title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-09 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Biochemical composition, β-glucan and phenolic content of a marine diatom Chaetoceros muelleri cultivated in Guillard’s modified medium link: https://peerj.com/articles/20098 last-modified: 2025-09-30 description: The biochemical compositions of diatoms are important for agricultural and pharmaceutical applications, and they vary according to nutrients and physical factors. To study the influence of carbonate and nitrogen source supplementation in the medium on the chemical composition of the marine diatom Chaetoceros muelleri, Guillard’s medium was modified for this study. Three types of Guillard medium were prepared including standard Guillard medium (T1), modified Guillard medium (0.005 g/L bicarbonate supplement, T2), and 50% nitrogen reducing medium (T3). Results showed that the maximum biomass was observed at T3 (5.75 × 106 cell/mL), which was significantly different (p < 0.05) from that at T1 (3.85 ± 0.13 × 106 cells/mL) but did not differ from that at T2 (4.03 ± 0.08 × 106 cells/mL). T3 contained the highest level of carbohydrates (13.71 ± 1.56 ), with a statistically significant difference (p < 0.05) from T1 (5.81 ± 0.50) and T2 (6.90 ± 1.14). The total lipid content in T3 (4.34 ± 0.03) was significantly greater (p < 0.05) than that in T1 (1.1 ± 0.08) and T2 (2.21 ± 0.62). The protein content in T1 (94.84 ± 0.08 mg/g) was significantly higher (p < 0.05) compared to that in T2 (31.39 ± 0.72 mg/g) and T3 (30.91 ± 0.38 mg/g). The highest β-glucan level was measured in T3 (0.4 1 ± 0.01 g/L), and statistical analysis revealed a significant difference (p < 0.05) from that in T1 (0.41 ± 0.01 gL−1) and T2 (0.41 ± 0.01 gL−1). The phenolic content in T1 was 14.91 ± 0.97, while those in T2 and T3 were 4.44 ± 0.11 and 4.16 ± 0.17 μg/mg gallic acid equivalents (GAE), respectively. Antioxidation examination revealed the highest value at 94.59 ± 0.04 mg mL−1 extract in T3, followed by T1 (89.21 ± 1.71 mg mL−1 extract) and T2 (10.66 ± 0.38). Phenolic content showed the values for T1, T2 and T3 were 49.44 ± 4.49, 47.61 ± 5.45, and 53.23 ± 6.61 mg ascorbic acid, respectively. Statistical analysis revealed that the phenolic content in T1 significantly higher differed (p < 0.05) from that in T2 and T3. In contrast, the 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) scavenging ability significantly differed (p < 0.05) among T3, T1, and T2 according to the 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging ability and reducing power. The presence of β-glucan in the diatom extracts was confirmed by the FTIR spectrum data at wavenumbers 1,065 and 1,038 cm−1, whereas the LCMS spectrum confirmed the presence of gluconic acid at m/z 198, 196, and 194. Our results demonstrate that the modified Guillard T3 medium is optimal for cultivating C. muelleri to enhance the production of carbohydrates, lipids, proteins, and β-glucan. These findings are critical for advancing the large-scale production of diatom-derived biochemical components, particularly for pharmaceutical applications. creator: Sulaiman Madyod creator: Suwit Wuthisuthimethavee creator: Patchara Pedpradab creator: Rachow Khaochamnan creator: Suwanna Pholmai creator: Thitikorn Prombanchong uri: https://doi.org/10.7717/peerj.20098 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Madyod et al. title: Identification and analysis of the expansin gene family in yam link: https://peerj.com/articles/20093 last-modified: 2025-09-30 description: Expansins are a group of proteins that loosen plant cell walls and cellulose materials and are involved in regulating plant cell growth and diverse developmental processes. However, a systematic study of the Dioscorea opposita expansin (DoEXP) gene family has not yet been conducted. In this study, we used publicly available genomic data from yam to identify members of the DoEXP gene family and analyse its physicochemical properties, phylogeny and expression pattern using bioinformatics software. Thirty EXP genes were identified from the yam genome and can be classified into four subfamilies, DoEXPA, DoEXPB, DoEXLA, and DoEXLB, which are distributed across 14 chromosomes. All EXP proteins contain two conserved structural domains (DPBB_1 and expansin_C) and have highly similar motif compositions and exon–intron structures. Examination of the promoter regions of these genes revealed the presence of cis-acting elements associated with growth and development, phytohormone signaling, and abiotic stress. The collinearity analysis revealed that segmental duplication is the primary cause of the expansion of the DoEXP gene family. Gene Ontology (GO) enrichment analysis revealed that DoEXP genes (DoEXPs) are significantly associated with root elongation and cell differentiation processes. Utilizing quantitative real-time polymerase chain reaction (qPCR), the expression patterns of nine selected DoEXPs were validated. The results of this study are helpful for understanding the molecular functions of expansin proteins in yam tuber expansion and provide a theoretical basis for revealing the molecular regulatory mechanism of yam tuber growth and development. creator: Xing Qiao creator: Shuai Yuan creator: Jing Wei creator: Changzhou Li creator: Lan Lan creator: Xuerui He creator: Aiqin Wang creator: Jie Zhan creator: Longfei He creator: Dong Xiao uri: https://doi.org/10.7717/peerj.20093 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Qiao et al. title: DNA damage-dependent mechanisms of ionizing radiation-induced cellular senescence link: https://peerj.com/articles/20087 last-modified: 2025-09-30 description: Cellular senescence can be broadly categorized into replicative senescence and stress-induced premature senescence. Replicative senescence mainly results from the progressive shortening of telomeres during successive cell divisions, eventually leading to the arrest of cell division and the onset of senescence. In contrast, stress-induced premature senescence is typically triggered by environmental factors, such as ionizing radiation (IR). While the DNA damage induced by IR has been extensively studied, the specific mechanisms by which IR induces cellular senescence via DNA damage remain incompletely understood. This review focuses on IR-induced cellular senescence, particularly in the context of DNA damage. Understanding these mechanisms provides insight into the long-term effects of radiation on cellular senescence and lays the groundwork for future research into the effects of radiation on aging processes. creator: Jiebing Guan creator: Tuo Li creator: Feifei Ma creator: Ning Wang creator: Huanteng Zhang creator: Jiale Li creator: Jianguo Li creator: Chang Xu creator: Qiang Liu uri: https://doi.org/10.7717/peerj.20087 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Guan et al. title: Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park link: https://peerj.com/articles/20081 last-modified: 2025-09-30 description: New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications. creator: Sally Kong creator: Eliana Abrams creator: Yehuda Binik creator: Christina Cappelli creator: Mathew Chu creator: Taiyo Cornett creator: Isayah Culbertson creator: Epifania Garcia creator: Jada Henry creator: Kristy Lam creator: D.B. Lampman creator: Grace Morenko creator: Illusion Rivera creator: Tanasia Swift creator: Isabella Torres creator: Rayven Velez creator: Elliot Waxman creator: Serena Wessely creator: Anthony Yuen creator: Casey K. Lardner creator: J.L. Weissman uri: https://doi.org/10.7717/peerj.20081 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kong et al. title: Spatially explicit models of density improve estimates of Eastern Bering Sea beluga (Delphinapterus leucas) abundance and distribution from line-transect surveys link: https://peerj.com/articles/20077 last-modified: 2025-09-30 description: We investigate spatially explicit models and ensemble modeling techniques for estimating animal abundance from line-transect survey data. Spatially explicit models are expected to be statistically more efficient, resulting in more precise abundance estimates, than design-based abundance estimators that rely heavily on assumptions about survey design and realization. Ensemble modeling reduces error by averaging among models, and allows for model selection uncertainty to propagate to the abundance estimator. We develop density surface models using Matérn covariance functions and spline-based smooths for a case study, belugas (Delphinapterus leucas) from the Eastern Bering Sea (EBS) stock. EBS belugas are upper trophic level predators in a rapidly changing ecosystem and are a vital nutritional and cultural resource for Alaska Natives. Effective management of this stock requires regular monitoring to derive accurate and unbiased estimates of abundance. Since 1992, aerial line-transect surveys have been the primary means of surveying and estimating abundance of EBS belugas in the region. We compare EBS beluga abundance estimates for 2017 and 2022 that were derived using post-stratified, design-based abundance estimators with analogous estimates the we derive using spatially explicit and ensemble modeling methods. The estimated precision in the abundance estimates from the individual density surface models (DSMs) and the ensemble average of DSMs is higher than for the design-based estimator in both survey years. The design-based models estimated that there were 12,269 belugas in 2017 (coefficient of variation (CV) = 0.118) and 19,811 belugas within a larger study area in 2022 (CV = 0.343). The ensemble spatial models estimate that there were 11,654 belugas in 2017 (CV = 0.118) and 13,313 belugas in 2022 (CV = 0.216). Among the individual spatially explicit models, abundance estimates range from 11,242 to 11,963 (CV = 0.111 to 0.114) in 2017 and 12,023 to 15,593 (CV = 0.172 to 0.198) in 2022. Because spatial models identify spatial patterns in beluga density at finer resolutions than design-based models, we argue that ensembles of spatially explicit density models provide a reasonable path forward for estimating EBS beluga abundance and distribution in a way that is useful to management and conservation efforts. creator: Megan C. Ferguson creator: Paul B. Conn creator: James T. Thorson uri: https://doi.org/10.7717/peerj.20077 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ferguson et al. title: Morphological, phytochemical, and pharmacological properties of the genus Tamarix in Kazakhstan species: a review link: https://peerj.com/articles/20059 last-modified: 2025-09-30 description: The tree-like plants of the genus Tamarix belong to the Tamaricaceae family and predominantly grow in subtropical areas, steppes, and saline soils. These plants exhibit various pharmacological properties, including antioxidant, antidiabetic, anti-inflammatory, and antimicrobial characteristics. The current flora of Kazakhstan also includes 13 Tamarix species. Despite the diversity of the Tamarix taxon, the species discovered in the region have received limited investigation. Therefore, this review analyzed Kazakhstan and international-related scientific studies concerning the morphological, phytochemical, and pharmacological properties of 13 species within the Tamarix genus. The plants’ biological features and potential applications were also comprehensively analyzed. Consequently, this review significantly contributed to botanical science and practical pharmacology. Conservation and sustainable employment of the Tamarix species for medical purposes could also be developed. creator: Arailym Daulbayeva creator: Gulnara Kadyrbayeva creator: Kaldanay Kozhanova creator: Shazlin Shaharudin creator: Nurgali Rakhymbayev creator: Zoya Allambergenova creator: Rabiga Anarbayeva creator: Urziya Alimova creator: Aigerim Kantureyeva creator: Ainash Baidullaeva creator: Vladimir An creator: Bakkonat Kydyrbai uri: https://doi.org/10.7717/peerj.20059 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Daulbayeva et al. title: Identification and verification of prognostic genes related to zinc homeostasis and zinc transport in breast cancer link: https://peerj.com/articles/20031 last-modified: 2025-09-30 description: PurposeZinc homeostasis and zinc transporter (ZHT) have been closely associated with the development of various cancers. Therefore, in this study, prognostic genes and their mechanisms related to ZHT in breast cancer (BC) were explored.Patients and methodsDifferential expression analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify genes associated with Zinc homeostasis and Zinc transporter-related genes (ZHTGs) in BC. Subsequently, independent prognostic factors and their correlations with clinical features were examined to investigate their association with the prognosis of BC. Finally, we further explored the pathways and immune cells associated with BC prognosis. We also verified gene expression in tissues and cells by quantitative polymerase chain reaction (qPCR).ResultsIn this study, six prognostic genes were identified. Patients were subsequently classified into high-risk and low-risk cohorts based on the median risk score, with the low-risk group presenting superior survival outcomes. Subsequently, riskScore, age, tumor/node/metastasis (T/N/M) stage showed significant associations with the prognosis of BC, and the constructed nomogram demonstrated strong predictive performance. Clinical analysis revealed differences in risk scores among sub-cohorts with different clinical characteristics, such as race (white and others) and T-stage (T1 and T2, T1 and T3). Furthermore, significant disparities were noted in immune cells and immune checkpoints across different risk cohorts. The results of reverse transcription quantitative PCR were basically consistent with the prediction. In addition, the IHC results from the Human Protein Atlas database further validated our prediction.ConclusionWe screened six prognosis genes related to ZHT in BC, providing a reference for the prognosis and personalized treatment of BC. creator: Mengxuan Li creator: Haoyi Zi creator: Jiajun Ding creator: Shuai Wang creator: Yujie Bai creator: Jianing Sun creator: Cong Fan creator: He Chen creator: Ting Wang uri: https://doi.org/10.7717/peerj.20031 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Li et al. title: Unlocking the genomic potential of historical and formalin-fixed specimens: phylogenetic insights from museum-preserved threadfin fishes (Teleostei: Polynemidae) link: https://peerj.com/articles/20029 last-modified: 2025-09-30 description: DNA sequencing continues to revolutionize our understanding of biodiversity, ecology, and evolution. While analyzing sequence data allows us to address countless questions, most of the world’s vertebrate museum specimens have been historically inaccessible for genetic sampling. This is partially due to the absence of modern genetic samples and/or the impact formalin has on DNA during the preservation of specimen vouchers. Recent studies have shown successful extraction of DNA from historic museum specimens using additional chemicals and/or exposing the sample(s) to heat, with these advances enhancing the possibility of capturing genomic information from type specimens, characterizing genetic diversity within species complexes, and incorporating rare samples into phylogenetic analyses. However, questions remain about the reliability of these data and utility of historic DNA in modern phylogenetic analyses. In this study, we use a commercial extraction kit that targets formalin-fixed, paraffin-embedded samples to successfully extract DNA from historic museum specimens of threadfin fishes (Teleostei: Polynemidae). These specimens represent rare, genetically uncharacterized taxa that have yet to be included in a phylogenetic analysis. Low-depth shotgun sequencing is then used to sequence mitochondrial loci from the historic samples. The resulting sequence data are assembled, validated, and incorporated into a newly generated mitochondrial dataset that is simultaneously analyzed with a previously published ultraconserved-element dataset to construct a phylogenetic framework. We then explore new and previously described morphological variation within this new evolutionary framework for threadfins, identifying several shared characters that warrant revision of the generic-level classification. These findings add to the growing body of literature that demonstrates sequencing historical DNA from museum specimens and analyzing these data with complementary datasets of molecular markers from modern genetic samples can provide reliable and comprehensive assessments of biodiversity, ecology, and evolution across fishes and other vertebrates. creator: Matthew G. Girard creator: Kevin R. Chovanec uri: https://doi.org/10.7717/peerj.20029 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Girard and Chovanec title: Undernutrition and feeding difficulties among children with disabilities in Zambia: insights for inclusive nutrition strategies link: https://peerj.com/articles/20023 last-modified: 2025-09-30 description: BackgroundUnderstanding the burden of undernutrition in children with disabilities is crucial for designing inclusive nutrition programs and policies. This study aimed to estimate the prevalence of undernutrition and risk for feeding difficulties and describe common feeding practices among children with disabilities living with families in Zambia and receiving services at selected health centers and community-based rehabilitation centers.MethodsWe analyzed cross-sectional program data from 483 children aged birth to 10 years with reported special healthcare needs, collected between June 2017 and August 2021 at three health centers and ten community-based rehabilitation centers. Data included demographics, weight, height, mid-upper arm circumference (MUAC), hemoglobin concentrations, risk for feeding difficulties, and reported caregiver feeding practices. Undernutrition was assessed using the World Health Organization z-scores for anthropometric measurements, MUAC cut-off points, and anemia criteria. ANOVA and Pearson’s chi-squared tests were used to compare groups.ResultsMore than half of the children were boys (54.2%) and under 5 years old (59.2%). Cerebral palsy was the most common special healthcare need (63.6%), followed by an unspecified “other” category (18.6%). Undernutrition was prevalent, with 62.8% underweight, 68.1% stunted, 22.6% wasted (using MUAC), and 60.5% anemic. Children with cerebral palsy had consistently lower anthropometric z-scores and higher rates of stunting, wasting, and underweight compared to children with other developmental disabilities or special healthcare needs. A risk for feeding difficulties was identified in 89.5% of the children, with common issues including coughing or choking and prolonged mealtimes. Despite these challenges, most caregivers reported practicing responsive feeding techniques at least some of the time.ConclusionThese findings highlight the significant risk of undernutrition and feeding difficulties among children with disabilities, underscoring the urgent need for disability-inclusive, community-based nutrition strategies in Zambia. Stakeholders should use this information to strengthen nutrition programs and policies that uphold the rights of children with disabilities. creator: Zeina Makhoul creator: Julie M. Long creator: Mulemba Ndonji creator: Carolyn Moore creator: Watson Shungu Mwandileya creator: Edgar Lunda creator: Kate Miller creator: Bradley S. Miller creator: Douglas Taren uri: https://doi.org/10.7717/peerj.20023 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Makhoul et al. title: Metabolomic and physiological analysis of bud differentiation in dense apple (Malus×domestica Borkh.) orchards following thinning and reshaping link: https://peerj.com/articles/20011 last-modified: 2025-09-30 description: BackgroundIn China, a majority of apple orchards were initially planted under arboriculture. The branch number increases, causing a deterioration of the canopy light conditions as the trees age. This phenomenon blocks bud differentiation, resulting in yield decrease and deterioration of fruit quality. Thinning and reshaping are effective strategies for addressing these issues. However, the impact of thinning and reshaping remains unclear. This study analyzed the physiological and metabolic aspects of flower bud differentiation following thinning and reshaping of an overcrowded orchard.MethodsPhysiological and metabolomic analyses were conducted on terminal flower bud samples collected during early (T1) and late (T2) bud differentiation following thinning and reshaping alongside controls CK1 and CK2.ResultsSucrose, glucose, fructose, and sorbitol contents in T1 and T2 groups were significantly higher than in CK1 and CK2. Metabolomic analysis revealed significant differences: 60 metabolites (32 up-regulated, 28 down-regulated) in T1 vs CK1 and 51 metabolites (26 up-regulated, 25 down-regulated) in T2 vs CK2. KEGG enrichment analysis revealed that the biosynthesis of secondary metabolites was the most enriched pathway, with the crucial compounds associated with flower bud differentiation. There was an accumulation of coumarin (C05851), eriodictyol (C05631), and histidine (C00135) during both the early and late stages of flower bud differentiation, underscoring their promoting role. In T1 vs CK1, 2-isopropylmalic acid (C02504), (+)-catechin (C09727), and trans-ferulic acid (C01494) were significantly up-regulated, highlighting their potential as metabolic activators. Conversely, 3’,5’-dimethoxy-3,5,7,4’-tetrahydroxyflavone (C11620) and 4-hydroxyphenylpyruvic acid (C01179) decreased, implying divergent regulatory mechanisms. Temporal specificity emerged in T2 vs CK2, with significant upregulation of myricetin (C10107) and isopimpinellin (C02162). In contrast, umbelliferone (C09315) and trans-caffeic acid (C01197) exhibited opposing trends. Moreover, jasmonic acid (C08491) and 6-phosphogluconic acid (C00345) increased sharply in T2, while trans-traumatic acid (C16308) declined.ConclusionsThinning and reshaping improved light penetration and increased the accumulation of nutrients and secondary metabolites. Sucrose, glucose, fructose, and sorbitol contents and the relative levels of coumarin, eriodictyol, and histidine increased during early and late flower bud differentiation stages, which suggested their positive roles during these stages. 2-isopropylmalic acid, (+)-catechin, and trans-ferulic acid exhibited metabolic activation potential, while 3’,5’-dimethoxyflavone and 4-hydroxyphenylpyruvic acid were distinctly regulated in T1 vs CK1. Myricetin, isopimpinellin, jasmonic acid, and 6-phosphogluconic acid exhibited activation potential, while trans-traumatic acid was distinctly regulated in T2 vs CK2. Metabolic changes and pathway-specific activation/inhibition patterns underlying flower bud differentiation exhibited a direct-indirect regulatory network in secondary metabolism. creator: Zehua Yang creator: Tianli Guo creator: Junqiang Niu creator: Xiaoning Yin creator: Ming Ma uri: https://doi.org/10.7717/peerj.20011 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: Interprofessional collaboration and associated factors among wound, ostomy, and continence nurses: a cross-sectional study in China link: https://peerj.com/articles/20006 last-modified: 2025-09-30 description: BackgroundWound, ostomy, and continence (WOC) nurses play a crucial role in providing cost-effective and high-quality care for an increasing number of people with acute and chronic wounds. WOC nursing is a multifaceted, evidence-based specialty practice requiring inter-professional collaboration (IPC). IPC is a core competency that ensures comprehensive and holistic wound management, yet few studies have examined IPC among WOC nurses in China. This study aimed to investigate the level and influencing factors of IPC among WOC nurses in China, providing insights into IPC education and intervention.MethodsA cross-sectional study was conducted among 247 WOC nurses recruited from various hospitals from January to February 2025. Participants completed an online questionnaire to assess their IPC competency, readiness for interprofessional learning, and work environment. Multiple linear regression was used to determine influencing factors for IPC competency.ResultsThe mean scores for IPC, readiness for inter-professional learning, and work environment were 134.49 ± 10.99, 81.15 ± 6.00, and 127.1 ± 18.78, respectively. A higher level of inter-professional learning readiness (β = 0.46, P < 0.001), a better work environment (β = 0.39, P < 0.001), and being a WOC team leader (β = 0.12, P = 0.008) were associated with a higher level of IPC competency, collectively explaining 55.1% of the total variance.ConclusionWOC nurses showed a generally good level of IPC, but there is still room for improvement. IPC may be effectively improved through optimizing the work environment, strengthening IPC learning, and empowering nurses with leadership responsibilities. creator: Lin Shi creator: Liqing Yue creator: Xiaowan Liu creator: Xueqin Gong creator: Bingfa Li uri: https://doi.org/10.7717/peerj.20006 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shi et al. title: Optimization of anther culture of awnless triticale link: https://peerj.com/articles/19951 last-modified: 2025-09-30 description: BackgroundCompared with traditional breeding methods, anther culture is an effective method for quickly obtaining homozygotes within one generation. The method of cultivating doubled haploid plants derived from the anthers of awnless triticale was studied and optimized.MethodsYoung awnless triticale spikes were pretreated at 4 °C for 5, 10, 15, 20, or 25 days, respectively, and then the anthers of different treatment days were cultured on cysteine heart blood (CHB) with antibiotics media with four different hormone concentrations, respectively.ResultsOverall, 15 days was the best low-temperature treatment, and CHB medium containing 1.5 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D) and 1.5 mg/L Kinetin (KT) was the best hormone concentration treatment. The callus induction rate (CIR) was highest (22.20%) for anthers pretreated for 15-days and inoculated on CHB medium containing 1.5 mg/L 2,4-D and 1.5 mg/L KT. The green plantlet differentiation frequency (DFG) was highest (30.20%) for anthers pretreated for 25-days and inoculated on CHB medium containing 0.5 mg/L 2,4-D+0.5 mg/L KT. Green plantlet production (PRG) was highest (4.58%) for anthers which were pretreated for 10-days and inoculated on CHB medium containing 0.5 mg/L 2,4-D+0.5 mg/L KT. The success rate of chromosome doubling for regenerated green plantlets was 52.8%. Nine of the thirteen DH1 plants (the first generation of double haploid plants) had tip and side awns shorter than 5 mm, implying that they may be used for cultivating awnless triticale.ConclusionTriticale anther culture technology was optimized in this work, enabling the rapid breeding of homozygous varieties of awnless triticale and accelerating the breeding of new varieties of awnless triticale. creator: Jun Ma creator: Fangyuan Zhao creator: Xinhui Tian creator: Wenhua Du uri: https://doi.org/10.7717/peerj.19951 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ma et al. title: Study on the diagnostic potential and molecular mechanism of hsa_circ_0000831 in oral squamous cell carcinoma link: https://peerj.com/articles/20082 last-modified: 2025-09-29 description: BackgroundCircular RNA (circRNA) are a new class of non-coding RNAs that are involved in the molecular pathology of cancer. This study aims to screen and validate key circRNAs with diagnostic potential in o ral squamous cell carcinoma (OSCC), and explore their possible molecular mechanism.MethodsThis study first integrated the GSE131182 dataset with clinically obtained OSCC sample data and used the limma package to identify differentially expressed circular RNAs (DEcircRNAs). Subsequently, circRNAs associated with head and neck squamous cell carcinoma were identified using CircNet2.0 and intersected with the differentially expressed circRNAs to determine the key circRNA. The diagnostic value of the key circRNA was evaluated using receiver operating characteristic (ROC) curves, followed by functional validation through in vitro assays including cell counting kit-8 (CCK-8), wound healing, transwell assay, and flow cytometry. Finally, target microRNAs (miRNAs) were predicted using CircNet2.0 and miRDB, a ceRNA network was constructed, and functional enrichment analysis of target genes was performed using Metascape tool.ResultsA total of 318 and 46 differentially expressed circRNAs (DEcircRNAs) were identified from the GSE131182 dataset and clinical samples, respectively. Through intersection analysis, the key circRNA hsa_circ_0000831 was identified. hsa_circ_0000831 was upregulated in OSCC samples, and ROC curve analysis indicated its high diagnostic performance. In vitro experiments showed that inhibition of hsa_circ_0000831 significantly reduced OSCC cell viability, migration, and invasion, while markedly enhancing apoptosis. ceRNA network analysis predicted that hsa_circ_0000831 targets five miRNAs (including hsa-miR-136-5p, hsa-miR-100-3p, hsa-miR-144-5p, hsa-miR-149-5p and hsa-miR-214-5p), with the associated target genes mainly enriched in cancer-related pathways.ConclusionThis work offer s a novel foundation for the early identification of OSCC and provides potential clues for finding new therapeutic targets. creator: Ting Liu creator: Xiaoze Chen creator: Shigeng Lin creator: Qitao Wen creator: Wei Deng creator: Daiying Huang uri: https://doi.org/10.7717/peerj.20082 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Factors influencing catheter-related infections in peritoneal dialysis patients: a meta-analysis link: https://peerj.com/articles/20063 last-modified: 2025-09-29 description: ObjectiveSystematic analysis of factors influencing catheter-related infections in patients undergoing peritoneal dialysis.MethodsA computerized search of Chinese and English databases was conducted to identify the factors affecting catheter-related infections in patients undergoing peritoneal dialysis. Studies with a search period from inception to July 31, 2024 were retrieved. Two researchers independently screened the literature using inclusion and exclusion criteria, and data extraction and quality assessments were performed. Meta-analysis was performed using RevMan5.4 and Stata software.ResultsIn total, 13 studies were included and meta-analysis revealed that comorbid diabetes mellitus, insecure catheter fixation, dialysis duration >2 years, body mass index >20 kg/m2, mechanical strain, lack of proper care, irregular caregivers, and history of catheter pulling (P < 0.05) were the influencing factors contributing to the incidence of catheter-related infections in patients undergoing peritoneal dialysis.ConclusionsClinicians should pay close attention to these influencing factors and provide targeted preventive measures to prevent catheter-related infections. creator: Juan Sun creator: Miaomiao Zhao creator: Yifang Zhang creator: Wenyu Zhang creator: Huimin Zhang creator: Qingzhu Bao uri: https://doi.org/10.7717/peerj.20063 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sun et al. title: A propensity score-matched retrospective study on sacubitril/valsartan use and 6-month readmission rates in patients with acute heart failure link: https://peerj.com/articles/20055 last-modified: 2025-09-29 description: BackgroundSacubitril/valsartan is a compound preparation commonly used for treating chronic heart failure with reduced ejection fraction. In clinical practice, it is also administered to patients with newly diagnosed acute heart failure. However, limited research exists on its benefits during hospitalization in this patient population.AimTo investigate the impact of in-hospital use of sacubitril/valsartan on the 6-month readmission rate in patients with newly diagnosed acute heart failure.MethodA retrospective study was conducted involving 176 patients admitted for the first time with acute heart failure at Xiaoshan Hospital Affiliated to Hangzhou Normal University. Patients were divided into two groups based on whether they received sacubitril/valsartan during hospitalization: a treatment group and a control group. Clinical data were collected, and propensity score matching (PSM) was used to balance baseline characteristics. Logistic regression analysis was performed to evaluate the effect of sacubitril/valsartan on 6-month readmission.ResultsAfter PSM, 53 matched pairs were obtained, with balanced covariates between the two groups. Before matching, the readmission rate was 10.47% in the treatment group and 25.56% in the control group. Multivariate logistic regression indicated that sacubitril/valsartan was associated with a reduced risk of readmission (OR = 0.339, 95% CI [0.116–0.994], P = 0.049). However, after matching, the readmission rate was 13.21% in the treatment group and 20.75% in the control group. Logistic regression analysis post-matching showed no statistically significant reduction in readmission risk (OR = 0.728, 95% CI [0.212–2.496], P = 0.252).ConclusionsIn-hospital use of sacubitril/valsartan does not significantly reduce the risk of 6-month readmission in patients with newly diagnosed acute heart failure. creator: Lingdi Zhang creator: Qinglian Chen creator: Guofei Ren uri: https://doi.org/10.7717/peerj.20055 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zhang et al. title: Robust statistical methods and the credibility movement of psychological science link: https://peerj.com/articles/20043 last-modified: 2025-09-29 description: The general linear model (GLM) is the most frequently applied family of statistical models in psychology. Within the GLM, the effects under study are estimated using the ordinary least squares (OLS) estimation. In certain situations, OLS produces parameter estimates that are unbiased and optimal (with least possible error) and hypothesis tests that retain the expected rate of false positives (Type I errors). This happens when (1) outliers and influential cases are absent, and (2) assumptions of linearity and additivity, spherical errors, and normal errors are met. This paper first provides a technical description of OLS and an overview of its statistical assumptions. We then discuss the methods commonly employed to detect and address violations of assumptions, and how the current application of these methods can compromise the reproducibility of findings by allowing too many data-driven decisions to be made as part of the data analytic pipeline. We briefly introduce several robust estimation methods—namely bootstrapping, heteroscedasticity-consistent standard errors, M-estimators, and trimming—that can improve the accuracy of parameter estimates and the power of statistical tests. We provide guidance on how these methods can be used to transparently preregister a sensitivity analysis, reducing the opportunity for problematic researcher degrees of freedom to enter the analytic pipeline. creator: Martina Sladekova creator: Andy P. Field uri: https://doi.org/10.7717/peerj.20043 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sladekova and Field title: In vitro assessment of the impact of 30 CYP2C19 variants on citalopram metabolism link: https://peerj.com/articles/20027 last-modified: 2025-09-29 description: BackgroundCYP2C19 polymorphisms are correlated with individual variability in response to citalopram treatment. The pharmacogenomic testing of CYP2C19 has been shown to optimize the safety and efficacy of citalopram medication. Exploration of the effect of novel CYP2C19 variants on citalopram could further enhance the potential for personalized citalopram treatment.ObjectivesThe main goal of this study was to functionally characterize 30 CYP2C19 variants in citalopram metabolism, most of which were rare or novel variants identified in the Chinese Han population.MethodsAn in vitro incubation system was set up using recombinant human CYP2C19 variants expressed in Sf21 insect cell microsomes to simulate the citalopram metabolic environment. A high-performance liquid chromatography with fluorescence detection method (HPLC-FLD) was established to quantitatively determine both citalopram and demethylcitalopram.ResultsIn this study, compared to the wild-type enzyme (CYP2C19*1), 73% (22/30) of the CYP2C19 variants showed significantly different metabolic activities in citalopram metabolism. Among them, two variants, CYP2C19*29 and L16F, showed significantly increased intrinsic clearance (nearly 5-fold and 1.5-fold, respectively). Eighteen variants–CYP2C19*2C, *2F, *2G, *2J, *6, *18, *30, *31, *32, *33, N231T, R124Q, R261W, I327T, A430V, R125G, M255T, and I331V–exhibited significantly decreased intrinsic clearance (18.02–63.16%). Two variants, CYP2C19*3 and 35FS, demonstrated weak or no activity. Moreover, the remaining 27% (8/30) of the CYP2C19 variants showed similar metabolic activities to that of the wild-type enzyme.ConclusionThese CYP2C19 variants require specific attention from physicians and researchers, as their altered metabolic activities may influence the safety and efficacy of citalopram treatment. This work greatly expands the previously underexplored knowledge about the metabolic activities of rare or novel CYP2C19 variants in relation to citalopram medication. These findings may further facilitate the precision use of citalopram in personalized medicine. creator: Peng Wang creator: Xiao-xia Hu creator: Jun-wei Li uri: https://doi.org/10.7717/peerj.20027 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Effectiveness of exercise as an intervention for internet addiction in adolescents: a meta-analysis link: https://peerj.com/articles/19999 last-modified: 2025-09-29 description: BackgroundInternet addiction, particularly among adolescents, has become a pressing global concern, impacting psychological well-being and daily functioning. This meta-analysis aims to evaluate the effectiveness of exercise interventions in mitigating symptoms of internet addiction among adolescents.MethodsA