title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-07 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Optimizing carbon nanoparticle staining for sentinel lymph nodes in rabbit lower limb models: concentration and time dependence link: https://peerj.com/articles/19799 last-modified: 2025-07-31 description: Background and ObjectivesCarbon nanoparticles (CNPs) have been used as a lymphatic imaging agent that can selectively enter lymphatic vessels. This experiment used CNPs for lower limb lymph node staining in rabbits, aiming to explore the suitable concentration and time of CNPs for sentinel lymph node (SLN) sufficient staining, and the biosafety of CNPs retention was preliminarily explored.MethodsStaining effect of SLN using different concentrations of CNP injection on the rabbit lower limb lymphatic model. To explore the temporal correlation of CNPs staining. We investigated the effects of long-term retention of CNPs in lymph nodes on lymph node tissue structure and mRNA expression of inflammatory factors (IL-6/TNF-α), apoptosis factors (Bcl-2/Bax), and fibrosis factors (Collagen-I/α-SMA).ResultsThe lowest concentration to achieve adequate lymph node staining is 0.0781 mg/0.8 mL, while the best staining results were observed at least 12 hours post-injection. Long-term CNPs retention has no significant negative impact on the structure and function of lymph nodes.ConclusionsCNPs are an effective and safe lymphatic tracer. It is a concentration-dependent and time-dependent lymphatic staining agent. 0.0781 mg/0.8 mL and 12 hours are suitable for the rabbit lower limb lymphatic staining model, which provides valuable data for further research on the application of CNPs in rabbit animal models. In addition, the results provide evidence for future clinical development of concentration and time standards for CNPs’ use. creator: Narbol Kylyshbek creator: Heng Wang creator: Shuning Feng creator: Yuxin Zhang creator: Dong Dong creator: Wangjaleoseop Han creator: Ayidana Ayoujiang creator: Liang Chen creator: Tianyi Liu uri: https://doi.org/10.7717/peerj.19799 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Kylyshbek et al. title: Relationships between different components of intolerance of uncertainty and symptoms of obsessive–compulsive disorder: a network analysis link: https://peerj.com/articles/19791 last-modified: 2025-07-31 description: BackgroundPrevious studies have shown that intolerance of uncertainty (IU) and obsessive–compulsive disorder (OCD) are closely interrelated. This reliance on scale totals to measure symptom severity obscures the distinctions and connections between different symptoms. In the present study, we explored the relationships between different components of IU and symptoms of OCD.MethodsWe recruited 1,616 participants and retained 1,529 pieces of valid data. Components of IU were measured by the Chinese version of the Intolerance of Uncertainty Scale-Short Form, and symptoms of OCD were measured by the Chinese version of the Obsessive-Compulsive Inventory-Revised. The present study employs network analysis to examine both core and bridging symptoms within the context of the IU and OCD networks.ResultsIn the overall network, the nodes with the highest expected influence (EI) were OCD3 (“I get upset if things don’t work out”), IU6 (“I can’t stand being taken by surprise”), and OCD6 (“It’s hard for me to control my thoughts”). The nodes with the highest bridge expected influence (BEI) were OCD3 (“I get upset if things don’t work out”), OCD9 (“I get upset when people change my plans”), and IU12 (“I must get away from all uncertain situations”). Within the IU community, the strongest edge was between IU1 (“Unforeseen events upset me greatly”) and IU2 (“It frustrates me not having all the information I need”). Within the OCD community, the strongest edge was between OCD10 (“I force myself to repeat certain numbers”) and OCD11 (“Sometimes, I force myself to bathe or wash myself because I feel dirty”). The strongest edge connecting the IU and OCD communities was between IU10 (“When I am uncertain I can’t function very well”) and OCD6 (“It’s hard for me to control my thoughts”). No significant gender differences were found in the network structure.ConclusionsThis study revealed specific component–symptom patterns between different facets of intolerance of uncertainty (IU) and various obsessive-compulsive symptoms. Understanding how distinct components of IU—an assumed risk factor—relate to specific OCD symptoms may inform targeted prevention and intervention strategies. For example, interventions aimed at OCD3, IU6, OCD9, and IU12 may effectively reduce the severity of obsessive-compulsive symptoms among Chinese university students, enhance their ability to cope with uncertainty, and help disrupt the reciprocal influence between IU components and OCD symptoms. creator: XiaoBin Ding creator: Ze Zhao creator: Jie Wang creator: Chen Chen creator: ShuChan Ding creator: JingYi Gao creator: Jun Deng creator: Dan Liu uri: https://doi.org/10.7717/peerj.19791 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ding et al. title: Influence of 4-week lower extremity high-intensity interval training on energy metabolism and maximal oxygen uptake of elite swimmers link: https://peerj.com/articles/19788 last-modified: 2025-07-31 description: ObjectivesThis study examines the effects of a 4-week high-intensity interval training (HIIT) program on energy metabolism and maximal oxygen uptake (VO2max) in elite swimmers, aiming to provide empirical evidence for optimizing competitive swimming training.MethodsTwenty-four competitive swimmers were randomly assigned to either an HIIT experimental group or a control group. The experimental group underwent a structured 4-week lower-limb HIIT program, while the control group continued their regular training regimen. Energy metabolism parameters and VO2max were assessed using a Lode lower-limb power cycle and a gas metabolism analyzer. Repeated measures analysis was used to examine interaction effects, with data analysis conducted at a significance level of P < 0.05.ResultsThe HIIT group exhibited significant improvements in all energy metabolism parameters and VO2max. Phosphagen energy supply increased from 40.39 ± 9.46 kJ to 58.27 ± 9.12 kJ (P < 0.001), glycolytic energy supply increased from 41.81 ± 9.81 kJ to 59.06 ± 10.86 kJ (P < 0.001), and aerobic energy supply increased from 132.29 ± 25.12 kJ to 173.32 ± 29.50 kJ (P < 0.001). Consequently, total energy supply rose from 214.48 ± 38.58 kJ to 290.65 ± 42.01 kJ (P < 0.001). Additionally, VO2max significantly improved from 51.48 ± 3.85 ml/min/kg to 55.03 ± 4.90 ml/min/kg (P = 0.041), whereas no significant changes were observed in the control group.ConclusionThe findings confirm that a 4-week lower-limb HIIT program significantly enhances energy metabolism and VO2max in elite swimmers. These results underscore the efficacy of HIIT in improving metabolic adaptability, thereby supporting its application as a key training strategy for optimizing competitive swimming performance. creator: Rangxi Jin creator: Junhui Sun creator: Na Jiang creator: Chao Chen uri: https://doi.org/10.7717/peerj.19788 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jin et al. title: The association between the extracellular water-to-total body water ratio and albuminuria in Chinese type 2 diabetes mellitus patients link: https://peerj.com/articles/19780 last-modified: 2025-07-31 description: BackgroundDiabetic kidney disease (DKD) is a common complication in patients with type 2 diabetes (T2DM), and early screening and diagnosis are crucial for preventing end-stage renal disease (ESRD). The extracellular water/total body water (ECW/TBW), as measured by bioelectrical impedance analysis (BIA), may be closely associated with the development of DKD. This study aimed to evaluate the relationship between ECW/TBW and albuminuria in T2DM patients and to explore its potential as an early diagnostic tool.Materials and methodsThis study included 1,034 T2DM patients. Demographic information, medical history, medication use, and laboratory test results were collected, including glycated hemoglobin (HbA1c), creatinine, lipid profile, and the urine albumin-creatinine ratio (UACR). BIA was used to measure parameters such as ECW/TBW. Multivariate logistic regression analysis explored the correlation between ECW/TBW and UACR. Ultimately, two simple nomograms were established to predict macroalbuminuria from patients with normoalbuminuria and microalbuminuria, respectively.ResultsThe ECW/TBW increased significantly with rising UACR levels. Multivariate logistic regression analysis showed that ECW/TBW was significantly associated with macroalbuminuria compared to both normo-albuminuria and microalbuminuria (OR = 2.082, 95% CI [1.476–2.937], P < 0.001; and OR = 1.642, 95% CI [1.129–2.386], P = 0.009, respectively). In the analysis stratified by renal function, a similar relationship was found only in patients with eGFR ≥ 60 mL/min/1.73 m2 (OR = 2.108, 95% CI [1.479–3.004], P < 0.001) but not in patients with eGFR < 60 mL/min/1.73 m2. Finally, two nomograms for predicting macroalbuminuria were established. The C-index of the nomogram model for predicting the macroalbuminuria in patients with normoalbuminuria was 0.795 (95% CI [0.752–0.838]), and the C-index of the nomogram model for predicting the macroalbuminuria in patients with microalbuminuria was 0.761 (95% CI [0.711–0.812]).ConclusionsThis study demonstrated a significant correlation between the ECW/TBW and UACR levels in Chinese T2DM patients. In patients with normal or mildly impaired renal function (eGFR ≥ 60 mL/min/1.73 m2), ECW/TBW was significantly associated with macroalbuminuria, potentially serving as a diagnostic marker for macroalbuminuria. creator: Aili Yang creator: Xinwen Yu creator: Zhiqiao Fan creator: Yuxin Jin creator: Fei Sun creator: Xin Wang creator: Xi Yuan creator: Langlang Liu creator: Guohong Zhao creator: Bin Gao uri: https://doi.org/10.7717/peerj.19780 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: Habitat composition near linear landscape structures across Poland: perspectives on pollinator conservation link: https://peerj.com/articles/19765 last-modified: 2025-07-31 description: Landscape management intensification is a major driver of global decline in insect pollinators and the ecosystem services they provide. Part of the proposed solution is to take advantage of the potential benefits of existing human-made habitats such as linear landscape structures (LLSs) associated with highways verges, railway embankments, or levees. We explored the surrounding landscape composition of different LLSs across Poland using geographic information system (GIS) methodology, examining spatial scales reflecting typical foraging distances of key pollinator groups (bees, butterflies, flies). We found that land cover composition around LLSs closely mirrored the overall national land cover distribution in Poland with right-skewed distributions of tree, grass, crop, and built cover across all LLS types. Highway verges exhibited the highest landscape diversity, while railways and levees showed more similar patterns to each other. Our study revelated that land cover changes occur unidirectionally at the studied scales, suggesting consistent habitat transitions around these linear features. Based on these findings, we propose prioritising two approaches for pollinator conservation in Poland: (1) using levee verges as supplementary habitat in wetland areas due to their lowest traffic level and reduced cost; (2) developing highway verges as a supplementary habitat to support pollinator ecosystem services in farmland and urban landscapes. Since LLSs are managed by relatively few stakeholders, primarily public bodies and government agencies, which provides an opportunity to implement management plans supporting biodiversity and ecosystem services at the national and regional scale. creator: Emilia Marjańska creator: Dawid Moroń uri: https://doi.org/10.7717/peerj.19765 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Marjańska and Moroń title: ASB3 ablation has no detectable effects on spermatogenesis and fertility in male mice link: https://peerj.com/articles/19738 last-modified: 2025-07-31 description: BackgroundAs a member of the Ankyrin repeat and SOCS box (Asb) family, the Asb3 is enriched in the testes and highly conserved in multiple species. The knockout of the Asb12 gene not significantly affect spermatogenesis, but led to a compensatory increase in the mRNA expression level of the Asb3. Although it has been reported that the Asb12 is not required for spermatogenesis and male fertility in mice, the functional role of Asb3 remains not to be clearly elucidated.Methods and resultsAsb3 was predominantly expressed in mouse testis and primarily localized to the elongated spermatids, as determined by real-time fluorescent quantitative PCR and fluorescence in situ hybridization. The Asb3-KO mice were successfully generated using CRISPR Cas9 technology. Sperm quantity and motility from the cauda epididymidis were assessed via the hemocytometer. Histological analysis and immunostaining confirmed that normal fertility, normal spermatozoa and normal spermatogenesis in Asb3-KO mice. Additionally, no significant differences were observed between Asb3-KO mice and heterozygous mice regarding seminiferous tubule apoptosis via the TUNEL analysis.ConclusionsThere is no significant difference in fertility between Asb3-KO mice and heterozygous mice. Despite a significant increase in the relative mRNA expression level of the Asb3 gene due to the absence of the Asb12, the deficiency of ASB3 did not adversely affect fertility or spermatogenesis in males. Hence, we demonstrated that ASB3 ablation has no detectable effects on spermatogenesis and fertility in male mice. creator: Changtong Xu creator: Xiya Qiu creator: Aiyan Zheng creator: Yan Pu creator: Tiantian Wu creator: Jie Ding creator: Bo Zheng uri: https://doi.org/10.7717/peerj.19738 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Xu et al. title: Evaluating the antibacterial properties of deep-sea sponges Dactylospongia elegants, Stelletta fibrosa, and Haliclona manglaris from the Jordanian Gulf of Aqaba link: https://peerj.com/articles/19735 last-modified: 2025-07-31 description: Marine sponges are known for their rich variety of secondary metabolites, many of which show potential for pharmaceutical applications. In this study, three deep-sea sponge species—Stelletta fibrosa, Dactylospongia elegans, and Haliclona manglaris—were identified using DNA barcoding, and their ethanolic extracts were tested for antibacterial activity. The extracts were evaluated against Gram-positive (e.g., Bacillus pumilus, Staphylococcus aureus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus, MRSA) and Gram-negative bacteria (e.g., Escherichia coli and Klebsiella aerogenes) using the agar well diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined. Among the extracts, D. elegans exhibited the most potent antibacterial activity, with inhibition zones ranging from six to 21 mm against gram-positive bacteria and low MIC/MBC values from 0.25 to three mg/ml. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis of D. elegans revealed the presence of bioactive compounds such as gallic acid, caffeic acid, bolinaquinone, dactyloquinone, and others, which are known for their antimicrobial properties. These findings suggest that D. elegans has promising antibacterial properties that could be valuable in combating antimicrobial resistance. creator: Razan Ataallah Abuassaf creator: Fatima F. Al-Jamal creator: Osama H. Abusara creator: Malek Zihlif creator: Ahmad A. Deeb creator: Mamoon M.D. Al-Rshaidat uri: https://doi.org/10.7717/peerj.19735 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Abuassaf et al. title: Motor competence development of children in Singapore: a cross-sectional and longitudinal study link: https://peerj.com/articles/19698 last-modified: 2025-07-31 description: IntroductionUnderstanding the motor competence development of young children requires both cross-sectional and longitudinal analyses. This is crucial for identifying relative age effects and tracking individual developmental trajectories. However, there are limited data in Southeast Asia, particularly in Singapore.MethodsThis study monitored the development of motor competence of 75 children in Singapore, aged 3–4.5 years, over an 18-month period. Four data points were conducted using the Movement Assessment for Children, 2nd Edition (MABC-2) at six-month intervals. Data were analyzed using repeated measures multivariate analysis of variance (MANOVA), two-way analysis of variance (ANOVA), and post-hoc multiple comparisons.ResultsCross-sectional analysis revealed a positive age effect across all eight motor tasks, with older children demonstrating higher fine and gross motor competence. Longitudinal analysis showed significant improvement in seven out of eight motor tasks over the 18-month period, except for the task of jumping on mats.ConclusionThe most pronounced age effect was observed between children aged 3.5 and 4.0 years, suggesting a potential period of accelerated motor development within this age range. The significant improvements in motor competence observed over the 18-month period underscore the critical nature of early childhood for motor skill acquisition. Additionally, the study highlights the importance of frequent monitoring (e.g., every 6 months) to identify children with motor delays and facilitate timely interventions. creator: Jernice S.Y. Tan creator: Michael Y.H. Chia uri: https://doi.org/10.7717/peerj.19698 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tan and Chia title: A new theory of tree sap flow link: https://peerj.com/articles/19670 last-modified: 2025-07-31 description: IntroductionThe theory of water transport in trees, according to which the main driving force of water movement is the suction created by the evaporation of water by the meniscus (the curved surface of the capillary liquid column) on the evaporating elements, supported from below by root pressure, is controversial. The main physics argument against it is that the capillary effect in nature is around 1 m. In the case of open-air gaps, the leaf cannot suck in the water against gravity because, in this case, the plant would not be sucking in water, but air through the open-air gap.AimTo present a new theory of three-sap flow and to support it with practical observations, previous data from decades of experimental measurements, and direct measurement data obtained by the authors.New theoryWhen evaporation occurs, there is no suction towards the canopy, but pressure is due to a reduction in the cross-section of the water pipe caused by heat loss through evaporation. At night, when evaporation stops, a thermal equilibration process is triggered, restoring the pipe’s original cross-section. This generates suction and draws water from the soil. As the hydrostatic pressure in the pipe is high for tall trees, the pipe is segmented.Materials and MethodsTo study the change in the wood’s cross-section, a mechanical pressure-sensing transmitter-amplifier instrument was used. The instrument is designed to convert changes in the diameter of a millimeter-sized tree into easily detectable data by increasing the diameter by an order of magnitude. We also used high-resolution computer tomography (CT) to measure the cross-sectional image of oak trees to explore areas rich in water.ResultsThe experimental results show that the tree diameter increases during the night (suction phase) and decreases during the day (pressure phase). Many measurements in the literature show a similar phenomenon. The CT scan results showed that the outer, living one-ring area of the tree is rich in water, from which passages lead to the passive water storage inside the tree.ConclusionsSeveral examples have been given to prove this theory. Water transport is not based on physical mechanical laws alone. Complex physiological, biochemical, and biophysical processes may be behind the operation of the pipe system. creator: András Török creator: Anikó Anna Hajduné Kubovje creator: Balázs Hardi creator: Ralf Bergmann creator: Krisztián Szigeti creator: Domokos Máthé creator: Imre Hegedüs uri: https://doi.org/10.7717/peerj.19670 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Török et al. title: Effects of irrigation and nitrogen management on phyllosphere microbial communities of silage maize link: https://peerj.com/articles/19663 last-modified: 2025-07-31 description: Silage maize (Zea mays) is a significant source of animal roughage in many countries. Few studies have revealed the specific impacts of agronomic measures on harmful or beneficial microbial species (based on plant health or utilization) in silage maize. The aim of the present study was to investigate the effects of three maturity stages (big trumpet, milk, and dough) × two irrigation amounts (1,200 m3 hm−2 (IA1,200) and 2,400 m3 hm−2 (IA2,400)) × three nitrogen (N) application rates (160 kg hm−2 (low), 240 kg hm−2 (medium), and 320 kg hm−2 (high)) on the bacterial community structure of the silage maize phyllosphere. Irrigation amounts and N application rates did not affect silage maize leaves’ chemical or physiological properties, but influenced the bacterial community structure of silage maize phyllosphere. There were higher relative abundances of beneficial (Pseudomonas, Rhodococcus, Achromobacter, and Myroides) or harmful (Bordetella and Ralstonia) microbial in IA2,400 compared with IA1,200. Plant pathogenic bacteria (Erwinia and Serratia) were found to have the highest relative abundance at the low N application rates. In meta-analysis, some bacteria impacted the phytosanitation and nutrition quality of forage, encompassing Ralstonia, Pantoea, Dokdonella, Vogesella, Erwinia, Serratia, Pseudomonas, and Bordetella. Based on the yield, plant health, and potential fermentation quality of silage maize, we recommend using an irrigation amount of 2,400 m3 hm−2 and an N application rates of 240 kg hm−2 for agricultural production and harvesting silage maize at the milk stage. creator: Liuxing Xu creator: Changjing Chen creator: Chenggang He creator: Ahmed M. Abd El Tawab creator: Qinhua Liu creator: Hua Jiang uri: https://doi.org/10.7717/peerj.19663 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Xu et al. title: PCK1 as a potential hub gene in distinguishing lactate metabolism between rheumatoid arthritis and osteoarthritis link: https://peerj.com/articles/19661 last-modified: 2025-07-31 description: BackgroundLactate is notably involved in the advancement of rheumatoid arthritis (RA) and osteoarthritis (OA). Nevertheless, the causal association between these conditions and lactate remains uncertain. This study aims to use Mendelian randomization (MR) to investigate their relationship with lactate and understand the genetic differences in lactate metabolism between them.MethodsGenetic data for RA, OA, and lactate metabolism were obtained from GWAS, GEO, and MSigDB databases. MR analysis was performed using the inverse variance weighted (IVW) method. Differential gene expression analysis was conducted using the “limma” package, and Gene Set Enrichment Analysis (GSEA) was performed with GSEA software. Immune cell infiltration was assessed using the CIBERSORT platform. Validation of differentially expressed genes was carried out via Western blotting. Additionally, weighted gene co-expression network analysis (WGCNA) was employed to identify hub genes, while GO and KEGG analyses were performed to compare mechanistic differences between RA and OA. In vitro experiments were conducted to assess the effects of PCK1 on lactate secretion and cellular functions in RA-FLS.ResultsMR analysis indicated a causal relationship between RA and OA with lactate levels. Differential gene expression analysis revealed that PCK1 is a key gene underlying the metabolic differences in lactate levels between RA and OA. In vitro experiments demonstrated that knocking down PCK1 in RA-FLS affected lactate secretion, inhibited cell migration, and promoted apoptosis, suggesting its critical role in lactate metabolism. Additionally, GSEA analysis showed significant enrichment of PCK1 in the citrate cycle and gluconeogenesis signaling pathways in RA.ConclusionThis study provides genetic evidence supporting the causal relationship between RA, OA, and lactate levels. Additionally, PCK1 is identified as a pivotal target implicated in the metabolic disparities of lactate between RA and OA, highlighting its potential significance in RA therapeutics. creator: Pengfei Xin creator: Shaoqiang Pei creator: Nanshan Ma creator: Lianbo Xiao uri: https://doi.org/10.7717/peerj.19661 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xin et al. title: Effects of core strength training on the technical skill performance of striking combat sport players: a systematic review link: https://peerj.com/articles/19615 last-modified: 2025-07-31 description: Research purposeThis review investigated the effects of core strength training on the competitive performance of players participating in striking combat sports. By analyzing karate, taekwondo, boxing, Chinese martial arts, and Muay Thai, the study examined the effects of core strength training on the number of kicks, striking force, and impact speed of players. The aim of this study was to provide a theoretical basis for training methods in striking combat sports and to explore the role of core strength in improving players’ actual competitive performance.MethodsData for this study were reported using the Preferred Reporting Project for Systematic Review and Meta-Analysis (PRISMA) guidelines. On November 1, 2023, a full search was conducted on SCOPUS, PubMed, Web of Science, EBSCO, CNKI (only core academic journals were included in the search, specifically those listed in recognized Chinese journal evaluation systems such as the Beijing University Core Journals or CSSCI, thereby excluding non-academic or low-tier publications.) and Google Scholar (via EBSCOhost) searching engine. PICOS determined the inclusion criteria: (1) Combat sports player; (2) core strength training; (3) the enhancement intervention was compared with the control group or other exercise groups, and a single-group test was conducted; (4) test at least one technical skill performance; (5) non-randomised research trials and randomised controlled designs. Only eight of the 826 studies met all inclusion criteria and were included in the systematic review.ResultsIn karate, wheel kick scores were significantly increased after core strength training; in taekwondo training groups, the number of kicks in 30 seconds was increased considerably; in boxing, 10-second and 20-second sandbag strikes and performance in 1 minute were significantly increased, and backhand punch strikes were enhanced; in martial arts, the striking power and relative striking power of straight punches and whip kicks were increased considerably; and in Muay Thai, jabs were made possible by both static and dynamic training; the knee strike and other manoeuvres had significant increases in striking power and impact speed. Overall, core strength training positively affected the frequency of kicks, striking power, and impact speed in all striking combat sports.ConclusionThe number of kicks, striking force, and impact speed in karate, taekwondo, boxing, Chinese martial arts, and Muay Thai have all improved, with particularly notable improvements in roundhouse kicks, straight punches, and whip kicks. core strength training has enhanced players’ strength and physical stability, improving movement control and explosive power. Therefore, incorporating core strength training into striking combat sports training can comprehensively improve players’ practical performance and physical fitness levels. creator: Shuai Zhang creator: Wanyu Huang creator: Kim Geok Soh creator: Shengyao Luo creator: Long Li creator: Xinzhi Wang uri: https://doi.org/10.7717/peerj.19615 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhang et al. title: Optimizing planting dates and irrigation schedules to enhance wheat production in Fars Province under future climate scenarios using the CERES-Wheat model link: https://peerj.com/articles/19592 last-modified: 2025-07-31 description: BackgroundClimate change poses significant threats to wheat production, particularly in regions prone to increasing temperatures and water scarcity. This study aimed to explore the optimum planting date and irrigation schedule that increases winter wheat productivity under the potential adverse impacts of climate change.MethodsA combination of data from 2-year field experiments (2018–2019 and 2019–2020) and simulation data of the Crop Environment Resource Synthesis (CERES)-Wheat model was employed in this research. The weather data emanating from eight global climate models (GCMs) of Climate Model Intercomparison Project 5 and 6 (CMIP5 and CMIP6) under Representative Concentration Pathways (RCP-4.5 and RCP-8.5) and Shared Socioeconomic Pathways (SSP-245 and SSP-585) were used to predict rainfall and temperature variations in two future periods (2041–2070 and 2071–2100).ResultsThe findings demonstrated that the annual maximum and minimum temperatures (T(max) and T(min)) would respectively increase by 3.14 °C and 3.50 °C in the 2050s, based on averaging all models of CMIP5 and CMIP6 with the highest T(max) values projected for June to August. In the 2080s, further warming of 4.54 °C and 4.66 °C was anticipated in the annual T(min) and T(max), again peaking in June to August, respectively. As opposed to the baseline period, precipitation over the growing season (October to May) is projected to be reduced by 23.03% and 29.48% in the 2050s and 2080s, respectively, with the lowest rainfall occurring in May. The anthesis date was projected to decline by 27, 37, 17, and 31 days under RCP-4.5, RCP-8.5, SSP-245, and SSP-585 scenarios, respectively. Additionally, the findings indicated that the period in which the wheat is grown decreased by 23, 32, 22, and 29 days under RCP-4.5, RCP-8.5, SSP-245, and SSP-585, respectively. Planting wheat from October 22 to November 11 recorded the highest value of grain yield in all irrigation treatments. On average, across all scenarios, with a 3-week early planting date compared to October 22, the grain yield was predicted to decrease by 22–44%. Therefore, adjusting the planting date and the irrigation time as the adaptation strategy during climate change slightly increased wheat grain yield in semi-desert regions like the Fars province. This advancement is linked to the crop’s ability to utilize cooler temperatures during critical growth phases when sown earlier. creator: Farkhondeh Ebrahimi creator: Mohsen Edalat creator: Ruhollah Naderi uri: https://doi.org/10.7717/peerj.19592 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ebrahimi et al. title: New evidence for the co-occurrence of two genera of Paleoparadoxiidae (Mammalia, Desmostylia) from the Middle Miocene of Japan: insights into taxonomic status and paleodiversity in Desmostylia link: https://peerj.com/articles/19578 last-modified: 2025-07-31 description: Desmostylia, an extinct order of marine mammals, includes two major families: Paleoparadoxiidae and Desmostylidae. Within Paleoparadoxiidae, three genera—Archaeoparadoxia, Paleoparadoxia, and Neoparadoxia—have been identified, with Paleoparadoxia being the only genus found on both coasts of the North Pacific Rim. In Akan, Hokkaido, Japan, one of the largest Paleoparadoxia fossil assemblages in the world has been discovered from the Middle Miocene Tonokita Formation. Previous studies suggested the presence of two congeneric species of Paleoparadoxia, while recent taxonomical revisions raise the possibility that two genera, Paleoparadoxia and Neoparadoxia, were present in Akan. Here, we describe three paleoparadoxiids specimens from Akan, which consist of two partial crania and a mandible. Based on morphological comparisons and phylogenetic analysis, we identified these specimens as Paleoparadoxia sp. and Neoparadoxia sp. This represents the first record of two genera of Paleoparadoxiidae in the same locality and horizon, with the potential to provide valuable insights into cladogenesis and morphological diversification within this family. In addition, the Akan specimens exhibit mosaic characteristics of Paleoparadoxia and Neoparadoxia, suggesting that a reassessment of their morphological features for