerj.19178 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Goodnight et al. title: iSeqSearch: incremental protein search for iBlast/iMMSeqs2/iDiamond link: https://peerj.com/articles/19171 last-modified: 2025-04-28 description: BackgroundThe advancement of sequencing technology has led to a rapid increase in the amount of DNA and protein sequence data; consequently, the size of genomic and proteomic databases is constantly growing. As a result, database searches need to be continually updated to account for the new data being added. However, continually re-searching the entire existing dataset wastes resources. Incremental database search can address this problem.MethodsOne recently introduced incremental search method is iBlast, which wraps the BLAST sequence search method with an algorithm to reuse previously processed data and thereby increase search efficiency. The iBlast wrapper, however, must be generalized to support better performing DNA/protein sequence search methods that have been developed, namely MMseqs2 and Diamond. To address this need, we propose iSeqsSearch, which extends iBlast by incorporating support for MMseqs2 (iMMseqs2) and Diamond (iDiamond), thereby providing a more generalized and broadly effective incremental search framework. Moreover, the previously published iBlast wrapper has to be revised to be more robust and usable by the general community.ResultsiMMseqs2 and iDiamond, which apply the incremental approach, perform nearly identical to MMseqs2 and Diamond. Notably, when comparing ranking comparison methods such as the Pearson correlation, we observe a high concordance of over 0.9, indicating similar results. Moreover, in some cases, our incremental approach, iSeqsSearch, which extends the iBlast merge function to iMMseqs2 and iDiamond, provides more hits compared to the conventional MMseqs2 and Diamond methods.ConclusionThe incremental approach using iMMseqs2 and iDiamond demonstrates efficiency in terms of reusing previously processed data while maintaining high accuracy and concordance in search results. This method can reduce resource waste in continually growing genomic and proteomic database searches. The sample codes and data are available at GitHub and Zenodo (https://github.com/EESI/Incremental-Protein-Search; DOI: 10.5281/zenodo.14675319). creator: Hyunwoo Yoo creator: Mohammadsaleh Refahi creator: Robi Polikar creator: Bahrad A. Sokhansanj creator: James R. Brown creator: Gail L. Rosen uri: https://doi.org/10.7717/peerj.19171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yoo et al. title: Redescription of four Epiperipatus species with an update on the distribution of Epiperipatus acacioi (Marcus & Marcus, 1955) link: https://peerj.com/articles/19168 last-modified: 2025-04-28 description: Due to recent phylogenetic studies on Neopatida over the last ten years, the genus Epiperipatus has become the most diverse within Peripatidae. Such an expansion occurred due to nomenclatural acts based on evidence from anatomical characters that had not been well supported for genera and species included in the last Epiperipatus revision. Among these species are Epiperipatus brasiliensis (Bouvier, 1900), E. acacioi (Marcus & Marcus, 1955), E. cratensisBrito et al., 2010 and Peripatus bouvieriFuhrmann, 1913. Here, we provide the redescription of these three species previously included in Epiperipatus, besides presenting Epiperipatus bouvieri as a new combination. We extended the distribution of E. acacioi for the Serra da Moeda in the municipalities of Rio Acima, Nova Lima, and Itabirito (Minas Gerais, Brazil). The molecular data showed that specimens from these locations are closely related to E. acacioi, forming a clade deeply nested within the Epiperipatus group. Hitherto, the distribution of the species was restricted to the Estação Ecológica do Tripuí in the municipality of Ouro Preto. However, based on our results, the natural porosity of the rocks associated with the iron ore deposits of this region may have allowed the dispersal of the species along the mountains in this region for tens of kilometers. creator: Cristiano Sampaio Costa creator: Robson de Almeida Zampaulo creator: Santelmo Vasconcelos creator: Michele Molina creator: Igor Cizauskas creator: Ricardo Pinto-da-Rocha uri: https://doi.org/10.7717/peerj.19168 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Costa et al. title: Time perception and lived experience in personality disorders: differences across types, dimensions and severity link: https://peerj.com/articles/19403 last-modified: 2025-04-25 description: BackgroundAltered temporal experience lies at the core of various psychiatric conditions, including borderline personality disorder (BPD). Mainstream research in psychopathology tends to explore BPD with scrutiny while neglecting other personality disorders (PD). At the same time, the dimensional approach to PD proposes looking through the disorders’ subtypes and tracing lived experience-based commonalities. This study is the first to explore the temporality of PD by investigating the relationship between symptom severity and lived time and combining objectified measures of time perception with phenomenological interpretation.MethodsA total of 63 participants of various educational backgrounds, with personality disorders (36.5% male), following ICD-10 coding diagnosed with paranoid (3.2%), borderline (41.3%), narcissistic (33.3%), avoidant (4.8%), dependent (1.6%) and unspecified (15.9%) personality disorder. Levels of personality functioning and intensity of maladaptive trait domains were controlled with Level of Personality Functioning—Brief Scale 2.0 and Personality Inventory for ICD-11, respectively, resulting in the overall sample classification as comprising nine subclinical, 13 mild, 20 moderate, 16 severe, and five extremely severe conditions. Polish Short Version of the Zimbardo Time Perspective Inventory (PS-ZTPI) and Cottle’s Circles Test (CT) were used to assess the temporal experience.ResultsIn comparison to healthy individuals, those with PD are more oriented toward past negative (4.01 vs. 2.98) and less toward past positive (2.31 vs. 3.71) and future (3.04 vs. 3.47), as measured with PS-ZTPI; their pre-reflective temporal experience, as measured with CT, is dominated either by the past or the future, while the present remains marginalized. BPD distinctiveness among other PD lies in higher orientation toward hedonistic present and lower orientation toward the future. While the general temporal profile of PD is independent of age and duration of hospitalization, it is related to the severity of the condition. The more severe the impairments in self-functioning, the higher the negative past perspective and pre-reflective past dominance, and the lower the positive and future perspective. The results of this study highlight temporality as an essential aspect of lived experience in PD, being possibly related to disturbed self-experience. creator: Anna Sterna creator: Eisuke Sakakibara creator: Marcin Moskalewicz uri: https://doi.org/10.7717/peerj.19403 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sterna et al. title: Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China link: https://peerj.com/articles/19384 last-modified: 2025-04-25 description: BackgroundChaohu Lake (CL) is one of the most polluted areas in China due to its high content of antibiotics. However, the distribution and influencing factors of antibiotic resistance genes (ARGs) in this lake are still controversial.MethodsTo solve this problem, we used metagenomic sequencing to investigate the distribution and in-fluencing factors of ARGs in CL.ResultsOur findings revealed the existence of nine kinds of ARGs, including 45 specific genes. The most abundant types were multidrug, bacitracin, polymyxin, macrolide lincosamide streptogramin, and aminoglycoside. Multiple microorganisms were undeniable ARG reservoirs, although they were not dominant species in the microbiota. Our results also showed that both the microbiota and physiochemical factors played important roles in shaping the distributions of ARGs in CL. Specifically, the levels of PO4-P (0.5927) and total phosphorus (0.4971) had a greater impact than total nitrogen (0.0515), NO3-N (0.0352), NO2-N (−0.1975), and NH3-N (−0.0952).ConclusionsThese findings provide valuable insights into the distribution and influencing factors of ARGs in lakes. creator: Yan Zhang creator: Guoao Ding creator: Yue Gao creator: Ying Li creator: Peng Zhou creator: Li Wu creator: Minghui Zhou creator: Jingjing Wang creator: Jun Tang uri: https://doi.org/10.7717/peerj.19384 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Normal feeding movements expressed by dimensionality reduction of whole-body joint motions using principal component analysis link: https://peerj.com/articles/19324 last-modified: 2025-04-25 description: BackgroundUnderstanding elementary feeding movements and postures is essential for improving assessment and intervention strategies in occupational therapy, particularly for individuals with eating difficulties, and for educating caregivers and students. However, the current assessment tools lack precision in evaluating complex feeding movements and often rely on subjective judgments rather than objective measures. We aimed to determine elementary movements and postures corresponding to different feeding phases using principal component analysis (PCA).MethodsThis cross-sectional observational study was conducted at a Local National University Hospital and included 45 healthy, right-handed adult volunteers (23 men and 22 women) aged 20–39 years (mean age, 27.3 years), with no neurological or musculoskeletal impairments. Movements during yogurt feeding using a spoon were captured with a three-dimensional inertial sensor motion capture system. Principal components (PCs) and their scores were derived from PCA of whole-body joint motion data across four feeding phases. PC scores were compared between phases using Friedman’s and post-hoc tests.ResultsThe primary PC, representing whole-body movement, accounted for 50.0% of the variance; the second PC, associated with hand direction changes, accounted for 13.7%. The cumulative variance of the first five PCs was 83.1%, including individual body-part movements and fixations or combinations of these. Significant differences existed between feeding phases, particularly in the reaching and transport phases, which showed greater whole-body movement than that during the spooning and mouth phases. Hand direction changes were more prominent during the spooning phase than during the mouth phase.ConclusionsPCA helped determine key elementary movements and their corresponding feeding phases, which can be used to assess patients with feeding difficulties and guide occupational therapy interventions. Portions of this text were previously published as part of a preprint (https://doi.org/10.1101/2024.09.14.24313686). creator: Jun Nakatake creator: Shigeaki Miyazaki creator: Hideki Arakawa creator: Etsuo Chosa uri: https://doi.org/10.7717/peerj.19324 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nakatake et al. title: Expression and molecular characterization of an intriguing hyaluronan synthase (HAS) from the symbiont “Candidatus Mycoplasma liparidae” in snailfish link: https://peerj.com/articles/19253 last-modified: 2025-04-25 description: BackgroundHyaluronan synthases (HASs) are ubiquitous in living organisms, and the hyaluronic acid (HA) synthesized by them are important to their body and well used in medicine, cosmetics and other fields. HAS from deep-sea creatures has not yet been explored before. The study aims to analyse the characteristics and enzyme kinetics of a novel hyaluronan synthase derived from the symbiont “Candidatus Mycoplasma liparidae” found in deep-sea snailfish (snHAS).MethodologysnHAS was over-expressed using His 6 as tag in the study. The sequence alignment was conducted by Cluster W and then the phylogenetic analyse of HASs was performed by Mega 6.0 to investigate the position of snHAS during evolution. Km and Vmax were detected to study the enzyme kinetics of snHAS wildtype and its mutant. The molecular weight of HA was evaluated by high performance gel permeation chromatography (HPGPC). The cardiolipin was added to investigate whether it had a promoting effect on the snHAS.ResultsThe length of snHAS was 933 bp with an open reading frame (ORF) of 310 amino acids. Unlike other repoted HASs, snHAS had no transmembrane region and was not classified into the currently known Class I or Class II. snHAS could synthesize hyaluronan with lower molecular weights using the substrates of uridine-diphosphate—N-acetylglucosamine (UDP-GlcNAc) and uridine-diphosphate—glucuronic acid (UDP-GlcA) in vitro. The Km values of snHAS were 258 ± 45 µM and 39 ± 5 µM for UDP-GlcNAc and UDP-GlcA, respectively, much lower than those from mice (Km for UDP-GlcA: 55 ± 5 µM; Km for UDP-GlcNAc: 870 ± 60 µM). The kcat/Km values of snHAS were 163.5 s−1 mM−1 and 8.08 s−1 mM−1 for UDP-GlcA and UDP-GlcNAc, respectively. Furthermore, the activity of snHAS was independent of cardiolipin.ConclusionssnHAS was a novel HAS based on the characteristics of the animo acid sequence, which could produce low molecular weight of HA with high efficiency. This provides a molecular basis for the biosynthesis of low molecular weight of HA. creator: Lulu Guo creator: Shaolu Wang creator: Chunang Lian creator: Lisheng He uri: https://doi.org/10.7717/peerj.19253 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Guo et al. title: Telehealth satisfaction among patients with chronic diseases: a cross-sectional analysis link: https://peerj.com/articles/19245 last-modified: 2025-04-25 description: BackgroundThe study aims to assess telehealth satisfaction among patients with chronic diseases focusing on key demographic and clinical factors that influence satisfaction.MethodsA descriptive cross-sectional study was conducted using a self-reported online questionnaire between December 1, 2023, and January 30, 2024. The study targeted chronic patients who had been using telehealth for at least three months. After screening for eligibility and ensuring data completeness, responses from 1,070 patients from three non-governmental hospitals were included in the analysis. The questionnaire covered demographic, socio-economic, and technology-related data, as well as a telehealth satisfaction scale.ResultsA total of 62.9% of patients reported being satisfied with the telehealth services they received, while 37.1% expressed dissatisfaction. Logistic regression analysis identified several factors associated with patient satisfaction. The constant term was significantly positive (coefficient = 4.129, p < 0.001), indicating a baseline high level of satisfaction. Age negatively impacted satisfaction (coefficient = −0.191, p < 0.001), with older patients being less satisfied. Male patients showed a higher satisfaction rate (coefficient = 0.473, p = 0.047), while education level, particularly having a bachelor’s degree, was strongly associated with increased satisfaction (coefficient = 1.977, p < 0.001). Marital status (married) was not a significant predictor (p = 0.403), whereas employment status (working) had a positive association with satisfaction (coefficient = 1.445, p < 0.001). Income level (sufficient and save) did not significantly affect satisfaction (p = 0.561). Having children was positively associated with satisfaction (coefficient = 1.189, p < 0.001).ConclusionAddressing demographic, socio-economic, and technological needs can enhance patient satisfaction with telehealth services. Tailoring services to specific patient preferences, especially for older patients and those needing continuous training, can improve telehealth effectiveness and acceptance. creator: Abdelaziz Hendy creator: Sally Mohammed Farghaly Abdelaliem creator: Ahmed Zaher creator: Bothayna N. Sadek creator: Abdulqadir J. Nashwan creator: Mohammed Musaed Ahmed Al-Jabri creator: Ahmad Ahmeda creator: Ahmed Hendy creator: Amany Anwar Saeed Alabdullah creator: Shaban Majed Sinnokrot uri: https://doi.org/10.7717/peerj.19245 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hendy et al. title: A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed link: https://peerj.com/articles/19120 last-modified: 2025-04-25 description: The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems. creator: Aman Deep creator: Guido Sieber creator: Lisa Boden creator: Gwendoline M. David creator: Daria Baikova creator: Dominik Buchner creator: Jörn Starke creator: Tom L. Stach creator: Torben Reinders creator: Una Hadžiomerović creator: Sára Beszteri creator: Alexander J. Probst creator: Jens Boenigk creator: Daniela Beisser uri: https://doi.org/10.7717/peerj.19120 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Deep et al. title: A phylogeographic pattern of the trans-Palaearctic littoral water flea Pleuroхus truncatus (O.F. Müller, 1785) (Cladocera: Chydoridae) link: https://peerj.com/articles/19355 last-modified: 2025-04-24 description: Water fleas (Crustacea: Cladocera) are recently regarded as models for phylogeographic studies, but most such publications are concerned the planktonic genera, first of all, Daphnia O.F. Müller. The aim of our article is to study the phylogeographic pattern of a very common littoral chydorid Pleuroxus truncatus (O.F. Müller) based on sequences of two mitochondrial (cytochrome oxidase (COI) and 16S) and two nuclear (18S and 28S) genes. All totality of the sequences could be subdivided into two major clades, A, having a predominantly European distribution with a single exclusion, and B, having a predominantly Asian distribution, but with few populations in European Russia; the clade B is subdivided into three subclades (B1–B3) with a moderate support. Earlier derived phylogroups (subclades B1 and B2) are distributed in south portion of Western Siberia. This pattern is known for previously studied daphniids. Estimations of the major clade (A and B) and subclade differentiation time in P. truncatus based on different methods lie in the interval of ca. 0.01–0.3 Mya. Therefore, the whole revealed pattern is very young, related to Late Pleistocene and more shallow as compared to previously studied daphniids. Probably, the total population of P. truncatus was not so strongly split by the unfavorable conditions during the Pleistocene cold phases. creator: Alexey A. Kotov creator: Petr G. Garibian creator: Anna N. Neretina creator: Dmitry P. Karabanov uri: https://doi.org/10.7717/peerj.19355 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kotov et al. title: Research progress of nano drug delivery systems in the anti-tumor treatment of traditional Chinese medicine monomers link: https://peerj.com/articles/19332 last-modified: 2025-04-24 description: Tumors pose a serious threat to global public health and are usually treated from two aspects: tumor cells and tumor microenvironment. Compared with traditional chemotherapy drugs, traditional Chinese medicine (TCM) monomers have advantages in tumor treatment, such as multiple targets, multiple levels and synergistic intervention. However, most TCM active ingredients have disadvantages such as poor water solubility and stability, which restrict their clinical application. Nano drug delivery systems have the functions of improving the bioavailability of TCM anti-tumor active ingredients, enhancing tissue targeting, achieving controlled drug release, and inhibiting tumor multidrug resistance. Compared with free monomers, they have higher therapeutic effects and fewer side effects. This article summarizes five commonly used anti-tumor TCM monomer nanocarriers, including lipid nanomaterials, exosomes, polymer micelles, carbon nanotubes, and dendrimers, and explains their anti-tumor mechanisms after combining with TCM, such as inhibiting tumor cell proliferation and metastasis, regulating tumor microenvironment, etc. At the same time, the potential of nano drug delivery systems combined with radiotherapy and immunotherapy is discussed, as well as the current problems of potential toxicity, long-term stability, and complex amplification process, as well as future development directions, aiming to provide a reference for promoting the clinical application of nano drug delivery systems for TCM anti-tumor active ingredients. creator: Bocui Song creator: Li Shuang creator: Shuang Zhang creator: Chunyu Tong creator: Qian Chen creator: Yuqi Li creator: Meihan Hao creator: Wenqi Niu creator: Cheng-Hao Jin uri: https://doi.org/10.7717/peerj.19332 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Song et al. title: Three distinct classes of myenteric ganglia in mice and humans: insights from quantitative analyses link: https://peerj.com/articles/19329 last-modified: 2025-04-24 description: BackgroundThe myenteric plexus primarily consists of the myenteric ganglia, which include enteric neurons, synaptic neuropils, and glial cells. Abnormal myenteric plexus formation can result in gastrointestinal disorders. Comprehensive morphological classification studies of myenteric ganglia remain limited.MethodsWhole-mount immunofluorescence staining was used to label myenteric ganglia in colon tissue of mice and children. The ganglionic area and the number of intraganglion neurons were quantified by the K-means clustering algorithm. The guts of embryonic day 11.5 (E11.5) mouse were cultured and immunostained to observe the characteristics of developing myenteric ganglia.ResultsMyenteric ganglia can be categorized into three groups in the colon tissues of mice and normal children. A similar classification was observed for Tuj1-positive neuronal cell clusters in the midgut of E11.5 mouse. Culture of the E11.5 mouse midgut revealed that the area of post-cultured clusters of developing neurons also fell into three distinct categories, with a noticeable increase compared to pre-culture.ConclusionsThe myenteric ganglia in mice and humans can be categorized into three groups based on both the ganglionic area and intraganglion neuron count, and distinct classes of myenteric ganglia may be present during early development. creator: Luyao Wu creator: Lei Xiang creator: Yingjian Chen creator: Handan Mao creator: Xinyao Meng creator: Jing Wang creator: Honglin Li creator: Xuyong Chen creator: Jiexiong Feng creator: Jun Xiao uri: https://doi.org/10.7717/peerj.19329 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wu et al. title: Quality of life and parental stress related to executive functioning, sensory processing, and activities of daily living in children and adolescents with neurodevelopmental disorders link: https://peerj.com/articles/19326 last-modified: 2025-04-24 description: The quality of life (QoL) of families caring for children with neurodevelopmental disorders is influenced by the severity of the disorder, family support, and access to specialized services. Parental stress also affects family dynamics and QoL due to the additional demands of care, particularly focusing on the management of activities of daily living (ADLs). This study aimed to analyze the relationship between parents’ QoL and stress, involving 46 parents of children aged 3 to 12 years with neurodevelopmental disorders, while also examining the relationship with the performance in ADLs, sensory processing, and executive functioning of children with neurodevelopmental disorders. Significant positive associations were found between factor 1 of the “Assessment of Sensory Processing and Executive Functions in Childhood” (EPYFEI) with perceived stress (r = 0.401, p ≤ 0.01), and parents physical component summary (PCS) (r = 0.330, p ≤ 0.05). Significant negative correlations were observed between ADL performance and parents’ physical component summary (PCS) of SF-12 (r =  − 0.356, p ≤ 0.05). Conversely, a significant negative association was found between factors 1 and 4 of the EPYFEI and ADL performance (r =  − 0.392, p ≤ 0.01 and r =  − 0.660, p ≤ 0.01). Furthermore, a significant positive association was found between parents’ perceived stress and the PCS of SF-12 (r = 0.471, p ≤ 0.01), and a negative association between perceived stress and parents’ mental component summary (MCS) (r =  − 0.300, p ≤ 0.05). The study revealed that QoL and parental stress are closely linked to functioning in ADLs and executive functioning of children with neurodevelopmental disorders. Interventions to strengthen these areas might improve parents’ well-being and QoL. Additionally, it underscores the importance of teaching these parents stress management strategies. creator: Vanesa Lobato-Ruiz creator: Dulce Romero-Ayuso creator: Abel Toledano-González creator: José Matías Triviño-Juárez uri: https://doi.org/10.7717/peerj.19326 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lobato-Ruiz et al. title: The effect of diluted 1% baby shampoo on biofilm reduction in chronic rhinosinusitis with nasal polyposis link: https://peerj.com/articles/19134 last-modified: 2025-04-24 description: BackgroundBiofilm has been identified as the contributing factor for refractory chronic rhinosinusitis with nasal polyposis (CRSwNP). Nasal douching using baby shampoo was thought to be effective in patients with CRSwNP. We aimed to study the in-vitro reduction of biofilm using diluted 1% baby shampoo.MethodsSixty nasal polyps taken from patients who met the inclusion and exclusion criteria were sent for histopathological examination using haematoxylin and eosin staining. Another portion of the same samples was sent for tissue culture and tissue culture plate assay to identify S. aureus and P. aeruginosa and determine their biofilm forming capacity. The efficacy of diluted 1% baby shampoo versus normal saline was tested on the biofilm in vitro where the optical density readings were compared pre- and post-treatment.ResultsThe prevalence of biofilm in patients with CRSwNP is 21.7%. Thirteen samples were positive for biofilm; P. aeruginosa 23% (n = 3), S. aureus 15% (n = 2), no bacterial growth 54% (n = 7) and others 8% (n = 1). Biofilm formation was significant in both S. aureus and P. aeruginosa (p < 0.001) whilst a significant reduction of biofilm was seen in diluted 1% baby shampoo (p = 0.043).ConclusionIn conclusion, diluted 1% baby shampoo is an effective treatment in the reduction of biofilm for CRSwNP. creator: Farah Dayana Zahedi creator: Mun Yee Soo creator: Muttaqillah Najihan Abdul Samat creator: Suria Hayati Md Pauzi creator: Salina Husain creator: Aneeza Khairiyah Wan Hamizan creator: Baharudin Abdullah creator: Balwant Singh Gendeh creator: Abdul Samat Ismail creator: Rocky Vester Richmond uri: https://doi.org/10.7717/peerj.19134 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zahedi et al. title: Liver stiffness and serum galectin 3 level significantly increases in patients with prediabetes: a fibroscan study link: https://peerj.com/articles/19377 last-modified: 2025-04-23 description: AimDiabetes mellitus (DM) is associated with the development and progression of metabolic dysfunction-associated steatotic liver disease (MASLD). In our study, we aimed to evaluate the relationship between liver stiffness (LS) and galectin-3 levels in patients diagnosed with prediabetes.MethodsA total of 120 participants were included in this prospective and cross-sectional study, comprising 40 patients with prediabetes, 40 patients with type 2 DM and 40 individuals with normal glucose metabolism. Human galectin-3 levels were measured using Enzyme-Linked Immunosorbent Assay (ELISA) with Human Galectin-3 kits. LS measurements were performed using the FibroScan® Mini 430 device (Echosens, France).ResultsIn our study, we found that Fib-4 index, LS and galectin-3 levels were increased in patients with prediabetes. Another significant finding was that hemoglobin A1c (HbA1c) and galectin-3 levels were higher in patients with LS value ≥8 kPa and both HbA1c and galectin-3 levels were independently associated with LS.ConclusionConsidering the increased prevalence of MASLD in prediabetes, we recommend early assessment of LS and measurement of galectin-3 levels in these patients. creator: Huseyin Ali Ozturk creator: Hilmi Erdem Sumbul uri: https://doi.org/10.7717/peerj.19377 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ozturk and Sumbul title: Effects of exercise on glycolipid metabolism in adolescents with overweight and obesity: a systematic review and meta-analysis of 26 randomized controlled trials link: https://peerj.com/articles/19365 last-modified: 2025-04-23 description: ObjectiveThe aim of this meta-analysis was to investigate the effect of exercise intervention on glycolipid metabolism in overweight and obese adolescents.MethodsA systematic review and meta-analysis of randomized trials were conducted. The review adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and was registered (ID: CRD42024623686). Electronic searches were performed using the following databases: Web of Science, PubMed, Scopus, Cochrane and Embase. Randomized controlled trials of exercise interventions were included. Data on fasting blood glucose (FBG), fasting insulin (FINS), total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C) and high-density lipoprotein cholesterol (HDL-C) before and after exercise interventions were extracted for overweight and obese adolescents. Risk of bias was assessed using the Cochrane risk of bias tool. The Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) tool was used to evaluate the quality of the evidence. Standardized mean differences (SMDs) were calculated to compare differences between exercise and conventional control groups. Subgroup analyses were performed to assess whether effects differed by exercise type, intervention duration, supervision, and intervention frequency.ResultsA total of 984 participants (576 in experimental groups and 408 in control groups) were included across 26 studies. The analysis revealed that exercise interventions significantly improved key metabolic parameters: FBG (SMD: −0.42 95% CI [−0.73 to −0.12]), FINS (SMD: −0.81 95% CI [−1.13 to −0.49]), TC (SMD: −0.18 95% CI [−0.34 to −0.01]), TG (SMD: −0.46 95% CI [−0.56 to −0.25]), LDL-C (SMD: −0.28 95% CI [−0.44 to −0.12]), and HDL-C (SMD: 0.26 95% CI [0.11–0.40]). Subgroup analysis indicated that exercise type, supervision and intervention frequency influenced the effectiveness.ConclusionThe analysis suggests that exercise interventions improve glycolipid metabolism in adolescents with overweight and obesity. Continuous endurance training demonstrated greater efficacy in improving blood glucose parameters, whereas hybrid-type exercise showed advantages in improving lipid metabolism. Engaging in three supervised training sessions weekly may be the optimal approach to enhance glycolipid metabolism in obese adolescents. These findings provide evidence for clinicians and healthcare professionals (e.g., exercise physiologists, physical therapists) to guide exercise prescriptions for obese adolescents, thereby preventing worsening metabolic imbalances. creator: Xinyu Fan creator: Weihao Sun creator: Song Gu uri: https://doi.org/10.7717/peerj.19365 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Fan et al. title: Kinematic and neuromuscular responses to different visual focus conditions in stand-up paddleboarding link: https://peerj.com/articles/19362 last-modified: 2025-04-23 description: PurposeThis study analyzed the kinematics and muscle activity during the stand-up paddleboarding (SUP) under different visual focus points in three conditions: i) eyes on the board nose, ii) looking at the turn buoy, and iii) free choice.MethodsFourteen male paddleboarders (24.2 ± 7.1 years) performed three trials covering 65 m, and the electromyographic (EMG) activation patterns and kinematic parameters in four cycle strokes for the left and right sides were analyzed. Surface EMG of the upper trapezius, biceps brachii, triceps brachii, tibialis anterior, and gastrocnemius medialis were recorded. The data were processed according to the percentage of maximum voluntary contraction (%MVC). Speed, stroke frequency (SF), stroke length, and stroke index (SI) were analyzed.ResultsThe speed, SF, and SI (p < 0.01, η2 ≥ 0.42) showed significant variance between conditions, with the free condition achieving the highest speed (1.20 ± 0.21 m/s), SF (0.65 ± 0.13 Hz) and SI (2.25 ± 0.67 m2/s). This condition showed greater neuromuscular activity, particularly in the triceps brachii during both the left (42.25 ± 18.76 %MVC) and right recoveries (32.93 ± 16.06 %MVC). During the pull phase, the free choice presented higher biceps brachii activity (8.51 ± 2.80 %MVC) compared to the eyes on the board nose (6.22 ± 2.41 %MVC; p < 0.01), while showing lower activity in the triceps brachii (10.02 ± 4.50 %MVC vs. 16.52 ± 8.45 %MVC; p < 0.01) and tibialis anterior (12.24 ± 7.70 %MVC vs. 17.09 ± 7.73 %MVC; p < 0.01) compared to looking at the turn buoy.ConclusionThese results suggest that a free visual focus allows paddleboarders to enhance their kinematics and muscle activation, highlighting the significance of visual focus strategies in improving both competitive and recreational SUP performance. creator: João Freitas creator: Ana Conceição creator: Jan Stastny creator: Jorge E. Morais creator: Diogo L. Marques creator: Hugo Louro creator: Daniel A. Marinnho creator: Henrique P. Neiva uri: https://doi.org/10.7717/peerj.19362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Freitas et al. title: Constructing a neural network model based on tumor-infiltrating lymphocytes (TILs) to predict the survival of hepatocellular carcinoma patients link: https://peerj.com/articles/19351 last-modified: 2025-04-23 description: BackgroundHepatocellular carcinoma (HCC) is the most common primary liver cancer worldwide, and early pathological diagnosis is crucial for formulating treatment plans. Despite the widespread attention to pathology in the treatment of HCC patients, a large amount of information contained in pathological images is often overlooked.MethodsWe retrospectively collected clinical data and pathological slide images from (a) 331 HCC patients at Qingdao University Affiliated Hospital between January 2013 and December 2016 and (b) 180 HCC patients from The Cancer Genome Atlas (TCGA). After data screening, precise quantification of various cell types was achieved using QuPath software. Key factors related to the survival prognosis of pathologically confirmed HCC patients were identified through Cox regression and neural network models, and potential therapeutic targets were screened.ResultsOur study showed that tumour-infiltrating lymphocytes (TILs) had a protective effect. We quantified the TILs index by machine learning and built a neural network model to predict the prognostic risk of patients (ROC = 0.836 for training set ROC validation set). 