comprehensive literature search was conducted across PubMed, Web of Science (WoS), Cochrane Library, Embase, Scopus, and China National Knowledge Infrastructure (CNKI) databases up to January 1, 2025. The search yielded 266 records, of which nine studies involving 654 adolescents met the inclusion criteria. The quality of the included studies was assessed using the Cochrane Risk of Bias tool. Meta-analyses, subgroup analyses, and sensitivity analyses were conducted using Review Manager 5.4 and Stata 17.0. Publication bias was evaluated using Egger’s tests. This study is registered with PROSPERO (CRD42025632958).ResultsThe random effects model revealed that exercise interventions significantly reduced internet addiction scores compared to the control group (standardized mean difference (SMD) = −1.11, 95% CI [−1.60 to −0.62], p < 0.000). Subgroup analyses indicated that the type of exercise, duration, frequency, and intensity of interventions did not significantly contribute to heterogeneity. Sensitivity analysis confirmed the stability of these findings. Tests for publication bias yielded non-significant results (Egger’s test, p = 0.226). Exercise-based interventions demonstrate significant efficacy in reducing symptoms of internet addiction among adolescents.ConclusionsThese findings underscore the importance of integrating physical activity into therapeutic strategies for managing internet addiction. The findings of this study will be useful for healthcare workers and adolescents with Internet addiction. However, due to the high heterogeneity of the included literature, these findings should be interpreted with caution. creator: Luqiu Wang creator: Yonghuan Chen creator: Jin Ho Cho creator: Humin Yang creator: Jae Chul Seo uri: https://doi.org/10.7717/peerj.19999 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Development and evaluation of a deep learning model for occlusion classification in intraoral photographs link: https://peerj.com/articles/20140 last-modified: 2025-09-26 description: BackgroundMalocclusion affects oral health and aesthetics, traditionally classified using systems like Angle’s, which depend on physical exams or casts. Digital dentistry has shifted towards intraoral photography for documentation and assessment, though interpretation requires clinical expertise. The application of artificial intelligence (AI), and specifically deep learning, in medical imaging has been successful but remains largely unexplored in occlusal classification from intraoral photos. This study introduces a deep learning model to automate the classification of occlusal types from intraoral photographs, aiming to improve efficiency and objectivity in orthodontic diagnosis and treatment planning.ObjectivesOcclusal classification is a crucial prerequisite for designing orthodontic treatment plans. Therefore, this study aims to develop an evaluation tool utilising a deep learning approach to automatically identify occlusal types reflected in digital oral photographs.MethodsUsing a large-scale dataset with high-quality annotations (comprising 5,000 orthodontic intraoral photographs at a 45° lateral view and 2,200 at a 90° lateral view from 6,100 patients), three deep-learning models were developed based on Swin Transformer for the identification of various occlusal classifications: Molar occlusal relationships (M1, M2, M3), canine occlusal relationships (C1, C2, C3), and anterior overbite relationships (normal overbite, deep overbite, edge-to-edge bite, open bite, anterior crossbite, single-tooth crossbite or segmental crossbite).ResultsOur model achieved weighted average F1-scores of 0.90 and 0.87 for molar and canine occlusal relationships, respectively. Regarding anterior overbite relationships, the model attained a weighted average f1-score of 0.89, with subclass F1-score ranging from 0.86 for edge-to-edge bite to 0.94 for deep overbite.ConclusionsOur deep learning model has successfully achieved the primary objectives of identifying molar and canine occlusal relationships, as well as anterior overbite relationships, using intraoral digital photographs. The demonstrated performance of this model highlights its potential for clinical applications.Clinical significanceThe application of deep learning models for occlusal classification depicted in digital intraoral photographs, which enables clinicians to extract key information rapidly, holds significant implications for patient management and treatment monitoring in orthodontic practices. creator: Rongxiu Zhang creator: Lin Zhang creator: Di Zhang creator: Ying Wang creator: Yongsong Huang creator: Dong Wang creator: Li Xu uri: https://doi.org/10.7717/peerj.20140 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Teacher preparedness regarding autism spectrum disorder in the Jazan region, Saudi Arabia: a cross-sectional study link: https://peerj.com/articles/20044 last-modified: 2025-09-26 description: BackgroundAutism spectrum disorder (ASD) is a multifaceted neurodevelopmental condition marked by distinct behavioral patterns, impaired social interaction, and communication challenges. Early recognition and appropriate intervention are pivotal for improving outcomes. This study aims to comprehensively evaluate the understanding, attitudes, and teaching methodologies of kindergarten and primary school teachers in the Jazan region, Kingdom of Saudi Arabia, regarding children with ASD.MethodologyA cross-sectional study was conducted using a multistage cluster random sampling technique. An interview-based questionnaire was administered to kindergarten and primary school teachers in the Jazan region. The target sample size was 800 teachers.ResultsAmong the 870 participating teachers, 87.8% reported lacking prior training on effectively addressing the needs of children with ASD. However, 74.8% demonstrated substantial understanding of the social communication difficulties faced by autistic children, and 76.2% were aware of the attention-related challenges these children encounter. Additionally, 77.7% of participants recognized the pivotal role of open communication between teachers and families in facilitating quality educational experiences and enhancing academic outcomes for students with ASD.ConclusionThe study highlights the critical need for targeted training programs to equip teachers with essential skills for supporting students with ASD. These findings underscore the importance of policy interventions to ensure adequate resources and expertise for effectively accommodating the unique needs of students with ASD in mainstream schools. creator: Maged El-Setouhy creator: Ahmad Y. Alqassim creator: Mohammad Zaino creator: Essam A. AlAmeer creator: Anwar Makeen creator: Mohammed A. Muaddi creator: Abdullah A. Alharbi creator: Renad H. Hamzi creator: Amaal A. Hamdi creator: Hanan N. Abu Summah creator: Norah K. Najmi creator: Raghad M. Sharahily creator: Maram A. Zuqayli creator: Fatimah A. Khubrani creator: Kholod Wasli uri: https://doi.org/10.7717/peerj.20044 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 El-Setouhy et al. title: Odontometric analysis of permanent mandibular first and second premolars in an Indian population using cone beam computed tomography link: https://peerj.com/articles/20039 last-modified: 2025-09-26 description: BackgroundDifferences in tooth size across populations can significantly influence dental diagnosis, treatment planning, and forensic identification. Despite its relevance, comprehensive region-specific odontometric data—particularly for the Indian population—remain limited. This study aimed to obtain odontometric measurements of permanent mandibular first and second premolars in the Indian population using cone beam computed tomography (CBCT), and to compare these measurements with Wheeler’s dental morphology standards, focusing on crown length, root length, and total tooth length.MethodsIn this retrospective study, 300 high-quality CBCT scans were analyzed. Measurements of crown, root, and overall tooth lengths for mandibular first and second premolars were obtained using CS 3D Imaging (Version 3.9.3). A one-sample t-test was performed to compare the mean values with Wheeler’s reference standards.ResultsStatistically significant differences were observed in all measured dimensions (p < 0.001). For first premolars, crown, root, and total lengths were shorter by 2.3 mm, 1.1 mm, and 3.4 mm, respectively. Second premolars showed reductions of 1.9 mm, 1.2 mm, and 3.0 mm, respectively.ConclusionsThis odontometric analysis highlights distinct dental morphological characteristics in the Indian population. These findings offer valuable insights for applications in anthropology, evolutionary biology, forensic science, and clinical dentistry. creator: Fiza Hamdulay creator: Ajinkya M. Pawar creator: Shivani Singh creator: Suraj Arora creator: Luca Testarelli creator: Asok Mathew creator: Alexander Maniangat Luke creator: Mohmed Isaqali Karobari uri: https://doi.org/10.7717/peerj.20039 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hamdulay et al. title: Integrating network pharmacology, molecular docking, and molecular dynamics simulations to explore potential compounds and mechanisms of Coptis chinensis in treating streptococcal infections link: https://peerj.com/articles/19960 last-modified: 2025-09-26 description: BackgroundCoptis chinensis, a prominent herb in traditional Chinese medicine, is widely utilized for its therapeutic effects against Streptococcus infections, though its precise mechanisms of action remain insufficiently understood. This study aims to clarify the potential mechanisms and active compounds of C. chinensis in the treatment of Streptococcus.MethodsActive compounds of C. chinensis were identified using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database, and their potential targets were predicted from multiple public resources. These targets were intersected with streptococcus-related genes to identify overlapping targets, which were then used to construct a protein–protein interaction (PPI) network and screen for key hub genes. To investigate the pharmacological mechanisms, Gene Ontology and KEGG pathway enrichment analyses were performed. Molecular docking was employed to evaluate the binding affinities between active compounds and core target proteins, followed by molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations to assess binding stability and free energy.ResultsA total of 24 active compounds were identified, along with 180 overlapping targets related to streptococcal infection. PPI network analysis revealed ten key hub genes, including IL1β, IL6, and MMP9. Enrichment analysis suggested that C. chinensis may inhibit the TLR4/NF-κB inflammatory pathway to modulate host immunity and mediate lipid metabolism reprogramming to restrict pathogen proliferation. Several core targets were also enriched in pathways related to extracellular matrix remodeling and immune regulation, indicating potential indirect effects on host–pathogen interface interactions. Molecular docking and simulation confirmed stable binding between major active ingredients and streptococcus-associated proteins.ConclusionThis study provides mechanistic insights into the multi-component, multi-target, and multi-pathway effects of C. chinensis against streptococcal infections. The findings offer a theoretical basis for future experimental validation and clinical translation. creator: Wanxiang Qi creator: Bin Shi creator: Wenqiang Tang creator: Jiangyong Zeng creator: Ma Zhuo creator: Hongcai Ma uri: https://doi.org/10.7717/peerj.19960 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Qi et al. title: Anticancer potential of ethanolic sidr leaf extracts against MCF-7 breast cancer cells: phytochemical, nutritional, and antimicrobial profile comparisons of different plant parts link: https://peerj.com/articles/19858 last-modified: 2025-09-26 description: BackgroundTraditional medicine has long utilized natural plants to treat diseases and promote overall health. They have contributed significantly to the creation of modern medications. To supplement existing information, therefore, this current investigation aimed to understand the potential therapeutic properties of the sidr plant against triple negative breast cancer (TNBC) on MCF-7 breast cell line by conducting phytochemical, nutritional, and antimicrobial profile comparisons of different plant parts.MethodsPhytochemical analyses involved soluble sugar composition and oxidation profile, whereas nutritional analysis involved the proximate chemical analysis. Additionally, antimicrobial analyses involved six kings of food-borne bacterial strains.ResultsAccording to the study, leaves possessed the highest amounts of protein (12.44%) and ash (8.17%), as well as the highest amounts of ascorbic acid and total chlorophyll. On the other hand, pulps exhibited the highest flavonoid concentration in their ethanolic extract and had higher sugar contents. Furthermore, at a dosage of 100 µg/mL, the ethanolic extract of leaves showed potent antimicrobial action and suppressed over 50% of MCF-7 breast cancer cell survival.ConclusionsBioactive components, antioxidant, antimicrobial and nutritional elements of sidr plant appears a promising medicinal candidate to fight breast cancer cells. creator: Roqayah H. Kadi creator: Nashi K. Alqahtani creator: Ahmed M. Abdulfattah creator: Fayez Alsulaimani creator: Ahmed M. Basri creator: Reham M. Algheshairy creator: Hend F. Alharbi creator: Rokayya Sami creator: Amal Alyamani creator: Roua S. Baty creator: Ruqaiah I. Bedaiwi creator: Hala M. Abo-Dief creator: Nahid A. Osman creator: Nouf H. Alsubhi creator: Ashwaq M. Al-Nazawi creator: Manal Malibary uri: https://doi.org/10.7717/peerj.19858 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kadi et al. title: Relationship between locomotive syndrome risk test and height and weight in infancy and toddlerhood: a preliminary study link: https://peerj.com/articles/20114 last-modified: 2025-09-25 description: IntroductionThe Japanese Medical Science Federation’s declaration highlighted that locomotive syndrome (LS) precedes frailty, emphasizing the importance of early intervention beginning in childhood and continuing throughout life. To date, no study has examined the relationship between LS in adults and height and weight during infancy and toddlerhood. As a preliminary investigation, this study aimed to clarify how height and weight during early life stages are related to LS among young adults.MethodsIn this study, 62 students enrolled at a health sciences university were administered the locomotive syndrome risk test, and their grip strength was measured. Height and weight at birth, at 1 year, and at 3 years of age were obtained from the Maternal and Child Health Handbook. All participants were born via normal delivery. The relationships between the LS risk test results, height, and weight were analyzed using correlation and multivariate analyses.ResultsCorrelation analysis revealed significant associations between height and weight in infancy and toddlerhood and the following variables: two-step length, two-step test value, 25-question geriatric locomotive function scale score, and grip strength. Multiple regression analysis showed a significant relationship between two-step length and height at birth (p = 0.002), and between grip strength and weight at age 3 (p = 0.021).ConclusionsA weak-to-moderate relationship was found between LS and height and weight in infancy and toddlerhood. These findings suggest that preventive measures for LS should not be delayed until adulthood; rather, early-life interventions beginning in infancy, toddlerhood, and childhood may be crucial. creator: Shuntaro Tsuji creator: Tamaki Hirose creator: Yohei Sawaya creator: Runa Kawano creator: Takumi Sugiura creator: Riona Takimoto creator: Yuto Nishimura creator: Masafumi Itokazu uri: https://doi.org/10.7717/peerj.20114 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tsuji et al. title: Geographic distributions and patterns of co-occurrence among black-bellied and shovel-nosed salamanders (Desmognathus spp.) in the Great Smoky Mountains National Park link: https://peerj.com/articles/20110 last-modified: 2025-09-25 description: The southern Appalachian Mountains are a global hotspot for salamander diversity. Recent taxonomic revisions driven by a growing understanding of cryptic diversity and advancements in genomic technology have increased the number of described species in the area significantly, raising questions about biogeography and community structure. Recently described species in the Desmognathus quadramaculatus-marmoratus complex are morphologically cryptic but diagnosable by mitochondrial DNA. The complex includes multiple species within each of two distinct ecomorphs, the highly aquatic ‘shovel-nosed’ (SN) ecomorph and the semi-aquatic ‘black-bellied’ (BB) ecomorph. Here, we use mitochondrial DNA and Bayesian phylogenetic analysis to clarify distributions and patterns of co-occurrence of recently described species in the Great Smoky Mountains. We present new data showing more extensive co-occurrence of two cryptic species of the black-bellied ecomorph than previously recognized. Our results are also consistent with earlier work indicating shared variation between ecomorphs within one clade. In addition, we identified a divergent mitochondrial lineage of the shovel-nosed ecomorph related to D. aureatus, a species not previously known to inhabit the Great Smoky Mountains. These results reveal a more complex and diverse assemblage of ecomorphs than previously recognized in this hotspot of salamander diversity. creator: Aidan Shaw creator: Rebecca Chastain creator: Benjamin M. Fitzpatrick uri: https://doi.org/10.7717/peerj.20110 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shaw et al. title: Establishment and verification of a nomogram model based on the inflammatory indicators of patients with cervical cancer for predicting the risk of their lymph node metastasis link: https://peerj.com/articles/20069 last-modified: 2025-09-25 description: Based on inflammatory indicators, this study aimed to predict the risk of lymph node metastasis (LNM) in patients with cervical squamous cell carcinoma (CSCC) and establish a predictive nomogram model.MethodsThis retrospective study analyzed the clinical data of 194 patients with stage IA2-IIA2 who underwent surgery at Hebei General Hospital (between January 2017 and August 2023). Patients were divided into two groups based on the presence of LNM or not. Clinical data of the participants were gathered and analyzed to compare the two groups. Logistic regression analysis was used to analyze the factors influencing LNM in patients with CSCC. R software was used to construct a nomogram model to predict LNM in patients with CSCC, and its accuracy was verified.ResultsSquamous cell carcinoma antigen (SCC-Ag) level, D-dimer level, platelet (PLT) count, and platelet-to-lymphocyte ratio (PLR) index were significantly higher in patients with LNM than in those without LNM (P < 0.05). There was a significant association between lymph vascular space invasion (LVSI) in patients with CSCC and their LNM (P < 0.05). Logistic regression analysis showed that SCC-Ag, PLR, and LVSI in patients with CSCC were independent risk factors for LNM (P < 0.05). A predictive nomogram model was constructed, and the prediction probability was consistent with the actual observed value (Hosmer–Lemeshow P = 0.313). Analyses using the receiver operating characteristic (ROC) curve revealed that the combination of the SCC-Ag, PLR, and LVSI values of patients with CSCC significantly improved the diagnostic efficiency of their LNM (AUC = 0.792, P < 0.001).ConclusionEstablishing a nomogram model based on preoperative inflammatory indicators of patients with CSCC can accurately predict the risk of LNM, providing evidence for implementing a clinical diagnosis and treatment scheme. creator: Liyun Song creator: Kaiyun Qin creator: Suning Bai creator: Qi Wu creator: Jing Zhao creator: Jie Qi creator: Junmei Zhang creator: Yazhuo Wang creator: Yuan Zhang creator: Ren Xu uri: https://doi.org/10.7717/peerj.20069 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Song et al. title: Selection of suitable wheat genotypes under thermal stress and complex genotype-environment interaction using stability analyses and selection indices link: https://peerj.com/articles/20061 last-modified: 2025-09-25 description: Thermal stress is a consequence of climate change that threatens food security, causes plant tissue damage, and harms crop production, particularly during the pollination and fertilization period and in grain-filling stages negatively impacting the number of grains, grain size, and quality. Genotype-environment interaction (GEN: ENV) complicates the selection of optimal wheat genotypes due to the complex genetic basis of yield under varying conditions. Diversified approaches were put forth in response to the pressing demand for simultaneous enhancements in high-yield performance combined with stability. This study investigates the selection of ideal wheat genotypes under thermal stress and complex GEN: ENV using stability analyses and selection indices to assess genotype performance and stability. Twenty wheat genotypes were evaluated across optimal conditions (OC) and thermal stress conditions (TSC) over three growing seasons with six ENVs. Results demonstrated significant GEN: ENV, revealing genetic variations in thermal tolerance. The additive main effects and multiplicative interaction (AMMI2) biplot indicated a combined variance of 99.00%, and eleven genotypes showed stable grain yield (GY) with six ENVs, three (G05, G09, and G17) were more stable. The G04, G05, G06, G09, and G18 genotypes were chosen for GY as perfect (stable and high-performance) genotypes by weighted average of absolute scores biplot (WAASB) and were also identified as the best genotypes group by WAASB-GY, with the exception of G18. Ten selection indices showed significant positive associations under GYoc and GYtsc, so they can be leveraged to detect the genotype’s high yield of GYtsc indirectly. The heritability, accuracy, and rgen: env values for most indices were high, indicating a major role of the genotypic effect in their inheritance, with the exception of the stress-non-stress production index (SNPI) index. Out of the five that were examined by WAASB, G04, G05, G06, and G09 were the top-ranking genotypes by the multi-trait genotype ideotype distance index, either before or after removing variables. This suggests that they could be examined for validation stability measures. The findings of this study offer valuable insights for ENVs variety selection, facilitating the identification of improved cultivars and supporting the development of thermal stress-resilient breeding programs. creator: Abdelhalim Ghazy creator: Walid Ben Romdhane creator: Majed Alotaibi creator: Abdullah Al-Doss creator: Omar Dahrog creator: Nasser Al-Suhaibani creator: Abdullah Ibrahim creator: Adel M. Al-Saif creator: Khalid A. Al-Gaadi creator: Ahmed M. Zeyada creator: Khalid F. Almutairi creator: Ibrahim Al-Ashkar uri: https://doi.org/10.7717/peerj.20061 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ghazy et al. title: Association of circulating branched-chain amino acids with risk of pre-diabetes: a systematic review and meta-analysis link: https://peerj.com/articles/20054 last-modified: 2025-09-25 description: ObjectiveRecent investigations have looked at the systemic concentrations of branched-chain amino acids (BCAA), which they consider prospective indicators for health conditions and the likelihood of chronic diseases. To elucidate the equivocal link between systemic BCAA concentrations and prediabetes, our study undertook a meta-analytical investigation.Materials and MethodsElectronic databases were comprehensively searched in April 2024, and the study quality evaluation relied on the Newcastle-Ottawa Scale (NOS). The I2 statistic was used for heterogeneity assessment, and data analysis relied on Review Manager 5.4 and Stata 12.0. Standard mean difference (SMD) was used as the effect size to account for varying units of measurement across the included studies. Sensitivity assessment was instituted to evaluate result tenacity, and subgroup examinations were concomitantly carried out, with funnel plots, Egger’s regression analysis, and Begg’s rank-correlation methodology deployed to discern publication bias. PROSPERO registration (CRD42024572760) validates this review’s protocol compliance.ResultsMeta-analysis was conducted on 15 studies that involved 3,849 participants. Most individuals were over 40 years old. The prediabetes (PreDM) group exhibited significantly elevated levels of valine (Val) (SMD = 0.29; 95% confidence interval (CI) [0.14–0.45]; P = 0.0002), leucine (Leu) (SMD = 0.34; 95% CI [0.18–0.49]; P < 0.0001), and isoleucine (Ile) (SMD = 0.24; 95% CI [0.15–0.32]; P < 0.00001) compared to controls. Affirming the soundness of the results, sensitivity analysis indicated the lack of significant publication bias.ConclusionsThis meta-analysis supports the hypothesis that circulating BCAA levels increase in PreDM, suggesting that measuring BCAA levels could be investigated as a potential biomarker for the diagnosis of PreDM and a target for its treatment. creator: Yu Wang creator: Jiang-Hong Xiao creator: Xi-Mei Zhang creator: Wen-Xiao Wang creator: Qiao Zhang creator: Yu-Ping Tang creator: Shi-Jun Yue uri: https://doi.org/10.7717/peerj.20054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Identification of immunological and prognostic value of SHROOM2 in pan-cancer and experimental verification of its role in promoting malignant phenotypes in breast cancer link: https://peerj.com/articles/20051 last-modified: 2025-09-25 description: ObjectiveThis study aimed to investigate the relationship between Shroom Family Member 2 (SHROOM2) expression and immune features, survival outcomes, and tumor mutational burden (TMB) across various cancer types, as well as its impact on the aggressive behavior of breast cancer (BC).MethodsRNA sequencing and clinical survival data were retrieved from the TCGA-BRCA and TCGA-PANCANCER datasets within The Cancer Genome Atlas (TCGA) database. Survival analyses were performed to assess the association between SHROOM2 expression and clinical outcomes across different cancer types. Gene set enrichment analysis (GSEA) was applied to identify potential mechanisms associated with differentially expressed genes in BC. Spearman correlation and Wilcoxon tests were used to evaluate the relationships between SHROOM2 levels and immune characteristics, TMB, or drug sensitivity. Additionally, the effects of SHROOM2 on BC cells were assessed through reverse transcription-quantitative polymerase chain reaction (PCR), cell counting kit-8 (CCK-8) assay, transwell assay, and wound healing assay.ResultsSHROOM2 was overexpressed in a range of cancers, and its upregulation was associated with poor clinical outcomes. It was significantly correlated with immunomodulators, immune checkpoints, and immune cell infiltration in pan-cancer. Moreover, it showed an association with TMB and drug sensitivity in BC. Increased SHROOM2 expression enhanced the proliferative, migratory, and invasive capabilities of BC cells in vitro.ConclusionHigh SHROOM2 expression is linked to poor prognosis in BC, supporting its potential as both an immunological and predictive biomarker. creator: Yaya Wang creator: Yuechao Ren creator: Xiaoyan Zheng creator: Yan Wang creator: Haoqi Wang creator: Xi Zhang creator: Sainan Li uri: https://doi.org/10.7717/peerj.20051 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Effect of cirrhosis on prognosis in patients with acute-on-chronic liver failure: a systematic review and meta-analysis link: https://peerj.com/articles/20049 last-modified: 2025-09-25 description: BackgroundAcute-on-chronic liver failure (ACLF) is a prevalent complication among cirrhosis patients, whose high mortality is linked to cirrhosis combined with ACLF. Nevertheless, there is a paucity of systematic reviews. This study aimed to illustrate whether cirrhosis is a prognostic factor for ACLF.MethodologyPubMed, Embase, and Cochrane Library were searched for observational studies that explored the connection between cirrhosis and ACLF prognosis from database inception to January 10, 2025. Pooled relative risk (RR) and 95% confidence interval (CI) were utilized for data analyses. Publication bias was estimated using Egger’s tests. The protocol was registered in the PROSPERO (CRD42025639557).ResultsThis meta-analysis included 17 articles and 8,488 patients of ACLF under different diagnostic criteria. The analyses indicated that cirrhosis did not correlate with 28-day mortality of ACLF patients (RR = 1.08, 95% CI [0.84–1.39], p = 0.550, I2 = 88.8%) but independently predicted 90-day mortality (RR = 1.33, 95% CI [1.10–1.61], p = 0.004, I2 = 92.6%). Subgroup analyses of cirrhosis discovered no significant difference in 28-day and 90-day mortality between non-cirrhosis patients and those with compensated cirrhosis (p > 0.05). The 90-day mortality in decompensated cirrhosis patients was markedly higher than that in non-cirrhosis individuals (RR = 1.33, 95% CI [1.14–1.56], p < 0.001, I2 =64.2%).ConclusionsCompensated cirrhosis did not correlate with the 28-day mortality of ACLF patients, while it was an independent risk factor for 90-day mortality. creator: Chunyang Dong creator: Xiaoxiao Liu creator: Dongshuai Zhang creator: Deyou Jiang uri: https://doi.org/10.7717/peerj.20049 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dong et al. title: Elevational surveys of Sulawesi herpetofauna 2: Mount Katopasa on the Eastern Peninsula of Sulawesi island, Indonesia link: https://peerj.com/articles/20024 last-modified: 2025-09-25 description: The unique geologic and biogeographic history of the island of Sulawesi in Indonesia has produced one of the world’s most endemic biota, much of which is still unknown to science. The biogeography of the island is influenced both by its unique shape, a confluence of four peninsulas, as well as its extremely mountainous topography, and its upland ecosystems are poorly understood by science. Here, we report the second full-mountain checklist from a series of herpetological surveys of Sulawesi’s Mountains conducted by an international team of researchers. During 3 weeks of work on Gunung Katopasa, a 2,825 m asl peak on Sulawesi’s Eastern Peninsula in the province of Sulawesi Tengah, we recovered 45 species of reptiles and amphibians. Among these, we believe that at least eight represent undescribed species. Our efforts to survey Gunung Katopasa highlight that greater herpetological diversity will likely be discovered upon future assessments of species richness and abundance on the Eastern Peninsula of Sulawesi. creator: Isaac W. Krone creator: Benjamin R. Karin creator: Jeffrey H. Frederick creator: Sina S. Amini creator: Simon G. Scarpetta creator: Amir Hamidy creator: Syahfitri Anita creator: Awal Riyanto creator: Evy Arida creator: Wahyu Tri Laksono creator: Umilaela Arifin creator: Bryan H. Bach creator: Collin Bos creator: Charlotte K. Jennings creator: Alexander L. Stubbs creator: Kinsington Peterson creator: Sucheng Shi creator: Jimmy A. McGuire uri: https://doi.org/10.7717/peerj.20024 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Krone et al. title: Interactive effects of acacia biochar, maize hybrids, and irrigation levels on soil health and crop productivity link: https://peerj.com/articles/20048 last-modified: 2025-09-24 description: The demand for sustainable agricultural solutions has increased because of issues like declining soil fertility from inorganic soil changes, increasing crop water demands, shifting weather patterns, and decreasing water resources. The addition of activated acacia biochar to degraded soil can significantly influence soil health by improving its moisture and nutrient retention capacity, as well as crop productivity under water-limited conditions. At present, field experiment under split-plot design was conducted to explore the suitable level of activated biochar (A0, 0 tons ha−1; A1, 5 tons ha−1; A2, 10 tons ha−1;) for maize hybrids (DK-2088, YH-5427, and DK-6317) under different moisture regimes (100% ETC; full irrigation (FI), 70% ETC; partially deficit irrigation (PDI), and 50% ETC; severely deficit irrigation (SDI)) during maize growing year 2023 from February to June. The results showed that the addition of 10 tons ha−1 activated biochar caused a maximum improvement in soil organic matter (109%), saturation percentage (13%), and mineral profile particularly carbon (83%) and calcium (52%). Under full irrigation (FI), activated acacia biochar amendment in the soil caused an improvement in the physiological and biochemical parameters such as sugar (55%) and protein content (136%), and yield attributes of all maize hybrids, particularly DK-6317. However, under severely deficit irrigation (SDI), the highest improvement in protein content, and yield per hectare was found in DK-2088, i.e., 11% to 29% higher in 5 tons ha−1, 10 tons ha−1 activated biochar amended soil, respectively. The average economic gain percentage was highest in DK-6317, i.e., 1-fold, and 2.5-fold higher under PDI, and SDI in 10 tons ha−1 activated biochar amended soil. The present study indicates the significance of organically activated acacia biochar amendments in soil for improving its water retention capacity and enhancing maize growth and yield under moisture-deficit conditions. creator: Zarghoona Naz creator: Audil Rashid creator: Summera Jahan uri: https://doi.org/10.7717/peerj.20048 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Naz et al. title: From Abstainers to Dependent Drinkers: alcohol consumption patterns and risk factors among Portuguese university students link: https://peerj.com/articles/20026 last-modified: 2025-09-24 description: BackgroundAlcohol is the most prevalent psychoactive substance consumed around the world. In Portugal, alcohol consumption is deeply embedded in social and cultural practices, contributing to high prevalence rates among university students, with binge drinking emerging as a predominant consumption pattern. Despite the associations between this drinking behaviour and numerous social, physical, and psychological problems, research on alcohol consumption in Portuguese university populations remains limited. Thus, this study aimed to provide a comprehensive description of alcohol use patterns among a large sample of Portuguese university students, focusing on adolescents and young adults.MethodsA total of 1,746 students, aged 17–24 years, participated in a cross-sectional study and were surveyed using the Alcohol Use Disorders Identification Test (AUDIT) and additional questionnaires regarding socio-demographic information, alcohol and illicit drug use, smoking habits, and alcohol cravings. Statistical analyses included descriptive statistics, group comparisons, and multinomial logistic regressions to obtain odds ratios (ORs) for group membership.ResultsAlcohol consumption was reported by 83.2% of students over the past year. Based on their drinking patterns and AUDIT score, participants were distributed across five drinking groups: Abstainers (16.8%), Moderate Drinkers (35.1%), Hazardous Drinkers (25.8%), Binge Drinkers (20.8%), and Dependent Drinkers (1.5%). Nearly 47% of students revealed harmful drinking patterns, and 1.5% exhibited symptoms of alcohol dependence. A progressive increase in the severity of alcohol consumption characteristics was observed across the groups, with Dependent Drinkers reporting the highest levels of all assessed characteristics. Significant predictors of group membership included polydrug use, standard weekly consumption, earlier drinking onset, and higher levels of alcohol craving. Polydrug use, reported by 27.3% of students, was the strongest predictor for being a Hazardous Drinker (OR = 10.75), Binge Drinker (OR = 13.20), and Dependent Drinker (OR = 21.40). Binge Drinkers displayed standard weekly consumption and craving levels comparable to Dependent Drinkers, while Moderate Drinkers exhibited the least risky patterns among drinkers, including a later age of onset of drinking. Male students reported significantly greater consumption and craving levels than their female peers.ConclusionsThis study highlights the prevalence of harmful drinking behaviours among Portuguese university students and identifies critical risk factors, such as polydrug use and early drinking onset. These findings underscore the need for prevention programmes focused on delaying the onset of alcohol use, reducing drug use, and promoting healthier behaviours within academic settings. creator: Lucas Saldanha creator: Alberto Crego creator: Natália Almeida-Antunes creator: Rui Rodrigues creator: Adriana Sampaio creator: Eduardo López-Caneda uri: https://doi.org/10.7717/peerj.20026 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Saldanha et al. title: Impact of nonalcoholic fatty liver disease on the functional cure of nucleos(t)ide analogues-treated chronic hepatitis B patients add-on pegylated interferon therapy: a retrospective study link: https://peerj.com/articles/19972 last-modified: 2025-09-24 description: BackgroundThis study aimed to determine whether nonalcoholic fatty liver disease (NAFLD) influences the functional cure of nucleos(t)ide analogues (NAs)-treated chronic hepatitis B (CHB) patients in combination with pegylated interferon (PEG-IFN) therapy.MethodsA retrospective analysis was conducted on CHB patients treated with nucleos(t)ide analogues (NAs) who received PEG-IFN combination therapy at a single center. Patients were stratified into a CHB group and a CHB-NAFLD group based on the presence of fatty liver comorbidity. The primary endpoint was the difference in hepatitis B virus surface antigen (HBsAg) seroclearance rates between the two groups, and the secondary endpoint was the differences in biochemical parameters and adverse events.ResultsA total of 158 NAs-treated CHB patients were enrolled, comprising 91 CHB -only patients and 67 CHB-NAFLD