taxonomic identification and phylogenetic analysis is required. To better understand species-level diversity patterns in Desmostylia, we conducted stage-binned analysis and richness curve analysis. Our analysis revealed three significant points in their diversification history: (1) Desmostylidae reached peak diversity at the Oligocene-Miocene boundary, coinciding with a glacial event; (2) Paleoparadoxiidae achieved peak diversity during the Middle Miocene global warming event; (3) both families declined in diversity and went extinct during the Middle to Late Miocene global cooling event. These findings indicate that desmostylian diversity could have been closely linked to climatic events, with the differing peak diversities of Paleoparadoxiidae and Desmostylidae reflecting their respective preferences for warmer and cooler climates. Our analysis provides a valuable baseline for understanding the diversity and evolutionary history of Desmostylia. creator: Yuma Asai creator: Tatsuro Ando creator: Hiroshi Sawamura creator: Shoji Hayashi uri: https://doi.org/10.7717/peerj.19578 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Asai et al. title: Rnf32 is not essential for spermatogenesis and male fertility in mice link: https://peerj.com/articles/19794 last-modified: 2025-07-30 description: BackgroundRing finger motifs are found in a variety of proteins with diverse functions, often involved in protein-DNA or protein–protein interactions. The Rnf32-encoded protein contains two such motifs and is predominantly expressed in the testes and ovaries, suggesting that its expression may be regulated by elements within the Rnf32 promoter region. Rnf32 is active during spermatogenesis, mainly in spermatocytes and spermatids, indicating a potential role in sperm development.MethodsWe established an Rnf32 knockout (Rnf32−/−) mouse model using CRISPR/Cas9 technology. Gene expression was analyzed via reverse transcription quantitative polymerase chain reaction (RT-qPCR). Testicular and epididymal phenotypes were assessed through histological and immunofluorescence staining, and fertility and sperm motility were evaluated.ResultsHere, we successfully established an Rnf32 knockout mouse model using CRISPR/Cas9 technology. Surprisingly, male Rnf32−/− mice exhibited normal fertility, with no significant differences in testicular and epididymal histology, spermatogenesis, sperm count, or motility compared to Rnf32+/+ mice. These findings suggest that Rnf32 may not be essential for male fertility in mice, and its potential functions warrant further investigation. creator: Hao Kong creator: Yufeng Yin creator: Ni Zeng creator: Yunfei Zhu creator: Yiqiang Cui uri: https://doi.org/10.7717/peerj.19794 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kong et al. title: Comparative effects of square-stepping and strengthening exercises on cognitive and balance functions in chronic obstructive pulmonary disease: a randomized clinical trial link: https://peerj.com/articles/19792 last-modified: 2025-07-30 description: BackgroundCognitive impairment and balance dysfunction are common in individuals with chronic obstructive pulmonary disease (COPD), yet targeted interventions remain limited. Square-stepping exercise (SSE), a structured multitasking intervention involving progressive, multi-directional step patterns, combines cognitive and motor challenges. This study aimed to compare the effects of SSE and traditional strengthening exercises (SE) on cognitive function and balance in individuals with COPD through a telerehabilitation model.MethodsThis randomized clinical trial included 34 male individuals with mild to moderate COPD (mean age: 63.91 ± 6.98 years), randomly assigned to SSE and SE groups (n = 17 each). Both groups participated in supervised telerehabilitation sessions three times per week for eight weeks. Cognitive function was assessed using the Montreal Cognitive Assessment (MoCA; 0–30 points, with higher scores indicating better cognition), while the Standardized Mini-Mental State Examination (SMMSE; 0–30, cutoff < 23) was used as a screening tool to exclude significant cognitive impairment. Balance performance was evaluated using the Biodex Balance System, including the overall stability index, anterior/posterior index, and medial/lateral index (lower scores indicate better balance). Perceived breathlessness (dyspnea) was assessed with the Modified Medical Research Council (mMRC) scale (0–4), and disease impact with the COPD Assessment Test (CAT; 0–40, ≥10 indicating high symptom burden). Comorbidity severity was evaluated using the modified Charlson Comorbidity Index (CCI; higher scores indicate greater severity). Data normality was assessed using the Shapiro–Wilk test. Independent sample t-tests were used for parametric between-group comparisons, and Mann–Whitney U tests were applied for non-parametric data. Paired sample t-tests and Wilcoxon signed-rank tests were used for within-group comparisons. The level of statistical significance was set at p < 0.05.ResultsBoth groups showed significant within-group improvement in MoCA scores (p = 0.01 for both). However, the SSE group demonstrated greater improvements in balance parameters, particularly in the overall stability index (p = 0.014) and anterior/posterior stability index (p = 0.05), compared to the SE group. The SE group showed limited improvements, primarily in static balance conditions (p = 0.029). Although cognitive gains were similar between the groups, balance improvements were more pronounced in the SSE group.ConclusionsWhile both exercise modalities improved cognitive function in individuals with COPD, SSE led to superior outcomes in balance control. The multitasking design of SSE, requiring simultaneous cognitive processing and motor coordination, may underlie its enhanced impact on postural stability. These findings support SSE as a technically advantageous and accessible intervention in telerehabilitation for individuals with COPD. creator: Alp Özel creator: Eylem Tütün Yümin creator: Suat Konuk uri: https://doi.org/10.7717/peerj.19792 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Özel et al. title: New and known free-living nematode species (Nematoda: Chromadorea) from offshore tsunami monitoring buoys in the Southwest Pacific Ocean link: https://peerj.com/articles/19789 last-modified: 2025-07-30 description: Deep-ocean Assessment and Reporting of Tsunami (DART) buoys are deployed across the Southwest Pacific and provide substrates for biofouling communities. Two new free-living nematode species, Atrochromadora tereroa sp. nov. and Euchromadora rebeccae sp. nov. (family Chromadoridae), and one known species, Halomonhystera refringens (Bresslau & Schuurmans Stekhoven, 1933) comb. nov. (family Monhysteridae), are described from buoys deployed off Raoul Island in the Kermadec/Rangitāhua region and off New Zealand’s East Cape. Thalassomonhystera refringens (Bresslau & Schuurmans Stekhoven, 1933) Jacobs, 1987 and T. anoxybiotica (Jensen, 1986) Jacobs, 1987 are transferred to Halomonhystera based on the presence of precloacal and caudal papillae in males. In addition, Halomohystera zhangi Li, Huang & Huang, 2024 is synonymised with Halomonhystera refringens. Updated keys to Atrochromadora, Euchromadora and Halomonhystera species are provided. The presence of nematodes on buoys located more than 100 km from the nearest landmass and in deep waters (>3,500 m water depth) shows that some nematode species are capable long-distance dispersal to colonise new substrates. Such dispersal by Atrochromadora, Euchromadora and Halomonhystera species likely occurs via drifting macroalgal fragments. creator: Daniel Leduc uri: https://doi.org/10.7717/peerj.19789 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Leduc title: The tip of the iceberg: extraordinarily high diversity while examining two infralittoral nematode communities on Okinawa-jima Island, Japan, using morphology and DNA barcoding link: https://peerj.com/articles/19757 last-modified: 2025-07-30 description: BackgroundNematodes are among the most diverse and abundant metazoans in aquatic habitats, contributing significantly to global biodiversity. Despite their abundance and importance, the presumed number of undescribed species is high and their diversity is often underestimated.MethodsIn this research, sediment samples were collected from three microhabitats (bare sand, seagrass, coral) in two sites around Okinawa-jima Island in subtropical southern Japan. Nematode specimens were obtained by filtering the sediment and were then used to determine meiofaunal assemblages with morphology and molecular methods at the two sites and to compare them with environmental variables.ResultsThe results showed an overwhelmingly high biodiversity of nematofauna with both methods. The morphological identification of free-living nematodes was partly supported by molecular analyses, with the results varying more regarding less common taxa. The discrepancies between different methods may be due to low success of DNA amplifications, high nucleotide variability, and overestimation of congeneric specimens. We observed that coral reef habitats clearly differed from nearby sand and seagrass beds in terms of nematode genus-level assemblages. We identified at least 10 orders and 38 genera of nematodes from our samples that only span two different sites, and it is highly likely these samples include undescribed taxa. Our results strongly suggest that coral reefs and neighboring areas are hot-spots for nematode diversity, at least around Okinawa-jima Island if not also in other coral reef regions. creator: Marilyn Carletti creator: Nuria Viñuela Rodríguez creator: Gaia Rossetti creator: Virginia Rossi creator: Bryan Gabriel Pulido Tan creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.19757 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Carletti et al. title: Pain without gain? A randomized crossover study on the impact of active and passive foam rolling on jump height and pain intensity link: https://peerj.com/articles/19747 last-modified: 2025-07-30 description: BackgroundFoam rolling has become increasingly popular for its proposed benefits on physical performance and recovery. This study investigated the effects of single bouts of active foam rolling and passive foam rolling on vertical jump height, perceived pain, and applied pressure during treatment.MethodsTwenty physically active participants (10 males, 10 females) completed a randomized crossover design study, undergoing one active and one passive foam rolling session. Jumping performance was assessed via countermovement jump (CMJ) height at baseline, pre-treatment (PRE), and post-treatment (POST). Pain intensity was evaluated using a visual analog scale, while applied pressure was measured via force plates for active foam rolling and the weight applied to a custom device for passive foam rolling.ResultsThe CMJ height post-treatment was reduced after both foam rolling treatments (p < 0.001, ωp2 = 0.29), with no significant interaction or condition effect observed. The applied pressure during active was significantly higher than during passive foam rolling for the thigh (p < 0.001, Hedges’ g = 1.14). In contrast, perceived pain was greater in passive than in active rolling (p = 0.002, Hedges’ g = 0.96). CMJ height improved following the initial warm-up (baseline to PRE, p = 0.014, 95%, Hedges’ g = −0.11).ConclusionThis study highlights the biomechanical and psychological complexities of foam rolling, suggesting that both active and passive rolling may temporarily impair power performance. The observed jump height reduction could stem from decreased tissue stiffness, while the initial warm-up benefits reinforce the effectiveness of traditional warm-up protocols. creator: Lars Heinke creator: Sasha Javanmardi creator: Janis Alexander Zemke creator: Ludwig Rappelt creator: Jürgen Freiwald creator: Christian Baumgart creator: Daniel Niederer uri: https://doi.org/10.7717/peerj.19747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Heinke et al. title: Identification of potential inhibitors of the main protease from feline infectious peritonitis virus using molecular docking and dynamic simulation approaches link: https://peerj.com/articles/19744 last-modified: 2025-07-30 description: BackgroundFeline infectious peritonitis virus (FIPV) is one of cats’ most serious viral infections. The FIPV infection induces a complicated syndrome in the affected cats, including immunosuppression and severe inflammatory conditions. Unfortunately, vaccines are unable to provide complete prevention in cats from getting infected with these viral infections. There is ongoing research on preparing antiviral therapies against FIPV in cats. However, these are still in clinical trials and have not been fully approved by the drug authorities in many countries, including the USA. Targeting the main viral proteases is one of the promising trends in the drug design of many viral diseases, including coronaviruses. The main goal of the current study was to repurpose and test the efficacy of some known antiviral drugs to treat FIPV infection in cats by targeting the FIPV main protease (Mpro).MethodsWe used the in-silico prediction and molecular docking tools to screen and identify some drugs targeting FIPV-MPro to achieve these goals. The research method was started by building a screening pharmacokinetic associated variables of the compound, then used to design a new potential inhibitor by employing the docking and molecular dynamic simulation to evaluate the interaction of all complexes using the standard dynamics cascade protocol of Biovia Discovery studio.ResultsOur results show that out of the 15 antiviral and immunomodulatory compounds, the top-ranked inhibitors for the FIPV-Mpro are reference standard inhibitor (N3), Sofosbuvir, and the GS-441524, out of which GS-441524 was suggested as Mpro-inhibitor on the basis of further investigation through molecular dynamics simulation method. In conclusion, our results confirmed the potential applications of the predicted FIPV-Mpro inhibitors either independently or in combination with other immune-modulatory compounds. Further in vitro and in vivo studies are encouraged to test the efficacy of these identified compounds as potent inhibitors for the Mpro of the FIPV in cats. This study will pave the way for the development of novel drugs that treat FIPV infection in cats. creator: Mohd Yasir Khan creator: Abid Ullah Shah creator: Nithyadevi Duraisamy creator: Nadine Moawad creator: Reda Nacif ElAlaoui creator: Mohammed Cherkaoui creator: Maged Gomaa Hemida uri: https://doi.org/10.7717/peerj.19744 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Khan et al. title: The role of mast cells in allergic rhinitis link: https://peerj.com/articles/19734 last-modified: 2025-07-30 description: IntroductionIn recent decades, mast cells and their mediators have been increasingly recognized as central players in the pathogenesis of allergic rhinitis (AR), a complex chronic nasal disease characterized by pathological changes influenced by genetic factors, various immune cells, and environmental exposures. Mast cells are pivotal in allergic reactions, orchestrating inflammation and airway contraction through the secretion of diverse mediators. Prominent among these mediators are histamine and bioactive lipids, whose physiological effects are prominently observed during the acute phase of allergic reactions. The accumulation of mast cells in specific areas of allergic rhinitis may correlate with the disease’s phenotype, progression, and severity. In vivo experiments in mice have demonstrated that mast cells develop from mast cell progenitor cells, which are induced by inflammatory stimuli and subsequently migrate to the airway. Human mast cell progenitor cells have been identified in the bloodstream, with a high proportion potentially reflecting the persistent pathological changes associated with allergic rhinitis. The primary activation of mast cells in allergic rhinitis occurs via the cross-linking of IgE high-affinity receptors (Fcɛ RI) mediated by IgE in conjunction with allergens. However, mast cells can also be activated by a variety of other stimuli, including toll-like receptors and MAS-related G protein-coupled receptor X2.Rationale for this reviewDespite the substantial progress in understanding the role of mast cells in allergic rhinitis, several critical gaps remain in our knowledge. The complex interplay between mast cells, their mediators, and the immune system in the context of AR is still not fully elucidated. Moreover, the specific mechanisms underlying the recruitment and activation of mast cell progenitor cells in the nasal mucosa remain poorly understood. Addressing these gaps is essential for developing more effective therapeutic strategies for allergic rhinitis. This review aims to provide a comprehensive and up-to-date synthesis of the current literature on the role and development of mast cells and their progenitor cells in allergic rhinitis, including the activation pathways implicated in the pathogenesis.Target audienceThis review is intended for a broad audience, including researchers in the fields of immunology, allergy, and respiratory medicine, as well as clinicians who manage patients with allergic rhinitis. By summarizing the latest findings and highlighting the unresolved questions, this review aims to serve as a valuable reference for future research directions in mast cells and allergic rhinitis, ultimately contributing to improved patient care and outcomes. creator: Jin Zhang creator: Xiaofei Xie creator: Ruixia Ma creator: Peng Liu uri: https://doi.org/10.7717/peerj.19734 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Analysis of combining ability and stability of yield characteristics of upland cotton in two years link: https://peerj.com/articles/19716 last-modified: 2025-07-30 description: ObjectiveCombining ability analysis forms the basis for selecting suitable parents and hybrid combinations. The performance of combining ability is influenced significantly by environmental conditions. Therefore, it is essential to comprehensively evaluate advantageous parents and hybrid combinations through multi-year experiments.MethodsIn this study, seven parental lines were crossed using a complete diallel design [p(p−1)/2], producing 21 combinations. Yield-related traits, including boll number per plant, seed cotton per plant, lint cotton per plant, boll weight, lint percentage, and seed index, were measured in the parental lines and their hybrid F1 generations over two consecutive years. Combining ability and interannual stability were subsequently analysed.ResultsCotton yield traits were significantly influenced by environmental factors such as weather, temperature, and soil conditions. Interannual variation and genotype-year interactions contributed substantially to variation in yield traits. The interactions between year and both general combining ability (GCA) and specific combining ability (SCA) were significant or highly significant, with GCA stability being relatively low. Yield traits were governed by both additive and dominance genetic effects, with additive effects being predominant. The comparison coefficients for stability of GCA for lint cotton per plant and seed cotton per plant across years were relatively high (51.372% and 55.187%, respectively), whereas SCA stability coefficients for lint percentage and boll weight were comparatively lower (44.986% and 48.645%, respectively). Parent Xinluzao62 (Parent 7) exhibited both high and stable GCA and can therefore be recommended as a backbone parent for yield improvement. Additionally, eight hybrid F1 combinations showing excellent and stable SCA were identified, suitable for use as dominant combinations.ConclusionThe GCA and SCA for yield traits in upland cotton are notably influenced by environmental factors such as climate and soil. Yield performance varies considerably across different years and locations. Therefore, selections based on multi-year and multi-location trials provide more reliable results, offering a solid theoretical basis for developing high-yield cotton varieties. creator: Xiaoman Ma creator: Weifeng Guo creator: Liangrong He creator: Xinchuan Cao uri: https://doi.org/10.7717/peerj.19716 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ma et al. title: Analytical performance evaluation of a multiplex real-time RT-PCR kit for simultaneous detection of SARS-CoV-2, influenza A/B, and RSV link: https://peerj.com/articles/19693 last-modified: 2025-07-30 description: Differentiating between influenza, respiratory syncytial virus (RSV), and SARS-CoV-2 based on clinical symptoms alone can be challenging due to their overlap. This cross-sectional study, conducted from September to November 2023, evaluated the analytic performance of the LabTurbo multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) kit for the simultaneous detection of these viruses. Nasopharyngeal swab specimens were tested using the LabTurbo kit, the Cobas Liat SARS-CoV-2 influenza A/B assay, and the Cobas influenza A/B and RSV assays. RNA standards were serially diluted and tested with the LabTurbo kit to determine the limit of detection (LOD). This cross-sectional study involved the analysis of 350 nasopharyngeal swab samples, which included 250 positive cases (50 cases each of influenza A, influenza B, and RSV, along with 100 cases of SARS-CoV-2) and 100 negative cases. The LabTurbo kit demonstrated 100% positive percent agreement and negative percent agreement with the reference assays for detecting SARS-CoV-2, influenza A/B, and RSV. The LODs for SARS-CoV-2, influenza A, influenza B, and RSV were 8,333, 3,333, 6,667, and 8,333 copies/mL, respectively. These findings confirm the diagnostic accuracy and analytic performance of the LabTurbo multiplex real-time RT-PCR kit for the detection of SARS-CoV-2, influenza A/B, and RSV, simultaneously. This assay could substantially improve the rapid identification and differentiation of these pathogens, thereby enabling more timely and appropriate treatment measures to control the spread of co-circulating viruses. creator: Chi-Sheng Tai creator: Ming-Jr Jian creator: Tai-Han Lin creator: Hsing-Yi Chung creator: Chih-Kai Chang creator: Cherng-Lih Perng creator: Po-Shiuan Hsieh creator: Hung-Sheng Shang uri: https://doi.org/10.7717/peerj.19693 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tai et al. title: A sustainable approach for smallholder farmers: evaluation of plant by-products and industrial waste in wheat cultivation link: https://peerj.com/articles/19775 last-modified: 2025-07-29 description: Large amounts of waste and by-products are generated during the extraction of essential oils, leading to disposal challenges. Integrating these by-products into the production systems of smallholder farmers may help reduce yield losses caused by environmental stress factors. This study investigated the potential use of plant waste and by-products from aromatic plants as bioregulators in wheat cultivation. Greenhouse and field experiments were conducted to evaluate the effects of these materials on yield parameters and biochemical markers in wheat. The treatments included: T0 (control), T1 (plant extract), T2 (plant biomass), and T3 (plant extract + plant biomass). In the greenhouse experiment, the T3 treatment advanced the onset of tillering by 5.4 days, stem elongation by 5.6 days, and heading by 12 days compared to the control. In the field experiment, T3 reduced the heading onset by an average of 5.27 days relative to the control. Additionally, the highest yield was recorded in the T3 treatment, reaching 264.96 kg da−1. These findings suggest that by-products from aromatic and medicinal plants can serve as cost-effective, sustainable, and environmentally friendly biostimulants to enhance yield in agricultural production. creator: Muhammet Cagri Oguz uri: https://doi.org/10.7717/peerj.19775 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Oguz title: Epidemiological characteristics of invasive meningococcal disease and carriage prevalence of Neisseria meningitidis in the Xinjiang Uygur Autonomous Region, China, 2004–2023: a retrospective study link: https://peerj.com/articles/19772 last-modified: 2025-07-29 description: ObjectiveThe Xinjiang Uygur Autonomous Region (Xinjiang) currently exhibits the high incidence rates of invasive meningococcal disease (IMD) in China. Current epidemiological data on meningococcal carriage rates among asymptomatic individuals remain sparse, with limited population-based studies systematically investigating the prevalence of Neisseria meningitidis colonization in the general population. This study employs a dual-pronged epidemiological approach to systematically characterize the clinical-epidemiological profile of IMD in Xinjiang and quantify the nasopharyngeal carriage prevalence of N. meningitidis among asymptomatic populations, while identifying region-specific sociodemographic and behavioral determinants of carriage dynamics.MethodsEpidemiological characteristics were analyzed using descriptive epidemiological methods. N. meningitidis strains isolated from asymptomatic carriers underwent serogroup characterization via multiplex real-time polymerase chain reaction (real-time PCR) targeting conserved capsular biosynthesis loci (serogroups A, B, C, W, X, and Y), with reaction conditions optimized per WHO standardized protocols for meningococcal molecular typing. The ${\chi^2}$χ2 test was used to compare the N. meningitidis carriage rates. A multivariable logistic regression model was used to analyze the risk factors associated with the carriage of N. meningitidis.ResultsFrom 2004 to 2023, 1,100 cases of IMD were reported in Xinjiang, with the annual incidence rate fluctuating between 0.00/100,000 and 1.15/100,000 per year. The peak incidence occurred from February to May. The incidence was primarily concentrated in individuals under 20 years old (80.36%). Among 3,075 oropharyngeal swab specimens analyzed, 411 (13.37%; 95% CI [12.18–14.62]) yielded culture-confirmed N. meningitidis isolates. Serogroup B (168, 40.88%) emerged as the predominant meningococcal serogroup. Binomial multivariate logistic regression analyses indicated significant associations between the carriage rate of N. meningitidis and age, sex, year, region, and vaccination history (p < 0.05).ConclusionEpidemiological surveillance data from 2004 to 2023 revealed a significant decline in the incidence of IMD across Xinjiang, with the epidemiological profile transitioning from cyclic epidemic peaks to sporadic case clusters. Despite this decline, the carriage rate of N. meningitidis remained at elevated levels among healthy populations. The risk of carrying N. meningitidis was relatively high among the healthy population in the southern region of Xinjiang, people aged over 16, and those without a vaccination history. Strengthening IMD surveillance in high-risk areas is essential to prevent future outbreaks. creator: Halimubieke Nazhaerbieke creator: Wenhui Fu creator: Zhaoguo Lan creator: Yesitai Muheiyati creator: Tian Tian creator: Caipilima Wuqierjiafu creator: Na Xie uri: https://doi.org/10.7717/peerj.19772 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Nazhaerbieke et al. title: Knowledge and application of sonographic scoring models for ovarian cancer management among gynecologists in Saudi Arabia: a cross-sectional study link: https://peerj.com/articles/19746 last-modified: 2025-07-29 description: BackgroundOvarian cancer is a significant global health concern, ranking as the seventh most common cancer and the eighth leading cause of cancer-related deaths among women. Annually, it claims the lives of approximately 207,000 women worldwide. Early detection is crucial, as most cases are diagnosed at advanced stages, resulting in a 5-year survival rate of less than 20%. Common diagnostic tools include Cancer Antigen 125 (CA125) and ultrasound, but these methods are limited by sensitivity, specificity, and operator dependence. The Risk of Malignancy Index (RMI) and the Assessment of Different NEoplasias in the Adnexa (ADNEX) model, which integrates ultrasound and CA125, offer improved diagnostic accuracy. This study aims to assess the knowledge and application of these models among gynecologists in Saudi Arabia.MethodsA cross-sectional study was conducted involving 148 gynecologists from various hospitals in Saudi Arabia. Participants completed a structured questionnaire that was distributed online, designed to evaluate their knowledge and application of the RMI and ADNEX models. Data were analyzed using descriptive statistics, and factors influencing the utilization of these models were identified through multivariate logistic regression analysis.ResultsThe study found that 72% of the gynecologists were familiar with the RMI, and 58% were aware of the ADNEX model. However, only 46% reported regularly using the RMI, and 32% used the ADNEX model in their practice. Key barriers to the application of these models included a lack of training (56%), and limited access to necessary diagnostic tools (48%). Gynecologists with more than 10 years of experience were significantly more likely to use the RMI (odds ratio (OR): 2.5, 95% confidence interval (CI) [1.3–4.8]) and the ADNEX model (OR: 2.1, 95% CI [1.1–4.0]).ConclusionIn Saudi Arabia, gynecologists show moderate knowledge of sonographic scoring models for ovarian cancer management, with higher familiarity for RMI than ADNEX. However, application in clinical practice is limited. Experience level influences usage, while lack of training and diagnostic access remain key barriers. Targeted educational efforts and improved resource availability are needed to support broader clinical adoption. creator: Rana Aldahlawi uri: https://doi.org/10.7717/peerj.19746 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Aldahlawi title: Factors associated with incomplete latent tuberculosis infection preventive treatment in Sabah, Malaysia link: https://peerj.com/articles/19736 last-modified: 2025-07-29 description: BackgroundLatent tuberculosis infection (LTBI) is a critical public health issue in Malaysia, particularly in regions like Sabah, where the incidence of tuberculosis (TB) remains high. LTBI can progress to active TB if left untreated, making preventive treatment essential in reducing TB transmission. However, adherence to LTBI preventive treatment remains a significant challenge, with incomplete treatment potentially undermining efforts to control TB. This study aimed to determine the proportion of individuals with LTBI who did not complete preventive treatment and to identify associated factors.MethodsA retrospective record review was conducted among individuals with LTBI registered in the Sabah State Health Department’s LTBIS 401A registry. Multiple logistic regression analyses were applied to determine the factors associated with incomplete preventive treatment.ResultsA total of 895 individuals with LTBI were included in the study. The proportion of incomplete LTBI preventive treatment was 9.2%. Factors that were significantly associated with the incomplete preventive treatment were non-HCW occupation (adj.OR = 4.21, 95 CI [1.25–14.22]), residents of Tawau Division (adj.OR = 2.00, 95% CI [1.10–3.65]), and individuals with LTBI without contact to TB patients (adj.OR = 2.79, 95% CI [1.42–5.48]).ConclusionThe proportion of incomplete preventive treatment among individuals with LTBI in Sabah was comparatively lower than many previous studies. Targeted interventions should be developed to address the specific needs of the groups with higher odds of having incomplete preventive treatment. It includes tackling the social determinants of health, like improving healthcare system accessibility. A prospective study to evaluate these interventions’ effectiveness in improving preventive treatment completion rate is recommended. creator: Ahmad Firdaus Mohamed creator: Mohd Nazri Shafei creator: Wan Mohd Zahiruddin Wan Mohammad creator: Roddy Teo creator: Amabel Seow Min Hui uri: https://doi.org/10.7717/peerj.19736 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Mohamed et al. title: Review of the genus Microlaimus de Man, 1880 with an illustrated guide for species identification link: https://peerj.com/articles/19611 last-modified: 2025-07-29 description: Among the representatives of the family Microlaimidae, the genus Microlaimus is the most species richeness. However, the most recent literature on this genus presents species lists that diverge, in terms of