95% CI [0.7688–0.896], and there was a significant difference in prognosis in the high-low risk group predicted by the model (p = 2.6e−18, HR = 0.18, 95% CI [0.12–0.27], and TNFSF4 was identified as a possible immunotherapy target.ConclusionThis study included a total of 511 patients, divided into a training cohort of 331 cases (from Qingdao University Hospital between January 2013 and December 2016) and a validation cohort of 180 cases (TCGA). The results revealed that tumor-infiltrating lymphocytes (TILs) have a protective effect and successfully predicted the survival risk of liver cancer patients using machine learning and neural network technology. The discovery of TNFSF4 provides a new potential target for immunotherapy. creator: Wenqing Zhong creator: Ziyin Zhao creator: Xin Fang creator: Jingyi Sun creator: Yanbing Wei creator: Fengda Li creator: Bing Han creator: Cheng Jin uri: https://doi.org/10.7717/peerj.19351 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zhong et al. title: A revised turtle assemblage from the Upper Cretaceous Menefee Formation (New Mexico, North America) with evolutionary and paleobiostratigraphic implications link: https://peerj.com/articles/19340 last-modified: 2025-04-23 description: The middle Campanian Menefee Formation (Fm.) of the San Juan Basin of New Mexico is a relatively understudied terrestrial deposit in southern Laramidia preceding the fossil-rich upper Campanian Fruitland and Kirtland formations that have been studied for more than a century. Previous collection efforts have revealed a diverse dinosaurian and crocodyliform fauna in the Menefee Fm., including ankylosaurian, tyrannosaurid, hadrosaurid, ceratopsian, and neosuchian taxa. Nearly a decade has passed since the last description of the Menefee turtle fauna, and we present new material that provides insight into turtle evolution during the Campanian in the Colorado Plateau, with implications for Late Cretaceous turtle paleobiostratigraphy in Laramidia. In particular, we extend the stratigraphic ranges of the baenids Neurankylus baueri and Scabremys ornata backwards from younger San Juan Basin strata, along with the nanhsiungchelyid Basilemys. Additional material increases Menefee representation of the relict helochelydrid Naomichelys, and the regionally prevalent derived baenids Denazinemys and Thescelus. Additionally, we report new pan-trionychian specimens, which provide insight into the persistence of Adocus and multiple trionychid and plastomenid species through the remainder of the Campanian in the San Juan Basin. A cluster analysis of turtle diversity across early-middle Campanian sites in Laramidia shows distributions consistent with latitudinal provinciality in some groups. For instance, derived baenids were restricted to latitudes south of southern Utah, along with marine taxa (bothremydids and protostegids) and pan-kinosternoids. Basin-scale endemism is also suggested by some baenid and trionychid distributions. Otherwise, the turtle fauna of the Menefee most closely resemble those of the similarly-aged Wahweap Fm. in southern Utah, and the Aguja Fm. in the Big Bend area of Texas and Mexico to a lesser extent. The Menefee turtle assemblage is consistent with reconstructed paleoenvironments characteristic of the western shoreline of the Western Interior Seaway. Recurrent cyclothems in these settings shaped the development of fluviodeltaic deposits that preserved distal components of large channels with surrounding floodplains and swamps, along with evidence of freshwater, brackish, and possibly shallow marine influence. creator: Brent Adrian creator: Heather F. Smith creator: Andrew T. McDonald uri: https://doi.org/10.7717/peerj.19340 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Adrian et al. title: Development and validation of COVID-19 vaccination perception (CoVaP) instrument among healthcare workers in Malaysia link: https://peerj.com/articles/19318 last-modified: 2025-04-23 description: BackgroundHealthcare workers (HCWs) play an essential role in facilitating coronavirus disease 2019 (COVID-19) vaccination, and their confidence in vaccination is crucial. Nevertheless, valid instruments for assessing the HCWs’ perceptions of COVID-19 vaccination were lacking. This study aims to develop and validate the COVID-19 Vaccination Perceptions (CoVaP) instrument among HCWs in Malaysia.MethodsA literature review and discussion with research teams were conducted to identify the content to be considered. The instrument was developed in Malay language and underwent back-to-back translations to the English version. The initial CoVaP instrument was unidimensional with 12 items. The Malay and English versions underwent a content validation process by seven expert panels. However, only the Malay version underwent face and construct validation. Face validity was assessed using 30 HCWs. The construct validation was conducted in a two-step process using data from two cross-sectional study samples, including 125 and 300 HCWs for exploratory factor analysis (EFA) and confirmatory factor analysis (CFA), respectively. It was a self-administered questionnaire, and the data were collected using both face-to-face and online platforms. The data were analysed using Analysis of Moment Structure version 28.0 and Statistical Packages for the Social Sciences version 26.ResultsThe analysis showed excellent content (item content validity index (I-CVI) = 0.83 to 1.0, average content validity index (S-CVI/Ave) = 0.97) and face (item face validity index (I-FVI) = 0.87 to 1.0, average face validity index (S-FVI/Ave) = 1.02) validity. The EFA analysis revealed seven items with two domains. Subsequent analysis using CFA demonstrated a two-factor model of seven items with an acceptable level of goodness of fit indexes (comparative fit index = 0.999, Tucker-Lewis index = 0.999, incremental fit index = 0.987, chi-squared/degree of freedom = 1.039, and root mean square error of approximation = 0.011). Finally, the Cronbach’s alpha was satisfactory for both domains (0.899 and 0.815).ConclusionThe CoVaP instrument is a valid and reliable tool for measuring perceptions of COVID-19 vaccination among HCWs. The high validity and reliability of the CoVaP instrument underscore its utility in capturing the unique cultural and contextual factors influencing vaccine perceptions among Malaysian HCWs. Understanding these factors is essential for designing effective public health interventions to address vaccine hesitancy and improve vaccination rates. creator: Siti Nur Aisyah Zaid creator: Azidah Abdul Kadir creator: Mohd Noor Norhayati creator: Basaruddin Ahmad creator: Muhamad Saiful Bahri Yusoff creator: Anis Safura Ramli creator: Jasy Suet Yan Liew uri: https://doi.org/10.7717/peerj.19318 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zaid et al. title: Impact of Nordic hamstring breaking point angle on football player performance link: https://peerj.com/articles/19275 last-modified: 2025-04-23 description: BackgroundFootball demands both aerobic and anaerobic capacities due to its dynamic movements, which include jumps, directional changes, ball control, and sprints. The Nordic hamstring exercise (NHE) enhances eccentric strength, which is crucial for high-intensity movements. However, the relationship between Nordic breaking point angle (NHEbpa), which is associated with eccentric hamstring peak torque during Nordic hamstring exercise, and sprint, countermovement jump (CMJ), and change of direction (COD) speed in soccer players has not been sufficiently investigated.ObjectiveThis analysis examines the relationship between the Nordic breaking point angle and critical performance indicators—sprint speed, COD ability, and vertical jump—in football players.MethodsFifty-eight male soccer players volunteered for the study. Assessments included anthropometric measurements, CMJ tests, 10-20-30 m sprint tests, and COD (zig-zag) tests. NHEbpa was measured using motion analysis software. Correlation analysis was used to determine the relationship between variables. A multiple linear regression analysis was conducted to evaluate the individual effects of the sprint, CMJ, and COD performances on NHEbpa, with data analyzed using JASP 0.18.ResultsCorrelation analysis showed strong positive correlations between NHEbpa and sprint performances (r = 0.633 to 0.666), moderate negative correlation between NHEbpa and CMJ (r = −0.406), and moderate positive correlation between NHEbpa and COD (r = 0.580). Regression analysis results were used to analyze the independent coefficients of multiple variables more comprehensively, revealing significant predictors for performance: 20-m sprint (β = 24.166, p = 0.030), 10-m sprint (β = 22.564, p = 0.047), 30-m sprint (β = 10.677, p = 0.027), and CMJ (β = 4.974, p = 0.034). Conversely, COD performance (β = −0.154, p = 0.470) did not demonstrate a significant effect.ConclusionsThe study identified significant relationships between NHEbpa and sprint/CMJ performances (p < 0.05), while no meaningful effect was observed for COD speed (p > 0.05). These findings highlight the importance of eccentric strength in sprint performance, suggesting that other factors may play a more prominent role in COD. Incorporating eccentric-focused training, particularly through Nordic exercises, is recommended to enhance sprint performance and hamstring strength, which are essential for football players. creator: Murat Koç creator: Niyazi Sıdkı Adıgüzel creator: Barışcan Öztürk creator: Hakan Engin creator: Aydın Karaçam creator: Umut Canli creator: Bekir Erhan Orhan creator: Pablo Prieto-González creator: Peter Sagat creator: Jason Perez creator: Maria Isip creator: Peter Bartik uri: https://doi.org/10.7717/peerj.19275 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Koç et al. title: A novel approach to assessing the bioavailability of biopeptide inhibitor of HMG CoA reductase from germinated and ungerminated Kara Kratok (Phaseolus lunatus L.) link: https://peerj.com/articles/19262 last-modified: 2025-04-23 description: BackgroundThe bioavailability of biopeptide compounds is a development challenge, mainly because of their resistance to the digestion system. This study aimed to determine the bioavailability of HMG CoA reductase biopeptide inhibitors from germinated and ungerminated Kara Kratok (Phaseolus lunatus L.).MethodsGerminated and ungerminated brown P. lunatus were simulated for digestion enzyme in vitro (120 minutes for pepsin and pancreatin), followed by an in situ method for absorption. Perfusate samples were measured for the absorption percentage, inhibition of HMG CoA reductase, molecular weight (MW), peptide concentration, and hydrolysis degree (%DH).ResultsThe results showed that germinated brown P. lunatus exhibited the highest absorption (32.42%), and the percentage of HMG CoA reductase inhibition during enzymatic digestion was at 210 minutes (87.51%), with MW < 10 kDa, peptide concentration of 2.39 mg/mL, and %DH of 48.90%. These findings suggest that germinated brown P. lunatus is a potent HMG CoA reductase inhibitor with significantly higher bioavailability than that of its ungerminated counterpart. This finding underscores its superiority in this context and open new possibilities for biopeptide research. creator: Cahyo Budiyanto creator: Andriati Ningrum creator: Agnes Murdiati creator: Retno Indrati uri: https://doi.org/10.7717/peerj.19262 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Budiyanto et al. title: A cross-sectional study on perceptions towards safe disposal of unused/expired medicines and its associated factors among the public in Saudi Arabia—a threat to the environment and health link: https://peerj.com/articles/19258 last-modified: 2025-04-23 description: BackgroundThe unsafe disposal of pharmaceutical waste poses significant health hazards and causes environmental pollution on a global scale. The lack of specifically authorized guidelines in Saudi Arabia for the disposal of unused medicines available at home creates an undue economic burden and potentially threatens the environment and healthcare.AimThe current study aimed to determine the presence, disposal practices, and perceptions of unused or expired household medicines. Furthermore, it identifies the association between demographic characteristics and the presence, disposal practices, and perceptions of the safe disposal of unused/expired medicines. The study also intended to obtain opinions on methods to control the hazardous effects of waste medicines and promote awareness among the public about the safe disposal of unused/expired medicines.MethodsThis study is a web-based, cross-sectional questionnaire-based survey conducted in Saudi Arabia. The authors of the current study developed a questionnaire based on relevant literature. The study questionnaire comprises various domains such as demographic characteristics, presence and disposal of unused/expired medicines, perception of safe disposal of unused/expired medicines, and recommended improvement plan for safe disposal of used/expired medicines. Estimating internal consistency, expert review, and retranslation methods ensured reliability, face validity, and language validation. The results are expressed as frequency and percentages for categorical data. In addition, a chi-square test was also performed to find the association between the independent variables and the survey responses.ResultsAmong the total population, 643 reported having unused/expired medicines at home, with antibiotics being the most common (79.4%). Symptom improvement is associated with accumulating unused medicines at home (71.7%). Age group, educational level, and occupational status were the predictors of the prevalence of waste medicines available at home (p < 0.05). The method selection for disposing of unused medicines was influenced by gender, age group, marital status, and educational level (p < 0.05), and the preferred method was putting them in the garbage (86.1%). Educational level is the most prominent factor associated with the perception of disposal of unused/expired medicines (p < 0.001).ConclusionOur study reveals a positive perception of the safe disposal of used or expired medicines, but practice requires improvement. The initiatives to improve the safe disposal practice should be tailored based on gender, educational level, and occupational status. Patient education during medicine dispensing could be an appropriate intervention and can be done by the pharmacist. Introducing medicine waste collection programs or safe medicine disposal guidelines for the public in Saudi Arabia could effectively prevent potential environmental and health hazards. creator: Noohu Abdulla Khan creator: Vigneshwaran Easwaran creator: Khalid Orayj creator: Krishnaraju Venkatesan creator: Sirajudeen Shaik Alavudeen creator: Saad Ali Alhadeer creator: Abdulbari Ali Al Nazih creator: Ibrahim Hadi Saeed Al Afraa creator: Abubakr Taha Hussein creator: Sultan Mohammed Alshahrani creator: Mohammad Jaffar Sadiq Mantargi creator: Sivakumar Vijayaraghavalu uri: https://doi.org/10.7717/peerj.19258 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Khan et al. title: The Hippo pathway in bone and cartilage: implications for development and disease link: https://peerj.com/articles/19334 last-modified: 2025-04-22 description: Bone is the main structure of the human body; it mainly plays a supporting role and participates in metabolic processes. The Hippo signaling pathway is composed of a series of protein kinases, including the mammalian STE20-like kinase MST1/2 and the large tumor suppressor LATS1/2, which are widely involved in pathophysiological processes, including cell proliferation, differentiation, apoptosis and death, especially those related to biomechanical transduction in vivo. However, the role of it in regulating skeletal system development and the evolution of bone-related diseases remains poorly understood. The pathway can intervene in and regulate the physiological activities of bone-related cells such as osteoclasts and chondrocytes through its own or other bone-related signaling pathways, such as the Wnt pathway, the Notch pathway, and receptor activator of nuclear factor-κB ligand (RANKL), thereby affecting the occurrence and development of bone diseases. This article discusses the role of the Hippo signaling pathway in bone development and disease to provide new insights into the treatment of bone-related diseases by targeting the Hippo signaling pathway. creator: Chenwei Shao creator: Hao Chen creator: Tingting Liu creator: Chun Pan uri: https://doi.org/10.7717/peerj.19334 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shao et al. title: Comparing the Postural Assessment Scale for Stroke and Berg Balance Scale for predicting community walking ability at discharge in subacute stroke: a prospective cohort study link: https://peerj.com/articles/19322 last-modified: 2025-04-22 description: BackgroundBalance assessment is crucial for predicting community ambulation outcomes in subacute stroke patients undergoing rehabilitation. This study aims to compare the accuracy of the Postural Assessment Scale for Stroke Patients (PASS) and the Berg Balance Scale (BBS) in predicting community walking ability at discharge from rehabilitation.MethodsThis prospective cohort study included 47 stroke patients admitted to a 4-week inpatient rehabilitation program. Patients were assessed with PASS and BBS at admission. Discharge assessments included the Functional Ambulation Categories and 6-Min Walk Distance tests. Statistical analysis involved calculating the area under the receiver operating characteristic curve (AUC), sensitivity, specificity, likelihood ratios, and cut-off scores.ResultsPASS and BBS demonstrated excellent predictive accuracy, with AUC values of 0.955 (95% CI [0.850–0.994]) for PASS and 0.991 (95% CI [0.906–1.000]) for BBS. Cut-off scores were >28 for PASS and >46 for BBS. Sensitivity was high for both (94.44%, 95% CI [72.7–99.9]), while BBS had superior specificity (96.43%, 95% CI [81.7–99.9]) compared to PASS (85.71%, 95% CI [67.3–96.0]). BBS also had a higher positive likelihood ratio (26.44 vs. 6.61). The difference in AUC values was non-significant (p = 0.093).ConclusionsPASS and BBS assessed at admission are highly accurate tools for predicting community ambulation at discharge in subacute stroke patients, with BBS demonstrating a slight advantage, particularly in its positive predictive value. These findings support the use of both scales to guide rehabilitative clinical decision-making. creator: Chutipa Worraridthanon creator: Maria Justine creator: Akkradate Siriphorn uri: https://doi.org/10.7717/peerj.19322 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Worraridthanon et al. title: Decoding biomaterial-associated molecular patterns (BAMPs): influential players in bone graft-related foreign body reactions link: https://peerj.com/articles/19299 last-modified: 2025-04-22 description: Bone grafts frequently induce immune-mediated foreign body reactions (FBR), which hinder their clinical performance and result in failure. Understanding biomaterial-associated molecular patterns (BAMPs), including physicochemical properties of biomaterial, adsorbed serum proteins, and danger signals, is crucial for improving bone graft outcomes. Recent studies have investigated the role of BAMPs in the induction and maintenance of FBR, thereby advancing the understanding of FBR kinetics, triggers, stages, and key contributors. This review outlines the stages of FBR, the components of BAMPs, and their roles in immune activation. It also discusses various bone grafting biomaterials, their physicochemical properties influencing protein adsorption and macrophage modulation, and the key mechanisms of protein adsorption on biomaterial surfaces. Recent advancements in surface modifications and immunomodulatory strategies to mitigate FBR are also discussed. Furthermore, the authors look forward to future studies that will focus on a comprehensive proteomic analysis of adsorbed serum proteins, a crucial component of BAMPs, to identify proteins that promote or limit inflammation. This understanding could facilitate the design of biomaterials that selectively adsorb beneficial proteins, thereby reducing the risk of FBR and enhancing bone regeneration. creator: Carel Brigi creator: K.G. Aghila Rani creator: Balachandar Selvakumar creator: Mawieh Hamad creator: Ensanya Ali Abou Neel creator: A.R. Samsudin uri: https://doi.org/10.7717/peerj.19299 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Brigi et al. title: Long non-coding RNA CYTOR promotes the progression of melanoma via the miR-485-5p/GPI axis link: https://peerj.com/articles/19284 last-modified: 2025-04-22 description: BackgroundRecent research has underscored the critical role of long non-coding RNAs (lncRNAs) in tumorigenesis and malignancy development. Nevertheless, the role of lncRNA cytoskeleton regulator RNA (CYTOR) in the progression of melanoma remains only partially elucidated. This research seeks to explore the impact of CYTOR on melanoma development and to elucidate the molecular mechanisms involved.MethodsIn vitro and in vivo models were used to assess CYTOR expression levels by QPCR and Western blotting. Melanoma cell proliferation, migration, and invasion were assessed by CCK-8 assay, scratch wound assay and transwell invasion experiments. The mechanism of CYTOR promoting melanoma progression was verified in a xenograft tumor mouse model.ResultsOur investigation identified a marked increase in CYTOR expression levels in both melanoma tissues and cells. Experiments conducted both in vitro and in vivo revealed that CYTOR markedly stimulated melanoma cell proliferation, migration, and invasion. Dual-luciferase reporter assays confirmed the direct binding of miR-485-5p to CYTOR, and glucose-6-phosphate isomerase (GPI) was identified as a direct target of miR-485-5p. creator: Haitao Lu creator: Yunhua Zhao creator: Yanli Zhang creator: Shaomin Shi creator: Huanrong Hu creator: Xuefei Li creator: Yandong Niu creator: Haihua Qi creator: Shang Ji creator: Xinsuo Duan creator: Yaling Liu uri: https://doi.org/10.7717/peerj.19284 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Lu et al. title: Chemical analysis and angiotensin I-converting enzyme inhibitory activity of enzymatic hydrolysates derived from meat of goat-kids with supplemental selenium link: https://peerj.com/articles/19261 last-modified: 2025-04-22 description: BackgroundThe effects of selenium (Se) on animal health due to its antioxidant and immune system regulatory properties are very well-documented. However, there is still a lack of scientific evidence about the effect of Se on muscle tissue. Se supplementation in ruminants will enhance the antioxidant activity of myocytes and increase angiotensin-converting enzyme (ACE) inhibitory activity. Generating bioactive peptides derived from meat could prevent the production of angiotensin II, a key player in the development of cardiovascular diseases.MethodsForty-five suckling goat kids were randomized into one of three groups: (1) CG: group without Se supplemented in the diet; (2) GSS: group with a single injectable dose subcutaneously of sodium selenite (Na2SeO3) at a dose of 0.25 mg/kg of body weight; (3) GSM: group with an oral administration of selenomethionine (SeMe) at a dose of 0.3 mg/kg of body weight). The effect of both sources of Se was evaluated on the proximate composition of meat and liver and the angiotensin I-converting enzyme inhibitory activity of meat-derived enzymatic hydrolysates.ResultsThe kids-goat meat from the GSM group had a higher protein content (p < 0.05). The fat content gradually increased over time in the treatment GSM, which increased ca. two-fold (from 1.77 to 3.68). The degree of hydrolysis of the meat samples decreased (p < 0.05) in the treatments supplemented with Se (GSS and GSM). The degree of hydrolysis increased significantly (p < 0.05) over time in treatments with Se (GSS and GSM). The electrophoretic patterns of the enzymatic hydrolysates at two h showed a molecular weight between 23.44 and 27.5 kDa, the bands with more intensity. At 21 d of slaughter, a major degree of hydrolysis was observed in the treatments supplemented with Se (GSS and GSM) compared to the CG. Meat protein content and rate of ACE inhibition after hydrolysis improved (50% and 2%, p < 0.05) with GSM at 7 d of slaughter. After hydrolysis, the IC50 of the selenium-supplemented groups decreased (p < 0.05) the amount of CAE and IC50 values.ConclusionThis is the first report describing the ACE inhibitory activity of bioactive peptides derived from goat-kids meat with supplemental. These results indicate the presence of ACE in goat meat; however, the percentage of ACE inhibition after hydrolysis was only improved with selenomethionine dosing at 7 days of slaughter. The study’s novelty indicates that supplemented selenium synergized with ACE in goat meat. It is necessary to continue these studies to identify specific bioactive peptides, antioxidant activities, and goat meat’s biological and functional value, considering it a functional food that can prevent metabolic diseases and be a healthy alternative for the human population. creator: Silvia C. Pérez-Ramirez creator: Rosy Cruz-Monterrosa creator: Mayra Diaz-Ramirez creator: Erika B. León-Espinosa creator: José E. Aguilar-Toalá creator: Monzerrat Rosas-Espejel creator: J. Efren Ramirez-Bribiesca uri: https://doi.org/10.7717/peerj.19261 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pérez-Ramirez et al. title: eDNA metabarcoding shows highly diverse but distinct shallow, mid-water, and deep-water eukaryotic communities within a marine biodiversity hotspot link: https://peerj.com/articles/19249 last-modified: 2025-04-22 description: As the impact of human activities continues to move beyond shallow coastal waters into deeper ocean layers, it is fundamental to describe how diverse and distinct the eukaryotic assemblages from the deep layers are compared to shallow ecosystems. Environmental DNA (eDNA) metabarcoding has emerged as a molecular tool that can overcome many logistical barriers in exploring remote deep ocean areas. We analyzed shallow water samples (<30 m) collected via SCUBA diving and adjacent deeper samples (mid-water 30–150 m, deep-water >200 m) obtained with Niskin samplers within 16 locations in a recognized hotspot of marine biodiversity (Gulf of California, Mexico). We sequenced an eDNA metabarcoding library targeting a fragment of the COI gene of eukaryotes. We demonstrated that the diversity of operational taxonomic units (OTUs) did not peak at shallow coastal regions and that the mid-water and deep-water benthic and pelagic samples had similar levels of biodiversity compared to shallow sites, but detected a significant vertical zonation between shallow and deeper habitats. Our results suggest that the deep refugia hypothesis, which posits that deep environments protect biodiversity during environmental changes, enabling species to survive and repopulate shallower regions, is not supported for most taxa and only applies to about a third (34.9%) of the 5,495 OTUs identified that were shared between the shallow and deeper layers. In comparison, the rest of the taxa were exclusive to either shallow (30.8%) or deeper zones (34.28%). The observation that mid-water and deep-water benthic and pelagic communities were as rich but quite distinct as shallow communities supports extending spatial management and conservation tools to deeper habitats to include a significant fraction of unique phylogenetic and functional diversity. creator: Patricia Cerrillo-Espinosa creator: Luis Eduardo Calderón-Aguilera creator: Pedro Medina-Rosas creator: Jaime Gómez-Gutiérrez creator: Héctor Reyes-Bonilla creator: Amílcar Leví Cupul-Magaña creator: Ollin Tezontli González Cuellar creator: Adrian Munguia-Vega uri: https://doi.org/10.7717/peerj.19249 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cerrillo-Espinosa et al. title: An integrated health management model to improve the health of professional e-sports athletes: a literature review link: https://peerj.com/articles/19323 last-modified: 2025-04-21 description: BackgroundWith the rapid development of the esports industry, an increasing number of esports athletes face various health issues due to occupational characteristics such as a prolonged sedentary lifestyle, high-intensity training, and multi-cycle competitions. Effectively managing and improving the health status of esports athletes has become an urgent need. As a systematic and multidisciplinary collaborative management strategy, the Integrated Health Management Model has been widely applied to various occupational groups, but its application among esports athletes has not yet been systematically reviewed.MethodologyThis study adopted a narrative literature review method to collect and analyze the existing literature on the health issues and health management of esports athletes. This study aimed to identify the major health problems of esports athletes and explore the role of the Integrated Health Management Model in improving and preventing these health problems.ResultsThis study resulted in two main findings: (1) The main health issues faced by esports athletes include musculoskeletal disorders, visual fatigue, metabolic disorders, and psychological stress; (2) the Integrated Health Management Model, through the integration of physical activity and fitness training, psychological counseling, ergonomic optimization, vision protection, and health education, can effectively alleviate common health problems among esports athletes and promote overall health improvement.ConclusionThe Integrated Health Management Model can effectively improve the overall health level of esports athletes through the integration and synergy of multiple strategies. creator: Yunxuan Mi creator: Siyuan Zhao creator: Fangyuan Ju uri: https://doi.org/10.7717/peerj.19323 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mi et al. title: Barriers to seeking consultation at public service and medical facilities among pregnant and postpartum women in Japan: a cross-sectional study link: https://peerj.com/articles/19320 last-modified: 2025-04-21 description: BackgroundPregnant and postpartum women often experience parenting problems which may affect their mental health and children’s health and development. However, their ability to seek consultation at public service or medical facilities remains unclear. This study aimed to identify the characteristics associated with women who refrain from visiting these facilities for consultation and their reasons for it.MethodsThis cross-sectional internet-based survey was conducted in Japan between July and August 2021, involving 7,326 women (1,639 pregnant and 5,687 postpartum women). The study outcome was defined as refraining from seeking consultation on family or parenting issues at public service or medical facilities despite a perceived need. We identified women’s characteristics associated with refraining from consultation using multivariable logistic regression and conducted a descriptive analysis of 13 listed reasons for refraining from the consultation.ResultsThe percentage of women who reported refraining from seeking consultation at public service or medical facilities was 8.6% and 5.1%, respectively. Common factors associated with refraining from seeking consultation at these facilities included having a child(ren) and being in the postpartum period, low health literacy, lack of partner support, and current disability. “Difficulty taking child(ren) to the consultation” and “uncertainty about the seriousness of the problem” were major reasons for refraining from consultation.DiscussionHealthcare workers at public service and medical facilities should offer prenatal education on the importance of seeking help. An online consultation service and an improved facility environment may mitigate women’s perceived barriers to seeking consultation. creator: Sumiyo Okawa creator: Kaori Seino creator: Hiroyasu Iso creator: Takahiro Tabuchi uri: https://doi.org/10.7717/peerj.19320 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Okawa et al. title: Knowledge and attitudes toward pediatric pain management among nursing interns from a selected university in Riyadh, Saudi Arabia: a descriptive cross-sectional quantitative study link: https://peerj.com/articles/19288 last-modified: 2025-04-21 description: IntroductionPediatric pain is often not addressed properly in the literature, which suggests a research gap in pediatric health-care providers’ knowledge and attitudes toward the treatment of pain experienced by children in various health-care settings. To improve future practice in this area, nursing interns should be well versed in pediatric pain assessment and management to improve pediatric pain management practices in collaboration with other health-care professionals.PurposeThis study aimed to assess the levels of knowledge and attitudes toward pediatric pain management among nursing interns at a specific academic institution.MethodsThis descriptive cross-sectional quantitative study employed an online questionnaire to collect data from 119 female nursing interns in Riyadh, Saudi Arabia. In addition to collecting the participants’ demographic profiles, the questionnaire gathered data using the Pediatric Nurses’ Knowledge and Attitudes Survey Regarding Pain instrument. Descriptive and inferential statistics were calculated using SPSS for Windows (v. 21.0).ResultsThe nursing interns’ overall knowledge and attitudes toward pediatric pain management were found to be poor, with a mean score of 36.59% (standard deviation, 13.2).ConclusionAdditional education and clinical training for nursing interns is essential to enhance their knowledge and attitudes toward pediatric pain management. creator: Sumathi Robert Shanmugam creator: Amany Anwar Saeed Alabdullah creator: Maha Hanis Alenezi creator: Shahad Khalid Aldughyshim creator: Maryam Fahad Alnemer creator: Wedad Khalid Almutairi creator: Ghaida Saad Alhadyan creator: Rasha Zaid Albugomi creator: Fatimah Abdullah Alkhulayfi uri: https://doi.org/10.7717/peerj.19288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shanmugam et al. title: Effects of phosphorus-solubilizing fungi on bulb quality and the Fritillaria taipaiensis rhizosphere soil environment link: https://peerj.com/articles/19283 last-modified: 2025-04-21 description: BackgroundFritillaria taipaiensis P.Y. Li is commonly used in Chinese medicine for its cough-suppressing and expectorant properties. Due to over-excavation and ecological damage, the wild resources of F. taipaiensis have suffered serious damage. Understanding and improving the inter-root soil environment plays an important role in improving the success rate of artificial cultivation of F. taipaiensis and the quality of medicinal herbs.MethodsThis study employed a pot experiment to inoculate three strains of phosphorus-solubilizing fungi from the Aspergillus genus for a total of seven treatment groups, with sterile physiological saline serving as the control group (CK). The research aims to examine the impact of inoculating phosphorus-solubilizing fungi on the biomass of F. taipaiensis, alkaloid concentration in its bulbs, and characteristics of the rhizosphere soil environment. The specific inoculation treatments included: Aspergillus tubingensis (Z1); Aspergillus niger (Z2); Aspergillus fumigatus (Z3); a combination of A. tubingensis and A. niger (Z12); a combination of A. niger and A. fumigatus (Z13); a combination of A. tubingensis and A. fumigatus (Z23); and a combination of all three fungi, A. tubingensis, A. niger, and A. fumigatus (Z123).ResultsInoculation with phosphorus-soluble fungi significantly increased the biomass of F. taipaiensis, and the largest increase was in the Z123 group, which was 62.85% higher than that of the CK group. Total alkaloid content increased the most (0.11%) in the Z3 group, which was an 83.87% increase compared with the CK group. The total content of monomer alkaloids in the Z3, Z13, and Z123 groups increased by 10.53%, 12.48%, and 9.61%, respectively, compared with those in the CK group, indicating that the quality of F. taipaiensis could be significantly improved after applying phosphorus-solubilizing fungi. The soil environment improved after inoculation with different phosphorus-solubilizing fungi. The Z23 and Z123 groups had the greatest effect on the rhizosphere soil bacteria and Actinomyces. Overall, the soil nutrient content of the Z13 group increased the most, and the contents of available phosphorus, available potassium, available nitrogen, total phosphorus, and organic matter increased by 47.71%, 27.36%, 26.78%, 25.13%, and 31.72%, respectively, compared with those in the CK group.ConclusionThese results show that the treatment groups that included different combinations of strains were superior to the single-strain treatment groups, and the Z123 group was the best treatment group when considering bulb biomass and alkaloid and soil nutrient contents. Applying phosphorus-solubilizing fungus fertilizer is highly feasible during F. taipaiensis production in the field. creator: Xueyang Ren creator: Lin Yuan creator: Huan Yao creator: Yuhan Wang creator: Huan Wang creator: Dongqin Guo creator: Nong Zhou uri: https://doi.org/10.7717/peerj.19283 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ren et al. title: A study of diel and seasonal patterns of loss of commercial lychee fruits to vertebrate frugivores: implications for mitigating a human-wildlife conflict link: https://peerj.com/articles/19269 last-modified: 2025-04-21 description: Human-wildlife conflicts pose a growing threat to biodiversity, particularly when the targeted species plays an ecological keystone role. Mauritius has repeatedly mass-culled an endemic and threatened flying fox species (the Mauritian flying fox; Pteropus niger) failing the intended objectives of crop protection and elevating the species’ extinction risks. In this context, the ecology of this species should be better understood to develop non-lethal management strategies. Here we investigated foraging patterns of vertebrate frugivores over 24 hour cycles in lychee orchards and backyard gardens. We assessed all agents of damage (mainly flying fox, alien bird, alien mammal) and the temporal variation of flying fox and bird foraging (take and amount eaten relative to fruit ripeness) on lychee trees. The most important frugivores foraging on lychees were flying foxes (78.3%) and birds (16.1%), namely ring-necked parakeets (Alexandrinus krameri), red-whiskered bulbuls (Pycnonotus jocosus), village weavers (Ploceus cucullatus) and common mynas (Acridotheres tristis) while damage by alien mammals was negligible (<1%). Flying foxes consumed more fruits in the early night (59%) compared to the late night and this was