patients. After 48 weeks of PEG-IFN therapy, 20.9% of patients achieved HBsAg seroclearance. Before and after propensity score matching (PSM), differences in cumulative HBsAg seroclearance probability between groups were non-significant (25.3% vs. 14.9% , P = 0.121; 32.4% vs. 13.5%, P = 0.063). Similarly, cumulative hepatitis B e antigen (HBeAg) seroconversion incidence showed no intergroup differences before and after PSM (P = 0.618 and P = 0.954, respectively). Logistic regression analysis indicated that baseline HBeAg status was independently associated with HBsAg seroclearance. Further analysis confirmed that NAFLD did not significantly affect HBsAg loss, regardless of HBeAg status, both before and after PSM (P > 0.05). Moreover, the NAFLD group exhibited higher rates of abnormal alanine aminotransferase (ALT) at weeks 24 and 48 versus the CHB-only group (31.9% vs. 12.3%, P = 0.009; 70.8% vs. 47.4%, P = 0.007). However, ALT normalization rates 24 weeks post-treatment showed no significant difference (88.9% vs. 77.2%, P = 0.074).ConclusionNAFLD does not affect the achievement of functional cure with PEG-IFN therapy in NAs-treated chronic hepatitis B patients. However, CHB patients with NAFLD show a reduced likelihood of ALT normalization during treatment. creator: Huili Li creator: Ling Li creator: Yiru Zhao creator: Guangde Yang creator: Xia Wang creator: Juanjuan Fu creator: Li Li creator: Xiucheng Pan uri: https://doi.org/10.7717/peerj.19972 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Li et al. title: Individualized responses to velocity-based versus percentage-based resistance training in combat sports athletes: the influence of baseline characteristics link: https://peerj.com/articles/19928 last-modified: 2025-09-24 description: BackgroundTraditional percentage-based resistance training (PBRT) is a cornerstone of strength development, but its fixed nature may not account for daily fluctuations in athlete readiness. Velocity-based resistance training (VBRT) has been proposed as a superior alternative for power development due to its auto-regulatory capabilities, but its efficacy in highly trained combat sports athletes remains contested.ObjectiveThis study aimed to compare the effects of velocity-based resistance training (VBRT) and percentage-based resistance training (PBRT) on upper limb strength, general power, and sport-specific power in combat sports athletes, and to explore individualized training responses.MethodsA randomized parallel-group controlled trial was conducted, recruiting 24 male university combat sports athletes (age: 21.5 ± 2.1 years; training experience: 4.8 ± 1.5 years; baseline bench press one-repetition maximum (1RM): 95.4 ± 10.2 kg). Participants were randomly assigned to either a VBRT group (n = 12) or a PBRT group (n = 12) for an 8-week bench press intervention. Pre- and post-intervention tests included bench press 1RM, medicine ball throws, and power in the Seoi-nage (shoulder throw).ResultsA 2 × 2 mixed-model analysis of variance (ANOVA) revealed that while both groups significantly improved in most metrics, the PBRT group demonstrated significantly greater improvements in several key areas. Significant Group × Time interactions were found favoring the PBRT group for 4kg medicine ball velocity (p < .001), power (p = .012), and distance (p = .020), as well as for sport-specific power in both the left (p < .001) and right (p = .018) Seoi-nage. Crucially, at post-test, the PBRT group’s left Seoi-nage power was significantly higher than the VBRT group’s (p = .035). Exploratory cluster analysis identified three distinct athlete subgroups, and PBRT elicited superior or comparable training adaptations across all of them.ConclusionFor the cohort of university-level combat sports athletes in this study, PBRT was a more effective training methodology than VBRT for enhancing both general and sport-specific power. These findings challenge the assumption of VBRT’s universal superiority for power development and highlight the continued efficacy and robustness of traditional PBRT for strength and conditioning in this population. creator: JiaYong Chen creator: Beiwang Deng creator: Tianyuan He creator: Jiaxin He creator: Duanying Li creator: Min Lu creator: Jian Sun uri: https://doi.org/10.7717/peerj.19928 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Effects of 4-week velocity-based HIIT on athletic performance in youth soccer players link: https://peerj.com/articles/20066 last-modified: 2025-09-23 description: ObjectiveYoung soccer players need to enhance their athletic performance, including speed and endurance. Traditional training methods may not be effective enough to improve athletic performance in these young athletes. Velocity-based high-intensity interval training (vHIIT) workouts can increase the efficiency of energy systems and improve athletic performance. This study aimed to investigate the effects of four weeks of vHIIT on athletic performance in young soccer players.MethodA total of 14 male soccer players participated in the study (mean age: 18.9 ± 1.0 years, body mass: 76.5 ± 5.3 kg, height: 1.81 ± 0.08 m). Participants were randomly assigned to either an experimental group (n = 7) or a control group (n = 7). While the control group continued their regular soccer training without additional vHIIT intervention, the experimental group underwent vHIIT training at 85–90% intensity twice a week for 4 weeks in addition to their regular training. Change of direction speed (COD), maximum sprint speed (MSS), maximum oxygen consumption (VO2max), and the 30-15 intermittent fitness test (VIFT) were assessed twice, in the control and experimental groups, both at pre-test and post-test measurements.ResultsThe findings indicated a significant decrease in COD time (p < 0.001, η2p = 0.682) and 30-15 IFT (p < 0.001, η2p = 0.735) in the experimental group. However, no statistically significant change was observed in these parameters between the pre-test and post-test in the control group. Additionally, group-time interaction effects were found to be significant in favor of the experimental group in all parameters.ConclusionFour weeks of speed-based vHIIT training led to improvements in sprint performance, COD, and aerobic capacity in young soccer players. Incorporating vHIIT workouts into conditioning programs for youth soccer players may be an effective strategy for enhancing physical performance components, including speed, agility, and endurance, which are requirements of soccer. creator: Murat Koç creator: Niyazi Sıdkı Adıgüzel creator: Hakan Engin creator: Barışcan Öztürk creator: Umut Canli creator: Aydın Karaçam creator: Bekir Erhan Orhan creator: Pablo Prieto-González creator: Peter Bartik creator: Shahad Alghemlas creator: Maria Isip creator: Peter Sagat uri: https://doi.org/10.7717/peerj.20066 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Koç et al. title: Effectiveness of gamma-oryzanol in glycaemic control and managing oxidative stress, inflammation, and dyslipidaemia in diabetes: a systematic review of preclinical studies link: https://peerj.com/articles/20062 last-modified: 2025-09-23 description: BackgroundDiabetes mellitus (DM) and associated complications remain a global public health challenge despite many confrontational aspects of the disease, and its prevalence is projected to rise in the coming decades. Thus, there is an urgent need to intensify the current efforts to address both the prevalence and adverse effects of diabetes, including the use of natural products. Increasing evidence from the scientific literature has revealed the beneficial effects of gamma oryzanol for treating diabetes and its related complications.AimTo investigate the effectiveness of gamma oryzanol (γ-oryzanol) in managing hyperglycaemia, oxidative stress, inflammation, and dyslipidaemia in a rodent model of diabetes mellitus.MethodologyThe review was conducted by searching PubMed, ScienceDirect, Scopus, and Web of Science for articles published from inception to July 12, 2025, with the terms (Gamma-oryzanol OR γ-oryzanol OR Oryzanol OR Cycloartenyl ferulate OR Gammariza) AND (Diabetes mellitus OR Type 2 diabetes mellitus OR hyperglycemia OR oxidative stress OR inflammation OR dyslipidaemia). The review included only articles that used rat and mouse models of diabetes mellitus and γ-oryzanol as treatments; articles that did not meet these criteria were excluded. A total of nine articles were identified, encompassing a total population of 394 rodents. SyCLE’s risk of bias tool was used to assess the methodological quality of the studies.ResultsOut of 1,989 records initially identified through the systematic search, nine studies met the eligibility criteria. All included studies were assessed to have an unclear to low risk of bias. The synthesised findings indicate that γ-oryzanol (γ-ORZ) exerts beneficial effects on glycaemic control by enhancing insulin secretion and sensitivity, as well as by reducing fasting blood glucose (FBG) levels. Additionally, γ-ORZ demonstrates antioxidant activity by elevating endogenous antioxidant enzyme levels and decreasing oxidative stress markers. Its lipid-modulatory effects include the elevation of beneficial lipid fractions and the reduction of atherogenic lipids, thereby alleviating diabetic dyslipidaemia. Moreover, γ-ORZ exhibits anti-inflammatory properties through the downregulation of proinflammatory biomarkers. Despite these promising results in preclinical models, further high-quality investigations, particularly well-designed clinical trials, are essential to validate these findings and support the potential integration of γ-ORZ into diabetes management strategies.ConclusionMost included studies reported that γ-ORZ positively affected hyperglycaemia, oxidative stress, dyslipidaemia, and inflammation under diabetic conditions. Further research, particularly rigorously designed clinical trials, is strongly recommended to confirm and translate these preclinical findings into clinical practice. creator: Mustapha Ismail Radda creator: Norsuhana Omar creator: Siti Fairuz Mohd Yusof creator: Rozaziana Ahmad creator: Abdul Jalil Rohana creator: Wan Rosli Wan Ishak creator: Anani Aila Mat Zin creator: Aminah Che Romli uri: https://doi.org/10.7717/peerj.20062 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Radda et al. title: Estimating ankle joint angle from skeletal geometry: a mechanical model of the calcaneal lever in terrestrial mammals link: https://peerj.com/articles/20056 last-modified: 2025-09-23 description: BackgroundThe ankle joint angle, typically measured between the tibia and metatarsus, shows only a small range of movement during the stance phase and remains relatively constant within species, but varies across taxa. This variation influences traits such as stride length, posture, and locomotor function. While joint angles are readily observable in living animals, they cannot be directly measured in extinct species, for which only skeletal remains are available. Therefore, estimating ankle joint posture from skeletal geometry is important for reconstructing locomotion in both extant and extinct mammals. In this study, we propose a mechanical model of the ankle extensor apparatus to estimate ankle joint angle from bones and test whether the muscle-lever system aligns consistently with skeletal features across taxa.MethodsWe developed a simplified mechanical model of the ankle extensor apparatus to calculate ankle extensor moment arm defined as the perpendicular distance from the ankle joint center to the muscle force line of action, which was assumed to be parallel to the tibia. To verify the Achilles tendon runs parallel to the tibia across taxa, dissections were performed on cadavers of 24 species in seven orders. We compared observed angle (θobs) from 26 species of zoo-kept terrestrial mammals, covering various body mass and locomotor modes, with estimated angle (θest) from skeletal specimens of the same species. θobswas the mean tibia–metatarsus angle during the stance phase, recorded laterally with a high-speed camera. θestwas measured on reassembled skeletal specimens as the ankle joint angle that maximized the extensor moment arm in the model. Phylogenetic comparative methods, including phylogenetic ANOVA and PGLS, were applied to analyze relationships among θobs, θest, body mass, and locomotor mode based on a time-calibrated phylogeny.ResultsDissections confirmed the Achilles tendon runs nearly parallel to the tibia across species. Stance phase ankle joint rotations were small. Therefore, θobs could be considered as representative for each species. Over 85% of the studied species maintained their ankle joint angle at which the mechanical advantage of the calcaneal lever was greater than 0.9. No significant differences in the mechanical advantage of the calcaneal lever were found among locomotor modes or taxonomic orders. A strong positive correlation was observed between θobs and θest (ρ = 0.70, p < 0.001).ConclusionOur mechanical model could estimate θest from skeletal morphology that closely match θobs during stance phase. Despite interspecific variation of θobs, the mechanical advantage of the calcaneal lever remains within a narrow range, suggesting mechanical optimization of the ankle extensor apparatus across terrestrial mammals. This model informs postural reconstruction in extinct species. creator: Fumihiro Mizuno creator: Shin-ichi Fujiwara uri: https://doi.org/10.7717/peerj.20056 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mizuno and Fujiwara title: On the composition and temporal dynamics of a snake community at the Cerrado-Amazonia ecotone link: https://peerj.com/articles/20025 last-modified: 2025-09-23 description: Understanding the factors shaping the temporal dynamics of ecological communities is crucial for biodiversity conservation during the Anthropocene. In this study, we describe the species composition of a snake community within the Cerrado-Amazonia transition, the largest forest-savanna transition zone in the world, and a highly threatened ecosystem in Brazil. We also analyzed community structure over time using temporal diversity indices. The community had a balanced mix of forest and savanna species, with the Dipsadidae family exhibiting the highest diversity, including two potentially new taxa. Our research, conducted through extensive fieldwork and literature records, documented 53 species across seven families. This comprehensive approach provided a detailed picture of the snake diversity in this unique transitional zone. The results corroborate previous observations that snake richness is high during wet seasons and show that the community has complex temporal dynamics tied to seasonal shifts. The snake community was active throughout all seasons, with species turnover higher during the wet and dry seasons, marked by a high appearance rate during wetter periods and a high disappearance rate of species during the dry season. The community exhibited positive covariance among species, with each species fluctuating independently over time. However, ongoing deforestation in the region may impact species abundance. These characteristics may be attributed to the unique ecological pressures and adaptations of the transition zone. The presence of species with diverse distribution patterns and habitat preferences underscores the environmental and biogeographic complexity of the region, indicating that the Cerrado-Amazonia transition serves as a critical habitat for a wide range of snake species. We also identified two potential new species, emphasizing the urgent need for further research on the effects of environmental changes on local snake populations and biodiversity. Our findings contribute to understanding Neotropical patterns of herpetofauna diversity and underscore the importance of protecting transitional ecosystems. As these areas face increasing threats from human activities, understanding their ecological dynamics becomes essential for developing effective conservation strategies. Our study serves as a call to action for preserving the unique biodiversity of the Cerrado-Amazonia transition zone and mitigating the adverse impacts of anthropogenic changes. creator: Arthur Sena creator: Guarino Rinaldi Colli uri: https://doi.org/10.7717/peerj.20025 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sena and Colli title: Identification of key pathways and genes underlying melatonin-enhanced drought tolerance in cotton link: https://peerj.com/articles/20005 last-modified: 2025-09-23 description: Drought stress is a significant environmental constraint that adversely affects the growth of upland cotton (Gossypium hirsutum) by inducing complex physiological disruptions. Emerging research evidence indicates that melatonin (MT), as a plant growth regulator, is extensively involved in the process of plant stress resistance regulation. This study explored the role of exogenous MT in enhancing drought tolerance in cotton, employing both physiological parameter analysis and transcriptomic profiling to unravel the underlying mechanisms of its stress mitigation effects. The results demonstrated that MT treatment significantly enhanced drought resistance in cotton plants by upregulating leaf superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities, elevating proline (PRO) content, and decreasing malondialdehyde (MDA) accumulation, thus confirming its physiological role in alleviating drought stress. Transcriptome analysis revealed that MT specifically modulates the “plant circadian rhythm”, “thiamine metabolism”, and “taurine and hypotaurine metabolism” pathways under drought stress conditions, thereby playing a pivotal role in drought adaptation. Further analysis of the 276 differentially expressed genes (DEGs) specifically modulated by MT under drought stress, combined with co-expression network analysis, identified two MT-specific induced Basic Helix-Loop-Helix (bHLH) family transcription factors (GhPIF8 and GhMYC5, gene IDs: Ghi_A11G05431 and Ghi_D03G05926) as key regulatory candidates in MT-mediated drought tolerance. This study establishes a theoretical framework for understanding the physiological and molecular mechanisms underlying MT-mediated drought tolerance in cotton, while also informing practical applications of MT in cotton agriculture. creator: Xingyue Zhong creator: Aixia Han creator: Yunhao Liusui creator: Xin Zhang creator: Wanwan Fu creator: Ziyu Wang creator: Yuanxin Li creator: Jing Cao creator: Yanjun Guo creator: JingBo Zhang uri: https://doi.org/10.7717/peerj.20005 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhong et al. title: How urban impervious surface shapes bird foraging behavior in an arid city link: https://peerj.com/articles/19980 last-modified: 2025-09-23 description: Wildlife behavior and interactions in urban ecosystems can vary across landscape types and species, with some birds dominating human-derived resources. This study investigates the relationship between urbanization, measured as impervious surface cover, and bird foraging behavior in the Phoenix metropolitan area in Arizona, USA. We conducted 126 feeding trials across 13 sites along a gradient of urbanization and bird interactions with anthropogenic food sources present. Trials were conducted using popcorn placed at random distances and orientations from a trash can. We recorded bird species visiting feeding stations and time to first visit during 20-minute trials and then quantified relationships among visitation timing (latency), species richness, and impervious surface coverage. Time to first visit was negatively correlated with the amount of impervious surface, with the highly urban areas having birds arrive at the feeding station the soonest. Great-tailed Grackles (Quiscalus mexicanus) comprised the most common visitor across all impervious surface levels. Non-native doves like Rock Pigeons (Columbia livia) and Eurasian Collared-doves (Streptopelia decaocto) were quicker to visit feeding stations compared to native doves like Mourning Doves (Zenaida macroura), Inca doves (Columbina inca), and White-winged Doves (Z. asiatica). Small urban-adapted generalists, like House Sparrows (Passer domesticus) and House Finches (Haemorhous mexicanus), tended to be more frequent visitors at highly urbanized sites compared to larger birds. These emphasize how species-specific foraging behaviors can differentiate resource use by birds in urban areas. creator: Simone Vega Rabelo creator: Jeffrey D. Haight creator: Heather L. Bateman uri: https://doi.org/10.7717/peerj.19980 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vega Rabelo et al. title: Bacterial microbiome profiles of the inflamed terminal ileum mucosa in active Crohn’s disease patients link: https://peerj.com/articles/19959 last-modified: 2025-09-23 description: BackgroundThe dysbiosis of the intestinal microbiome relates to the pathogenesis of Crohn’s disease (CD). Previous studies have focused on microbiota diversity and composition in CD patients in comparison with healthy individuals. Nonetheless, intestinal flora varies greatly among individuals. This study aimed to characterize the bacterial microbiome profiles of inflamed mucosa in comparison with those of noninflamed mucosa from Crohn’s disease patients.MethodsSequencing of 16S rDNA V4 was used to identify the bacterial microbiome profiles of twelve pairs of inflamed and noninflamed mucosa from active CD patients.ResultsA total of 753 OTUs were specific to inflamed tissues. Alpha diversity demonstrated that the biodiversity of the bacterial microbiota in the inflamed mucosa was increased, but it was not significantly different from that in the noninflamed mucosa. Linear discriminant analysis effect size (LEfSe) Clustergram showed Micrococcaceae, Bifidobacteriaceae, Bifidobacteriales, Flavobacteriaceae, and Methylobacteriaceae as microbes that were significantly different in the inflamed mucosa of active CD patients. Wilcox test results of genus differences indicated Methylobacterium, Rothia, Shinella, Capnocytophaga, Actinomyces, Gardnerella, Leucobacter, and Bifidobacterium as significantly upregulated genera in the inflamed mucosa of active CD patients compared with their noninflamed mucosa. These findings provide new evidence that the dysbiosis of mucosa-associated microbiota contributes to CD development, from a self-comparison perspective. creator: Juan Yin creator: Tong Hu creator: Liping Zhang creator: Lijuan Xu creator: Jianyun Zhu creator: Yulan Ye creator: Zhi Pang uri: https://doi.org/10.7717/peerj.19959 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Yin et al. title: Evaluation of cross-generational exposure to microplastics and co-occurring contaminants on embryonic and larval behavior in fathead minnows, Pimephales promelas link: https://peerj.com/articles/19927 last-modified: 2025-09-23 description: Microplastics (MPs) are ubiquitous in freshwater systems, and understanding their effects on aquatic organisms is increasingly important. Microplastics also have unique surface properties that allow them to act as vectors for common environmental pollutants, such as endocrine-disrupting chemicals (EDCs), and can serve as an additional route of exposure to those contaminants. However, few studies have considered the cross-generational effects of microplastics on early life-stage behaviors in aquatic vertebrates. In this study, adult fathead minnows, Pimephales promelas, were exposed to microplastics alone (MPVirgin) or in association with one of two environmentally relevant concentrations of 17 α-ethinyl estradiol (low; MPEE2 10 and high; MPEE2 50) for 30 days and then were allowed to spawn. Embryonic activity was assessed for F1 offspring of MP-exposed adults at 4 days post-fertilization. After hatching, half of these larvae received continued exposure to MPs for 21 days, and larvae were tested in open-field swimming trials for swimming performance and space use at 14 and 21 days post-hatch. Before hatching, MPEE2 10 F1 individuals showed reduced activity compared to other groups. After hatching, larvae from MP-exposed parents were more active than control larvae, but no changes in space use were observed. Evidence was limited for the effects of continued MP exposure on larvae after hatching, or combined effects of MPs and EE2. These results indicate that parental exposure to MPs induces subtle, sublethal effects on embryos and larvae that have the potential to affect individual fitness. creator: Mackenzie Persinger creator: Jessica Ward uri: https://doi.org/10.7717/peerj.19927 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Persinger and Ward title: Prognostic utility of submental B/M-Mode ultrasonography for swallowing function assessment in post-stroke pharyngeal dysphagia: a preliminary study link: https://peerj.com/articles/20046 last-modified: 2025-09-22 description: ObjectiveTo evaluate the prognostic value of hyoid bone kinematic parameters measured via submental B/M-mode ultrasonography in post-stroke pharyngeal dysphagia, aiming to identify reliable predictors of swallowing recovery.MethodsThis study included 46 stroke patients with pharyngeal dysphagia, diagnosed via videofluoroscopic swallowing study (VFSS), and treated at the Department of Rehabilitation Medicine, Affiliated Brain Hospital of Nanjing Medical University (June 2020–August 2024). Swallowing function was assessed using seven pharyngeal phase parameters from the Videofluoroscopic Dysphagia Scale (VDS) at baseline and post-rehabilitation. Patients were stratified into favorable (n = 26) and unfavorable (n = 20) prognosis groups based on post-treatment VDS and Functional Oral Intake Scale (FOIS) scores. Submental B/M-mode ultrasonography quantified hyoid bone displacement parameters pre- and post-rehabilitation, including maximum displacement, anterior displacement, superior displacement, total movement duration, and hyoid-thyroid cartilage approximation ratio (ASR).ResultNo significant differences were observed between groups in baseline characteristics. Post-treatment, the favorable group showed significantly lower Rosenbek scores (p = 0.000), reduced VDS scores (p = 0.000), and decreased feeding tube dependency (p = 0.000). Post-treatment, the favorable group exhibited greater anterior displacement (p = 0.011), higher ASR (p = 0.000), and shorter total movement duration (p = 0.005). Logistic regression identified hyoid anterior displacement (odds ratio (OR) = 9.539, p = 0.011) and ASR (OR = 14.238, p = 0.001) as independent prognostic predictors. ROC curve analysis indicated that hyoid anterior displacement (area under the curve (AUC) = 0.720) and ASR (AUC = 0.816) were significant discriminators of favorable outcomes, with optimal cutoff values of 0.865 cm (92.3% sensitivity, 50.0% specificity) and 31.5% (84.6% sensitivity, 65.0% specificity), respectively. The combined model further improved predictive accuracy (AUC = 0.854, 84.6% sensitivity, 85.0% specificity).ConclusionImpaired hyoid anterior displacement and reduced ASR are critical pathophysiological mechanisms in post-stroke dysphagia. Combined assessment of these parameters provides significant clinical utility for prognosis and treatment planning. creator: Meng Huang creator: Tong Wu uri: https://doi.org/10.7717/peerj.20046 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang and Wu title: Safety of outpatient vs. inpatient anterior cervical discectomy and fusion: a systematic review and meta-analysis link: https://peerj.com/articles/20045 last-modified: 2025-09-22 description: ObjectiveTo evaluate and compare the safety of outpatient and inpatient anterior cervical discectomy and fusion (ACDF) regarding complications and related outcomes.MethodsPubMed, Embase, and Scopus were systematically searched for retrospective cohort studies published between January 1, 2000, and December 31, 2024, comparing outpatient and inpatient ACDF. Pooled relative risks (RRs) and weighted mean differences (WMDs) were calculated using a random-effects model. Study quality and certainty of evidence were assessed using the Newcastle–Ottawa Scale (NOS) and GRADE, respectively.ResultsA total of 21 studies involving 164,541 patients (36,361 outpatient and 128,180 inpatient) were included. Outpatient ACDF resulted in significantly lower incidence of overall complications (RR 0.45, 95% CI [0.35–0.57]), mortality (RR 0.35, 95% CI [0.16–0.77]), deep vein thrombosis (RR 0.56, 95% CI [0.37–0.85]), and wound complications (RR 0.59, 95% CI [0.52–0.68]). Reduced risks were also observed for unplanned reoperations (RR 0.33, 95% CI [0.24–0.46]), readmissions (RR 0.57, 95% CI [0.46–0.70]), and pulmonary complications (RR 0.43, 95% CI [0.27–0.68]). Risks of stroke, dysphagia, hematoma, and renal and cardiac complications were comparable between the groups. The certainty of evidence was rated low to very low due to high heterogeneity, retrospective study designs, and indirectness.ConclusionOutpatient ACDF is associated with fewer complications as compared to inpatient procedures for carefully selected patients. However, the retrospective nature of the studies, the possibility of selection bias, and low-certainty evidence underscore the need for high-quality prospective research to validate these results and inform clinical practice. creator: Lili Ding creator: Mengzhu Yin creator: Wenhua Yuan uri: https://doi.org/10.7717/peerj.20045 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ding et al. title: Practitioner training and user experience of Seeking Safety for people with complex post-traumatic stress disorder and substance use disorder link: https://peerj.com/articles/20010 last-modified: 2025-09-22 description: BackgroundPost-traumatic stress disorder (PTSD) develops because of a profoundly traumatic experience such as combat situations, interpersonal violence, accidents, and natural disasters. Symptom manifestation may include recurring intrusive thoughts and memories, low mood, hypervigilance, disrupted sleep patterns, emotional dysregulation, and reduced attention span. Individuals affected by complex PTSD may withdraw from society or engage in harmful, risky and dangerous behaviours or develop substance use disorder (SUD). The purpose of this scoping review is to consider available evidence around the use of Seeking Safety as a treatment modality in individuals with complex PTSD and SUD. In particular it aims to identify the available evidence relating to Seeking Safety with regards to (i) gaps in knowledge around implementation; (ii) which healthcare professionals (HCPs) deliver Seeking Safety; (iii) knowledge and training required to deliver it; and (iv) the experience of individuals completing Seeking Safety treatment.MethodsA scoping review methodology was used to identify qualitative, quantitative, and grey literature of Seeking Safety as a treatment modality in individuals with PTSD and SUD.ResultsA total of 451 studies were identified. Following deduplications, 431 records were screened for inclusion, the full-text of 24 articles were reviewed for eligibility and 18 were included in the review. Extracted data was synthesized and six overarching themes were identified: (i) Seeking Safety as a treatment; (ii) meeting the needs of a diverse patient population group; (iii) factors impacting success; (iv) empowerment of self and agency over life; (v) measuring treatment success; and (vi) knowledge gaps of Seeking Safety treatment.ConclusionThis scoping review considers the gaps in knowledge around Seeking Safety, specifically relating to which HCPs are best suited to delivering it in clinical practice; the knowledge and training required to deliver it; and the experience of individuals undertaking Seeking Safety. creator: Luise V. Marino creator: Osahon Ogbeiwi creator: Melanie Mott creator: Matthew Jordan creator: Tracey Smith creator: Wajid Khan creator: Martin Webber uri: https://doi.org/10.7717/peerj.20010 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Marino et al. title: Predicting the prognosis of hepatocellular carcinoma based on genes related to polyamine metabolism link: https://peerj.com/articles/19985 last-modified: 2025-09-22 description: BackgroundHepatocellular carcinoma (HCC) is a highly prevalent malignant tumor worldwide. Evidence showed that polyamine metabolism plays a crucial part in the regulation of cancer onset and development, however, its clinical significance in HCC remains unclear.MethodsBulk RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq) data of HCC were collected from public databases. Polyamine metabolism-related genes (PMRGs) were obtained from the MSigDB database. The molecular subtypes of HCC were classified by ConsensusClusterPlus package, and differentially expressed genes (DEGs) of the molecular subtypes were identified by the limma package, followed by enrichment analysis with clusterProfiler package. Univariate Cox and Lasso Cox regression analyses were performed to screen core genes, construct risk model, and develop a nomogram integrating clinical characteristics for survival prediction. The obtained biomarkers were validated using in vitro experiments (CCK8, wound healing, and Transwell assay). The Tumor Immune Estimation Resource (TIMER), MCP-counter, and Cell Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) methods were employed for immune cell infiltration analysis. Finally, drug sensitivity of the HCC samples was analyzed with the oncoPredict package.ResultsThis study identified two molecular subtypes (C1 and C2), with C2 demonstrating a more favorable prognosis. Glucose-6-phosphate dehydrogenase (G6PD), alcohol dehydrogenase 4 (ADH4), S100 calcium binding protein A9 (S100A9), aldo-keto reductase family 1 member B15 (AKR1B15) were predicted as the biomarkers for HCC. Cell experiment results showed that the expressions of G6PD, AKR1B15, and S100A9 were all notably elevated in HuH-7 cells. Moreover, the loss of G6PD gene expression reduced the viability, migratory, and invasive capabilities of HCC cells. Patients with a high RiskScore had a lower survival rate than those with a low RiskScore. Scores of immune cells such as Tregs and M0 macrophages were higher in the high-risk group, and 13 drugs were found to be significantly linked to the RiskScore. Single-cell analysis showed that G6PD and S100A9 were high-expressed mainly in hematopoietic progenitor cells (HPCs) and macrophages.ConclusionIn conclusion, this study screened four key genes based on PMRGs and constructed a risk model to effectively predict the prognosis of HCC, providing novel potential targets and theoretical basis for the molecular subtyping and individualized treatment of HCC. creator: Chengli Liu creator: Meng Pu creator: Yingbo Ma creator: Shuhan Zhang creator: Qike Huang creator: Haoming Li creator: Tian Xia creator: Jingchen Zhang uri: https://doi.org/10.7717/peerj.19985 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Liu et al. title: The braincase anatomy of Simosaurus gaillardoti (Diapsida: Sauropterygia) revealed with X-ray micro-computed tomography link: https://peerj.com/articles/19932 last-modified: 2025-09-22 description: Sauropterygia is a clade of Mesozoic marine reptiles that includes the eosauropterygian Simosaurus gaillardotiVon Meyer, 1842, classically considered to be a member of Nothosauroidea. The braincase of this species has thus far only been studied in acid-prepared specimens. Acid preparation is a destructive technique prone to information loss, e.g., through the dissolution of thin braincase bones. Here, one well-preserved skull (SMNS 16363) that remains partially embedded in matrix has been visualised using X-ray micro-computed tomography, and the braincase region has been virtually extracted. This braincase provides valuable information on the general shape of the endocast, the existence and shape of epipterygoids, which were previously considered absent in the taxon, the course of cranial nerves and the bifurcation of the internal carotid arteries along an expanded and broad parabasisphenoid, the latter extending in a tapering cultriform process to the level of the external and internal narial openings. The arrangement of the semicircular canals of the inner ear confirms previously hypothesised adaptations for near-shore aquatic life in the species. The anatomical similarities of the braincases between Simosaurus gaillardoti and Nothosaurus marchicus, including a jugular foramen that is framed by the exoccipital medially and by the opisthotic laterally, support the current phylogenetic placement of the former as an early branching member of Nothosauroidea. The cranial flattening observed in nothosaurs relative to the less dorsoventrally flattened skull of Simosaurus reflects diverging feeding strategies. Most nothosaurs were fish-trap ambush predators, whereas Simosaurus gaillardoti had durophagous, as well as (opportunistic) piscivorous capacities. These results might indicate that specialised piscivorous predation using fish-trap dentition could be independently derived in nothosaurs and in pistosauroids (including plesiosaurs). creator: Elisa H. London creator: Dennis F.A.E. Voeten creator: Henning Blom creator: Torsten M. Scheyer uri: https://doi.org/10.7717/peerj.19932 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 London et al. title: Distribution and evolution of the western European water frogs (genus Pelophylax) from Catalonia, northeastern Spain link: https://peerj.com/articles/19895 last-modified: 2025-09-22 description: European water frogs from the genus Pelophylax are particular among amphibians as they can produce hybrids (named kleptons) reproducing by hybridogenesis. Four klepton species have been described in Europe: Pelophylax kl. esculentus, P. kl. hispanicus, P. kl. grafi, and the putative klepton PK. While most of these kleptons originated naturally in areas where the parental species occur in sympatry, human-mediated translocations of water frogs across Europe have altered this dynamic. As a result, several Pelophylax species and kleptons are now found outside their natural ranges, posing a threat to autochthonous water frogs. Additionally, the subtle morphological differences between Pelophylax species make hybrid identification and, thus, conservation difficult. In the