composition and the number of species considered valid for Microlaimus. The morphological characteristics of this genus overlap with those of other genera of Microlaimidae, making the taxonomy of this genus complex. In the present study, we reviewed the species of the genus Microlaimus, as well as species included in genera of Microlaimidae that are morphologically similar to this taxon. Groups of species that share certain characteristics were created and represented in an illustrated guide for intraspecific identification of Microlaimus. The position of the amphidial fovea in relation to the anterior end of the body, provided important taxonomic information that was used to distinguish Microlaimus species. The presence or absence of cuticular ornamentation, the size of the spicules, the absence/presence of gubernaculum and the amphidial fovea position in relation to the anterior end of the body were characteristics used to separate the groups. Furthermore, the morphology of the male copulatory structures, as well as the composition of the cephalic arrangement (papillae, setiform papillae and setae) and the length of the cephalic setae in relation to head diameter, were also relevant for the characterization of the species. creator: Andre M. Esteves creator: Alex Manoel creator: Patricia F. Neres uri: https://doi.org/10.7717/peerj.19611 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Esteves et al. title: Biological maturation determines the beneficial effects of high-intensity functional training on cardiorespiratory fitness in male adolescents link: https://peerj.com/articles/19756 last-modified: 2025-07-28 description: BackgroundDuring adolescence, between 15–18 years of age, biological maturation is associated with changes in body composition, blood pressure (BP), and cardiorespiratory fitness (CRF). Also, environmental factors may influence the trajectory of these changes. The rising prevalence of physical inactivity calls for the identification of effective exercise modalities to mitigate adverse health outcomes in youth. Although high-intensity training regimens are increasingly recognized for their benefits in school settings, the specific role of biological maturation in determining adolescent responses to such intervention in health outcomes remains insufficiently understood.AimThis quasi-experimental study investigated the effects of chronological age (CA) and maturity offset (MO), defined as the time before/after peak height velocity, on changes in body fat (BF), BP, and CRF induced by high-intensity functional training (HIFT) and assessed the contribution of MO on these outcomes.MethodsThe sample consisted of 116 males, grouped by CA years (y) (15y [n = 30], 16y [n = 29], 17y [n = 30], 18y [n = 27]). The biological maturation effects were studied after separating the participants by quartiles of MO into four classes: late, middle late, middle early, and early matured. Participants were randomly allocated to experimental (EG) and control groups (CG). The EG performed HIFT for 8 weeks (6–14 min/twice a week). Changes in BF, BP, and CRF before and after the intervention were calculated. The MO role in the HIFT intervention was tested by MANCOVA and ANCOVA with post hoc detailed comparisons.ResultsMO contributed to the studied model more than CA (Wilk’s Λ = 0.49, ηp2 = 0.24, p < 0.001; Wilk’s Λ = 0.83, ηp2 = 0.07, p < 0.063, respectively). When controlling for age, MO was the main determinant (in comparison to CA) of the delta in CRF (F = 8.76, p < 0.001). Those who matured earliest (MO > 3.59 years after APHV) benefited more from HIFT intervention than biologically younger, independent of CA (improvement by 194.7 ± 151.5 m in the CRF test). Maturity offset was the primary contributor to the variance in ΔCRF (β = 0.71, r2sp = 9.3%, p = 0.014). When MO was combined with CA, both independent variables together explained 15% of the variance (p = 0.004).ConclusionBiological maturation plays a more important role than CA in determining HIFT-induced improvements in CRF among male adolescents: those who matured earliest exhibited the greatest gains, whereas changes in BP and BF were not significantly related to either factor. Tailoring HIFT-based interventions can be achieved by adjusting intensity, progression, and load according to each one maturity level, ensuring more developmentally appropriate exercise programs. Future research should investigate the feasibility of these maturity-focused strategies in broader adolescent populations, thereby informing larger-scale interventions and maximizing long-term health benefits. creator: Jarosław Domaradzki creator: Cristian Alvarez creator: Rafał Szafraniec creator: Dawid Koźlenia uri: https://doi.org/10.7717/peerj.19756 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Domaradzki et al. title: Cross-tolerance evolution is driven by selection on heat tolerance in Drosophila subobscura link: https://peerj.com/articles/19743 last-modified: 2025-07-28 description: The evolution of heat tolerance is crucial for the adaptive response to global warming. However, it depends on the genetic variation present in populations and the intensity of thermal stress in nature. Experimental selection studies have provided valuable insights into the evolution of heat tolerance. However, the impact of the heat stress intensity on the correlated changes in resistance traits under selection of heat tolerance has not yet been explored. In this study, the correlated response of increasing knockdown temperature in Drosophila subobscura was evaluated on the knockdown time at different stressful temperatures, the thermal death time (TDT) curves, and the desiccation and starvation resistance. Selection for increased heat tolerance was conducted using different ramping temperatures to compare the effect of heat intensity selection on resistance traits. An evolutionary increase of high temperature tolerance also confers the ability to tolerate other stresses such as desiccation and starvation. However, the extent to which these correlated responses depend on the intensity of thermal selection and sex may limit our ability to generalize these results to natural scenarios. Importantly, this study confirms the value of the experimental evolutionary approach in exploring and understanding the adaptive responses to global warming. creator: Luis E. Castañeda uri: https://doi.org/10.7717/peerj.19743 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Castañeda title: Using PLUS-InVEST-OPGD model to explore spatiotemporal variation of ecosystem carbon storage and its drivers in Jinsha river basin, China link: https://peerj.com/articles/19681 last-modified: 2025-07-28 description: Land-Use/Land-Cover Change (LUCC) is a key disturbance factor of the carbon cycle in terrestrial ecosystems, and the study on the coupling mechanism between LUCC and carbon storage is of great scientific value for implementing a regional carbon-neutral strategy. In this study, the Jinsha River Basin in Yunnan Province, which has outstanding ecological vulnerability, is taken as the research object, and a synergistic analytical framework of “spatial and temporal pattern drivers” is constructed by integrating multi-temporal remote sensing data and multi-model coupling method. Based on the high-precision 30 m land use data from 1990 to 2020, the PLUS-InVEST-OPGD multi-model coupled system was used to simulate and predict the characteristics of spatial and temporal carbon storage differentiation in 2030 under four development scenarios, namely, natural development (ND), ecological protection (EP), farmland protection (FP), and economic development (ED), and to analyze the driving mechanism using the Optimal Parameter Geodetic Probe (OPGP). The driving mechanism is analyzed using an optimal parameter geodetector. The main findings were: (1) The land use structure of the watershed in the study area showed a significant ecological-productive dichotomy, with forest land (60.58%), grassland (28.85%) and cultivated land (7.19%) constituting the core carbon sink carriers (the average proportion of which was 96.62% from 1990 to 2020). Still, the area of forest and grassland decreased by a total of 2,757.84 km2 in the past 30 years, and the expansion of construction land amounted to 2,321.91 km2; (2) the spatial and temporal evolution of carbon storage shows the heterogeneous characteristics of “overall decreasing and local optimization”, in which the carbon loss from forest to grassland conversion is as high as 30% of the total carbon loss, and the expansion of construction land leads to irreversible decay of carbon sinks of about 50%; (3) a multi-scenario simulation shows that the EP scenario minimizes the loss of carbon storage (−2.46 × 106 t) by maintaining a 96.82% ecological land share in 2030, reducing the carbon deficit by 7.79 × 106 t compared with the ND scenario; (4) the average annual temperature is the largest single factor affecting carbon storage, and its interaction with the population factor has a high q value of 0.84. This study innovatively reveals the nonlinear threshold effect of LUCC-carbon storage response in the Jinsha River Basin of Yunnan Province, and the proposed optimization model of “ecological protection” can provide decision support and corresponding reference for the construction of ecological security barriers in the upper reaches of the Yangtze River. creator: Lichang Huang creator: Xue Ding creator: Jinliang Wang creator: Shuangyun Peng uri: https://doi.org/10.7717/peerj.19681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Validation of the Malay version of the Diabetes Health Literacy Scale among Malaysian adults with type 2 diabetes mellitus link: https://peerj.com/articles/19660 last-modified: 2025-07-28 description: BackgroundThe aims of this study were to translate and adapt the Diabetes Health Literacy Scale (DHLS) to Malay, and to determine the validity and reliability of the Malay version of the DHLS (DHLS-M) among Malaysian adults with type 2 diabetes mellitus (T2DM).MethodsThe DHLS was translated and culturally adapted to Malay, followed by a cross-sectional study which was conducted using a self-administered questionnaire among the adults with T2DM in Hospital Universiti Sains Malaysia (USM). The participants were recruited by convenience sampling. Confirmatory factor analysis (CFA) and correlation analysis were performed.ResultsA total of 250 adults with T2DM participated in this study. The median age of the participants was 63.0 years old (IQR = 12.3) and most of the participants were male (51.2%). The final measurement model of DHLS-M with removal of one problematic item, fit the data well based on several fit indices: Relative chi-square (χ2/df) = 3.858, comparative fit index (CFI) = 0.981, Tucker–Lewis index (TLI) = 0.976. The composite reliability of the three subscales based on Raykov’s rho were 0.962, 0.836 and 0.828 respectively. The subscales of DHLS-M were significantly correlated with the Malay version of the Michigan Diabetes Knowledge Test (MDKT) (r = 0.26 to 0.31) and the Malay version of the short form Health Literacy Survey Questionnaire (HLS-SF12) (r = 0.43 to 0.66).ConclusionThe DHLS-M, which consisted of three subscales and 13 items, is a valid and reliable instrument for measuring diabetes health literacy among adults with T2DM in Malaysia. Its validity was further strengthened by the convergent validity with the Malay version of the MDKT and the Malay version of the HLS-SF12. creator: Pei Ling Ng creator: Wan Nor Arifin creator: Wan Mohd Izani Wan Mohamed creator: Rosnani Zakaria creator: Yee Cheng Kueh uri: https://doi.org/10.7717/peerj.19660 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ng et al. title: Validation of three functional tests against the 6-minute walk test in individuals with obesity link: https://peerj.com/articles/19755 last-modified: 2025-07-25 description: BackgroundThe six-minute walk test (6MWT) is one of the most commonly-used assessments of functional capacity. However, its length and space requirements can limit feasibility in busy clinical settings. There is limited evidence on the validity of shorter or alternative functional tests compared to the 6MWT in individuals with obesity. Therefore, this study aimed to evaluate the concurrent validity of the distance covered during the first two minutes of the 6-minute walk test (2’6MWT), the 2-minute step test (2MST) and the 1-minute sit-to-stand test (1STST) against the full 6MWT in individuals with obesity.MethodsThis was a cross-sectional study. Participants with obesity completed three functional tests—6MWT, 2MST and 1STST—on the same day. Spearman’s rank correlation was used to assess the concurrent validity of the 2’6MWT, 2MST and 1STST in relation to the 6MWT.ResultsA total of 59 individuals with obesity (16 men) participated in the study. Age was 34 (8.5) years (mean (standard deviation)), and body mass index was 40.9 (6.5) kg/m2. The 2’6MWT demonstrated a strong correlation with the 6MWT (Spearman’s rank correlation, rs = 0.87, p < 0.001), while the 2MST and the 1STST showed moderate and weak correlations, respectively (rs = 0.45, p < 0.001; rs = 0.31, p = 0.02).ConclusionThe 2’6MWT may serve as a valid alternative to the 6MWT for assessing functional capacity in individuals with obesity, offering a shorter duration and potentially reducing fatigue. The 2MST may be a more suitable alternative to the 1STST in settings with limited space for walking tests. creator: Thapanun Mahisanun creator: Jittima Saengsuwan uri: https://doi.org/10.7717/peerj.19755 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mahisanun and Saengsuwan title: The value of inflammatory indices in the diagnosis of acute appendicitis and prediction of complicated appendicitis: a retrospective study link: https://peerj.com/articles/19754 last-modified: 2025-07-25 description: BackgroundAcute appendicitis is a common cause of acute abdominal pain, typically treated surgically, although medical management is also an option. Laboratory investigations play a valuable role in diagnosis and predicting prognosis. We aimed to investigate and compare the effectiveness of indices such as the Systemic Immune-Inflammation Index (SII), Systemic Inflammatory Response Index (SIRI), and Pan-Immune-Inflammatory Value (PIV), all derived from complete blood count, in diagnosing acute appendicitis and distinguishing between complicated and uncomplicated cases.MethodsWe retrospectively analyzed data from 334 patients diagnosed with acute appendicitis and 350 healthy individuals. The SII, SIRI, and PIV parameters were compared between the acute appendicitis group and the healthy group. The SII, SIRI, and PIV parameters were also compared between the complicated and uncomplicated groups.ResultsAll three parameters demonstrated good performance in predicting the diagnosis of appendicitis. An SII value above 1,008.43 (p < 0.0001, AUC = 0.707), a SIRI value above 2.60 (p < 0.0001, AUC = 0.743), and a PIV value above 904.85 (p < 0.0001, AUC = 0.726) were found to support the diagnosis of appendicitis. For predicting complicated appendicitis, thresholds were identified as SII values above 2501.13 (p = 0.0012, AUC = 0.634), SIRI values above 7.98 (p = 0.0005, AUC = 0.645), and PIV values above 1,869.66 (p = 0.0012, AUC = 0.635).ConclusionsAll three indices showed good predictive performance for diagnosing appendicitis and acceptable performance for predicting complicated cases. Among the indices, SIRI was slightly superior to the other two in both scenarios. creator: Akif Yarkaç creator: Çiğdem Öncü Güldür creator: Seyran Bozkurt creator: Ataman Köse creator: Çağrı Safa Buyurgan creator: Semra Erdoğan creator: Tuba Kara uri: https://doi.org/10.7717/peerj.19754 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yarkaç et al. title: First report of microplastics in the gastrointestinal tracts of North American insectivorous bats link: https://peerj.com/articles/19740 last-modified: 2025-07-25 description: BackgroundMicroplastics (MPs) are among the many ubiquitous environmental contaminants of emerging concern for both aquatic and terrestrial species. Bats have integral roles in aquatic-terrestrial food webs on almost every continent, are exposed to a wide variety of environmental contaminants, and yet have received limited investigation about the threat of MPs. While MPs have been detected in numerous bird species and in bats of the Amazon, there are no published studies documenting the dietary MP exposure of North American bats that consume many terrestrial and aquatic arthropods or the possible adverse effects of exposure.MethodsWe chemically digested bat gastrointestinal tracts (GITs) to extract, quantify, and characterize MPs that accumulated in insectivorous Eptesicus fuscus (big brown bats). We quantified MPs in procedural blanks to account for background contamination in the lab for controls and compared concentrations in bat GITs to controls. We measured the mass of bat carcasses, minus the brains, prior to necropsy to determine body condition. We investigated the relationship between MP concentrations in bat GITs to body condition to determine if higher concentrations indicated reduced bat body condition using linear regression.ResultsOur results indicate that the ingestion of MPs by bats could lead to lower bat mass, potentially related to poorer body condition or ability to store fat. The ability to store and use fat is crucial for the survival of these migrating and cave-hibernating species. Moreover, bats with higher fat stores are more likely to survive multiple stressors such as the non-native fungal disease white-nose syndrome. This study will allow future research to build off baseline information and further explore the effects of MPs to individuals and populations of bats of conservation concern. creator: Ashleigh B. Cable creator: Emma V. Willcox creator: Leah N. Crowley creator: Christy Leppanen uri: https://doi.org/10.7717/peerj.19740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cable et al. title: Factors influencing natural regeneration of Fagus hayatae link: https://peerj.com/articles/19761 last-modified: 2025-07-24 description: BackgroundNatural regeneration is pivotal for sustaining evolutionary processes in plant species. Identifying determinants that shape recruitment dynamics could elucidate key factors governing this critical biological process. However, the relationship between environmental variables and recruitment patterns in Fagus hayatae remains uninvestigated, despite its dual significance as a species endemic to China and a National Grade II Protected Plant. This knowledge gap persists even though understanding such ecological interactions could enhance conservation management for this vulnerable endemic tree species.MethodsThis study employed Pearson correlation analysis, redundancy analysis (RDA), and structural equation modeling (SEM) to examine environmental factors of natural regeneration in Fagus hayatae populations across ontogenetic stages (seedling, sapling, small tree) within three stratified elevational bands (low: 1,670–1,700 m; mid: 1,770–1,800 m; high: 1,890–1,940 m) of Micangshan Nature Reserve, located in Sichuan Province, China.ConclusionsStructural equation modeling (SEM) revealed altitude-specific environmental regulation of Fagus hayatae regeneration dynamics. In low-altitude stands (1,670–1,700 m), the litter layer emerged as the primary limiting factor for seedling density (direct effect: −0.80), while diameter at breast height (DBH) suppressed sapling density through direct negative pathways (−0.63). Soil pH exhibited indirect positive mediation on seedling establishment via litter layer modification (0.42), suggesting synergistic management of litter removal and soil acidity regulation enhances regeneration success. Mid-elevation populations (1,770–1,800 m) demonstrated contrasting dynamics: DBH positively influenced sapling density (0.57), small tree density (0.89), and height growth (0.38), whereas available potassium indirectly reduced regeneration capacity through cascading effects involving canopy structure (DBH-mediated) and soil moisture, necessitating balanced canopy light penetration and weak acidic pH maintenance. High-altitude ecosystems (1,890–1,940 m) exhibited distinct nutrient-temperature synergies: available potassium exerted the strongest direct positive effect on small tree density (0.70), while air temperature (0.58) and litter thickness (0.53) jointly promoted vertical growth, highlighting the dual importance of organic layer preservation and thermal constraint mitigation in alpine forest regeneration. These findings delineate elevation-dependent multifactorial interaction networks governing Fagus hayatae population dynamics, establishing mechanistic frameworks for natural regeneration prediction while informing altitude-specific silvicultural interventions to optimize conservation outcomes. creator: Chun Qin creator: Meng Tang creator: Xue-mei Zhang uri: https://doi.org/10.7717/peerj.19761 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Qin et al. title: Effects of unstable training on muscle activation: a systematic review and meta-analysis of electromyographic studies link: https://peerj.com/articles/19751 last-modified: 2025-07-24 description: ObjectiveTo systematically evaluate the effects of unstable training (UT) on muscle activation and provide activation prescriptions for different muscle regions, offering more targeted guidance for different populations in muscle activation.MethodsData extraction and meta-analysis were conducted using RevManager 5.3, Stata 16.0, and R software. Subgroup analyses were performed on five variables: exercise equipment, exercise intensity, exercise mode, exercise experience, and contraction mode. Heterogeneity and publication bias were also examined.ResultsA total of 28 studies were included, involving 579 participants. Comparison of activation effects between unstable training and stable training: Significant increases in core muscle activation, including rectus abdominis (SMD = 0.32, 95% CI [0.18–0.46], P < 0.01), internal oblique (SMD = 0.38, 95% CI [0.20–0.56], P < 0.01), external oblique (SMD = 0.38, 95% CI [0.20–0.56], P < 0.01), and erector spinae (SMD = 0.60, 95% CI [0.17–1.02], P < 0.01); Significant increases in upper limb muscle activation, including biceps brachii (SMD = 0.52, 95% CI [0.23–0.80], P < 0.01), trapezius (SMD = 0.23, 95% CI [0.12–0.35], P < 0.01), serratus anterior (SMD = 0.33, 95% CI [0.07–0.59], P = 0.01), and triceps brachii (SMD = 0.24, 95% CI [0.04–0.45], P = 0.02); Significant increases in lower limb muscle activation, including soleus (SMD = 0.65, 95% CI [0.42–0.87], P < 0.01), gluteus medius (SMD = 0.28, 95% CI [0.05–0.52], P = 0.02). In subgroup analysis, the core muscles with the great effect were: rectus abdominis (Bosu ball, body weight, sit-ups), internal oblique (Swiss ball, relative load, bench press), external oblique (Swiss ball, body weight, sit-ups), erector spinae (TRX suspension, body weight, bridging); the upper limb muscles with the great effect were: biceps brachii (more than 1 year of training experience, TRX suspension, body weight, muscle-up), trapezius (less training experience, Bosu ball, body weight, push-ups), triceps brachii (body weight). The lower limb muscles with the great effect were: soleus (squats). Negative activation effects: erector spinae (Swiss ball, 60% 1RM load, and shoulder press), serratus anterior (Swiss ball), triceps brachii (more than 1 year of training experience), Swiss ball, >60% 1RM; rectus femoris (Bosu ball, squats).ConclusionUnstable training is an excellent choice for rehabilitation after sports injuries, pre-exercise activation, and enhancing specific sports abilities. It can significantly activate core, upper limb, and lower limb muscles. In the future, more rigorous research should be carried out, providing a larger sample size and more meticulous evaluation methods for further comparative analysis. creator: Zihan Bao creator: Shun Wang creator: Ziyang Li uri: https://doi.org/10.7717/peerj.19751 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bao et al. title: Prevalence and associated factors of physical-psychological-cognitive multimorbidity in Chinese community-dwelling older adults: a cross-sectional study link: https://peerj.com/articles/19750 last-modified: 2025-07-24 description: BackgroundThe rising prevalence of physical-psychological-cognitive (PPC) multimorbidity among older adults poses significant challenges. Understanding its prevalence and associated risk factors is crucial for the development of targeted and effective care strategies.MethodsThis cross-sectional study utilized convenience sampling to survey older adults residing in two cities in Sichuan Province and Chongqing, Southwest China, between September 2024 and December 2024. Data were collected using the General Information Questionnaire, EQ-5D-5L, HALFT scale, Patient Health Questionnaire-9, and the 8-item Ascertain Dementia tool. Univariate and multivariate logistic regression analyses were performed to identify predictors of PPC multimorbidity.ResultsA total of 437 participants were included, with 75 having PPC multimorbidity and 362 without, resulting in a prevalence of PPC of 17.2%. Social frailty was observed in 17.8%. Multivariate logistic regression identified long-term medication use (OR = 3.24, 95% CI [1.28–8.21]), higher multimorbidity burden (OR = 7.31, 95% CI [3.27–16.36]), social frailty (OR = 3.49, 95% CI [174–7.01]), and lower EQ-5D scores (OR = 0.07, 95% CI [0.02–0.26]) as significant predictors of PPC status (all p < 0.05).ConclusionThis study highlights the burden of PPC multimorbidity in older adults in China, with key factors including long-term medication use, advanced multimorbidity, social frailty, and poor quality of life. It calls for a patient-centered care approach that addresses these issues, with future research focusing on larger, diverse samples to guide targeted interventions. creator: Lin Lin creator: Di-fei Duan creator: Linjia Yan creator: Hai yan He uri: https://doi.org/10.7717/peerj.19750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lin et al. title: NRF2 polymorphism and susceptibility to ischemic stroke in a Chinese population link: https://peerj.com/articles/19742 last-modified: 2025-07-24 description: BackgroundIschemic stroke (IS) is a major health concern in the Chinese population. Previous studies have highlighted the role of NRF2 in IS. This study investigates the association between NRF2 polymorphisms and IS susceptibility in a Chinese population.MethodsThis retrospective study included Chinese patients diagnosed with IS based on clinical symptoms, neurological examinations, and brain imaging findings from computed tomography or magnetic resonance imaging. Age- and sex-matched unrelated individuals with no family history of stroke, tumors, or genetic diseases served as controls. Peripheral blood samples were collected to genotype seven single-nucleotide polymorphisms (SNPs) in NRF2 (rs13005431, rs4893819, rs6721961, rs35652124, rs6726395, rs2364723, rs2706110) using the SNaPshot method. Binary logistic regression analysis was used to assess associations between these SNPs and IS risk. NRF2 and reactive oxygen species (ROS) levels in peripheral blood were measured. The relationship between rs35652124 and NRF2 expression was evaluated using expression quantitative trait locus (eQTL) analysis.ResultsAll seven NRF2 SNPs conformed to Hardy–Weinberg equilibrium. Six SNPs (rs13005431, rs4893819, rs6721961, rs6726395, rs2364723, and rs2706110) showed no significant differences in distribution between the case and control groups (p > 0.05). However, the TC genotype of rs35652124 in the co-dominant model was significantly associated with increased IS risk. The distribution of this genotype aligned with trends observed in East Asia and the Chinese Han population but varied across other global populations. The CCTTGGC haplotype was the most common in both groups. Stratified analysis of rs35652124 showed no association with confounding factors such as age, sex, hypertension, diabetes, or lipid levels. NRF2 and ROS levels were higher in IS patients than in controls, but did not differ by rs35652124 genotype. Concurrently, eQTL analysis indicated that rs35652124 did not affect NRF2 expression in peripheral blood.ConclusionThe NRF2 rs35652124 polymorphism is associated with IS susceptibility, suggesting it may be a potential genetic risk factor for IS. creator: Pengyu Wang creator: Junxiu Lu creator: Min Wang creator: Guangming Wang creator: Huaqiu Chen uri: https://doi.org/10.7717/peerj.19742 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Curcumin inhibits type III secretion of Pseudomonas aeruginosa link: https://peerj.com/articles/19725 last-modified: 2025-07-24 description: Pseudomonas aeruginosa is a remarkable opportunistic bacterium that represents a global health concern, due to its ubiquity and high levels of antibiotic resistance. Hence, the development of novel antimicrobials or alternative therapies against its infections is urgent. In this regard, anti-virulence therapies are a promising option to minimize pathogen mediated damage to the host rather than directly kill pathogenic bacteria. To date several natural and synthetic compounds had shown activity against quorum sensing regulated virulence factors of P. aeruginosa; nevertheless, the type three secretion system (T3SS), also known as injectisome, represents one of the main virulence factors of this bacterium, and a major contributor for acute infections. Importantly, the expression and activity of the injectisome appears not to be positively regulated by quorum sensing, and hence the use of specific quorum quenching enzymes does not inhibit type three secretion. In this work, we characterized the type three secretion profile of effector proteins in a collection of clinical isolates of P. aeruginosa isolated from burn patients and respiratory infections. Immunoblotting showed that the presence of an active T3SS is common in these strains, confirming it is an important determinant for its infections. Furthermore, we demonstrate that the natural compound curcumin can effectively inhibit the secretion of the main effectors ExoS and ExoU in PA01 and PA14, the main reference strains of this bacterium, as well as in representative clinical isolates. This inhibition of effectors secretion occurs despite their intracellular accumulation upon curcumin treatment, suggesting that curcumin do not work by impeding effectors expression but rather by interfering with either the assembly or the function of the T3SS. creator: Miguel Diaz-Guerrero creator: Luis Esaú López-Jácome creator: Rafael Franco-Cendejas creator: Rafael Coria-Jiménez creator: María Guadalupe Martínez-Zavaleta creator: Bertha González-Pedrajo creator: Daniel Huelgas-Méndez creator: Rodolfo García-Contreras uri: https://doi.org/10.7717/peerj.19725 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Diaz-Guerrero et al. title: GEDTM30: global ensemble digital terrain model at 30 m and derived multiscale terrain variables link: https://peerj.com/articles/19673 last-modified: 2025-07-24 description: Production and validation of an open global ensemble digital terrain model (GEDTM30) and derived terrain variables at 1 arc-s spacing grid ($\sim$∼30 m spatial resolution) is described. Copernicus DEM, ALOS World3D, and object height models were combined in a data fusion approach to generate a globally consistent digital terrain model (DTM). This DTM was then used to compute 15 standard terrain variables across six scales (30, 60, 120, 240, 480 and 960 m). A global-to-local transfer learning model framework with 5° × 5° tiling leveraged globally distributed lidar datasets: ICESat-2 ATL08 (best-fit terrain height) and GEDI02 (lowest mode elevation), totaling over 30 billion training points. A global model was initially fitted using ICESat-2 and GEDI, followed by locally optimized models per tile, ensuring both global consistency and local accuracy. Independent validation shows that GEDTM30 reduces Copernicus DEM RMSE by about 25.4% in built-up areas, 10.0% in regions with 10–50% tree cover, and 27.3% in areas with over 50% tree cover. Compared to state-of-the-art DTMs (MERIT DEM, FABDEM and FathomDEM), GEDTM30 achieves the lowest vertical errors when assessed with GNSS station records, yielding a standard deviation of 7.77 m, an RMSE of 10.69 m, and a mean error of 7.34 m. FathomDEM exhibited the lowest vertical RMSE when validated against independent