statistically significant in one orchard and backyards. However, the difference in damage was on average one to three fruits per tree per night. Bird damage at both orchards was highest during the first half of the day (64%). Flying foxes ate fewer fruits towards the end of the fruiting season while birds followed the opposite trend. As fruit ripeness increased from unripe to fully ripe, flying foxes ate 39–42% more lychee pulp per fruit at the two orchards. Parakeets ate 7% more fruit pulp with increasing ripeness at one orchard only. Deliberate disturbances involving smoke, noise or light to deter flying foxes were common in orchards. The weak difference in the extent of flying fox damage to fruits between early and late night suggested at best minor advantages of concentrating deliberate disturbances in early night, and that netting would be a better strategy as it would also protect against diurnal frugivores. Additionally, trees should be protected from the sixth week after fruit set as most damage occurred when fruits were unripe. Such an improved timing of crop protection should play an important role in reducing fruit losses and thereby alleviate the human-wildlife conflict around the flying fox’s diet. creator: Geetika Bhanda creator: Ryszard Z. Oleksy creator: Raphaël D. Reinegger creator: Cláudia Baider creator: F.B. Vincent Florens uri: https://doi.org/10.7717/peerj.19269 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bhanda et al. title: Occult zonulopathy detected during cataract surgery in patients with acute primary angle closure: a retrospective study link: https://peerj.com/articles/19330 last-modified: 2025-04-18 description: BackgroundWhether occult zonulopathy contributes to the development of acute primary angle closure (APAC) remains elusive. This study aimed to determine the association between occult zonulopathy detected during cataract surgery and APAC and to investigate the biometric characteristics of APAC patients with or without occult zonulopathy.MethodsRetrospective case-control study. A total of 27 Chinese unilateral APAC subjects and 132 control subjects with comprehensive ophthalmic examinations were recruited. Occult zonulopathy was identified with the intraoperative signs during cataract surgery. The proportion of occult zonulopathy was compared between the APAC and control groups. A multivariate logistic analysis was conducted to determine the association between occult zonulopathy and APAC. The ocular biometric parameters were compared between APAC and the contralateral eyes in APAC patients with or without occult zonulopathy.ResultsAPAC patients (63.0%) had a significantly larger proportion of occult zonulopathy than control subjects (1.5%, P < 0.001). In the multivariate logistic analysis, occult zonulopathy was significantly associated with APAC after adjusting the axial length (AL) and sex (OR = 126.49, 95% CI [20.89–766.02]; P < 0.001). Compared to contralateral eyes, shallower central anterior chamber depth, more anterior lens position and relative lens position were found in APAC eyes both with and without occult zonulopathy (all P < 0.05), but no difference in AL and lens thickness.ConclusionA larger proportion of occult zonulopathy was significantly associated with APAC. Occult zonulopathy could be a risk factor for APAC by inducing forward shifting of the lens. creator: Jiawei Chen creator: Xiang-Ling Yuan creator: Xinyue Zhang creator: Yanjun Huang creator: Xiaona Huang creator: Xuanchu Duan uri: https://doi.org/10.7717/peerj.19330 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Acute effects of optimal power load flywheel half-squat training on lower limb explosive power under different load volumes link: https://peerj.com/articles/19321 last-modified: 2025-04-18 description: BackgroundTo explore the effects of flywheel half-squat interventions with different volumes of optimal power load (OPL) on post-activation performance enhancement (PAPE) in countermovement jump (CMJ) height and 30 m sprint performance among collegiate athletes.MethodsA randomized crossover design was employed, recruiting 20 collegiate athletes to participate in the experiment. After determining each participant’s OPL, four different training load schemes were arranged for eight formal experiments, including four CMJ tests and four 30 m sprint tests. The differences between baseline and post-intervention at 0, 4, 8, and 12 min were compared. A two-factor repeated measures ANOVA was used for data analysis, with a significance level set at P < 0.05, and Cohen’s d value was used to represent the effect size (ES).Results(1) The improvement in CMJ height for different flywheel half-squat load volumes peaked at 8 min of recovery. In terms of ES, the improvement was Group B > Group C > Group A. (2) The improvement in 30 m sprint speed for Group A peaked at 4 min post-intervention, while the improvement for Groups B and C peaked at 8 min post-intervention. In terms of ES, the improvement was Group B > Group C > Group A.ConclusionUsing two sets × six repetitions of OPL flywheel half-squat arrangement can induce a more reliable PAPE effect compared to higher load volumes. However, when using half-squats as a pre-stimulation exercise, the PAPE effect on CMJ height is superior to that on 30 m sprint speed. creator: Haonan Qi creator: Mushuai Hao creator: Boyang Qu creator: Liang Zhao creator: Wei Han uri: https://doi.org/10.7717/peerj.19321 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Qi et al. title: Therapeutic strategy and prognostic analysis of inflammatory myofibroblastic tumor in the head and neck: a retrospective study link: https://peerj.com/articles/19315 last-modified: 2025-04-18 description: ObjectiveThis study aimed to investigate the clinical features, treatment methods, and prognosis of head and neck inflammatory myofibroblastic tumor (HNIMT).MethodsA retrospective analysis was conducted using the clinical data of 12 HNIMT patients who were admitted to Shanxi Cancer Hospital between January 2016 and December 2023. This analysis focused on their clinical manifestations, pathological characteristics, treatment strategies, and prognosis.ResultsAmong the 12 cases analyzed, four involved inflammatory myofibroblastic tumors (IMT) located in the nasal sinuses or nasopharynx, with symptoms including nasal congestion, rhinorrhea, and maxillofacial swelling. Two cases each in the salivary glands and oral cavity presented as localized, painless masses. One right cervical IMT case also presented as a painless lump. Two laryngeal IMT cases had hoarseness, and one subglottic endotracheal IMT case showed inspiratory dyspnea. All patients received surgery, with postoperative pathology confirming IMT. During follow-up, four cases recurred. Finally, nine patients were disease-free, two survived with disease, and one died.ConclusionsHNIMT is a rare, low-grade malignant or borderline tumor that is generally associated with a favorable prognosis. Accurate diagnosis relies on pathological examination, and surgical resection remains the primary treatment for HNIMT. The need for adjuvant therapy following surgery should be determined by clinicians based on tumor location, surgical approach, and the presence of high-risk factors. creator: Feng Liu creator: Yanchao Qin creator: Zhiwei Zhang creator: Mengru Li creator: Bowei Feng creator: Wei Ding creator: Shubin Dong uri: https://doi.org/10.7717/peerj.19315 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Ex-situ avian sex skews: determinants and implications for conservation link: https://peerj.com/articles/19312 last-modified: 2025-04-18 description: With over half of all avian species in decline globally, zoo-based recovery programs are increasingly relied upon to save species from extinction. The success of such programs not only rests with political will, but also in our understanding of species’ breeding biology and how individuals and populations respond to changes in their environment. Sex skews, that is, an imbalance in the optimal number of males to females, is an underlying mechanism of population decline in some threatened species. Ex-situ (i.e., zoo-based) management practices will need to become more efficient to support the growing number of conservation reliant species and manage sex skews to amend, repair and restore population stability both in- and ex-situ. In this article, we analysed data from over 182,000 birds in global ex-situ collections. We interpreted sex ratio variation by observing the proportion of males within and between orders, International Union for Conservation of Nature (IUCN) threat status and housing inside and outside of a species’ natural range. Overall, our results showed that male-biased sex skews are more prevalent ex-situ than they are in the wild and although they vary greatly at the institutional level, were closer to parity at a global level. The variation amongst threat status and housing outside of range were less significant. These findings have implications for the conservation management of threatened birds and the potential of ex-situ populations to function with maximum effect in an integrated management system. creator: Clancy A. Hall creator: Gabriel C. Conroy creator: Dominique A. Potvin uri: https://doi.org/10.7717/peerj.19312 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hall et al. title: Tailored lymph node dissection in right hemicolectomy: a retrospective study focusing on the anterior tissue of the superior mesenteric vein surgical trunk link: https://peerj.com/articles/19290 last-modified: 2025-04-18 description: BackgroundThe optimal extent of lymph node dissection in right hemicolectomy for colon cancer remains a topic of debate. This study aimed to refine lymph node dissection strategies by investigating the histopathological characteristics of the anterior tissue of the superior mesenteric vein (SMV) surgical trunk.MethodsOne hundred sixty-two patients underwent surgery, with their medial resection border determined to be either to the right or left of the SMV. Pathological and perioperative variables were assessed, and the anterior tissue of the SMV was analyzed to quantify lymph nodes and nerve fibers.ResultsOf the patients included, 84 were in the SMV-right group and 78 in the SMV-left group. After propensity score matching (PSM), the SMV-left group with dissection extending to the left side of the SMV and removal of the anterior tissue of SMV surgical trunk, retrieved more lymph nodes (36.9 vs. 26.8, P < 0.001) than the SMV-right group. However, there was no difference in node-positive staging. The SMV-left group also experienced more postoperative complications (16.7% vs. 1.7%, P = 0.011) and prolonged postoperative defecation times (4.2 vs. 3.5, P = 0.035), accompanied by a higher resection of nerve fibers (12.1 ± 4.2/case). Multivariate analysis identified tumor location above the ileocolic vein (ICV) root and elevated preoperative CA 19-9 levels as independent risk factors for metastasis to main lymph nodes.ConclusionRight hemicolectomy with extended lymph node dissection improves lymph node retrieval but increases complication risks and prolongs bowel recovery time. For patients with tumors located below the ICV root, a more limited dissection with the right side of the SMV as the medial boundary may be a preferable option, given the low rate of main lymph node metastasis. creator: Xianda Chi creator: Xuejie Li creator: Qiong Liang creator: Pinjie Huang creator: Jianpei Liu uri: https://doi.org/10.7717/peerj.19290 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xianda et al. 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. title: Analysis of factors influencing hookwire dislodgement in CT-guided hookwire localization: a retrospective study using variable importance analysis with a random forest model link: https://peerj.com/articles/19231 last-modified: 2025-04-16 description: BackgroundVideo-assisted thoracoscopic surgery (VATS) is a minimally invasive and safe procedure. However, lung deflation during the operation causes anatomic landmark distortion, complicating small nodules detection. Computed tomography (CT)-guided hookwire localization promotes the success rates of VATS, but faces issues with hookwire dislodgement, potentially losing intraoperative tumor reference. This study was conducted to identify the relative importance ranking of potential factors influencing dislodgement in CT-guided hookwire localization.MethodsThis retrospective study reviewed 123 cases of CT-guided hookwire localization followed by VATS resection. Variables analyzed included sex, age, nodule size, emphysema, chest wall/muscle/total depth, distance from the nodule (DNP) or wire tip to the pleura (DWP), procedure time, nodule subtypes, multiple localization, post-procedural hemorrhage, pneumothorax, nodule penetration, and time intervals between completion of procedure to initiation of surgery (PS interval). Variables were compared using chi-square tests or Mann-Whitney tests. A random forest model, enhanced with the Synthetic Minority Over-sampling Technique (SMOTE) for oversampling, was employed to determine the relative importance of each variable. The relative importance of variables was presented using the mean decrease Gini and mean decrease accuracy metrics. For sensitivity analysis, relative variable importance was analyzed using extreme gradient boosting (XGBoost) model, and the relative importance of variables was presented using the gain metric.ResultsAmong the 123 cases, dislodgement occurred in 15. In univariable analysis, only the PS interval was statistically significant (134.1 ± 73.1 vs. 104.1 ± 46.1 minutes in dislodgement or non-dislodgement, p = 0.031). The random forest and XGBoost model identified the top five important variables as the PS interval, DWP, DNP, total depth, and age. The top five factors demonstrated a distinct difference when compared to the other factors.ConclusionsThe study identified the PS interval as the most critical factor in hookwire dislodgement, along with DNP, DWP, total depth, and age. These results identified the presence of modifiable factors within the hospital and can assist practitioners and surgeons in recognizing the dislodgement risk of procedures based on various patient factors. creator: Kiook Baek creator: Jin Young Kim creator: Jung Hee Hong uri: https://doi.org/10.7717/peerj.19231 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Baek et al. title: The tadpole of Chiasmocleis altomontana (Anura: Microhylidae) link: https://peerj.com/articles/19220 last-modified: 2025-04-16 description: BackgroundDescribing the morphology of anuran larvae contributes towards filling gaps in taxonomy and natural history. This is especially relevant for explosive breeders, in which adults remain at the reproduction site for only a short period, while tadpoles may be more conspicuous. Here, we describe the larval external morphology and internal oral anatomy of the microhylid frog Chiasmocleis altomontana from near its type locality in southeastern Brazil.MethodsWe took 13 linear morphometric measurements of 11 tadpoles between stages 35 and 39 from four ponds. To compare the larval external morphology of the genus, we also built a morphospace based on the log-shape ratio of linear measurements provided by the original descriptions. To impute missing data, we used a trait imputation method that considered the phylogenetic relationships and a Brownian Motion model of multivariate trait evolution. Finally, we provide novel quantitative and qualitative data on the tadpole of Chiasmocleis anatipes based on museum specimens.ResultsThe tadpole of C. altomontana is the largest among the Atlantic Forest species and the second largest of the genus, after C. anatipes. Like all species of the genus, the tadpole of C. altomontana is exotrophic, suspension feeder, Orton type II, and occurs in lentic temporary environments. Overall, C. altomontana shows subtle differences in dorsal fin height, dorsal fin insertion, tail tip, and snout in lateral view from its congeners. The spiracle of C. anatipes is ventral, single, covering the vent tube, as in all other microhylids. The species has a larger tail and interorbital distance than its congeners. All species of the Atlantic Forest clade are clustered together in the morphospace, suggesting little disparity, while those of the Amazonian clade are more spread, suggesting higher morphological disparity. Chiasmocleis altomontana was close to its sister species, Chiasmocleis mantiqueira, while C. anatipes differs greatly in terms of shape from the remaining species of the genus. Our results can improve our understanding of the morphological diversity of microhylid tadpoles and reduce the diversity shortfall in anuran larval forms. creator: Leandro B. C. Menezes creator: Marcos R. Severgnini creator: Tiago L. Pezzuti creator: Michel V. Garey creator: Diogo B. Provete uri: https://doi.org/10.7717/peerj.19220 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Menezes et al. title: Optimization of cultural conditions for pectinase production by Diaporthe isolate Z1-1N and its pathogenicity on kiwifruit link: https://peerj.com/articles/19207 last-modified: 2025-04-16 description: Diaporthe Z1-1N, the primary causal agent of soft rot disease in kiwifruit, exhibited higher pectinase activity compared to cellulase activity in both in vitro and in vivo incubation models. To gain deeper insights into the role of pectinases in the pathogenicity of this fungus, we evaluated the effects of incubation temperature (ranging from 18 to 38 °C), duration (1 to 7 days), and medium pH (4.0 to 9.0) on the activities of two crucial pectinases: polygalacturonase (PG) and polymethylgalacturonase (PMG). Our single-factor experiments revealed that the optimal conditions for maximizing PMG yield were a pH of 7.5 and a temperature of 28 °C, with peak activity occurring after three days of incubation. Notably, PG activity peaked on the fourth day under the same pH and temperature conditions. Under the optimal conditions identified through an orthogonal experimental design, PMG exhibited higher activity than PG. Further analysis showed that temperature was the most influential factor on PMG activity, followed by incubation duration and pH. The lesion size caused by the purified pectinase extracts was 50% the lesion size that caused by the fungal mycelium of Diaporthe Z1-1N. These findings underscore the significance of PG and PMG as key virulence factors in the pathogenicity of Diaporthe Z1-1N, providing a solid scientific basis for future research into the functions of these enzymes. creator: Shu-Dong Zhang creator: Ling-Ling Chen creator: Chao-Yue Li creator: Xiao-Qing Long creator: Xue Yang creator: Xiao-Duo He creator: Li-Wen Du creator: Heng-Feng Yang creator: Li-Zhen Ling uri: https://doi.org/10.7717/peerj.19207 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Azov-type spits: long-term monitoring of morphodynamics and vegetation in response to changing environment link: https://peerj.com/articles/18369 last-modified: 2025-04-16 description: BackgroundAzov-type spits (ATS) are unique landforms located along the Northern coast of the Sea of Azov (NA) that have no global analogs. They play a vital role in delivering essential ecosystem services and significantly contribute to the economy of southern Ukraine. ATS are highly sensitive and dynamically responsive to environmental changes, including global and local climate changes, rising sea levels, geological shifts in the Ukrainian crystalline shield, internal shifts in the Sea of Azov and various anthropogenic influences. These factors significantly shape the ATS, influencing their capacity to accumulate biogenic material and sediments, thereby impacting vegetation cover, resilience and functioning within their ecological context.MethodsOur study on ATS morphodynamics and vegetation changes is based on a 95-year dataset that incorporates retrospective vegetation maps (1927–1929, 1934, 1996–1999), grassland releves (1995–1999) and satellite imagery (1975–2022) using specific standardized indices (NDVI, NDWI, NDMI, Thermal). We employed Earth Remote Sensing (ERS) tools due to the impracticality of field research amid the ongoing military occupation of ATS territories. Climate change vulnerability was assessed by examining surface air temperature and precipitation changes for the periods 1900–2021 and 1991–2021.ResultsMeteorological data for NA shows a consistent climate change trend, including rising annual surface temperatures (1.14 ± 0.3 °C/100 years) and increased annual precipitation (98 ± 35 mm/100 years) over the last 120 years. Recent decades have witnessed intensified aridization, with up to a 15% drop in precipitation and a 0.8 °C per decade temperature increase, accompanied by increased evaporation. Our study reveals the ongoing transformation of ATS and their vegetation, primarily driven by inundation, aggravated by climate change and rising sea levels. ERS tools demonstrated their effectiveness in monitoring environmental changes under challenging circumstances, identifying general trends in the state of plant communities and validating our earlier forecasts for changes in vegetation cover. The increase in the area of halophytic meadow and marsh plant communities occurred alongside a certain decrease in their productivity, while the reduction in sandy-steppe plant community areas was accompanied by an increase in their productivity. The study provides a complex evaluation of the current anthropogenic impacts on the spits and their vegetation. creator: Oksana Tyshchenko creator: Volodymyr Tyshchenko creator: Svitlana Boychenko creator: Andrii Tarieiev creator: Vasyl Tkachenko uri: https://doi.org/10.7717/peerj.18369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tyshchenko et al. title: Potential relationship of the gut microbiome with testosterone level in men: a systematic review link: https://peerj.com/articles/19289 last-modified: 2025-04-15 description: The gut microbiome influences the metabolism and health of several organs beyond the gut and has recently gained considerable attention. The gut plays a central role in food digestion, absorption, nutrition, and general health. Hence, the gut microbiome has become a research subject for almost all health conditions. Imbalance or dysbiosis in the gut microbiome can cause different health issues in men, including reproductive and sexual health issues associated with testosterone levels. Several studies have investigated the relationship between the gut microbiome and testosterone levels. In this systematic review, we aimed to examine the relationship between the gut microbiome and testosterone levels in men. Literature searches were conducted by scanning PubMed, ProQuest, EBSCO, Taylor & Francis Online, Wiley Online, Springer Link, Web of Science, Google Scholar, and Science Direct databases for relevant keywords following the preferred reporting items for the systematic review guidelines. This review included cross-sectional, case-control, retrospective, and prospective cohort studies. Quality assessment was conducted using the Newcastle-Ottawa Scale. We found a significant positive correlation between the gut microbiome and testosterone levels in men. Several microbes play substantial roles in testosterone production. Mechanisms have been proposed as factors that contribute to testosterone levels, namely the hypothalamus-pituitary-gonad axis modulation, androgen metabolism, and intestinal homeostasis, by balancing the bone morphogenic protein (BMP) and the Wnt diverse microbiome. Ruminococcus showed a stronger correlation with testosterone levels than other microorganisms. The gut microbiome has complex correlations with testosterone metabolism. However, the microbiome with the most significant influence on testosterone levels cannot be easily identified and requires further research. creator: Cennikon Pakpahan creator: Geraldo Laurus creator: Markus Christian Hartanto creator: Rajender Singh creator: Ankur Saharan creator: Darmadi Darmadi creator: Andri Rezano creator: Gito Wasian uri: https://doi.org/10.7717/peerj.19289 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pakpahan et al. title: Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data link: https://peerj.com/articles/19270 last-modified: 2025-04-15 description: The regulation of residual feed intake (RFI) in beef cattle involves brain-gut mechanisms due to the interaction between neural signals in the brain and hunger or satiety in the gut. RNA-Seq data contain an extensive resource of untapped SNPs. Therefore, hypothalamic and duodenal tissues from ten extreme RFI individuals were collected, and transcriptome sequenced in this study. All the alignment data were combined according to RFI, and the SNPs in the same group were identified. A total of 270,410 SNPs were found in the high RFI group, and 255,120 SNPs were found in the low RFI group. Most SNPs were detected in the intronic region, followed by the intergenic region, and the exon region accounts for 1.11% and 1.38% in the high and low RFI groups, respectively. Prediction of high-impact SNPs and annotation of the genes in which they are located yielded 83 and 97 genes in the high-RFI and low-RFI groups, respectively. GO enrichment analysis of these genes revealed multiple NADH/NADPH-related pathways, with ND4, ND5, and ND6 significantly enriched as core subunits of NADH dehydrogenase (complex I), and is closely related to mitochondrial function. KEGG enrichment analysis of ND4, ND5, and ND6 genes was enriched in the thermogenic pathway. Multiple genes, such as ATP1A2, SLC9A4, and PLA2G5, were reported to be associated with RFI energy metabolism in the concurrent enrichment analysis. Protein-protein interaction analysis identified multiple potential candidate genes related to energy metabolism that were hypothesized to be potentially associated with the RFI phenotype. The results of this study will help to increase our understanding of identifying SNPs with significant genetic effects and their potential biological functions. creator: Zonghua Su creator: Chenglong Li creator: Chaoyun Yang creator: YanLing Ding creator: Xiaonan Zhou creator: Junjie Xu creator: Chang Qu creator: Yuangang Shi creator: Cong-Jun Li creator: Xiaolong Kang uri: https://doi.org/10.7717/peerj.19270 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Su et al. title: Comprehensive analysis of groundwater hydrochemistry and nitrate health risks in the Baiquan basin, Northern China link: https://peerj.com/articles/19233 last-modified: 2025-04-15 description: Groundwater is a crucial water source and strategic resource, essential for sustaining both urban and rural livelihoods, supporting economic and social development, and maintaining ecological balance. This study investigates the hydrochemical properties and controlling factors of groundwater in the Baiquan basin (BQB) by analyzing water quality data collected during both dry and wet periods. Additionally, the suitability of groundwater for drinking and agricultural irrigation was evaluated. The findings reveal that groundwater in BQB is generally weakly alkaline and primarily consists of hard-fresh water. Although there are seasonal variations in the main ion concentrations, HCO3− and Ca2+ are the predominant anions and cations, respectively. Consequently, the hydrochemical type is mainly HCO3-Ca⋅Mg type, with a secondary classification of SO4⋅Cl-Ca ⋅ Mg. The hydrochemical composition is primarily influenced by the dissolution of carbonate and silicate minerals, as well as cation exchange processes. Additionally, it is affected by anthropogenic inputs, particularly from the use of agricultural fertilizers. The water quality assessment results indicated that all water samples are classified as either good or moderate, with a significant majority falling into the good category. Additionally, the northern section of the BQB exhibited lower entropy weight water quality index (EWQI) values during the dry season in comparison to the wet season. For irrigated agriculture, groundwater in the BQB serves as a high-quality water source for irrigation throughout both the dry and rainy seasons. Furthermore, non-carcinogenic risks are notably concentrated in the north-western and south-eastern regions of the study area. Health risks associated with nitrates in groundwater are elevated during the rainy season. Notably, non-carcinogenic risks for infants were significantly high across both seasons and substantially exceeded those for children and adults. These results provide valuable scientific insights for the management and development of groundwater resources in the BQB. creator: Bo Li creator: Di Wu creator: Dalu Yu creator: Changsuo Li creator: Jinxiao Wang creator: Liting Xing creator: Shuai Gao creator: Zhe Zhang creator: Mingguo Wang creator: Yuwei Wang uri: https://doi.org/10.7717/peerj.19233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Endozoicomonas dominance and Vibrionaceae stability underpin resilience in urban coral Madracis auretenra link: https://peerj.com/articles/19226 last-modified: 2025-04-15 description: Coral resilience varies across species, with some exhibiting remarkable stability and adaptability, often mediated by their associated microbiomes. Given the species-specific nature of coral-microbiome interactions, investigating the microbiomes of urban-adapted corals provides critical insights into the health, dynamics, and functioning of coral holobionts. In this study, we examined the microbiome of Madracis auretenra, a Caribbean coral from Santa Marta, Colombia, across contrasting environmental conditions. Over two years, we compared the microbiomes of healthy and stressed coral colonies from two distinct reef habitats—urban and protected—using 16S rRNA gene sequencing (V4 region) to assess microbial diversity. Our findings revealed microbial richness and diversity were primarily influenced by seasonal and local factors rather than host-specific traits such as interaction with algae, health status, or microhabitat. These variations were not substantial enough to disrupt the overall microbial community structure, which remained stable across temporal and spatial scales. Dominant taxa included Endozoicomonas, along with Vibrionaceae and Rhodobacteraceae, which form dense ecological interaction networks. Notably, nutrient and oxygen levels emerged as key drivers of microbiome fluctuations, yet Vibrionaceae populations exhibited exceptional temporal stability. These findings highlight the presence of a well-structured and resilient coral microbiome with minimal seasonal variability, even in urban-influenced environments. We propose that the dominance of Endozoicomonas and the stability of Vibrionaceae populations play a pivotal role in maintaining microbiome balance, ultimately contributing to the ecological resilience of M. auretenra in dynamic reef habitats. creator: Jordan Ruiz-Toquica creator: Andrés Franco Herrera creator: Mónica Medina uri: https://doi.org/10.7717/peerj.19226 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ruiz-Toquica et al. title: Evidence of rare occurrences of the Phoenix effect in the Hawaiian corals Porites compressa and Montipora capitata following mortality induced by a marine heatwave link: https://peerj.com/articles/19225 last-modified: 2025-04-15 description: Coral bleaching is a common stress response to extreme temperatures experienced during marine heatwaves. Bleached corals are left vulnerable without the nutritional support of their algal symbionts, and can often suffer partial or complete mortality. Bleaching-induced mortality is often accompanied by colonization of turf algae over the dead coral skeleton, which can be difficult for corals to regrow over. The Phoenix effect is a phenomenon of rapid recovery of live coral tissue following mortality, which is hypothesized to occur via the regrowth of tissue from deep within the coral skeleton that expands over the top of dead portions. Here, we found that the Hawaiian corals Porites compressa and Montipora capitata can display rapid tissue recovery suggestive of the Phoenix effect. During a marine heatwave that occurred in 2015 in Kāne’ohe Bay, Hawai’i, USA, 237 individuals (including bleached and non-bleached phenotypes) were identified and monitored for mortality and recovery over the next 2–7 years. Nearly 16% of P. compressa individuals and 34% of M. capitata exhibited substantial partial mortality, and approximately half of these affected individuals of each species had bleached during the heatwave. Partial mortality following the 2015 heatwave was followed by turf algae colonization over the exposed skeleton. Of the colonies with substantial mortality, six colonies (10% of affected individuals; five P. compressa and one M. capitata) subsequently recovered to over 90% live coral tissue within 2 years (2017), with an additional three colonies (two P. compressa and one M. capitata) recovering within 4 years of the 2015 marine heatwave (2019). We qualify colonies with rapid tissue recovery as those that meet two criteria: (1) substantial partial mortality (≥40%) in the first 12 months following the initial 2015 marine heatwave, and (2) recovery of any amount of live tissue at anytime before 2022. Interestingly, only colonies that had bleached in 2015 exhibited rapid tissue recovery. A consecutive, yet less severe marine heatwave occurred in 2019, and none of the previously recovered colonies observed experienced significant tissue loss, suggesting these individuals remained resilient amidst a secondary heat stress exposure. This phenomenon is an example of remarkable recovery and resilience that may be informative for further study of mechanisms of coral tissue regeneration in two important reef-building coral species. creator: Katelyn G. Jones creator: Katie L. Barott uri: https://doi.org/10.7717/peerj.19225 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Jones and Barott title: Ginsenosides and gut microbiota: differential effects on healthy individuals and irritable bowel syndrome subtypes link: https://peerj.com/articles/19223 last-modified: 2025-04-15 description: BackgroundIrritable bowel syndrome (IBS) is a common gastrointestinal disorder with poorly understood mechanisms. Variations in gut microbiota composition are observed in different IBS subtypes. Ginsenosides have shown potential in alleviating IBS symptoms, but their interactions with gut microbiota in different IBS subtypes are not well studied.MethodsIn this study, we investigated the effects of ginsenosides on the gut microbiota of both healthy participants and participants suffering from IBS characterized by diarrhea (IBS-D) or constipation (IBS-C), using in vitro fermentation alongside 16S rRNA sequencing and bioinformatics analyses.ResultsThe analysis demonstrated that there were no statistically significant alterations in α- or β-diversity between the ginsenosides-treated and control groups across all models. However, the microbial composition assessment revealed the presence of 51 shared genera, with notable variations in composition and a significant enrichment of specific taxa. Specifically, the LEfSe analysis revealed that, following ginsenosides treatment, the healthy model groups exhibited significant enrichment of Stenotrophomonas and Achromobacter, while the IBS-D model groups demonstrated significant enrichment of Pseudomonas and Stenotrophomonas.ConclusionsThe results elucidate the distinctive microbial signatures associated with ginsenosides treatment across both healthy and IBS-D groups, underscoring the potential therapeutic efficacy of ginsenosides in modulating gut microbiota. This study highlights the necessity for further investigation into targeted microbiome therapies for IBS, which may facilitate the development of more personalized and efficacious treatment strategies for gastrointestinal health. creator: Zhi Du creator: Chengman Zhao creator: Jiabin Li creator: Yan Shen creator: Guofei Ren creator: Jieying Ding creator: Jing Peng creator: Xiaoli Ye creator: Jing Miao uri: https://doi.org/10.7717/peerj.19223 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Du et al. title: Multiple instance learning-based prediction of programmed death-ligand 1 (PD-L1) expression from hematoxylin and eosin (H&E)-stained histopathological images in breast cancer link: https://peerj.com/articles/19201 last-modified: 2025-04-15 description: Programmed death-ligand 1 (PD-L1) is an important biomarker increasingly used as a predictive marker in breast cancer immunotherapy. Immunohistochemical quantification remains the standard method for assessment. However, it presents challenges related to time, cost, and reliability. Hematoxylin and eosin (H&E) staining is a routine method in cancer pathology, known for its accessibility and consistently reliability. Deep