present study, we analyzed 423 specimens from 54 populations sampled across Catalonia and implemented a two-step molecular method to identify all species of water frogs present in Catalonia. We also examined the mitochondrial genome of the hybrid Pelophylax kl. grafi to obtain new insights into their reproductive system and spatial structure. Despite the large number of samples analyzed, only the native P. perezi and its klepton P. kl. grafi were found, with the proportion of the latter being unexpectedly high. Results showed a high misidentification rate based on morphology compared to molecular methods, indicating that identification of P. kl. grafi through morphological characters is unreliable. Furthermore, the mitochondrial DNA of hybrid specimens entirely belonged to P. perezi and showed high intra-specific variability. This suggests either a single hybridization event involving a male P. ridibundus or P. kl. esculentus and a female P. perezi, or that P. ridibundus mitochondrial DNA has been eliminated from the P. kl. grafi germline by adaptive or non-adaptive processes. This study offers new insights into the distribution and composition of the North Iberian Pelophylax hybridogenetic complex, providing comprehensive sampling across one of the main entry points of the complex into the Iberian Peninsula. creator: Bernat Burriel-Carranza creator: Carolina Molina-Duran creator: Karin Tamar creator: Laia Pérez-Sorribes creator: Jhulyana López-Caro creator: Mar Cirac creator: Daniel Fernandez-Guiberteau creator: Salvador Carranza uri: https://doi.org/10.7717/peerj.19895 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Burriel-Carranza et al. title: Stress management strategies and controlling emotion among Polish nurses and midwives who suffer COVID: cross-sectional study link: https://peerj.com/articles/19816 last-modified: 2025-09-22 description: IntroductionStress management strategies and the ability of nursing staff to control their emotions is an important way to reduce emotional tension in a difficult situation.AimTo identify the dominant stress management strategy and emotion control modality in professionally active nurses and midwives during the COVID-19 pandemic.Material and MethodsA total of 137 nursing personnel from south-eastern Poland were studied. Sociodemographic and clinical data were collected with a questionnaire developed by the authors, stress management was assessed with the Coping Inventory for Stressful Situations (CISS), and control of emotions was examined with the Courtauld Emotional Control Scale (CECS).ResultsThe most common strategy for stress management strategy among nursing staff was the task-oriented strategy, the least frequently used was the avoidance. Only the avoidance style showed a significant difference in the group of midwives taking the form of seeking social contact (p = 0.016). CECS in none of the subcategories showed a significant difference for the profession. It turned out that the longer the time elapsed in nursing staff from having contracted COVID-19, the less often they chose the avoidance oriented coping (p = 0.022), and the presence of more post-COVID complications favoured focusing on emotions (p = 0.016) and avoidance (p = 0.005) in the form of initiating social contacts (p = 0.003).ConclusionsThe tendency to prefer a maladaptive style of coping with stress and suppression of emotions in nursing staff is associated with the risk of psychosomatic diseases and occupational burnout. The results indicate the necessity of providing interprofessional support combined with learning to “actively cope” with stress at work. creator: Barbara Zych creator: Anna Kremska creator: Anna Lewandowska creator: Małgorzata Nagórska uri: https://doi.org/10.7717/peerj.19816 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zych et al. title: Morphological diversity of Western Balkan durum wheat landraces link: https://peerj.com/articles/20068 last-modified: 2025-09-19 description: Wheat (Triticum spp.) is a vital food source for a substantial portion of the global population, with durum wheat (Triticum turgidum L. subsp. durum Desf) particularly significant in warmer regions like the Mediterranean. However, the aggressive introduction, spread and adoption of elite germplasm has led to crop genetic diversity loss, prompting efforts to preserve local durum wheat landraces. This study investigates the phenotypic diversity of 80 durum wheat landraces originating from the Western Balkan region, including accessions from Montenegro, Bosnia and Herzegovina, and Croatia. These landraces, locally known under traditional names such as ‘Rogosija’, ‘Grbljanka’, or ‘Velja pšenica’, represent a historical gene pool of durum wheat once widely cultivated until 1972 but subsequently abandoned. Historically, these landraces were valued for productivity, disease resistance, and resilience to drought and heat—traits well suited to Mediterranean conditions. Phenotypic traits were assessed across 17 morphological descriptors following International Union for the Protection of New Varieties of Plants (UPOV) guidelines. We observed wide trait variability, with high variation in ear and plant length, and limited variation in straw pith thickness and ear density. Strong correlations among certain traits suggest coordinated selection patterns or shared developmental pathways, while others may reflect distinct genetic or environmental influences. Our study identified 370 differentiated morphological types across 80 accessions, with most accessions displaying between four and six phenotypes. This demonstrates the extensive genetic variability within the collection. The normalized Shannon-Weaver index (H’) across 17 traits averaged 0.59, indicating moderate to high diversity. Maximum H’ values exceeded 0.80 for traits such as beak length, shoulder width of the lower glume, ear awn distribution, and recurved flag leaf frequency. Low variation in traits like straw pith thickness (H’ = 0.05) and ear density (H’ = 0.22) may indicate fixation or selection pressure. These findings provide valuable insights into Western Balkan durum wheat diversity, emphasizing the importance of considering both morphological traits and geographical origins in crop diversity studies. Overall, our study provides a foundation for future breeding efforts aimed at enhancing the agronomic performance and resilience of durum wheat cultivars. creator: Ana Velimirović creator: Sanja Mikić creator: Zoran Jovović creator: Dragan Mandić creator: Novo Pržulj uri: https://doi.org/10.7717/peerj.20068 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Velimirović et al. title: Uric acid to HDL cholesterol ratio as a novel predictor of carotid intima-media thickness: a cross-sectional study in rural China link: https://peerj.com/articles/20053 last-modified: 2025-09-19 description: PurposeCarotid intima-media thickness (cIMT) is a widely recognized marker for assessing carotid atherosclerosis, which is a significant predictor of cardiovascular diseases such as ischemic stroke. The serum uric acid to high-density lipoprotein cholesterol ratio (UHR) has recently emerged as a potential combined marker for metabolic and inflammatory processes related to cardiovascular risk. This study aims to investigate the association between UHR and cIMT in a rural Chinese population, with a particular focus on differences across age and sex groups.Patients and methodsA cross-sectional study was conducted using data from the 2019 general physical examination of residents in Jizhou District, Tianjin, China. A total of 3,280 participants aged 45 years and older were included after excluding those with incomplete data or specific health conditions. Demographic and clinical data were collected through face-to-face interviews and physical examinations. Serum levels of uric acid (SUA) and high-density lipoprotein cholesterol (HDL-C) were measured, and UHR was calculated. Carotid intima-media thickness was assessed using ultrasound. Multivariate linear and logistic regression analyses were performed to evaluate the association between UHR and cIMT, adjusting for potential confounders. Subgroup analyses were conducted to explore variations in this association by age and sex. Receiver operating characteristic (ROC) analysis was used to compare the predictive value of UHR, SUA, and HDL-C for cIMT thickening.ResultsThe study population had a mean age of 64.10 ± 8.02 years, with 45.2% males and 54.8% females. The prevalence rates of hypertension, diabetes, smoking, and alcohol consumption were 77.2%, 19.7%, 41.4%, and 36.3%, respectively. Univariate analysis showed significant associations between UHR, age, hypertension, diabetes, smoking, alcohol consumption, systolic blood pressure (SBP), pulse pressure (PP) difference, glucose (GLU), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and cIMT. Multivariate analysis revealed that UHR was an independent risk factor for increased cIMT (β = 0.06, 95% CI [0.01–0.10], P = 0.017) and carotid intima-media thickening, particularly in older men. Subgroup analysis indicated that the association between UHR and cIMT was more pronounced in participants aged 60 years or older and in males. ROC analysis demonstrated that UHR had a higher predictive value for cIMT thickening in older men (AUC = 0.577, 95% CI [0.510–0.644], P < 0.05) compared to SUA or HDL-C alone.ConclusionThis study identifies UHR as a significant predictor of cIMT and carotid intima-media thickening, with a particularly strong association observed in older men. These findings suggest that UHR could serve as a valuable marker for early detection and intervention of carotid atherosclerosis. creator: Guibao Luo creator: Haiying Wang creator: Yajun Cao creator: Juan Hao creator: Taofeng Tan creator: Yingzhe Shao creator: Xianjia Ning creator: Chunsheng Yang creator: Jinghua Wang creator: Yan Li uri: https://doi.org/10.7717/peerj.20053 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Luo et al. title: Driving factors of runoff and sediment yield effects of various slope ecological restoration measures in the middle reaches of the Yellow River link: https://peerj.com/articles/20040 last-modified: 2025-09-19 description: The middle reaches of the Yellow River, with an exceeding amount of coarse sediment compared to the stream flow and the lower reaches, with severe sediment deposition, are key regions for sediment control in the Yellow River Basin. Recent years have witnessed efforts to return farmland land to forest and grassland and the launch of the Three-North Shelterbelt Forest Program, but the effectiveness of these measures remains to be studied. Research on factors influencing runoff depth (RD) and sediment yield (SY) sheds light on the mechanism of soil erosion in the study area. The present study focuses on the standard runoff fields in the Kuye River Basin, where ecological restoration measures (arbor forest land, shrub grassland, natural grassland, artificial grassland, cultivated land, Bare land) for various slope steepness (S) have been taken. Based on a six-year observation of the SY and RD in these fields, we aim to identify the primary factors influencing soil erosion, based on rainfall data and slope gradients. Using rainfall data and slope steepness factors, we explored the dominant factors that influence runoff and SY. The results showed that: (1) the rainfall events with short-duration, medium rainfall, and medium rainfall intensity were the most frequent; (2) the rainfall events with medium duration, heavy rainfall, and heavy rainfall intensity produced the most serious runoff and sediment; (3) using machine learning methods, the researchers found that the gradient boosting decision tree (GBDT) model was the most suitable for the study area, as it provided the best simulation of soil erosion. The structural equation model reveals that there is a significant correlation between runoff depth (RD) and soil erosion modulus (SEM). Time of precipitation (T), average precipitation intensity (Iavg), maximum intensity of precipitation in thirty minutes (I30) and slope steepness (S) are factors that indirectly influence runoff SY. The present study provides technical guidance for the ecological restoration and improvement of different slope surfaces in major sections of the middle reaches of the Yellow River. creator: Xin Wang creator: Zhenqi Yang creator: Jianying Guo creator: Fucang Qin creator: Xinyu Liu creator: Dong Fan uri: https://doi.org/10.7717/peerj.20040 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wang et al. title: Microbial communities inhabiting the surface and gleba of white (Tuber magnatum) and black (Tuber macrosporum) truffles from Russia link: https://peerj.com/articles/20037 last-modified: 2025-09-19 description: The complex symbiotic relationships between truffles and their microbiota, coupled with their obligate mycorrhizal lifestyle, present significant challenges for obtaining axenic mycelium and achieving controlled cultivation. This study aimed to characterize the microbial communities within the surface and gleba of truffle ascomata using 16S and 18S rRNA gene sequencing and identify the taxonomic composition and ecological roles of these microbiota. Specimens of Tuber magnatum (white truffle) and Tuber macrosporum (smooth black truffle) were collected, with T. magnatum representing the first documented discovery of this species in Russia. Metabarcoding profiling identified both species-specific and shared microbial taxa, with the yeast-like fungus Geotrichum spp. emerging as a core symbiont in both truffle species. Its consistent detection in surface and gleba tissues suggests a critical role in mycorrhizal establishment and spore dispersal, potentially mediated by sulfur volatiles that attract mycophagous fauna. In T. magnatum, the bacterial community was dominated by Proteobacteria, particularly Alphaproteobacteria and Gammaproteobacteria, with the nitrogen-fixing genus Bradyrhizobium being especially abundant. The truffle microbiota predominantly comprised soil-derived microorganisms (e.g., nitrogen-fixing Rhizobiaceae spp., phenol-degrading Mycoplana spp.) and plant-associated symbionts (e.g., ectomycorrhizal Sebacina spp.), implicating these communities in nutrient cycling, xenobiotic degradation, and host plant interactions. By elucidating the taxonomic and functional profiles of truffle-associated microbiota, this study provides foundational insights into their ecological contributions. Chemical differences align with tissue-specific microbial communities, suggesting microenvironmental specialization in bioactive compound synthesis. These findings advance efforts to replicate critical symbiotic interactions in vitro, a prerequisite for developing sustainable cultivation protocols for T. magnatum and T. macrosporum under controlled conditions. creator: Ekaterina V. Malygina creator: Nadezhda A. Potapova creator: Natalia A. Imidoeva creator: Tatiana N. Vavilina creator: Alexander Yu Belyshenko creator: Maria M. Morgunova creator: Maria E. Dmitrieva creator: Victoria N. Shelkovnikova creator: Anfisa A. Vlasova creator: Olga E. Lipatova creator: Vladimir M. Zhilenkov creator: Anna A. Batalova creator: Elina E. Stoyanova creator: Denis V. Axenov-Gribanov uri: https://doi.org/10.7717/peerj.20037 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Malygina et al. title: Compounds from medicinal plants produced in hairy root and transgenic hairy root cultures: a review link: https://peerj.com/articles/19967 last-modified: 2025-09-19 description: BackgroundPlants produce a wide variety of molecules, and some of them are of medicinal importance. Biotechnological systems such as suspended cells and hairy roots (HR) are used to produce plant compounds in a stable and controlled manner. HRs are obtained through a genetic transformation mediated by Rhizobium rhizogenes (R. rhizogenes), a Gram-negative bacterium that randomly inserts the transfer DNA (T-DNA) from the root-inducing plasmid (pRI) into the chromosome of a plant cell. Gene expression of T-DNA in plant cells induces a metabolic change to promote HR syndrome. The primary benefits of producing medicinal plant compounds in these biotechnology systems include the large yield of organ-specific bioactive compounds, production of de novo secondary metabolites, and scaling up to bioreactors for the industrial production of medicinal plant compounds. This article aims to describe the applications and advantages of the biotechnological system of hairy root cultures, which is used to obtain specific or de novo compounds of plant secondary metabolism in the last fourteen years.MethodologyA broad bibliographic search was accomplished of articles that report the HR cultures to produce bioactive compounds of medicinal plants. To find the largest number of reports in the past fourteen years, different databases for web searchers, such as Scopus, PubMed, Google Scholar, Web of Science, Redalyc, and SciELO were used. The reports mentioned here were collected and selected to include those that were of great relevance.ResultsOne hundred and twelve research articles were selected to integrate this review. We highlight the principal advantages of hairy root cultures to produce secondary metabolites which are used as medicinal compounds. Hairy root cultures can produce a wide variety of organo-specific compounds, including de novo secondary metabolites, by activating complex metabolic pathways. This process is facilitated by the expression of rol genes which are inserted into the chromosome of the plant cell during genetic transformation mediated by R. rhizogenes. Therefore, stable and continuous molecules production over several years, as well as a higher yield than that in wild plants, have been observed. Another advantage is the easy scaling up into a bioreactor system.ConclusionsDifferent plant species have successfully produced HR. The root cells in HR cultures have a complicated endomembrane system that facilitates the production of a wide variety of bioactive molecules of the secondary metabolism, such as phenols, terpenes, and alkaloids. Due to the random insertion of the pRI rol genes, different secondary metabolism pathways are activated in each induced HR. Only a few HR lines synthesize higher concentrations of specific molecules found in the wild plant or de novo metabolites, including those used as medicinal compounds; and some of them are secreted into the culture medium. creator: Araceli Urquiza-López creator: Crescencio Bazaldúa creator: Alexandre T. Cardoso-Taketa creator: Maria Luisa Villarreal uri: https://doi.org/10.7717/peerj.19967 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Urquiza-López et al. title: Taxonomic status of Coryphophylax maximiliani Fitzinger in: Steindachner, 1867 with notes on Coryphophylax subcristatus (Blyth, “1860” 1861) link: https://peerj.com/articles/19841 last-modified: 2025-09-19 description: The insular agamid genus Coryphophylax Fitzinger in Steindachner, 1867, is endemic to the Andaman and Nicobar Islands in the Bay of Bengal, India. These diurnal lizards are currently represented by two putative species, Coryphophylax subcristatus (Blyth, “1860” 1861) and Coryphophylax brevicauda Harikrishnan, Vasudevan, Chandramouli, Choudhury, Dutta & Das, 2012. The species C. subcristatus is said to be distributed through the Andaman and Nicobar Islands, even across the Ten Degree Channel, which is a recognised biogeographic barrier. A reassessment of the taxonomy of C. subcristatus shows the population south of the Ten Degree Channel, for which the nomen Coryphophylax maximiliani Fitzinger in Steindachner, 1867 is available, to be distinct. The results are based on morphological data from museum material, including type specimens and mitochondrial 16S rRNA sequences. The members of the genus Coryphophylax are abundant and widespread across the islands and may serve as an illuminating example for studying the patterns of colonization and diversification across the Andaman and Nicobar Islands. creator: Zeeshan A. Mirza creator: Saunak Pal creator: Tejas Thackeray creator: Harshil Patel creator: Aaron M. Bauer uri: https://doi.org/10.7717/peerj.19841 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mirza et al. title: Toxic dinoflagellate Prorocentrum cordatum affects the filtration rate and enzymatic activities of Chinese razor clam (Sinonovacula constricta) link: https://peerj.com/articles/20072 last-modified: 2025-09-18 description: Harmful algal blooms represent a significant environmental challenge in various marine ecosystems worldwide. While marine filter-feeder bivalves can consume toxic phytoplankton, their capacity to mitigate the presence of harmful microalgae is not yet fully understood. In this study, we examined the filtration rates and enzymatic activities of Sinonovacula constricta, a commercially valuable bivalve, when exposed to varying levels of toxic dinoflagellates (Prorocentrum cordatum) and non-toxic diatoms (Skeletonema costatum) over a 12-h period. Chlorophyll a concentration was used to reflect the presence of these microalgae. In the initial 2 h, the filtration rate under toxic conditions was lower than under non-toxic conditions. However, after the first 2 h, the filtration rate under toxic conditions did not decline as rapidly as it did under non-toxic conditions, suggesting that S. constricta could adapt to the presence of toxic microalgae over time. Regarding enzymatic activities, digestive enzymes were not significantly affected by low concentrations of toxic microalgae, but lipase activity was inhibited at higher concentrations. Antioxidant enzyme activity showed no significant changes across all non-toxic microalgal concentrations. Superoxide dismutase (SOD) activity increased at higher toxic microalgal concentrations, but both low SOD and catalase activities indicated that the bivalve’s antioxidant defenses for detoxification may be limited. These results suggest that S. constricta can tolerate toxic microalgae through adaptive feeding behaviors and changes in digestive and antioxidant enzymatic activities. This study revealed S. constricta has a high filtration rate and is sensitive to high concentrations of toxic microalgae. Therefore, its bioremediation function requires further study. creator: Yanbin Tang creator: Zhibing Jiang creator: Yibo Liao creator: Lu Shou creator: Jiangning Zeng creator: Rongliang Zhang creator: Chenghua Li uri: https://doi.org/10.7717/peerj.20072 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tang et al. title: Expression characterization of the guanylate-binding protein gene family in breast cancer and its association with the immune microenvironment link: https://peerj.com/articles/20058 last-modified: 2025-09-18 description: BackgroundConsidering the complexity of prognostic assessment in breast cancer (BRCA) and the potential role of guanylate-binding protein (GBP) genes in immune regulation, the present research was designed to construct a prognostic model using GBP-related genes and to explore the mechanism of their role in BRCA.MethodsUsing RNA sequencing data of BRCA from public databases, GBP gene scores of BRCA samples were computed by single-sample GSEA (ssGSEA). The gene modules associated with the scores were identified by weighted gene co-expression network analysis (WCGNA). Subsequently, differentially expressed genes (DEGs) between BRCA samples and paraneoplastic samples were screened by the “limma” package and intersected with the modular genes. Key prognostic genes were further compressed by least absolute shrinkage and selection operator (LASSO), univariate and multivariate stepwise regression analyses were used to develop a risk model. Next, differences in the biological characteristics and immune infiltration between different risk groups were explored. Particularly, CCK-8, wound healing and transwell test were performed to examine the biological role of DACT2 in BRCA.ResultsLow GBP scores in BRCA patients were significantly linked to a poorer overall survival. Two gene modules were closely and positively correlated with GBP scores, and their module genes were enriched in immune-related pathways. Subsequently, four key genes (PSME2, DACT2, PIGR and STX11) were screened to construct a risk model, which showed strong diagnostic performance. Notably, the infiltration of immune cells (e.g., CD4/CD8 T cells, mast cells, and macrophages) was higher in low-risk BRCA patients. In addition, the RiskScore was significantly negatively correlated with ESTIMATE scores. In vitro cellular experiments demonstrated that PSME2 was significantly upregulated in BRCA cell lines, while DACT2, PIGR, and STX11 were all markedly downregulated in BRCA cells. In particular, overexpression of DACT2 markedly suppressed the survival, migration, and invasion of AU565 and MDA-MB-231 cells.ConclusionThis study constructed a prognostic model for BRCA based on GBP-related genes. The model was closely related to the immune microenvironment, contributing to the prognostic assessment and individualized treatment guidance in the management of BRCA. creator: Min Wei creator: Peng Sun creator: Xuemei Liu creator: Xuhua Liu creator: Jie Lei uri: https://doi.org/10.7717/peerj.20058 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wei et al. title: In situ study of environmental factors (temperature and salinity) affecting cohort patterns and growth rates in Ciona robusta link: https://peerj.com/articles/20034 last-modified: 2025-09-18 description: Assessing and understanding the ecological impacts of marine invasive species is important for managing marine ecosystems, especially since their rapid growth, short reproductive cycles, and wide range of water temperature adaptability pose major challenges. In this study, conducted in Mokpo, South Korea, we explored the cohort dynamics and environmental influences on the ascidian Ciona robusta, which is considered a widespread invasive species. Through biweekly field surveys and quantitative measurements (dry weight, wet weight and body length) conducted from June to October 2022, we identified five distinct cohorts, challenging existing assumptions about lifespan and cohort patterns. All separation index value (which quantify differences between cohorts) exceeded 2, indicating clear separation of cohorts during the study period. The cohorts had a lifespan of between 4 and 10 weeks, much shorter than the previously reported maximum of 2 years. These differences suggest that local climatic conditions can have a significant impact on lifespan parameters. In addition, growth rates were significantly positively correlated with environmental conditions, particularly temperature. This highlights that while C. robusta growth rates are particularly sensitive to temperature changes, they showed relative tolerance to the salinity variations observed in this study. Therefore, this study contributes to the understanding of the population ecology of C. robusta in temperate marine ecosystems. In particular, it provides valuable insights for developing management strategies to mitigate the impacts of C. robusta due to climate change. creator: Philjae Kim creator: Seongjun Bae uri: https://doi.org/10.7717/peerj.20034 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kim and Bae title: Influence of leaf morphological properties on epiphytic lactic acid bacteria counts in forage crops link: https://peerj.com/articles/20028 last-modified: 2025-09-18 description: The structural properties of leaves play a crucial role in the attachment of lactic acid bacteria (LAB) in forage corps. This study analyzed the effects of leaf morphological properties, on LAB counts in different wild forage crops. The LAB counts and morphologic features on adaxial or abaxial surfaces of leaves from twelve forage species (maize (Zea mays), beggarticks (Bidens pilosa), white goosefoot (Chenopodium album), common bean (Phaseolus vulgaris), morning glory (Ipomoea purpurea), perilla (Perilla frutescens), tomato (Solanum lycopersicum), chili pepper (Capsicum), sweet potato (Ipomoea batatas), peanut (Arachis hypogaea), potato (Solanum tuberosum), and mallow (Malva verticillata)) were investigated. White goosefoot (5.22 log10 CFU g−1 FM) and beggarticks (4.83 log10 CFU g−1 FM) had the highest LAB counts but shortest leaf lengths (5.06 cm and 4.97 cm, respectively), whereas maize (3.37 log10 CFU g−1 FM) and sweet potato (3.38 log10 CFU g−1 FM) had lower LAB counts but significantly greater leaf widths than the other crops except for mallow (P < 0.001). Linear regression analysis revealed that the coefficients of determination (R2) between LAB counts and contact angle of the adaxial and abaxial surfaces of leaf were 0.1424 and 0.175, respectively. Therefore, the morphological features of leaves have a relatively weak influence on the LAB counts in different forage crops. creator: Dan Wu creator: Guicong Tang creator: Gaofeng Liu creator: Ting Sun creator: Jinmei Yang creator: Guojian Tang creator: Liuxing Xu uri: https://doi.org/10.7717/peerj.20028 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: Effect of foliar application of microelements on chlorophyll content, canopy architecture indicators, and physiological parameters of Hordeum vulgare L. plants link: https://peerj.com/articles/19966 last-modified: 2025-09-18 description: BackgroundThe availability of nutrients determines the proper development and yield of plants. Microelements play an important role primarily as cofactors of important enzymes in the metabolic and physiological processes of plants. Barley (Hordeum vulgare L.) is one of the most popular cereals in the world. It is used mainly as animal feed and as a raw material for the brewing industry.MethodsA three-year field experiment was conducted to determine the effect of foliar spraying of plants with single-component fertilizers containing copper, manganese, molybdenum, and zinc on the physiological parameters of barley plants. In the experiment, three malting barley cultivars were tested: Baryłka, KWS Irina, RGT Planet. During the vegetation period of the plants after foliar fertilization, canopy architecture indices, chlorophyll content in leaves, and gas exchange and chlorophyll fluorescence parameters were measured.ResultsThe foliar application of each of the microelements tested caused a significant increase in the chlorophyll content in the leaves and canopy architecture parameters (LAI and MTA) compared to the control. Furthermore, a significant increase in gas exchange parameters was also observed: intercellular CO2 concentration (Ci), transpiration rate (E), stomatal conductance (gs), net photosynthetic rate (PN) and chlorophyll fluorescence parameters, maximum quantum yield of PSII photochemistry (Fv/Fm), fraction of active PSII reaction centers (RC/ABS), potential photochemical efficiency (Fv/F0), and performance index (PI). The highest results of physiological parameters such as CCI, Ci, E, Fv/Fm, Fv/F0 and PI were recorded after the application of zinc fertilizer. LAI and MTA were highest in plots with plants sprayed with molybdenum-based fertilizer. The foliar application of Cu caused the greatest increase in Ci and PN. The experiment showed significant genotypic differences. The RGT Planet cultivar had a higher chlorophyll content, E and PN parameters among the tested cultivars. The KWS Irina cultivar was characterized by the highest values of canopy architecture parameters and significantly lower values of CCI, Fv/Fm and Fv/F0 compared to the Baryłka and RGT Planet. creator: Barbara Stadnik creator: Renata Tobiasz-Salach creator: Dagmara Migut uri: https://doi.org/10.7717/peerj.19966 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Stadnik et al. title: Fine-tuning protein language models unlocks the potential of underrepresented viral proteomes link: https://peerj.com/articles/19919 last-modified: 2025-09-18 description: Protein language models (pLMs) have revolutionized computational biology by generating rich protein vector representations, or embeddings—enabling major advancements in de novo protein design, structure prediction, variant effect analysis, and evolutionary studies. Despite these breakthroughs, current pLMs often exhibit biases against proteins from underrepresented species, with viral proteins being particularly affected, frequently referred to as the “dark matter” of the biological world due to their vast diversity and ubiquity, yet sparse representation in training datasets. Here, we show that fine-tuning pre-trained pLMs on viral protein sequences, using diverse learning frameworks and parameter-efficient strategies, significantly enhances representation quality and improves performance on downstream tasks. To support further research, we provide source code for fine-tuning pLMs and benchmarking embedding quality. By enabling more accurate modeling of viral proteins, our approach advances tools for understanding viral biology, combating emerging infectious diseases, and driving biotechnological innovation. creator: Rajan Sawhney creator: Barbra D. Ferrell creator: Thibaut Dejean creator: Zachary Schreiber creator: William Harrigan creator: Shawn W. Polson creator: K. Eric Wommack creator: Mahdi Belcaid uri: https://doi.org/10.7717/peerj.19919 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sawhney et al. title: Movements of post-breeding royal terns (Thalasseus maximus) in Virginia, U.S.A link: https://peerj.com/articles/19898 last-modified: 2025-09-18 description: Seabirds use a variety of strategies to maximize survival during migration. We studied the post-incubation movements of royal terns (Thalasseus maximus) from the largest seabird colony in Virginia, U.S.A. to understand their behaviors after nesting. We affixed GPS/GSM transmitters to nine incubating adult royal terns near the end of incubation (late June 2022) until migration (early December 2022). We used a hidden Markov model to describe royal tern behavior from late incubation through part of the migration season. Royal terns were classified as either resting or exploratory (e.g., flying, foraging) based on their speed and turning angles. Royal terns spent most of their time in the exploratory state (0.711, 95% CI [0.710–0.711]). Royal terns tended to move north following the breeding season before migrating to the south in October and November. We speculate that the post-breeding movement north was to track Atlantic menhaden (Brevoortia tyrranus), a primary food source. As threats to royal terns on the Atlantic coast such as declining prey fish stocks and offshore energy development increase, knowledge of their behaviors and movements will be essential to their conservation. creator: Chelsea Weithman creator: Daniel Catlin creator: Sarah Karpanty creator: Kelsi Hunt creator: Camille Alvino creator: Joanna Morelli creator: Will Britton creator: Ruth Boettcher creator: Rebecca Gwynn creator: Michael Guilfoyle creator: James Fraser uri: https://doi.org/10.7717/peerj.19898 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Weithman et al. title: Salinity tolerance and growth response of redroot pigweed (Amaranthus retroflexus L.): a comprehensive evaluation link: https://peerj.com/articles/19717 last-modified: 2025-09-18 description: Amaranths (Amaranthus L.) are multi-use crop species known for their nutritional quality and tolerance to salinity stress. As soil salinity has become an increasing issue globally, we conducted a study to test the salinity tolerance of one cultivar of Amaranthus retroflexus L. (Redroot pigweed). The plants were grown for 30 days in pot culture conditions at different salinity levels: non-saline, slightly saline, moderately saline, highly saline, and extremely saline (using two different rates: extreme1 and extreme2. We assessed various growth parameters including plant height, stem diameter, root, stem and leaves fresh (FW) and dry weight (DW), water content (WC), photosynthesis rate (Pn), transpiration rate (E), water use efficiency (WUE), chlorophyll content index (CCI), nutrient content, phytodesalination potential, salt tolerance index (STI), and vegetation indices. Our findings indicated that at slight to moderate levels of salinity, growth parameters and other factors, such as STI and vegetation indices, were less affected compared to higher levels of salinity for A. retroflexus L. creator: Gohar Margaryan creator: Abhishek Singh creator: Vishnu D. Rajput creator: Mohamed Soliman Elshikh creator: Sapna Rawat creator: Karen Ghazaryan uri: https://doi.org/10.7717/peerj.19717 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Margaryan et al. title: Perianth symmetry in sexually differentiated flowers of Akebia quinata (Lardizabalaceae) link: https://peerj.com/articles/20060 last-modified: 2025-09-17 description: Sexual differentiation of monoecious plants usually involves differentiation in the size of female and male flowers produced on the same individuals. In the nectarless Akebia quinata (Houtt.) Decne (Lardizabalaceae), the trimeric, actinomorphic female flowers are larger than the males, which is explained as an adaptive trait to prevent self-pollination, as conspicuous female flowers are usually visited by pollinators earlier than smaller male flowers of the same individuals. This results in the plants being cross-pollinated rather than geitonogamously pollinated. However, it is also known that the development of the perianth in this species is genetically associated with the ontogeny of the petaloid sepals. These are thus developmentally linked to the ontogeny of the stamens. Therefore, it is possible that female flowers lacking fertile stamens also have less developmental control over the perianth ontogeny. Consequently, our study investigated whether female and male flowers of A. quinata differ in their overall shape features, in the amounts of variation among flowers, as well as in the extent of different types of asymmetry in perianth shapes. Geometric morphometric analyses of triradial perianth symmetry based on the generalised Procrustes analysis of a complete symmetry group of perianth shapes showed that female flowers were indeed significantly more variable in all different subspaces of their symmetric and asymmetric shape variation. This