reference DTMs. GEDTM30 was further used to generate multiscale variables of topography and hydrology through an optimized tiling workflow ($\sim$∼800 tiles of 600 × 600 km with $\sim$∼16% overlap) based on the Equi7 grid system. The entire workflow was implemented in Python using GDAL and Whitebox Workflows. Visual inspection confirmed the absence of boundary artifacts and the preservation of hydrologic connectivity. The tiling-based implementation significantly reduces computational costs of generating large-scale DTMs and derived terrain variables. The GEDTM30 dataset and code are publicly available as Cloud-Optimized GeoTIFFs via Zenodo and the OpenLandMap STAC. Further fusion with local lidar-based DTMs and national DTMs is recommended to enhance local accuracy and level of detail. creator: Yu-Feng Ho creator: Carlos H. Grohmann creator: John Lindsay creator: Hannes I. Reuter creator: Leandro Parente creator: Martijn Witjes creator: Tomislav Hengl uri: https://doi.org/10.7717/peerj.19673 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ho et al. title: The role of macrophages in renal fibrosis and therapeutic prospects link: https://peerj.com/articles/19769 last-modified: 2025-07-23 description: Monocytes/macrophages are the key regulators of tissue repair, regeneration, and fibrosis. Monocyte-derived macrophages, which are characterized by high heterogeneity and plasticity, are recruited, activated, and polarized throughout the process of renal fibrosis in response to the local microenvironment. Increasing evidence suggests that phenotypic changes in macrophages are essential for chronic kidney disease (CKD) development and progression. Advanced bioinformatics and single-cell RNA sequencing analyses have revealed the critical mechanisms of macrophage iron homeostasis dysregulation and macrophage-to-myofibroblast transition (MMT), which may be a novel therapeutic target for renal fibrosis. In this review, we systematically examine the dynamic phenotype transitions of macrophages across distinct phases of kidney injury progression. Notably, we provide new insights into the multifaceted crosstalk between renal macrophages and neighboring parenchymal cells, including tubular epithelial cells, fibroblasts, podocytes, mesangial cells, and endothelial cells, mediated through diverse mechanisms, including soluble factors, extracellular vesicles, and direct cell-cell contact, and highlight the therapeutic potential of targeting macrophages. creator: Di Niu creator: Jun Jie Yang creator: Dan Feng He uri: https://doi.org/10.7717/peerj.19769 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Niu et al. title: New Andean plump toad of the genus Osornophryne (Anura: Bufonidae) from Cerro Candelaria, Ecuador link: https://peerj.com/articles/19760 last-modified: 2025-07-23 description: The amphibian genus Osornophryne is endemic to the northern Andes of South America and has long been considered rare. Recent explorations in the humid montane forests of the upper Pastaza Valley have uncovered previously unknown species. Here, we describe a new Andean toad species from the central Ecuadorian Andes, identified through genetic analyses and distinctive morphological and cranial traits. Osornophryne backshalli sp. nov., from Cerro Candelaria in the upper Pastaza River basin, is closely related to O. sumacoensis from Sumaco Volcano. This new species is characterized by a uniquely short fifth toe relative to toes I–III, triangular papillae on the snout tip, an occipital fold, large subconical and conical warts on the body, dorsal surfaces Brownish Olive with Spectrum Yellow and Light Neutral Gray flecks, ventral surfaces Brownish Olive with Spectrum Yellow bright blotches. Our phylogenetic analyses revise the genus taxonomy by delimiting two well-supported clades: the Osornophryne bufoniformis species group and the Osornophryne guacamayo species group. Furthermore, we show that the Pastaza River does not constitute a geographical barrier for Osornophryne distribution. These findings emphasize the value of continued exploration to expand our understanding of this genus in the humid montane forests of the Ecuadorian Andes. creator: Juan P. Reyes-Puig creator: Miguel A. Urgiles-Merchán creator: H. Mauricio Ortega-Andrade creator: Diego F. Cisneros-Heredia creator: Julio C. Carrión-Olmedo creator: Mario H. Yáñez-Muñoz uri: https://doi.org/10.7717/peerj.19760 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Reyes-Puig et al. title: Impact of kombucha, coffee, and turmeric beverages on the color stability of a single-shade versus a multi-shade resin-based composite link: https://peerj.com/articles/19759 last-modified: 2025-07-23 description: Currently, patients place great significance on both the appearance and health benefits of dental treatments. Single-shade resin-based composites (RBC) are commonly used in clinical practice, but various popular caffeinated and healthy drinks can lead to staining. This study aimed to compare the resistance of a newly introduced single-shade RBC with an advanced polymerization system (APS) to turmeric, kombucha, and coffee staining as compared to that of a conventional multi-shade RBC. Sixty specimens (8 × 5 × 2 mm) were created using two types of RBCs: a single-shade (Vittra APS Unique, FGM Dental Group, Joinville, SC, Brazil) and a conventional universal RBC (Tetric N-Ceram, Ivoclar Vivadent, Germany). The samples were randomly divided into two main groups (N = 30) based on the RBC used. Each group was further divided into three subgroups (n = 10) based on the storage media, including turmeric, kombucha, and coffee (positive control). Color readings were recorded after 0, 6, and 12 days of immersion. The mean color change (ΔE (both ΔE*ab and ΔE00)) values were statistically analyzed using repeated measure mixed design ANOVA and Bonferroni multiple comparisons (p < 0.05). The results of the study indicated that time had a statistically significant effect on ΔE (p < 0.001). The three-way interaction (time*material*solution) was also found to be statistically significant (p = 0.005). Turmeric caused a significantly higher ΔE compared to both coffee and kombucha (p < 0.001). Tetric N-Ceram exhibited a significantly lower ΔE than Vittra APS Unique (p = 0.004). In conclusion, with consideration of the limitations of the study, it can be stated that single-shade RBCs with APS are less color-stable than universal RBCs. The study also indicates that both kombucha and coffee can affect the color stability of RBCs, whereas turmeric has the most detrimental effect on the color of dental composites. creator: Hanin E. Yeslam creator: Abdulaziz F. Bakhsh uri: https://doi.org/10.7717/peerj.19759 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yeslam and Bakhsh title: Identification and classification of Aquilaria (Thymelaeaceae): inferences from a phylogenetic study based on matK sequences link: https://peerj.com/articles/19752 last-modified: 2025-07-23 description: In the realm of Aquilaria classification and grading, a persistent market uncertainty persists, questioning whether the basis should be geographical distribution or biological origin. In this study, the effectiveness of matK molecular markers, particularly through eight stable polymorphic loci (e.g., +249C for Chinese origin, +435G for Aquilaria sinensis), emerges as a decisive tool for differentiating Aquilaria species. The integration of matK and trnL-trnF not only validates this efficacy but also streamlines the systematic categorization of 34 agarwood products into four biogeographic pedigrees: Chinese (C1: A. sinensis; C2: A. malaccensis), Indonesian (A. cumingiana), and Indochinese (A. rugosa). Molecular clock analyses trace the genus’s divergence to 6.78 million years ago (Ma) (A. hirta), with recent speciation of commercially pivotal species (A. sinensis:  0.9 Ma; A. malaccensis:  1.0 Ma). Notably, the redefined placement of Gyrinops walla (5.75 Ma) within Aquilaria challenges prior taxonomic assumptions, suggesting revised genus boundaries. The Median-Joining network further visualized these haplotypes, showing key evolutionary transitions, particularly from A. crassna to A. rugosa and A. malaccensis. These findings provide robust tools for species differentiation, insights into evolutionary history, and practical guidance for conservation and trade applications within the field of botany. creator: Zhaoqi Xie creator: Siqing Fan creator: Junyu Xu creator: Haijing Xiao creator: Jiaxin Yang creator: Min Guo creator: Chunsong Cheng uri: https://doi.org/10.7717/peerj.19752 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xie et al. title: West Nile Virus (Orthoflavivirus nilense) RNA concentrations in wastewater solids at five wastewater treatment plants in the United States link: https://peerj.com/articles/19748 last-modified: 2025-07-23 description: BackgroundOrthoflavivirus nilense, formerly known as West Nile Virus (WNV), has become endemic to the United States since its introduction in 1999. Current surveillance methods rely primarily on mosquito pool testing, which is both costly and time-intensive. Wastewater-based epidemiology (WBE) has proven an effective method for the surveillance of various pathogens, including other orthoflaviviruses such as Dengue. WBE for WNV represents a potentially valuable surveillance approach that has so far been underexplored.MethodsA targeted droplet digital reverse transcription-polymerase chain reaction (RT-PCR) approach (ddRT-PCR) was used to measure WNV concentrations in wastewater retrospectively from five locations and in over 600 samples. Three of these locations were in communities with multiple confirmed WNV infections, while two were not. Samples were collected during periods corresponding to typical WNV seasonality (spring to fall). SARS-CoV-2 RNA was measured simultaneously to assess nucleic acid degradation during sample storage. Publicly available confirmed WNV case data were compiled from the California and Nebraska departments of public health and their weekly arboviral reports.ResultsWNV RNA was detected in wastewater samples during periods of known viral circulation within a community. The adopted ddRT-PCR assay is highly specific and sensitive, and detections in wastewater solids correspond to the occurrence of cases in the season and location of sampling. WNV was detected in nine samples in three locations with known WNV clinical cases—wastewater positivity rates in these locations ranged from 3.3% to 13%. The results suggest that wastewater monitoring could serve as an effective complement to traditional surveillance methods, particularly for sentinel surveillance in locations which do not have extensive mosquito and clinical testing systems. creator: Alessandro Zulli creator: Dorothea Duong creator: Bridgette Shelden creator: Amanda Bidwell creator: Marlene K. Wolfe creator: Bradley White creator: Alexandria B. Boehm uri: https://doi.org/10.7717/peerj.19748 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zulli et al. title: Transcriptome and metabolome profiling reveal the inhibitory effects of food preservatives on pathogenic fungi link: https://peerj.com/articles/19737 last-modified: 2025-07-23 description: Sec-butylamine, potassium sorbate, and citric acid were selected as preservatives to investigate their inhibitory effects on common plant pathogens—Aspergillus flavus, Alternaria alternata, and Talaromyces funiculosus—as well as the inhibitory mechanism of sec-butylamine against A. flavus. The results showed that all three preservatives significantly inhibited the growth of the tested fungi. Under the experimental conditions, 0.6% sec-butylamine, 1.2% citric acid, and 0.2% potassium sorbate completely inhibited the growth of A. flavus. Similarly, 0.5% sec-butylamine, 1.0% citric acid, and 0.6% potassium sorbate completely inhibited A. alternata, while 1.0% sec-butylamine, 1.2% citric acid, and 0.8% potassium sorbate completely inhibited T. funiculosus. All three preservatives exhibited strong inhibitory activity against mycelial growth, with inhibition increasing alongside concentration under ex vivo conditions. To explore the inhibitory mechanism of sec-butylamine on A. flavus, transcriptomic and metabolomic analyses were conducted on A. flavus mycelia before and after treatment. The results revealed that key genes such as AFLA_053390, AFLA_121370, AFLA_024930, and AFLA_041970 were significantly downregulated following sec-butylamine exposure. Additionally, AFLA_002830 and AFLA_030450 also showed reduced expression levels. Metabolomic analysis identified several metabolites associated with sec-butylamine treatment. Compounds such as (3R)-4,4-dimethyl-2-oxotetrahydro-3-furanyl β-D-glucopyranoside (Com_5857_neg), trehalose (Com_3182_neg), D-glucosamine 6-phosphate (Com_4401_neg), and sucrose (Com_494_neg) were elevated, while D-gluconic acid (Com_9540_neg), D-glucose 6-phosphate (Com_723_neg), verbascose (Com_11501_neg), and D-(-)-fructose (Com_285_neg) were reduced after treatment. This study provides a reference for the practical application of food preservatives and lays a foundation for further research into their antifungal mechanisms. creator: Zhenxia Shi creator: Ni Zhan creator: Ming Ma creator: Zhen Wang creator: Xunyou Yan creator: Rumeng Li creator: Xuejuan Liu uri: https://doi.org/10.7717/peerj.19737 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shi et al. title: Effects of soy isoflavones on menopausal symptoms in perimenopausal women: a systematic review and meta-analysis link: https://peerj.com/articles/19715 last-modified: 2025-07-23 description: Soy isoflavones are phytoestrogens found mainly in soy and its derivatives. Given their estrogen-like and antioxidant-inhibiting inflammatory effects, they have been hypothesized to be effective in treating menopausal symptoms. We conducted a systematic review in accordance with the PRISMA guidelines. In October 2024, we screened 2,099 articles, of which 12 were eligible for meta-analysis, and found that soy isoflavones were effective for treating menopausal symptoms (seven studies, 533 participants, Hedges’ g = −0.25, 95% CI [−0.42 to −0.08], p = 0.00). Soy isoflavones showed significant effects on headache (three studies, 340 participants, Hedges’ g = −0.38, 95% CI [−0.60 to −0.17], p = 0.00), psychosocial symptoms (five studies, 416 participants, Hedges’ g = −0.29, 95% CI [−0.48 to −0.10], p = 0.00), palpitation (three studies, 356 participants, Hedges’ g = −0.42, 95% CI [−0.63 to −0.22], p = 0.00), and depression (four studies, 748 participants, Hedges’ g = −0.72, 95% CI [−1.17 to −0.28], p = 0.00), but no significant treatment effect on paresthesia symptoms, fatigue symptoms, physical symptoms, hot flushes, excessive sweating, insomnia, and vasomotor symptoms was observed. However, our results should be interpreted with caution owing to the small sample size. More trials should be conducted in the future to validate our findings. creator: Haodi Luan creator: Qianqian Liu creator: Yahui Guo creator: Hua Fan creator: Sileng A. creator: Jing Lin uri: https://doi.org/10.7717/peerj.19715 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Luan et al. title: Psychological distress and problematic internet use among language teachers: a latent profile analysis link: https://peerj.com/articles/19707 last-modified: 2025-07-23 description: BackgroundGiven the limited attention to psychological distress (PD) and problematic internet use (PIU) among language teachers, the study tried to reveal the different PD profiles and their association with PIU.MethodsWe first employed latent profile analysis (LPA) to identify the latent profiles within a cohort of language teachers in China and then utilized multivariate logistic regression analysis to explore the demographic characteristics associated with different PD profiles. After that, one-way analysis of variance (ANOVA) was conducted to examine the relationships between PD and PIU.ResultsThe LPA identified three distinct latent profiles of PD: the moderate-to-severe PD profile, the mild PD profile, and the mentally healthy profile. The results of multivariate logistic regression indicated that male and experienced language teachers were more likely to experience severe PD. The results of one way ANOVA suggested that language teachers experiencing PD reported notably higher levels of PIU, with those in the moderate-to-severe PD group scoring particularly high in internet gaming disorder.DiscussionResults of this study indicate the close association between PD and PIU in language teachers. These findings underscore the critical need to address PD among language teachers and emphasize the importance of education and training aimed at promoting teachers’ appropriate internet use. Breaking the “PD–PIU” vicious cycle is essential for fostering better mental health and well-being within this professional group. creator: Zizheng Shen creator: Honggang Liu creator: I-Hua Chen uri: https://doi.org/10.7717/peerj.19707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shen et al. title: Combining echocardiography with carotid ultrasound parameters in predicting major adverse cardiovascular events among older individuals with coronary artery disease link: https://peerj.com/articles/19688 last-modified: 2025-07-23 description: ObjectiveTo investigate the predictive value of combining echocardiography with carotid ultrasound for major adverse cardiovascular events (MACE) among older individuals with coronary artery disease.MethodsA total of 138 elderly individuals diagnosed with coronary artery disease and admitted to our facility from June 2020 to June 2021 were included in this study. These patients were categorized into two groups: a non-MACE group consisting of 84 patients and a MACE group with 54 patients, based on whether they experienced MACE within three years following their discharge. Additionally, a validation cohort of 141 patients was assembled, which was also divided into a non-MACE group with 90 patients and a MACE group with 51 patients. Upon admission, all participants underwent both transthoracic echocardiography and carotid ultrasound assessments. We then conducted a comparative analysis of the ultrasound parameters between the two groups.ResultsThe MACE group had higher left ventricular end-diastolic diameter (LVEDD), carotid intima-media thickness (IMT), and Crouse score, and lower left ventricular ejection fraction (LVEF) and A-wave velocity (all P < 0.05). LVEDD, IMT, and Crouse score were risk factors for MACE, while LVEF and A value were protective factors against MACE. Derivation area under the curve (AUC) = 0.755; validation AUC = 0.754.ConclusionEchocardiography and carotid ultrasound parameters can be used to predict the occurrence of MACE within 3 years in elderly patients with coronary artery disease, and combined detection can effectively improve the accuracy of prediction. creator: Tianli Jia creator: Xiaoxiao Li creator: Qianqian Xie uri: https://doi.org/10.7717/peerj.19688 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jia et al. title: Metagenomics-based analysis of mobile genetic elements and antibiotic/metal resistance genes carried by treated wastewater link: https://peerj.com/articles/19682 last-modified: 2025-07-23 description: Wastewater treatment plants in Tunisia are recognized as key locations for the spread of antibiotic and heavy metal resistance genes among bacteria. Despite the widespread presence of pollutants in these treatment systems, there is still a significant gap in our understanding of resistance dynamics. This study focused on analyzing the bacterial community and resistome-mobilome profiles of the Charguia wastewater treatment plant (WWTP). Using metagenomics sequencing, six samples from the influent, sludge, and effluent were thoroughly examined. Our research findings indicated the prevalence of Proteobacteria and high levels of Bacteroidota, Firmicutes, Campylobacterota, and Patescibacteria. After conducting a species level analysis, we identified important species such as Pseudomonas psychrophila, Pseudomonas fragi, Pseudomonas lundensis, Acinetobacter johnsonii, and Thiothrix unzii linked to antibiotic resistant genes (ARGs) like mdtA and merR1 and heavy metal resistance genes (MRGs), including czcA and cnrA. Our study illustrated the persistence of specific species in the effluent due to the co-occurrence of ARGs/MRGs and mobile genetic elements (MGE). Notably, IncQ and IncP were found to be associated with mdtA, mexR, arsR1, and merR. The conclusions drawn from our research suggest that the WWTP has been potentially effective in reducing multidrug resistance. creator: Chahnez Naccache creator: Chourouk Ibrahim creator: Abdennaceur Hassen creator: Maha Mezghani Khemakhem uri: https://doi.org/10.7717/peerj.19682 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Naccache et al. title: A study of salivary cortisol and glutamate after the cold pressor task in healthy adults link: https://peerj.com/articles/19625 last-modified: 2025-07-23 description: Nociception related salivary biomolecules can be a useful future aid in the assessment of acute pain. We have investigated changes in the levels of two salivary biomolecules, glutamate and cortisol, following the induction of acute cold pain using the cold pressor task (CPT). Saliva samples were collected from 18 healthy volunteers before, immediately after and then, every 10 minutes for one hour after CPT. Statistical analysis of the biomolecule concentrations across all participants and time points were done. This showed significant differences between salivary cortisol concentration before (median 0.14 µg/dL, Interquartile Range (IQR) = 0.1) and 10 minutes after termination of CPT (median 0.34 µg/dL, IQR = 0.4, p = 0.007). Male participants exhibited a greater increase in cortisol concentration after cold pain compared to females. The timeline and pattern of the rise in salivary cortisol concentration in this study are consistent with existing literature. Salivary glutamate concentration fluctuated but none of the changes were statistically significant except at t =  + 50 minutes, when the concentration had dropped below baseline. The findings do not support the use of glutamate as a useful biomarker in acute pain despite evidence that plasma and salivary glutamate levels are higher in people with chronic pain conditions such as migraine and temporomandibular disorder. creator: Roxaneh Zarnegar creator: Angeliki Vounta creator: Arisara Amrapala creator: Sara S. Ghoreishizadeh uri: https://doi.org/10.7717/peerj.19625 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zarnegar et al. title: Impact of P fertilizer and arbuscular mycorrhizal fungi on forage legume growth, chlorophyll content and productivity link: https://peerj.com/articles/18955 last-modified: 2025-07-23 description: Soil phosphorous (P) is the most limiting plant nutrient globally, reducing forage plant productivity. Although inorganic P fertilizers are used, about 75–90% of P becomes unavailable for plant uptake, hence, the strategies to enhance P uptake acquisition, such as the use of arbuscular mycorrhizal fungi (AMF) inoculation, are crucial. A greenhouse pot experiment was conducted under controlled environmental conditions at the University of Fort Hare, where three legume species (Vigna unguiculata, Lablab purpereus and Mucuna pruriens) were grown for 90 days under five P fertilizer levels (0; 0.68; 1.36; 2.04 and 2.72 g P/pot) with or without AMF-inoculation, resulting in 30 treatment factorial arrangement, each replicated 4 times. Agronomic responses to P fertilization and AMF-inoculation were assessed. Plant height, stem diameter, chlorophyll content, and leaf and stem yield were significantly influenced (p < 0.001) by the interaction of phosphorus (P) fertilizer levels, arbuscular mycorrhizal fungi (AMF) inoculation, and legume species. Inoculated plants showed remarkable growth, reaching heights of 94.2 to 159.0 cm compared to 61.1 to 117.0 cm in uninoculated plants. Additionally, inoculated plants had stem diameters twice as large as those of uninoculated plants when grown with 1.36 g P/pot, outperforming other P fertilizer levels by day 90 across all legume species. Likewise, chlorophyll content of inoculated plants (78.1–90.7 soil plant analysis development (SPAD)) was significantly higher than uninoculated plants (56.9–69.1 SPAD) at 1.63 P g/pot compared to 0, 0.68, 2.04 and 2.72 g P/pot. Moreover, inoculated plants attained relatively higher leaf (123.3–144.0 g/pot) and stem yield (75.2–121.8 g/pot) than uninoculated plants at 1.36 g P/pot compared to 0, 0.68, 2.04 and 2.72 g P/pot. Overall, AMF-inoculation improved growth and productivity of forage legumes, but its effects depended on the P fertilizer level, with 1.36 g P/pot being the potential optimum fertilizer rate for soil nutrition of legume pastures. creator: Sanele Mpongwana creator: Alen Manyevere creator: Conference Thando Mpendulo creator: Johnfisher Mupangwa creator: Wandile Mashece creator: Mthunzi Mndela uri: https://doi.org/10.7717/peerj.18955 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mpongwana et al. title: Tertiary lymphoid structures-driven immune infiltration patterns and their association with survival in neuroblastoma link: https://peerj.com/articles/19767 last-modified: 2025-07-22 description: BackgroundNeuroblastoma (NB), a diverse childhood cancer, needs better prognostic markers for personalized treatment. The current clinical risk stratification system does not fully explain the high heterogeneity of tumor patients. Tertiary lymphoid structures (TLS), key in tumor immunity, may serve as new biomarkers, but their impact on NB prognosis is unclear.MethodsWe combined transcriptome data from NB cohorts GSE49710 and GSE62564, analyzing 37 TLS-related genes. A prognostic signature (CMLS) was created using machine learning and validated with Kaplan-Meier and receiver operating characteristic (ROC) curves. We also studied immune infiltration and gene expression patterns in NB tissues using single-cell sequencing and quantitative real-time polymerase chain reaction (qRT-PCR).ResultsA 6-gene TLS signature predicted better survival in NB patients. High levels of CCL2, CCL4, CCL21, CD200, CXCR3, and IGSF6 correlated with improved survival. The low-TLS risk group showed better event-free and overall survival. Immune analysis indicated a higher immune cell presence, especially cytotoxic T cells, in this group. Single-cell sequencing revealed lower TLS gene expression in refractory recurrence samples. CD200 downregulation reduced NB cell invasiveness and migration.ConclusionOur study demonstrates that TLS-related genes play a crucial role in NB prognosis, with a 6-gene TLS signature (CCL2, CCL4, CCL21, CD200, CXCR3, and IGSF6) serving as a promising prognostic biomarker for NB. CD200 may be a potential target for inhibiting the biological behavior of NB cells. creator: Xuelian Liu creator: Jian Deng creator: Bingqing Yu creator: Jiaxiong Tan creator: Xiaoliang Lu creator: Minmin Zhang uri: https://doi.org/10.7717/peerj.19767 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Preoperative digital 6-minute walk test reveals risk of postoperative pulmonary complications in patients undergoing heart valve surgery: a pilot feasibility study link: https://peerj.com/articles/19732 last-modified: 2025-07-22 description: BackgroundPostoperative pulmonary complications (PPCs) are a significant concern in cardiac surgery, affecting patient prognosis. This pilot study explored the feasibility of developing a machine learning model for preoperative PPCs risk stratification by integrating dynamic respiratory physiology from the six-minute walk test (6MWT) with clinical parameters.MethodsA prospective study was conducted at the Department of Cardiovascular Surgery of West China Hospital, Sichuan University, from August 2021 to December 2022. We enrolled 142 consecutive patients undergoing valvular heart surgery. After quality control, 117 patients with complete synchronized respiratory monitoring during 6MWT and clinical data were included. We extracted 94 physiological features across 6MWT phases (baseline, walking, recovery) and clinical variables, developing predictive models using five machine learning algorithms evaluated through rigorous five-fold cross-validation.ResultsThe logistic regression model demonstrated promising discriminative performance (AUC 0.86, 95% CI [0.81–0.89]) in this exploratory cohort. Preliminary physiological patterns emerged, including associations between elevated expiratory tidal volume during recovery (OR 9.70, p = 0.006) and reduced baseline minute ventilation (OR 0.15, p = 0.002) with higher PPCs risk.ConclusionThese pilot findings suggest that continuous physiological monitoring during 6MWT, when combined with clinical data, may provide a feasible approach for preoperative PPCs risk assessment. While requiring multi-center validation, the results highlight the potential of wearable-enabled respiratory monitoring to guide prehabilitation strategies in cardiac surgery. creator: Lixuan Li creator: Yuqiang Wang creator: Zhengbo Zhang creator: Zeruxin Luo creator: Wenqing Wang creator: Jiachen Wang creator: Xiaoli Liu creator: Ying Shi creator: Tian Yuan creator: Yong Fan creator: Hong Liang creator: Yingqiang Guo creator: Buqing Wang creator: Jing Wang creator: Jiaoxue Deng uri: https://doi.org/10.7717/peerj.19732 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Li et al. title: Non-agriculturalization of cultivated land in densely populated areas at the watershed scale: a case study of the Minjiang River Basin, China link: https://peerj.com/articles/19722 last-modified: 2025-07-22 description: Zero hunger is a top priority in the Sustainable Development Goals, however, millions of people worldwide still face hunger. Over the years, China has experienced rapid population growth, industrialization and urbanization, leading to significant agricultural land loss, which threats the nation’s food supply. Understanding the patterns and driving factors of non-agriculturalization is crucial for its protection. The Minjiang River Basin, the largest tributary of the Yangtze River, is densely populated and experiencing rapid urbanization, making it a typical snapshot of the non-agriculturalization in China. This study comprehensively examines the characteristics and trends in the spatiotemporal evolution of cultivated land in the Minjiang River Basin, along with the drivers of non-agriculturalization. The results reveal the findings: (1) From 1990 to 2020, the cultivated land in the Minjiang River Basin has decreased and mainly concentrated in flat areas. The spatiotemporal evolution of cultivated land exhibits low dispersion and strong directionality, predominantly shifting northward, and the migration of cultivated land can be divided into three stages. (2) A consistent positive spatial correlation is observed in the non-agriculturalization areas of cultivated land in the Minjiang River Basin, with high-high (HH) clustering analysis revealing an aggregation pattern radiating outward from the city center. (3) Population growth and economic factors are the primary drivers of non-agriculturalization in the Minjiang River Basin. creator: Xi Zhao creator: Zhongwen Hu creator: Yinghui Zhang creator: Jingzhe Wang creator: Tiezhu Shi creator: Yanguo Liu creator: Jie Zhang creator: Guofeng Wu uri: https://doi.org/10.7717/peerj.19722 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Regulatory role of transcription factor c-Myc in the pathogenesis of psoriasis link: https://peerj.com/articles/19706 last-modified: 2025-07-22 description: Psoriasis is a chronic relapsing dermatosis characterized by hyperproliferation and poor differentiation of keratinocytes (KCs). The c-Myc gene is one of the main members of the Myc family and exerts multiple biological functions. C-Myc is highly expressed in psoriatic lesions. The co-expressed genes and coexisting factors of c-Myc determine the final survival of cells. The high expression levels of c-Myc in the skin lesions of psoriatic patients are associated with the continuous proliferation of KCs, and form an abnormal state of epidermal dynamics. C-Myc is also involved in the induction of metabolic reprogramming of cells in the development of psoriasis, thus exacerbating the excessive proliferation of psoriatic epidermis. In this review, we focus on the mechanisms of the transcription factor c-Myc in the pathogenesis of psoriasis and its clinical implications. creator: Yue Cao creator: Xu-Ping Niu creator: Kai-Ming Zhang uri: https://doi.org/10.7717/peerj.19706 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cao et al. title: A SNP-based genome-wide association study (GWAS) of seed-yield related traits in Psathyrostachys juncea using wheat as a reference genome link: https://peerj.com/articles/19617 last-modified: 2025-07-22 description: BackgroundPsathyrostachys juncea is an popular perennial grass for both mowing and grazing when used for pasture establishment in high latitude regions. P. juncea has the advantages of high yield, high quality, good palatability and high nutritional value. It is widely used in artificial grassland construction and ecological restoration in Inner Mongolia and other regions.MethodsThe current study aimed to identify genetic signals associated with seed yield in P. juncea germplasm through a genome-wide association study (GWAS) using wheat as a reference genome. 