learning has shown the potential in predicting biomarkers in cancer histopathology. This study employs a weakly supervised multiple instance learning (MIL) approach to predict PD-L1 expression from H&E-stained images using deep learning techniques. In the internal test set, the TransMIL method achieved an area under the curve (AUC) of 0.833, and in an independent external test set, it achieved an AUC of 0.799. Additionally, since RNA sequencing results indicate a threshold that allows for the separation of H&E pathology images, we further validated our approach using the public TCGA-TNBC dataset, achieving an AUC of 0.721. These findings demonstrates that the Transformer-based TransMIL model can effectively capture highly heterogeneous features within the MIL framework, exhibiting strong cross-center generalization capabilities. Our study highlights that appropriate deep learning techniques can enable effective PD-L1 prediction even with limited data, and across diverse regions and centers. This not only underscores the significant potential of deep learning in pathological artificial intelligence (AI) but also provides valuable insights for the rational and efficient allocation of medical resources. creator: Zhen Da creator: Heng Yang creator: Bianba Zhaxi creator: Kaixiang Sun creator: Guohui Bai creator: Chao Wang creator: Feiyan Wang creator: Weijun Pan creator: Rui Du uri: https://doi.org/10.7717/peerj.19201 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Da et al. title: Mehran vs. Mehran2 pre-procedure: which score better predicts risk of contrast-induced acute kidney injury in patients with acute coronary syndrome? link: https://peerj.com/articles/19166 last-modified: 2025-04-15 description: BackgroundContrast-induced acute kidney injury (CI-AKI) is a significant concern during percutaneous coronary intervention (PCI) procedures. The novel Mehran 2 pre-procedural risk score, an updated version of the original Mehran score, shows promise as a predictive tool. However, its effectiveness specifically in acute coronary syndrome (ACS) patients requires further investigation. This study aims to evaluate the performance of Mehran 2 pre-procedure risk score compared to original score in predicting CI-AKI risk in acute coronary syndrome patients undergoing PCI.Material and MethodsA prospective cohort study was conducted with patients with ACS undergoing PCI, who were followed up for 90 days (December 2019–February 2021). The Mehran 2 CI-AKI risk score with pre-procedure data was compared with the original Mehran score. Receiver operating characteristic (ROC) curve and area under the ROC curve (AUC-ROC) were used to evaluate the discriminative capacity.Results192 patients were analyzed and 33% (n = 64) developed CI-AKI. CI-AKI outcome was associated with advanced age, arterial hypertension, chronic kidney disease, troponin T, hemodynamic instability, serum hemoglobin, serum creatinine, and higher both Mehran scores. Both scores demonstrated good agreement. The original Mehran score demonstrated superior CI-AKI stratification with higher sensitivity (85.94%) and specificity (60.16%) compared to the Mehran 2 pre-procedural score (sensitivity 50%, specificity 75%). Significant differences were observed in the discriminative performance between both scores.ConclusionSociodemographic, clinical, and laboratory variables were associated with CI-AKI. The original Mehran score demonstrated more consistent discriminative capacity for predicting CI-AKI risk in ACS patients undergoing PCI compared to the Mehran 2 pre-procedural score. creator: Matheus Santos Moitinho creator: Dulce Barbosa creator: Attilio Galhardo creator: Adriano Caixeta creator: Eduesley Santana-Santos creator: Maximina Cunha creator: Beatriz Santana Prado creator: Cassiane Dezoti da Fonseca uri: https://doi.org/10.7717/peerj.19166 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Moitinho et al. title: CDCP1 knockdown suppresses PDGFRβ/AKT pathway-mediated vascular smooth muscle cell proliferation by inhibiting PDGFRβ endocytosis link: https://peerj.com/articles/19114 last-modified: 2025-04-15 description: CUB domain-containing protein 1 (CDCP1) is a type of cell surface glycoprotein that has been identified as being capable of regulating cell anchorage, migration, proliferation, and differentiation. However, the contributions of CDCP1 in intimal hyperplasia, specifically regarding the proliferation and migration of vascular smooth muscle cells (VSMC), are unclear. In this study, we analyzed CDCP1 expression on intimal hyperplasia through a focal carotid stenosis model in vivo. In vitro, we cultured mouse VSMCs and stimulated them with 20 ng/mL platelet-derived growth factor BB (PDGF-BB) for 24 h. Western blot analysis was performed to detect the expression of CDCP1 in the cells. Next, we knocked down the expression of CDCP1 in VSMCs and assessed its effects on cell proliferation and migration using CCK8 assays, EDU+ assay, and wound healing experiments. We then performed RNA-Seq analysis on the CDCP1-knockdown VSMCs. Based on the sequencing results, we utilized western blotting to investigate the impact of CDCP1 knockdown on the AKT signaling pathway. Additionally, we validated the interactions between Platelet-derived growth factor receptor (PDGFR)β with NEDD4, clathrin, and Rab5 using immunofluorescence and co-immunoprecipitation assays. The results discovered that CDCP1 levels were activated in the intimal hyperplasia tissues in vivo. CDCP1 knockdown significantly attenuated mouse VSMC proliferation and migration induced by PDGF-BB in vitro. Based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed proteins obtained from RNA-sequencing, we found that the knockdown of CDCP1 is related to the “PI3K-AKT signaling pathway”, “ubiquitin-mediated proteolysis”, and “endocytosis” pathways. The subsequent experiments demonstrated that CDCP1 knockdown inhibited AKT signaling pathway. CDCP1 knockdown promoted the binding of PDGFRβ and NEDD4, and PDGFRβ ubiquitin. Moreover, CDCP1 knockdown attenuated the binding of PDGFRβ to clathrin and Rab5. These data reveal that the absence of CDCP1 may enhance the binding of PDGFR to NEDD4 and promote the ubiquitination of PDGFR, thereby regulating the AKT signaling pathway and intimal hyperplasia. creator: Xin Ji creator: Xin Wang creator: Qianqian Dong creator: Wanqiu Li creator: Ning Zhou creator: Xiaole Yue creator: Dandan Zhao creator: Xiaolong Yang uri: https://doi.org/10.7717/peerj.19114 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ji et al. title: Changes in the spectrum of kidney diseases: a 14-year single-center retrospective renal biopsy study from southeast China link: https://peerj.com/articles/19302 last-modified: 2025-04-14 description: ObjectiveKidney disease has become a significant public health issue. Socioeconomic improvements and environmental changes in China have influenced the kidney disease spectrum. This study aims to examine the changing spectrum of biopsy-confirmed kidney diseases in a single center from southeastern China and explore their clinical-pathological correlations.MethodsPatients who underwent renal biopsy at the First Affiliated Hospital of Fujian Medical University from January 2010 to December 2023 were included in this retrospective study. Clinicopathological data were collected and analyzed.Results2,832 patients were enrolled. Primary glomerular diseases accounted for the majority of kidney diseases (69.0%), followed by secondary glomerular diseases, tubulointerstitial diseases, and others. Among primary glomerular diseases, membranous nephropathy (MN) was the most prevalent (34.9%), followed closely by IgA nephropathy (IgAN) (34.5%) and minimal change disease (18.5%), with an increasing trend for MN. For secondary glomerular diseases, lupus nephritis (34.3%), diabetic nephropathy (DN) (24.8%), and hepatitis B virus-associated nephropathy (HBVN) (9.0%) were the most common. HBVN showed a significant decrease, while DN increased annually. Nephrotic syndrome (NS) was the most frequent indication for renal biopsy (40.3%), followed by progressive chronic kidney disease (22.4%). MN (47.2%) was the leading pathology in NS, and IgAN (51.6%) was predominant in patients with proteinuria and hematuria.ConclusionsThe spectrum of kidney disease has changed within the last 14 years. The relative frequency of MN and DN increased significantly, while that of HBVN decreased significantly. These findings highlight the need for ongoing public health efforts tailored to the changing spectrum of kidney diseases. creator: Zishan Lin creator: Shidong Xie creator: Wenfeng Wang creator: Tao Hong creator: Bingjing Jiang creator: Caiming Chen creator: Xuan Tao creator: Dewen Jiang creator: Jianxin Wan creator: Hong Chen creator: Yanfang Xu uri: https://doi.org/10.7717/peerj.19302 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lin et al. title: Psidium guajava L. hydroethanolic extract as endodontic irrigant: phytochemical analysis, antioxidant activity, antimicrobial action and biocompatibility link: https://peerj.com/articles/19301 last-modified: 2025-04-14 description: BackgroundThe search for novel antimicrobial agents in Endodontics is constant to overcoming persistent infections. Psidium guajava L. is a medicinal plant little explored in Endodontics. The aim of this study was to produce hydroethanolic extract of P. guajava L. and to evaluate its phytochemical composition, antimicrobial and antibiofilm action against standard and clinical strains of Enterococcus faecalis and Candida albicans, and cytotoxicity and genotoxicity on human keratinocyte cultures (HaCaT cells). The findings provide new insights into the potential of P. guajava as an alternative endodontic antimicrobial agent, contributing to the development of more effective and biocompatible therapeutic strategies.MethodsP. guajava hydroethanolic extract was produced using young leaves of guajava and extracted using absolute ethanol and ultrapure water in a ratio (30 g:100 mL). The solid soluble, total flavonoid and total phenols content were determined. The chemical composition was determined via high-performance liquid chromatography (HPLC) analysis, then the free radical suppressive activity was assessed by determining the IC50 value, indicating the concentration required to eliminate 50% of free radicals. Later, the minimum inhibitory concentration (MIC) and minimum microbicidal concentration (MMC) of the extract was evaluated against the strains using clinical and laboratory standards institute (CLSI) guidelines (M27-S4 and M7-A9). Then, the antibiofilm activity was evaluated via MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay. Finally, the cytotoxicity of the extract was evaluated via Alamar Blue assay, and the genotoxicity via micronucleus assay on human keratinocyte cultures (HaCaT cells). Data were analyzed using ANOVA and Tukey’s test or Kruskal-Wallis and Dunn’s test.ResultsThe soluble solids content in the extract was 3.35%. Using the quercetin standard curve, the total flavonoid concentration was 0.130 ± 0.110 mg/mL. In addition, using standard curve for phenolic acids, the total phenolic concentration was 1.770 ± 1.540 mg/mL. HPLC analysis revealed peaks of rutin, quercetin and kaempferol as major flavonoids in the P. guajava L. extract. The extract demonstrated notable antioxidant activity, with an IC50 value of 10.39 µg/mL. The MMC values ranged 1.04–8.37 mg/mL. The extract at 8.37 mg/mL was effective in reducing the biofilms of standard and clinical strains of E. faecalis and C. albicans after 10 min. Cytotoxicity analysis revealed that all tested concentrations exhibited relatively low toxicity toward HaCaT cells. Genotoxicity assessment via the micronucleus assay indicated minimal DNA damage at all tested concentrations. Overall, P. guajava L. hydroethanolic extract at 8.37 mg/mL is the most effective concentration in reducing the biofilm of the standard and clinical strains of E. faecalis and C. albicans, while maintaining biocompatibility with HaCaT cultures. creator: Lara Steffany de Carvalho creator: Vanessa Marques Meccatti-Domiciano creator: Livia Ramos Dorta da Silva creator: Maria Cristina Marcucci creator: Cláudio Antonio Talge Carvalho creator: Amjad Abu Hasna creator: Luciane Dias de Oliveira uri: https://doi.org/10.7717/peerj.19301 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 de Carvalho et al. title: Behavioral adaptations of Caenorhabditis elegans against pathogenic threats link: https://peerj.com/articles/19294 last-modified: 2025-04-14 description: This review examines the behavioral adaptation mechanisms of Caenorhabditis elegans in response to pathogenic bacterial threats, emphasizing their ecological significance. It systematically explores how mechanisms such as avoidance behavior, transgenerational learning, and forgetting enable C. elegans to optimize its survival and reproductive strategies within dynamic microbial environments. C. elegans detects harmful signals through chemosensation and initiates avoidance behaviors. Simultaneously, it manages environmental adaptation and energy allocation through transgenerational memory and forgetting, allowing C. elegans to cope with selective pressures from environmental fluctuations. In contrast, pathogenic bacteria such as Pseudomonas aeruginosa and Salmonella influence C. elegans behavior through strategies such as toxin release and biofilm formation, highlighting the complex co-evolutionary dynamics between hosts and pathogens. Additionally, these pathogens employ “Trojan Horse-like” and “Worm Star” mechanisms to kill C. elegans, further complicating host-pathogen interactions. These processes are driven by behavioral adaptations, biochemical signaling, and evolutionary pressures, which emphasize the ecological niche of C. elegans within microbial ecosystems. C. elegans serves as a valuable model for studying host-pathogen interactions. This study provides crucial theoretical insights into adaptive evolution and ecosystem dynamics, offering valuable guidance for the development of biocontrol strategies and the effective management of microbial ecosystems. creator: Xin Zhao creator: Xinyu Li creator: Jiayi Gao creator: Shi Shen creator: Wei Zou uri: https://doi.org/10.7717/peerj.19294 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhao et al. title: The regulatory effect of blood group on ferritin levels in aging: a retrospective study link: https://peerj.com/articles/19281 last-modified: 2025-04-14 description: BackgroundFerritin plays a pivotal role in the ageing process. Previous studies have identified statistically significant differences in ferritin levels among various ABO blood groups. However, the interaction between the ABO blood group and ferritin levels during senescence remains underexplored.MethodsThis research was conducted as a retrospective study involving a cohort of 3,843 individuals aged 40 and over who underwent blood type and ferritin testing at Beijing Zhongguancun Hospital. Assumption testing is employed to assess the normal distribution of continuous variables in the context of regression analysis. Spearman correlation analysis was employed to examine the relationship between the non-normally distributed biochemical indicators and ferritin levels. Age was considered the independent variable, while gender and biochemical indicators related to ferritin served as control variables. Blood type was analyzed as a moderating factor to evaluate its impact on the relationship between age and ferritin levels.ResultsOur findings revealed a negative correlation between ferritin and age (ρ =  − 0.099, p < 0.001). Significant differences in ferritin levels were observed between genders (p = 0.005) and blood groups (p < 0.001). The influence of age on ferritin levels varied across different blood groups, particularly in individuals with blood types A (p = 0.003, β =  − 0.072) and B (p < 0.001, β =  − 0.110), where the negative association between age and ferritin was more pronounced.ConclusionABO blood type may influence ferritin levels as individuals age. Notably, in individuals with blood types A and B, the inverse relationship between age and ferritin levels was particularly significant among middle-aged and elderly individuals. These findings suggested the potential benefit of targeted iron supplementation for this population. creator: Ni Xiaolin creator: Fenghong Yao creator: Mingkang Pan uri: https://doi.org/10.7717/peerj.19281 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xiaolin et al. title: Downregulation of EB1 impedes Cx43 localization and cardiac conduction after hypothermic ischemia-reperfusion in rats link: https://peerj.com/articles/19276 last-modified: 2025-04-14 description: BackgroundHypothermic ischemia-reperfusion arrhythmia is a common complication after cardiopulmonary bypass heart surgery, which can lead to hemodynamic disorders and even sudden cardiac death and is still not effectively prevented. This study aims to investigate the role and mechanisms of EB1 in hypothermic ischemia-reperfusion arrhythmia.Methods4–6 week old male Sprague-Dawley (SD) rats were randomly assigned to four groups with a control group receiving no treatment. In the treatment groups, the rats received an injection of a negative control adenovirus (AAV9-CON) or an adenoviral vector containing Mapre1 gene (AAV9-EB1) or an equal volume of saline via the tail vein. After 4 weeks, untreated rat hearts underwent continuous isolated heart perfusion for 5 min, while the treatment groups were subjected to Langendorff isolated heart ischemia-reperfusion. The multi-electrode array (MEA) technique was used to measure the conduction heterogeneity of rat heart, evaluating the protective effects of EB1 overexpression against reperfusion arrhythmias. Additionally, histological staining and western blotting were used to explore the potential pathways by which EB1 exerts its anti-arrhythmic effects, potentially through promoting the localization of connexin 43 (Cx43) to the intercalated discs (IDs). Furthermore, western blot analysis was conducted to assess microtubule stability and evaluate the possible mechanism by which EB1 facilitates the localization of Cx43 to the IDs.ResultsFollowing ischemia-reperfusion, EB1 expression was downregulated, accompanied by a reduction in Cx43. Overexpression of myocardial EB1 reduced the incidence of reperfusion arrhythmias and shortened their duration, which was associated with improved myocardial conduction. Male SD rats injected with AAV overexpressing EB1 had significantly higher levels of both total myocardial Cx43 and gap junction Cx43 after ischemia-reperfusion compared to the non-overexpression groups. Histological staining revealed lateralization of Cx43 in ischemia-reperfusion myocardium, which was corrected by EB1 overexpression. Additionally, EB1 overexpression increased the distribution of Cx43 at the IDs, overall reducing Cx43 remodeling. Moreover, EB1 overexpression can also alleviate microtubule damage caused by ischemia-reperfusion, which may be an important mechanism for the transport of Cx43 to the IDs.ConclusionsEB1 downregulation following hypothermic ischemia-reperfusion was accompanied by a reduction in gap junction Cx43. EB1 overexpression improved cardiac conduction and reduced reperfusion arrhythmias by promoting Cx43 localization to IDs, facilitating gap junctions (GJs) formation. These findings contribute to the development of new therapeutic targets for reperfusion arrhythmias. creator: Chunlei Wen creator: Rongfeng Yang creator: Jing Yi creator: Ying Cao creator: Yuting Song creator: Li An creator: Zijun Wang creator: Hong Gao uri: https://doi.org/10.7717/peerj.19276 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wen et al. title: Treatment preferences of patients with chronic low back pain in physical therapy clinics in Saudi Arabia: a cross-sectional study link: https://peerj.com/articles/19274 last-modified: 2025-04-14 description: BackgroundLow back pain (LBP) is a prevalent musculoskeletal disorder that significantly contributes to disability and health care burden. Clinical practice guidelines (CPGs) recommend non-pharmacological interventions, such as those delivered by physical therapists, to improve clinical outcomes. Incorporating patient preferences into treatment decisions is essential for promoting patient-centered care and enhancing adherence to CPGs. This study aimed to explore the physical therapy treatment preferences of patients with chronic LBP (CLBP) in Saudi Arabia and to evaluate their alignment with CPG recommendations.MethodsThis cross-sectional survey-based study was conducted across three healthcare centers in Saudi Arabia. Patient preferences were assessed using a validated questionnaire that listed available physical therapy treatments for CLBP. The participants were provided with a standardized explanation of evidence-based treatment options based on the updated CPGs for LBP before selecting their preferred treatments. Data analysis included descriptive statistics and chi-square tests to assess the alignment of preferences with CPG recommendations.ResultsA total of 138 participants were included, with 60.1% of the selected treatments aligning with CPG recommendations (p < 0.001). Sociodemographic factors, such as sex, prior physical therapy experience, and body mass index (BMI), influenced treatment preferences. Exercise was the most preferred treatment, aligning with CPGs, while passive modalities, such as interferential therapy, were also frequently chosen despite not being recommended.ConclusionThis study highlights the importance of understanding patient preferences to improve adherence to CPGs and promote evidence-based care for CLBP. Educational interventions tailored to the cultural context can bridge the gap between patient preferences and evidence-based recommendations, empower patients, and enhance clinical outcomes. creator: Maryam Alasfour creator: Majd Bajnaid creator: Salhah Hobani creator: Muhammad Alrwaily uri: https://doi.org/10.7717/peerj.19274 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Alasfour et al. title: Effects of exercise intervention on executive function in children with overweight and obesity: a systematic review and meta-analysis link: https://peerj.com/articles/19273 last-modified: 2025-04-14 description: BackgroundWeight control in children depends on executive function. Previous studies have shown that exercise interventions can effectively improve children’s executive function. However, the effects of these interventions on children with overweight and obesity remain unclear and require further investigation. This systematic review and meta-analysis was conducted to evaluate the effects of exercise interventions on executive function-related indicators in children with overweight and obesity.MethodsRandomized controlled trials (RCTs) investigating the effects of exercise interventions on executive functions in children with overweight and obesity were included by searching PubMed, Web of Science, EMbase, Cochrane Library, ProQuest, Scopus, CNKI, China Wanfang, and VIP databases. The quality of the included studies was assessed using the Cochrane risk of bias assessment tool. RevMan 5.4 software was used for effect size pooling, forest plot creation, and subgroup analyses. Stata 16.0 software was employed for publication bias testing and sensitivity analysis. The evidence levels of the results were evaluated using the GRADEpro tool.ResultsThis meta-analysis included a total of 13 studies. The results indicate that exercise interventions may help improve executive functions in children with overweight and obesity. Specifically, inhibitory control (standardized mean (SMD) = −0.59, 95% confidence interval (CI) [−0.89 to −0.29], Z = 3.85, P < 0.001) and cognitive flexibility (SMD = −0.54, 95% CI [−1.06 to −0.01], Z = 2.01, P < 0.05) showed moderate effect sizes. Working memory exhibited a smaller effect size (SMD = 0.40, 95% CI [−0.69 to −0.10], Z = 2.61, P < 0.01), while attention did not show significant improvement (SMD = 0.13, 95% CI [−0.39 to 0.65], Z = 0.50, P > 0.05).ConclusionThe results of this meta-analysis indicate that exercise interventions have significant benefits for inhibitory control, working memory, and cognitive flexibility in children with overweight and obesity, but the impact on attention is not significant. Moreover, the effects of inhibitory control interventions are influenced by exercise duration, exercise intensity, exercise type, and age. creator: Pengfei Wang creator: Ying Meng creator: Jinnian Tong creator: Tiance Jiang uri: https://doi.org/10.7717/peerj.19273 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: The acidic latex protein from Hevea brasiliensis serves as an anionic antimicrobial peptide link: https://peerj.com/articles/19242 last-modified: 2025-04-14 description: BackgroundHev b5 is a unique acidic protein identified as an allergen in natural latex and latex gloves, known for stimulating histamine release from human basophils sensitized with serum from latex-allergic individuals. It is rich in glutamic acid and proline residues arranged in repeated motifs. The protein’s unusual amino acid composition includes 48% negatively charged residues and 13% positively charged residues.MethodsThe recombinant form of Hev b5 (rHev b5) was produced in Escherichia coli. Its chitinase activity, which may provide antifungal properties by breaking down chitin in phytopathogen cell walls, was assessed. Additionally, the antibacterial activity of rHev b5 against Gram-positive and Gram-negative bacteria, including Bacillus cereus, Staphylococcus aureus, E. coli and Salmonella typhi, was evaluated. The potential enhancement of this activity in the presence of calcium or zinc ions was investigated to understand the underlying mechanism involving binding to microbial membranes via metal ion-mediated cationic salt bridges.ResultsrHev b5 exhibited significant chitinase activity and demonstrated substantial antibacterial effects against both Gram-positive and Gram-negative bacteria. The antibacterial activity was notably enhanced in the presence of zinc or calcium ions, suggesting that rHev b5 binds to microbial membranes through metal ion-mediated cationic salt bridges, leading to cell lysis and microbial death.ConclusionAntimicrobial properties and chitinase activity of Hev b5 underline its potential as an anionic antimicrobial peptide, offering both antifungal and antibacterial defenses. These findings position Hev b5 as a promising candidate for further research in antimicrobial peptide applications. creator: Methaporn Meethong creator: Kitiya Ekchaweng creator: Sumalee Obchoei creator: Chanawee Jakkawanpitak creator: Phanthipha Runsaeng uri: https://doi.org/10.7717/peerj.19242 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Meethong et al. title: Prognostic value and immunotherapy analysis of immune cell-related genes in laryngeal cancer link: https://peerj.com/articles/19239 last-modified: 2025-04-14 description: BackgroundLaryngeal cancer (LC) is a prevalent head and neck carcinoma. Extensive research has established a link between immune cells in the tumor microenvironment (TME) and cancer progression, as well as responses to immunotherapy. This study aims to develop a prognostic model based on immune cell-related genes and examine the TME in LC.MethodsRNA-seq data for LC were sourced from The Cancer Genome Atlas (TCGA), and GSE27020 and GSE51985 datasets were retrieved from the Gene Expression Omnibus (GEO) database. Key genes were identified through the intersection of differentially expressed genes (DEGs) between normal and LC samples and module genes derived from weighted gene co-expression network analysis (WGCNA), followed by functional enrichment analysis. The prognostic risk model was constructed using univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO) analyses. Gene Set Variation Analysis (GSVA) was subsequently performed for hallmark and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses in high- and low-risk groups. Immune infiltration analysis between risk groups was conducted via Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) and single sample gene set enrichment analysis (ssGSEA). Finally, the relationship between the risk model and immunotherapy response was explored.ResultsA total of 124 key genes were identified through the overlap analysis, predominantly enriched in GO terms such as defense response to viruses and regulation of response to biotic stimuli, as well as KEGG pathways related to phagosome and Epstein-Barr virus infection. Machine learning indicated that the optimal prognostic model was constructed from two biomarkers, RENBP and OLR1. GSVA revealed that in the high-risk group, epithelial-mesenchymal transition and ECM-receptor interaction were the most significantly enriched pathways, while autoimmune thyroid disease, ribosome, and oxidative phosphorylation predominated in the low-risk group. Additionally, the stromal score was significantly higher in the high-risk group, while CD8+ T cells, cytolytic activity, inflammation promotion, and T cell co-stimulation were elevated in the low-risk group. Tumor Immune Dysfunction and Exclusion (TIDE) analysis showed higher TIDE and exclusion scores in the high-risk group, whereas the CD8 score was higher in the low-risk group. Finally, CD274 (PD-L1) expression was significantly elevated in the low-risk group.ConclusionsThis study identified two key prognostic biomarkers, RENBP and OLR1, and characterized TME differences across risk groups, offering novel insights into the diagnosis and treatment of LC. creator: Sen Zhang creator: Jianrui Pan creator: Huina Guo creator: Xiaoya Guan creator: Chenxu Yan creator: Lingling Ji creator: Xiansha Wu creator: Hui Huangfu uri: https://doi.org/10.7717/peerj.19239 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhang et al. title: Catecholamine exposure and the gut microbiota in obstructive sleep apnea link: https://peerj.com/articles/19203 last-modified: 2025-04-14 description: Patients with obstructive sleep apnea (OSA) have increased mortality from chronic inflammatory and cardiovascular diseases. Excess catecholamine exposure contributes to the disease associations of OSA, but the underlying mechanism is unknown. This study tested the hypothesis that increased catecholamine exposure is associated with Enterobacteriaceae abundance in OSA. We compared urinary norepinephrine and the fecal microbiota in 24 patients with OSA and 23 controls. Urinary norepinephrine was elevated in OSA patients, consistent with increased sympathetic activation in those patients. OSA patients did not show changes in the community structure of the microbiome or in Enterobacteriaceae abundance compared to controls. Longitudinal changes in Enterobacteriaceae abundance in OSA patients were significantly associated with within-subject changes in norepinephrine, but this association was absent in controls. These results provide a preliminary association between norepinephrine exposure and Enterobacteriaceae in patients with disordered sleep. creator: Joe Alcock creator: Dongdong Lin creator: Prashanth Setty creator: Lee K. Brown creator: Armand E.K. Dichosa creator: Benjamin J. Burnett creator: Cliff S. Han creator: Henry C. Lin uri: https://doi.org/10.7717/peerj.19203 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alcock et al. title: Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics link: https://peerj.com/articles/19158 last-modified: 2025-04-14 description: DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring. creator: Karlijn Doorenspleet creator: Amalia Aikaterini Mailli creator: Berry B. van der Hoorn creator: Kevin K. Beentjes creator: Annelies De Backer creator: Sofie Derycke creator: Albertinka J. Murk creator: Henning Reiss creator: Reindert Nijland uri: https://doi.org/10.7717/peerj.19158 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Doorenspleet et al. title: LASSO-derived nomogram prediction model for lymph node metastasis in colorectal cancer: a retrospective analysis link: https://peerj.com/articles/19148 last-modified: 2025-04-14 description: ObjectiveThis study aims to develop a prediction model for lymph node metastasis (LNM) in colorectal cancer (CRC) patients using common clinicopathologic data and a nomogram. The model seeks to uncover correlations between LNM and clinical indicators, providing an effective tool to identify high-risk patients, aiding clinical decision-making, and enhancing patient prognosis.MethodsWe conducted a retrospective analysis of CRC patients diagnosed between January 2021 and December 2023 at Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University. Risk predictors for LNM were identified through comparative analysis and Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression. Nomograms were then utilized to predict the probability of metastasis, and their performance was assessed using calibration curves, receiver operating characteristic (ROC) curves, and decision curve analysis.ResultsThe study comprised 869 CRC patients, with 435 cases allocated to the training set and 434 cases to the validation set. First, 12 potential risk factors for LNM in CRC patients were identified through comparative analysis in the training set. Next, nine independent predictors (T stage, vascular tumor thrombus, PMS2, MSH2, KRAS, BRAF, PIK3CA, leukocyte, and neutrophil) of LNM occurrence were refined using LASSO regression and multivariate logistic regression models. Subsequently, a clinical nomogram was developed based on these independent predictors of LNM. The nomogram exhibited a C-index of 0.751 (95% CI [0.728–0.774]), indicating its robust predictive value, which was further validated in the independent validation set.ConclusionT stage, vascular tumor thrombus, PMS2, MSH2, KRAS, BRAF, and neutrophil emerged as significant risk factors for LNM in CRC, while leukocytes appeared to be protective. These findings emphasize the importance of comprehensive risk assessment and personalized therapeutic strategies in CRC management. creator: Xiyun Quan creator: Yi Deng creator: Zhimin Liu creator: Zhenqin Gao creator: Huimei Yi creator: Ming Li uri: https://doi.org/10.7717/peerj.19148 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Quan et al. title: A retrospective study using machine learning to develop predictive model to identify rotavirus-associated acute gastroenteritis in children link: https://peerj.com/articles/19025 last-modified: 2025-04-14 description: BackgroundRotavirus is the leading cause of severe dehydrating diarrhea in children under 5 years worldwide. Timely diagnosis is critical, but access to confirmatory testing is limited in hospital settings. Machine learning (ML) models have shown promising potential in supporting symptom-based diagnosis of several diseases in resource-limited settings.ObjectivesThis study aims to develop a machine-learning predictive model integrated with multiple sources of clinical parameters specific to rotavirus infection without relying on laboratory tests.MethodsA clinical dataset of 509 children was collected in collaboration with the Regional Institute of Medical Sciences, Imphal, India. The clinical symptoms included diarrhea and its duration, number of stool episodes per day, fever, vomiting and its duration, number of vomiting episodes per day, temperature and dehydration. Correlation analysis is performed to check the feature-feature and feature-outcome collinearity. Feature selection using ANOVA F test is carried out to find the feature importance values and finally obtain the reduced feature subset. Seven supervised learning models were tested and compared viz., support vector machine (SVM), K-nearest neighbor (KNN), naive Bayes (NB), logistic regression (Log_R) , random forest (RF), decision tree (DT), and XGBoost (XGB). A comparison of the performances of the seven models using the classification results obtained. The performance of the models was evaluated based on accuracy, precision, recall, specificity, F1 score, macro F1, F2, and receiver operator characteristic curve.ResultsThe seven ML models were exhaustively experimented on our dataset and compared based on eight evaluation scores which are accuracy, precision, recall, specificity, F1 score, F2 score, macro F1 score, and AUC values computed. We observed that when the seven ML models were applied, RF performed the best with an accuracy of 81.4%, F1 score of 86.9%, macro F1-score of 77.3%, F2 score of 86.5% and area under the curve (AUC) of 89%.ConclusionsThe machine learning models can contribute to predicting symptom-based diagnosis of rotavirus-associated acute gastroenteritis in children, especially in resource-limited settings. Further validation of the models using a large dataset is needed for predicting pediatric diarrheic populations with