included the differences among individual flowers, their rotational and bilateral symmetry as well as the asymmetry among sepals within flowers. These results indicate that developmental control over perianth shape is systematically weaker in female flowers compared to male flowers of A. quinata. It is therefore likely that this phenomenon is related to the presence or absence of fertile male reproductive organs, whose development is linked to the ontogeny of the perianth and the maintenance of its trimeric symmetry. creator: Jiri Neustupa creator: Katerina Woodard uri: https://doi.org/10.7717/peerj.20060 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Neustupa and Woodard title: Advances and challenges in research methods on oral absorption mechanisms of nano-formulations link: https://peerj.com/articles/20032 last-modified: 2025-09-17 description: BackgroundNano-formulations show significant promise for oral administration, but their absorption mechanisms—including how nanoparticles traverse intestinal epithelium, whether enhanced absorption stems from solubilization or intact particle uptake, and the fraction of intact nanoparticles entering the bloodstream—remain poorly understood. This hinders their development and clinical application. Research methods are crucial for studying oral absorption mechanisms; however, systematic reviews addressing the research techniques and methods of these mechanisms are still scarce. Consequently, this review was compiled to provide practical methodological guidance for in-depth research on their absorption mechanisms.MethodologyThe literature published from 2018 to 2024 was searched in the Web of Science and PubMed databases using the topic ‘oral absorption mechanism’. A subset of significant reviews and articles pertaining to the oral absorption mechanism of nano-formulations was chosen from the vast collection of retrieved articles. This review was compiled through a systematic categorization and comparative analysis of the diverse research methods employed to investigate these mechanisms.ResultsThis review systematically compared the advantages, disadvantages, and rational applications of various experimental models and summarized current methods/techniques for investigating the oral absorption mechanisms of nano-formulations, including mucus layer penetration, endocytosis, intracellular transport and exocytosis pathways, paracellular transport, and lymphatic transport. Careful analysis showed that commonly used cell and tissue models are inadequate to fully simulate the complex gastrointestinal absorption environment; current detection techniques fail to capture the actual in vivo changes and absorption mechanisms of nano-formulations; existing research methods often dissect oral absorption processes in isolation, leading to fragmented results. Finally, the review anticipated new promising experimental models and cutting-edge technologies (e.g., organoid models, microphysiological systems, gene editing, and in vivo sub-cellular high-resolution imaging techniques) with potential to address these limitations.ConclusionsThe limitations of existing models, techniques, and research approaches underscore the need for innovative methods to advance understanding of oral nano-formulation absorption. Emerging technologies, despite being in the infant stage and facing many bottlenecks, offer transformative potential to overcome these challenges. They are expected to revolutionize research on oral absorption mechanisms of nano-formulations, thus ushering in a new era of comprehensive exploration. creator: Shu-jun Sun creator: Yi-Tong Liu creator: Jin-Yu Nie creator: Zheng-Yang Hu creator: Ze-Rong Liu creator: Hao Chen creator: Yong-zhi Hua creator: Shan Feng creator: Tao Yi creator: Ji-Fen Zhang uri: https://doi.org/10.7717/peerj.20032 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Sun et al. title: Gas chromatography-mass spectrometry and Fourier-transform infrared spectroscopy coupled to chemometrics for metabolome analysis of different milk types in the light of green analytical chemistry link: https://peerj.com/articles/19921 last-modified: 2025-09-17 description: BackgroundMilk is an important dietary source for a healthy and balanced diet, owing to its rich content of proteins, fats, sugars, vitamins, and minerals. Due to the importance of milk macronutrient content for consumers’ preferences, a multiplex metabolomics-based approach using Fourier-transform infrared spectroscopy (FTIR) and gas chromatography-mass spectrometry (GC-MS) fingerprinting platforms was employed for the characterization of metabolites in different types of buffalo (BM), cow (CM), goat (GM), and camel (LM) milk.MethodsGC-MS and FTIR coupled to chemometric tools (multivariate data analysis) were employed for the discriminative qualitative and quantitative analysis of BM, LM, CM, and GM milk, targeting their primary metabolites. A side-by-side comparative assessment of the performance of both the FTIR and GC-MS methods was implemented in the light of green analytical chemistry principle (GAC) and white analytical chemistry principles (WAC) using the 12 green analytical chemistry principles (12 GAC), analytical greenness metric approach (AGREE), national environmental methods index (NEMI), eco-scale assessment (ESA) and complementary green analytical procedure index (ComplexGAPI), and the red green blue (RGB) 12 algorithms.ResultsThe milk types were qualitatively identified by visual inspection of their characteristic FTIR spectra as a fingerprint for each milk type. Quantitatively, GC-MS revealed the presence of 87 peaks belonging to alcohols, amino acids/nitrogenous compounds, fatty acids, organic acids, sterols, sugars, and vitamins. Sugars, mainly lactose, appeared as the major component in all milk types. The highest lactose content was detected in CM 1.07-fold higher than LM making LM a potential alternative for lactose intolerance. Both BM and CM were found to contain the highest organic acid content 5.2-fold higher than that in LM, accounting for their acidity (sourness), while the lowest level was found in LM. On the other hand, LM had the highest vitamins content compared to other milks. Lastly, FTIR outperformed GC-MS in terms of greenness and whiteness, suggesting its utilization as an alternative to traditional chromatographic techniques such as GC-MS. creator: Mohamed A. Farag creator: Sherif M. Eid creator: Sherine El-Shamy uri: https://doi.org/10.7717/peerj.19921 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Farag et al. title: Analysis of the occupancy rates of İstanbul Dams and optimum water management strategies against climate change effects link: https://peerj.com/articles/20041 last-modified: 2025-09-16 description: İstanbul is facing an increasingly deepening water management crisis due to its growing population, rapid urbanization, and climate change. This study aims to assess the current status of urban water management using over 23 years of daily occupancy data from İstanbul’s ten main dams. The dataset, provided by the İstanbul Water and Sewerage Administration (İSKİ), underwent extensive preprocessing, including eliminating missing observations, cleaning of outliers, and normalization. Statistical analysis of occupancy rate differences among dams was performed using the nonparametric Friedman test (Q = 8,083.929; p < 0.0001), revealing significant performance inequalities with a high significance level. The inequitable distribution of water resources was measured using the Gini coefficient, and a value of 0.65 indicated a striking imbalance in the current system. Geographical analysis revealed that dams located in the north have stable occupancy rates, while dams closer to the city center and under urban pressure exhibit erratic and underperforming conditions. Time series analyses revealed distinct seasonal fluctuations across dams. These patterns reflect the dams’ responses to different climatic and spatial conditions, and no direct assessment has been made of factors such as climate change. The study revealed that the occupancy fluctuations and inequalities exhibited by the İstanbul dam system over time vary significantly depending on the dam’s location, basin characteristics, and operational conditions. This suggests that the current dam structure is far from a spatially homogeneous entity and that management approaches should consider this diversity. This study aims to contribute to developing sustainable and climate-adapted water policies for megacities like İstanbul through a data-driven governance approach. creator: Muhammed Ernur Akiner uri: https://doi.org/10.7717/peerj.20041 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Akiner title: Pre-harvest mango yield prediction using artificial neural networks based on leaf nutrient variability link: https://peerj.com/articles/20013 last-modified: 2025-09-16 description: Accurate pre-harvest mango yield prediction provides valuable insights for improving productivity, reducing food waste, enhancing food security, and supporting the farmer livelihoods. In this respect, nine mango orchards, which had different agricultural practices, were selected to attain the essential data to integrate yield and leaf nutrient variability using an artificial neural network model. In the mango leaves, noticeable variations were detected in concentrations of nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), calcium (Ca), chlorophyll a (Chl a), chlorophyll b (Chl b), and total carbohydrates (Carbs) fraction. The yield variation between seasons is high; the ON season gave a high yield, and the OFF season gave a low yield. The results revealed that at the pre-harvesting time, the relationship between the carbohydrate: nitrogen (C/N) ratio and the yield against the growing season had a reverse trend. The artificial neural network (ANN) mango yield model was created using eight inputs representative of the nutrient status of leaves. The ANN model achieved an accurate match in predicting mango yield from investigated parameters, with an R2 value of 0.975 using a testing dataset, and the mean absolute percentage error (MAPE) was 3.02%. The concentration of Chl a, Chl b, and the Carbs fraction had the greatest contribution in predicting mango productivity. It was concluded that the ANN model performed adequately and captured the non-linear effects of the interaction between the nutrition status of the mango leaves and mango productivity. creator: Abdullah Alebidi creator: Khalid F. Almutairi creator: Rashid S. Al-Obeed creator: Essa Makhasha creator: Abdulwahed M. Aboukarima creator: Mahmoud Abdel-Sattar uri: https://doi.org/10.7717/peerj.20013 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alebidi et al. title: Prognostic significance and pathogenesis of RFC3 gene expression in diffuse large B-cell lymphoma link: https://peerj.com/articles/20001 last-modified: 2025-09-16 description: BackgroundDiffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma (NHL) subtype in adults. Dysregulation of replication factor C subunit 3 (RFC3) gene expression were associated with disease progression and poor prognosis in various cancer types. However, its significance in DLBCL remains largely unexplored. This study aimed to characterize RFC3 expression patterns, clinical relevance, functional mechanisms, and potential therapeutic implications in DLBCL.MethodsMulti-omics analyses were performed using data extracted from the Gene Expression Omnibus (GEO) project (GSE181063, GSE10846, GSE32918, GSE31312, GSE32018, and GSE12453) and The Cancer Genome Atlas (TCGA). RFC3 expression was validated via immunohistochemistry (IHC) in DLBCL samples. Survival analysis was conducted using the Kaplan–Meier method. The chi-square test was used to assess the association between RFC3 expression and clinical characteristics of DLBCL. Gene Set Enrichment Analysis (GSEA) was employed to identify tumor signaling pathways associated with RFC3. Immune infiltration was evaluated using the Immuno-Oncology Biological Research (IOBR) package. Drug sensitivity analysis was performed using the oncoPredict package, and immunotherapy response was assessed via the IMvigor210 dataset. Pan-cancer analysis was conducted using the easyTCGA and TCGAplot packages available on the R software.ResultsRFC3 expression was significantly upregulated in DLBCL. High RFC3 expression was closely associated with poor prognosis, adverse clinical features, and adverse tumor microenvironment characteristics in DLBCL patients. Furthermore, multiple tumor proliferation and cancer-related signaling pathways were significantly enriched in the high RFC3 expression group. The pan-cancer analysis also revealed elevated RFC3 expression across several tumor types. Elevated RFC3 expression was strongly correlated with worse tumor prognosis.ConclusionsRFC3 may serve as a novel prognostic biomarker and a potential therapeutic target for DLBCL. Further investigations into the mechanisms underlying RFC3 dysregulation may provide important insights for future diagnostic and therapeutic strategies. creator: Zuguo Tian creator: Shuiyu Liu creator: Chunlan Weng uri: https://doi.org/10.7717/peerj.20001 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tian et al. title: Comparison of the antibacterial properties of peptides from the hepatopancreas of red king crab and snow crab and development of an approach for red king crab peptide isolation from the hepatopancreas link: https://peerj.com/articles/19989 last-modified: 2025-09-16 description: The hepatopancreas of crustaceans is an important immune organ involved in the secretion of immune effectors such as antimicrobial peptides. Crustacean antimicrobial peptides are very diverse and have a broad spectrum of activity, but are poorly explored. In this work, the activity of antibacterial peptides from the hepatopancreas of red king crab and snow crab was compared. Both peptides were found to be highly effective in inhibiting the growth of gram-positive bacteria. At the same time, the peptide from the red king crab was found to be highly sensitive to the presence of salt and a disulfide bond reducing agent, in contrast to the peptide from the snow crab. An approach for the chromatographic purification of the red king crab peptide from the hepatopancreas was developed. Both peptides are of interest for the development of novel antibacterial drugs. creator: Vladislav Molchanov creator: Alfiya Yunusova creator: Olesya Kazantseva creator: Alexander Yegorov creator: Alexander Lukin creator: Alexander Timchenko creator: Vitaly Novikov creator: Nikolay Novojilov creator: Maria Timchenko uri: https://doi.org/10.7717/peerj.19989 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Molchanov et al. title: Determination of metabolite differences between loquat nectar and honey by UPLC-MS/MS link: https://peerj.com/articles/19988 last-modified: 2025-09-16 description: Honey is a widely consumed natural agricultural product. Honey bees produce honey by collecting nectar from different flowers and then metabolising it to form honey which is stored in the hive. The current focus of research has been on the primary characteristic metabolites of monofloral honey from different plant sources. There is a lack of understanding of the differences in the transformation and composition of overall metabolites between plant nectar and the honey that is processed by bees after nectar feeding. In this study, loquat nectar and mature loquat honey were used for the detection of all non-volatile metabolites in both by ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Subsequently, an analysis was conducted on the primary metabolites, including saccharides, amino acids and their derivatives, nucleotides and their derivatives, lipids, and organic acids. In addition, the secondary metabolites, including flavonoids, phenolic acids, and terpenoid, were analysed. The results showed that there was a significant difference in the relative content of non-volatile metabolites between the two. We detected a total of 914 non-volatile metabolites, of which 834 were detected in loquat nectar and 759 in loquat honey. We analyzed the relative content of metabolites based on their classification and found that the relative content of primary and secondary metabolites showed different trends after processing by bees. Among them, the content of nucleotides and their derivatives and sugar metabolites in loquat honey was generally higher than that in loquat honey. This result presents a comprehensive picture of the non-volatile metabolite composition of loquat nectar and loquat honey, and systematically compares the changes in the relative content of the two substances. creator: Xin Sun creator: Rui Shu creator: Yuli Qu creator: Junjun Dai uri: https://doi.org/10.7717/peerj.19988 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Sun et al. title: Effects of perioperative intravenous esketamine on postoperative recovery quality in adult patients: a systematic review and meta-analysis link: https://peerj.com/articles/19977 last-modified: 2025-09-16 description: ObjectiveThis study aimed to evaluate the effects of perioperative intravenous esketamine on the quality of postoperative recovery in adult patients.MethodsThe primary outcome was post-anesthesia care unit (PACU) stay time. Secondary outcomes included extubation time, Quality of Recovery-40 (QoR-40) and Quality of Recovery-15 (QoR-15) scores, pain scores at 24 hours postoperatively, incidence of postoperative nausea and vomiting (PONV), postoperative sleep quality, anxiety and depression, and mental side effects. A comprehensive literature search was conducted in PubMed, EMBASE, Web of Science, the Cochrane Library, and China National Knowledge Infrastructure from inception through April 20, 2023, with an update on May 18, 2024. The study was registered on PROSPERO (Registration number: CRD42023399290). Mean differences (MD) or relative risks (RR) with 95% confidence intervals (CI) were used to estimate effect sizes. Meta-analysis was performed using RevMan 5.3 and Stata 16.0 software.ResultsNineteen studies involving 1,967 patients were included. No significant differences were observed between the esketamine and control groups in PACU stay time (MD = 0.99, 95% confidence interval (CI) [−2.31–4.30], P = 0.56) or extubation time (MD = 1.30, 95% CI [−1.10–3.17], P = 0.34). However, the esketamine group showed significantly higher postoperative QoR-40 scores (MD = 9.40, 95% CI [6.12–12.69], P < 0.00001) and QoR-15 scores (MD = 7.43, 95% CI [3.97–10.88], P < 0.0001) compared to the control group.ConclusionPerioperative intravenous esketamine does not significantly affect PACU stay time, extubation time, or the incidence of postoperative mental side effects. However, it can reduce pain within 24 hours after surgery, improve sleep quality, decrease the incidence of PONV, and enhance postoperative recovery as reflected by higher QoR scores. creator: Zibang He creator: Jin Wu creator: Chun Yang creator: Peng Jiang uri: https://doi.org/10.7717/peerj.19977 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 He et al. title: ybx1 acts upstream of atoh1a to promote the rapid regeneration of hair cells in zebrafish lateral-line neuromasts link: https://peerj.com/articles/19949 last-modified: 2025-09-16 description: Like the sensory organs of the human inner ear, the lateral-line neuromasts (NMs) of fish such as the zebrafish (Danio rerio) contain mechanosensory hair cells (HCs) that are surrounded by supporting cells (SCs). A damaged NM can quickly regenerate new HCs by expressing genes such as atoh1a, the master regulator of HC fate, in the SCs at the NM’s center. We used the supervised learning algorithm DELAY to infer the early gene-regulatory network for regenerating central SCs and HCs and identified adaptations that promote the rapid regeneration of lateral-line HCs in larval zebrafish. The top hub in the network, Y-box binding protein 1 (ybx1), is highly expressed in HC progenitors and young HCs and its protein can recognize DNA-binding motifs in cyprinids’ candidate regeneration-responsive promoter element for atoh1a. We showed that NMs from ybx1 mutant zebrafish larvae display consistent, regeneration-specific deficits in HC number and initiate both HC regeneration and atoh1a expression 20% slower than in wild-type siblings. By demonstrating that ybx1 promotes rapid HC regeneration through early atoh1a upregulation, the results support DELAY’s ability to identify key temporal regulators of gene expression. creator: Caleb C. Reagor creator: Paloma Bravo creator: A.J. Hudspeth uri: https://doi.org/10.7717/peerj.19949 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Reagor et al. title: Response inhibition and morphological awareness in children with attention deficit hyperactivity disorder: evidence from behavior and ERPs link: https://peerj.com/articles/19863 last-modified: 2025-09-16 description: BackgroundResponse inhibition is an important predictor of attention deficit hyperactivity disorder (ADHD), and many studies have shown that phonological awareness is associated with inhibition in native English-speaking children. Unlike English, which is phonetic, Chinese is an ideographic language. In the context of Chinese as a native language, do children with ADHD have deficits in morphological awareness? The present study explored the differences in response inhibition and morphological awareness between children with ADHD and typically developing (TD) children using behavioral data and event-related potentials (ERPs) to verify whether there is a morphological awareness deficit in children with ADHD.MethodGo/No-go task was used to verify the presence of response inhibition deficits in children with ADHD, in which participants were required to respond rapidly to a “Go” stimulus and inhibit responses to a “No-go” stimulus. The Morphological Awareness task was used to verify the presence of a morphological awareness deficit in children with ADHD, in which participants were required to make judgement about true word and pseudo-word.ResultsGo/No-go task shows children with ADHD had significantly lower correct No-go stimuli and longer reaction times than TD children, lower evoked N200 amplitudes, and significantly impaired inhibitory control in children with ADHD. The morphological awareness task required participants to recognize pseudo-words and true words, and to respond to pseudo-words. The results showed no difference between the two groups of children in terms of correct response rate, N400 wave amplitude, and latency on the morphological awareness test.ConclusionThe results of the study showed that children with ADHD have deficits in response inhibition compared to TD children and do not have significant deficits in morphological awareness. creator: Fang Cheng creator: Xinhui Hu creator: Yawen Chi creator: Jie Yang creator: Changzhou Hu creator: Beini Wang creator: Jingjing Cui creator: Taoping Wu creator: Lixian Chen creator: Rong Wang uri: https://doi.org/10.7717/peerj.19863 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cheng et al. title: Digitized endocasts and brains: a perspective on measurements and historical analyses of the evolution of 172 fossil and extant amniote specimens link: https://peerj.com/articles/19826 last-modified: 2025-09-16 description: This perspective paper is intended to stimulate future research and discussion of brain evolution in amniotes by sharing 172 digitized endocasts of extinct and extant species spanning 60 million years. Using 3D digital surface scans of physical (e.g., latex, plaster, resin) endocasts, we measured and compared relative endocranial volumes from dozens of extinct amniote taxa with those (endocasts or brain surface scans) of relevant extant species. Additionally, we offer calculated Encephalization Quotients and neocorticalization from digitized endocasts. Using historical methods of analysis, we find that, on average, neocortocalization of mammals increased over time, which is in agreement with recently published findings. Results also showed that, about 60 million years ago, mammalian neocorticalization averaged about 20%, increasing to a present average of 50%, and reaching a maximum of about 80% in primates within the past 10 million years. These results potentially redefine the allometric boundary between mammals and reptiles and confirm that measurements on a single species can adequately represent the brains of the entire species. We encourage other researchers to use our data, results, and conclusions as a springboard for more updated analyses. creator: Harry J. Jerison creator: Catherine M. Early creator: Andrew A. Farke creator: Ashley C. Morhardt uri: https://doi.org/10.7717/peerj.19826 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jerison et al. title: Azhdarchid pterosaur diversity in the Bayanshiree Formation, Upper Cretaceous of the Gobi Desert, Mongolia link: https://peerj.com/articles/19711 last-modified: 2025-09-16 description: Pterosaur remains are very rare in Mongolian Mesozoic deposits, in stark contrast with the great abundance of dinosaur fossils in the region. This contribution presents a reassessment of the azhdarchid pterosaur remains from the Bayanshiree Formation’s “upper beds” (Turonian–Santonian), represented by two specimens coming from two distinct localities: the Burkhant and the Bayshin Tsav azhdarchids. These specimens, collected by the Japanese−Mongolian Joint Paleontological Expedition and originally described in 2009, have been previously interpreted as indeterminate azhdarchids. Under the light of current knowledge on the morphological diversity of azhdarchid cervical vertebrae, as well as on the taxonomic and phylogenetic signals these skeletal elements carry, we herein identify diagnostic features and reassess the phylogenetic affinities of the Bayanshiree azhdarchids in further detail. Our results suggest that the Burkhant azhdarchid, hereby named Gobiazhdarcho tsogtbaatari gen. et sp. nov., represents a medium-sized (3.0–3.5 meters in wingspan) basal member of a Quetzalcoatlus-Arambourgiania lineage. The Bayshin Tsav azhdarchid, Tsogtopteryx mongoliensis gen. et sp. nov., is recovered as a basal member of a Hatzegopteryx-lineage and, surprisingly, seems to represent a small form under 2 m in wingspan. Our results shed fresh light on the diversity and phylogeny of azhdarchid pterosaurs, and reinforce the reoccurring pattern of coexistence between multiple, differently-sized azhdarchid species from a same deposit. creator: R. V. Pêgas creator: Xuanyu Zhou creator: Yoshitsugu Kobayashi uri: https://doi.org/10.7717/peerj.19711 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pêgas et al. title: Global species richness of dragonflies and damselflies (Odonata): latitudinal trends and insular colonization link: https://peerj.com/articles/20004 last-modified: 2025-09-15 description: Odonates are mainly “sun lover” insects, and therefore reach maximum diversity in tropical regions, particularly in rainforests. Here, worldwide patterns of species richness of the order are analysed, by compiling a database of species numbers for 255 continental regions and 243 islands. Area, distance to continents and elevation for all islands were estimated, and their effect analysed on odonate species richness by means of linear models. As expected, a clear effect of latitude and insularity on the species richness of Odonates was found, with a maximum of  550 species in the equator for continental areas but only  200 species in islands. In islands, latitude, area and distance to the continent clearly affect species richness, but elevation had no significant effect. The continental countries with highest richness are Venezuela (548) and Colombia (543 species). Brazil (863) and China (818) have higher richness, but given their size were included in the analysis as states and regions. Excluding very large islands (New Guinea, Sumatra or Borneo), which are considered continents in this paper, Japan (209) is the archipelago with highest richness, albeit Indonesia (737) and the Philippines (306) have more species, but were analysed subdivided by islands. The proportion of Zygoptera found at the different regions was negatively affected by latitude and positively by the area, but not by insularity. In contrast, in islands the proportion of Zygoptera was not affected by latitude, distance or elevation, but was positively affected by area. These analyses highlight the ability of odonates to colonize even the most remote islands, places that can be sources of rapid speciation, as occurred in Hawaii or Fiji. creator: Adolfo Cordero-Rivera uri: https://doi.org/10.7717/peerj.20004 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cordero-Rivera title: Mitochondrial and Wolbachia phylogenetics of the introduced Jorō spider, Trichonephila clavata (Araneae: Araneidae) in North America link: https://peerj.com/articles/19952 last-modified: 2025-09-15 description: The introduction of Trichonephila clavata (L. Koch, 1878) (Araneae: Araneidae: subfamily Nephilinae) in the United States was first recorded in Georgia in 2014. Since its introduction, T. clavata has become a prominent feature of the arthropod fauna in several southeastern US states. Many questions regarding the introduction event(s) remain unanswered; for instance, was the introduction a single discrete event followed by rapid spread, or were there multiple introductions? The mitochondrial cytochrome c oxidase subunit one gene region (COI), which was used to characterize the initial T. clavata observation in the US, has also been used to characterize within- and between-population genetic variation. One confounding factor for COI as a population genetic molecular marker, though, is the presence of cytoplasmic agents of selection such as intracellular bacteria in the genus Wolbachia. Given that Wolbachia infections have been detected in potential source populations of T. clavata, the present study sought to characterize mitochondrial genetic diversity and the status of Wolbachia infection in the North American population(s) closest to the originally proposed introduction site in Georgia. DNA sequencing revealed no mitochondrial genetic variation in the T. clavata population sampled in North America, and an exact sequence match to the previously reported T. clavata in Georgia and a sequence sample from Yunnan, China. Wolbachia was detected in the North American samples. However, phylogenetic analysis on a concatenated multi-locus type sequence suggested two distinct Wolbachia clades, one represented by samples collected in Georgia and another represented by a single sample collected in South Carolina. Sequence analyses of the multi-locus gene regions suggested that the Georgia T. clavata may be infected with two strains of Wolbachia (super-infection), and the South Carolina sample represented a separate single infection. The study’s results emphasize the need for further research, including expanded sampling in the introduced and potential source population regions, as well as a more detailed molecular characterization of the populations. creator: James E. Russell creator: Nicholas Mizera creator: Christopher G. Brown creator: Angela Chuang creator: David R. Coyle creator: David R. Nelsen uri: https://doi.org/10.7717/peerj.19952 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Russell et al. title: In vivo biotoxicological assessment of nanoplastics and microplastics predicted using the zebrafish model link: https://peerj.com/articles/19833 last-modified: 2025-09-15 description: Nanoplastics (NPs) and microplastics (MPs) are emerging environmental pollutants that have raised concerns due to their potential impacts on human health. Zebrafish (Danio rerio) have been widely used as a model organism to study the toxicity of NPs and MPs and to evaluate the effects of these pollutants on human health. This review summarizes recent studies on the toxicities and potential effects of NPs and MPs in zebrafish and discusses how findings from this model can help predict their impact on human health. Additionally, the mechanisms by which NPs and MPs affect biological processes, such as growth, development, behavior, immune function, reproduction, and the nervous system, in zebrafish are further illustrated. Taken together, zebrafish serve as a valuable model for predicting the potential effects of NPs and MPs on human health and highlight the growing concern surrounding these environmental pollutants. creator: Tao Ren creator: Libo Yan creator: Daogang Wang creator: Ning Xu creator: Weiming Zhang creator: Mengzhe Yang uri: https://doi.org/10.7717/peerj.19833 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ren et al. title: Neonatal hearing screening among high-risk newborns in Northwestern Nigeria link: https://peerj.com/articles/20002 last-modified: 2025-09-12 description: BackgroundNeonatal Intensive Care Unit (NICU) patients are at an increased risk of developing hearing loss. Given the critical role of normal hearing in speech and language development, early detection and treatment of this condition in children are paramount.MethodsHearing assessments were performed using transient evoked otoacoustic emission (TEOAE) and automated auditory brain stem response (AABR) tests on 60 neonates. The resulting data were analysed using R version 4.3.3.ResultsOut of the 60 neonates enrolled in the study, 57% were males and 43% were females, and their ages ranged from 1 to 30 days. A total of 43 (71.7%) neonates passed both hearing tests, while 17 (28.3%) failed. In the unadjusted analysis, low birth weight, prematurity, birth asphyxia, and gestational age were significantly associated with neonatal hearing screening failure. Premature neonates and those with low birth weight had markedly higher odds of failing the screening (Odds Ratio (OR) = 24.4; 95% confidence interval (CI) [5.85–135.0] and OR = 12.3; 95% CI [3.5–50.6], respectively), while gestational age was associated with lower odds of failure (OR = 0.59; 95% CI [0.43–0.76]). In the multivariable model, after accounting for multicollinearity, only gestational age remained a statistically significant predictor, with each additional week associated with reduced odds of screening failure (adjusted OR = 0.60; 95% CI [0.43–0.80]).ConclusionOur findings underscore the importance of early screening for hearing loss in high-risk neonates in the NICU to facilitate timely interventions. creator: Semen Stephen Yikawe creator: Nasir Aliyu creator: Joseph Hassan Solomon creator: Shuaibu Lawal creator: Musbau Adeyemi creator: Agatha Eileen Wapmuk creator: Andrew Musa Adamu creator: Anayochukwu Edward Anyasodor creator: Oyelola A. Adegboye uri: https://doi.org/10.7717/peerj.20002 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yikawe et al. title: The effects of repeated sprints on mid-range and three-point jump shot biomechanics in elite basketball players link: https://peerj.com/articles/19983 last-modified: 2025-09-12 description: BackgroundIn basketball, fatigue is a prevalent physiological state that significantly influences shooting mechanics. This study discusses the difference of kinematic parameters of mid-range and long-range basketball players before and after the onset of fatigue, providing a comprehensive analysis of how fatigue affects shooting performance at these distances.MethodsThis study involved 12 collegiate male basketball players of at least level I athlete status. Blood lactate levels, subjective exercise fatigue scores, and heart rate variability were used as indices for assessing fatigue. Kinematic data during basketball shooting were collected by inertia motion capture system (Xsens technologies BV, The Netherlands) and a high-speed camera (Sony, Tokyo, Japan). Differences in kinematic parameters between pre- and fatigue conditions during middle and long-range shooting were analyzed using a paired sample T-test.ResultsAfter fatigue, the shooting percentage of middle distance had no significant decrease compared with that before fatigue (P > 0.05), while the shooting percentage of long distance had a significant decrease (P < 0.05). In the fatigue state, significant decreases in the angular velocity of the wrist (P < 0.01) and elbow (P < 0.05) were recorded, while an increase was noted in the knee joint’s angular velocity (P < 0.05). For long-range shots, there was a significant reduction in wrist angular velocity (P < 0.01), with marked increases in the angular velocities of the ankle (P < 0.01), knee (P < 0.01), and elbow (P < 0.05).ConclusionFatigue has no significant effect on the shooting percentages for mid-range jump shots among elite collegiate athletes; however, it substantially reduced the success rate of long-range jump shots. This decline in performance led to reductions in both the shooting angle and incident angle, as well as the extension of shooting time. Fatigue can compromise the effectiveness of force transfer from the lower to upper extremities. Long-distance shooting requires exceptional lower limb explosive power and precise neuromuscular synchronization. creator: Shuairan Li creator: Jielin Yang creator: Jing Mi creator: Yue Li uri: https://doi.org/10.7717/peerj.19983 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Distribution and host range of viruses associated with the citrus leprosis disease complex in Mexico link: https://peerj.com/articles/19889 last-modified: 2025-09-12 description: Citrus leprosis virus C (CiLV-C) (Cilevirus) and orchid fleck virus citrus strain (OFV-Cit) (Dichorhavirus) are viruses associated with citrus leprosis disease. Although symptoms associated with CiLV-C were observed in orange in 2005 in Mexico, and confirmed using molecular techniques in 2011, no studies have been made on the distribution of either CiLV-C or OFV-Cit viruses. During 2017, we studied the geographical distribution and host range of these two viruses infecting citrus orchards in Mexico, specifically orange, lime, mandarin and grapefruit orchards in 15 Mexican states. Furthermore, in 2019 we sampled lime orchards in three Mexican states. Presence of CiLV-C and OFV-Cit was determined using reverse transcription polymerase chain reaction (RT-PCR) assays. During 