300 accessions of P. juncea germplasm from different countries were used as materials to assess eight seed yield-related traits in two environments for two consecutive years.ResultsAll the trait values varied considerably across genotypes. Across different locations, the coefficient of variation among genotypes was the highest for seed yield per plant, which exceeded 70%. Further correlation analysis of seed yield factors showed that seed yield per plant had a significant positive correlation with reproductive tiller number. The population exhibited five population structures (Q) assessed by using 84,024 single-nucleotide polymorphisms (SNPs). After controlling Q and K (subgroups), GWAS identified 121 SNPs significantly associated with eight traits. Among them, 19 SNPs were detected in multiple environments, and a total of 91 candidate genes were annotated, which involve the synthesis of cell wall polysaccharides and proteins, plant growth and development, photosynthesis, gibberellin regulation, hormone signal transduction, phenylalanine metabolism, and amino acid metabolism processes. The identification of SNP signals and related candidate genes could enrich the existing genomic resources and lay a foundation for the study of molecular breeding, mapping, and cloning of important genes in P. juncea. creator: Zhen Li creator: Tian Wang creator: Xiaomin Ren creator: Feng Han creator: Yingmei Ma creator: Lan Yun uri: https://doi.org/10.7717/peerj.19617 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Genome-wide characterization and expression analysis of the JRL gene family in response to hormones and abiotic stress in tomato (Solanum lycopersicum L.) link: https://peerj.com/articles/19724 last-modified: 2025-07-21 description: Jacalin-related lectins (JRLs), a newly discovered subfamily of plant lectins, play an important role in plant growth and development and abiotic stress response. However, in the most important model and economic plant, the tomato, little is known about this gene family. Here, we conducted a genome-wide identification and characterization of the JRL gene family in tomato. A total of eight JRL gene family members (SlJRL1–SlJRL8) were identified based on the tomato genome through bioinformatics analyses, which were unevenly distributed on four chromosomes. Chromosomal localization revealed four pairs of tandemly duplicated genes. Genome collinearity analyses showed that tomato JRL genes were more closely related to Arabidopsis than to rice and maize. Phylogenetic analysis showed that tomato JRL could be divided into seven subgroups, and members within each subgroup shared similar gene structures and conserved motifs. Promoter analysis revealed abundant cis-acting elements associated with stress-responsive and phytohormone-responsive. Finally, real-time quantitative polymerase chain reaction (qRT-PCR) was used to analyze the expression profile of SlJRL gene under various plant hormone and abiotic stress treatments. The results show that the SlJRL gene family exhibits tissue-specific expression patterns and responds to a variety of hormonal and stress conditions. This study systematically analyzed the genomic characteristics of tomato JRL family. Our results lay the foundation for further studies on the biological functions of tomato JRL genes. creator: Hui Li creator: Hongling Hu creator: Lina Cao creator: Yue Zhuo creator: Liting Wang creator: Hui Ma creator: Ming Zhong uri: https://doi.org/10.7717/peerj.19724 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: P21 activated kinase 6: a promising tool for predicting small cell lung cancer diagnosis and treatment response link: https://peerj.com/articles/19714 last-modified: 2025-07-21 description: ObjectiveBuilding upon the established role of P21 Activated Kinase 6 (PAK6) in tumor progression and chemoresistance pathways, we postulate its potential as a dual-function biomarker for small cell lung cancer (SCLC). This investigation aims to conduct a comprehensive evaluation of PAK6’s diagnostic validity and prognostic significance through comparative analysis of PAK6 serological levels across distinct clinical cohorts to determine diagnostic thresholds, and its clinical correlation with therapeutic responsiveness.Patients and MethodsThis study included 109 patients diagnosed with SCLC, 92 patients with non-small cell lung cancer (NSCLC), 85 patients with pulmonary nodules (PN), and 94 healthy individuals undergoing routine physical examinations as the normal control group (NC). Serum PAK6 concentrations were measured using enzyme-linked immunosorbent assay (ELISA). Additionally, levels of neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9), and pro-gastrin-releasing peptide (ProGRP) were quantified via chemiluminescence assays. Progression-free survival (PFS) data for SCLC patients were collected through case review and telephone follow-up.ResultsSerum PAK6 levels were significantly higher in the SCLC group compared to the other three groups (p < 0.01). Similarly, NSE and ProGRP levels were markedly elevated in the SCLC group compared to the other groups (p < 0.01). Correlation analysis revealed a positive association between PAK6 and variables such as gender, VA (Veteran’s Administration Lung Cancer Study Group) stage, age, smoking status, CEA, CA19-9, NSE, and ProGRP. The serum tumor markers (STMs) PAK6, NSE, and ProGRP exhibited superior diagnostic performance, with AUCs of 0.892, 0.834, and 0.935, respectively (95% confidence interval (CI) [0.857–0.927], [0.778–0.890], and [0.909–0.960]), compared to CEA and CA19-9 (AUCs = 0.676 and 0.611, respectively; 95% CI [0.622–0.731] and [0.547–0.675]) (p < 0.01). Furthermore, PAK6, NSE, and ProGRP levels significantly decreased after three months of treatment, while CEA and CA19-9 showed no significant changes. Survival analysis demonstrated that higher PAK6 levels were associated with poorer SCLC prognosis. Increased serum PAK6 expression correlated with shorter PFS (HR = 2.02 [1.33–3.07], P = 0.001).ConclusionSerum PAK6 holds significant clinical value for the diagnosis, treatment monitoring, and prognosis evaluation of SCLC and may serve as a potential therapeutic target for the disease. creator: Simei Chen creator: Kexin Han creator: Yinyi Chen creator: Liping Wei creator: Xinlu Sun creator: Yi Luo creator: Lili Wen creator: Liming Tan uri: https://doi.org/10.7717/peerj.19714 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Transcriptomic, and metabolic profiling reveals adaptive mechanisms of Auricularia heimuer to temperature stress link: https://peerj.com/articles/19713 last-modified: 2025-07-21 description: Temperature significantly influences the growth and development of edible mushrooms, including the popular Auricularia heimuer. Despite its economic importance, the molecular mechanisms that enable A. heimuer to withstand prolonged temperature stress are poorly characterized. Here, we performed a comprehensive morphologic, transcriptomic, and metabolic analysis of A. heimuer mycelium exposed to different temperatures over a long period of time. Low temperatures (LT) suppressed mycelial growth, while high temperatures (HT) promoted it. Extremely high temperatures (EHT) were highly detrimental, not only inhibiting growth but also potentially leading to mycelial mortality. The production of reactive oxygen species (ROS) and the activities of antioxidant enzymes such as superoxide dismutase (SOD) and catalase (CAT) were significantly altered by temperature. Transcriptomic profiling identified 1,024, 778, and 4,636 differentially expressed genes (DEGs) in LT, HT, and EHT, respectively, compared to normal temperature (NT). The response to LT was found to involve the regulation of protein synthesis and transport. Notably, HT and NT shared the highest degree of similarity, indicating that these two conditions represent a moderate temperature range that places less stress on the mycelium. In contrast, exposure to EHT resulted in the upregulation of genes related to ribosomal biogenesis, suggesting that A. heimuer may increase protein synthesis in response to heat stress. Furthermore, many genes related to carbohydrate metabolism were downregulated under EHT. Enzymatic assays further confirmed that thermal stress profoundly affects the synthesis of metabolic byproducts and the activities of key glycolytic enzymes, suggesting a restructured metabolic landscape under stressful conditions. In summary, our comprehensive analysis of the A. heimuer mycelial transcriptomic and enzymatic responses to sustained temperature fluctuations provides valuable insights into the molecular basis of thermotolerance. This work lays the foundation for future breeding efforts aimed at improving the resilience of cultivated A. heimuer and can serve as the basis for similar initiatives in other fungal species. creator: Chenhong Nie creator: Shiyan Wei creator: Shengjin Wu creator: Liangliang Qi creator: Jing Feng creator: Xiaoguo Wang uri: https://doi.org/10.7717/peerj.19713 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nie et al. title: Analysis of the optimal patterns of serum alpha fetoprotein (AFP), AFP-L3% and protein induced by vitamin K absence or antagonist-II (PIVKA-II) detection in the diagnosis of liver cancers link: https://peerj.com/articles/19712 last-modified: 2025-07-21 description: BackgroundLiver cancers are common malignancies that primarily include hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA). Currently, the most commonly used serum markers for HCC are alpha fetoprotein (AFP), AFP-L3% and protein induced by vitamin K absence or antagonist-II (PIVKA-II), while the most commonly used serum markers for CCA are carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9). In recent years, many HCC diagnostic models using the combined detection of serum AFP, AFP-L3% and PIVKA-II have been established. For serum AFP, AFP-L3%, PIVKA-II and their many diagnostic models, there has been no clear guidance on the selection of these markers and their various combinations in the diagnosis of liver cancers. The aim of this study was to evaluate and compare the efficacy of these markers and the models that incorporate them in diagnosing HCC and CCA. This could assist in identifying the optimal patterns of serum AFP, AFP-L3% and PIVKA-II for the diagnosis of liver cancers.MethodsClinical data and the results of serum AFP, AFP-L3%, PIVKA-II, CEA and CA19-9 were collected from 117 patients with HCC, 28 patients with CCA and 101 patients with benign liver diseases. Laboratory tests and detection of serum tumor markers in liver cancer patients were conducted prior to treatments. Recently published diagnostic models for AFP, AFP-L3% and PIVKA-II detection were collected; these included GALAD, ASAP, GALAD-C, GAAP, C-GALAD, C-GALAD II and GAP-TALAD.ResultsLevels of AFP-L3%, PIVKA-II, GALAD, ASAP, GALAD-C, GAAP, C-GALAD and C-GALAD II significantly differed between the patient cohorts, with the highest levels seen in HCC, followed by CCA and with the lowest levels seen in benign liver diseases (p < 0.05). Levels of CEA and CA19-9 significantly differed between cohorts, with the highest levels seen in CCA, followed by HCC and with the lowest levels seen in benign liver diseases (p < 0.05). Levels of AFP and GAP-TALAD in HCC patients were significantly higher than those in patients with CCA and patients with benign liver diseases (p < 0.05), but there were no significant differences in levels of AFP and GAP-TALAD between patients with CCA and benign liver diseases (p > 0.05). In the diagnosis of HCC, GAP-TALAD, GALAD, C-GALAD, ASAP and GALAD-C showed the highest efficacy. In the diagnosis of overall liver cancers (HCC and CCA), GALAD-C, GAAP, GALAD, ASAP and C-GALAD showed the highest efficacy. In the diagnosis of early liver cancers (early HCC and CCA), GALAD, GALAD-C, GAAP, C-GALAD and ASAP showed the highest efficacy.ConclusionsFor serum AFP, AFP-L3% and PIVKA-II, diagnostic models of combined marker detection improved efficacy in the diagnosis of liver cancers. Diagnostic models GALAD, ASAP, GALAD-C and C-GALAD showed the highest efficacy in the diagnosis of HCC, overall liver cancers (HCC + CCA) and early liver cancers, and can be used preferentially in clinical practice. creator: Ling Luo creator: Xiaochen Wang creator: Xujian Peng creator: Runqiang Zhong creator: Xuejing Xuan creator: Haixiong Lin creator: Xianghua Lin creator: Chaohui Duan uri: https://doi.org/10.7717/peerj.19712 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Luo et al. title: New approaches for capturing and estimating variation in complex animal color patterns from digital photographs: application to the Eastern Box Turtle (Terrapene carolina) link: https://peerj.com/articles/19690 last-modified: 2025-07-21 description: Color pattern plays a crucial role in various aspects of an organism’s biology, including camouflage, mating, and communication. Despite its significance, methods to quantify and study color pattern variation are often lacking, especially for complex patterns that defy simple categorization. In this study, we developed algorithms to capture and obtain data on 19 different pattern measurements from digital images of 55 individuals of the Eastern box turtle Terrapene carolina sampled in the field and in a museum. The Eastern box turtle is an ideal species to study variation of complex color patterns as this species is easily encountered in the field and in museum collections in Northeastern US, has a relatively easy to identify bright color pattern against a dark background, and has a rigid shell structure, which removes problems related to body distortion. The selected measurements capture the different aspects of the complexity of the color pattern, including the symmetry of the pattern on the turtles’ scutes, a critical component in developmental and evolutionary studies. We estimated the variation of each of these 19 measurements across our samples. We determined how much of this variation was influenced by the sensitivity of the pattern capture algorithm due to non-standardized elements of the image acquisition, lighting conditions, and animal shape on pattern variation. To our knowledge, this is the first study to use a comprehensive set of pattern measurements to capture variation in a complex color pattern while also assessing the susceptibility of each of these measurements to noise introduced during data collection. Additionally, we carried out a citizen science approach to characterize the complexity of the color pattern based on human perception and determine which of the 19 pattern measurements best describe this complexity. The most variable measurements across individuals were blue and yellow contrast between the pattern and non-pattern coloration and the average size of objects. From our estimates of the measurement noise due to image acquisition and analysis, we found that the contrast differences reflected true pattern variations between individual turtles, whereas differences in the average size of objects were influenced by both individual turtle variation and measurement inconsistencies. We found that due to the complexity of the patterns, measurements had lower variability if they did not depend on the algorithm defining a set of discrete objects. For example, total area had much less measurement variability than average object area. Our study provides a comprehensive workflow and tools to study variation in complex color patterns in organisms sampled under non-standardized conditions while also estimating the influence of noise due to biological and non-biological factors. creator: Erik Maki creator: Tilmann Glimm creator: Paramahansa Pramanik creator: Ylenia Chiari creator: Maria Kiskowski uri: https://doi.org/10.7717/peerj.19690 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Maki et al. title: Pectoral muscle area index is an independent protective factor for mortality in sepsis patients: a retrospective observational study link: https://peerj.com/articles/19689 last-modified: 2025-07-21 description: BackgroundSepsis is an infection-induced systemic inflammatory response involving multiple mediators. Identifying risk factors for mortality in patients with sepsis is important for determining treatment strategies. Sarcopenia is a systemic pathology of the skeletal muscles associated with poor outcomes in patients with sepsis. However, there exists a gap in the literature regarding the thoracic muscle area and early outcomes of sepsis. Thus, this study investigated the relationship between 28-day survival and indicators of sarcopenia (pectoral muscle area and pectoral muscle density) from chest computed tomography images of patients with sepsis.MethodsPatients (n = 134, median age = 75 years) who met the Sepsis-3 diagnosis criteria were included. Pectoral muscle area and density were measured in patients who underwent pulmonary computed tomography within ±3 days of admission. Univariate and multivariable factors associated with 28-day mortality were evaluated via Cox regression analysis. Factors with a single-factor p  <  0.05 were included in the multivariate Cox regression analysis to evaluate the factors associated with 28-day mortality in sepsis.ResultsIn this study, 88 patients survived, whereas 46 did not survive at the 28-day mark. Body mass index (BMI) (P = 0.044), pectoral muscle area (P = 0.005), pectoral muscle density (P = 0.008), and pectoral muscle area index (P = 0.003) significantly differed between patients who survived and those who did not survive. BMI was positively correlated with pectoral muscle area (r = 0.516, P  <  0.001) and index (r = 0.560, P  <  0.001). Acute Physiology and Chronic Health Evaluation II score (hazard ratio (HR) = 1.119, P  <  0.001) constituted an independent risk factor for 28-day mortality, whereas the pectoral muscle area index (HR, 0.847; P = 0.027) was a protective factor for 28-day mortality in patients with sepsis. The pectoral muscle area index was associated with a reduced risk of early mortality in patients with sepsis. creator: Xin Li creator: Meijiao Li creator: Yongchang Sun creator: Qingtao Zhou uri: https://doi.org/10.7717/peerj.19689 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Assesment of bone healing after surgical management of odontogenic cysts utilizing fractal analysis—a retrospective cross-sectional study link: https://peerj.com/articles/19745 last-modified: 2025-07-18 description: ObjectivesOdontogenic cysts, originating from inflammatory or developmental processes of the tooth germ epithelium, represent the most common intraosseous pathology in the head and neck region. This retrospective study aimed to evaluate bone healing following the surgical removal of odontogenic cysts using fractal analysis.Materials and MethodsBone changes in 17 patients who underwent cyst enucleation were assessed using fractal dimension and lacunarity measurements on digital panoramic radiographs obtained before and six months after surgery. Statistical analyses included the Shapiro–Wilk test, paired t-test, Wilcoxon signed-rank test, repeated measures ANOVA, and the Friedman test.ResultsAt six months postoperatively, bone structure differences had largely normalized. In the cyst center, there were no statistically significant differences in fractal dimension or lacunarity (P > 0.05). At the cyst edge, fractal dimension remained statistically unchanged (P = 0.446), while lacunarity significantly decreased from 0.06 to 0.04 (P = 0.04). In unaffected control regions, no significant changes were observed (P > 0.05). Preoperative fractal dimension values significantly differed between regions (P < 0.001), but these differences were no longer significant postoperatively (P = 0.077). Lacunarity values showed no significant regional differences at either time point (P > 0.05).ConclusionsFractal analysis offers valuable insights into bone regeneration and may surpass traditional radiographic evaluations. Despite limitations such as small sample size and potential subjectivity in region of interest (ROI) selection, the results support the utility of fractal dimension and lacunarity in tracking bone healing after cyst surgery. creator: Ayse Tas creator: Elif Celebi creator: Zeynep Çukurova Yilmaz uri: https://doi.org/10.7717/peerj.19745 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Tas et al. title: Cavy lifespan: survival analysis and lifetables for the pet guinea pig (Cavia porcellus, L.) in Britain link: https://peerj.com/articles/19702 last-modified: 2025-07-18 description: In Britain, an estimated number of 700,000 guinea pigs are currently kept as pets. Despite their widespread presence, research on pet guinea pig survivability remains limited. While demographic studies exist, they primarily focus on morbidity rather than lifespan analysis. This study aims to fill this gap by investigating factors influencing pet guinea pig longevity and constructing life tables, contributing valuable insights into their survival patterns and potential improvements in care practices. The study was conducted using publicly available data from the VetCompass™ UK Program, including 675 guinea pigs receiving veterinary care in the UK in 2019. The survival analysis was conducted using Kaplan–Meier models, with lifespan differences tested via the Log-Rank test. Key predictors included sex, neutering status, and breed classification.The results of the study indicate an average lifespan of the British pet guinea pigs is 4.022 (3.875; 4,170) years; a median survival time of 4.025 95% confidence interval (3.830; 4,290) years; and an interquartile range of (2.563; 5447) years. Unlike other companion animals, no significant differences in longevity were found between sexes, neutering status, or breed (log-rank Mantel-Cox χ2 p > 0.05), suggesting that these factors may play a less critical role in guinea pigs. The findings challenge common assumptions about lifespan determinants in domesticated species. The study also highlights low neutering rates, likely influenced by concerns over surgical risks. Additionally, breed classification remains inconsistent, indicating a possible lack of standardised identification among owners and veterinarians. This study is limited by potential selection bias, lack of environmental and husbandry data, few neutered animals, unclear breeding backgrounds, unaccounted cohort effects, and no geographical analysis of care variation across different regions of Britain. creator: Fernando Mata uri: https://doi.org/10.7717/peerj.19702 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mata title: Identification of Cassiopea sp. in Lake Macquarie, Australia and revision of the taxonomic status of Cassiopea maremetens Gershwin, Zeidler & Davie, 2010 (Cnidaria: Scyphozoa: Cassiopeidae) link: https://peerj.com/articles/19669 last-modified: 2025-07-18 description: Scyphozoans of the genus Cassiopea are notable for their unusual benthic habit of lying upside-down with their exumbrella resting on the substrate and oral arms facing upwards resulting in their common name “upside-down jellyfish”. Cassiopea includes species that have been historically confused because of taxonomic ambiguity. Additionally, some species are considered to be invasive, which can have significant economic and environmental consequences by impacting fisheries, tourism, and trophic structures. In temperate southeastern Australia, Cassiopea medusae were first reported in temperate Wallis Lake and Lake Illawarra in 2016, and then Lake Macquarie in 2017, though historically these jellyfish have a more northern tropical distribution in Queensland, eastern Australia. Owing to the invasive potential of Cassiopea, correct species identification is crucial for future management. To address this knowledge gap, this study used genetic comparison through the cytochrome c oxidase subunit I (COI) barcoding gene and morphometric analysis, together with revision of type and topotype material of Cassiopea maremetens Gershwin, Zeidler & Davie, 2010, an incompletely known nominal species from Queensland, to investigate the identity of Cassiopea occurring in Lake Macquarie. The morphometric analysis was also used to identify key features that distinguish the Lake Macquarie species from a second species, designated Cassiopea sp.3, that is also expanding its range southwards in eastern Australia, and which may be sympatric in some areas. The results of this study show the species occurring in Lake Macquarie is Cassiopea xamachana Bigelow, 1892, originally described from Jamaica and subsequently widely reported from the Western Atlantic and the Indo-West Pacific. Additionally, we demonstrate that Cassiopea maremetens, is a junior synonym of C. xamachana. Morphological characters that can be most readily used to distinguish mature specimens of C. xamachana from C. sp.3, which has an overlapping distribution on the Australian east coast, are: (1) the number of large appendages on the oral disc, which is much higher in Cassiopea sp.3 (at least 1 but up to 14) vs. a maximum of two in C. xamachana; (2) the oral arm branching pattern, which is usually alternating for C. xamachana, but a combination of alternating, bifurcating and pinnate for Cassiopea sp.3; (3) the length of the large appendage on the oral arm, which is proportionally longer relative to the bell diameter in C. xamachana. creator: Claire E. Rowe creator: Shane T. Ahyong creator: Will F. Figueira creator: Ingo Burghardt creator: Stephen J. Keable uri: https://doi.org/10.7717/peerj.19669 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Rowe et al. title: Electrical characteristics of the extracellular fluid in the body segments of Apis mellifera bees link: https://peerj.com/articles/19691 last-modified: 2025-07-17 description: This study investigates the electrical properties of the extracellular fluid in honeybees (Apis mellifera) and its relationship with different body segments. By characterizing resistance, capacitance, and electrical impedance, aspects such as ionic composition, molecular polarization, and the differential response of live bees to electrical stimuli were evaluated. The results show that electrical characteristics vary significantly depending on the body segment, with the head exhibiting high resistance values and the abdomen displaying high capacitance, reflecting differences in molecular composition and functionality. Additionally, experiments with live bees demonstrated the feasibility of measuring electrical parameters non-invasively, opening new possibilities for monitoring the health of these pollinators under controlled conditions and in natural environments. This work lays the foundation for developing innovative tools in ecological monitoring, the assessment of environmental stressors, and the sustainable management of bee colonies. creator: Juan Hernandez creator: Fredy Mesa creator: Anderson Dussan creator: Andre Riveros uri: https://doi.org/10.7717/peerj.19691 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hernandez et al. title: Core body temperature correlates of transition from aerobic to anaerobic metabolism in running link: https://peerj.com/articles/19686 last-modified: 2025-07-17 description: PurposeWe investigated core body temperature (CBT) during a graded exercise test (GXT) in comparison with gas exchange dynamics.MethodsThirty-two active males performed a treadmill GXT (0.5 km/h increments every 30 seconds, 1.5% incline) until exhaustion. Gas exchange data and rectal temperature (Tre) were continuously registered. Ten participants repeated the test for reliability assessment. The first and second gas exchange thresholds (VT1 and VT2) were determined by the simplified V-slope method, while CBT dynamics and eventual temperature thresholds (TT1 and TT2) were assessed according to the criteria defined in this study. Three independent evaluators determined gas exchange and temperature thresholds.ResultsIn 29 subjects, Tre increase was best fitted with a 3-phase segmented model of successively steeper slopes, with a linear relationship in all three segments (17 subjects), or in two segments, with a quadratic relationship for the remaining segment (12 subjects). The between-segment intersection points were considered as TT1 and TT2. In three participants, Tre was best fitted with a two-segment, single-breakpoint (TT1 or TT2) model. The evaluators’ objectivity was satisfactory for VT1 (α = 0.786), very high for TT2 (α = 0.941) and VT2 (α = 0.948). TT1 and VT1 were moderately correlated (ρ = 0.41, p = 0.021) while VT2 and TT2 were highly correlated (r = 0.78, p < 0.001) showing a small, yet statistically significant difference (12.95 ± 1.9 vs 13.43 ± 1.7 km/h, p = 0.039). However, test-retest reliability was low.ConclusionThe breakpoints in CBT increase observed during graded running may represent transitions between the three intensity domains of physical activity. creator: Marija Rakovac creator: Davor Šentija creator: Tošo Maršić creator: Vesna Babić uri: https://doi.org/10.7717/peerj.19686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Rakovac et al. title: Analysis of epidemic trend of respiratory pathogens in children after long-term pathogen isolation link: https://peerj.com/articles/19710 last-modified: 2025-07-16 description: BackgroundChina implemented strict prevention and control measures during the COVID-19 pandemic, leading to prolonged home confinement of children and significantly reduced exposure to respiratory pathogens. The ability of children under these conditions to resist respiratory pathogens post-lifting of containment measures remained unknown. The children’s ability to face respiratory pathogens post-isolation was assessed through collecting respiratory pathogens detection data, statistical analysis and comparing with pre-epidemic data. In this way, we addressed data gaps in related fields and provided empirical support for research and public health sectors.MethodsThe pathogen detection method was real-time polymerase chain reaction (PCR). Data analysis software: SPSS Statistics 23.ResultsFour environmental factors—temperature, humidity, wind speed and sunshine time—exerted interactive effects ton respiratory pathogens prevalence. Influenza A and B viruses, Mycoplasma pneumoniae and adenovirus exhibited seasonally prevalent patterns in winter, while respiratory syncytial virus showed lower prevalence in summer, and rhinovirus had no significant seasonal variation. The infection rate of respiratory syncytial virus and the number of expected infections decreased with the increase of age, whereas adenovirus, influenza virus, Mycoplasma pneumoniae and bacterial pathogens showed age-related increases in both metrics. Gender-related differences were observed in higher infection rates of Klebsiella pneumoniae, Haemophilus influenzae and Pseudomonas aeruginosa in men compared to women. Co-infection analysis revealed that respiratory syncytial virus exhibited the highest co-infection diversity, followed by influenza B virus, Mycoplasma pneumoniae, and Staphylococcus aureus. Pseudomonas aeruginosa showed inhibition of co-infection with Klebsiella pneumoniae. Streptococcus pneumoniae had been shown to inhibit co-infection with Haemophilus influenzae, Staphylococcus aureus, and Klebsiella pneumoniae. The lower respiratory tract infection rate of Mycoplasma pneumoniae and bacterial pathogens exceeded the overall infection rate. Infection rates of influenza B virus and adenovirus were lower than the overall rate, while those of influenza A and rhinovirus paralleled the overall rate. Analysis of statistical data from China and Gansu Provincial Centers for Disease Control and Prevention revealed that most respiratory pathogens showed an increase in the