optimum sensitivity and specificity. creator: Sourav Paul creator: Minhazur Rahman creator: Anutee Dolley creator: Kasturi Saikia creator: Chongtham Shyamsunder Singh creator: Arifullah Mohammed creator: Ghazala Muteeb creator: Rosy Sarmah creator: Nima D. Namsa uri: https://doi.org/10.7717/peerj.19025 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Paul et al. title: Genetic assessment of farmed Oreochromis mossambicus populations in South Africa link: https://peerj.com/articles/18877 last-modified: 2025-04-14 description: The global utilisation of Oreochromis spp. in freshwater aquaculture extends to South Africa. Here the native Mozambique tilapia (Oreochromis mossambicus) has been proposed as a priority species for regional aquaculture projects, although it is still not preferred over the non-native O. niloticus. There is limited understanding of the genetic diversity, and genetic differentiation of farmed O. mossambicus in South Africa. Using a suite of 14 microsatellite markers, the present study aimed to determine the origin and genetic diversity of four farmed O. mossambicus populations in KwaZulu-Natal and Mpumalanga provinces. Wild O. mossambicus from rivers surrounding the farms were included to trace the origin of farmed populations. Results revealed lower genetic diversity in farmed populations compared to wild populations. In particular, the University of Zululand population exhibited lower genetic diversity compared to the rest of the farmed populations. While most farmed populations closely resembled their local wild counterparts, the uMphafa ponds exhibited distinct genetic characteristics. Notably, some individuals from uMphafa shared genetic affinities with those from the Thukela River, suggesting that the Thukela River could be the source of this farmed population, or that farmed fish may have been introduced or escaped into the river. The study suggests that select farmed populations may have the potential for use in breeding and broodstock supplementation programs but emphasizes the importance of thorough genetic monitoring. However, before these populations can be considered for broodstock supplementation, further investigation is required to confirm their genetic integrity and rule out potential contamination from invasive species. creator: Mahlatse Fortunate Mashaphu creator: Gordon Craig O’Brien creator: Colleen Thelma Downs creator: Sandi Willows-Munro uri: https://doi.org/10.7717/peerj.18877 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mashaphu et al. title: Diversity and distribution of the caddisfly genus Atopsyche Banks, 1905 in Ecuador, with the description of seven new species (Trichoptera: Hydrobiosidae) link: https://peerj.com/articles/18769 last-modified: 2025-04-14 description: Atopsyche is the largest Hydrobiosidae genus on the South American continent. The genus previously included 27 species in Ecuador. In this work, we describe and illustrate seven new species of Atopsyche from the Andes of Ecuador: Atopsyche andinasp. nov., Atopsyche azuayanasp. nov., Atopsyche chocoandinasp. nov., Atopsyche jocotocosp. nov., Atopsyche papallactasp. nov., Atopsyche piburjasp. nov., and Atopsyche tapichalacasp. nov. Additionally, we provide distributional information for all Ecuadorian Atopsyche, including three new country records: A. kingi, A. mayucapac, and A. neotropicalis. With these additions, there are now 37 species of Atopsyche in Ecuador, or about 75% of species in the country, according to the CHAO 2 species estimator. Finally, we provide new and more detailed illustrations for A. bolivari, A. bravoi, and A. davidsoni. creator: Ernesto Rázuri-Gonzales creator: Ralph Holzenthal creator: Blanca Ríos-Touma uri: https://doi.org/10.7717/peerj.18769 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Rázuri-Gonzales et al. title: Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mitochondrial DNA copy number in songbird blood and sperm cells link: https://peerj.com/articles/19278 last-modified: 2025-04-11 description: Mitochondrial DNA (mtDNA) copy number varies across species, individuals, and cell types. In birds, there are two types of cells with a relatively low number of mitochondria: red blood cells and spermatozoa. Previous studies investigating variation of mitochondrial abundance in animal sperm have generally used quantitative PCR (qPCR), but this method shows potential limitations when quantifying targets at low abundance. To mitigate such issues, we investigated and compared the reliability and accuracy of qPCR, digital PCR (dPCR) and droplet digital PCR (ddPCR) to quantify high and low concentration DNA. We used synthetic DNA targets, to calculate the limit of detection and the limit of quantification and found that with both dPCR and ddPCR, these limits were lower than with qPCR. Then, to compare quantification accuracy and repeatability, we used DNA extracted from blood and sperm cells of Eurasian siskin. We found that qPCR, dPCR and ddPCR all reliably quantified mitochondrial DNA in sperm samples but showed significant differences when analyzing the typically lower levels of mtDNA in blood, with ddPCR consistently showing lower variation among replicates. Our study provides critical insights and recommendations for future studies aiming to quantify target mtDNA and indicates that dPCR and ddPCR are the preferred methods when working with samples with low abundance of mtDNA. creator: Laima Bagdonaitė creator: Erica H. Leder creator: Jan T. Lifjeld creator: Arild Johnsen creator: Quentin Mauvisseau uri: https://doi.org/10.7717/peerj.19278 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bagdonaitė et al. title: Association between polymorphisms of the adenylate cyclase 3 gene rs2241759 and the effect of high-intensity interval training on blood lipid profiles link: https://peerj.com/articles/19271 last-modified: 2025-04-11 description: BackgroundOne of the recognized effects of systematic physical activity is the improvement of physical fitness, with a negative correlation found between physical fitness and cardiovascular and cardiometabolic risk. The purpose of this study is to analyze the influence of single nucleotide polymorphisms (SNPs) of the adenylate cyclase 3 (ADCY3) gene on the effect of high-intensity interval training (HIIT) on blood lipids, and simultaneously screen out the genetic markers sensitive to HIIT in Chinese Han youth.MethodsIn the 12-week HIIT program, a total of 237 Chinese Han college students with non-regular exercise habits were recruited, and these volunteers participated in the training three times a week. Baseline and after the HIIT program, total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) were measured, respectively. DNA was extracted from the white blood cells of volunteers and genotyping was carried out. The PLINK v1.09 software was used to conduct quality control screening on the obtained SNPs, and a linear regression model was constructed to analyze the association between ADCY3 gene SNPs and the effect of HIIT on blood lipids. ANOVA multiple comparison (LSD) was performed to test the difference between groups (P < 0.05).Results(1) Through the analysis of Illumina CGA chip scanning, a total of 22 SNPs of the ADCY3 gene were identified. Following rigorous quality control screening, 15 SNPs were included in the subsequent analysis. Notably, it was found that the rs2241759 locus is associated with the effect of HIIT on blood lipid profiles. (2) Among male volunteers, significant differences in the baseline HDL-C values were observed among the three genotypes at the rs2241759 locus of the ADCY3 gene (β =  − 0.019, P = 0.040). The baseline value for the GG genotype was higher than that AA/AG genotypes. (3) After HIIT, the total levels of TC and HDL-C in volunteers increased significantly (P < 0.05). In contrast, the total levels of TG and LDL-C decreased significantly (P < 0.05). Further statistical analysis categorized by gender revealed that, with the exception of TC values in men, significant changes were observed for TC, TG, HDL-C, and LDL-C across both genders (P < 0.05). (4) Compared to male volunteers with the GG genotype, male volunteers carrying the A allele exhibited a more pronounced change in TC values following training (β = 0.044, P = 0.038). (5) The rs2241759 locus demonstrated a significant association with the effect of HIIT on LDL-C (β =  − 0.065, P = 0.04363).Conclusion(1) The implementation of a 12-week HIIT regimen can significantly enhance the blood lipid status of college students. (2) The locus rs2241759 of the ADCY3 gene is significantly associated with the sensitivity of LDL-C to HIIT. creator: Junren Lai creator: Li Gong creator: Yan Liu creator: Yanchun Li creator: Jing Ni creator: Duoqi Zhou uri: https://doi.org/10.7717/peerj.19271 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lai et al. title: Circulating microRNAs demonstrate limited diagnostic potential for diabetic retinopathy in the population of Kazakhstan link: https://peerj.com/articles/19259 last-modified: 2025-04-11 description: BackgroundDiabetic retinopathy (DR) is the most common complication of diabetes, leading to blindness. The asymptomatic onset and the existing difficulties in diagnosing warrant the search for biomarkers that can facilitate the early diagnosis of DR. The aim of this study was to evaluate the potential of plasma microRNAs (miRNAs), which have previously been shown to be involved in the pathogenesis of DR and differentially expressed in plasma/serum of patients, as biomarkers for DR in the Kazakhstani population.Materials and MethodsUsing quantitative RT-PCR, we compared the levels of ten candidate miRNAs in plasma among three groups: type 2 diabetes mellitus (T2DM) patients with DR (DR patients, N = 100), T2DM patients without DR (noDR patients, N = 98), and healthy controls (N = 30).ResultsLevel of miR-423-3p was significantly reduced in DR patients compared to noDR patients (pFDR = 5.4 × 10−3). Levels of miR-423-3p and miR-221-3p were significantly reduced in DR patients compared to controls (pFDR = 5.4 × 10−3 and 0.024, respectively ), level of miR-23a-3p was significantly reduced in noDR patients compared to controls (pFDR = 0.047), levels of miR-221-3p and miR-23a-3p were significantly reduced in T2DM patients (combined group) compared to controls (pFDR = 0.047, and 0.049, respectively). Also, there were several significant differences between groups formed based on clinical-pathological characteristics, but none of these results remained significant after adjustment for multiple comparisons. Correlation analysis revealed weak associations between the levels of miR-423 and miR-221-3p and DR staging (pFDR = 1.3 × 10−3 and 0.026, respectively), and fair associations between the levels of miR-29b-3p and miR-328-3p and diabetes duration in noDR patients (pFDR = 8.8 × 10−3 and 0.016, respectively). According to receiver operating characteristic (ROC) analysis, only miR-23a-3p can be considered a potential biomarker with moderate informativeness for diagnosing proliferative DR (PDR); however, a larger sample size is needed to verify this finding. Furthermore, the small magnitude of observed changes in miRNA levels between groups significantly complicates classification.ConclusionsDue to the low specificity and small magnitude of deviations from the norm, the studied miRNAs have low potential in the diagnosis of DR. creator: Aizhan Magazova creator: Yeldar Ashirbekov creator: Arman Abaildayev creator: Kantemir Satken creator: Gulzhakhan Utegenova creator: Ayaz Belkozhayev creator: Altynay Balmukhanova creator: Zaure Dzhumatayeva creator: Ainagul Beissova creator: Iryna Shargorodska creator: Aigul Balmukhanova creator: Kamalidin Sharipov uri: https://doi.org/10.7717/peerj.19259 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Magazova et al. title: Differences in depression prevalence among older adults in China before and during the COVID-19 pandemic: a systematic review and meta-analysis link: https://peerj.com/articles/19251 last-modified: 2025-04-11 description: ObjectiveChanges in the prevalence of depression during the COVID-19 (Coronavirus disease 2019) pandemic among older adults in China have not been systematically evaluated. We aimed to systematically summarize existing evidence to conduct a meta-analysis to quantify changes in the prevalence of depression before and during the COVID-19 pandemic.MethodsThe PubMed, Web of Science, Scopus, Embase, PsycINFO, China National Knowledge Infrastructure (CNKI), WangFang Data, CQVIP, and China Biology Medicine disc (CBMdisc) databases were searched from January 1, 2017, to November 20, 2024. Studies reporting the prevalence of depression among Chinese individuals aged 60 or older using validated diagnostic tools were included. A random-effects model was applied to estimate pooled prevalence, with subgroup analyses performed by demographic and socio-economic factors. Relative risks (RR) were calculated to compare prevalence across different pandemic stages.ResultsA total of 101 studies involving 264,758 participants were included. The pooled prevalence of depression among older adults was 25.8% (95% CI [21.7–29.9]) from 2017–2019 and 23.8% (95% CI [19.8–27.8]) from 2020–2023. During the early pandemic stage (January–April 2020), prevalence significantly decreased (RR = 0.849, P < .001) but increased in later stages, reaching 24.4% by 2021–2023. The prevalence of depression among older adults during the COVID-19 pandemic showed a significant increasing trend (Ptrend < .001). Subgroup analyses revealed higher prevalence among females, rural residents, individuals with lower education levels, and those living alone.ConclusionDepression prevalence among older adults in China decreased during the early pandemic response but showed an increasing trend over time, reflecting the complex mental health impact of prolonged public health measures. Effective interventions are needed to address the specific needs of vulnerable subgroups during and beyond public health crises. creator: Xin Zhao creator: Xiaojing Du creator: Shuliang Bai creator: Pianpian Zheng creator: Xun Zhou creator: Zhenjie Wang uri: https://doi.org/10.7717/peerj.19251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Effects of gait speed on paraspinal muscle activation: an sEMG analysis of the multifidus and erector spinae link: https://peerj.com/articles/19244 last-modified: 2025-04-11 description: BackgroundThe paraspinal muscles, such as the multifidus muscles and erector spinae muscles, play an important role in trunk stabilization and pelvic mobility during gait. Understanding how they are activated according to the speed of locomotion can facilitate the diagnosis and treatment of patients with these conditions. This study aimed to comprehensively analyze the activity of postural muscles (multifidus and erector spinae) using surface electromyography (sEMG) across a range of gait speeds.MethodsThe study group consisted of 31 students of physiotherapy at the Pomeranian University in Słupsk, including 20 women (64.51%) and 11 men (35.48%). The research process included an interview and participation in the sEMG survey. The sEMG examination of the musculus erector spinae (MES) and musculus multifidus (MM) was carried out in the supine, standing position, while walking on a treadmill, maintaining speeds: 1 km/h, 3 km/h, 5 km/h and 6 km/h, for 60 s at each stage and at maximum voluntary isometric contraction (MVIC). The percentage value of the amplitude of the sEMG recording in relation to maximum voluntary isometric contraction (%MVIC) was determined. The average rate of change in muscle activity was also assessed in relation to the respective changes in locomotion speed for MES and MM.ResultsThe results show significant differences in the %MVIC parameter between sides (left vs right) for both muscle groups (MES and MM) in the supine position and in the standing position for the multifidus muscles. At the set speeds of 1 km/h, 3 km/h, 5 km/h and 6 km/h, the differences are not statistically significant. A decreasing trend in the rate of change in muscle activity was also observed for both muscle groups as gait speed increased. The most significant decrease is observed at average gait speeds of 3–5 km/h.ConclusionsIn the sEMG examination during rest, standing and walking, the activity of the right and left MES and MM muscles examined is not always equal. The activity of the muscles studied (MES and MM) increases with increasing gait speed. The rate of change in muscle activity decreases as gait speed increases. creator: Aleksandra Bryndal creator: Wojciech Nawos-Wysocki creator: Agnieszka Grochulska creator: Karol Łosiński creator: Sebastian Glowinski uri: https://doi.org/10.7717/peerj.19244 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Bryndal et al. title: An update on Aenocyon dirus in the interior of North America: new records, radiocarbon dates, ZooMS spectra, and isotopic data for an iconic late Pleistocene carnivore link: https://peerj.com/articles/19219 last-modified: 2025-04-11 description: Aenocyon dirus played a crucial role as a predator in late Quaternary megafaunal communities throughout southern North America. This article presents two new occurrences of the species from southwest Iowa on the eastern Great Plains, updates the Peccary Cave record in the southern Ozark Highlands, and amends the fossil record of the species. In southern North America, there are 166 occurrences of A. dirus, spanning Marine Isotope Stage (MIS) 2-19, with at least two-thirds (n = 112) of the occurrences dating to MIS 2-3 (11,600–57,000 cal B.P.). A. dirus fossils are found across this region, with notable concentrations in California, Florida, the Ozark Highlands, and broadly across the southern Great Plains. Consideration of Canis specimens from the lead region (covering contiguous parts of Illinois, Wisconsin, and Iowa) previously identified as Canis mississippiensis (and sometimes synonymized with A. dirus or C. lupus) reveals they are actually C. lupus. The terminal extinction of A. dirus occurred sometime after 12,800 cal B.P.The Iowa finds, consisting of a radius and a partial cranium, are the first records for the state. Zooarchaeology by mass spectrometry confirms these records, as well as the Peccary Cave record, are A. dirus, as opposed to C. lupus. The Iowa specimens are directly dated to 29,040–28,410 cal B.P. and 14,325–14,075 cal B.P., while Peccary Cave is dated to 25,350–21,405 cal B.P. These results place A. dirus in the interior of southern North America before, during, and after the Last Glacial Maximum (26,500–19,000 cal B.P.). Stable nitrogen isotope (δ15N) values of bone collagen from the younger of the two Iowa records suggest this individual did not regularly compete for prey with Smilodon fatalis during the Bølling-Allerød Chronozone (14,640–12,850 cal B.P.). To the south, at Peccary Cave, considerations of prey size, prey abundance, and isotopic data strongly suggest Platygonus compressus was the focal prey species. creator: Matthew G. Hill creator: Christopher C. Widga creator: Todd A. Surovell creator: Kurt M. Wilson creator: Sarah A. Allaun creator: McKenna L. Litynski creator: Jason Titcomb uri: https://doi.org/10.7717/peerj.19219 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hill et al. title: RAD51 expression and prognostic impact in patients with stomach adenocarcinoma link: https://peerj.com/articles/19179 last-modified: 2025-04-11 description: BackgroundStomach adenocarcinoma (STAD) is the most common gastrointestinal cancer. A clear diagnosis and molecular targeted therapy have important implications for prolonging survival of patients. RAD51 is the central catalyst of homologous recombination that plays important role in maintaining genomic integrity. However, the clinical significance of RAD51 expression in STAD patients remains unclear. This study aimed to assess the association of RAD51 expression with clinicopathological characteristics and patient outcomes.MethodsIn this study, RAD51 mRNA expression in STAD patients was assessed using the UALCAN and GEPIA databases. The diagnostic value of RAD51 was evaluated by analyzing the ROC curve (data from the The Cancer Genome Atlas (TCGA) database). The protein expression level of RAD51 in STAD patients and its relationship with clinicopathological characteristics and prognosis were evaluated by immunohistochemistry. Co-expression analysis of RAD51 in STAD was performed by Coexpedia and Gene Expression Profiling Interactive Analysis (GEPIA) databases. The associations of RAD51 and its co-expression genes with immune infiltrates were analyzed in TIMER database.ResultsOur bioinformatic analysis revealed that RAD51 demonstrates elevated expression in STAD. The ROC curve analysis yielded an AUC value of 0.9366 (95% CI [0.9075–0.9658]), confirming its potential as a biomarker for STAD. Immunohistochemical assessments validated the up-regulation of RAD51 in STAD, highlighting its significant correlation with TNM stage and T stage, but not with age, sex, grade, N stage, M stage, or P53 expression. Patients exhibiting high RAD51 expression exhibited significantly reduced overall survival. Multivariate analysis identified RAD51 expression may serve as an independent prognostic biomarker of poor prognosis in patients with STAD. Additionally, our bioinformatic analysis identified eight RAD51 co-expression genes (AURKA, CKS1B, NUSAP1, PFDN4, CCNE1, CDCA4, KIF4A, and MCM10) in STAD. Moreover, we discovered that RAD51 and its main co-expressed genes were significantly negatively associated with most or all immune cell infiltration.ConclusionsRAD51 overexpression was related to disease progression and poor prognosis, as well as infiltration of immune cells in gastric cancer. creator: Baiyu Jian creator: Hao Zhang creator: Li Fan creator: Yang Li creator: Nan Wu creator: Ningning Wang creator: Lingmin Li creator: Xueyan Li creator: Pengling Ge creator: Yingcai Niu creator: Jicheng Liu uri: https://doi.org/10.7717/peerj.19179 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Jian et al. title: Phytochemical production and antioxidant activity improvement of Rhinacanthus nasutus (L.) Kurz calli by in vitro polyploidization link: https://peerj.com/articles/19160 last-modified: 2025-04-11 description: BackgroundRhinacanthus nasutus (L.) Kurz is a multipurpose ethnomedicinal shrub containing various bioactive compounds and phytochemicals. Inducing polyploidy is an alternative way to enhance the production of secondary metabolites in medicinal plants. The main objectives of this research were to study the effect of polyploidization on the phytochemical content and antioxidant activity of R. nasutus calli.MethodsIn vitro polyploidy was induced by soaking calli in colchicine at different concentrations and for different exposure times. To determine callus polyploidy, the relative DNA contents of each sample were examined using flow cytometry. Diploid, tetraploid, and mixoploid calli were extracted to determine the total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity.Results and conclusionResults showed that the callus survival rate decreased with increasing colchicine concentration and exposure time. The highest percentage of induced tetraploid (66.67%) and mixoploid (66.67%) calli were obtained at 0.05% and 0.2% colchicine with exposure times of 48 and 24 h, respectively. Tetraploid calli showed the highest TPC (81.28 mg GAE/g extract), TFC (35.33 mg QE/g extract), and antioxidant activity compared to diploid and mixoploid calli. Additionally, tetraploid calli demonstrated an approximately twofold greater increase in TPC and TFC compared to diploid calli. The analysis of polyploid callus samples revealed that tetraploid calli exhibited the highest antioxidant activity, whereas diploid calli demonstrated the lowest antioxidant activity across all applied assays. Therefore, inducing a tetraploid of R. nasutus calli plays a critical role in modifying phytochemical content and antioxidant activity. creator: Wipa Yaowachai creator: Prathan Luecha creator: Worasitikulya Taratima uri: https://doi.org/10.7717/peerj.19160 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yaowachai et al. title: Maize leaves salt-responsive genes revealed by comparative transcriptome of salt-tolerant and salt-sensitive cultivars during the seedling stage link: https://peerj.com/articles/19268 last-modified: 2025-04-10 description: Maize (Zea mays) is a crop of significant global importance, yet its productivity is considerably hindered by salt stress. In this study, we investigated two maize cultivars, one exhibiting high salt tolerance (ST) and the other showing salt sensitivity (SS) at the seedling stage. The ST cultivar demonstrated superior seedling survival rates, higher relative water content, and lower electrolyte leakage and malondialdehyde levels in its leaves after both 3-day and 7-day salt treatments, when compared to the SS cultivar. To explore the molecular basis of these differences, we performed comparative transcriptome sequencing under varying salt treatment durations. A total of 980 differentially expressed genes (DEGs) were identified. Gene ontology (GO) functional enrichment analysis of DEGs indicated that the oxidation-reduction process, phosphorylation, plasma membrane, transferase activity, metal ion binding, kinase activity, protein kinase activity and oxidoreductase activity process is deeply involved in the response of ST and SS maize varieties to salt stress. Further analysis highlighted differences in the regulatory patterns of transcription factors encoded by the DEGs between the ST and SS cultivars. Notably, transcription factor families such as AP2/ERF, bZIP, MYB, and WRKY were found to play crucial roles in the salt stress regulatory network of maize. These findings provide valuable insights into the molecular mechanisms underlying salt stress tolerance in maize seedlings. creator: Mingfang Ji creator: Sirui Xu creator: Zhongxian Ma creator: Chengnan Xiao creator: Jiangting Xu creator: Yanfang Zhu creator: Ronghao Cai creator: Chen Bo uri: https://doi.org/10.7717/peerj.19268 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ji et al. title: Genome-wide identification and characterization of the KNOX gene family in Vitis amurensis link: https://peerj.com/articles/19250 last-modified: 2025-04-09 description: BackgroundThe KNOX (KNOTTED1-like homeobox gene) gene family plays a pivotal role in controlling plant growth, maturation, and morphogenesis. However, the function of KNOX in Vitis amurensis has not yet been reported. This study identified and characterized the entire KNOX gene family in Vitis amurensis.MethodsBy employing bioinformatic approaches, the phylogenetic relationships, chromosomal positions, gene architectures, conserved motifs, cis-regulatory elements present in promoter regions, and gene expression profiles of KNOX gene family members in Vitis amurensis were identified and analyzed.ResultsTen KNOX genes spanning nine chromosomes were discovered, and these genes were subsequently categorized into two distinct subclasses. The promoter regions of members of the KNOX gene family include cis-acting elements that are involved in plant growth, hormonal regulation, and stress and light responses. An examination of the expression profiles of KNOX genes in different tissues of Vitis amurensis revealed that genes in Class I presented tissue-specific expression patterns, whereas genes belonging to Class II presented more ubiquitous expression across various tissues. The expression levels of Vitis amurensis KNOTTED1-like homeobox (VaKNOX)2, VaKNOX3, and VaKNOX5 were highest in fruits. VaKNOX2, VaKNOX3, and VaKNOX5 can serve as candidate genes for enhancing fruit quality. The expression levels of VaKNOX6 and VaKNOX7 were much higher in cold environments than in normal conditions. Through in-depth research into the functions of VaKNOX6 and VaKNOX7, we aimed to improve the cold resistance of grapevine varieties. creator: Linling Liu creator: Wenpeng Lu creator: Shutian Fan creator: Yiming Yang uri: https://doi.org/10.7717/peerj.19250 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Machine learning-based prediction of LDL cholesterol: performance evaluation and validation link: https://peerj.com/articles/19248 last-modified: 2025-04-09 description: ObjectiveThis study aimed to validate and optimize a machine learning algorithm for accurately predicting low-density lipoprotein cholesterol (LDL-C) levels, addressing limitations of traditional formulas, particularly in hypertriglyceridemia.MethodsVarious machine learning models—linear regression, K-nearest neighbors (KNN), decision tree, random forest, eXtreme Gradient Boosting (XGB), and multilayer perceptron (MLP) regressor—were compared to conventional formulas (Friedewald, Martin, and Sampson) using lipid profiles from 120,174 subjects (2020–2023). Predictive performance was evaluated using R-squared (R2), mean squared error (MSE), and Pearson correlation coefficient (PCC) against measured LDL-C values.ResultsMachine learning models outperformed traditional methods, with Random Forest and XGB achieving the highest accuracy (R2 = 0.94, MSE = 89.25) on the internal dataset. Among the traditional formulas, the Sampson method performed best but showed reduced accuracy in high triglyceride (TG) groups (TG > 300 mg/dL). Machine learning models maintained high predictive power across all TG levels.ConclusionMachine learning models offer more accurate LDL-C estimates, especially in high TG contexts where traditional formulas are less reliable. These models could enhance cardiovascular risk assessment by providing more precise LDL-C estimates, potentially leading to more informed treatment decisions and improved patient outcomes. creator: Jing-Bi Meng creator: Zai-Jian An creator: Chun-Shan Jiang uri: https://doi.org/10.7717/peerj.19248 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Meng et al. title: Caregiver factors influencing family-based treatment for child and adolescent eating disorders: a systematic review and conceptual model link: https://peerj.com/articles/19247 last-modified: 2025-04-09 description: IntroductionThe need to assess and manage familial factors influencing family-based treatment (FBT) has been identified in the literature in the context of improving outcomes. While some studies have attempted to address this need, results have not been unified into a framework and to date, no conceptual model exists to bring these factors together for use in clinical practice. A systematic review was conducted to fill this gap and addressed the following question: which caregiver factors influence FBT outcome for child and adolescent eating disorders?MethodologyThe protocol was registered in PROSPERO (CRD42022338843) and utilized the PRISMA framework. A total of 1,994 results were returned from EBSCO Host, Embase, ProQuest, PubMed Central, SCOPUS and Web of Science. Screening returned 164 studies for full-text-review with third-party replication to reduce risk of bias. Thirty-nine articles were included and organized in an evidence hierarchy including both quantitative and qualitative methodologies. Heterogeneity of the data precluded meta-analysis; results were synthesized and grouped using a systematic-narrative approach.ResultsInfluential caregiver factors were identified and grouped into eight domains: caregiver capacity, confidence, readiness, internalizing factors, externalizing factors, food-related factors, support network and family function. Factors within each domain and their influence on treatment outcome were reported. A conceptual model, caregiver factors influencing treatment (Care-FIT) was produced as a graphical representation of the identified domains and factors by frequency of appearance.ConclusionCaregiver factors can significantly impact FBT outcome, and given the importance of their role in treatment, effective identification and management of caregiver factors is warranted. The conceptual model can be used in clinical case formulation and to support further exploration of the degree to which factors are influential. Identifying caregiver factors likely to influence treatment can facilitate support to enhance treatment and recovery. creator: Alex McCord creator: Kylie Rice creator: Adam Rock uri: https://doi.org/10.7717/peerj.19247 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 McCord et al. title: Unveiling the potentials of Lawsonia inermis L.: its antioxidant, antimicrobial, and anticancer potentials link: https://peerj.com/articles/19170 last-modified: 2025-04-09 description: BackgroundLawsonia inermis L., commonly known as henna, is a traditional medicinal Indian plant used for anti-dandruff and antifungal purposes. The plant is rich in phytochemicals and is believed to have significant bioactivity potential. However, limited information is available on the phytochemical compositions of L. inermis cultivars in Thailand. Therefore, this study aims to assess the phytochemical constituents and investigate the bioactivity of L. inermis extract.MethodsL. inermis leaf extracts were prepared by macerating in ethanol (HenE), methanol (HenM), chloroform (HenC), hexane (HenH), and water boiling (HenW). The phenolic and flavonoid contents were determined by Folin-Ciocalteu and aluminum chloride colorimetric methods. High-performance liquid chromatography (HPLC) was performed to qualify polyphenolic contents. Antioxidant activities were evaluated by using 2,2-Diphenyl-1-picrylhydrazyl (DPPH), 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and ferric reducing antioxidant power (FRAP) methods. Moreover, antibacterial activity was tested against two gram-positive and four gram-negative bacteria by the agar well diffusion and the broth dilution methods, and antifungal activity was carried out using the poisoned food technique. Additionally, the cytotoxicity of the extracts against MDA-MB-231, SW480, A549 and A549RT-eto cancer cell lines was determined by using (3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide) (MTT) assay. The scratch wound healing assay was performed to determine the effect of anti-migration on A549 cells.ResultsQuantitative analysis revealed that HenE and HenM extracts had high phenolic and flavonoid contents. Gallic acid, catechin, ellagic acid, apigetrin, lawsone and quercetin were identified by HPLC. The HenE and HenM extracts exhibited strong antioxidant properties, and the extracts showed different inhibition growth against bacteria tested, especially B. cereus and S. aureus. In addition, all extracts had potential inhibitory activity to all fungal strains, especially HenE and Hen M, which exhibited strong antifungus activity against Penicillium sp. All extracts showed cytotoxic effects in the cell lines MDA-MB-231, SW480, A549 and A549RT-eto, except HenH. The HenE and HenM exhibited the best IC50 values of 57.33 ± 5.56 µg/ml and 65.00 ± 7.07 µg/ml against SW480 cells, respectively. The HenC, HenW, and HenH were found to suppress A549 cells migration.Discussion and ConclusionThis study revealed that the L. inermis extracts, particularly those obtained from polar solvents (HenE and HenM), had a strong potency for antioxidant, antibacterial, and anticancer properties. Our findings highlight the valuable biological properties of extracts that can be promoted through additional investigation into their applications in Thailand for medicinal and industrial purposes. creator: Nantikan Joyroy creator: Lukana Ngiwsara creator: Siriporn Wannachat creator: Ratchanee Mingma creator: Jisnuson Svasti creator: Jintanart Wongchawalit uri: https://doi.org/10.7717/peerj.19170 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Joyroy et al. title: Psychometric properties of the Chinese version physical literacy assessment questionnaire among high school students in Gansu, China link: https://peerj.com/articles/19093 last-modified: 2025-04-09 description: IntroductionThe concept of physical literacy (PL) originated from the philosophy of lifelong sports, and its development is crucial for achieving lifelong sports goals. The Portuguese Physical Literacy Assessment Questionnaire (PPLA-Q) is a tool designed to assess the physical literacy of high school students, demonstrating good reliability and validity. The aim of this study is to translate and adapt the PPLA-Q into Chinese (PPLA-Q-C) and validate its applicability among adolescents in Gansu, China through confirmatory factor analysis (CFA).MethodsA total of 780 middle school students from Gansu Province, China, aged 15–18, participated. After screening, the final sample size was 729. The English PPLA-Q was translated into Chinese and validated through expert review and pre-testing. Data were collected in September 2022 via a self-reported survey, with an effective response rate of 93.5%. Data analysis was conducted using Mplus 8.3 with the