2017 the proportion of leaves infected by either CiLV-C or OFV-Cit was significantly affected by geographical origin. However, only a few samples were obtained from mandarin and grapefruit so these data were excluded from statistical analysis; orange had significantly higher rates of infection with CiLV-C than lime and the opposite was observed for OFV-Cit. Using RT-PCR, some asymptomatic leaves from 2017 samples were positive for the viruses of interest. In 2019 no symptoms associated with leprosis were observed in any of the leaves sampled from lime orchards. However, low infection rates were detected, with 6% of samples testing positive for CiLV-C and 3% for OFV-Cit. To confirm the identity of the CiLV-C isolate found in lime leaves collected in 2019, we sequenced nearly the complete RNA2 genomic region of the virus. Basic Local Alignment Search Tool (BLAST) search revealed 98.99% similarity with previously reported CiLV-C sequences from other citrus species. The implications of our results for field monitoring and disease detection are discussed. creator: Hugo Enrique González-García creator: Ma. Teresa Santillán-Galicia creator: Laura Delia Ortega-Arenas creator: Guadalupe Valdovinos-Ponce creator: Alberto Enrique Becerril-Román creator: Pedro Luis Robles-García creator: Ariel Wilbert Guzmán-Franco creator: Alfredo Sánchez-Villarreal uri: https://doi.org/10.7717/peerj.19889 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 González-García et al. title: Bone-tissue decomposition of a single X-ray image via solving a Laplace equation link: https://peerj.com/articles/20016 last-modified: 2025-09-11 description: Because bones are often enveloped by soft tissues, their visibility in X-ray images is compromised, resulting in a lack of clarity. Addressing this challenge, our article introduces an innovative approach to virtually decompose an X-ray image into distinct components: one representing soft tissues and the other, the bone structure. To achieve this separation, we have formulated a novel mathematical model. With proper assumptions, the model is reduced to a standard Laplace equation, which has fast numerical solvers. Our method has two important properties. First, the bone image derived from this process is theoretically guaranteed to have enhanced contrast relative to the original, thereby accentuating the visibility of bony details. Second, our method is computationally fast. Our method can process a $2\hbox{,}044 \times 1\hbox{,}514$2,044×1,514 resolution image within 0.35 s on a laptop (8.8 million pixels per second). Our methodology has been validated through a series of numerical experiments, demonstrating its efficacy and efficiency. With such performance, this technique holds promise for a broad spectrum of X-ray imaging applications, including but not limited to clinical diagnostics, surgical planning, pattern recognition, and advanced deep learning applications. creator: Zhili Wei creator: Wenming Tang creator: Yuanhao Gong uri: https://doi.org/10.7717/peerj.20016 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wei et al. title: Functional characteristics, intercellular interactions and pathophysiological associations of astrocytes in Parkinson’s disease link: https://peerj.com/articles/19998 last-modified: 2025-09-11 description: Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorder, and its incidence rate is increasing at an alarming rate. Astrocytes exhibit a complex array of functions that play a critical role in the pathogenesis and progression of PD. These multifaceted functions substantially influence disease development and exacerbation. Although numerous studies have investigated the role of astrocytes in PD, the interactions between astrocytes and other cellular or molecular factors during the course of neurological deterioration in PD have not been comprehensively characterized. Therefore, this review aims to highlight the roles and functional characteristics of astrocytes in PD. Astrocytes are involved in maintaining the blood-brain barrier, clearing α-synuclein, metabolizing glutamate and fatty acids, and protecting neurons. The interactions among astrocytes, microglia, and oligodendrocytes exert dual effects on PD progression. Additionally, the recently recognized phenomena of ferroptosis and cuproptosis have been associated with astrocytic activity. The interplay and regulatory mechanisms linking these forms of cell death to apoptosis and pyroptosis of immune cells in the brain warrant further investigation. This review is intended for researchers, healthcare professionals, and clinicians involved in the study and treatment of PD and its related complications. To ensure comprehensive and unbiased coverage, a systematic literature search was conducted using major scientific databases such as PubMed, Scopus, and Web of Science. Keywords included “Parkinson’s disease”, “astrocyte”, “brain”, “signaling mechanisms”, and “α-synuclein”. Articles were selected based on their relevance to astrocyte–PD interactions, while studies lacking scientific rigor or relevance were excluded. In summary, this review synthesizes current understanding of astrocytic function and mechanisms in PD and proposes potential therapeutic directions based on these insights. creator: Ziying Li creator: Mengran Cao creator: Zhaoyang Yin creator: Xiaolei Li creator: Qinglu Wang creator: Panpan Dong creator: Caixia Zhou uri: https://doi.org/10.7717/peerj.19998 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: The effects of shoe structural features on agility and stability tasks during walking link: https://peerj.com/articles/19930 last-modified: 2025-09-11 description: BackgroundFootwear can accommodate foot pathologies, alleviate symptoms of musculoskeletal injury, provide environmental protection and, for orthopedic or aging consumers, enhance agility or stability to improve daily locomotion. Independent of the specific characteristics underlying footwear selection, shoes are often called upon to support the performance of many different types of activities.PurposeThe purpose of this study was to investigate the extent to which shoe design features intended for stability versus agility affect walking tasks that would disproportionately depend on those features.MethodsFourteen adults completed two walking tasks intended to disproportionately require greater agility or greater stability. Participants completed walking tasks while wearing each of two footwear designs: a supportive hiking boot and a flexible sneaker.ResultsWe found no significant performance differences between footwear designs in either the agility task metrics or stability task metrics. Conversely, participant perceptions reflected differences in footwear design features.ConclusionsThe results of this study suggest that shoe design features intended for stability versus agility minimally bias walking performance towards either respective benefit. Our results may improve consumer confidence in footwear selection, often thereafter called upon to meet the needs of a variety of activities of daily living. creator: Kavya Katugam-Dechene creator: Ava Cook creator: Anh Nguyen creator: Ross Smith creator: Andrew Shelton creator: Jason R. Franz uri: https://doi.org/10.7717/peerj.19930 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Katugam-Dechene et al. title: Interventional treatment for azygos vein steal syndrome after bidirectional Glenn procedure in cyanotic congenital heart disease: a retrospective study link: https://peerj.com/articles/20022 last-modified: 2025-09-10 description: ObjectivesPatients with cyanotic congenital heart disease (CCHD) may continue to experience hypoxia and worsening cyanosis after undergoing a bidirectional Glenn procedure (BGP). Azygos or hemiazygos vein steal syndrome is a common cause of these complications. This study aimed to evaluate the safety and efficacy of transcatheter closure for azygos or hemiazygos vein steal syndrome following BGP in patients with CCHD.MethodsA retrospective analysis was conducted on clinical data from 13 patients with CCHD who underwent transcatheter closure for azygos or hemiazygos vein steal syndrome after BGP at Fuwai Hospital between December 2007 and September 2019.ResultsAll azygos or hemiazygos veins were successfully closed. Femoral artery oxygen saturation (SFAO2%) significantly increased after closure compared to before closure (86.94 ± 2.63% vs 74.98 ± 3.53%, P < 0.001). The mean pulmonary arterial pressure (mPAP) also showed a statistically significant increase after closure but remained within normal ranges (12.08 ± 2.75 mmHg vs 10.54 ± 3.28 mmHg, P = 0.020). The superior vena cava pressure (SVCP) showed almost no change before and after closure (11.08 ± 3.62 mmHg vs 12.31 ± 3.25 mmHg, P = 0.059). During an average follow-up period of 25.69 ± 9.60 months, all patients showed significant improvement in cyanosis, and none experienced facial or neck edema. The saturation of pulse oximetry (SpO2) was above 90% in all patients.ConclusionsTranscatheter closure of azygos or hemiazygos vein steal syndrome in CCHD patients after BGP is a safe and effective intervention. It offers high technical success and favorable short- to mid-term outcomes, while avoiding the physical and psychological trauma associated with repeat thoracotomy. creator: Zhengwei Li creator: Luxi Guan creator: Dong Luo creator: Meijun Liu creator: Haibo Hu creator: Xiangbin Pan uri: https://doi.org/10.7717/peerj.20022 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Effects of seed priming with salicylic acid on cuticular wax deposition in sweet sorghum under drought stress link: https://peerj.com/articles/20014 last-modified: 2025-09-10 description: BackgroundSeed priming is an affordable and effective method to enhance crop drought tolerance by improving seed germination and seedling vigor. However, whether seed priming alters cuticle formation, which could contribute to drought resistance in seedlings, remains unclear.Materials and MethodsIn this study, sweet sorghum seeds belonging to three varieties were primed with salicylic acid (SA) and the seedlings were exposed to drought stress. The seeds were primed with SA with concentrations of 50, 100, 150, 200, 250 mg L−1. For drought treatment (35% field capacity, 80% of field capacity as the normal condition), both SA-primed and non-primed seeds were planted in a soil mixture.ResultsUnder drought conditions, SA priming at 150 mg L−1 significantly increased total wax content (12.3%–33.3%), primary alcohol content (42.0%–57.0%), proline content (70.9%–119%), leaf water content (9.8%–36.6%), water use efficiency (28.4%–120%), and biomass (25%–30%). Additionally, leaf water loss rate and chlorophyll leaching rate were significantly reduced. Correlation analysis revealed strong positive associations (r = 0.79–0.86, P < 0.001) between total wax content and water status as well as proline content. Furthermore, under both well-watered and drought conditions, SA priming at 150 mg L−1 significantly increased leaf wax content and biomass in all sorghum varieties.ConclusionSeed priming with salicylic acid at 150 mg L−1 not only promotes normal growth under well-watered conditions, but also enhances sorghum’s adaptability to drought stress, ultimately contributing to drought tolerance without penalizing growth. creator: Luhua Yao creator: Yitao Wu uri: https://doi.org/10.7717/peerj.20014 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Yao and Wu title: Physiological response mechanism of Machilus faberi Hemsl under drought stress and rewatering link: https://peerj.com/articles/19855 last-modified: 2025-09-10 description: Drought stress is a predominant environmental challenge that significantly limits plant growth and survival, particularly affecting agricultural productivity and ecological stability in arid and semi-arid regions. This study aimed to elucidate the physiological responses of one-year-old Machilus faberi Hemsl seedlings to various degrees of drought stress, thereby aiding their cultivation and application in challenging environments. To simulate real-world drought conditions, four levels of drought stress were defined based on soil moisture content: control (80% soil moisture), mild drought (LD, 50–60% soil moisture), moderate drought (MD, 40–50% soil moisture), and severe drought (SD, 20–30% soil moisture). These thresholds were selected to represent a gradient from optimal water availability to extreme water scarcity, reflecting conditions commonly encountered in drought-prone regions. The results revealed that drought stress profoundly inhibited growth, primarily affecting plant height and reducing the number and length of new shoots. Notably, leaves under moderate and SD conditions demonstrated significant wilting and subsequent death. Photosynthetic pigment content and photosynthesis-related parameters initially increased but subsequently experienced a sharp decline as drought stress persisted. Biochemical analyses indicated elevated levels of relative conductivity and malondialdehyde, indicating extensive cell membrane damage. In the meanwhile, the activities of key antioxidant enzymes (superoxide dismutase, peroxidase, and ascorbate peroxidase) increased, alongside higher accumulations of soluble sugars, soluble protein, and proline, albeit with a sluggish recovery observed under severe stress conditions. Anatomical studies highlighted the thickening of both the upper and lower epidermis, as well as a reduction in the density of palisade and spongy tissues. Recovery following rewatering was more effective under LD and MD conditions than under SD stress, indicating that M. faberi possesses strong drought tolerance but is not suitable for highly arid regions. This study elucidates the adaptive mechanisms of M. faberi under drought stress and provides practical guidance for its management and cultivation in drought-prone areas, enhancing its ecological and economic viability. creator: Wei Tang creator: Qiong Mo creator: Yangyang Fu creator: Damao Zhang creator: Yang Liu creator: Mingtong Ren creator: Tingting Li creator: En Wu creator: Dingding Su creator: Xiaoying Yu creator: Lihong Yan creator: Yanlin Li uri: https://doi.org/10.7717/peerj.19855 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tang et al. title: The potential biofertilization effect of H2 is accompanied by a modest impact on the composition of microbial communities in the rhizosphere of common vetch link: https://peerj.com/articles/20019 last-modified: 2025-09-09 description: BackgroundN2-fixing nodules release molecular hydrogen (H2) in the rhizosphere of legumes. The process activates H2-oxidizing bacteria (HOB) in soil, leading to multiple effects on biogeochemical processes and a potential biofertilization effect. The legacy effect of the energy potential of H2 on the soil microbial community structure and the population density of HOB has received little attention. The aim of the current study is to evaluate how the legacy effect of HOB, previously activated in soil microcosms exposed to elevated H2 concentrations (eH2), affects biomass production yield of common vetch (Vicia sativa), the abundance of HOB, and the composition of the rhizosphere microbiome.MethodsContrasting soil samples displaying more than 60% difference in H2 oxidation activity were used as growth substrate for vetch. Soil microbial community composition and diversity were examined by bacterial 16S rRNA polymerase chain reaction (PCR) amplicon sequencing, and dry weight (DW) of the above- and below-ground biomass of vetch was analyzed to assess the impact of HOB enrichment on plant growth. The population density of high-affinity HOB was estimated by using the droplet digital polymerase chain reaction (ddPCR) technique to target the hhyL gene, encoding for the large subunit of group 1H/5 [NiFe]-hydrogenase.ResultsThe abundance of HOB possessing group 1H/5 [NiFe]-hydrogenase was indistinguishable between the treatments, indicating that soil nutrient content (inorganic and organic carbon) and the energy potential of H2 were insufficient to support their growth. Aeromicrobium spp. and Ramlibacter spp. were favored by eH2 exposure at the activation stage, but their response was lost after vetch growth. The root biomass and the root/shoot ratio were reduced in soil conditioned with eH2 compared to control soil exposed to ambient H2, suggesting that the plant growth-promotion activity of HOB reduces root proliferation for nutrient prospection. These results provide new experimental evidence suggesting the biofertilization effect of H2 is not universal and requires specific conditions that are yet to be identified. creator: Diana Dip creator: Philippe Constant uri: https://doi.org/10.7717/peerj.20019 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dip and Constant title: Comparative study of gut microbiota on fat deposition in European meat pigeons and Yuzhong pigeons link: https://peerj.com/articles/20008 last-modified: 2025-09-09 description: The rate of fat deposition is a critical indicator for assessing the quality of roast squab. Fat deposition in meat pigeons is closely related to their intestinal flora. However, few studies have examined the relationship between gut microbiota structure and fat synthesis in pigeons. This study focused on 28-day-old roast squabs of European meat pigeons and Yuzhong pigeons, which exhibit significant differences in fat synthesis and weight. We analyzed the molecular mechanisms by which the intestinal microbiota of different meat pigeons influences fat deposition. Additionally, we evaluated the effects of intestinal digesta from these pigeons on pigeon milk digestion and absorption using a monogastric animal simulation digestive system. Results indicated that the intestinal microflora structures of European meat pigeons and Yuzhong pigeons were significantly different. In European meat pigeons, Romboutsia promoted fat absorption and utilization by influencing lipid metabolism. In contrast, Lactobacillus and Turicibacter in Yuzhong meat pigeons facilitated fat decomposition in roast squab by affecting bile acid transformation and β-oxidation. Furthermore, gut microbiota can influence the enzymatic activity of acetylCoA carboxylase through biotin synthesis, thereby affecting fat synthesis and the overall transport and deposition of fat in the body. This study reveals, for the first time, the influence of meat pigeons’ gut microbiota on fat digestion and absorption, laying the foundation for developing specialized probiotic products for meat pigeons. creator: Zhen Zhang creator: Xinghui Song creator: Dingding Zhang creator: Na Luo creator: Liheng Zhang creator: Runzhi Wang creator: Zhanbing Han creator: Guirong Sun creator: Pengkun Yang uri: https://doi.org/10.7717/peerj.20008 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Can the triglyceride-glucose index predict the risk of stroke? A meta-analysis of high-quality studies with 12.8 million participants link: https://peerj.com/articles/19994 last-modified: 2025-09-09 description: ObjectiveThe triglyceride-glucose index (TyG) has been actively researched for predicting several diseases. However, high-quality evidence assessing its ability to predict stroke is lacking. We conducted a meta-analysis of high-quality studies examining if TyG can predict stroke in the general population.MethodsEmbase, PubMed, CENTRAL, Web of Science, and Scopus databases were searched until 13th January 2025. Cohort studies on the general population, excluding those with baseline stroke or cardiovascular disease, with a minimum follow-up of four years and reporting an adjusted association between TyG and stroke were included. TyG was assessed as both a categorical and continuous variable.ResultsA total of 13 studies with 12,898,434 individuals were eligible. The overall incidence of stroke was 0.89%. Meta-analysis indicated a statistically significant increased risk of stroke between higher vs lower values of TyG (risk ratio (RR): 1.27 95% confidence interval (CI) [1.19–1.35] I2 = 66%). Per unit increase in TyG was also associated with a statistically significant increase in the risk of stroke (RR: 1.16 95% CI [1.07–1.27] I2 = 89%). Most results remained unchanged on subgroup analysis based on location, excluded population, stroke diagnosis, TyG data, and follow-up. Meta-regression using moderators sample size, age, male gender, diabetes mellitus, hypertension, TyG cut-off, stroke incidence, and follow-up also failed to reveal significant results.ConclusionHigh TyG is associated with increased risk of stroke in the general population. creator: Gang Xin creator: Huiya Li creator: Ji Jiang uri: https://doi.org/10.7717/peerj.19994 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xin et al. title: Beneficial dose-dependent effects of Ag nanoparticles on germination do not compromise growth and metabolic profiles of Capsicum annuum seedlings link: https://peerj.com/articles/19974 last-modified: 2025-09-09 description: This study evaluates the effects of silver nanoparticles (AgNPs) as a nanopriming agent and their potential detrimental impacts on growth and physiology in wild and domesticated chili (Capsicum annuum) seeds. We compared the responses of wild (C. annuum var. glabriusculum) and domesticated (Serrano) plants. Seeds were soaked for 24 hours in AgNP solutions at concentrations of 0 ppm, 50 ppm, 100 ppm, and 250 ppm. Germination was monitored daily over a 14-day period in replicated Petri dishes under controlled growth chamber conditions. A subsample of germinated seedlings from each treatment was transplanted into plastic pots to assess plant growth and secondary metabolism at 28 and 42 days after germination. On each sampling day, three randomly selected plants per treatment were evaluated for shoot and root length, as well as wet and dry biomass. Physiological measurements included both primary and secondary metabolites, specifically chlorophyll and polyphenols. Potential genotoxic effects were assessed by exposing meristematic root tissue to a 5 ppm AgNP solution for 72 hours and analyzing mitotic activity. The results showed that AgNPs significantly increased germination in wild chili, reaching 90% compared to 77% in the control, without negative effects on plant development. No significant differences were observed in growth traits or polyphenol content, or the number of dividing cells. Furthermore, no chromosomal aberrations were detected. The beneficial effects of nanopriming were limited to the germination stage in wild plants, and no enhancement was observed in the domesticated variety. These results suggest that domestication may reduce sensitivity to nanopriming. Overall, our findings support the potential benefits and safety of AgNP-based nanopriming in agriculture, even at high concentrations. creator: Berenice Cortes Espinoza creator: Alejandro Sánchez-González creator: María Evarista Arellano-García creator: Rafael Bello-Bedoy uri: https://doi.org/10.7717/peerj.19974 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cortes Espinoza et al. title: Macular function measured by Nidek MP-3 microperimeter in normal Chinese individuals across age groups link: https://peerj.com/articles/19961 last-modified: 2025-09-09 description: BackgroundMicroperimetry has emerged as a tool for assessing retinal function, especially macular function in recent years. In this study, the MP-3, a widely adopted device, was employed to analyze macular sensitivity and fixation stability across various age groups.MethodsThe research involved evaluating the macular sensitivity and fixation stability of 182 healthy eyes free from ocular disorders. The relationship between macular sensitivity, fixation pattern, and age was determined through generalized estimating equations.ResultsMacular sensitivity and percentage of fixation stability within 2° and 4° were measured for 182 eyes (mean age: 45.24 ± 17.03 years) using MP-3. The mean macular sensitivity was 29.5 ± 1.6, while the mean percentage of fixation points within a 2° circle was 93.0 ± 7.5%, and within a 4° circle was 98.3 ± 2.8%. Macular sensitivity, as well as the percentage of fixation points within the central 2° and 4° areas, tended diminish with advancing age.ConclusionIn conclusion, among normal subjects, macular sensitivity and fixation values decrease with age. MP-3 emerges as a reliable instrument for measuring macular function. creator: Dan Hu creator: Qiuhai Wang creator: Qingcui Liu creator: Emmanuel Eric Pazo creator: Zhe Liu creator: Shuang Wu creator: Wen Zhang creator: Yan Xing creator: Bo Yu uri: https://doi.org/10.7717/peerj.19961 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hu et al. title: Analysis of imaging data on seasonal changes in the population structure and vertical distribution of two dominant planktonic copepod species in the western subarctic Pacific link: https://peerj.com/articles/19956 last-modified: 2025-09-09 description: Traditionally, zooplankton analyses have relied on stereomicroscopes, but recent advancements in imaging analysis have offered significant advantages, including the simultaneous collection of abundance, size, and biovolume data. In this study, formalin-preserved samples were collected from depths of 0 to 1,000 m across four seasons at a station in the western subarctic Pacific, using the imaging device ZooScan. Two dominant copepod genera, Metridia and Eucalanus, were examined for seasonal changes in abundance, biovolume, and diurnal vertical distribution. ZooScan measurements were taken for each developmental stage to obtain information on the equivalent spherical diameter (ESD). Four Metridia species were identified: M. pacifica, M. okhotensis, M. asymmetrica, and M. curticauda. M. pacifica, the dominant species, had an ESD of 2 mm or less, while the other three species exceeded 2 mm. M. pacifica exhibited diurnal migration to surface layers (0–50 m) at night, while the larger species were primarily located in the deeper layer (750–1,000 m) both day and night. Only one species, E. bungii, was identified in the genus Eucalanus, with size cohorts corresponding to each developmental stage. Its vertical distribution was consistent day and night across seasons, but seasonal changes were evident. In October and February, E. bungii was found at depths of 200–500 m. In April, later developmental stages migrated to shallower depths of 50–200 m, while in July, younger stages (C1–C4) were found at 0–50 m, indicating recent reproduction during the spring phytoplankton bloom. Although it was clear that new individuals emerged in July, understanding the dynamics of later stages and generation time was difficult due to overlapping size distributions, particularly in C5 and C6. The differences in vertical distribution between copepod species reveal important ecological trends: M. pacifica performs diel vertical migration (DVM), while E. bungii exhibits seasonal vertical migration (SVM). M. pacifica shows no clear seasonality in population structure, whereas E. bungii has distinct seasonal patterns. This indicates that both species reproduce near the surface, but E. bungii follows annual life cycles due to its larger size, while M. pacifica reproduces opportunistically throughout the year. Using ZooScan offers significant advantages for studying copepod ecology, enabling precise estimations of ecological fluxes—such as feeding, production, and egestion—through accurate measurements of body sizes and masses. Adopting these methods will enhance our understanding of copepod populations and their ecosystems. creator: Tian Gao creator: Atsushi Yamaguchi uri: https://doi.org/10.7717/peerj.19956 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gao & Yamaguchi title: Mimicry between adult rove beetles and assassin bug nymphs with unequal defenses: antagonistic or mutualistic? link: https://peerj.com/articles/19942 last-modified: 2025-09-09 description: Defensive mimicry encompasses a continuum ranging from Batesian to Müllerian mimicry. Batesian mimicry involves antagonistic interactions between undefended and defended species, whereas Müllerian mimicry represents mutualistic interactions between species with comparable levels of defense. When mimicry occurs between species with unequal defensive abilities, it is termed quasi-Batesian mimicry, though whether such interactions are antagonistic or mutualistic remains debated. Despite their common occurrence in nature, few quasi-Batesian mimicry systems have been experimentally studied. Here, we investigated the mimetic interaction between two chemically defended insect species, the rove beetle Paederus fuscipes Curtis, 1826 (Coleoptera: Staphylinidae) and the assassin bug Sirthenea flavipes (Stål, 1855) (Hemiptera: Reduviidae), through behavioral assays with their potential predator, the pond frog Pelophylax nigromaculatus (Hallowell, 1861) (Anura: Ranidae), which naturally co-occurs with these insects in Japan. Adult P. fuscipes resemble S. flavipes nymphs in their conspicuous reddish-orange and black coloration. Under laboratory conditions, 45.8% of pond frogs rejected P. fuscipes adults, whereas 70.8% rejected S. flavipes nymphs, suggesting that the assassin bug nymphs are better defended. Prior exposure to S. flavipes increased frog rejection of P. fuscipes, whereas exposure to P. fuscipes slightly reduced rejection of S. flavipes. These results indicate that adult P. fuscipes may gain protective benefits from mimicry of S. flavipes nymphs, while the latter may incur a small cost. creator: Shinji Sugiura creator: Masakazu Hayashi uri: https://doi.org/10.7717/peerj.19942 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sugiura and Hayashi title: A lack of open data standards for large infrastructure projects hampers social-ecological research in the Brazilian Amazon link: https://peerj.com/articles/19926 last-modified: 2025-09-09 description: New infrastructure projects are planned or under construction in several countries, including in the bioculturally diverse Amazon, Mekong, and Congo regions. While infrastructure development can improve human health and living standards, it may also lead to environmental degradation, such as deforestation, and social change, such as loss of livelihoods. Accessible, high-quality data about infrastructure projects is essential for both monitoring these projects and studying their social and environmental impacts. As a case study, we investigated the availability and quality of data on infrastructure projects in the Brazilian Amazon by reviewing the academic literature and surveying researchers from the conservation and development community. We used the results of these surveys to identify recommended steps for the gathering, organizing, and sharing of infrastructure data by social-ecological researchers and practitioners. Although data on infrastructure in the Brazilian Amazon were generally available, they were often of poor quality and lacked information critical for monitoring and research. Data were often difficult to find on government and non-government websites as well as reformat, resulting in loss of time and resources for researchers and other stakeholders. Discrepancies between researchers’ survey responses on data needs and the types of data used in peer-reviewed articles on infrastructure projects indicate the following information was often missing: geographic extent of the project, construction and operation dates, and project type (e.g., paved vs. unpaved road). Including these data in a standardized format, along with making them more readily accessible by hosting them in public repositories and ensuring they are current and comprehensive, would facilitate research and improve planning, decision-making, and monitoring of operational and planned infrastructure projects in Brazil and other developing countries. creator: Jacy L. Hyde creator: Christine Swanson creator: Stephanie A. Bohlman creator: Simone Athayde creator: Emilio M. Bruna creator: Denis R. Valle uri: https://doi.org/10.7717/peerj.19926 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hyde et al. title: The farther, the better? The effect of attentional focus distance on motor performance: a systematic review and meta-analysis link: https://peerj.com/articles/20012 last-modified: 2025-09-08 description: BackgroundMotor skill performance is influenced by attentional focus, and recent studies suggest that external focus, particularly a more distal external focus, may enhance performance more than an internal or a proximal external focus. However, the optimal distance for external focus and the influence of expertise level remain unclear. This systematic review and meta-analysis aimed to evaluate the effect of attentional focus distance on motor performance across various tasks and expertise levels.MethodsThis systematic review and meta-analysis followed established guidelines (PRISMA) and was registered with the International Prospective Register of Systematic Reviews (CRD42024595116). Comprehensive literature searches were performed in PubMed, Web of Science, Embase, and Cochrane Library databases. Data extraction followed the PICOS framework, and analyses were conducted using Stata and Review Manager.ResultsA total of 20 randomized controlled trials with 497 participants were included. The results indicated that a distal external focus significantly improved motor performance compared to both external proximal focus (standardized mean difference, S = 0.3, 95% CI [0.07–0.53], p = 0.01) and internal focus (SMD = 0.59, 95% CI [0.14–1.05], p = 0.01). However, no significant difference was observed between the distal and proximal external focus in novices. Subgroup analyses showed that skill level significantly moderated the effectiveness of attentional focus.ConclusionsA distal external focus improves motor performance in experienced although its effectiveness in novices requires further study. Future research should explore the mechanisms underlying these effects and skill-specific guidelines for optimal attentional focus distance. creator: Le Zang creator: Wei Guo creator: Biye Wang uri: https://doi.org/10.7717/peerj.20012 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zang et al. title: Sex-based influence of morphological and physical attributes on serve performance in adolescent volleyball players link: https://peerj.com/articles/19992 last-modified: 2025-09-08 description: This study examined sex differences in anthropometric and physical attributes, and their relationships with volleyball serve accuracy and speed among adolescent volleyball players. Fifty athletes (age: 13.1 ± 0.4 years; peak height velocity: −2.2 ± 0.3 years) voluntarily participated in this study. Anthropometric attributes, physical performances, and technical performance (i.e., serve accuracy and speed) were measured. The result showed that boys were taller, leaner, and had greater leg length than girls (all p < 0.001). Boys also outperformed girls in change of direction (p < 0.01), vertical jump (p < 0.0001), upper limb strength (p < 0.005), balance, and serve speed (both p < 0.0001). Height, arm length, lower limb length, and hand length were positively correlated with serve accuracy and speed for both boys and girls (range: r = 0.497 to 0.789; all p < 0.05). Serve accuracy and speed were associated with all physical performance measures (range: r = 0.402 to 0.908; all p < 0.05), except 10-meter sprint time, which was only significantly correlated with serve speed in girls (r =  − 0.403; p < 0.05). The main anthropometric factor influencing serve accuracy was height in boys (R2 = 0.901; p < 0.0001) and hand length in girls (R2 = 0.650; p < 0.0001); the opposite was true for serve speed. For physical performance, change of direction, flexibility, and balance were the main factors influencing accuracy in boys (R2 = 0.717; p < 0.0001) and girls (R2 = 0.820; p < 0.0001). Serve speed was influenced by hand grip force, upper limb strength, and balance in boys (R2 = 0.770; p < 0.0001), while hand grip force was the main factor in girls (R2 = 0.722; p < 0.0001). In conclusion, body span and physical abilities, such as balance, flexibility, and strength are essential for volleyball serve accuracy and speed in adolescent players. creator: Rani Asfour creator: Hamza Marzouki creator: Ibrahim Ouergui creator: Jabeur Methnani creator: Khalifa Al-Jadidi creator: Majid Al-Busafi creator: Yung-Sheng Chen creator: Nabil Gmada creator: Ezdine Bouhlel uri: https://doi.org/10.7717/peerj.19992 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Asfour et al. title: Progress in biostimulation-based remediation of TPH-contaminated soils: a comprehensive review link: https://peerj.com/articles/19991 last-modified: 2025-09-08 description: BackgroundPetroleum pollution in soils poses a significant global environmental threat, primarily due to increased industrial activities and oil spills. Biostimulation, a bioremediation strategy that enhances indigenous microbial activity through nutrient amendment, has gained prominence for its sustainability and effectiveness.MethodsThis review consolidates findings from 276 peer-reviewed studies published between 2000 and 2025, covering the application of organic amendments, mineral nutrients, and biochar. It further analyzes microbial community responses, degradation efficiency, and synergistic treatment outcomes under varied environmental conditions.ResultsBiostimulants such as compost, nitrate, and phosphate significantly enhance microbial degradation of total petroleum hydrocarbons (TPHs), especially when used in combination. Biochar improves soil aeration and supports functional gene expression. Integrated treatments demonstrate superior removal efficiencies compared to single-agent approaches.ConclusionBiostimulation is a promising, scalable solution for TPH-contaminated soils. However, optimization of nutrient ratios, consideration of site-specific variables, and real-time monitoring systems are essential for effective field deployment. creator: Yuanyuan Li creator: Jinqiang Yang creator: Yaru Song creator: Mingli Wei uri: https://doi.org/10.7717/peerj.19991 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Study on the correlation between multiple object tracking ability