infection rates post-COVID-19, particularly respiratory syncytial virus, indicating altered prevalence patterns in children due to prolonged exposure to isolated pathogens. creator: Ping Chen creator: Yahong Li creator: Shiwei Li creator: Xin Hua creator: Yu Liu uri: https://doi.org/10.7717/peerj.19710 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Influence of phragmites density, algal concentration and water velocity on cyanobacterial bloom dynamics link: https://peerj.com/articles/19704 last-modified: 2025-07-16 description: BackgroundCyanobacterial blooms present a significant global water challenge, often accumulating in lakeside wetlands and impacting water quality. Despite this, wetland characteristics influencing bacterial diversity during cyanobacterial bloom degradation remain unclear.MethodsTo address this gap, we conducted a 30-day simulation experiment near Lake Taihu, China, to investigate the effects of Phragmites density, algae concentration and water velocity on bacterial diversity and water quality. An orthogonal design with three factors and levels was used with 18 tanks, each with a soil layer. Phragmites density, algae concentration and water velocity were adjusted to simulate lake conditions. Physicochemical parameters were measured within a month, and water samples were collected for bacterial biomass and DNA extraction. Bacterial 16S rRNA gene sequencing was performed to assess diversity, and statistical analyses including α-diversity, β-diversity, and analysis of similarities (ANOSIM) were conducted to evaluate the impact of the experimental factors on water quality and bacterial community structures.ResultsAlgal concentration and water velocity had a greater impact on water quality than Phragmites density. Employing 16S rRNA gene sequencing technology, we discovered that bacterial α-diversity was significantly affected by phragmites density, water velocity, and time (P < 0.01), whereas bacterial β-diversity was significantly influenced by algal concentration and time (P < 0.001). The bacterial community structure was significantly impacted by phragmites density, water velocity, algal concentration, and time (P < 0.001). During the degradation of cyanobacterial blooms, the most abundant bacteria were Proteobacteria (36.8%), Bacteroidetes (20.4%), Cyanobacteria (19.1%), and Actinobacteria (10.3%). Algal density had a stronger influence on bacterial community structure than Phragmites density or water velocity. Orthogonal test results indicated that high algal concentration, coupled with reduced Phragmites density and increased water velocity, rapidly decreased nitrogen, phosphorus concentrations, and bacterial diversity. These findings deepen our understanding of Phragmites wetland effects on cyanobacterial blooms, offering insights for water ecological conservation and resource management in cyanobacteria-affected lakes. creator: Jiaming Lv creator: Guijun Yang creator: Yuqing Zhang creator: Keqiang Shao creator: Xiangming Tang uri: https://doi.org/10.7717/peerj.19704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lv et al. title: Association between vitamin D receptor gene polymorphisms and athletic performance in Chinese male youth soccer players link: https://peerj.com/articles/19696 last-modified: 2025-07-16 description: BackgroundThe relationship between the vitamin D receptor (VDR) gene and muscle strength has been extensively investigated; however, the findings of this research remain inconclusive. The aim of this study was to evaluate the association between VDR variants (ApaIrs797523, BsmI rs1544410, and FokIrs2228570 genotypes) and athletic performance in youth soccer players in China.Materials and MethodsA total of 142 male soccer players (73 from an elite group and 69 from a sub-lite group) aged 13–15 years, and 107 controls (13- to 14-year-old students) were recruited for this study. We measured height, weight, speed, explosive power, anaerobic endurance, and aerobic endurance in both the elite and sub-elite athletes. ApaI, BsmI and FokI genotypes were detected in controls, elite, and sub-elite soccer players with the single-nucleotide polymorphism (SNP) technique. The χ2 test was applied to analyze the correlation between genotype distribution and allelic frequency in elite and sub-elite athletes and controls. One-way analysis of variance and Bonferroni’s post hoc test were implemented to analyze the differences in parameters among groups, and statistical significance was set at p ≤ 0.05.Results(1) The genotype distributions of the ApaI, BsmI, and FokI in controls, elite, and sub-elite soccer players were consistent with the Hardy–Weinberg equilibrium (HWE) results, except for the BsmI genotype distribution in control s (χ2 = 7.396, df = 1, p = 0.025). (2) The BsmI AG frequency in the controls and sub-elite players was significantly higher than in the elite players (χ2 = 6.4, df = 1, p = 0.011; χ2 = 4.50, df = 1, p = 0.034, respectively). The frequency of the FokI TT genotype in the controls was significantly higher than in the elite and sub-elite players (χ2 = 12.737, df = 1, p < 0.001, χ2 = 8.805, df = 1, p = 0.003, respectively). The frequency of the ApaI A in the elite players was significantly lower than that in the controls and sub-elite players (χ2 = 3.765, df = 1, p = 0.05; χ2 = 12.19, df = 1, p < 0.001 respectively). (3) ApaI CC players had longer distances in the standing long jump (SLJ) (p = 0.026) and shorter times in the 30-m run (p = 0.003) than ApaI AC players. Additionally, ApaI AA players had significantly longer Yo-Yo Intermittent Recovery Test Level 1 (YYIR1) running distances compared to ApaI AC players (p = 0.002).ConclusionChinese elite youth soccer players are more likely to possess the ApaI CC genotype and are less likely than sub-elite players to have the BsmI A alleles. Additionally, the ApaI CC genotype is associated with better speed and explosive power among Chinese elite youth soccer players. creator: Shidong Yang creator: Wei Zhang creator: Meng Jia creator: Haichun Chen uri: https://doi.org/10.7717/peerj.19696 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: Development and validation of a risk prediction model for hypoproteinemia after adult cardiac valve surgery: implications for clinical care link: https://peerj.com/articles/19676 last-modified: 2025-07-16 description: ObjectiveTo construct and validate a risk prediction model for hypoproteinemia in adults following cardiac valve surgery with cardiopulmonary bypass (CPB), providing medical staff with an effective tool for early identification and intervention.MethodsThis retrospective cohort study analyzed clinical data from 259 patients who underwent CPB-assisted heart valve surgery at the Department of Cardiovascular Surgery, First Affiliated Hospital of China University of Science and Technology, between January and December 2023. Patients were divided into two groups based on whether their serum albumin levels fell below 35 g/L within 48 hours postoperatively: the hypoproteinemia group (n = 144) and the non-hypoproteinemia group (n = 115). Least absolute shrinkage and selection operator (LASSO) regression was used to identify candidate predictors, followed by multivariate logistic regression to determine independent risk factors.ResultsAmong the 259 patients, 144 developed hypoproteinemia, yielding an incidence rate of 55.60%. LASSO regression identified nine variables associated with hypoproteinemia, and multivariate logistic regression confirmed eight independent predictors. Hypertension, chest infection, frailty, and preoperative heart failure were identified as independent risk factors (OR > 1, P < 0.05), while higher body mass index (BMI), red blood cell (RBC) count at admission, platelet count at admission, and albumin level at admission were protective factors (OR < 1, P < 0.05). The predictive model constructed using the nine LASSO-selected variables demonstrated good discrimination, with an area under the ROC curve (AUC) of 0.823 (95% CI [0.774–0.873]). The Hosmer–Lemeshow test showed no significant difference between predicted and observed outcomes (P = 0.737), indicating good model calibration.ConclusionThe incidence of postoperative hypoproteinemia in this cohort was 55.60%. The developed nomogram model, based on key clinical predictors, demonstrated strong calibration and discrimination, offering a practical tool for identifying patients at high risk of hypoproteinemia following valve surgery. creator: Fang Wang creator: Zhen-zhen Su creator: Xiao-qian Guo creator: Man Li creator: Rui Wang creator: Yan-jun Xu uri: https://doi.org/10.7717/peerj.19676 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Evaluating the effectiveness of participatory science dog teams to detect devitalized Spotted Lanternfly (Lycorma delicatula) egg masses link: https://peerj.com/articles/19656 last-modified: 2025-07-16 description: The spotted lanternfly (Lycorma delicatula, SLF) is an invasive planthopper first detected in the United States in 2014, with initial sightings in Pennsylvania. SLF poses a serious threat to agriculture, particularly targeting grapevines, hops, and ornamental plants, resulting in substantial annual economic losses. Due to its life cycle, the early detection and removal of egg masses are the most effective strategies for preventing long-distance dispersal. However, visual detection by humans is time-consuming and inefficient. Detection dogs have demonstrated high accuracy in locating SLF egg masses and differentiating them from environmental distractors. Despite their effectiveness, the number of dogs available through governmental channels is insufficient to meet demand. This study evaluated whether community scientist dog-handler teams could meet standardized detection criteria using SLF egg masses. Teams from across the U.S. were recruited and trained using devitalized egg masses, with oversight provided by local trainers. Following a 3- to 6-month independent training period, team performance was assessed through an odor recognition test and a field trial. Dogs demonstrated a sensitivity of 82% in controlled testing and 58% in field conditions. These results provide proof of concept; community scientist dog teams could play a significant role in protecting their local environments and agriculture from invasive species. creator: Sally Dickinson creator: Mizuho Nita creator: Edgar O. Aviles-Rosa creator: Nathan Hall creator: Erica N. Feuerbacher uri: https://doi.org/10.7717/peerj.19656 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dickinson et al. title: Optimal cultivation measures for maize production in the drylands of the Loess Plateau link: https://peerj.com/articles/19654 last-modified: 2025-07-16 description: Proper nutrient management and planting density can effectively improve crop yields and economic efficiency. Optimized fertilization and high-density planting measures have gained attention for their ability to balance high crop yields with efficient nitrogen utilization. High and stable yield of maize is an important guarantee for global food security, and fertilizer and planting density are important factors affecting yield components. In this study, dryland maize (Zea mays L.) in the Loess Plateau was used as the research material, and a three-factor, five-level quadratic orthogonal rotated combination design with organic fertilizer, nitrogen fertilizer and density were set up for a field trial. Regression models of organic fertilizer, nitrogen fertilizer, density and maize yield were established. The results showed that the contribution of each factor to maize yield was in the order of density > nitrogen fertilizer > organic fertilizer. The contribution rates are as follows: 90.02, 89.23, and 79.66, respectively. The univariate analysis concluded that maize yield increased with increasing application of organic fertilizer. Nitrogen fertilizer and density positively affected maize yield within a certain range. Maximum yield is achieved when nitrogen fertilizer and planting density are set at levels 150 kg hm−2 and 82,500 plants hm−2, respectively. The analysis of the intercropping effects showed that organic fertilizer-nitrogen fertilizer, organic fertilizer-density, and nitrogen fertilizer-density intercropping had a synergistic effect on maize yield. Optimisation analysis of different cultivation measures was used to obtain the optimum range of treatments for yields higher than 15,000 kg hm−2: 6,429.30–7,895.10 kg hm−2 for organic fertilizer application, 159.30–203.55 kg hm−2 for nitrogen fertilizer application, and 72,465–80,940 plants hm−2 for planting density. This study explored the effects of different ratios and interactions of organic fertilizer, nitrogen fertilizer and density on maize yields, and screened out the scientific level of dense fertilizer to provide theoretical basis and practical experience for the standardised cultivation of maize in the Loess Plateau. creator: Wenbo Mi creator: Gang Zhao creator: Jianjun Zhang creator: Yi Dang creator: Lei Wang creator: Gang Zhou creator: Shuying Wang creator: Shangzhong Li creator: Tinglu Fan creator: Jingyu Hu creator: Xujiao Zhou uri: https://doi.org/10.7717/peerj.19654 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mi et al. title: Sex- and age-related morphological and functional differences in the skull of Eira barbara (Linnaeus, 1758) (Carnivora, Mustelidae) link: https://peerj.com/articles/19730 last-modified: 2025-07-15 description: BackgroundMorphological differences related to age and sex have been extensively documented in Nearctic and Palearctic mustelids, largely due to the interest in the commercial management of species such as martens and fishers. However, sexual dimorphism and ontogenetic development in Neotropical species, such as the tayra (Eira barbara), remain poorly studied.MethodsWe investigated the skull development and sexual differences in E. barbara through qualitative and morphometric analyses of 376 skull specimens from museum collections. Specimens were classified into four age classes based on tooth eruption, cranial suture closure, and skull morphology. Linear measurements were used to assess biomechanical parameters related to the masticatory function, including temporal and masseter muscle force indices.ResultsThe results show that male and female tayras follow two distinct growth pathways. While juveniles (Age Classes I–II) share nearly identical skull proportions, males rapidly surpass females in size and robustness by the subadult stage (Age Class III). Fully mature males (Age Class IV) develop broader zygomatic arches, thicker sagittal crests, and significantly stronger bite forces driven by enlarged temporal muscles. On the other hand, E. barbara adult females exhibit a narrower post-orbital constriction and palatal region which denotes distinct ontogenetic trajectories between males and females. Multivariate statistical analyses (principal component analysis/discriminant function analysis) confirmed these morphological trends, highlighting allometric growth patterns and functional differences in masticatory biomechanics. Males exhibit greater bite force, particularly in the temporal muscle system, which may be linked to territorial defense or mating behaviors. These findings align with patterns observed in other Guloninae species, such as fishers (Pekania pennanti) and wolverines (Gulo gulo), but highlight unique aspects of E. barbara’s tropical ecology, including non-seasonal breeding, flexible growth patterns, and broad habitat use. Additionally, tayras’ asynchrony in sexual maturity and sexual dimorphism in skull biomechanics may be related to distinct ecological roles for the sexes. We hypothesize that these differences are adaptative responses to the dynamic and resource-rich environments of the Neotropics. Our work underscores the role of ontogenetic and sexual variation in understanding the evolutionary and ecological adaptations of Neotropical mustelids, providing new light on E. barbara’s morphology and masticatory function. creator: Fernando Araujo Perini creator: Fernando L. Sicuro uri: https://doi.org/10.7717/peerj.19730 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Perini and Sicuro title: Study on the induction of exogenous plant hormones to enhance the weed suppression ability of allelopathic and non-allelopathic rice accessions link: https://peerj.com/articles/19700 last-modified: 2025-07-15 description: BackgroundIncreasing the induced-allelopathic potential of rice at the seedling stage by chemical induction is an important strategy in weed management. More in-depth work is needed to find inducing agents for effectively improving the weed-suppressive activity of allelopathic and non-allelopathic rice accessions via the modulation of root morphology and allelochemicals production.MethodsGrown in Hoagland’s solution, two rice cultivars—allelopathic PI312777 (PI) and non-allelopathic Lemont (LE)—were treated using various phytohormones to evaluate root growth and allelopathic potential. Optimal phytohormones (ABA and EBL) were selected based on root growth responses. Extraction of rice leaf and root exudates, subsequently assessed on lettuce seedlings, revealed induced allelopathy. WinRHIZO software was used to investigate root morphologies; HPLC and GC-MS evaluated phenolic acids and terpenoids in rice tissues. The transcription of genes related to phenolic acid and terpenoid biosynthesis was measured by qPCR. ANOVA and correlation analysis were applied in data analysis.ResultsThe results showed that the optimal induction conditions were abscisic acid (ABA, three µmol/L) or 24-epibrassinolide (EBL, 0.5 nmol/L) for 3 days. Under these conditions, the induced-allelopathy (IA) values of rice root exudates induced by three µmol/L ABA were 9.62% in PI31277, and 13.76% in Lemont, while the IA values of PI31277 and Lemont after 0.5 nmol/L EBL treatment were 7.83% and 11.51%, respectively. ABA mainly affected the root length and volume at 0–0.2 mm diameter, while EBL mostly affected root length and volume at 0–1.0 mm diameter. The total content of phenolic acids in root-exudates of PI31277 and Lemont induced by EBL were 1.16 and 2.33 times greater, respectively, while ABA induction also increased the phenolic acid content by 1.48 and 1.87 times, respectively. Most genes related to phenolic acid and terpenoid synthesis, such as PAL, C4H, F5H, MK, SQS, and PS, were upregulated after EBL induction, while most genes were downregulated after ABA treatment. Moreover, correlation analysis confirmed that root morphology, allelochemicals production, and related gene expression levels were significantly correlated with induced-allelopathy caused by ABA or EBL treatment. creator: Ting Wang creator: Xinyi Ye creator: Yuhui Fan creator: Shuyu Chen creator: Huayan Ma creator: Jiayu Li uri: https://doi.org/10.7717/peerj.19700 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Analysis of ergot alkaloid gene expression and ergine levels in different parts of Ipomoea asarifolia link: https://peerj.com/articles/19692 last-modified: 2025-07-15 description: BackgroundErgot alkaloids are renowned for their pharmacological significance and were historically attributed to fungal symbioses with cereal crops and grasses. Recent research uncovered a symbiotic relationship between the fungus Periglandula ipomoea and Ipomoea asarifolia (Convolvulaceae), revealing a new source for ergot alkaloid synthesis. While past studies have emphasized the storage of both the fungus and alkaloids in leaves and seeds, recent work has found they also occur in other plant parts. This study aimed to examine expression of the dmaW gene, which plays a crucial role in ergot alkaloid biosynthesis, and to quantify ergot alkaloid levels across various organs and growth stages of I. asarifolia.ResultsOur findings revealed the highest levels of dmaW gene expression in young seeds and young leaves, whereas the highest ergine concentrations were found in mature leaves followed by young leaves. In light of previous studies, we propose three hypotheses to reconcile these conflicting results: the possibility of an inefficient ergot alkaloid biosynthesis pathway, the possibility that different types of ergot alkaloids are produced, and the existence of an ergot alkaloid translocation system within the plant. Furthermore, ergine concentration and ergot alkaloid biosynthesis gene expression were detected in stems, roots, and flowers, indicating that ergot alkaloids are produced and accumulated in all studied parts of I. asarifolia, rather than being solely confined to the leaves and seeds, as previously reported.ConclusionsOverall, our study reveals that ergot alkaloids are produced and accumulated in most parts of I. asarifolia, suggesting a plant-wide biosynthesis and potential transport system, challenging the previous belief that biosynthesis was confined to glandular trichomes on leaves. creator: Yanisa Olaranont creator: Alyssa B. Stewart creator: Wisuwat Songnuan creator: Paweena Traiperm uri: https://doi.org/10.7717/peerj.19692 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Olaranont et al. title: Exploring the impact of curiosity and sport commitment on creativity among fitness coaches: the mediating role of knowledge-sharing and flow experience link: https://peerj.com/articles/19684 last-modified: 2025-07-15 description: The creativity of fitness coaches is crucial for maintaining the competitiveness of fitness enterprises. This study aimed to explore the factors, mechanisms, and moderating effects influencing the creativity of fitness coaches (n = 732) in Chinese fitness businesses, using partial least squares structural equation modeling (PLS-SEM) analysis. The results indicate that curiosity and sport commitment have a positive impact on knowledge-sharing and flow experience. In addition, knowledge-sharing and flow experience positively influence creativity. Importantly, the curiosity and sport commitment of fitness coaches affect creativity through knowledge-sharing and flow experience. Finally, social media usage positively moderates the relationship between knowledge-sharing and creativity. The findings of this study provide meaningful information and decision-making references for professionals in the fitness industry and academic researchers. Future efforts should emphasize the protection of fitness coaches’ creative achievements, with policymakers encouraged to establish relevant legal frameworks to safeguard innovation within the industry. creator: Ying Chen creator: Bin Chen uri: https://doi.org/10.7717/peerj.19684 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Chen and Chen title: SARS-CoV-2-specific humoral and cellular immunity assessment in Peruvian vaccinated population: a cross-sectional study link: https://peerj.com/articles/19651 last-modified: 2025-07-15 description: BackgroundEvaluating both humoral and cellular immunity is essential for optimizing vaccination strategies and preventing post-pandemic SARS-CoV-2 outbreaks. This cross-sectional study assessed cellular immunity by measuring CXCL10 mRNA expression and humoral immunity through SARS-CoV-2-specific IgG antibodies.MethodWhole blood samples were collected from 40 Peruvian volunteers. CXCL10 expression was evaluated in blood samples stimulated with Spike protein peptides from the Wuhan strain and Omicron BA.5 variant using RT-qPCR. Anti-spike IgG levels were measured with a semi-quantitative ELISA.ResultsThe median age was 31 years, with 62.5% females. A heterologous vaccination scheme was reported by 73%, but only 25% received their last dose within the past 6 months, and 55% completed three doses. The BNT162b2 vaccine was included in 88% of vaccination schemes, serving as the first and second dose in 48% of cases. All participants had detectable anti-spike IgG antibodies; 90% exhibited cellular responses to Wuhan peptides and 97.5% to Omicron peptides. CXCL10 mRNA expression (2−ΔΔCT) was significantly higher for Omicron (median: 565.97; IQR: 565,148.34) compared to Wuhan (median: 18.55; IQR: 62,898.67). Higher anti-spike IgG levels correlated with age and the number of vaccine doses. Males had significantly higher CXCL10 and anti-spike IgG levels (p < 0.05). Antibody levels were greater in those recently boosted or vaccinated with mRNA-1273 (p = 0.001, p = 0.002).ConclusionMost participants exhibited robust immunity, characterized by elevated levels of CXCL10 and anti-SARS-CoV-2 IgG antibodies. These findings highlight the importance of boosters in enhancing immunity and the need for diverse techniques for measuring immunity. creator: Marlon Yuri Garcia-Paitan creator: Salyoc Tapia-Rojas creator: Hector Santiago Alvarez Vega creator: Javier Enciso-Benavides creator: Maria J. Pons creator: Ana Mayanga-Herrera uri: https://doi.org/10.7717/peerj.19651 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Garcia-Paitan et al. title: The lncRNA MAGI2-AS3 in peripheral blood mononuclear cells: a valuable biomarker for diagnosis and prognosis prediction of breast cancer link: https://peerj.com/articles/19694 last-modified: 2025-06-30 description: BackgroundExisting research has shown that long non-coding RNA (lncRNA) MAGI2 antisense RNA3 (MAGI2-AS3) expression is significantly decreased in breast cancer tissues and can inhibit breast cancer progression. However, the relationship between MAGI2-AS3 expression levels in peripheral blood mononuclear cells (PBMCs) and breast cancer remains unclear. This study aimed to explore the clinical significance of MAGI2-AS3 expression in PBMCs for diagnosing breast cancer and predicting patient prognosis.MethodsReal-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to detect MAGI2-AS3 expression in PBMCs from healthy donors and breast cancer patients. The chi-square test analyzed the associations between MAGI2-AS3 expression and breast cancer clinicopathological parameters. The Kaplan-Meier method evaluated the impact of MAGI2-AS3 on patients’ overall survival (OS), and receiver operating characteristic (ROC) analysis assessed its diagnostic accuracy for breast cancer.ResultsMAGI2-AS3 expression was significantly downregulated in breast cancer patients’ PBMCs compared to the control group. Its expression decreased with the advancement of tumor-node-metastasis (TNM) stage and elevation of pathological grade, and was remarkably lower in patients with distant metastasis (DM). Low MAGI2-AS3 expression in PBMCs was correlated with shorter OS. ROC curve analysis showed that MAGI2-AS3 in PBMCs had good diagnostic accuracy.ConclusionMAGI2-AS3 expression in breast cancer patients’ PBMCs is reduced and negatively correlated with patient outcomes. Thus, it has the potential to be a valuable biomarker for breast cancer diagnosis and prognostic evaluation. creator: Shanmei Du creator: Hong Yang creator: Yong Yang creator: Kui Liu uri: https://doi.org/10.7717/peerj.19694 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Du et al. title: Factors associated with the intention to vaccinate and price sensitivity to the human papillomavirus (HPV) vaccine among Chinese male medical college students: a cross-sectional survey link: https://peerj.com/articles/19699 last-modified: 2025-06-30 description: BackgroundCollege students, particularly males, face a high risk of the human papillomavirus (HPV) infection, yet vaccination rates remain low in China. This study aims to explore the willingness to receive HPV vaccine among Chinese male medical college students based on health literacy (HL) theory and price sensitivity.MethodsA cross-sectional survey was conducted from June 16 to July 16, 2024, to assess socioeconomic status and HL among college students at Guangdong Medical University. The survey was distributed via WeChat using convenience sampling through the Chinese online survey platform “Wenjuanxing” (http://www.wjx.cn). A Van Westendorp price sensitivity meter (PSM) was used to determine male medical college students’ price sensitivity to HPV vaccines.ResultsAmong 1,631 valid participants, 59.4% (n = 969) expressed willingness to receive HPV vaccination. The key influencing factors included graduate status (OR: 1.82; 95% CI [1.00–3.32]; p = 0.049), family history of cancer (OR: 1.29; 95% CI [1.01–1.66]; p = 0.041), moderate daily exercise (OR: 53; 95% CI [1.21–192]; p < 0.001), peers’ HPV vaccination status (OR: 1.42; 95% CI [1.15–1.75]; p < 0.001), and HL levels (OR: 1.03; 95% CI [1.01–1.05]; p = 0.002). The Van Westendorp PSM analysis demonstrated high price sensitivity: the market price of the quadrivalent vaccine aligned closely with the lowest price point for male medical college students, whereas the nine-valent vaccine’s market price exceeded the acceptable price range.ConclusionsHL levels directly increased HPV vaccination intentions, and PSM analysis revealed the nine-valent vaccine’s market price exceeded the acceptable price range, contrasting with the affordability-aligned quadrivalent vaccine. Interventions should prioritize HL programs and cost-reduction strategies (e.g., subsidies for the nine-valent vaccine), while addressing nonprice barriers (including family history of cancer, moderate daily exercise and peer influence networks), particularly for the quadrivalent vaccine. creator: Yuan Li creator: Hiromi Kawasaki creator: Zhengai Cui creator: Sae Nakaoka uri: https://doi.org/10.7717/peerj.19699 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: MAPK/ERK signaling pathway in rheumatoid arthritis: mechanisms and therapeutic potential link: https://peerj.com/articles/19708 last-modified: 2025-07-14 description: Rheumatoid arthritis (RA) is a multifaced autoimmune disorder characterized by chronic joint inflammation, leading to progressive disability and significantly impacting patients’ quality of life. Despite advances in treatment, finding a cure or preventing disease progression remains a major clinical challenge, underscoring the urgent need for novel therapeutic strategies. Among various pathways involved in the pathophysiology of RA, the mitogen-activated protein kinases/extracellular regulated protein kinases (MAPK/ERK) pathway is of particular importance. As the central cascade within the broader MAPK signaling pathways, MAPK/ERK plays a critical role in regulating numerous physiological and pathological processes, with a well-established and prominent involvement in RA. Unlike p38 MAPK and c-Jun-N-terminal kinase (JNK), whose role in RA have been well-documented, the specific contributions of the MAPK/ERK pathway to RA remains comprehensively unreviewed. Furthermore, the MAPK/ERK pathway does not act in isolation but interacts synergistically with other major pathways, including NF-κB, Janus kinase-signal transducer and activator of transcription (JAK/STAT), sonic hedgehog (SHH), and PI3K/AKT, which further enhance its pathological effects. This review offers a comprehensive analysis of MAPK/ERK signaling pathway, focusing on its molecular components and its contribution to RA pathophysiology. Furthermore, we explore the cross-talk between MAPK/ERK and other pathways in the context of RA, and evaluates the therapeutic potential of targeting this pathway with small molecule inhibitors, natural compounds and biomolecules. By elucidating the mechanistic role of MAPK/ERK in RA, this article aims to highlight the pathway’s therapeutic relevance and provide a foundation for the developing more effective, targeted therapies for RA. creator: Jun Xie creator: Sijuan Sun creator: Qingzhou Li creator: Yuhui Chen creator: Lijun Huang creator: Dong Wang creator: Yumei Wang uri: https://doi.org/10.7717/peerj.19708 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al. title: Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean link: https://peerj.com/articles/19674 last-modified: 2025-07-14 description: DNA barcoding is a widely used tool for species identification, with its reliability heavily dependent on reference databases. While the quality of these databases has long been debated, a critical knowledge gap remains in their comprehensive evaluation and comparison at regional scales. Marine metazoan species in the western and central Pacific Ocean (WCPO), a region characterized by high biodiversity and limited sequencing efforts, are an example of this gap. This study developed a systematic workflow to assess mitochondrial cytochrome c oxidase subunit I (COI) barcode coverage and sequence quality in two commonly used reference databases for DNA barcoding: the nucleotide reference database from the National Center for Biotechnology Information (NCBI); and from the Barcode of Life Data System (BOLD). Comparative analyses across marine phyla and WCPO regions identified significant barcode gaps and quality problems, providing insights to guide future barcoding efforts. NCBI exhibited higher barcode coverage, but lower sequence quality compared to BOLD. Quality issues, including over- or under-represented species, short sequences, ambiguous nucleotides, incomplete taxonomic information, conflict records, high intraspecific distances, and low inter-specific distances were identified in both databases, likely resulting from contamination, cryptic species, sequencing errors, or inconsistent taxonomic assignment. The barcode identification number (BIN) system in BOLD demonstrated potential for identifying and addressing problematic records, highlighting the benefits of curated databases. Significant barcode deficiencies and quality issues were observed in the south temperate region of WCPO and phyla such as Porifera, Bryozoa, and Platyhelminthes. Additionally, the COI barcode showed limited species-level resolution for certain taxa, including Scombridae and Lutjanidae. Addressing barcode coverage gaps, improving taxonomic representation, and enhancing sequence quality will be essential for strengthening future barcoding initiatives and advancing biodiversity monitoring and conservation in the WCPO and beyond. This study highlights the need for standardized database curation and sequencing practices to improve the global reliability and applicability of DNA barcoding. creator: Yufei Zhou creator: Alejandro Trujillo-González creator: Simon Nicol creator: Roger Huerlimann creator: Stephen D. Sarre creator: Dianne Gleeson uri: https://doi.org/10.7717/peerj.19674 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhou et al. title: Validation of improved cytochrome c oxidase I (COI) primers for comprehensive biodiversity assessment of ascidians link: https://peerj.com/articles/19671 last-modified: 2025-07-14 description: Reliable molecular tools are needed for effective biodiversity assessment of marine organisms. These tools can be used in ascidians species, which are one of the most invasive taxa worldwide and morphologically difficult to identify. This study aimed to redesign and improve ascidian-specific primers and validate the new primer pair (AscCOI2) for comprehensive biodiversity assessment. To design an optimized primer, 3,948 COI sequences from 273 ascidian species were used as a dataset. The AscCOI2 pair was developed through strategic modifications to the binding site and validated using in silico and in vitro approaches. Analysis of penalty scores showed the improved efficiency of the redesigned AscCOI2 pair, with ascidians scoring less than 150 points for both forward and reverse primers and the non-target groups maintaining a score above 480. Primer-binding analysis results showed a significant improvement in amplification success rate from 47.99% to 82.42% at the species level. In vitro validation using conventional polymerase chain reaction (PCR) confirmed the successful amplification of six ascidian species and failure for a non- ascidian taxon. Barcoding gap analysis showed a clear gap of 0.015 between intraspecific and interspecific genetic distances. The species detection capability of the redesigned AscCOI2 pair greatly improved, and the high taxonomic specificity of ascidians is maintained. Overall, this study demonstrates that the AscCOI2 pair is an effective tool for both metabarcoding and mini-barcode applications in biodiversity assessment and molecular systematics research of ascidians. creator: Seongjun Bae uri: https://doi.org/10.7717/peerj.19671 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bae title: Optimizing nutrient management protocol for Ophiopogon japonicus-corn intercropping: impacts on growth, yield, and medicinal quality link: https://peerj.com/articles/19655 last-modified: 2025-07-14 description: Ophiopogon japonicus is a valuable medicinal plant commonly intercropped with corn due to limited arable land in its primary cultivation areas. Optimizing fertilization management to enhance both crop yields and medicinal quality is a key research focus. This study investigates the effects of different fertilization treatments—nitrogen sources (urea and ammonium nitrate), micronutrient supplementation (magnesium and manganese), and phosphorus-potassium (P+K) fertilization—on the growth, yield, and medicinal quality of O. japonicus and corn in an intercropping system. A randomized complete block design was employed to evaluate eight treatments. Agronomic traits, biomass production, and medicinal quality indicators were analyzed using cluster analysis, correlation analysis, and principal component analysis (PCA). Results showed that nitrogen source significantly affected corn height, with ammonium nitrate outperforming urea. Micronutrients and P+K had significant interactive effects on stem diameter and leaf development. Fresh biomass and silage yield were primarily influenced by nitrogen source and P+K, while stem biomass was affected by micronutrient supplementation. The highest corn yield and biomass were recorded in treatments T5 (urea + P + K), T7 (urea + Mn + Mg + P + K), and T8 (ammonium nitrate + Mn + Mg + P + K). For O. japonicus, micronutrient applications significantly increased tuberous root numbers, while P+K fertilization promoted plant height and fibrous root growth. All three fertilization factors significantly impacted tuber biomass, the main determinant of medicinal yield. T8 showed the highest overall yield of O. japonicus, followed by T5 and T7. Medicinal quality evaluation through cluster analysis and PCA identified T5 as the optimal treatment for enhancing key medicinal components. The optimal strategy for maximizing yield in the intercropping system includes ammonium nitrate (150 kg N/ha), magnesium sulfate (45 kg/ha), manganese sulfate (15 kg/ha), superphosphate (75 kg P2O5/ha), and potassium sulfate (450 kg K2O/ha). For improving medicinal quality, the best treatment includes urea (150 kg N/ha), superphosphate (75 kg P2O5/ha), and potassium sulfate (450 kg K2O/ha). Future studies should assess the adaptability of this intercropping system across different soil and climatic conditions. Incorporating precision agriculture technologies may further refine fertilization strategies, while long-term monitoring is recommended to evaluate impacts on soil health and environmental sustainability. creator: Xiaoyang Cai creator: Heling Fan creator: Hongmei Deng creator: Wenjing Li creator: Haohan Wang creator: Jiaming Zhang creator: Min Li uri: https://doi.org/10.7717/peerj.19655 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cai et al. title: Revisiting Drymaeus germaini (Ancey, 1892) (Gastropoda, Bulimulidae): ecological niche and first anatomical description of a poorly known land snail species from Brazil link: https://peerj.com/articles/19641 last-modified: 2025-07-14 description: BackgroundTerrestrial gastropods are one of the most imperiled animal groups in the world. However, information on population size and structure, geographic range and their trends over time, which is necessary to assess species conservation status, is unavailable or insufficient for most land snail taxa, making it difficult to apply the IUCN criteria. Ecological niche modelling (ENM) has been used to predict geographic distribution, allowing better characterization of the distribution ranges of endemic or rare species, offering the necessary information for stating their conservation status and planning for conservation measures.MethodsWe compiled occurrence records of Drymaeus germaini and D. suprapunctatus (herein proposed as a junior synonym of D. germaini) associated with museum collections and human observation. A distribution map including geographic boundaries and Brazilian biomes was made with QGis version 3.10.14. For niche modelling, seven bioclimatic variables were used as predictors. The models were performed using different packages in R environment version 4.2.0.Results and DiscussionWe have redescribed Drymaeus germaini based on the inner anatomy and shell sculpture, also providing the first comparative conchological analysis with congeneric species. We also updated the current distribution of the species within the main Brazilian biomes and estimated its potential geographic distribution using the ENM approach. The ENM results revealed a belt of mid-to-high suitability areas from Northeast to South Brazil in the Atlantic Forest, the most degraded biome in Brazil. In the Northeast these areas extended from the Atlantic Forest to the Caatinga and in the South, from the Atlantic Forest to the Pampas. Additional areas of mid-suitability were found in Cerrado, the second most degraded biome in Brazil. Our results also revealed a continuous area of mid-to-high environmental suitability for D. germaini within the Arc of Amazon deforestation. Our results evidence the scarcity of occurrence records for this species and most of these records do not correspond to protected areas. Also the ecologically suitable areas for D. germaini are in regions disturbed by deforestation, fires, urbanization, habitat loss, mining, and flooding, which may represent the main threats for this species. Nonetheless, the information necessary to apply the IUCN criteria for D. germaini is still incipient and this species should be classified as data deficient. creator: Maria Isabel Pinto Ferreira Macedo creator: Ximena Maria Constanza Ovando creator: Sthefane D’ávila uri: https://doi.org/10.7717/peerj.19641 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Macedo et al. title: Developing a threat risk register based on the IUCN threat hierarchy for five tropical Important Plant Areas in Guinea link: https://peerj.com/articles/19629 last-modified: 2025-07-14 description: A pilot study to develop a threat risk register for Tropical Important Plant Areas in Guinea using the IUCN threat hierarchy is outlined. Guinea lost 92% of its total original forest before the end of the 20th Century. In addition, in the Guinée Forestière region alone, a further 25% of the remaining forest has been lost between 2000 and 2018, primarily driven by agriculture. One of the obstacles to effective protected area management in Guinea is the lack of quantitative measurements of the characteristics and location of the threats. Data was collected from five areas in Guinée Forestière to create individual risk registers for mapping and monitoring threats. The results show that the biggest threat is from agriculture, followed by biological resource use and intrusions and human disturbance. The level of threat of agriculture varies between sites but is the greatest threat at Mt Béro and Southern Simandou Mountains, though results could be skewed by sampling density. Further training of conservators and ecoguards on identification and classification of threats is needed to ensure consistency of recording across areas. This is a novel technique for recording and quantifying threats to plants in protected areas in Africa as no equivalent has been found during the course of this research. This tool has potential uses, both nationally and internationally, to improve monitoring of threats to rare plants and the forest landscape and can feed into IUCN Red List species and ecosystem assessments, as well as Protected Area Management Effectiveness systems. creator: Charlotte Couch creator: Faya Julien Simbiano creator: Mamadou Diawara creator: EdgarFrançois Loua creator: Léonce Mamy creator: Martin Cheek creator: Sékou Magassouba uri: https://doi.org/10.7717/peerj.19629 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Couch et al. title: Intraspecific and spatial variation in habitat use by sperm whales (Physeter macrocephalus) along the west coast of Martinique link: https://peerj.com/articles/19614 last-modified: 2025-07-14 description: For a deep-diving cetacean species like the sperm whale, acoustics is a vital tool for research. This need is especially pressing in the eastern Caribbean, where the habitat of marine mammals overlaps with heavy maritime traffic, leading to noise pollution and an increased risk of vessel collisions. To mitigate this risk, understanding their habitat use is essential. Mature males are generally solitary and migrate over long distances, while females and immatures form stable social units in subtropical and tropical waters. In this study, we examined intraspecific variation in distribution and habitat use among individuals along the Caribbean coast of Martinique, using both visual and acoustic data. Over the course of 24 surveys, 19 aggregations involving a total of 74 individual sightings were characterised, recognizing that some individuals may have been recorded multiple times. Using the inter-pulse interval (IPI) of clicks, we estimated individual size, which provided insights into the age and/or sex of each individual. Habitat characteristics included bathymetry, distance from the coast, and seabed slope. Our results on social structure are in line with previous literature: 37% of the aggregations were made up of females and/or juveniles, immatures, with a mature male nearby, with temporal changes in aggregations linked to male migration patterns. Spatial distribution and habitat use appeared consistent across aggregation types, regardless of group size, average individual size, or the presence of immatures. However, specific areas were identified for hunting and socialising based on bathymetry. This study highlights the importance of bathymetry and/or distance from the coast and temporal dynamics related to variations in weather conditions and movements of breeding males, in understanding habitat use by sperm whales in the eastern Caribbean. The lack of observed influence of seabed slope suggests that our spatial scale may have been too limited, or that finer details regarding seabed characteristics are needed. These findings could inform traffic management strategies to reduce the risk of vessel collisions with sperm whales. creator: Séréna Laurent creator: Marion Poupard creator: Célia Ortolé creator: Céline Valin creator: Benjamin de Montgolfier uri: https://doi.org/10.7717/peerj.19614 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Laurent et al. title: Spatiotemporal prediction of soil organic carbon density in Europe (2000–2022) using earth observation and machine learning link: https://peerj.com/articles/19605 last-modified: 2025-07-14 description: This article describes a comprehensive framework for soil organic carbon density (SOCD, kg/m3) modeling and mapping, based on spatiotemporal random forest (RF) and quantile regression forests (QRF). A total of 45,616 SOCD observations and various Earth observation (EO) feature layers were used to produce 30 m SOCD maps for the EU at four-year intervals (2000–2022) and four soil depth intervals (0–20 cm, 20–50 cm, 50–100 cm, and 100–200 cm). Per-pixel 95% probability prediction intervals (PIs) and extrapolation risk probabilities are also provided. Model evaluation indicates good overall accuracy (R2 = 0.63 and CCC = 0.76 for hold-out independent tests). Prediction accuracy varies by land cover, depth interval and year of prediction with the worst accuracy for shrubland and deeper soils 100–200 cm. The PI validation confirmed effective uncertainty estimation, though with reduced accuracy for higher SOCD values. Shapley analysis identified soil depth as the most influential feature, followed by vegetation, long-term bioclimate, and topographic features. While pixel-level uncertainty is substantial, spatial aggregation reduces uncertainty by approximately 66%. Detecting SOCD changes remains challenging but offers a baseline for future improvements. Maps, based primarily on topsoil data from cropland, grassland, and woodland, are best suited for applications related to these land covers and depths. We recommend that users interpret the maps in conjunction with local knowledge and consider the accompanying uncertainty and extrapolation risk layers. All data and code are available under an open license at https://doi.org/10.5281/zenodo.13754343 and https://github.com/AI4SoilHealth/SoilHealthDataCube/. creator: Xuemeng Tian creator: Sytze de Bruin creator: Rolf Simoes creator: Mustafa Serkan Isik creator: Robert Minarik creator: Yu-Feng Ho creator: Murat Şahin creator: Martin Herold creator: Davide Consoli creator: Tomislav Hengl uri: https://doi.org/10.7717/peerj.19605 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tian et al. title: Effectiveness of Rhizophagus intraradices and Acinetobacter calcoaceticus on soybean growth and thiram residues in soybean grains and rhizosphere soil link: https://peerj.com/articles/19701 last-modified: 2025-07-11 description: Soybean root rot has a serious effect on soybean yield. Pesticides such as thiram are used to prevent soybean root rot, but thiram remains in the soil, which seriously threatens food safety and human health. Microbial fertilizers can effectively control root rot, promote crop growth, and degrade pesticide residues. This study aimed to evaluate the synergistic effects of arbuscular mycorrhizal fungi and phosphorus-solubilizing bacteria in a controlled environment, specifically investigating their potential for prevention and control of soybean root rot and pesticide degradation. In this pot-based study, we investigated the effects of Rhizophagus intraradices, Acinetobacter calcoaceticus, and thiram on the incidence of root rot, soybean biomass, the number of bacterial colonies in rhizosphere soil, and thiram residues in soybean grains and rhizosphere soil. The results showed that inoculation with R. intraradices and A. calcoaceticus significantly increased arbuscular mycorrhizal fungi spore density (445%), arbuscular mycorrhizal fungi infection rate (103%), soybean biomass such as fresh weights (59%), nodule number (237%), and total bacterial colony number in the rhizosphere soil of soybean plants (133%) and presented the lowest incidence of root rot (20%) (P < 0.05), compared with the control group. A single inoculant significantly reduced the residual amount of thiram in soybean grains and rhizosphere soil, and a mixed inoculation (R. intraradices and A. calcoaceticus) produced the most significant reduction, relative to the group sprayed with only thiram, thiram residues were reduced by 73% and 69%, respectively (P < 0.05). These findings provide a foundation for the biological control of soybean root rot and the degradation of pesticides and contribute to the sustainable development of agricultural ecosystems. creator: Weiguang Jie creator: Yiwen Tan creator: Houze Lin creator: Min Zhang creator: Lianbao Kan uri: https://doi.org/10.7717/peerj.19701 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jie et al. title: Antibacterial potential and chromatographic profiling of bioactive compounds from endophytic Streptomyces sp. strain MIRK71 isolated from Mirabilis jalapa (L.) link: https://peerj.com/articles/19683 last-modified: 2025-07-11 description: Multidrug-resistant bacteria pose an alarming global health threat. The persistent rise in antibiotic-resistant infections continues to challenge healthcare systems worldwide. This study aims to evaluate the antimicrobial potential of 18 endophytic actinobacteria isolated from Mirabilis jalapa (L.) against clinically relevant multidrug-resistant pathogens. Among these, strain MIRK71 exhibited the strongest activity in secondary antimicrobial screening and was selected for further investigation. Molecular characterization using 16S rRNA gene sequencing identified MIRK71 as a Streptomyces species. Morphological analysis via scanning electron microscopy (SEM) revealed branched, filamentous colonies with microspore chains. Antimicrobial compounds were extracted from the culture filtrate grown in ISP1 broth using methanol under reduced pressure in a rotary evaporator. Gas chromatography-mass spectrometry (GC-MS) analysis detected 20 volatile compounds. Further profiling was conducted using high-performance thin-layer chromatography (HPTLC) with three optimized solvent systems: ethyl acetate:methanol:water (20:3:2) for glycosides (SS1), cyclohexane:ethyl acetate:formic acid (4:6:1) for phenols (SS2), and toluene:ethyl acetate:methanol:acetic acid (3:5:1:0.5) for anthracenes (SS3). Five peaks were recorded in SS1 and SS3, while seven peaks were observed in SS2 at 254 nm. Overall, this study contributes to the growing body of knowledge on endophytic actinobacteria and underscores their potential applications in antimicrobial therapy. creator: Lalrokimi creator: Purbajyoti Deka creator: William Carrie creator: Lallawmsangi creator: Christine Vanlalbiakdiki Sailo creator: Lalrosangpuii creator: Felicia Lalremruati creator: Awmpuizeli Fanai creator: Yasangam Umbon creator: Esther Lalnunmawii creator: Zothanpuia uri: https://doi.org/10.7717/peerj.19683 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lalrokimi et al. title: A new neornithischian dinosaur from the Upper Jurassic Tiaojishan Formation of northern China link: https://peerj.com/articles/19664 last-modified: 2025-07-11 description: The Middle and Late Jurassic Yanliao Biota is different from other contemporaneous fossil assemblages in that it lacks neornithischian dinosaurs. Here, we report a new, early-diverging neornithischian, Pulaosaurus qinglong gen. et sp. nov., from the Upper Jurassic Tiaojishan Formation of Qinglong, Hebei Province, of northern China. Diagnostic or noteworthy morphological characteristics of P. qinglong include: five premaxillary teeth; a small boss is present on the caudoventral corner of the dorsal ramus of the jugal; a nuchal crest is located along the parietal; the manus has five digits; a supra-acetabular crest is present on the ilium; the paired arytenoids are gracile and leaf-like in form; the obturator process along the ischium is located near the pubic peduncle; a notch-like shaped obturator opening is present within the pubis; a robust fibular condyle forms a dorsoventrally extending crest on the tibia; a subtriangular flange on the anterior surface of the astragalus extends dorsolaterally along three distal tarsals; three of the distal tarsals are unfused, including a small drop-shaped distal tarsal 3; distal tarsal 3 is pierced by a foramen. A phylogenetic analysis places P. qinglong as one of the earliest-diverging neornithischians yet described. Moreover, P. qinglong represents the second known dinosaur to preserve ossified laryngeal elements, thus suggesting that a bird-like vocalization evolved early in non-avian dinosaur evolution. creator: Yunfeng Yang creator: James L. King creator: Xing Xu uri: https://doi.org/10.7717/peerj.19664 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: An R package for survival-based gene set enrichment analysis link: https://peerj.com/articles/19489 last-modified: 2025-07-11 description: Functional enrichment analysis is usually used to assess the effects of experimental differences. However, researchers sometimes want to understand the relationship between transcriptomic variation and health outcomes like survival. Therefore, we suggest the use of Survival-based Gene Set Enrichment Analysis (SGSEA) to help determine biological functions associated with a disease’s survival. Despite the availability of this method to researchers, there are no standard tools or software to perform this analysis. We developed an R package and Shiny app called SGSEA and presented a study of kidney renal clear cell carcinoma (KIRC) to demonstrate the approach. In Gene Set Enrichment Analysis (GSEA), the log-fold change in expression between treatments is used to rank genes, to determine if a biological function has a non-random distribution of altered gene expression. SGSEA is a variation of GSEA using the hazard ratio instead of a log fold change. Our study shows that pathways enriched with genes whose increased transcription is associated with mortality (NES > 0, adjusted p-value < 0.15) have previously been linked to KIRC survival, helping to demonstrate the value of this approach. This method allows rapid identification of disease variant pathways and provides supplementary information to standard GSEA, all within a single R package at https://github.com/ShellsheDeng/SGSEA or via the convenient app at https://biostats-shinyr.kumc.edu/SGSEA/. creator: Xiaoxu Deng creator: Jeffrey Thompson uri: https://doi.org/10.7717/peerj.19489 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Deng and Thompson title: Integrated platform for structural and functional analysis of terpene synthases of Cannabis sativa link: https://peerj.com/articles/19723 last-modified: 2025-07-10 description: Terpenoids are the largest and most diverse family of natural products. Volatile terpenes from Cannabis sativa are crucial in flavours, fragrances, and pharmaceuticals due to their unique odours and biological activities, including antimalarial, antibacterial, and insecticidal properties. Their synthesis is catalysed by terpene synthase (TPS) enzymes, which perform cyclisation and rearrangement reactions of over 55,000 distinct terpene compounds. However, low catalytic efficiency of C. sativa TPSs limits their use in large-scale commercial production. The complex biochemistry of these reactions is not well understood due to limited enzyme structure information. To address this, we have developed an integrated platform for the systematic expression, purification, enzymatic characterisation, and crystallisation of TPS enzymes from C. sativa. This workflow combines kinetic, thermostability, and structural analyses with a data-mining-informed crystallisation screen that enabled the production of diffraction-quality crystals. As a demonstration of the platform’s utility, ten C. sativa TPS enzymes were functionally characterised, revealing turnover rates (kcat) ranging from 0.0011 to 0.0204 s−1 and diverse substrate specificities, with each enzyme producing a distinct product profile, highlighting the need for systematic characterisation of C. sativa terpene biosynthesis. Our findings provide a framework for the structural and functional study of C. sativa TPSs. The developed platform sets the stage for future metabolic engineering aimed at optimising terpene production for pharmaceutical, pest management, and synthetic biology applications. creator: Danielle Wiles creator: James Roest creator: Bhuvana Shanbhag creator: Julian Vivian creator: Travis Beddoe uri: https://doi.org/10.7717/peerj.19723 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wiles et al. title: Vocal constraints on song amplitude in star finches Bathilda ruficauda link: https://peerj.com/articles/19705 last-modified: 2025-07-10 description: Given the two main functions of birdsong, mate attraction and territory defence, song amplitude is crucial for communication because it determines the communication range and it can also carry information. To understand the evolution of signals, it is helpful to consider the constraints on signal production, as physical constraints set the limits for signal plasticity and how signals can respond to selection. Previous work on the constraints of song amplitude was restricted to species that use loud vocalisations for long-distance communication. However, the low song amplitudes of some non-territorial species may hint at unknown limitations considering that females may prefer loud song. The star finch (Bathilda ruficauda) is one such species. In this study, we recorded the songs of male star finches in the laboratory and investigated the relationship between vocal amplitude and other acoustic parameters of their song syllables. We found that vocal amplitude was linked to the phonetic structure of the syllables. More complex sounds (measured as higher syllable bandwidth and higher Wiener entropy) were produced at lower amplitudes than less complex sounds. To the best of our knowledge, this is the first report of a trade-off between song complexity and vocal amplitude. More complex song syllables possibly require a more intricate control of the syrinx and vocal tract, which might only be possible at lower amplitudes. We speculate that if female star finches prefer complex songs, this would cause males to sing quietly, as they cannot produce complex syllables with high amplitudes. We also provided a phonetogram (vocal range profile) for the star finch, indicating a positive correlation between amplitude and peak frequency. This finding corroborates earlier studies on species that use loud vocalisations for long-range communication, which, like the star finches in our study, were also unable to produce low frequencies at high amplitudes. This suggests that the frequency-amplitude correlation is a more general phenomenon in bird vocalisations, independent of the overall source amplitude of a species. While the evolution of birdsong is often viewed as constrained by neural costs and body size, or selective pressures from predators and social aggression, our results emphasise the importance of understanding phonetic features as well. At the same time, our study fills an important gap on non-territorial species that produce soft songs. The absence of the ecological demands for long-distance signalling has probably led birds to use soft yet complex songs that function within the pair bond, as we report here for star finches. creator: Hana Goto creator: Masayo Soma creator: Ayumi Mizuno creator: Henrik Brumm uri: https://doi.org/10.7717/peerj.19705 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Goto et al. title: A Jack of All Trades—Tawaki/Fiordland penguins are able to utilise diverse marine habitats during winter migration link: https://peerj.com/articles/19695 last-modified: 2025-07-10 description: Migration and non-breeding movements are common across animal groups and are often driven by seasonal changes in habitat conditions. This behaviour is prevalent in crested penguins (Eudyptes sp.), which have evolved in and still primarily inhabit the subantarctic regions of the Southern Hemisphere. These species migrate outside the reproductive phase due to the limited year-round productivity around the breeding sites. Tawaki/Fiordland penguins (Eudyptes pachyrhynchus) are unusual in that they breed in temperate, continental New Zealand, an environment that appears productive enough to support year-round residency, yet they undertake extensive migrations during the non-breeding period. To investigate the drivers and patterns behind this behaviour, we used satellite telemetry to track 14 adult tawaki from across their breeding range during the winter of 2019. We examined whether migration routes differed by breeding location, and used maximum entropy (Maxent) modelling to identify environmental predictors of habitat use during the non-breeding period. All penguins followed a similar south-westerly trajectory toward the subantarctic waters south of Tasmania, irrespective of origin. Birds reached maximum distances of up to 2,193 km from their colonies, traveling a median total distance of 6,086 km over 135 days. Maxent models showed that mixed layer depth (i.e., the mixing height at the ocean surface) around 80 m was the strongest predictor of habitat suitability, aligning with known foraging depths in this species. Tawaki were associated with oceanic habitats ranging from polar to subtropical regions—a broader environmental range than other crested penguins, which tend to remain within a single water mass. These findings highlight the flexibility of tawaki in their use of marine habitats. This behavioural plasticity may suggest resilience to environmental variability, offering insights into why tawaki appear to be maintaining stable population trends while other New Zealand crested penguins are in decline. creator: Thomas Mattern creator: Klemens Pütz creator: Pablo Garcia Borboroglu creator: Ursula Ellenberg creator: David M. Houston creator: Bernhard Lüthi creator: Philip J. Seddon uri: https://doi.org/10.7717/peerj.19695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mattern et al. title: Expression of the IL-18-related gene PTX3 correlates with clinicopathological features and prognosis in glioma patients link: https://peerj.com/articles/19675 last-modified: 2025-07-10 description: BackgroundGlioma, a highly aggressive brain tumor, presents significant challenges in prognosis and treatment. This study investigates the role of PTX3 expression in glioma and its correlation with patient outcomes, addressing a gap in current research regarding its molecular mechanisms.Materials and MethodsRNA sequencing data and