robust maximum likelihood (MLR) estimator. Confirmatory factor analysis (CFA) assessed model fit using standardized root mean square residual (SRMR), root mean square error of approximation (RMSEA), Tucker-Lewis index (TLI), and comparative fit index (CFI) indices. Construct validity was evaluated through composite reliability (CR), average variance extracted (AVE), and factor correlations. The study followed ethical guidelines and received approval from Universiti Sains Malaysia’s ethics committee.ResultsAll observed items exhibited high factor loadings, confirming that the assumed model, consisting of 40 items grouped into four latent variables, was consistent with the original model. The CFA model demonstrated a good fit with the data, as indicated by fit indices: RMSEA = .024 (90% CI [.020–.027]), CFI = .978, TLI = .977, SRMR = .032.ConclusionThe final measurement model comprised 40 items, all retained and considered acceptable for the sample. The study results suggest that the Chinese version of PPLA-Q (PPLA-Q-C) is effective and reliable for assessing the PL of high school students in Gansu Province, China. Education practitioners and policymakers can utilize the PPLA-Q-C framework in their future work to assess the PL of Chinese-speaking students. creator: Zilu Qu creator: Jiarun Wu creator: Yee Cheng Kueh creator: Dongqing Ye creator: Garry Kuan uri: https://doi.org/10.7717/peerj.19093 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Qu et al. title: Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing link: https://peerj.com/articles/19260 last-modified: 2025-04-08 description: The gut microbiota is integral to an animal’s physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China’s temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome’s composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota’s contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning. creator: Jing Cao creator: Shengze Wang creator: Ruobing Ding creator: Yijia Liu creator: Baodong Yuan uri: https://doi.org/10.7717/peerj.19260 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Cao et al. title: Optimizing sowing time and weather conditions for enhanced growth and seed yield of chia (Salvia hispanica L.) in semi-arid regions link: https://peerj.com/articles/19210 last-modified: 2025-04-08 description: BackgroundClimate influenced weather events, especially during the flowering, grain filling, and maturity stages, can adversely influence crop yield and quality. Therefore, understanding how the phenological behaviour and yield potential of new crops such as chia are influenced by weather and sowing dates is crucial for maximizing crop yield. This study aimed to assess the impact of sowing dates on the flowering behaviour, and yield attributes of chia morphotypes, as well as to identify optimal weather conditions for achieving higher yields.MethodsThe study was conducted during 2021–22 and 2022–23 and consisted of fifteen sowing windows from 1st July to 1st February (at 15 days intervals), with two chia morphotypes (white and black seed) arranged in a replicated split-plot design. Phenological events, flowering characters and seed yield traits were recorded regularly. Weather parameters at the experimental location (Maharashtra, India) were recorded.ResultsThe results revealed that weather conditions such as relative humidity (RH) and rainfall favoured the flowering phenology, yield attributes, and seed yield of chia, whereas maximum temperature (Tmax), bright sunshine hours, and accumulated growing degree days had negative effects. Weather parameters significantly influenced the chia seed yield during the cropping period: RH (positive, R2 = 86.1%), Tmax (negative, R2 = 67.4%), rainfall (positive, R2 = 52.9%), and diurnal temperature range (negative, R2 = 74.9%). Black-seeded chia morphotypes consistently produced higher seed yields (10.8% greater) and better yield-contributing traits compared to white types across various sowing dates. The maximum chia seed yield (811–793.1 kg ha−1) was achieved with sowing dates between August 1st and September 1st in this semi-arid region of India. The performance of chia was good under congenial weather conditions, including relative humidity (∼67–72%), maximum temperature (∼30–31 °C), day length (<12.0 h), rainfall (∼200–350 mm), and accumulated growing degree days (∼1,521–1,891). The present study findings can help identify the best suitable regions for chia cultivation by revealing relationships between the performance of chia morphotypes and weather conditions. creator: CB Harisha creator: KM Boraiah creator: PS Basavaraj creator: Hanamant M. Halli creator: Ram Narayan Singh creator: Jagadish Rane creator: K Sammi Reddy creator: GR Halagundegowda creator: Amresh Chaudhary creator: Arvind Kumar Verma creator: Y Ravi creator: Honnappa Asangi creator: E Senthamil uri: https://doi.org/10.7717/peerj.19210 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Harisha et al. title: Nanoparticle-based antifungal therapies innovations mechanisms and future prospects link: https://peerj.com/articles/19199 last-modified: 2025-04-08 description: Fungal infections present an increasing global health challenge, with a substantial annual mortality rate of 1.6 million deaths each year in certain situations. The emergence of antifungal resistance has further complicated treatment strategies, underscoring the urgent need for novel therapeutic approaches. This review explores recent advances in nanoparticle-based therapies targeting fungal infections, emphasizing their unique potential to enhance drug solubility, bioavailability, and targeted delivery. Nanoparticles offer the ability to penetrate biological barriers, improve drug stability, and act as direct antifungal agents by disrupting fungal cell walls and generating reactive oxygen species. Despite their promising applications, challenges such as potential toxicity, scalability of production, and the need for controlled drug release remain. Future research should focus on optimizing nanoparticle properties, evaluating long-term safety profiles, developing environmentally sustainable synthesis methods, and exploring synergistic approaches with existing antifungal drugs. Nanotechnology offers a transformative opportunity in the management of fungal diseases, paving the way for more effective and targeted treatments. creator: Qinglin Wu creator: Fulan Cen creator: Ying Xie creator: Xianjia Ning creator: Jinghua Wang creator: Zhenghao Lin creator: Jia Huang uri: https://doi.org/10.7717/peerj.19199 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: DLEU2 facilitates bladder cancer progression through miR-103a-2-5p/SOS1 axis link: https://peerj.com/articles/18995 last-modified: 2025-04-08 description: BackgroundBladder cancer (BC) represents a life-threatening malignancy within the urinary system. Dysregulated long non-coding RNAs (lncRNAs) play pivotal roles in the advancement of BC. LncRNA deleted in lymphocytic leukemia 2 (DLEU2) is implicated in the development of various cancers. However, its role and regulatory mechanisms in BC remain unclear. This research aimed to explore the expression, biological function, and molecular mechanisms of DLEU2 In BC progression.MethodsExpression profiles of lncRNAs, microRNAs (miRNAs), and mRNAs in normal and BC tissues were examined by leveraging the raw data sourced from the NCBI GEO database. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) validated expression levels in BC cells. To evaluate the proliferation and migration capabilities of BC cells, assays such as CCK-8, EdU, Transwell, and scratch were carried out. Luciferase reporter assays examined interactions between DLEU2 and miR-103a-2-5p and between miR-103a-2-5p with SOS1. Protein expression of SOS1 in BC cells was analyzed via western blotting.ResultsDLEU2 was markedly increased in BC tissues. Functionally, DLEU2 overexpression elevated BC cell proliferation and migration, while its knockdown produced the opposite effects. Mechanistically, DLEU2 acted as a molecular sponge for miR-103a-2-5p, which targeted SOS1. miR-103a-2-5p knockdown enhanced proliferation and migration, while co-knockdown of miR-103a-2-5p and DLEU2 reversed these effects. Overexpression of SOS1 also promoted proliferation and migration, which were counteracted by miR-103a-2-5p overexpression. Conversely, SOS1 knockdown inhibited these processes, with miR-103a-2-5p knockdown reversing this inhibition.ConclusionsThese findings demonstrate that DLEU2 facilitates BC progression via the miR-103a-2-5p/SOS1 axis. This study reveals a novel regulatory mechanism underlying BC development and highlights DLEU2 as a potential therapeutic target for BC treatment. creator: Yinlong Liu creator: Jian Hu creator: Baochun Liao creator: Zhijian Zhu creator: Yong Liu creator: Qinghua Pan uri: https://doi.org/10.7717/peerj.18995 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Prediction of yield and quality in medicinal plant Ligusticum chuanxiong Hort. using uncrewed aerial vehicle multispectral measurement link: https://peerj.com/articles/19264 last-modified: 2025-04-07 description: Accurate predicting the yield and quality of medicinal materials before harvest can effectively guide post-harvest process, including processing and storage, thereby ensuring the final quality of medicinal materials. Currently, traditional experimental methods for yield and quality estimation are inadequate to offer reliable guidance for harvesting and processing of medicinal plan. Uncrewed aerial vehicle (UAV) multispectral can quickly and accurately estimate the yield and quality of field crops. Based on the UAV multispectral data of Ligusticum chuanxiong Hort. obtained about half a month before and near harvest, this study predicted the rhizome yield and the content of active components such as ferulic acid, Z-ligustilide and senkyunolide A. Additionally, the quality discriminant models of chuanxiong rhizoma were constructed according to the ferulic acid content index stipulated in Pharmacopoeia of the People’s Republic of China (2020). The results performed on the independent validation set show that the best prediction effects of fresh weight and dry weight of rhizome were NRMSE = 23.76%, MAPE = 14.75% and NRMSE = 34.65%, MAPE = 21.73%, respectively. And the best predictive effects of ferulic acid, Z-ligustilide and senkyunolide A were as follows: NRMSE = 13.35%, MAPE = 10.25%; NRMSE = 34.35%, MAPE = 23.40%; and NRMSE = 45.26%, MAPE = 25.48%. Furthermore, the quality discriminant models XGBoost and AdaBoost had effective performances (Accuracy = 0.7083, AUC = 0.7214). These results suggest that UAV multispectral can be effectively employed to predict both yield and quality before harvest, thereby guiding the harvest and processing of L. chuanxiong. creator: Yun-Fan Li creator: Chen Wu creator: Hong-Mei Jia creator: Xi Chen creator: Jin-Niu Xing creator: Wei-Ping Gao creator: Zhu-Yun Yan uri: https://doi.org/10.7717/peerj.19264 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Association between receiving the Aksi Bergizi Social Behavioral Change Communication (SBCC) intervention and hygiene behaviors among secondary school students in Padang, Indonesia link: https://peerj.com/articles/19256 last-modified: 2025-04-07 description: BackgroundThe Government of Indonesia and UNICEF introduced the Aksi Bergizi Social Behavioral Change Communication (SBCC) intervention to promote healthy eating and hygiene behaviors among adolescents. However, no systematic assessment of the program’s effect has been made. This study aims to assess the association between exposure to the Aksi Bergizi nutrition promotion program and hand, oral, and nail hygiene behaviors among secondary school students in Padang, Indonesia.MethodsWe conducted a school-based cross-sectional study in Padang Municipality, Indonesia, collecting data from 253 students attending Aksi Bergizi target schools and 253 students from non-target schools using a self-administered questionnaire. We compared hygiene behaviors between students in the two groups using descriptive statistics and multivariable logistic regression with adjustment for demographic and socioeconomic characteristics.ResultsAll students reported brushing their teeth at least twice per day, so there was no observable difference regarding oral hygiene. However, we found that students in target schools were significantly more likely than those in non-target schools to always use soap when washing their hands both before eating (75% vs. 21%; Adjusted odds ratio (OR) = 6.03; 95% confidence interval (CI) [3.96–9.19]) and after using the toilet (74% vs. 21%; Adjusted OR = 5.74, 95% CI [3.78–8.72]). However, there was no statistically significant difference with regard to nail hygiene, i.e., cutting nails at least once per week.ConclusionWe found differences between target and non-target schools regarding self-reported handwashing but no differences in nail-clipping. The findings of this study have implications for stakeholders in infectious diseases and nutrition. Future studies should consider ways to reduce social desirability bias and increase the generalizability of the study findings. creator: Ricvan Dana Nindrea creator: Wit Wichaidit uri: https://doi.org/10.7717/peerj.19256 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nindrea and Wichaidit title: Efficiency improvement of Juniper trees mass propagation through in vitro shoot multiplication link: https://peerj.com/articles/19255 last-modified: 2025-04-07 description: Juniperus procera is an endangered medicinal tree found in Saudi Arabia. Juniper trees face numerous challenges with seed production, germination and limited clonal propagation potential. Therefore, alternate techniques for reproducing Juniperus procera are essential for large-scale production. The main propose of the current research was establishment of an in vitro shoot multiplication protocol for J. procera. Explants were initially cultured in Murashige and Skoog (MS) media with varying combinations of benzyl amino purine (BAP), than the sprouted shoots were sub-cultured on MS media with different combination of BAP and naphthaleneacetic acid (NAA); rooting potential was examined on both MS and olive medium (OM) media supplemented with indole-3-butyric acid (IBA). The concentration of BAP at 1.0 mg/l showed the highest survival rate (70%) followed by 0.5 mg/l then the control treatment. Similarly, concentration of BAP at 1.0 mg/l produced a higher number of responded explants (2.66) and shoot number (2.67) compared with the other treatments. In multiplication media BAP at 2.0 mg/l without NAA produced higher percent of responded shoots; the lower concentrations of BAP gave lower response. The highest shoot number was observed into multiplication medium supplemented with BAP at 2.0 mg/l then by BAP at 2.0 mg/l +0.2 mg/l NAA. Meanwhile, shoot length showed a different trend in this experiment, as the highest shoot length occurred at the control treatment (0.0 BAP +0.0 NAA) followed by all BAP treatments, while addition of NAA to BAP into multiplication medium gave lower shoots length. Juniper shoots are hardly to root as, most of the treatments were inefficient. OM medium was responsible for rooting only when addition of IBA was implemented. The maximum percentage of rooted shoots was obtained with olive medium supplemented with IBA at 1.0 mg/l. According to the obtained results Juniper is a recalcitrant species to in vitro conditions; the multiplication rate highly depends on BAP concentration. Also, Juniper shoots have a low rooting potential, and most of the examined treatments were inefficient. Future studies are required to improve the current in vitro propagation potential. creator: Alae Ahmed Jabbour creator: Abdulaziz Alzahrani uri: https://doi.org/10.7717/peerj.19255 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jabbour and Alzahrani title: An evaluation of migration fidelity of Ruby-throated Hummingbirds inferred from stable isotope methods link: https://peerj.com/articles/19252 last-modified: 2025-04-07 description: Knowledge of spatial connectivity between breeding and non-breeding locations of migratory birds and their breeding site fidelity are important for avian conservation. Ruby-throated Hummingbirds (RTHU, Archilochus colubris) breed in eastern Canada west to the Rocky Mountains and in the USA east of the Mississippi River and spend the non-breeding period in Mexico, Central America, and southern Florida, USA. We measured the hydrogen and oxygen stable isotopic compositions of adult RTHU tailfeathers (fourth rectrix) from three breeding locations in North America to estimate migratory connectivity between breeding and non-breeding grounds where feathers are grown. Feather δ2H values showed no statistical difference among the three sampling locations as well as disparate geographic assignments from one location on the non-breeding grounds in Costa Rica. Therefore, only weak evidence of migratory connectivity between breeding and non-breeding grounds could be ascertained for our sample of this species. The lack of migratory connectivity detected for Ruby-throated Hummingbirds using stable isotopes is consistent with origins from broad regions on the non-breeding grounds. However, it may also imply that precipitation δ2H values on the non-breeding grounds do not vary enough to detect a difference among our study populations. Sampling of additional populations in the eastern and southern portion of the species’ breeding range and the non-breeding grounds may reveal differences in migratory connectivity among populations and requires further investigation. The δ18O values of feathers correlated poorly to their δ2H values, an effect that may reflect the balance between metabolically driven processes and environmental water on the δ18O values of hummingbird tissues. This study provides the foundations for further investigations into migratory connectivity of RTHU using δ2Hf values and suggests potential avenues of study for use of δ18O values of tissues in metabolic research. creator: Geoff Koehler creator: Kevin J. Kardynal creator: Ron E. Jensen creator: Keith A. Hobson uri: https://doi.org/10.7717/peerj.19252 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: ©2025 Koehler et al. title: Environmental conditions influencing the abundance of the salmonid ectoparasite Salmincola californiensis across upper Willamette River Reservoirs, Oregon link: https://peerj.com/articles/19228 last-modified: 2025-04-07 description: The freshwater copepod Salmincola californiensis is an ectoparasite of Pacific salmon and trout (Oncorhynchus spp.). High levels of infection by this parasite can significantly damage gills and result in blood loss, affecting the fitness and survival of hosts, and it may hinder recovery efforts of threatened and endangered salmonids. Juvenile salmonids that rear in reservoirs have been reported to experience higher rates of infection than their stream-dwelling counterparts. To date, the relationship between reservoir environmental conditions and infection rates remains poorly understood. Here, we evaluated sampling methods designed to capture S. californiensis copepodids, the free-swimming infectious life stage of this parasitic copepod, and develop predictive models of parasite abundance in reservoirs. We used light traps to collect 675 zooplankton samples from various sites and depths in Cougar, Lookout Point, and Fall Creek reservoirs, Oregon, USA during five months in 2020. We tested several predictive models of parasite abundance using environmental covariates obtained concurrently during plankton surveys (e.g., temperature, ambient light and water clarity, reservoir plankton profiles, and water flow). Our models showed a strong influence of water temperature on abundance of copepodids, with maximum initial abundance occurring at the mean water temperature 15.2 °C. At that temperature, August abundance was estimated to be 58.6 copepodids per site in Cougar Reservoir, 43.8 copepodids per site in Fall Creek Reservoir, and 3.5 copepodids per site in Lookout Point Reservoir. Water temperature and reservoir outflow both affected population growth of copepodids: increased water temperature was associated with an increase in population growth rate while an increased reservoir outflow was associated with a decrease in population growth rate. The efficacy of our sampling method was influenced by percent of moon fullness, whether the sample site was above or below the thermocline, water temperature, and number of juvenile sculpin fishes (Cottus spp.) captured in the trap. The mean probability of detecting a single copepodid if one was present was 0.042, but detection probability increased to 0.29 under ideal trap set conditions of warmer water, location above the thermocline, and a full moon. Biologists and managers could use these methods to assess the presence and abundance of S. californiensis in other locations, or to inform reservoir operations to reduce potential salmonid infections. creator: Kelsi Antonelli creator: Christina Murphy creator: Amanda Pollock creator: Ivan Arismendi uri: https://doi.org/10.7717/peerj.19228 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2025 Antonelli et al. title: The gut microbiota in mice with erythropoietin—induced abdominal aortic aneurysm link: https://peerj.com/articles/19222 last-modified: 2025-04-07 description: BackgroundIn recent years, a novel animal abdominal aortic aneurysm (AAA) model was established by administering erythropoietin (EPO) to wild-type (WT) mice. However, the influence of EPO on the murine fecal microbiota remains uninvestigated. Therefore, this study aims to explore the potential association between gut microbiota changes and AAA development in this model.Methods and resultsAdult male C57BL/6 mice were used to establish the AAA model by intraperitoneal administration of recombinant human EPO at a dosage of 10,000 IU/kg daily for 28 consecutive days. Hematoxylin and eosin (H&E) and Elastin Van Gieson (EVG) staining revealed that EPO administration increased aortic wall thickness and diameter, accompanied by enhanced degradation of the elastic lamina. The 16S rRNA—sequencing data were deposited in the Sequence Read Archive (PRJNA1172300). LEfSe analysis revealed that Akkermansia, Lawsonibacter, Clostridium, and Neglectibacter were significantly associated with EPO-induced AAA development, while Lactobacillus, Alistipes, Limosilactobacillus, and Eisenbergiella showed significant negative correlations. Analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) prediction module revealed significant differences in metabolic pathways between the two groups, including alanine, aspartate and glutamate metabolism; cysteine and methionine metabolism; pyrimidine metabolism; carbon metabolism; ABC transporters; and oxidative phosphorylation pathways.ConclusionsEPO-induced gut dysbiosis, particularly changes in Akkermansia, Lactobacillus, and Alistipes abundance, may contribute to AAA formation via inflammation, oxidative stress, and metabolic dysfunction. While this model advances AAA research, its limitations underscore the need for human validation and mechanistic studies. Future work should prioritize multi-omics integration and cross-model comparisons to unravel the complex microbiota-AAA axis. creator: Xinyi Lyu creator: Mingjun Jiang creator: Jiahao Shi creator: Qi Liu creator: Xilian Liu creator: Yulan Li creator: Shu-Qin Ding creator: Xianpeng Dai uri: https://doi.org/10.7717/peerj.19222 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lyu et al. title: Combined microbiome and metabolomics analysis of yupingfeng san fermented by Bacillus coagulans: insights into probiotic and herbal interactions link: https://peerj.com/articles/19206 last-modified: 2025-04-07 description: BackgroundYupingfeng san is a traditional Chinese medicine formula composed of siler, atractylodes, and astragalus. The herbal medicine fermentation process relies on the role of probiotics. Bacillus coagulans is a probiotic commonly used to ferment food and drugs. It produces a variety of beneficial metabolites during fermentation. However, the study on the interaction between B. coagulans and yupingfeng san is still blank.MethodsDuring solid-state fermentation of yupingfeng san, we used metabolomics technology and 16S rDNA sequencing to analyze the differential metabolites and microbial flora of B. coagulans at 0, 3, 7, 11, and 15 d, which corresponded to groups A0, B3, B7, B11, and B15, respectively. This research explored the correlation between microorganisms and metabolites in fermented compound Chinese medicine.ResultsThe results revealed a significant difference in species β diversity between group A0 and the B groups (P < 0.01). At the phylum level, in fermentation groups B3, B7, B11, and B15, the Cyanobacteria relative abundance decreased by 6.69%, 9.09%, 5.74%, and 2.24%, respectively (P < 0.05). The Firmicutes relative abundance increased by 39.73%, 35.65%, 49.09%, and 68.66% (P < 0.05), respectively. The Proteobacteria relative abundance decreased by 39.86% and 26.70%, respectively, in groups B11 and B15 (P < 0.05). The relative abundance of Actinobacteria increased initially with extended fermentation time, and then gradually decreased after reaching its peak in group B7. At the genus level, compared with group A0, the relative abundance of Actinobacteria increased to its highest level of 21.12% in fermentation group B3 and decreased to 9.51% after a fermentation time of 15 d. The abundance of Leuconostoc in fermentation groups B3, B7, and B11 was significantly higher than in group A0 (20.93%, 20.73%, and 21.00%, respectively, P < 0.05). Pediococcus in fermentation groups B3, B7, B11, and B15 was also significantly higher than in group A0 (4.20%, 2.35%, 18.84%, and 52.01%, P < 0.05). Both Pediococcus and Leuconostoc, which belong to lactic acid bacteria, increased fivefold, accounting for a total abundance of 62%. After yupingfeng san fermentation, using nontargeted metabolomics, we identified 315 differential metabolites. This results showed a decrease in the content of alkene and an increase in the contents of acids, lipids, ketones, and amino acids. In addition, in group B3, the contents of quercetin, paeoniflorin-3-O-glucoside, netin, iristin, anthocyanin, caffeic acid, rosmarinic acid, liquiritin, and isoliquiritin were significantly upregulated.ConclusionIn this study, the composition and metabolic profile of yupingfeng san after the fermentation of B. coagulans were studied, and it was found that the fermentation group showed rich species diversity, in which the abundance of Leuconostoc and Weisseria increased significantly, while the opportunistic pathogens such as Pseudomonas aeruginosa and Enterobacter decreased significantly. The analysis of metabolic products showed that the contents of acids, lipids and ketones were significantly increased, rich in a variety of beneficial microorganisms and small molecular compounds with antibacterial effects, and these changes worked together to inhibit the growth of pathogens and maintain intestinal health. The study not only helps to elucidate the assembly mechanism and functional expression of microorganisms after Chinese traditional medicine fermentation, but also provides a solid scientific basis for the development of efficient and safe micro-ecological feed additives. creator: Yu Kang creator: Yanting Sun creator: Jinzhong Cui creator: Yuzhen Song creator: Zilong Sun creator: Huan Li creator: Ruiyan Niu creator: Hongxing Qiao uri: https://doi.org/10.7717/peerj.19206 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kang et al. title: Prognostic value of neutrophil-lymphocyte ratio in gastroenteropancreatic neuroendocrine neoplasm: a systematic review and meta-analysis link: https://peerj.com/articles/19186 last-modified: 2025-04-07 description: PurposeA high neutrophil-to-lymphocyte ratio (NLR) might be connected with an unfavorable tumor prognosis. We sought to conduct a meta-analysis of published studies exploring the prognostic value of NLR in patients with gastroenteropancreatic neuroendocrine neoplasm (GEP-NEN).MethodsWe have referred to the PRISMA 2020 for the Abstracts checklist and have registered our review at the International Prospective Register of Systematic Reviews (registration number CRD42020187679). The PubMed, Embase, and Web of Science databases were screened using words like ‘neutrophil to lymphocyte ratio’, ‘neuroendocrine tumors’, and others up to July 2024. In our study, we evaluated the significance of NLR on overall survival (OS), recurrence-free survival (RFS), and progression-free survival (PFS) of patients with GEP-NEN. Subgroup analysis were conducted to identify the origins of heterogeneity and examine the impact of factor grouping.ResultsWe gathered 18 cohorts with 2,995 cases. All included studies were high quality, with Newcastle Ottawa Scale (NOS) scores ranging from 6 to 8. The pooled analysis revealed that a higher NLR related to worse OS (hazard ratio (HR): 4.59, 95% confidence interval (CI) [3.35–6.29], p < 0.00001) and poor RFS (HR: 4.05, 95% CI [2.78–5.90], p < 0.00001) in patients with GEP-NEN. Subgroup analysis of race, tumor sites, and therapy showed good predictive significance, however, NLR is not effective in predicting the overall survival time of non-operative patients.ConclusionThis meta-analysis showed that a high NLR predicted poor OS, RFS, and PFS in patients with GEP-NEN and can be used as a promising predictor. creator: Yajie Wang creator: Bei Wen creator: Yuxin Zhang creator: Kangdi Dong creator: Shubo Tian creator: Leping Li uri: https://doi.org/10.7717/peerj.19186 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: New role for an old acquaintance: miR-1246 as a new inflammatory and prognostic marker in polytrauma patients link: https://peerj.com/articles/19185 last-modified: 2025-04-07 description: BackgroundBased on a literature analysis, we hypothesized that miR-1246 has a high potential as new biomarker after trauma. This miRNA is already established in oncology but has not yet been described in polytrauma.MethodsPlasma samples from polytraumatized patients with an ISS ≥ 16 were collected in the emergency room (ER) and 48 hours after trauma. The patients were divided into two groups: a group affected by polytrauma with a leading traumatic brain injury (TBI) (abbreviated injury scale head, AIShead > 4) and a group with a polytrauma without TBI (AIShead = 0). The expression of miR-1246 was measured using qRT-PCR in plasma and plasma extracellular vesicles (EVs). Lastly, we isolated CD171 + EVs by using a magnetic bead-based method and measured miR-1246 expression.ResultsIn plasma, there was a significant increase in miR-1246 in the ER in polytrauma patients, but not in TBI patients. The EV miRNA expression was also significantly increased in the ER samples of the polytrauma patients (*p ≤ 0.0001), while an increase in the expression in the TBI patients (*p ≤ 0.01) was only observed after 48 hours. The systemic expression of miR-1246 correlated with the Injury Severity Score (ISS), creatine kinase and creatinine kinase MB (CK-MB), myoglobin, Interleukin (IL)-6 and the length of hospital stay. In CD171+neuro-EVs, the miR-1246 expression was also significantly increased.ConclusionMiR-1246 was shown to be a marker for the patients’ injury severity, the early inflammatory phase and the patients’ outcome. creator: Liudmila P. Leppik creator: Melissa Manamayil creator: Cora Schindler creator: Ramona Sturm creator: Philipp Störmann creator: Dirk Henrich creator: Ingo Marzi creator: Birte Weber uri: https://doi.org/10.7717/peerj.19185 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Leppik et al. title: In silico detection of dysregulated genes and molecular pathways in Alzheimer’s disease as basis for food restoring approach link: https://peerj.com/articles/19100 last-modified: 2025-04-07 description: Forty-eight million people worldwide suffer from dementia, often associated with the growth of the elderly population. There are also concerns about the younger population, where increasing acute and chronic abuse of alcohol and neurotoxic substances may contribute to brain damage and the early onset of dementia. Alzheimer’s disease (AD) accounts for 60% of dementia cases and most therapies used so far have been unsuccessful. Genetic, epigenetic and vascular factors contribute to the pathogenesis of AD. Among the epigenetic mechanisms, modulation of microRNA (miRs) plays an important role. To detect genes and pathways involved in AD, we performed an original bioinformatic analysis of published Alzheimer’s dysregulated miRs using MIcroRNA ENrichment TURned NETwork (MIENTURNET) followed by Reactome tools. The interrogation of these platforms allowed us to discover common putative genes (by MIENTURNET) targeted by the dysregulated miRs and the pathways in which the set of altered genes are involved (by Reactome tool). Our in silico analysis showed that the β-catenin phosphorylation cascade and Netrin-1 signalling, resulted as the most significant. Lastly, based on the assumption that food bioactive compounds (BC) modulate miRs, which in turn modulate dysregulated genes and pathways associated with AD, a literature search demonstrated that some BC are indeed able to modulate dysregulated pathways and genes. Curcumin, osthole, puerarin, xanthoceraside, sulforaphane, salvianolic acid A, resveratrol and andrographolide lead to upregulation of the Wnt/β-catenin pathway. Choline, methionine, folate and vitamin B6/B12 modulate the upregulation of the Netrin-1 pathway. In conclusion, our in silico analysis of miRs identified dysregulated genes and their associated pathways, paving interesting and new insights for diagnosis and for potential therapeutic interventions. creator: Ilaria Petrignani creator: Alessandra Pasquo creator: Roberto Bei creator: Paolo Di Nardo creator: Felicia Carotenuto creator: Noemi Pappagallo creator: Daniele Fraternale creator: Maria Cristina Albertini creator: Laura Teodori uri: https://doi.org/10.7717/peerj.19100 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Petrignani et al. title: Discovery of two new weevil species of Pholicodes Schoenherr, 1826 (Coleoptera: Curculionidae: Entiminae) from eastern Turkey link: https://peerj.com/articles/19026 last-modified: 2025-04-07 description: Weevils are beetles belonging to the superfamily Curculionoidea, known for their elongated snouts commonly named as rostrum. This superfamily is the most species-rich group in Insecta as well as Animalia kingdom, all they are considered phytophagous. The broad nosed weevil genus of Pholicodes Schoenherr, 1826 is solely Palearctic distribution with forty species. In this study, two new species Pholicodes artemisiae sp. nov. and Pholicodes hakkaricus sp. nov. are described from eastern Turkey. Morphological taxonomic characters are digitally illustrated. The new species Ph. artemisiae sp. nov. is associated with Artemisia plant and Ph. hakkaricus sp. nov. collected on Inula helenium L. in the habitat mountain slopes. creator: Levent Gültekin creator: Neslihan Gültekin uri: https://doi.org/10.7717/peerj.19026 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gültekin and Gültekin title: Impact of parental marital status on self-harm in Chinese primary school students: the mediating role of depression and the moderating effect of classmate relationships link: https://peerj.com/articles/19307 last-modified: 2025-04-04 description: BackgroundSelf-harm is an increasing global public health concern, with a growing prevalence in younger children. This study investigates the associations between parental marital status and self-harm behaviors among primary school students, with a focus on the mediating role of depressive symptoms and the moderating effect of classmate relationships.MethodsA cross-sectional survey was conducted among 33,285 students (grades 3–6; mean age = 10.36 years) in the Shapingba District of Chongqing, China, from September to December 2020. Self-report measures included the Children’s Depression Inventory (CDI), general demographic data, self-harm behaviors, and parental marital status. Data were analyzed using SPSS 26.0 for descriptive statistics and Mplus 8.1 for structural equation modeling (SEM), assessing the effects of parental marital status on self-harm.ResultsThe reporting rates of depression and self-harm in grades 3–6 of primary school are 16.3% and 12.7%, respectively. Parental separation exhibited a more pronounced overall impact on self-harm (β = 0.120) compared to divorce (β = 0.105). Positive classmate relationships mitigated the indirect effect of separation on self-harm mediated by depression, reducing it from 0.098 to 0.072. Additionally, these relationships attenuated the direct effect of divorce on