and eye- tracking characteristics in sports decision making among basketball players link: https://peerj.com/articles/19984 last-modified: 2025-09-08 description: BackgroundVariations in attention and search strategies can partially explain the differences in players’ decision-making capabilities. This study aims to explore the correlation between basketball players’ multiple object tracking (MOT) ability and visual search in sports decision-making tasks using the expert-novice paradigm.MethodsForty-eight college students were selected and divided into two groups: the expert group (24 basketball players) and the novice group (24 general college students). Using different numbers and speeds in MOT tasks, the Eyelink eye tracker was employed to record the visual search process during sports decision-making tasks. The correlation coefficient between MOT accuracy and eye-tracking indicators was then analyzed.Results(1) The accuracy of MOT in both the expert and novice groups was negatively correlated with average fixation time and average fixation frequency. The correlation between MOT accuracy and average fixation time for passing intuition and passing cognition in the expert group was stronger than that in the novice group. (2) When tracking three–six targets at a speed of 10°/s, a strong correlation was observed between the MOT accuracy in both groups and the eye movement indicators of the sports decision-making task. (3) The correlation between MOT accuracy in the expert group and the proportion of fixation time in irrelevant areas during intuitive decision-making was lower than in the novice group. Similarly, the correlation with the proportion of fixation frequency in irrelevant areas during cognitive decision-making was also lower in the expert group compared to the novice group.ConclusionsThe multiple object tracking ability of basketball players is negatively correlated with fixation time and fixation frequency in sports decision-making tasks, and positively correlated with fixation time during passing decisions. creator: Qifeng Gou creator: Sunnan Li uri: https://doi.org/10.7717/peerj.19984 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gou and Li title: Analysis of the resistance level and target site resistance mechanisms of Echinochloa crus-galli to penoxsulam from Hubei Province, China link: https://peerj.com/articles/19973 last-modified: 2025-09-08 description: Echinochloa crus-galli is a grass weed that infests rice fields and causes significant crop yield losses. In this study, we surveyed 15 resistant E. crus-galli populations collected from rice fields in Hubei Province, China, and investigated the resistance levels and target site resistance mechanisms to the acetolactate synthase (ALS) inhibitor penoxsulam. The results of whole-plant bioassay experiments revealed that 15 populations presented different levels of resistance to penoxsulam. The Trp-574-Leu mutation was detected in ten resistant populations, and the Pro-197-Leu mutation was detected in one resistant population. Additionally, the in vitro ALS activity in resistant populations (18-ETF, 18-WJJ, and 18-WMJ) was 51.28-, 5.51-, and 8.46-fold greater than that in the susceptible population. The ALS from these resistant populations requires a much higher penoxsulam concentration for activity inhibition. ALS gene expression in three resistant populations (18-ETF, 18-WJJ, and 18-WMJ) was 1.53-, 1.58-, and 1.41-fold greater than that in the susceptible population 18-NJ before penoxsulam treatment. Our results indicated that target-site mutation in ALS is at least partially responsible for barnyardgrass resistance to penoxsulam in Hubei Province. creator: Qiongnan Gu creator: Jing Shen creator: Shihai Chu creator: Qichao Huang creator: Anan Chen creator: Lin Li creator: Ruhai Li uri: https://doi.org/10.7717/peerj.19973 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gu et al. title: The platelet and coagulation function parameters in late pregnancy are associated with preeclampsia and its severity: a single-center retrospective study link: https://peerj.com/articles/19916 last-modified: 2025-09-08 description: ObjectiveThis study aimed to explore the correlation between platelet and coagulation function during late pregnancy with preeclampsia (PE) as well as its severity, and concurrently establish an effective risk model to predict PE.MethodsAs a retrospective case-control study, this research encompassed a sample of 594 patients of late pregnancy in Hangzhou Women’s Hospital from January 2021 to April 2024, including 198 cases diagnosed with mild-PE, 198 with severe-PE, and 198 healthy pregnant women. Utilizing both univariate and multivariate analysis, this study conducted a comparison of demographic and laboratory data among these groups to uncover the correlation between platelet parameters, coagulation function, and PE as well as the severity. Ultimately, a receiver operating characteristic (ROC) curve was drawn to evaluate the predictive power of the risk model for PE.ResultsUnivariate analysis revealed statistically significant differences in platelet count (PC), mean platelet volume (MPV), plateletcrit (PCT), thrombin time (TT), and fibrinogen mean (FIB). Multivariate analysis showed that MPV (adjusted odds ratio (AOR) = 1.882 for mild-PE group and AOR = 2.141 for severe-PE group) and TT (AOR = 3.071 for mild-PE group and AOR = 4.154 for severe-PE group) were associated with PE. The area under curve (AUC) of the risk model of MPV combined with TT, as depicted by the ROC curve, amounted to 0.827, exhibiting a sensitivity of 0.657 and a specificity of 0.879.ConclusionsMPV and TT are independent risk factors for PE and are associated with its severity. The risk model consisting of MPV and TT possesses a certain predictive capability for PE. creator: Jindi Zhang creator: Jie Liu creator: Pei Wang uri: https://doi.org/10.7717/peerj.19916 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Exploring differential gene expression and biomarker potential in systemic lupus erythematosus: a retrospective study link: https://peerj.com/articles/19891 last-modified: 2025-09-08 description: BackgroundSystemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by inflammation and immune-mediated multi-organ system damage, accompanied by clinical manifestations such as fever, hair loss, skin rash, oral ulcers, and joint pain and swelling. SLE has been reported to affect more than 3.4 million people worldwide, of which approximately 90% are women.PurposeThis study aims to identify and characterize key hub genes implicated in SLE through comprehensive bioinformatics analyses, providing a theoretical foundation for the development of more effective therapeutic strategies.MethodsTwo datasets were procured from the Gene Expression Omnibus (GEO) database: GSE13887 and GSE10325. Differentially expressed genes (DEGs) were identified and subjected to functional enrichment analysis, protein-protein interaction (PPI) network construction, and receiver operating characteristic (ROC) curve analysis to evaluate potential hub genes. The top 20 significantly upregulated and downregulated DEGs, alongside the top 15 enriched Gene Ontology (GO) terms and five Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, were screened from both datasets. Quantitative real-time PCR (RT-q PCR) was utilized to validate hub gene expression in CD3 + T cells from peripheral blood samples of SLE patients. Concurrently, flow cytometry was employed to quantify inflammatory cytokines in peripheral blood samples.ResultsBioinformatics analyses identified 1,912 DEGs in GSE13887 and 52 DEGs in GSE10325, with eight DEGs common to both datasets. Functional enrichment analysis underscored critical biological processes, notably cell-mediated cytotoxicity and cell killing. PPI network and enrichment analyses highlighted seven hub genes, among which FCER1A and RGS1 demonstrated consistent expression trends across datasets and clinical samples—FCER1A was significantly downregulated, while RGS1 was upregulated in SLE patients. ROC curve analysis confirmed their strong diagnostic potential (AUC > 0.7). Principal component analysis (PCA) further highlighted distinct gene expression profiles differentiating SLE patients from healthy controls. Clinical validation via RT-q PCR and flow cytometry corroborated these findings, demonstrating decreased FCER1A expression and increased RGS1 expression in CD3 + T cells from SLE patients. Moreover, elevated plasma levels of IL-6 and TNF-α, coupled with diminished IL-10 levels, were observed in SLE patients. These findings suggest that FCER1A and RGS1 are promising biomarkers for SLE diagnosis.ConclusionsFCER1A and RGS1 are significantly associated with SLE and serve as potential biomarkers for distinguishing SLE patients from healthy individuals. Their involvement in SLE pathogenesis underscores their potential as targets for future diagnostic and therapeutic interventions. creator: Jie Xiao creator: Yuhong Luo creator: Lina Duan creator: Xinru Mao creator: Lingyue Jin creator: Haifang Wang creator: Hongxia Wang creator: Jie Pan creator: Ying Gong creator: Haixia Li uri: https://doi.org/10.7717/peerj.19891 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xiao et al. title: Effects of dietary supplements on bone turnover markers in women after menopause: a network meta-analysis link: https://peerj.com/articles/19882 last-modified: 2025-09-08 description: BackgroundDiminished estrogen levels in women after menopause contribute to an elevated risk of decreased bone mineral density (BMD) and disturbed bone metabolism. Dietary supplements are extensively employed as substitutes for prescription drugs, serving as a significant approach to modulate bone metabolism and improve bone health. Nevertheless, a lack of robust evidence prevents clinicians and patients from making the best-informed choices at present. Accordingly, a network meta-analysis (NMA) was performed to provide a comprehensive comparison of the effects of different dietary supplements on bone turnover biomarkers among postmenopausal women.MethodsPubMed, Embase, Cochrane Library, and Web of Science databases were retrieved from their inception to November 20, 2024. Randomized controlled trials (RCTs) assessing the strength of dietary supplements in women after menopause were adopted in this research. Primary outcome indicators encompassed C-terminal telopeptide of type I collagen (CTX), procollagen type I N-terminal propeptide (P1NP), osteocalcin (OC), bone alkaline phosphatase (BAP), alkaline phosphatase (ALP), and N-terminal telopeptide of type I collagen (NTX). Risk of bias assessment was performed for each enrolled trial utilizing the ROB 2.0. A Bayesian NMA was conducted utilizing the R software (V4.4.1). Publication bias was assessed utilizing Stata 15.1.ResultsForty-three RCTs involving 5,184 postmenopausal women were adopted. Research findings revealed that CTX levels decreased most substantially with vitamin E supplementation (SUCRA: 82.37%). Combining vitamin D and vitamin K most effectively elevated P1NP (SUCRA: 100.00%) and OC (SUCRA: 97.05%) levels. The greatest increase in BAP levels (SUCRA: 95.50%) was observed with vitamin K supplementation. Calcium supplementation yielded the largest elevation in ALP levels (SUCRA: 96.68%). Furthermore, protein supplementation resulted in the most significant reduction in NTX levels (SUCRA: 81.20%).ConclusionDietary supplementation may serve as an important strategy for enhancing bone health in women after menopause by regulating bone metabolism. By promoting bone formation and inhibiting bone resorption, vitamin D, vitamin E, vitamin K, calcium, and protein may help mitigate the progression of osteoporosis. creator: Yan Wei creator: Congjie Lei creator: Yue Zhong creator: Hongchun Shen uri: https://doi.org/10.7717/peerj.19882 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wei et al. title: Vampyromorph coleoid predation by an ichthyosaurian from the Early Jurassic Lagerstätte of Bascharage, Luxembourg link: https://peerj.com/articles/19786 last-modified: 2025-09-08 description: Many Early Jurassic marine predators were seemingly adapted to hunt soft and fast prey items such as cephalopods. However, deciphering what these animals ate and, therefore, the intensity of their competition is challenging, as fossilised gut content is biased by multiple factors. In this paper, we report a loligosepiid vampyromorph coleoid in the gut of a specimen of the ichthyosaurian Stenopterygius triscissus from the early Toarcian Bascharage Lagerstätte of Southern Luxembourg. This is the first report of octobrachian predation in ichthyosaurians. The coeval pachycormid teleosts Pachycormus macropterus and Saurostomus esocinus have recently been reported to feed on loligosepiid octobrachians as well. We use this opportunity to compare the functional anatomy of these taxa and re-evaluate the affinities of coleoids preserved as ichthyosaurian gut content. creator: Valentin Fischer creator: Robert Weis creator: Dominique François Delsate creator: Francesco Della Giustina creator: Pierre Wintgens creator: Dirk Fuchs creator: Ben Thuy uri: https://doi.org/10.7717/peerj.19786 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fischer et al. title: Transcriptome analysis of substrate temperature effects on adventitious root formation in peach rootstocks link: https://peerj.com/articles/20015 last-modified: 2025-09-05 description: The propagation of peach rootstocks, particularly adventitious root (AR) formation, is influenced by multiple factors, with substrate temperature being crucial. This experiment studied the differential gene expression patterns of GF677 rootstock cuttings treated with 200 mg L−1 indole-3-butyric acid (IBA) under various substrate temperatures (ambient temperature (CK), 19 °C, 22 °C, 25 °C, and 28 °C) and cutting periods (7, 14, and 21 days). The results showed a maximum rooting rate of 91% when assessed at 40 days under 25 °C, while RNA sequencing was performed at earlier stages (7, 14, and 21 days). The highest number of differentially expressed genes (DEGs) observed between 22–25 °C. Therefore, the optimal substrate temperature for propagation was determined to be 25 °C. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlighted “starch and sucrose metabolism (photosynthesis processes)” and “plant hormone signal transduction (especially auxin)” as enriched pathways. Specifically, 26 plant genes (ARFs, LBDs, SAURs, and GH3) and 22 AR formation-related genes (AUR3, LRP1, RGF1, AIR9, AP2, and NAC) were identified from these DEGs. Weighted gene co-expression network analysis (WGCNA) clarified the involvement of various transcription factors (WRKYs, ERFs, NACs, bHLHs, bZIPs, and MYBs) in AR formation. These findings indicate significant differences in gene expression under different combinations of substrate temperatures and cutting periods. Overall, this study enhances our understanding of the molecular mechanisms underlying peach rootstocks asexual reproduction. creator: Fan Zhang creator: Hong Wang creator: Chenbing Wang creator: Xiaoshan Wang creator: Jiaxuan Ren creator: Meimiao Guo uri: https://doi.org/10.7717/peerj.20015 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Association between levels of trimethylamine N-oxide and cognitive dysfunction: a systematic review and meta-analysis link: https://peerj.com/articles/20000 last-modified: 2025-09-05 description: BackgroundPrevious studies have shown that the differential expression of trimethylamine N-oxide (TMAO) is closely related to the prognosis of cognitive dysfunction, but the conclusion is still controversial. Therefore, we conducted a meta-analysis to investigate the difference of TMAO levels between patients with and without cognitive dysfunction.MethodsFrom the beginning to January 25, 2024, we search for correlational studies on PubMed, Embase, Scopus, the Cochrane Library, and Web of Science. We sought to evaluate the association between TMAO, a major gut microbial metabolite, and cognitive function.ResultsTo investigate the differences in TMAO values between patients with and without cognitive dysfunction. The database search identified 229 studies. After applying exclusion criteria, seven studies involving 1,675 people (352 patients with cognitive dysfunction and 1,323 controls) were finally included in the meta-analysis. Compared with the control group, patients with cognitive dysfunction had significantly higher TMAO (standard mean differences (SMD): 1.21, 95% confidence interval (CI) [0.53–1.89], p = 0.0005, I2:96%).ConclusionPatients with cognitive dysfunction have elevated TMAO levels, and TMAO levels are correlated with cognitive dysfunction. creator: Zhendong Ren creator: LuMeng Mo uri: https://doi.org/10.7717/peerj.20000 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ren and Mo title: New Paleogene records of cartilaginous fishes (Chondrichthyes) from central Chile, including the oldest lamnid diversity from the southeastern Pacific link: https://peerj.com/articles/19996 last-modified: 2025-09-05 description: BackgroundThe Paleogene chondrichthyan diversity of the southern hemisphere is mostly known in Antarctica, southernmost South America and New Zealand, but records from the southeastern Pacific remain sparse to date. Among these, lamnid sharks (the lineage of the great white shark) are one of the scarcer groups in the southern hemisphere prior to the Eocene; moreover, their occurrences prior to the Neogene remained unreported in the southeastern Pacific. This contribution presents new Paleogene chondrichthyans recovered from two different horizons at Loanco, central Chile, including the first local records of lamnids, with the description of a new species of the genus Lethenia.MethodsSections of two geologic units were studied. These provided new teeth of chondrichthyans, as well as a single associated tooth set plus fragments of jaw cartilage and vertebrae. The material was taxonomically identified and compared with other local occurrences and other coeval assemblages from the southern hemisphere.ResultsThis research recognizes a lower Paleocene-lower Eocene assemblage including material referable to Palaeohypotodus sp., Megasqualus sp. and Hexanchidae indet., the latter being the oldest known record in the southwestern Pacific. In addition, material from upper Eocene-lower Oligocene levels include dental pieces referable to the lamnids Macrorhizodus praecursor Leriche, and to a new species, Lethenia carranzaensis sp. nov., the latter represented by an exceptional specimen preserving a dental set, mandibular cartilage and vertebrae. Although discrete, this fauna shows the presence of Paleocene- lower Eocene elements commonly present in Antarctica and the Austral Basin, suggesting a typical Weddellian distribution during that timespan. On the contrary, the presence of the genus Lethenia reinforces the evidence of vertebrate interchange with the north Atlantic between the upper Eocene—lower Oligocene, previously suspected by the shared presence of blochiid billfishes. Evidence of such marine interchange is also present during the late Paleocene, based on the previous reports of Palaeogaleus, Physogaleus, and Premontreia, genera with similar known geographic occurrences. The new records of Macrorhizodus and Lethenia also represent the oldest known record of Lamnidae in the southwestern Pacific, proving its early presence previous to its widespread and abundant occurrence during the Neogene. creator: Rodrigo A. Otero uri: https://doi.org/10.7717/peerj.19996 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Otero title: Species variability of Pinus elliottii, P. elliottii×P. caribaea, and P. massoniana in response to pinewood nematode infection link: https://peerj.com/articles/19990 last-modified: 2025-09-05 description: Pine wilt disease (PWD), caused by Bursaphelenchus xylophilus, poses a severe threat to global pine forests. This study evaluated the susceptibility of one-year-old seedlings of three pine species—Pinus massoniana, P. elliottii × P. caribaea, and P. elliottii—to PWD through artificial inoculation. Results showed that all species were generally susceptible at the seedling stage, developing symptoms and experiencing high mortality within a short period. However, P. elliottii, native to North America, exhibited the highest resistance, with slower disease progression and reduced pinewood nematode spread. P. elliottii × P. caribaea showed intermediate susceptibility, while the native P. massoniana was the most vulnerable, with rapid symptom onset and extensive xylem damage. These findings provide insights into species-specific resistance and inform breeding strategies for PWD management. creator: Ming Zeng creator: Xiaoliang Che creator: Zhe Wang creator: Yang Liu creator: Leping Deng creator: Yehuang Guo creator: Ting Huang creator: Wenbing Guo uri: https://doi.org/10.7717/peerj.19990 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zeng et al. title: Building heat-resilient Caribbean reefs: integrating thermal thresholds and coral colonies selection in restoration link: https://peerj.com/articles/19987 last-modified: 2025-09-05 description: Caribbean reefs face increasingly frequent and intense bleaching events, adding to the numerous other threats impacting these ecosystems. Addressing these challenges requires global action to reduce climate drivers, along with local efforts like reef restoration. Active restoration using thermotolerant coral colonies offers a potential strategy to alleviate these impacts; however, gaps remain in identifying context-specific temperature thresholds to guide colony selection and standardize thermotolerance assessment methods. This study addressed these gaps in two phases. First, by determining practical thresholds to differentiate species responses to heat stress; and second, by developing a framework to identify and prioritize resilient colonies for restoration. In the first phase, 70 colonies of Acropora cervicornis, Diploria labyrinthiformis, Montastraea cavernosa, Orbicella annularis, O. faveolata, Porites astreoides, and P. porites were sampled from reefs in the southeastern Dominican Republic. Heat stress responses were assessed through 3-hour heat pulse assays above the local maximum monthly mean (MMM) temperature, combining visual bleaching ranks, pixel intensity as a proxy for chlorophyll loss, and pulse amplitude modulated (PAM) fluorometry. Species-specific T50 thresholds were identified as the temperatures where 50% of colonies showed signs of stress. In the second phase, intraspecific thermotolerance was further examined for D. labyrinthiformis, M. cavernosa, O. annularis, O. faveolata, and P. astreoides using 99 colonies from known parent sources. Heat pulse assays at control (MMM) and T50 temperatures were repeated four times to assign colony-specific thermal performance scores. This study integrates inter- and intraspecific thermotolerance data into a practical selection framework, offering valuable insights to guide restoration under climate change. creator: Macarena Blanco Pimentel creator: Johanna Calle-Triviño creator: Daniel J. Barshis creator: Sancia E.T. van der Meij creator: Megan K. Morikawa uri: https://doi.org/10.7717/peerj.19987 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Blanco Pimentel et al. title: Drivers of microplastic pollution in soil sediments at fish landing centers in Sri Vijaya Puram (Port Blair), South Andaman Island link: https://peerj.com/articles/19965 last-modified: 2025-09-05 description: Microplastic pollution poses a growing global threat to marine ecosystems, and soil sediments at fish landing centres are an often-overlooked reservoir of microplastics. Sri Vijaya Puram (Port Blair), located in South Andaman Island, is critical for fisheries and marine biodiversity, making it an important area for studying microplastic pollution. This study aims to identify the key drivers of microplastic pollution in soil sediments at fish landing centers. The specific objectives included assessing microplastic abundance, characterizing polymer types, and identifying potential pollution sources, such as fishing gear, plastic packaging, and urban runoff. Sediment samples were collected from six fish landing centres such as Junglighat, Dignabad, Chatham, Guptapara, Wandoor and Chidiyatapu. The study revealed significant spatial variation in microplastic concentrations, with higher contamination in the northern region. Notably, the northern region (centers) had a significantly higher mean abundance of 251.4 ± 110.3 particles/kg compared to the southern region’s (centers) 105.0 ± 57.1 particles/kg. The Mann–Whitney U Test (U = 283.0, p-value = 0.00014) substantiated this significant difference. Dominant polymer types included aramid fiber, acrylonitrile-butadiene rubber, and polyisoprene, indicating industrial and consumer waste sources. Potential sources were linked to urban runoff, fishing activities, and inadequate waste management. This study contributes to understanding microplastic pollution drivers in tropical coastal environments. The findings highlight the impact of anthropogenic activities and land use patterns on microplastic pollution in fish landing centres. This information is crucial for developing targeted mitigation strategies in similar coastal regions. creator: Ajit Kumar creator: Akshatha Soratur creator: Sumit Kumar creator: R Kiruba-Sankar creator: Dilip Kumar Jha creator: Balu Alagar Venmathi Maran uri: https://doi.org/10.7717/peerj.19965 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kumar et al. title: Elucidation of the adaptability of Cinnamomum camphora seedlings from different provenances via analyzing photosynthetic characteristics and anatomical structure link: https://peerj.com/articles/19934 last-modified: 2025-09-05 description: Understanding intraspecific variation in photosynthetic capacity and leaf structure is critical for optimizing provenance selection of Cinnamomum camphora in afforestation and urban landscaping programs. In this study, we assessed the adaptability of C. camphora seedlings from four provenances (Fuzhou, Wuhan, Shenzhen, and Shanghai) by examining their physiological and anatomical traits under a common garden environment in Henan Province. A total of n = 80 three-year-old seedlings (twenty per provenance) were evaluated for photosynthetic parameters, stomatal characteristics, and leaf structural features. The results revealed that the net photosynthetic rates of C. camphora seedlings from four different provenance sites exhibited a “double-peak” curve and a photosynthetic “lunch break” phenomenon, which was strongly positively correlated with stomatal conductance, transpiration rate, and Soil Plant Analysis Development (SPAD) value. Significant differences in stomatal characteristics were observed among the seedlings from four provenances. The seedlings from Fuzhou and Wuhan exhibited larger stomatal width, area, resulting in superior stomatal gas exchange than that in the seedlings from other provenances. Conversely, C. camphora seedlings from Shanghai exhibited smaller stomatal area and density, indicating poorer gas exchange and reduced adaptability. The stem cortex cells, stem phloem, stem pith diameter, leaf palisade tissue thickness, and leaf thickness of the seedlings from Shanghai were significantly lower than those of the seedlings from other provenances, indicating that these structural characteristics do not exhibit any photosynthetic advantages over other provenances. In contrast, the seedlings from Fuzhou and Wuhan exhibited larger stem pith diameter, thicker mesophyll cell, and greater leaf thickness, which enhanced their photosynthetic capabilities. Among the seedlings from the four different origins, those from Fuzhou and Wuhan exhibited the best overall photosynthetic ability and strongest adaptability. Conversely, the seedlings from Shanghai exhibited the poorest overall photosynthetic ability and weakest adaptability. Despite similarities in climate, the environmental conditions of different provenances did not appear to have a significant correlation with leaf anatomy. This study provided valuable insights for the introduction of C. camphora in various regions in China. creator: Yufeng Liu creator: Ruobing Zou creator: Yanmeng Guo creator: Yu Ji creator: Mengyuan Li creator: Yang You uri: https://doi.org/10.7717/peerj.19934 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Development of a prognostic RiskScore model using efferocytosis-related signature genes for lung adenocarcinoma link: https://peerj.com/articles/19892 last-modified: 2025-09-05 description: BackgroundLung adenocarcinoma (LUAD) has high incidence and mortality rates. Efferocytosis is involved in the progression of various cancers. The current work set out to develop a prognosis signature using efferocytosis-related genes (ERGs) for LUAD.MethodsPublic databases were accessed to obtain bulk and single-cell data of LUAD. Molecular subtyping of LUAD was performed using ConsensusClusterPlus, and efferocytosis-related candidate genes were screened by weighted gene co-expression network analysis (WGCNA) in combination with differential analysis. Subsequently, Least Absolute Shrinkage and Selection Operator (LASSO) regression was applied to construct a prognostic RiskScore model, followed by evaluating the relationship between the RiskScore, immune infiltration, and drug sensitivity. Single-cell transcriptomic profiling of LUAD was performed with the Seurat package to elucidate the cellular origins of the key genes. The expression and potential function of the representative genes were verified by reverse transcriptional quantitative polymerase chain reaction (qPCR) (RT-qPCR), Cell Counting Kit-8 (CCK-8), wound healing, and Transwell assays.ResultsTwo molecular subtypes of LUAD with different outcomes and clinical features were identified. Candidate ERGs were mainly enriched in inflammatory and immune-related pathways. Subsequently, seven key genes (CD200R1, BTN2A2, STAP1, DNASE2B, SAMD9, SEMA7A, BIRC3) associated with efferocytosis in LUAD were identified to establish a RiskScore model, which exhibited high robustness in predicting patient prognosis. Notably, high-risk group had lower immune scores and more unfavorable prognosis than low-risk group. Moreover, eight drugs were closely linked to the RiskScore, and low-risk group was more sensitive to Doramapimod_1042. Single-cell atlas of LUAD showed that the prognostic ERGs were mainly expressed in mast cells. In vitro experiments revealed that most of the seven ERGs were overexpressed in LUAD cells, and that SEMA7A knockdown could suppress LUAD cell proliferation, migration and invasion.ConclusionsOur results provided novel insights for the prognosis prediction and personalized treatment of LUAD. creator: Zengmin Dai creator: Shaofeng Jin creator: Shanshan Huang creator: Bingyang Liu creator: Xingkai Shen creator: Yuhong Jin uri: https://doi.org/10.7717/peerj.19892 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dai et al. title: Comparative effectiveness of anti-inflammatory and antiviral therapies on NLR and survival outcomes in severe COVID-19: multicenter retrospective study link: https://peerj.com/articles/20003 last-modified: 2025-09-04 description: BackgroundThe COVID-19 pandemic has highlighted the critical role of immune dysregulation and systemic inflammation in disease severity, particularly in patients with severe respiratory illness. Elevated levels of pro-inflammatory cytokines, such as IL-6, and biomarkers like the neutrophil-to-lymphocyte ratio (NLR) have been associated with worse outcomes. This study enrolled laboratory-confirmed SARS-CoV-2 patients with acute respiratory illness requiring intestive care unit (ICU) admission, including mechanical ventilation, to evaluate the effect of different treatments on NLR, neutrophil count (NC), and lymphocyte count (LC).MethodsA retrospective, multicenter, observational cohort study was conducted across 15 tertiary hospitals in Saudi Arabia, involving 1,490 ICU-admitted COVID-19 patients between March 1, 2020, and October 30, 2020. Data on patient demographics, comorbidities, laboratory results, and treatment outcomes were collected using the Research Electronic Data Capture (REDCap) system. The study evaluated the effect of different treatments on NLR, neutrophil count (NC), and lymphocyte count (LC).ResultsThis study utilized 1,490 patients in the study of whom 73.6% were male and 26.1% were female. The average age of patients was 56.2 years, with a mean NLR of 8.77 ± 8.64, showing significant systemic inflammation. Tocilizumab (p = 0.031), oseltamivir (p = 0.004), and linezolid (0.029) showed statistically significant effects on NLR. Tocilizumab demonstrated the highest mean survival time with 60.813 days, compared to linezolid (49.359 days) and ostilomavir (40.635 days). However, patients not getting linezolid or ostilomavir had longer mean survival times, suggesting potential limitations in their efficacy. Tocilizumab also showed a weak positive correlation with NC (r = 0.086, p = 0.001), further supporting its role in modulating inflammation and improving the immune system.ConclusionAmong the evaluated therapies, tocilizumab and oseltamivir showed a consistent trend of lower NLR values in both survivors and non-survivors, compared to those not receiving these treatments. These findings suggest that tocilizumab and oseltamivir may offer some efficacy in modulating immune response (as measured by NLR) and potentially improving outcomes. However, due to observed weak correlations no single therapy alone appears sufficient to predict or reduce mortality, emphasizing the need for multimodal treatment strategies and further investigation into combined biomarker models. creator: Abbas Al Mutair creator: Muhammad Daniyal creator: Sameer A. Alkubati creator: Hamdan Albaqawi creator: Awatif M. Alrasheeday creator: Bushra Alshammari creator: Kawthar Alsaleh creator: Richard Mottershead creator: Hanan Alyami creator: Hanan F. Alharbi creator: Awad Al-Omari uri: https://doi.org/10.7717/peerj.20003 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mutair et al. title: Screening of MYB1R1 interaction with LDOX promoter to regulate anthocyanin biosynthesis in peaches link: https://peerj.com/articles/19975 last-modified: 2025-09-04 description: BackgroundThe floral color variegation of cultivar ‘Sahong Tao’ is distinctive and possesses significant ornamental value. Currently, there are no relevant reports on how MYB transcription factors (TFs) interact with LDOX promoter to regulate the flower color variegation in peach.MethodsIn this study, we screened for proteins that interact with the LDOX promoter using yeast one-hybrid (Y1H) and next-generation sequencing (NGS). The NGS data were aligned with the Arabidopsis database (TAIR10) utilizing Python 3.10.4. PlantTFDB was employed to identify TFs, while PlantRegMap was used to predict TFs that interact with the LDOX promoter. The Y1H assay verified MYB1R1 interaction with LDOX promoter, and Y1H-AOS predicted their binding sites. The physicochemical properties, structure and interacting proteins of MYB1R1 were analyzed using bioinformatics methods. Sequence alignment and phylogenetic tree analyses of MYB1R1 were performed. Finally, the tissue expression specificity of MYB1R1 and LDOX in ‘Sahong Tao’ was examined using qRT-PCR.ResultsThe Y1H and NGS results indicate that 1,190 proteins interact with the LDOX promoter. Among these, 20 TFs were identified, including ERF, MYB, NF-YB, SBP, S1Fa-like, TCP, bHLH, LBD, ZF-HD, C3H, DBB, MYB-related, and HD-ZIP. Of the 1,190 proteins, 1,146 exhibit high similarity to homologs in Arabidopsis, with 332 classified as RNA binding proteins and 124 as DNA binding proteins. A comparison with the NGS results identified seven TFs that align with predictions from PlantRegMap. Based on these findings, we selected MYB44 (PRUPE_6G229000, PRUPE_1G430000) and MYB1R1 (PRUPE_5G182000) as candidate members. Y1H assays demonstrated that MYB1R1 interacts with the LDOX promoter. Y1H-AOS was used to confirm 24 interaction binding sites. MYB1R1 consists of an 897 bp full-length CDS, encoding 298 amino acids, with a predicted molecular weight of 32.49 kDa and a theoretical isoelectric point of 7.20. MYB1R1 features a typical SANT-MYB domain, and its secondary structure is predominantly composed of irregular coils. Phylogenetic analysis indicates a close evolutionary relationship between MYB1R1 from ‘Sahong Tao’ and both Prunus avium and Prunus speciosa. Promoter prediction analysis for MYB1R1 reveals multiple hormone- and stress-related cis-acting elements. MYB1R1 may interact with bHLH and other proteins to perform its functions. In variegated petals, MYB1R1 expression is higher and LDOX expression is lower compared to red petals, suggesting that MYB1R1 negatively regulates anthocyanin synthesis by interacting with LDOX. This study contributes to elucidating the function of MYB1R1 and the regulatory mechanism of MYB- LDOX in the flower color of ‘Sahong Tao’. creator: Xinxin Wu creator: Tong Du creator: Yan Li creator: Weibing Zhuang creator: Naixin Kang creator: Jiaxin Zeng creator: Cong Yan creator: Zhenzhu Hu creator: Zewen Cao uri: https://doi.org/10.7717/peerj.19975 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: High prevalence and risk factors of undernutrition in adult cancer patients at Hawassa University Hospital: a call for targeted interventions link: https://peerj.com/articles/19925 last-modified: 2025-09-04 description: BackgroundCancer, a condition marked by the uncontrolled growth of abnormal cells, remains a major global health concern and is the second most common cause of death worldwide. Both the disease itself and its treatments can negatively impact taste, smell, appetite, and nutrient absorption, increasing the risk of malnutrition. This study aimed to determine the prevalence and factors associated with undernutrition among adult cancer patients, with the goal of identifying key characteristics that could inform targeted interventions to address nutritional challenges in this population.MethodA cross-sectional study involving 393 participants was conducted at a hospital using a convenient sampling method. Data collection took place over a two-month period from April to June 2023 through face-to-face interviews, utilizing a structured questionnaire. Quantitative data were gathered using both the questionnaire and the Patient-Generated Subjective Global Assessment short form (PG-SGA-SF). Data were analyzed with SPSS version 20, applying both bivariate and multivariate logistic regression analyses to identify associated factors. Variables with a p-value less than 0.05 were considered statistically significant predictors.ResultsBased on the PG-SGA-SF score, 58% of cancer patients were found to be malnourished. According to BMI measurements, 21% of participants were classified as underweight, while over 41% reported low dietary diversity, and nearly 78% were in advanced stages (III and IV) of cancer. Undernutrition showed significant associations (p < 0.01) with BMI below 18.5 kg/m2 (AOR = 2.81, 95% CI [1.29–6.08]), poor dietary diversity (AOR = 4.54, 95% CI [2.41–8.53]), consumption of semisolid and liquid diets (AOR = 4.41, 95% CI [2.41–8.10]), presence of nausea (AOR = 10.71, 95% CI [5.48–20.94]), and constipation (AOR = 6.42, 95% CI [2.95–13.97]).ConclusionThe findings of this study reveal a considerable burden of undernutrition among adult cancer patients, emphasizing the critical need for routine nutritional screening as part of cancer care. Early identification of malnutrition is essential to effectively manage associated symptoms, prevent nutrition-related complications, and improve treatment outcomes. Integrating comprehensive nutritional assessment and support into oncology services is recommended to enhance the quality of care and overall prognosis for cancer patients. creator: Simret Girma Worku creator: Zelalem Tafese Wondimagegne uri: https://doi.org/10.7717/peerj.19925 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Worku et al. title: Epibiotic Vibrio bacteria from crustaceans and macroalgae in a subantarctic ecosystem, and their future thermal suitability link: https://peerj.com/articles/19881 last-modified: 2025-09-04 description: Marine organisms harbor diverse microbial communities on their surface, yet studies exploring the epibiotic bacteria of marine hosts remain largely unexplored, particularly in subantarctic ecosystems. Here, we cultured and isolated bacteria from the surface of three marine hosts: the centolla (the southern king crab; Lithodes santolla), a squat lobster (Grimothea gregaria), and a brown macroalgae (Macrocystis pyrifera), from a subantarctic ecosystem, the Magellan Strait. Bacteria were inoculated in Petri dishes with Thiosulfate-Citrate-Bile Salts-Sucrose (TCBS) agar medium, and a fragment of the grown colonies was used to extract their DNA and sequence the whole 16S rRNA gene. We detected 14 different bacterial taxa, 11 from crustaceans, most of which were found only in the squat lobster. Vibrio spp. was detected in all marine hosts, but V. tasmaniensis was only detected in crustaceans. Phylogenetic comparisons revealed that epibiotic Vibrio formed a clade related to environmental Vibrio species, such as V. tasmaniensis, V. echinoidereum, and V. atlanticus. Given the ongoing climate change the world is experiencing, we explore the future sea surface temperatures that these bacteria might experience in the Magellan Strait. Oceanographic predictions indicate that the maximum sea surface temperatures will be 1 °C warmer in the future decades, and they could reach values above 14 °C in the last decades of the century. Our results increase the distribution and ecology of Vibrio bacteria and give insights about the temperatures that these microbes will face in future decades, which could have relevant consequences for aquaculture activities. creator: Manuel Ochoa-Sánchez creator: Rosalinda Tapia-López creator: Ulises E. Rodriguez-Cruz creator: Eliana Paola Acuña Gomez creator: Luis E. Eguiarte creator: Valeria Souza uri: https://doi.org/10.7717/peerj.19881 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ochoa-Sánchez et al. title: Easy-to-use nomogram to predict neonatal hyperbilirubinemia link: https://peerj.com/articles/20017 last-modified: 2025-09-03 description: BackgroundNeonatal hyperbilirubinemia is a common condition and a leading cause of hospitalization in newborns in their first week of life. Thus early identification of infants at risk is particularly important. In this study, we explored risk factors for its development of neonatal hyperbilirubinemia, and then constructed and validated an easy-to-use nomogram for the early prediction.MethodsThis study was conducted retrospectively and non-interventionally, involving 646 neonates born at the Second Hospital of Dalian Medical University between January 2021 and January 2024. The study population was systematically partitioned through cluster sampling into a training set comprising of 454 neonates and a validation set of 192 neonates, adhering to a 7:3 ratio, utilizing the R-4.4.0 program. Independent predictors of neonatal hyperbilirubinemia were identified using least absolute shrinkage and selection operator (LASSO) regression from the training set, and a nomogram was constructed based on these predictors. The performance of the nomogram was assessed using receiver operating characteristic (ROC) curves, calibration curves and decision curve analysis (DCA).ResultsAmong 646 newborns, there were 350 males and 296 females, with a mean gestational age (GA) of 38.4 ± 1.4 weeks and birth weight (BW) of 3,264.1 ± 490.7 g. Six independent factors associated with hyperbilirubinemia were identified: GA, BW, premature rupture of membranes (PROM) ≥ 18 hours or concurrent maternal fever, maternal-infant blood type incompatibility with positive direct Coombs test, supplementation with probiotics, and weight loss > 9% within 3 days. Calibration curves indicated that the nomogram closely matched the actual observed values in both the training and validation sets. The areas under the ROC curves for predicting hyperbilirubinemia were 0.825 (95% confidence interval (CI) [0.777–0.874]) in the training set and 0.829 (95% CI [0.757–0.901]) in the validation set. DCA showed that the nomogram has clinical applicability.ConclusionThe nomogram constructed in this study has good differentiation, calibration and clinical applicability, and has the potential to be used for predicting neonatal hyperbilirubinemia. creator: Shanshan Wang creator: Chan Wang creator: Siqi Zheng creator: Haiping Dou creator: Danyang Qu creator: Yuqian Wang creator: Liu Yang uri: https://doi.org/10.7717/peerj.20017 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Genome-wide identification of SHMT family genes in C3, C3-C4, and C4 Salsoleae s.l. species link: https://peerj.com/articles/19978 last-modified: 2025-09-03 description: C4 photosynthesis is a carbon-concentrating mechanism that evolved to enhance photosynthetic efficiency under conditions favoring photorespiration, such as high temperature, low atmospheric CO2, and aridity. Photorespiration is considered the primary driving force on the evolution of C4 photosynthesis. Serine hydroxymethyltransferase (SHMT) plays a crucial role in one-carbon metabolism and photorespiration. However, there is a lack of comprehensive bioinformatics investigation on the SHMT gene family across different photosynthetic types, specifically comparing C3, C4, and C3-C4 intermediate species. In this study, we conducted a systematic analysis of the SHMT gene family regarding gene structure, phylogenetic relationships, expression patterns, and cis-acting element in four Salsoleae species, including C3 species Salsola junatovii, C3-C4 intermediate species Oreosalsola laricifolia, and two C4 species Xylosalsola arbuscula and Soda foliosa. The results indicated that 4–5 SHMT members were identified in these four species. No fragment duplication were identified, which may explain the lower number of SHMT members in each Salsoleae species. The range of exon numbers varied from 4 to 15. Phylogenetic analysis showed that the SHMTs from Salsoleae species can be classified into four distinct classes, with most members displaying conserved gene structure and motif numbers, except for OlSHMT3 and XaSHMT3, which had divergent gene structures. The SHMTs in Salsoleae species did not exhibit organ-specific expression patterns; however, variations in expression were observed among the different members. Analysis of newly sequenced Salsoleae transcriptomes data and published data from five other genera (Flaveria, Heliotropium, Mollugo, Alternanthera, and Neurachne) revealed that, compared to C3 and C3-C4 intermediate species, only mitochondrial-localized, leaf preferential SHMT1 showed a low expression among SHMT members, probably evolved in C4 photosynthesis evolution. The MYB transcription factors were predicted to be the most significant regulators of SHMT1 in three Salsoleae species and the second most significant in X. arbuscula. These results may provide valuable information for further analyses, particularly in the evolutionary study of Salsoleae SHMT1. creator: Peng Peng creator: Qian Qin creator: Guzailinuer Kuerban creator: Ting Peng creator: Mao Wang creator: Zhibin Wen uri: https://doi.org/10.7717/peerj.19978 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Peng et al. title: surveyjoin: a standardized database of scientific trawl surveys in the Northeast Pacific Ocean link: https://peerj.com/articles/19964 last-modified: 2025-09-03 description: Fisheries management faces challenges due to political, spatial, and ecological complexities, which are further exacerbated by variation or shifts in species distributions. Effective management depends on the ability to integrate fisheries data across political and geographic boundaries. However, such efforts may be hindered by inconsistent data formats, limited data sharing, methodological differences in sampling, and regional governance differences. To address these issues, we introduce the surveyjoin R package, which combines and provides public access to bottom trawl survey data collected in the Northeast Pacific Ocean by NOAA Fisheries and Fisheries and Oceans Canada. This initial database integrates over 3.3 million observations from 14 bottom trawl surveys spanning Alaska, British Columbia, Washington, Oregon, and California from the 1980s to present. This database standardizes variables such as catch-per-unit-effort (CPUE), haul data, and in-situ measurements of bottom temperature. We demonstrate the utility of this database through three case studies. Our first case study develops a coastwide biomass index for Pacific hake (Merluccius productus) using geostatistical index standardization, comparing results to independent acoustic survey estimates. The second case study examines spatial patterns in groundfish community structure, highlighting breakpoints between assemblages in their mixture of life histories and trophic compositions. Our third example applies spatially varying coefficient models to assess sablefish (Anoplopoma fimbria) biomass trends, identifying regional variability in increases in occurrence and biomass. Together, these case studies demonstrate how the surveyjoin R package and database may improve species and ecosystem assessments by providing insights into population trends across geopolitical boundaries. This database and package represent an important step toward offering a scalable framework that can be extended to include additional data types, surveys, and species. By fostering collaboration, transparency, and data-driven decision making, surveyjoin supports international efforts to sustainably manage shared marine resources under dynamic environmental conditions. creator: Eric J. Ward creator: Philina A. English creator: Christopher N. Rooper creator: Bridget E. Ferriss creator: Curt E. Whitmire creator: Chantel R. Wetzel creator: Lewis A. K. Barnett creator: Sean C. Anderson creator: James T. Thorson creator: Kelli F. Johnson creator: Julia Indivero creator: Emily H. Markowitz uri: https://doi.org/10.7717/peerj.19964 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: BMP2 alterations in mucinous cystadenocarcinoma of the breast: insights from whole-exome sequencing link: https://peerj.com/articles/19948 last-modified: 2025-09-03 description: BackgroundMucinous cystadenocarcinoma (MCA) of the breast is a rare and distinct type of mammary tract adenocarcinoma. Molecular alterations in breast MCA remain poorly characterized in current epidemiological data.MethodsWe summarized the clinicopathological characteristics and performed exome sequencing on formalin-fixed, paraffin-embedded blocks from three patients with mammary MCA culled from the surgical pathology archives of Chongqing University Cancer Hospital. The tumor mutation landscape of these patients was determined using whole-exome sequencing. We assessed cancer effect sizes and analyzed the contribution of mutational processes to each oncogenic variant, quantifying the extent to which each process contributed to tumorigenesis/cancer effects.ResultsOur analysis revealed that one of the three patient cohorts with advanced-stage breast MCA demonstrated aggressive clinical behavior, which contrasts with the typically reported indolent course of this rare malignancy. We also identified a significant mutant gene, bone morphogenetic protein 2 (BMP2), that is associated with breast MCA. Furthermore, we evaluated the expression by immunohistochemistry in patients with breast MCA and predicted the potential molecular functions of BMP2 in breast cancer through in silico analyses.ConclusionThis study provides new insights into the clinical and molecular features of breast MCA, suggesting that tumor stage is an important prognostic indicator. BMP2 emerged as a potential driver of tumor progression, and its utility as a predictive or prognostic biomarker warrants further investigation in larger cohorts. These findings may pave the way for improved prognostic assessment and novel therapeutic strategies targeting BMP2 in breast MCA. creator: Zhenyu Li creator: Yi Gong creator: Guangxin Li creator: Qingming Jiang creator: Juanhui Dong creator: Rui Chen uri: https://doi.org/10.7717/peerj.19948 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Insight into the PmrB structures of colistin-resistant Gram-negative bacteria through the multi-template ligand-guided homology modeling and in silico mutagenesis link: https://peerj.com/articles/19945 last-modified: 2025-09-03 description: The increasing prevalence of colistin-resistant Gram-negative bacteria necessitates the development of novel therapeutic strategies. PmrB, a histidine kinase involved in colistin resistance, represents a promising drug target. However, the absence of experimentally resolved PmrB structures limits structure-based drug design efforts. This study employed a multi-template, ligand-guided homology modeling approach to construct full-length PmrB models for four pathogens: Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The resulting models demonstrated high structural integrity, with over 95% of residues located in favored regions and QMEANDisCo global scores ranging from 0.55 to 0.57. Molecular docking simulations guided the selection of representative ligand-bound states for adenosine triphosphate (ATP)-binding site prediction and yielded superior docking scores compared to models generated by AlphaFold, I-TASSER, and SWISS-MODEL. Molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) analysis confirmed the stability and binding affinity of the PmrB–ATP complexes, with ΔG values ranging from −27.72 to −47.71 kcal/mol. In silico mutagenesis revealed that the T246A and L344P mutations in K. pneumoniae enhanced ATP binding affinity and protein stability, potentially contributing to colistin resistance. Analysis of the PmrB–ATP complexes identified both conserved and species-specific interactions. This research provides valuable structural models and mechanistic insights into PmrB, supporting future structure-based drug design and the development of novel interventions against colistin-resistant infections. creator: Nuttapat Anuwongcharoen creator: Chuleeporn Phanus-umporn creator: Chawalit Chatupheeraphat creator: Kamonlak Weakwiweak creator: Noramon Kaewsai creator: Warawan Eiamphungporn uri: https://doi.org/10.7717/peerj.19945 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Anuwongcharoen et al. title: An assessment of CO2 and CH4 emissions in a tropical river: from the Kenyir Reservoir to the estuary link: https://peerj.com/articles/19929 last-modified: 2025-09-03 description: This study investigates the spatial and seasonal variations in CO2 and CH4 emissions from the Kenyir hydropower reservoir and its downstream Terengganu River system in Malaysia. Understanding these variations is crucial for assessing whether the greenhouse gas (GHG) budget for this aquatic continuum significantly contributes to global emissions. Malaysia’s distinct monsoonal climate presents a unique opportunity to explore the influence of seasonal hydrological changes on GHG emission dynamics in inland waters. Five sampling campaigns were performed at the reservoir to investigate this, involving three longitudinal surveys from the reservoir downstream along the Terengganu River, and two time-series samplings at the estuary between November 2017 and August 2019. Our findings reveal that GHG emissions from the Kenyir Reservoir are notably higher during the wet season (97 mmol CO2 m−2 d−1 and 2 mmol CH4 m−2 d−1) than during the dry season (54 mmol CO2 m−2 d−1 and 0.8 mmol CH4 m−2 d−1). This increase coincides with increased wind speed and potential surface mixing during the wet season. Despite operating since 1985, the Kenyir Reservoir’s total GHG emissions remain high compared to other global reservoirs, likely due to its tropical location and high organic carbon content. Elevated GHG emissions were recorded along the Terengganu River, near the dam discharge outlets, with gradual reductions observed downstream. Despite the estuary’s smaller surface area, more GHGs are emitted there than in the river. Overall, the Terengganu River catchment emits approximately 572 Gg CO2-equivalent annually, with the Kenyir Reservoir accounting for the majority (94%). The river and the estuary contribute 0.5% and 5.5%, respectively. This study highlights the substantial role of tropical hydropower reservoirs and their downstream river networks in the global GHG budget, emphasizing the need for further investigation into the factors influencing GHG dynamics in tropical river systems. creator: Daryl Jia Jun Lee creator: Siti Farhain Mohd Ludin creator: Wei Wen Wong creator: Liyang Zhan creator: Seng Chee Poh uri: https://doi.org/10.7717/peerj.19929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lee et al. title: Processing characteristics of visuospatial working memory in map cognition by orienteering athletes: evidence from behavioral and EEG studies link: https://peerj.com/articles/19817 last-modified: 2025-09-03 description: Through maps, the objects on the Earth’s surface are abstracted and represented on a plane, achieving the integration of physical entities and conceptual representations, thereby facilitating individuals’ rapid understanding and profound cognition of their surroundings. As a system for the storing and processing of visual and spatial information, visuospatial working memory (VSWM) provides individuals with the capacity to temporarily store and process map-related information within a spatial framework. To explore the temporal features of storing and retrieving in VSWM during map-related tasks among orienteers with varying skill levels, 22 orienteers were enrolled in the expert group, while 22 members from orienteering training teams were placed in the novice group. Employing electroencephalography (EEG) technology, this study developed a set of VSWM tasks to examine behavioral performance variations and EEG characteristics between experts and novices. The results revealed that experts exhibited enhanced rationality and superior response efficiency during the map cognition task relative to novices. Neurophysiological evidence further indicated distinct neural resource management patterns in experts, characterized by reduced θ neural oscillations in the frontal regions coupled with enhanced α oscillations in both the frontal and temporal lobes. The empirical outcomes confirm competitive advantages in expert athletes’ map processing, response speed, and optimized neural resource allocation. These findings not only deepen insights into the neural mechanisms underlying orienteers’ map cognition, but also provide strong theoretical support for orienteering training practices. creator: Deyu Zhu creator: Limin Guo creator: Yang Liu uri: https://doi.org/10.7717/peerj.19817 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhu et al. title: Soil copper sources and biogeochemical processes under different land uses: insights from stable copper isotopes in the Cambisols of Southwest China link: https://peerj.com/articles/19982 last-modified: 2025-09-02 description: Copper (Cu), a toxic trace element, has extensively accumulated in soils due to intensive human activities. Yet current knowledge on Cu sources and biogeochemical processes in Cambisols under varying land uses is scant. In this study, Cu contents, stable isotope compositions (δ65Cu) and their correlations with soil physicochemical properties in soil profiles across different land uses were analyzed, including cropland, abandoned cropland and orchard, shrub-grass land, and secondary forest in a karst watershed of Southwest China. Soil Cu contents in cropland (mean 44.9 mg kg −1) were significantly higher than those in abandoned cropland and orchard (mean 37.7 mg kg −1), and much higher than those in natural lands (mean 26.3 mg kg −1). In agricultural lands, cropland soils (mean –0.216‰) were significantly 65Cu-depleted compared to abandoned cropland and orchard (0.020‰), resulting from applying 65Cu-depleted fungicides. Soil δ65Cu values in shrub-grass land and secondary forest land exhibited within a wide range, from –0.627‰ to 0.338‰, attributed to Cu isotope fractionations during pedogenic processes. Soil δ65Cu values decreased with increasing soil depth and were positively correlated with soil organic carbon (SOC) contents, but negatively correlated with the chemical index of alteration (CIA), indicating the influences of clay mineral sorption, organic complexation, and leaching processes on soil δ65Cu patterns. In different regions, δ65Cu values in Cambisols increased in sub-humid climate, but decreased in humid climate with increasing annual precipitation. This study underscores the key roles of mineral sorption, organic complexation, and leaching processes in affecting δ65Cu patterns in Cambisols. creator: Man Liu creator: Guilin Han creator: Qian Zhang uri: https://doi.org/10.7717/peerj.19982 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Pregnancy-associated plasma protein A in maternal serum for predicting early gestational diabetes mellitus: a systematic review and meta-analysis link: https://peerj.com/articles/19825 last-modified: 2025-09-02 description: ObjectiveThis study assessed the effectiveness of pregnancy-associated plasma protein A (PAPP-A) in maternal serum in predicting gestational diabetes mellitus (GDM) in different geographical regions.MethodsPubMed, Web of Science, EMBASE, and Cochrane Library databases were searched for articles assessing the diagnostic utility of PAPP-A for GDM up to December 3, 2024. Two independent researchers screened the literature. Study quality was appraised using the QUADAS-2 instrument and RevMan 5.4 software. Stata 15.1 software was leveraged to calculate the combined sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and heterogeneity. The summary receiver operating characteristic curve was plotted to calculate the area under the curve (AUC). Subgroup analysis was also conducted to determine the source of heterogeneity.ResultsThis study included eight cohort studies, one cross-sectional study, and three case-control studies. A total of 25,183 participants were involved, including 5,993 GDM patients and 19,190 non-GDM patients. Deek’s test suggested no notable publication bias (P = 0.400). All included studies were rated as “low risk” or “unclear”. The combined sensitivity was 0.71 (95% CI 0.60–0.80), specificity was 0.62 (95% CI [0.55–0.68]), positive likelihood ratio was 1.9 (95% CI [1.4–2.5]), negative likelihood ratio was 0.47 (95% CI [0.30–0.72]), and diagnostic odds ratio was 4 (95% CI [2–8]). Subgroup analysis found that sample size might be the source of heterogeneity (p < 0.05). The AUC was 0.70 (95% CI [0.65–0.73]).ConclusionsPAPP-A has a certain diagnostic value for GDM and is helpful for more accurately identifying GDM and reducing the risk of related chronic diseases. Future articles with larger sample sizes and across multiple centers are warranted to explore the combined application of PAPP-A with other biomarkers. This approach may enhance the accuracy of GDM diagnosis. Registry number: PROSPERO (CRD42024617462). creator: Yuge Gao creator: Jihong Chen creator: Jia Mi uri: https://doi.org/10.7717/peerj.19825 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gao et al. title: Estimating density of native carnivores in central Chile landscapes using a simulated movement model, cameratrapR: insights on their potential exotic prey dietary subsidy link: https://peerj.com/articles/19946 last-modified: 2025-09-01 description: BackgroundSpecies-specific density is an essential parameter for evaluating population stability and ecosystem health. We estimate the population density of native carnivores, South American gray and culpeo foxes (Lycalopex spp.), guiña (Leopardus guigna) and Andes skunk (Conepatus chinga), in central Chile, inferring on the potential influence of the availability of introduced exotic prey on their population dynamics.MethodsMonitoring with camera traps was conducted from March 1, 2021, to March 31, 2022, across three distinct landscapes representative of the coastal mountain range of central Chile: Mediterranean coastal thorn forest, Mediterranean coastal sclerophyllous forest, and exotic monoculture tree plantations. We estimated density using an R package, cameratrapR, where animal movement was simulated using a correlated random walk within the camera grids. Simulations were run for a range of numbers of individuals, representing a gradient of population densities. We matched these results and the observed photo records using a machine learning algorithm, random forest, thereby estimating population density and its 95% confidence intervals.ResultsA total of 10,046 trap days resulted in 9,120 photographs of carnivores, with 3,888 independent records. Our findings indicate that Lycalopex spp. are the carnivore species with the highest population density in central Chile (4.1–4.8 individuals/km2). Furthermore, their density was higher in the exotic monoculture tree plantation ecotype compared to native forests, suggesting a dietary subsidy from non-native prey. We report the first population density estimates for Conepatus chinga (1.8–2.2 individuals/km2) and Leopardus guigna (0.7–1.3 individuals/km2) in the three landscapes, showing different habitat preferences and resource availabilities across landscapes. The results highlight the complex interactions between carnivores and their environments, particularly the role of exotic introduced species as prey items in shaping native carnivore populations. These findings also provide insights into carnivore adaptability and the implications for biodiversity conservation. creator: Diego Ramírez-Alvarez creator: Xinhai Li uri: https://doi.org/10.7717/peerj.19946 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ramírez-Alvarez and Li title: Integrative analyses of single-cell and bulk RNA sequencing to construct the tumor-associated macrophage-related prognostic signature in lung adenocarcinoma link: https://peerj.com/articles/19920 last-modified: 2025-09-01 description: BackgroundTumor-associated macrophages (TAMs) are a type of tumor-infiltrating immune cell that play a crucial role in tumor progression. However, the roles of TAMs and their regulatory mechanisms in lung adenocarcinoma (LUAD) remain poorly understood. Therefore, we aimed to develop a novel TAM-related prognostic signature to predict survival outcomes and constructed a lncRNA-miRNA-mRNA network based on these genes.MethodsTranscriptomic data, clinical data, and single-cell RNA-sequencing (scRNA-seq) data were obtained from LUAD patients were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Differentially expressed-lncRNAs (DE-lncRNAs), miRNAs (DE-miRNAs), and mRNAs (DEGs) were identified in LUAD. Differentially expressed TAM-related genes (DE-TAMGs) were selected and used to construct prognostic signatures. A TAM-related risk score was calculated, and patients were stratified into high- and low-risk groups based on the median risk score. Then, biological functions, immune characteristics, and responses to immunotherapy and chemotherapy were assessed across the risk groups. A TAM-related lncRNA-miRNA-mRNA network was constructed based on DE-lncRNAs, DE-miRNAs, and TAM-related signatures. Quantitative polymerase chain reaction (qPCR) was used to validate the expression of TAM-related genes, and scRNA-seq analysis was used to examine cell-type-specific expression of these genes.ResultsA total of 316 DE-lncRNAs, 162 DE-miRNAs, and 2,601 DEGs were screened in LUAD. Among these, 147 DE-TAMGs were selected. KLF4, GAPDH PDGFB, TIMP1, CD74, and CCL20 were identified as the key prognostic markers in LUAD. Patients were divided into high- and low-risk groups based on the median risk score. Enrichment analysis revealed several cancer-related pathways associated with the high-risk group, and significant differences in terms of immune cell infiltration, HLA-related gene expression, immune checkpoints expression, and therapeutic responses were observed between high- and low-risk groups. We also constructed a lncRNA-miRNA-mRNA network, which included 36 DE-lncRNAs, 23 shared miRNA, and four TAMGs (PDGFB, CD74, KLF4, and CCL20). The qPCR results indicated the increased expression of PDGFB, CD74, and KLF4 but decreased expression of CCL20 in LUAD tumor tissues compared with adjacent normal tissues. scRNA-seq analysis revealed that CD74, KLF4, CCL20, PDGFB were specifically expressed in macrophages.ConclusionsIn conclusion, we identify the TAM-related prognostic signature that predicts the survival outcome in patients with LUAD. This signature may offer a novel effective therapeutic strategy for LUAD patients. creator: Chaoqun Yu creator: Jun Chen creator: Jianming Deng creator: Hui Li creator: Qianru Zhuang creator: Bingqing Luo creator: Hua Ye creator: Hui Tian uri: https://doi.org/10.7717/peerj.19920 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Yu et al. title: Management of calcified canals during root canal treatment. A systematic review of case reports link: https://peerj.com/articles/19900 last-modified: 2025-09-01 description: Background and ObjectivesCalcified canals pose substantial challenges in endodontic treatment because of narrowing of pulp chambers and canal lumens, reducing accessibility and biomechanical preparation. Nevertheless, with advanced techniques and well-devised strategies, successful management of calcified canals is achievable. This comprehensive analysis aims to rigorously assess extant literature concerning the clinical management of teeth affected by pulp canal obliteration that necessitates root canal therapy and to formulate a comprehensive, updated algorithm for clinical decision-making strategies.Materials and MethodsThe study adhered to the PRISMA 2020 guidelines, the Cochrane Handbook (version 5.1.0), and Fourth Edition of the JBI Reviewer’s Manual, and was registered with PROSPERO (CRD42023460967). Electronic data sources consulted included Central, Medline, Embase, PsycINFO, Scopus, ERIC, and ScienceDirect, using standardized keywords and open-text phrases. The JBI checklist was used to evaluate the quality of case reports and case series.ResultsThirty-four case reports involving 41 patients were selected. For calcified canals, non-surgical endodontic treatment utilizing chelating agents and flexible rotary instruments has proven highly effective. Furthermore, the employment of a dental operating microscope in conjunction with ultrasonic tips has been reported to improve clinical outcomes in several cases. Also, the use of cone beam computed tomography (CBCT) along with 3D print guides considerably increased success rates in managing these cases.ConclusionsThis review highlights techniques like ultrasonic instruments, flexible nickel-titanium (Ni-Ti) files, and newer methods such as advanced imaging (CBCT) and 3D printed guides. Many case reports show that these approaches lead to higher success rates. Dentists should get familiar with these methods to improve patient outcomes and monitor for any complications. Future research should focus on creating standard protocols and exploring new tools and imaging to advance endodontics. creator: Kunal Giri creator: Kulvinder Banga creator: Suraj Arora creator: Firas Elmsmari creator: Ajinkya M. Pawar uri: https://doi.org/10.7717/peerj.19900 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Giri et al. title: Brain virtual histology and volume measurement of a lizard species (Podarcis bocagei) using X-ray micro-tomography and deep-learning segmentation link: https://peerj.com/articles/19672 last-modified: 2025-09-01 description: There is an increasing emphasis on understanding individual variation in brain structure—such as overall brain size and the size of specific regions—and linking this variation to behaviour, cognition, and the driving social and environmental factors. However, logistical challenges arise when studying the brain, especially in research involving wild animals, such as dealing with small sample sizes and time-consuming methods. In this study, we used wild lizards, Podarcis bocagei, as our model. We developed an efficient and accurate method that combines X-ray micro-tomography and deep-learning segmentation to estimate the volume of six main brain areas: the olfactory bulbs, telencephalon, diencephalon, midbrain, cerebellum, and brain stem. Through quantitative comparisons, we show that a sufficiently trained deep-learning neural network can be developed with as few as five samples. Using this trained model, we obtained volume data for the six brain regions from 29 brain samples of Podarcis bocagei. This approach drastically reduced the time needed for manual segmentation from several months to just a few weeks. We present a comprehensive protocol detailing our methods, which includes sample preparation, X-ray tomography, and 3D volumetric segmentation. This work collectively provides valuable resources that can assist researchers not only in animal behaviour and physiology, but also in biomedical research and computer sciences. creator: Tunhe Zhou creator: Yulia Dragunova creator: Zegni Triki uri: https://doi.org/10.7717/peerj.19672 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhou et al. title: Effects of bilateral low-load resistance training with blood-flow restriction on post-activation performance enhancement in male collegiate athletes link: https://peerj.com/articles/19272 last-modified: 2025-09-01 description: BackgroundWhile the effects of blood-flow restriction (BFR) training on various performance outcomes have been widely studied, the combination of BFR with low-load (LL) resistance training for post-activation performance enhancement (PAPE), particularly in vertical jump performance, has not been fully explored. This study aimed to investigate whether combining BFR with LL resistance training can enhance vertical jump performance in male collegiate athletes.MethodsFifteen male strength trainers (mean ± standard deviation (SD): age 21.7 ± 1.4 years, body mass 77.2 ± 6.3 kg, and height 179.1 ± 5.7) with at least two years of resistance training experience participated in three experimental trials using a randomized crossover design with 72-hour intervals: (a) low-load resistance exercise at 30% one repetition maximum (1RM) back squat combined with BFR for four sets of 15 repetitions (BFR+LL); (b) low-load resistance exercise without BFR for 4 sets of 15 repetitions (LL); and (c) a control condition involving passive rest (CON). Countermovement jump (CMJ) performance , including vertical jump height (VJH), relative peak power output (RPP), force impulse (FI), and rate of force development (RFD), was assessed at baseline, immediately after, and at 3-, 6-, 9-, and 12-minutes post-protocol. Both peak and mean CMJ were measured to evaluate performance changes.ResultsThe repeated measures analysis of variance (ANOVA) revealed significant condition × time interactions (p < 0.001) for VJH, RPP, and FI. Post-hoc comparisons demonstrated that BFR+LL resulted in significant improvements in VJH, RPP, and FI at 12 minutes post-protocol relative to both the CON and LL conditions (p < 0.05). Specifically, VJH increased by 7.17% (effect size (ES) = 0.79), RPP by 2.26% (ES = 0.31), and FI by 3.21% (ES = 0.29) compared to CON at 12 minutes following the BFR+LL protocol. In contrast, a significant decline in performance (p < 0.05) was observed immediately after BFR+LL, with VJH decreasing by −9.1 ± 5.1% (ES = −1.12), RPP by −8.3 ± 4.3% (ES = −1.16), and FI by −5.0 ± 2.2% (ES = −0.44) compared to baseline. No significant changes in RFD or peak CMJ performance were observed across the three conditions (p > 0.05).ConclusionThe study suggests that BFR+LL resistance training may enhance acute vertical jump performance 12 minutes post-exercise, despite an initial decline in performance immediately following the protocol. creator: Zhanfei Zheng creator: Zhipeng Wang creator: Changyuan Duan creator: Yu Zhang creator: Xiaowei Wang creator: Xixi Miao creator: Haiping Liu uri: https://doi.org/10.7717/peerj.19272 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zheng et al.