self-harm, decreasing it from 0.088 to 0.043. Depression significantly mediates the relationship between parental separation and children’s self-harm, with direct and indirect effects accounting for 53% (β = 0.057) and 47% (β = 0.063) of the total effect, respectively.ConclusionThe marital status of parents, especially in cases of separation, has a significant impact on self-harm behaviors among primary school students, with depression acting as a key mediating factor. Supportive classmate relationships can alleviate this effect, highlighting their importance in mental health interventions. These findings offer valuable insights for the development of policies aimed at reducing self-harm and enhancing psychological well-being among children. creator: Ming Ai creator: Xiao-Ming Xu creator: Wo Wang creator: JianMei Chen creator: Jinglan He creator: Qi Zhang creator: Su Hong creator: Yao Gan creator: Jun Cao creator: Daqin Ding creator: Jinhui Hu creator: Shuang Zhang creator: Li Kuang uri: https://doi.org/10.7717/peerj.19307 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ai et al. title: Biomass allocation, carbon content change and carbon stock distribution of Scots pine (Pinus sylvestris var. mongholica) plantation forests at different stand ages and densities in the sandy area of western Liaoning Province, China link: https://peerj.com/articles/19232 last-modified: 2025-04-04 description: Scots pine (Pinus sylvestris var. mongholica) is one of the main afforestation species in the southeastern edge of the Horqin Sandy Land, which not only effectively prevents the expansion of the sandland, but also serves as an important carbon reservoir. Uncovering the biomass allocation, carbon content changes and carbon stock distribution among organs of Scots pine at different ages and densities can provide a theoretical basis for rational afforestation and management in the western Liaoning sandy area. In this study, the biomass and carbon content of four organs, namely, trunk, branch, leaf and root, were measured at different age classes (young stage, half-mature stage, near-mature stage, mature stage and over-mature stage forests) and densities, and the carbon stock of Scots pine plantations in the western Liaoning sandy area was estimated. The results showed that the biomass of all organs except leaves increased with the increase of stand age, but the rate of increase of each organ was not consistent. To resist wind and sand, the biomass was preferentially allocated to the trunk and roots, which was in line with the theory of allometry and optimal allocation. The carbon content of each organ of Scots pine increases and then decreases with the rise of forest age classes, and the root carbon content is the lowest in five forest ages, and the plant carbon is mainly stored in the aboveground part. The biomass of each organ in both near mature and mature forests increased with the decrease in density. Still, the root carbon content decreased with the decrease of density, and the PCA analysis showed that near mature and mature forests had better carbon sequestration capacity in low density. The carbon stock of Scots pine plantation forests in the sandy area of western Liaoning was mainly concentrated in Fuxin and Chaoyang cities, and the lowest carbon stock was found in Jinzhou. The age and density of the forest stand are important factors affecting the biomass and carbon content of Scots pine, therefore, when operating Scots pine plantation forests in the sandy areas of western Liaoning, different stand densities should be retained at different age stages, so that their biomass and carbon content can be sufficiently accumulated and distributed to improve the local environment. creator: Xin Ai creator: Xiangyu Yang creator: Zhaowei Zhang creator: Hao Chen creator: Wenhui Tang creator: Qingyu Wang creator: Yutao Wang creator: Ping Liu uri: https://doi.org/10.7717/peerj.19232 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ai et al. title: Comparison of electromagnetic navigation bronchoscopic localization and computed tomographic imaging-guided methylene blue localization in the resection of pulmonary nodules: a retrospective cohort study link: https://peerj.com/articles/19224 last-modified: 2025-04-04 description: BackgroundAccurate localization of small-to-medium pulmonary nodules before video-assisted thoracoscopic surgery (VATS) is essential for success. Traditional imaging methods face challenges in the thoracic cavity. This study compares electromagnetic navigational bronchoscopic (ENB), computed tomography (CT)-guided localization effectiveness and safety with methylene blue marker dye.Materials and MethodsThis study, approved on May 4, 2024 by the Institutional Review Board of Wuhan Union Hospital (IRB ID UHCT240340) affiliated with Tongji Medical College, included patients with pulmonary nodules scheduled for VATS. Methylene blue was used as a marker dye and injected via CT-guided percutaneous or ENB techniques. The study compared clinical parameters, success rates, and complications between the two localization methods.ResultsOut of 378 patients who underwent preoperative localization, 254 received electromagnetic navigational bronchoscopy (ENB) and 124 had CT-guided percutaneous marker dye injections. Nodules were significantly larger in the ENB group (p < 0.001). Success rates were similar: ENB at 97.24% and CT-guided at 97.58%. ENB was more effective in the upper lobes than the lower lobes (p = 0.005), with no lobar preference for CT-guided localization (p = 0.073). ENB also had significantly fewer complications than CT-guided procedures (p < 0.001).ConclusionsENB localization success rates are comparable to CT-guided methods, but ENB carries lower risks, particularly for puncture-related complications. CT-guided localization is more effective than ENB for lower lobe nodules. creator: Babou Sowe creator: Junhao Wan creator: Fengjing Yang creator: Chuangyan Wu creator: Sihua Wang creator: Song Tong uri: https://doi.org/10.7717/peerj.19224 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sowe et al. title: Increasing leaf sizes of the vine Epipremnum aureum (Araceae): photosynthesis and respiration link: https://peerj.com/articles/19214 last-modified: 2025-04-04 description: The canopy leaves of allomorphic aroid vines can exceed 2,000 cm2, up to 30 times larger than respective understorey leaves. In the literature, this allomorphic increase in leaf area of aroid vines was hypothesized to improve its light foraging capacity. The viability of these large leaves depends on carbon acquisition obtained from their larger area and on the respective costs of production, maintenance and support. To evaluate and understand how leaf enlargement affects performance, we analyzed the photosynthesis and respiration of Epipremnum aureum leaves of different sizes via photosynthetic response light curves, morpho-physiology and anatomical parameters. Leaf size was increased by varying growth direction (horizontal vs. vertical) and light conditions (low vs. high). Vertical plants in high light produced leaves 9–13 times larger than those under other conditions. Saturated photosynthetic rates per area were similar across leaves of E. aureum, regardless of size, but respiration rates increased while specific leaf area decreased in larger leaves. This may suggests that larger leaves do not offset their costs per unit area in the short term, despite field observations of continuous enlargement with increased plant size. However, the high light levels able to saturate photosynthesis under field conditions are achieved only by larger leaves of E. aureum positioned at canopies (PPFD around 1,000 µmol m−2 s−1), not occurring at understory where smaller leaves are positioned (PPFD around 100 µmol m−2 s−1). This is confirmed by the higher values of the relative growth rate (RGR) and net assimilation rate (NAR) parameters exhibited by the vertical plants in high light. The saturated photosynthetic rates found here under experimental conditions for the smaller leaves of E. aureum could be related to their high invasive capacities as alien species around the world. We propose that the costs of larger aroid leaves might be outweighed by a strategy that optimizes size, morphophysiology, anatomy, photosynthesis and, lifespan to maximize lifetime carbon gain in tropical forests. creator: Carolina Brito creator: Dulce Mantuano creator: Karen L.G. De Toni creator: André Mantovani uri: https://doi.org/10.7717/peerj.19214 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Brito et al. title: Advances in solubilization and stabilization techniques for structural and functional studies of membrane proteins link: https://peerj.com/articles/19211 last-modified: 2025-04-04 description: Membrane proteins (MPs) are indispensable in various biological processes, including material transport, signal transduction, immune response, and cell recognition. Unraveling the intricate interplay between MP structure and function is pivotal for advancing fundamental biology and pharmaceutical research. However, the inherent hydrophobicity and complex lipid interactions of MPs pose significant challenges in determining their three-dimensional configurations. In recent years, cryo-electron microscopy (cryo-EM) has emerged as a powerful alternative for structural elucidation, overcoming the challenges faced by traditional techniques such as X-ray crystallography and nuclear magnetic resonance (NMR). This review centers on advanced solubilization and stabilization techniques for MPs, as well as MP functions and expression systems, highlighting the strengths and limitations of conventional detergents, liposomes, bicelles, and nanodiscs, alongside emerging alternatives like styrene-maleic acid (SMA) and diisobutylene-maleic acid (DIBMA). Notably, SMA and its derivatives provide promising detergent-free alternatives that preserve protein stability and native conformation, which is particularly valuable for accurate cryo-EM characterization of complex MPs. This work is designed to serve as both an updated resource for researchers already immersed in the field and an accessible entry point for those new to MP research. By consolidating recent advancements and highlighting critical gaps, this review aims to inspire future investigations that push the boundaries of MP structural and functional studies, ultimately driving innovations in drug discovery and therapeutic development. creator: Zhuanghan Zhou creator: Zheng Chen creator: Yiran Li creator: Xingyue Mao creator: Junjie Chen creator: Xuan Zhou creator: Bo Zhang uri: https://doi.org/10.7717/peerj.19211 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhou et al. title: Autonomous wave gliders as a tool to characterize delphinid habitats along the Florida Atlantic coast link: https://peerj.com/articles/19204 last-modified: 2025-04-04 description: As climate change and anthropogenic activities continue to impact cetacean species, it becomes increasingly urgent to efficiently monitor cetacean populations. Continuing technological advances enable innovative research methodologies which broaden monitoring approaches. In our study, we utilized an autonomous wave glider equipped with acoustic and environmental sensors to assess delphinid species presence on the east Florida shelf and compared this approach with traditional marine mammal monitoring methods. Acoustic recordings were analyzed to detect delphinid presence along the glider track in conjunction with subsurface environmental variables such as temperature, salinity, current velocity, and chlorophyll-a concentration. Additionally, occurrences of soniferous fish and anthropogenic noise were also documented. These in-situ variables were incorporated into generalized additive models (GAMs) to identify predictors of delphinid presence. The top-performing GAM found that location, sound pressure level (SPL), temperature, and chlorophyll-a concentration explained 50.8% of the deviance in the dataset. The use of satellite environmental variables with the absence of acoustic variables found that location, derived current speed and heading, and chlorophyll-a explained 44.8% of deviance in the dataset. Our research reveals the explanatory power of acoustic variables, measurable with autonomous platforms such as wave gliders, in delphinid presence drivers and habitat characterization. creator: Jessica Carvalho creator: Laurent M. Chérubin creator: Greg O’Corry-Crowe uri: https://doi.org/10.7717/peerj.19204 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Carvalho et al. title: Appraisal of healthcare students and professionals’ knowledge and intention to educate the public regarding monkeypox (Mpox) link: https://peerj.com/articles/19162 last-modified: 2025-04-04 description: BackgroundIn light of the increasing prevalence of monkeypox (Mpox) infections worldwide, it is critical to assess the level of awareness regarding the disease and its transmission among healthcare students and professionals. Understanding the knowledge gaps within these groups is essential, as they play a vital role in infection prevention and public education.ObjectivesThis study aimed to assess healthcare students and professionals’ knowledge and intention to educate the public regarding Mpox.MethodsAn anonymous survey consisting of 37 items was constructed utilizing scientific information pertaining to Mpox, obtained from sources such as the World Health Organization (WHO), Centers for Disease Control and Prevention (CDC), and previous studies. The study sample comprised healthcare professionals and students who were residents of the Al-Jouf province in Saudi Arabia. Significant associations between sociodemographic data and the knowledge and intention to educate the public about Mpox were compared using statistical methods. The comparison of means for two or more than two groups were performed using Student t-test and one-way ANOVA, respectively. Furthermore, ordinal logistic regression was employed for further analysis.ResultsOut of 545 responses, 437 (80.2%) were incorporated into the final analysis. Almost half of the participants in the study were female (51.5%) and 44.2% fell within the age range of 20 to 25 years. Moreover, 49.7% of the participants were unmarried and 29.5% held a bachelor’s degree. Over seven in ten participants were cognizant of the fact that Mpox is a public health emergency of international concern, whereas less than half of the participants were cognizant of the fact that Mpox has been reported in Saudi Arabia. The overall mean knowledge score was 10.40 ± 4.88 (score range: 0 to 21). Approximately 3.9% of the participants possess excellent knowledge (score > 17) and 44.9% possess average knowledge (score 12–17). The male gender, older participants, married, healthcare professionals and those in the medicine field were more knowledgeable. More than half of the study participants are willing to educate the public regarding Mpox, where overall intention score was 21.39 ± 6.84 (range 6 to 30). The female, married and those in the physiotherapy field showed more positive attitude and intention to educate the public regarding Mpox.ConclusionsDespite the fact that the majority of participants had a high or moderate intention to educate the public about Mpox, their knowledge ranged from average to poor. In light of these findings, educational programs aimed at enhancing the knowledge and awareness of healthcare professionals and students regarding Mpox are required. creator: Malik Suliman Mohamed creator: Mona Timan Idriss creator: Nasser Hadal Alotaibi creator: Yusra Habib Khan creator: Tauqeer Hussain Mallhi uri: https://doi.org/10.7717/peerj.19162 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Suliman Mohamed et al. title: First three new species of free-living marine nematodes of the Molgolaimus (Nematoda: Desmodoridae) from the continental shelf of the Brazilian coast (Atlantic Ocean) link: https://peerj.com/articles/19156 last-modified: 2025-04-04 description: Three new species of the Molgolaimus (Nematoda: Desmodoridae) are described from sample sediments collected in the South Atlantic, along the continental shelf break of Northeastern Brazil. This is the first time that new species of Molgolaimus have been described from sample sediments collected in the Brazilian coast. Molgolaimus sigmoidessp. nov. is characterized by four small cephalic sensillae, a buccal cavity with three small teeth, S-shaped spicules and gubernaculum with dorsal-caudal apophysis. Molgolaimus paralongispiculumsp. nov. possesses four setiform cephalic sensillae, a buccal cavity with three teeth, thin and elongated spicules and gubernaculum with anteriorly oriented apophysis. Molgolaimus brevispiculumsp. nov. is characterized by its possession of four setiform cephalic sensillae, an unarmed buccal cavity, short spicules and absent gubernaculum. We propose to amend the diagnosis of the genus, redistribute Molgolaimus species into subgroups 1b1 and 1b2, and to rearrange the order of presentation of subgroups 4a and 4b. creator: Alex Manoel creator: Patrícia F. Neres creator: Andre M. Esteves uri: https://doi.org/10.7717/peerj.19156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Manoel et al. title: Root fragment weight and carbohydrate dynamics of two weedy thistles Cirsium arvense (L.) Scop. and Sonchus arvensis L. during sprouting link: https://peerj.com/articles/19155 last-modified: 2025-04-04 description: Understanding the carbohydrate dynamics of sprouting Cirsium arvense (L.) Scop. and Sonchus arvensis L. ramets can assist in optimizing perennial weed management. However, detailed knowledge about general reserve dynamics, minimum values in reserves (compensation point) and different reserve determination methods remains sparse. We present novel insights into reserve dynamics, which are especially lacking for S. arvensis. We uniquely compare root weight changes as a proxy for carbohydrates with direct carbohydrate concentration measurements using high-performance liquid chromatography (HPLC). In a greenhouse study, ramets of two sizes (20 and 10 cm) were planted in pots. Subsequent creeping roots of sprouted plants were destructively harvested and analyzed for carbohydrates 12 times between planting and flowering. Efficiency in storing carbohydrates and the replenishing rate of root weight and carbohydrates was much higher in S. arvensis than in C. arvense. Thus, our study urges to evaluate perennial weed species individually when investigating root reserves. Determining root reserves by either using root weight changes as a proxy for carbohydrates or directly measuring carbohydrate concentrations by HPLC differed in the minimum values of reserves referred to as compensation points. For both species, these minimum values occurred earlier based on root weight than based on carbohydrate concentrations. Cutting ramets into 20 or 10 cm sizes did not significantly affect carbohydrate concentration or root weight changes for both species. We conclude that any practical applications targeting perennial weeds by fragmenting roots into small ramets through belowground mechanical control must be evaluated for trade-offs in soil structure, soil erosion, and energy consumption. creator: Marian Malte Weigel creator: Sabine Andert creator: Manuela Alt creator: Kirsten Weiß creator: Jürgen Müller creator: Bärbel Gerowitt uri: https://doi.org/10.7717/peerj.19155 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Weigel et al. title: Selective enrichment of active bacterial taxa in the Microcystis associated microbiome during colony growth link: https://peerj.com/articles/19149 last-modified: 2025-04-04 description: The toxic cyanobacterium Microcystis causes worldwide health concerns, being frequently found in freshwater and estuarine ecosystems. Under natural conditions, Microcystis spp. show a colonial lifestyle involving a phycosphere populated by a highly diverse associated microbiome. In a previous study, we have proposed that colony formation and growth may be achieved through mechanisms of multispecies bacterial biofilm formation. Starting with single-cells, specific bacteria would be recruited from the environment to attach and create a buoyant biofilm or colony. This progression from a few single cells to large colonies would encompass the growth of the Microcystis community and bloom formation. In order to test this, we applied 16S rDNA metabarcoding to evaluate the changes in bacterial community structure (gDNA) and its active portion (cDNA) between different sample sizes obtained from a Microcystis bloom. Bloom sample was sieved by size, from one or a few cells (U fraction) to large colonies (maximum linear dimension ≥ 150 µm; L fraction), including small (20–60 µm, S fraction) and medium size (60–150 µm, M fraction) colonies. We found that gDNA- and cDNA-based bacterial assemblages significantly differed mostly due to the presence of different taxa that became active among the different sizes. The compositional variations in the communities between the assessed sample sizes were mainly attributed to turnover. From U to M fractions the turnover was a result of selection processes, while between M and L fractions stochastic processes were likely responsible for the changes. The results suggest that colony formation and growth are a consequence of mechanisms accounting for recruitment and selection of specific bacterial groups, which activate or stop growing through the different phases of the biofilm formation. When the final phase (L fraction colonies) is reached the colonies start to disaggregate (bloom decay), few cells or single cells are released and they can start new biofilms when conditions are suitable (bloom development). creator: Carolina Croci creator: Gabriela Martínez de la Escalera creator: Carla Kruk creator: Angel Segura creator: Susana Deus Alvarez creator: Claudia Piccini uri: https://doi.org/10.7717/peerj.19149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Croci et al. title: Attitudes towards communication and perceived self-efficacy in nursing students: a longitudinal observational study link: https://peerj.com/articles/19139 last-modified: 2025-04-04 description: BackgroundCommunication is recognised as a critical component of all nursing interventions. For nurses to be able to communicate effectively, they need to develop communication skills during their training. Despite this recognition, there is still a lack of consensus about where and when in the syllabus this content should be covered, and how much time should be devoted to this competence, resulting in a inadequate and inconsistent training. Consequently, students develop negative or positive attitudes towards communication. The aim of this study was to analyse the evolution of attitudes towards communication and perceived self-efficacy in a cohort of undergraduate nursing students.MethodsWe conducted a prospective longitudinal observational study with three measurement points. Attitudes towards communication and self-efficacy were measured until the 2022–2023 academic year.ResultsParticipants included 131 undergraduate nursing students with a mean age of 20.44 years (SD = 6.08). The scores for attitudes towards communication were not linear. Baseline scores were higher than those recorded at the second assessment, and then scores increased again after the training. Scores for perceived self-efficacy increased progressively over the course of the training programme.ConclusionAttitudes towards communication and perceived self-efficacy do not intrinsically improve with age, course progression or clinical experience. When specific training in communication skills is not provided, students perceive their communication skills to be moderate and regard communication as a clinical competence of limited relevance . However, after receiving specific person-centred training in their final year, students perceived their ability to be highly in what is a very relevant competence in the healthcare context. creator: Rocío Juliá-Sanchís creator: Silvia Escribano creator: Juana Perpiñá-Galvañ creator: Sofía García-Sanjuán creator: María Sánchez-Marco creator: María José Cabañero-Martínez uri: https://doi.org/10.7717/peerj.19139 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Juliá-Sanchís et al. title: Fecal glucocorticoid metabolite and T3 profiles of orphaned elephants differ from non-orphaned elephants in Zambia link: https://peerj.com/articles/19122 last-modified: 2025-04-04 description: BackgroundElephants provide valuable insight into how early-life adverse events (ELAEs) associate with animal health and welfare because they can live to advanced ages, display extensive cognitive and memory capabilities, and rely heavily on social bonds. Although it is known that African savanna elephants that experienced ELAEs, such as being orphaned due to human activities, have altered behavioral outcomes, little is known regarding the physiological consequences associated with those stressors.MethodsWe compared fecal glucocorticoid (fGCM) and thyroid (fT3) metabolites as well as body condition scores (BCS) in rescued and rehabilitated orphaned (early-dry season: n = 20; late-dry season: n = 21 elephants) African savanna elephants in Kafue National Park, Zambia to age- and sex-matched wild non-orphaned controls groups (early-dry season: n = 57; late-dry season: n = 22 elephants) during the early- (May/June) and late- (September/October) dry seasons, respectively. Age and sex were known for orphans. For non-orphan controls, age was estimated based on dung diameter, and sex was determined based on external genitalia. Hormone concentrations were compared between groups by age class to account for developmental and nutritional transitions experienced in early life. Given that environmental stressors (e.g., availability of food and water sources) change over the course of the dry season, early- and late-dry seasons were separated in the analyses.ResultsfGCM concentrations were higher in orphans at younger ages than non-orphaned controls of any age. This may be due to the younger orphans being temporally closer to the traumatic event and thus not having had sufficient time to establish meaningful social bonds that could buffer the negative outcomes associated with ELAEs. Alternatively, orphans could have acclimated to living under human care, resulting in fGCM concentrations that were not different from wild controls at older ages. Orphans also had significantly higher mean fT3 concentrations than non-orphans, suggesting increased caloric intake during rehabilitation. There was no difference in BCS between orphan and non-orphan elephants at any age or time period, possibly reflecting the limitations associated with BCS assessments in younger elephants.ConclusionsTogether, these results provide insight into possible physiological responses underlying ELAEs and/or living under human care, including alterations in fGCM and fT3 concentrations, particularly in younger orphans. While these hormonal changes suggest a physiological response to trauma, the support of social bonds and acclimation to human care may mitigate long-term stress effects, highlighting the critical role of social integration in elephant rehabilitation and conservation efforts. creator: Daniella E. Chusyd creator: Janine L. Brown creator: Steve Paris creator: Nicole Boisseau creator: Webster Mwaanga creator: Moses Kasongo creator: Lisa Olivier creator: Stephanie L. Dickinson creator: Bailey Ortyl creator: Tessa Steiniche creator: Steven N. Austad creator: David B. Allison creator: Michael D. Wasserman uri: https://doi.org/10.7717/peerj.19122 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chusyd et al. title: Advancing medicinal plant agriculture: integrating technology and precision agriculture for sustainability link: https://peerj.com/articles/19058 last-modified: 2025-04-04 description: To strengthen the agriculture sector, it is crucial to combine the efforts of industrialization (field mechanization and fertilizer production), technology (genome editing and manipulation), and the information sector (for the application of current technologies in precision agriculture). The challenge of modern sustainable agriculture is increasing agricultural output while using the least amount of resources and capital expenditure possible and considering the variables contributing to environmental damage. Different environmental factors adversely affect medicinal plant populations, leading to the extinction of these valuable medicinal species. These difficulties drew the attention of the international scientific community to farm sustainability and energy efficiency studies that put forth the idea of precision agriculture (site-specific crop management) in medicinal plants. It is a systems-based method that monitors and responds to changes in intra- and inter-field conditions for environmentally friendly and optimum crop output. Farming systems have significantly benefited from the visualization and morphological analysis of agricultural areas (both open fields and greenhouse experiments) using remote sensing technology, geographic information systems (GIS), crop scouting, variable rate technology (VRT), and Global Positioning System (GPS). These technologies form the backbone of the fourth agricultural technological revolution, Agriculture 4.0. This review concisely summarizes these innovative technologies’ current use and potential future advancements in medicinal plants. The review is intended for researchers, professionals in medicinal plant cultivation, herbal medicine research, crop science, and related fields. creator: Vinay Kumar creator: Ashwini Zadokar creator: Pankaj Kumar creator: Rohit Sharma creator: Rajnish Sharma creator: Mohammed Wasim Siddiqui creator: Mohammad Irfan creator: Rahul Chandora uri: https://doi.org/10.7717/peerj.19058 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kumar et al. title: Contrast in the density and biomass of fish in a reef system with different fishing intensity in the Mexican Caribbean link: https://peerj.com/articles/19031 last-modified: 2025-04-04 description: A wide range of fish species are caught in reef fisheries. However, fishing efforts tend to be highly selective in favor of large species, which generally have low population growth rates, making them more vulnerable to overfishing. When the decline of large predators occurs, fishing efforts start to focus on catching species from lower trophic levels, which can cause a trophic cascade effect. The objective of this research was to detect changes in the density and biomass of fish communities in areas with different fishing intensity in the study area. This study was carried out in the Banco Chinchorro Biosphere (BCBR) in the Mexican Caribbean and analyze the effect of fishing intensity on fish density and biomass, comparing data obtained from visual censuses with dependent information of the fishery. Evidence was found of a relationship between high fishing exploitation and low levels of density and biomass for Epinephelus striatus, E. guttatus and Lachnolaimus maximus. The decline of predators had no evident effect on the density and biomass of non-commercially important species. The density and biomass of commercially important fish species were influenced by the presence of algae, octocorals, hydrocorals and by variations in their catch per unit of effort (CPUE). This study detected that density and biomass have decreased in some species belonging to the Serranidae and Lutjanidae families in areas with high fishing intensity. On the other hand, little evidence was found that the density and total biomass of families of noncommercially important species increased through the decline of their predators. These results are consistent with previous work documenting how fishing activity affects fish species with high trophic levels. The information generated will help the Reserve’s managers make decisions towards better management and conservation of fishery resources. creator: José Manuel Castro-Pérez creator: Carmen Amelia Villegas-Sánchez creator: Alejandro Medina-Quej creator: Rigoberto Rosas-Luis creator: Jesús E. Arias-González uri: https://doi.org/10.7717/peerj.19031 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Castro-Pérez et al. title: Implications of high-dose vitamin D3 with and without vitamin C on bone mineralization and blood biochemical factors in broiler breeder hens and their offspring link: https://peerj.com/articles/18983 last-modified: 2025-04-04 description: As broiler breeder hens age, they often experience a decline in bone mineralization and calcium absorption, especially during the later stages of egg production. This issue not only affects the hens’ health, making them more prone to conditions like osteoporosis, but it also impacts the quality of their offspring. To tackle this problem, our study explores whether supplementing these hens with a combination of vitamins D3 and C could help improve their bone health and overall biochemical balance, both for them and their progeny. The goal of this research was to evaluate the effects of high doses of vitamin D3, with and without added vitamin C, on bone mineralization and key blood parameters in aging broiler breeder hens and their offspring. In this experiment, 240 hens and 24 roosters from the Ross 308 strain, aged between 49 and 61 weeks, were used, and a two-way ANOVA (2 × 2) design was applied. This involved two levels of vitamin D3 (3,500 IU and 5,500 IU) and two levels of vitamin C (0 and 150 mg/kg), with six replications of 10 hens and one rooster per group. At the end of the study, blood samples were collected from hens and their offspring for biochemical analysis, and tibia bones were taken for ash content and mineralization assessment. The findings showed that vitamin D3 supplementation significantly lowered blood cholesterol, alkaline phosphatase (ALP), and parathyroid hormone (PTH) levels (P < 0.05), while boosting calcium, 25-hydroxycholecalciferol (25(OH)D3), and 1,25-dihydroxycholecalciferol (1,25(OH)2D3) (P < 0.05). Higher doses of vitamin D3 also improved the strength, resistance, and ash content of the hens’ tibia bones, and increased calcium in the carcasses of their offspring. Adding 150 mg/kg of vitamin C to the diet also had a positive effect, reducing cholesterol, ALP, and PTH, while enhancing plasma calcium, total antioxidant capacity, and the active form of vitamin D3 (P < 0.05). Vitamin C supplementation significantly strengthened the tibial bones of the hens and improved plasma calcium and PTH levels in their offspring (P < 0.05). Interestingly, combining elevated doses of both vitamins D3 and C resulted in even greater improvements in tibial bone strength (P < 0.05). In conclusion, giving hens 150 mg of vitamin C along with 5,500 IU of vitamin D3 leads to substantial improvements in the calcium content and structural integrity of their bones, and also boosts calcium and ash content in the carcasses of their offspring. creator: Ruhollah Kianfar creator: Reza Kanani creator: Hossein Janmohammadi creator: Majid Olyaee creator: Maghsoud Besharati creator: Maximilian Lackner uri: https://doi.org/10.7717/peerj.18983 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kianfar et al. title: Saudi radiology trainees’ insights on safety and professionalism in the workplace link: https://peerj.com/articles/19257 last-modified: 2025-04-03 description: Introduction/PurposeIn the radiology department, where advanced technologies and multidisciplinary collaboration are crucial, establishing a strong safety culture is particularly challenging. The present cross-sectional study examines the challenges of establishing a safety culture in radiology, focusing on how Saudi radiology trainees perceive and respond to safety and unprofessional conduct. It evaluates their willingness to voice concerns and the influencing factors, including workplace culture, potential patient risks, and demographics.MethodsThe present study surveyed Saudi radiology residents and interns at two tertiary hospitals using a validated questionnaire. A non-probability total population purposive sampling method was employed. Descriptive statistics, Mann-Whitney U test, and Kruskal-Wallis H test were used to analyze differences in willingness to speak up across demographic groups.ResultsParticipants felt encouraged by colleagues to address patient safety and unprofessional behavior, with over 70% and 56% respectively agreeing. Residents demonstrated significantly greater support for raising concerns about safety and unprofessional conduct compared to interns (mean rank = 47.58 vs. 33.91, p = 0.009). Furthermore, residents expressed a stronger belief that speaking up leads to meaningful changes (mean rank = 46.24 vs. 35.36, p = 0.033) and reported observing others addressing these issues more frequently (mean rank = 46.98 vs. 34.56, p = 0.015). Trainees from different hospitals exhibited significantly varied perceptions regarding support from colleagues in addressing patient safety and unprofessional behavior (mean rank = KAMC 54.53 vs. KSMC 33.04, p < 0.0001), the perceived impact of raising concerns (mean rank = KAMC 50.50 vs. KSMC 35.41, p = 0.004), and the frequency of observing these concerns being addressed (mean rank = KAMC 55.28 vs. KSMC 32.60, p < 0.0001). Radiology trainees are particularly vigilant about unintentional breaches of sterile technique, often addressing these issues with nurses (66.7%).ConclusionThe clinical environment supports safety concerns but less so for unprofessional behavior, with residents being more proactive. Promoting open communication in radiology requires leadership education, multifaceted strategies, alternative channels for concerns, and future research to assess and track cultural attitudes. The findings highlight the need to cultivate a supportive culture for speaking up in clinical settings, particularly in radiology, where trainee involvement can enhance patient safety and professional conduct. The present study lays the groundwork for future research and interventions to strengthen safety and professionalism among medical trainees in Saudi Arabia. creator: Khalid M. Alshamrani creator: Elaf K. Basalamah creator: Ghadah M. AlQahtani creator: Manar M. Alwah creator: Rahaf H. Almutairi creator: Walaa Alsharif creator: Awadia Gareeballah creator: Adnan AS Alahmadi creator: Shrooq T. Aldahery creator: Sultan A. Alshoabi creator: Abdulaziz A. Qurashi uri: https://doi.org/10.7717/peerj.19257 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alshamrani et al. title: Tumor marker elevations in chronic kidney disease: a retrospective study link: https://peerj.com/articles/19240 last-modified: 2025-04-03 description: AimTo investigate the changes in tumor markers such as carbohydrate antigen 125 (CA125), carbohydrate antigen 153 (CA15-3), carbohydrate antigen 19-9 (CA19-9), carbohydrate antigen 72-4 (CA72-4), pro-gastrin-releasing peptide (proGRP), and human epididymis protein 4 (HE4) in patients with chronic kidney disease (CKD) as compared to healthy individuals, and to analyze the potential indicators that can be utilized for monitoring early renal dysfunction, was the aim of this study.MethodsThis retrospective study involved 522 participants from our hospital, including 172 patients with CKD and 350 controls. CKD patients were divided into CKD1, CKD2, CKD3, CKD4, and CKD5 stages according to the estimated glomerular filtration rate (eGFR). Plasma creatinine and general clinical data were collected upon admission.ResultsThe level of tumor biomarkers, including carcinoembryonic antigen (CEA), CA125, CA15-3, CA19-9, NSE, proGRP, and HE4, were elevated in patients with CKD (p < 0.05). There were differences in CEA, CA125, CA19-9, NSE, proGRP, and HE4 between the control and CKD groups. The subgroup study showed that CEA, CA15-3, CA19-9, NSE, proGRP, and HE4 were elevated in patients with CKD having normal serum creatinine compared with those in the control group (p < 0.05). ProGRP and HE4 have high predictive values for early renal insufficiency with area under the curve of 0.736 and 0.931, respectively (p < 0.05). Furthermore, HE4 and proGRP were positively correlated with the stages of CKD, with correlation coefficients of 0.623 and 0.712, respectively.ConclusionsPatients with CKD have higher tumor markers, some of which are helpful for the early diagnosis of renal impairment. creator: Liuxia You creator: Zhongying Xu creator: Qiaoling Liu creator: Guoming Jin creator: Changting Wang uri: https://doi.org/10.7717/peerj.19240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 You et al. title: A multi-center cross-sectional investigation of BRAF V600E mutation in Ameloblastoma link: https://peerj.com/articles/19137 last-modified: 2025-04-03 description: BackgroundB-Raf proto-oncogene, serine/threonine kinase (BRAF) V600E mutation stands as a pivotal genetic alteration strongly associated with several neoplasms and contributes significantly to their pathogenesis as well as potential targeted treatment strategies.ObjectiveThis cross-sectional study aimed to determine the frequency of BRAF V600E mutation in ameloblastoma in a multi-center of Thailand.MethodAnti-BRAF V600E (clone VE1) immunohistochemistry was performed on 227 conventional ameloblastoma (AM) and 113 unicystic ameloblastoma (UA) samples collected from four major dental schools located in the Central, North, South, and Northeast regions of Thailand. Tumor cells from randomly chosen AM cases were also micro-dissected from the FFPE sections and subjected to DNA sequencing to confirm the immunohistochemical results.ResultsBRAF V600E mutation was detected in 71.8% of the AM samples, while 65.5% of samples with UAs demonstrated BRAF V600E positivity. The BRAF V600E mutation was significantly different in the histological subtypes of AMs in the four centers (p = 0.012) and the location of UA in three centers (p = 0.013). There was no significant association between the BRAF V600E mutation and the location of ameloblastoma in the overall prevalence of our multi-center study; nonetheless, a statistically significant association was found between the BRAF V600E mutation and the mandible location of AMs from the Central Faculty of Dentistry, Mahidol University (MU) center (p = 0.033), as well as with the histological subtypes of AMs from the Southern Faculty of Dentistry, Prince of Songkla University (PSU) center (p = 0.009). No statistical association was observed between the BRAF V600E mutation and AM and UA recurrence (p = 0.920 and p = 0.312), respectively. The results of DNA sequencing performed in randomly selected 40 BRAF V600E-positive and 20 BRAF V600E-negative ameloblastoma tissues were in accordance with the immunohistochemical findings.ConclusionAs a result of a notable prevalence of BRAF V600E in Thai individuals diagnosed with ameloblastoma, they may benefit from the utilization of adjunctive anti-BRAF targeted therapy for treatment. creator: Khin Mya Tun creator: Puangwan Lapthanasupkul creator: Anak Iamaroon creator: Wacharaporn Thosaporn creator: Poramaporn Klanrit creator: Sompid Kintarak creator: Siwaporn Thanasan creator: Natchalee Srimaneekarn creator: Nakarin Kitkumthorn uri: https://doi.org/10.7717/peerj.19137 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tun et al. title: Advanced superimposition method to evaluate the marginal and internal fit of ceramic crowns fabricated using heat pressing techniques link: https://peerj.com/articles/19117 last-modified: 2025-04-03 description: BackgroundDigital technologies can enhance the success of permanent crowns. The present study aimed to evaluate marginal adaptation and internal fit of permanent crowns fabricated using stereolithography (SLA) and digital light processing (DLP) 3D printing technologies following scans using two different intraoral scanners (IOS) (Medit i700, shape (TRIOS 3)).MethodsThree typodont #14 teeth were prepared for full veneer all ceramic crowns with three types of margins—chamfer (CFL), rounded shoulder (RSFL) and rounded shoulder with bevel (RSBFL). A total of 360 study models were made and divided into two groups based on the type of intraoral scanner used for digital impressions. Group A in which the intraoral scanner MEDIT i700 was used, and Group B in which intraoral scanner TRIOS 3 was used (n = 360/group). The subgroups were made as Medit i700-SLA, Medit i700-DLP, TRIOS 3-SLA and TRIOS 3-DLP (n = 180/subgroup). These were further divided into three sub-subgroups based on the finish lines: CFL, RSFL, and RSBFL (n = 30 each sub-subgroups). All ceramic crowns were made on models and scanned to assess discrepancies (marginal adaptation and internal fit) at nine zones (Z1–Z9). Three-way analysis of variance and pairwise comparison was done (Tukey HSD test) (α = 0.05).ResultsThe mean marginal gap and internal fit values were lowest for Group A-1 with RSBFL in each zone. The intergroup comparison showed values for marginal gap and the internal fit were minimum for Group A-1 for each finish line design, with the lowest for RSBFL at zone Z2 0.04 ±0.001.ConclusionsRegardless of the IOS and 3D printing techniques, the smallest gap was observed in RSBFL, followed by RSFL and CFL. The all-ceramic crowns fabricated using a Medit intraoral scanner with an SLA 3DPrinter with a rounded shoulder finish line had the best marginal and internal fit. creator: Nasser M. Alqahtani creator: Saurabh Chaturvedi creator: Mohamed Khaled Addas creator: Manar Fahad A. AlQahtani creator: Arwa Ahmed M. Alhudiry creator: Shahrah H. Qahtani creator: Mohammad A. Zarbah creator: Asim Elsir Elmahdi creator: Marco Cicciù creator: Giuseppe Minervini uri: https://doi.org/10.7717/peerj.19117 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alqahtani et al. title: Evaluation of non-invasive hair snares for North American beavers (Castor canadensis): placement, efficiency, and beaver’s behavioral response link: https://peerj.com/articles/19080 last-modified: 2025-04-03 description: Although the commercial demand for North American beaver (Castor canadensis) hair shaped much of the socio-ecological landscape of North America, use of beaver hair in wildlife research has focused on the Eurasian beaver (Castor fiber) and collection methods have largely involved handling animals alive or sampling dead animals. In 2022 and 2023, we tested the utility of barbed-wire hair snares to non-invasively collect hair from beavers around ponds in Northern Minnesota. At 56 different beaver ponds, we deployed 64 hair snares with remote cameras. From these data, we determined the efficiency of hair snares to collect samples, from what side of the body samples are collected, the weight and dirtiness of samples collected, the potential for bycatch, and if snares impede beavers’ ability to travel on land. We collected beaver hair samples from 94% of snares deployed, with snares sampling beaver legs and back most often. Forty-two percent of samples collected had no dirt on them, and the most productive snare collected on average 3.4 mg of clean hair per day. Muskrats were the second most sampled animal, but only made up on average 16% of total samples recorded on video per snare. Snares inhibited beaver travel in 0.1% of videos (n = 5,627 videos of beavers recorded, n = 6 videos where beaver travel was inhibited). We did not find any predictive variable that influenced the collection of beaver hair (e.g., location of snare at pond, presence of wire brushes on snare, number of times beavers touched snares, or location on the beaver’s body that was sampled). Our study provides in depth evidence of passive hair snare methods used to collect North American beaver hair, and serves as a guide to non-invasive hair snaring for multiple objectives such as hormone, genetic, and stable-isotope sample collection. creator: Dani R. Freund creator: Joseph K. Bump uri: https://doi.org/10.7717/peerj.19080 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Freund and Bump title: A retrospective study on safety and clinical outcomes of unilateral biportal endoscopic technique for spinal degenerative diseases link: https://peerj.com/articles/19076 last-modified: 2025-04-03 description: Background and ObjectiveUnilateral biportal endoscopy (UBE) has been developing rapidly in coincidence with the popularization of minimally invasive spine surgery (MISS). However, the clinical outcome and invasiveness of UBE-assisted spinal surgery (UBESS) are undefined. The aim of the present study was to summarize the clinical outcome and surgical invasiveness of UBE for the treatment of various spinal degenerative diseases in a single center to validate the safety and application value of UBESS.MethodsIncluded in this study were 105 patients who received UBESS from November 2021 to June 2022 in our center. All patients were followed up postoperatively for at least 12 months. All basic information was recorded to depict the demographic and surgical variables. Clinical outcomes were assessed in terms of the operation time, complications, days of hospital stay, total blood loss, intraoperative blood loss, postoperative drainage volume, hidden blood loss, biochemical changes associated with surgical injury, comparison of the visual analogue scale (VAS) for back and leg pain, Japanese Orthopedic Association (JOA) scores for cervical diseases at preoperative and postoperative stage, as well as Oswetry Disability Index (ODI), and modified MacNab scores one year after treatment.ResultsOf the 105 included patients, 68 patients were with single-level lumbar degenerative diseases, 22 with two-level diseases, two with three-level diseases, 10 with single-level isthmic spondylolisthesis, and three with single-level cervical spondylotic radiculopathy. UBE was performed by using five surgical approaches. The operation time, days of hospital stay, blood loss, postoperative immobilization time and prognosis were all estimated in consideration of the surgical approaches and the number of operated segments. The mean operation time ranged from 80 min to 214 min for single-level spinal diseases, and 112 min to 330 min for two-level ones. Total blood loss was higher in multilevel spinal surgery and single-level UBE-assisted lumbar interbody fusion+discectomy (ULIFD). The postoperative immobilization duration was between 0.5 and 2 days for single level spinal diseases, 1 and 3 days for 2-level diseases, fewer than 2 days for three-level diseases, and 1.5–12 days for isthmic spondylolisthesis (IS). The VAS and ODI for lumbar diseases decreased significantly and the JOA scores for cervical diseases improved after operation. The satisfaction rate was 89.70%, 85.71%, 90.00%, 66.67%, and 90.00% for the five surgical approaches respectively.ConclusionsUBESS has proved to be a safe, reliable and minimally invasive option for spinal degenerative diseases, with significant benefits of pain control, rapid functional recovery, short hospitalization, and early rehabilitation. However, postoperative hidden blood loss should be put under the careful management when performing UBESS. creator: Haitao Sun creator: Qi Zhang creator: Kehan Xu creator: Zihuan Zhou creator: Dongjie Jiang creator: Shaohui He creator: Jilu Liu creator: Haifeng Wei uri: https://doi.org/10.7717/peerj.19076 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sun et al. title: Seasonal genetic variation and genetic structure of Spodoptera exigua in Liaoning Province, Northeast China: insights from 11 years of microsatellite data link: https://peerj.com/articles/19243 last-modified: 2025-04-02 description: BackgroundThe beet armyworm (BAW), Spodoptera exigua, is a destructive migratory pest worldwide that has caused severe economic losses in China’s major crop-producing regions. To control this pest effectively, it is crucial to investigate its seasonal genetic variation and population genetic structure in northern China.MethodsIn this study, we used eight nuclear microsatellite loci to investigate the seasonal genetic variation and genetic structure of BAW in Shenyang, Liaoning Province, Northeast China, from 2012–2022, collected from a single location on Welsh onion.ResultsMicrosatellite data revealed moderate levels of genetic variation among 50 seasonal populations of BAW sampled from 2012–2022, along with significant genetic differentiation among these populations. Neighbor-joining dendrograms, STRUCTURE analysis, and principal coordinate analysis (PCoA) revealed two genetically distinct groups: the SY2012–2018 group and the SY2019–2022 group. Our results revealed seasonal variation in the genetic subconstruction at this location, which may be related to the presence of different migratory individuals throughout the year. Accordingly, our unique insights into the population genetics of BAW will contribute to the development of effective management strategies for this migratory pest. creator: Ming-Li Yu creator: Xian-Zhi Xiu creator: Jin-Yang Wang creator: Xin-Yi Cao creator: Fa-Liang Qin creator: Xing-Ya Wang creator: Li-Hong Zhou uri: https://doi.org/10.7717/peerj.19243 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Yu et al. title: A new metriacanthosaurid theropod dinosaur from the Middle Jurassic of Yunnan Province, China link: https://peerj.com/articles/19218 last-modified: 2025-04-02 description: Metriacanthosaurid theropods represent a basal-branching lineage of tetanurans. Members of this clade are mainly medium to large-sized and lived in Laurasia during the Middle Jurassic to the Early Cretaceous. In this clade, Sinraptor dongi, Sinraptor hepingensis, and Yangchuanosarus shangyouensis from the Late Jurassic are well represented by the nearly complete specimens, but the incompleteness of Middle Jurassic taxa hinders our knowledge of the origin and early evolution of Metriacanthosauridae. This paper describes a new genus and species of metriacanthosaurids, Yuanmouraptor jinshajiangensis gen. et sp. nov, from the Middle Jurassic Zhanghe Formation of Yunnan Province, China. The new taxon is represented by a cranium and the anterior section of the vertebral column including the complete cervical series and the first dorsal vertebra. Yuanmouraptor jinshajiangensis can be diagnosed based on the following autapomorphies: the anterior process of postorbital sheet-shaped and keeping consistent depth; ventral ramus of postorbital bearing a laterally twisted trough running along its lateral surface; ventral surface of axial intercentrum parallel with that of axial centrum; discontinuity of inclination on anterodorsal margin of the third and fourth cervical vertebrae; strongly posteriorly elongated epipophyses of anterior cervical vertebrae; deeply excavated pneumatic foramina on the third cervical vertebra; sheet-shaped and subrectangular neural spines of posterior cervical vertebrae. Phylogenetic analysis recovers Yuanmouraptor as the most basal-branching member within Metriacanthosauridae and provides a new alternative phylogenetic topology of non-coelurosaurian tetanurans. creator: Yi Zou creator: Li Chen creator: Tao Wang creator: Guo-Fu Wang creator: Wei-Gang Zhang creator: Xiao-Qin Zhang creator: Zhen-Ji Wang creator: Xiao-Chun Wu creator: Hai-Lu You uri: https://doi.org/10.7717/peerj.19218 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zou et al. title: The role and mechanism of aerobic glycolysis in nasopharyngeal carcinoma link: https://peerj.com/articles/19213 last-modified: 2025-04-02 description: This review delves into the pivotal role and intricate mechanisms of aerobic glycolysis in nasopharyngeal carcinoma (NPC). NPC, a malignancy originating from the nasopharyngeal epithelium, displays distinct geographical and clinical features. The article emphasizes the significance of aerobic glycolysis, a pivotal metabolic alteration in cancer cells, in NPC progression. Key enzymes such as hexokinase 2, lactate dehydrogenase A, phosphofructokinase 1, and pyruvate kinase M2 are discussed for their regulatory functions in NPC glycolysis through signaling pathways like PI3K/Akt and mTOR. Further, the article explores how oncogenic signaling pathways and transcription factors like c-Myc and HIF-1α modulate aerobic glycolysis, thereby affecting NPC’s proliferation, invasion, metastasis, angiogenesis, and immune evasion. By elucidating these mechanisms, the review aims to advance research and clinical practice in NPC, informing the development of targeted therapeutic strategies that enhance treatment precision and reduce side effects. Overall, this review offers a broad understanding of the multifaceted role of aerobic glycolysis in NPC and its potential impact on therapeutic outcomes. creator: Zhiyong Pan creator: Yuyi Liu creator: Hui Li creator: Huisi Qiu creator: Pingmei Zhang creator: Zhiying Li creator: Xinyu Wang creator: Yuxiao Tian creator: Zhengfu Feng creator: Song Zhu creator: Xin Wang uri: https://doi.org/10.7717/peerj.19213 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pan et al. title: A case for myoglobin-macromolecular rate theory applied to pseudo peroxidase kinetics link: https://peerj.com/articles/19205 last-modified: 2025-04-02 description: This study explores the well-known catalytic behavior of myoglobin as a pseudo-peroxidase by applying macromolecular rate theory (MMRT) to assess its temperature-dependent enzyme kinetics. While myoglobin is primarily recognized for its oxygen-binding properties in muscle tissues, with a characterized pseudo-peroxidase ability to catalyze the degradation of hydrogen peroxide in the presence of electron donors, the claim that myoglobin is actually a true peroxidase can be explored by analyzing the heat capacity changes (ΔCp‡) in the catalyzed reaction at different temperatures and fitting the results to the expanded Eyring equation (MMRT equation). This research uses the MMRT equation to compare myoglobin’s catalytic activity (a pseudo-peroxidase) with that of lactoperoxidase (a true peroxidase) and copper ions (a non-enzymatic catalyst) across a range of temperatures at pH 5, after which the biological catalysts are compared again at pH 7. By analyzing the ΔCp‡ of these catalysts, it was found that myoglobin exhibits a significant catalytic contribution at both pH levels, suggesting a structural/vibrational or some other relatively significant transition during the reaction. The study’s findings provide a new perspective into myoglobin’s enzymatic role in peroxide decomposition and highlight the utility of MMRT in quantifying the contribution of polypeptide chains in enzyme-catalyzed peroxidase reactions. Additionally, our research notes the pH-dependence of myoglobin’s catalytic efficiency compared to traditional peroxidases, offering implications for understanding its broader biological roles. creator: Collin Tuttle creator: Michael Hannesson creator: Amy Henrichsen creator: Lily Hainsworth creator: Camille Condie creator: Aj Whitesides creator: Archel Oren creator: Simeon Tanner creator: Benjamin Terry creator: Jacob Cannon creator: Jeremy Johansen creator: Alisha Bhatia creator: Daniel Scott uri: https://doi.org/10.7717/peerj.19205 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tuttle et al. title: Measurements of white-to-white corneal diameter and anterior chamber parameters using the Pentacam AXL wave and their correlations in the adult Saudi population link: https://peerj.com/articles/19227 last-modified: 2025-04-01 description: BackgroundAssessment of eye parameters such as the white-to-white (WTW) corneal diameter, anterior chamber depth (ACD), and anterior chamber angle (ACA) are essential for preoperative evaluation of refractive surgery and diagnosing and managing some ocular diseases.ObjectiveTo report the distribution and association between white-to-white corneal diameter and anterior chamber parameters in the Saudi adult population.MethodsCross-sectional prospective study consisting of 82 Saudi adults. White-to-white corneal diameter, anterior chamber angle, anterior chamber depth, and axial length were collected from healthy subjects using the Pentacam AXL Wave in a tertiary eye care setting.ResultsMean white-to-white corneal diameter, anterior chamber angle, anterior chamber depth, and axial length were 11.95 ± 0.39 mm, 37.94 ± 5.01°, 2.97 ± 0.31 mm and 23.93 ± 0.97 mm, respectively. A significant moderate correlation was found between white-to-white corneal diameter and anterior chamber angle (r = 0.31, p ≤ 0.01), anterior chamber depth (r = 0.49, p ≤ 0.01), and axial length (r = 0.50, p ≤ 0.01) and between anterior chamber angle and anterior chamber depth (r = 0.71, p ≤ 0.01). Furthermore, age was moderately correlated with anterior chamber angle (r = 0.44, p 0.01) and anterior chamber depth (r = 0.39, p 0.01) and weakly correlated with white-to-white corneal diameter (r =0.17, p = 0.12). Males had a significantly (p < 0.01) higher white-to-white corneal diameter (12.12 ± 0.38 mm) than females (11.84 ± 0.36.mm).ConclusionReference values for white-to-white corneal diameter and anterior chamber parameters would help eye care professionals choose the right lenses for cataract and refractive surgeries as well as in diagnosing glaucoma and corneal disorders. creator: Wafa M. Alotaibi creator: Naveen Challa creator: Saif Hassan Alrasheed creator: Rahaf Nasser Abanmi uri: https://doi.org/10.7717/peerj.19227 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alotaibi et al. title: Comparative larval morphology of four Pteroptyx (Coleoptera, Lampyridae, Luciolinae) species in Thailand link: https://peerj.com/articles/19190 last-modified: 2025-04-01 description: BackgroundFireflies in the genus Pteroptyx are renowned for their significance in firefly tourism initiatives. Their occurrence and abundance have been extensively studied to facilitate sustainable utilization and conservation of their populations. As a group of highly charismatic insects, Pteroptyx fireflies play an important role in raising awareness and advocating for the conservation of mangrove forests. Previous taxonomic studies on these fireflies have primarily focused on adult while the larvae remain limited. Therefore, this study aimed to compare the larval morphology of four Pteroptyx species found in Thailand.MethodsThe characteristics of the larvae were examined under a microscope, and the species were identified by rearing the larvae to adult and comparing the adult males with previously identified male specimens. Additionally, morphometric analysis of the protergites was conducted to support identification efforts.ResultsLarval descriptions and an identification key for four Pteroptyx species were developed through the comparison of larval morphology, focusing on tergite texture, protergum shape, color patterns, mouthparts, and the holdfast organ (pygopod). Among the species, P. valida is uniquely characterized by lacking tubercles on the thoracic tergites and has a holdfast organ composed of more than 10 retractable filaments, clearly distinguishing it from the other three Pteroptyx species. Most species have a protergum length much longer than its width, except P. tener. An overview description of Pteroptyx larvae is provided with supplementary files summarizing the key characteristics of these four Pteroptyx larvae.DiscussionSpecies-specific traits are evident among the four species, likely reflecting their specific biological and ecological requirements. Pteroptyx valida Olivier, 1909 displays distinct morphological characteristics, including features of the holdfast organ. creator: Suparada Boonloi creator: Parichart Laksanawimol creator: Soraya Jaikla creator: Marc A. Branham creator: Anchana Thancharoen uri: https://doi.org/10.7717/peerj.19190 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Boonloi et al. title: Untangling the taxonomic knot of Croton anomalus (Euphorbiaceae), a Neotropical dry forest shrub link: https://peerj.com/articles/19176 last-modified: 2025-04-01 description: Croton anomalus was described by Henri Pittier in 1930 from a collection made in Estado Lara, Venezuela, and the use of the name has so far been restricted to several states in this country. A reevaluation of the species has led to its recircumscription and recognition in several other countries, including Bolivia, Brazil, Colombia, French Guiana, Guyana, Mexico, and Suriname. Previously, it was confused with species referred to here as the “Croton anomalus group”, namely C. acapulcensis, C. blanchetianus, C. chiapensis, C. jacobinensis (=C. sonderianus), and C. stahelianus. We integrated morphological, phylogenetic, and ecological evidence to understand species limits and relationships within the Croton anomalus group. We first studied ca. 650 herbarium specimens covering the geographic range of the group, and we inferred species phylogenetic relationships using DNA sequences from the nuclear and plastid regions (ITS and trnL-F). We also used ecological niche modeling to infer potential suitable areas for the occurrence of the studied species and to determine the variables that most contribute to their distribution model. Both morphological and phylogenetic data provide evidence for the synonymization of C. acapulcensis, C. chiapensis, and C. stahelianus under C. anomalus. On the other hand, our results support the recognition of C. blanchetianus and C. jacobinensis as two independent lineages, both distinct from C. anomalus. An emended description of C. anomalus is provided, as well as the designation of lectotypes, illustrations, updates of distribution data, and morphological comparisons with closely related species. Regarding niche modeling, annual precipitation and the precipitation of the warmest quarter were the most important variables explaining species distributions. Croton anomalus showed suitable areas in most seasonally dry tropical forests in the Neotropics, while C. blanchetianus and C. jacobinensis had their most suitable areas restricted to the Caatinga Dry Forest (Brazil), and Caatinga + northern South America, respectively. Our study shows the importance of taxonomic revisions using integrative approaches to disentangling species boundaries and to elucidate their biogeography and conservation status. creator: Yuri Rossine creator: Ricarda Riina creator: Otávio L.M. Silva creator: Rafael Louzada uri: https://doi.org/10.7717/peerj.19176 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Rossine et al. title: Association of metallic elements with telomere length in children with autism spectrum disorder link: https://peerj.com/articles/19174 last-modified: 2025-04-01 description: BackgroundImbalances in metal elements have been identified as a potential risk factor for autism spectrum disorder (ASD), and shortened telomere length (TL) is commonly observed in children with ASD. Metal elements may influence telomere homeostasis through oxidative stress, which could contribute to the pathogenesis of autism. However, studies examining the combined effects of metal elements on TL in children with ASD are limited. To fill the gaps in the current literature, this study aimed to investigate the relationship between six metallic elements: manganese (Mn), copper (Cu), zinc (Zn), calcium (Ca), magnesium (Mg), and iron (Fe), and TL in the whole blood of children with ASD.MethodsA total of 83 children with ASD and 95 typically developing children were recruited. TL was measured using digital PCR, while metal concentrations were assessed using inductively coupled plasma mass spectrometry (ICP-MS). Linear regression analysis was first conducted to explore the correlations between metal elements and TL in both groups. Additionally, Bayesian Kernel Machine Regression (BKMR) was used to further examine the combined effects and potential interactions of these metals on TL in the ASD group.ResultsIn the ASD group, Ca was found to have a protective effect on TL (β = 0.07, 95% CI [0.01–0.13], P = 0.027). In contrast, Mg showed a protective effect on TL in the control group (β = 0.10, 95% CI [0.01–0.18], P = 0.027). The BKMR model revealed a significant positive combined effect of the metal mixtures on TL in the ASD group, with Ca having the largest individual effect (PIP = 0.45). Further analysis indicated that increases in Zn and Mn concentrations from the 25th to the 75th percentile were negatively correlated with TL, while higher concentrations of Cu, Ca, Mg, and Fe were positively associated with TL. No significant interactions among the metals were observed.ConclusionsThis study suggests a potential link between metallic elements and TL in children with ASD, with Ca having the greatest effect. Our findings highlight the potential benefits of appropriate calcium supplementation as a protective strategy for lengthening telomeres in children with ASD, emphasizing the importance of early nutritional interventions to improve their overall health. creator: Qiuyan Zhu creator: Tong Zhang creator: Yanan Sun creator: Jinming Liu creator: Zizi Liu creator: Fengxiang Wei creator: Yu Jin uri: https://doi.org/10.7717/peerj.19174 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhu et al. title: A cross-sectional study on the effects of bedtime administration of selective α1 adrenoceptor antagonists on nocturnal blood pressure in elderly patients with benign prostate hyperplasia link: https://peerj.com/articles/19165 last-modified: 2025-04-01 description: BackgroundIt remains uncertain whether a bedtime dose of selective α1 adrenoceptor antagonist could result in nocturnal hypotension in elderly patients with benign prostate hyperplasia (BPH).MethodsA total of 253 older men with BPH who had taken selective α1 adrenoceptor antagonists before sleep were consecutively recruited from the Geriatric Department of Shanghai Ninth People’s Hospital. A total of 221 patients were finally included in the analysis with qualified data including office blood pressure examinations, biochemical tests of blood, and 24-hour ambulatory blood pressure monitoring. Nocturnal hypotension was defined according to the nighttime average systolic blood pressure of ambulatory blood pressure ≤ 100 mmHg and/or diastolic blood pressure ≤ 60 mmHg. Explore the presence of night hypotension, compare the characteristics of the two groups with or without nocturnal hypotension, and analyze the related risk factors.ResultsAmong all 221 patients included in the analysis, nocturnal hypotension occurred in 38 patients (17.2%). Compared with those without, patients with nocturnal hypotension were older, had less body mass index, lower office diastolic blood pressure, and lower ambulatory blood pressure in a 24 hour day, and night systolic and diastolic blood pressure, and were less likely to have hypertension. Age (OR 1.064, 95% CI [1.012–1.118], P = 0.015) and no hypertension (OR 2.548, 95% CI [1.211–5.359], P = 0.014) were independently associated with the presence of nocturnal hypotension.DiscussionNocturnal hypotension was common in men 60 years and older with BPH treated with selective α1 adrenoceptor antagonists before sleep. Age and no hypertension were independently associated with nocturnal hypotension positively. Related factors may help clinicians identify hypotension tendencies in the elderly when prescribing such drugs. creator: Chao-Ting Chen creator: Shao-Jun Ma creator: Hai-Ya Wang creator: Hai-Jun Yao uri: https://doi.org/10.7717/peerj.19165 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Multimodal dataset for sensor fusion in fall detection link: https://peerj.com/articles/19004 last-modified: 2025-04-01 description: The necessity for effective automatic fall detection mechanisms in older adults is driven by the growing demographic of elderly individuals who are at substantial health risk from falls, particularly when residing alone. Despite the existence of numerous fall detection systems (FDSs) that utilize machine learning and predictive modeling, accurately distinguishing between everyday activities and genuine falls continues to pose significant challenges, exacerbated by the varied nature of residential settings. Adaptable solutions are essential to cater to the diverse conditions under which falls occur. In this context, sensor fusion emerges as a promising solution, harnessing the unique physical properties of falls. The success of developing effective detection algorithms is dependent on the availability of comprehensive datasets that integrate data from multiple synchronized sensors. Our research introduces a novel multisensor dataset designed to support the creation and evaluation of advanced multisensor fall detection algorithms. This dataset was compiled from simulations of ten different fall types by ten participants, ensuring a wide array of scenarios. Data were collected using four types of sensors: a mobile phone equipped with a single-channel, three-dimensional accelerometer; a far infrared (FIR) thermal camera; an $8×8$ LIDAR; and a 60–64 GHz radar. These sensors were selected for their combined effectiveness in capturing detailed aspects of fall events while mitigating privacy issues linked to visual recordings. Characterization of the dataset was undertaken using two key metrics: the instantaneous norm of the signal and the temporal difference between consecutive frames. This analysis highlights the distinct variations between fall and non-fall events across different sensors and signal characteristics. Through the provision of this dataset, our objective is to facilitate the development of sensor fusion algorithms that surpass the accuracy and reliability of traditional single-sensor FDSs. creator: Carla Taramasco creator: Miguel Pineiro creator: Pablo Ormeño-Arriagada creator: Diego Robles creator: David Araya uri: https://doi.org/10.7717/peerj.19004 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Taramasco et al.