clinical information for glioma patients were obtained from The Cancer Genome Atlas (TCGA). A multigene prognostic signature based on IL-18 signaling-related genes (ISRGs) was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression method. The functional roles of PTX3 were analyzed through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). Single-sample GSEA (ssGSEA) was used to assess the association between PTX3 expression and immune cell infiltration. The relationship between PTX3 expression and clinicopathological features was also examined. Prognostic relevance was evaluated using univariate and multivariate Cox regression models, and Kaplan–Meier survival analysis was performed. PTX3 protein expression was validated via immunohistochemistry in 56 glioma specimens.ResultsThe LASSO Cox regression model identified a nine-gene prognostic signature, including BMP2, NCF1, HSPB1, PIGT, PTX3, CCNA2, CCNB2, CCN4, and DES. Functional enrichment analysis revealed that PTX3-associated differentially expressed genes were significantly enriched in pathways such as cytokine–cytokine receptor interaction and PI3K-Akt signaling, which are critical for immune response and cell proliferation in glioma. PTX3 expression showed a strong correlation with immune cell infiltration, particularly macrophages, neutrophils, T cells, and natural killer cells, suggesting a role in modulating the tumor microenvironment. Pan-cancer analysis indicated that PTX3 is markedly upregulated in various cancers, especially gliomas, highlighting its potential as a biomarker. PTX3 expression was also associated with clinical features such as WHO grade, IDH mutation status, and 1p/19q co-deletion, with higher PTX3 levels linked to poorer survival outcomes. Immunohistochemistry confirmed elevated PTX3 protein expression in both lower-grade glioma and glioblastoma multiforme.ConclusionsThese findings highlight the critical role of PTX3 in glioma and suggest its potential as both a prognostic biomarker and therapeutic target. This study provides a foundation for future research into targeted therapies involving PTX3. creator: Delin Wang creator: Cuimei Liu creator: Bohao Sun creator: Xiaodong Zhang creator: Yejun Zhou creator: Zhonglin Hu creator: Duanzheng Cao creator: Jing Zhang creator: Jinfang Xu uri: https://doi.org/10.7717/peerj.19675 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Cryptic diversity on the genus Caenolestes (Caenolestidae: Paucituberculata) in the Ecuadorian Andes link: https://peerj.com/articles/19648 last-modified: 2025-07-10 description: The shrew-opposums of the genus Caenolestes (Thomas, 1895) belong to a group of Ameridelphian marsupial mammals in the order Paucituberculata, an order in which most of its representatives are extinct. This genus contains five formally described species: C. caniventer, C. convelatus, C. condorensis, C. fuliginosus, and C. sangay, all with type localities in Ecuador, plus at least three candidate species from Colombia now recognized as subspecies C. convelatus barbarensis, C. fuliginosus centralis and C. fuliginosus obscurus. Records of this genus are not abundant, both in biological collections and in sequence repositories (GenBank); thus, showing a discontinuous geographical distribution that could be a consequence of incomplete sampling. Systematic expeditions by the Instituto Nacional de Biodiversidad (INABIO) have increased the geographic sampling of this genus in Ecuador, which allowed us to reevaluate its genetic diversity. We obtained 43 sequences of cytb and 30 of RAG1 from 28 Ecuadorian localities in 12 Provinces, including novel topotypical material from C. caniventer, C. convelatus, and C. condorensis. We present a new hypothesis on the genetic diversity of Caenolestes using maximum likelihood inference for phylogenetic analysis, estimate p-genetic distances and divergence times for the genus. We found a species complex in the C. fuliginosus clade, with at least three candidate new species, having a threshold above 5% for the estimated genetic distance of the cytb among them. Also, we found two additional lineages hidden within C. caniventer. We expect that future work, with similar or larger sampling efforts in Colombia and Peru would reveal greater phylogenetic diversity and more complete evolutionary relationships. creator: Julio C. Carrión-Olmedo creator: Jorge Brito uri: https://doi.org/10.7717/peerj.19648 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Carrión-Olmedo and Brito title: Neuroprotective effects of essential oils in animal models of Alzheimer’s and Parkinson’s disease: a systematic review link: https://peerj.com/articles/19643 last-modified: 2025-07-10 description: Essential oils (EOs), derived from aromatic plants, have garnered significant attention for their potential neuroprotective properties in neurodegenerative diseases. This systematic review evaluates recent advancements in understanding the neuroprotective role of EOs against Alzheimer’s disease (AD) and Parkinson’s disease (PD). Following PRISMA guidelines, we conducted a comprehensive literature search across three major databases (PubMed, Virtual Health Library, and Web of Science) from inception to January 2024, resulting in thirteen high-quality in vivo studies for qualitative analysis. The review assessed various EOs, with hydrodistillation being the predominant extraction method (66.66% of studies). Studies primarily utilized Wistar rats (46.15%) and various mouse strains, employing diverse disease induction methods including β-amyloid administration (30.7% of AD models), rotenone (7.7% of PD models), and 6-hydroxydopamine (7.7% of PD models). Administration routes varied, with oral administration being most common (38.4%), with gavage and inhalation each accounting for 23.1% of studies. Key findings revealed that EOs exhibit multifaceted neuroprotective mechanisms. In AD models (69.3% of studies), EOs reduced oxidative stress markers, decreased pro-inflammatory cytokine levels, and increased neuroprotective protein expression. In PD models (30.7% of studies), EOs demonstrated significant dopaminergic neuroprotection, with improvements in behavioral outcomes. Behavioral assessments showed consistent enhancements in memory, learning, and motor functions across studies. The systematic analysis provides compelling evidence for EOs’ neuroprotective efficacy, particularly in early-stage intervention. However, limitations include the predominance of animal studies, variability in dosing, and administration methods. The most promising EOs identified were from Pinus halepensis, Citrus limon, and Acorus species, showing particular efficacy in reducing cognitive deficits and oxidative stress. Chemical analysis revealed that compounds such as α-pinene, limonene, and β-caryophyllene were predominantly responsible for the observed therapeutic effects. The molecular mechanisms underlying these effects included modulation of cholinergic transmission, reduction of amyloid-β aggregation, and enhancement of antioxidant enzyme activities. These findings suggest that EOs could serve as valuable complementary therapeutic agents, particularly when standardized for specific bioactive compounds. Future research should focus on standardizing EO compositions, conducting human clinical trials to establish safety and efficacy profiles, and investigating potential synergistic effects with conventional treatments. creator: Adrielle do Espírito Santos Macedo creator: Thayná Moraes Ferreira creator: Lane Viana Krejcová creator: Fernando Allan de Farias Rocha creator: Joyce Kelly R. da Silva creator: Laís Resque Russo Pedrosa creator: Bruno Duarte Gomes uri: https://doi.org/10.7717/peerj.19643 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Macedo et al. title: Correlation between preoperative uric acid levels and lymph node metastases in patients with papillary thyroid cancer: a retrospective study link: https://peerj.com/articles/19410 last-modified: 2025-07-10 description: BackgroundIn the past decade, numerous studies have highlighted a notable correlation between the prognosis of various cancers and uric acid (UA). Nevertheless, scientific literature regarding the association between central lymph node metastasis (CLNM) and UA remains lacking. This study sought to examine the association between UA and the likelihood of CLNM in individuals with papillary thyroid cancer (PTC) and to determine the UA threshold.MethodsThree hundred and seventy individuals with confirmed PTC who underwent surgery at the First People’s Hospital of Kunshan from October 2018 to July 2024 were included in this study. Initially, UA levels were measured, and the incidence of CLNM in PTC patients was assessed through postoperative pathology. Propensity score-matched (PSM) analysis was used to match patients. Multivariate logistic regression and a two-piecewise linear regression model were utilized to analyze the relationship between UA and CLNM and identify the threshold effect of UA concentrations on CLNM.ResultsThe correlation between UA and CLNM in PTC patients was found to be positive. Upon adjusting for various confounding factors, it was determined that, relative to the referential level, the odds ratio for CLNM was 4.01 at peak UA levels. After PSM analysis, the odds ratio for CLNM was 5.23 at the highest levels to the lowest levels. A non-linear relationship between UA and CLNM emerged following adjustment for potential confounding factors. The study identified 219.20 µmol/L as the UA threshold, serving as the optimal inflection point. The effect sizes and confidence intervals on both sides of the inflection point were −4.43 (−9.69–0.84) and 3.78 (1.70–5.85), respectively.ConclusionThe study concludes that the association between UA and CLNM is non-linear. A positive relationship between UA and CLNM was observed when UA levels exceeded 219.20 µmol/L. creator: ShaoKun Sun creator: Qin Zhou creator: Tao Hu uri: https://doi.org/10.7717/peerj.19410 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sun et al. title: Survival benefit from adjuvant chemoradiotherapy in local advanced gastric cancer without accurate D2 confirmation: a real-world retrospective study (TJ-ARK01) link: https://peerj.com/articles/19363 last-modified: 2025-07-10 description: The role of adjuvant chemoradiotherapy (CRT) is controversial following D2 dissection in advanced gastric cancer. Also, the extent of “D2 surgery” varied geographically due to the diversity in surgical techniques of radical lymphadenectomy and pathological accuracy in detecting positive lymph nodes detection. The purpose was to explore the role of adjuvant chemoradiation for gastric cancer and focus on patient stratification strategy. We retrospectively collected information of patients underwent surgery in Tongji Medical Cancer Center from January 2013 to December 2017 (2,489 in total). Propensity score match was applied to the chemotherapy (CT) group enrollment with well-balanced clinicopathological distributions. In total, 162 and 166 eligible patients were recruited into CT and CRT groups, nearly 75% diagnosed with advanced stage. The median follow-up duration was 61.3 months (4.0 to 109.0 months), 201 recurrence events occurred and 194 deaths events occurred. The 5-year disease-free-survival (DFS) rates were 32.0% in CT group and 44.0% in CRT group (P = 0.031), while 5-year overall survival (OS) rates were 36.0% in CT group and 50.0% in CRT group (P = 0.043). In the subgroup analysis, all patients were regrouped as subgroup 1 (positive lymph node (LN) ratio 0–50%) and subgroup 2 (positive LN ratio 51%–100%). There was a prolongation in 5-year DFS rates in subgroup 1 (40.0% in CT group, 61.0% in CRT group, P = 0.012) and in 5-year OS rates (48% in CT group, 64.0% in CRT group, P = 0.047). Further, patients with negative HER-2 expression had longer 5-year DFS (38% in CT, 49% in CRT, P = 0.115) and 5-year OS (36% in CT, 43% in CRT, P = 0.047). While previous studies found that the survival benefits were gained from chemoradiotherapy (CRT) inpatients of intestinal-type gastric cancer with lymph node metastasis, our findings highlight a distinct subgroup—patients with a lymph node ratio (LNR) ≤ 0.5 and HER2-negative tumors—for whom adjuvant chemoradiation may offer significant improvements in disease-free survival (DFS). This contrast underscores the potential role of molecular biomarkers (HER-2 status) and quantitative nodal burden (LNR) in refining therapeutic strategies, shifting the paradigm from histology-driven approaches to precision-based patient selection. creator: Xiao-Xiao Luo creator: Ben Zhao creator: Li Sun creator: Yu-Hong Dai creator: Hong Qiu creator: Xiang-Lin Yuan uri: https://doi.org/10.7717/peerj.19363 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Luo et al. title: Victory above all: the weight loss practices and perceptions of Chinese male kickboxers link: https://peerj.com/articles/19709 last-modified: 2025-07-09 description: ObjectivesKickboxing is a dynamic combat sport (CS) in which two competitors engage in full-force strikes using their hands, elbows, knees, shins, and feet. To ensure athletes compete against opponents of similar body size and weight for fairness, kickboxing competition is classified according to weight classes. Previous studies revealed that CS athletes tend to intentionally lose weight to gain a competitive advantage over their opponents. However, little is known about weight loss (WL) practices in kickboxers and the perceptions of CS athletes about WL. The aim of this study is to investigate the WL practices and perceptions of Chinese male kickboxers.MethodsA total of 152 Chinese male kickboxers completed the adapted Rapid WL Questionnaire. Participants were categorized by age group, weight category, competitive level, attitude toward impact of WL on health, and performance.ResultsSixty-eight percent of kickboxers purposefully engaged in WL practices. The average habitual WL was 6.0% of body mass (BM), with the average highest WL being 8.8% of BM. Most participants reduced 41–60% of their total planned magnitude of WL between 60 days and 9 days before the weigh-in, 21–40% between 8 days and 2 days before the weigh-in, and 0–20% within 1 day before the weigh-in. Coaches (67%) were most reported as the primary guides for WL. The primary reason kickboxers engage in WL is competing against lighter opponents to increase the chances of winning (70%). Most participants believed that WL had no impact on health (42%), improved performance (57%), and did not lead to unfair competition (73%). Significant differences were observed in both the highest WL% (p = 0.005, p = 0.018), the habitual WL% (p = 0.005, p = 0.018), the age beginning WL (p = 0.005, p = 0.018), and the annual WL times (p = 0.005, p = 0.018) across age and competitive level, but not observed across weight category, and attitudes toward both the health and performance impacts of WL (all p > 0.05). No significant differences were found in habitual weight regain after weigh-in/habitual WL (%) after weigh-in across all groups (all p > 0.05).ConclusionsThe prevalence of WL among Chinese male kickboxers is relatively low when compared to other CS, but the magnitude is relatively higher compared with previous studies. Their WL practices are mainly guided by kickboxing coach, and the primary reasons of WL is to gain a competitive advantage and improve performance. creator: Fanjie Meng creator: Yuming Zhong creator: Zhao Zhang creator: Zihan Ren uri: https://doi.org/10.7717/peerj.19709 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Meng et al. title: Clinical significance and heterogeneity of circulating tumor cells and clusters in breast cancer subtypes link: https://peerj.com/articles/19703 last-modified: 2025-07-09 description: The marked heterogeneity of breast cancer results in substantial variations in clinical characteristics, metastatic patterns, and prognosis across molecular subtypes. However, circulating tumor cells (CTCs) and circulating tumor cell clusters (CTC clusters), pivotal mediators of metastasis, have not been comprehensively evaluated for their biological characteristics and clinical significance across molecular subtypes. This review synthesizes recent research advancements to comprehensively examine the distribution characteristics, biological functions, and prognostic associations of CTCs and CTC clusters in luminal A, luminal B, HER2-positive breast cancer, and triple-negative breast cancer (TNBC). It was observed that HER2-positive breast cancer is associated with elevated CTC counts, whereas TNBC, despite lower CTC counts, exhibits CTCs and CTC clusters with enhanced invasiveness and metastatic potential due to Notch1 signaling pathway activation, elevated PD-L1 expression, and desialylation modifications. In luminal subtypes, the scarcity of CTC clusters is linked to a reduced metastatic risk; however, luminal B exhibits a greater propensity for CTC cluster formation than luminal A, suggesting prognostic differences. Clinical data demonstrate that CTC cluster counts are significantly inversely correlated with overall survival (OS) and disease-free survival (DFS), and that dynamic monitoring of CTC clusters enables prediction of treatment resistance and recurrence risk. Furthermore, the molecular profiles of CTCs (e.g., HER2 status, ESR1 mutations) facilitate personalized guidance for targeted and endocrine therapies. However, current detection technologies exhibit limitations in capturing CTC clusters with high efficiency and sensitivity, necessitating further optimization through microfluidic sorting, single-cell omics, and artificial intelligence approaches. This review underscores the heterogeneity of CTCs and CTC clusters across breast cancer subtypes, alongside their potential for clinical translation, offering theoretical support for prognostic evaluation and individualized treatment strategies in precision medicine. This study may be of considerable value to researchers and clinicians in the field of cancer metastasis. creator: LiangYu Hao creator: Lixiang Zheng uri: https://doi.org/10.7717/peerj.19703 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hao and Zheng title: Effect of modulating the extracellular matrix cross linkage by genipin on tumor cell resistance and survival in thioacetamide-induced hepatocellular carcinoma in rats link: https://peerj.com/articles/19680 last-modified: 2025-07-09 description: BackgroundPrevious studies on patients and rats with hepatocellular carcinoma (HCC) have shown significant changes in the extracellular matrix (ECM). Versican, a component of the ECM, forms extensive multimolecular interactions with other ECM components, particularly hyaluronan, through specific domains in its core protein. However, disturbances in the hyaluronan-versican interaction may affect cancer development. We aimed to examine the effect of modulating matrix cross-linkage between hyaluronan and versican using genipin on tumor cell survival, resistance, and renewal.MethodsFollowing the induction of HCC in rats using thioacetamide, an oral dose of 10 mg/kg of genipin was administered. Liver impairment was evaluated by measuring serum α-fetoprotein (AFP) levels and examining liver sections stained with hematoxylin/eosin and anti-versican and anti-fibronectin antibodies. Additionally, hepatic expression levels of mRNA and proteins, including epidermal growth factor (EGF), epidermal growth factor receptor (EGFR), fibronectin, glycogen synthase kinase-3 beta (GSK-3β), protein kinase B (PKB), and versican, were analyzed.ResultsGenipin enhances rats’ survival, leading to reduction in serum AFP levels and number of hepatic nodules. Micro-imaging examinations reveal that genipin reduces vacuolated cytoplasm, apoptotic nuclei, and necrotic nodules. Additionally, it significantly lowers EGF, EGFR, fibronectin, GSK-3β, PKB, and versican expression levels.ConclusionGenipin may be considered novel anticancer agent with hepatoprotective effects. This is achieved by reducing versican-free forms. Additionally, genipin decreases tumor cells’ resistance by lowering the expression of EGF, EGFR, PKB, and GSK-3β. Finally, it reduces tumor cell survival by decreasing the expression of fibronectin. creator: Hanan M. Hassan creator: Mohammed Baradwan creator: Alaa Bagalagel creator: Reem Diri creator: Ahmed Basilim creator: Mohammed Z. Nasrullah creator: Abdulhamid Althagafi creator: Hussam I. Kutbi creator: Abdulaziz A. Mohammed creator: Hanan M. Alshan creator: Mohammed M.H. Al-Gayyar uri: https://doi.org/10.7717/peerj.19680 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hassan et al. title: The reading difficulties in Chinese for individuals with attention deficit hyperactivity disorder: the role of executive function deficits link: https://peerj.com/articles/19679 last-modified: 2025-07-09 description: BackgroundAttention-deficit/hyperactivity disorder (ADHD) and reading disability (RD) are prevalent childhood conditions that together affect millions of children worldwide. In China, the prevalence of ADHD is approximately 6.4%, whereas the prevalence of RD ranges from 3.45% to 8%. Approximately 18–45% of children with ADHD also display comorbid RD, which further compromises their academic success and social functioning. Executive-function (EF) deficits are a core feature of ADHD and are known to affect reading in RD, yet their specific impact on Chinese reading remains under-explored.ObjectiveThis study investigated how EF deficits influence Chinese reading in children with ADHD, with the goal of informing diagnosis and intervention for ADHD-RD comorbidity.MethodsThis study recruited 160 Chinese-speaking children who met DSM-5 criteria for ADHD and allocated them to two groups—ADHD-only (n = 80) and ADHD + RD (n = 80). ADHD symptoms were rated with the Swanson, Nolan and Pelham Teacher and Parent Rating Scale (SNAP-IV), whereas Chinese reading was evaluated with the Dyslexia Checklist for Chinese Children (DCCC). Executive functions were measured with tasks tapping visuospatial working memory, verbal working memory, and response inhibition (Go/No-Go).ResultsBoth groups showed no significant differences in ADHD symptom scores. Compared with the ADHD-only group, the ADHD + RD group obtained higher total and subscale DCCC scores and lower accuracies on EF tasks. Total DCCC scores correlated negatively with EF performance, especially on visuospatial working-memory and response-inhibition tasks.ConclusionThis study suggests that individuals with ADHD comorbid with Chinese reading disabilities (RD) exhibit more pronounced deficits in executive function, particularly in verbal and visual-spatial working memory, and response inhibition tasks, compared to individuals with ADHD alone. These cognitive deficits are significantly negatively correlated with Chinese reading abilities, emphasizing the importance of not only focusing on traditional ADHD symptoms but also prioritizing training to enhance executive functions, especially visual-spatial working memory and response inhibition, when diagnosing and treating patients with ADHD comorbid with RD, in order to improve their reading abilities. creator: Jia Wei creator: Dengxian Yang creator: Fang Cheng creator: Wenwu Zhang uri: https://doi.org/10.7717/peerj.19679 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wei et al. title: Gender differences in peak medial joint contact forces during activities of daily living link: https://peerj.com/articles/19677 last-modified: 2025-07-09 description: Women are more likely to suffer from knee osteoarthritis as compared to men. For men and women, greater peak knee medial joint contact force is associated with greater rates of knee osteoarthritis. However, it is unclear if the increased rates of knee osteoarthritis in women is associated with greater medial joint contact force. We hypothesize that because women experience greater rates of knee osteoarthritis, they would experience greater peak medial joint contact force. Fifty-two healthy, young participants (26 women, 26 men) performed sit-to-stand, stand-to-sit, self-selected speed walking, self-selected speed running, and set speed running trials over force plates while motion capture data was recorded. Medial joint contact force, scaled by bodyweight, was calculated with a reduction modeling approach from inverse dynamics data and ultrasound measured distances. Differences in peak medial joint contact force between men and women were tested with one-tailed unpaired Student’s t-tests with a Bonferroni correction. No significant differences were seen between groups peak medial joint contact force in any of the tested movements. Medial joint contact force may not be able to explain the disparity in knee osteoarthritis rates between men and women. creator: Samantha J. Snyder creator: Maliheh Fakhar creator: Jae Kun Shim creator: Ross H. Miller uri: https://doi.org/10.7717/peerj.19677 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Snyder et al. title: Chronic sleep deprivation is associated with delayed puberty onset in rats, activation of proinflammatory cytokines and gut dysbiosis link: https://peerj.com/articles/19668 last-modified: 2025-07-09 description: Chronic sleep deprivation (CSD) in adolescents has become a trend with adverse health outcomes. Previous studies have demonstrated that sleep deprivation causes inflammation, alters puberty onset, and changes the gut microbiome composition; however, the relationship between these is still unknown. Therefore, we hypothesized that CSD delays the onset of puberty via elevating proinflammatory cytokines and alter ation of gut microbiome composition. Using the modified multiple platform method, we conducted a 4-week CSD experiment in juvenile rats and assessed pubertal markers, antioxidant activity, cytokine levels, and gut microbiome profiles. CSD significantly reduces body weight, delays onset of puberty, and elevated antioxidant enzyme activities in both sexes. In the sleep-deprivation female (SDF) rats, plasma levels of lipopolysaccharide–binding protein (LBP), interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) were significantly elevated; mRNA levels of TNF-α and IL-1β were also significantly elevated in the colon and reproductive organs, respectively. In the sleep-deprivation male (SDM) rats, only plasma levels of IL-6 were elevated considerably; in addition, mRNA levels of IL-1β and TNF-α were also significantly elevated in the colon and reproductive organs, respectively. Gut microbiome analysis revealed that the predominant bacteria at the genus level were Muribaculaceae, Prevotellaceae UCG-001, and Ruminococcaceae UCG-005 in the SDF rats; Prevotellaceae NK3B31, Ruminococcaceae UCG-010, Eubacterium coprostanoligenes, and Shuttleworthia in the SDM rats. CSD rats with abundant genera were positively correlated with antioxidant enzyme activities and mRNA levels of proinflammatory cytokines. Overall, CSD is associated with delayed puberty onset, possibly via an increase in the expression levels of proinflammatory cytokines and altering the gut microbiome composition, indicating proinflammatory cytokines and gut microbiome play an important role in pubertal timing change. These findings may guide the future studies to intervene sleep deprivation-related delays in the onset of puberty. creator: Shirley Priscilla Gunawan creator: Shih-Yi Huang creator: Jhih-Wei Hsu creator: Chia-Yuan Lin creator: Nam Nhat Nguyen creator: Te-Hsuan Tung creator: Shu-Ling Liang creator: Gilbert Aaron Lee creator: Chien-Tien Su creator: Yang Ching Chen uri: https://doi.org/10.7717/peerj.19668 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gunawan et al. title: Enhancing physical activity in older type 2 diabetic adults through remote patient monitoring: a pre-post study in Taiwan link: https://peerj.com/articles/19659 last-modified: 2025-07-09 description: BackgroundType 2 diabetes (T2D) is a growing concern among older adults, increasing the risk of frailty, and functional decline. In Taiwan, the convergence of population aging and high diabetes prevalence calls for innovative care strategies. This study evaluated the effectiveness of incorporating wearable step-count devices into the diabetic pay-for-performance (P4P) program to enhance physical activity and explore associations with related health outcomes.MethodsThis prospective, single-arm interventional study was conducted from February to September 2023 at a medical center in central Taiwan. T2D participants in P4P who were able to use smart phone were enrolled. At baseline, comprehensive geriatric assessment was performed to measure participants’ physical, mental functions and nutritional status. Daily step data were collected via Garmin trackers and synced automatically. Participants received weekly remote feedback from diabetes educators to encourage adherence in 2 months. The Wilcoxon signed-rank test assessed changes in step counts over time, and Spearman’s rank correlation examined associations with baseline health indicators. An association of daily step counts with metabolic controls factors, biochemical data, disease severity, functional performance, frailty, nutritional and mood were analyzed.ResultsThe study involved 66 participants, median age 72 years, with 24 males (36.4%) and 42 females (63.6%). Metabolic indicators showed fasting plasma glucose at 110.0 mg/dL (interquartile range, IQR: 97.0–137.5) and hemoglobin A1c at 6.1 (IQR: 5.7–7.2). Additionally, low-density lipoprotein was 86.5 mg/dL (IQR: 67.3–104.5), and triglycerides were 98.5 mg/dL (IQR: 76.8–139.8). Urine albumin-creatinine ratio was 15.3 (IQR: 7.6–84.9), and estimated glomerular filtration rate (eGFR) was 70.7 mL/min/1.73 m2 (IQR: 48.9–78.1). Functional capacity varied, with 47.0% having low muscle strength and 92.0% showing low physical performance. 15.2% showed symptoms of depression. Malnutrition and frailty were observed in 6.1% and 13.6%, respectively. Median daily steps significantly increased from 1,560.8 (IQR: 955.9–3,301.5) in week 1 to 2,652.9 (IQR: 1,271.8–4,139.3) in the final week (p < 0.001). Higher daily step counts were positively correlated with physical and nutritional status and negatively correlated with age, depressive symptoms, and frailty. Remote monitoring led to a significant and consistent increase in daily step counts across all tracking periods (p < 0.001).ConclusionsThe study found that digital mobile health monitoring improved daily step counts over time in older diabetic patients, and baseline physical functions, and nutritional status were related to the changes. Whether incorporating this wearable technology into diabetes education program improves long metabolic controls needs further researches. creator: Cheng-Fu Lin creator: Hui-Min Chang creator: Chiann-Yi Hsu creator: Chao-Tung Yang creator: Shih-Yi Lin uri: https://doi.org/10.7717/peerj.19659 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lin et al. title: Associations between squalene epoxidase gene polymorphisms and obesity link: https://peerj.com/articles/19635 last-modified: 2025-07-09 description: BackgroundAmong the known control points of cholesterol synthesis, squalene epoxidase (SQLE) is considered a key factor influencing cholesterol metabolism.MethodsA total of 1,045 consecutive participants were divided into an obese group and a control group. Blood biochemical markers were measured, and deoxyribonucleic acid (DNA) was extracted from all participants. Statistical analyses were conducted to assess the associations between SQLE gene single nucleotide polymorphisms (SNPs) and obesity.ResultsThe C/C genotype of SQLE SNP1 (rs10104486) was significantly more associated with obesity compared to the A/A genotype. A significant difference in genotype distribution frequency for rs10104486 was observed between the obese and control groups. The recessive model (CC vs. AC + AA) also showed a statistically significant difference. For SQLE SNP2 (rs2288312), differences were found in genotype distribution frequency, allele frequency, and the recessive model (GG vs. AA + AG) between the two groups.ConclusionsThis study indicates a correlation between the SQLE gene polymorphisms rs10104486 and rs2288312 and obesity in a young population. Participants carrying the C allele of rs10104486 were more likely to develop obesity than those carrying the A allele, with the CC genotype identified as a predisposing factor. creator: Jia-Qing Yu creator: Feng-Xia Wang creator: Shuai Liu creator: Bing Zhu creator: Yi-Tong Ma uri: https://doi.org/10.7717/peerj.19635 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Yu et al. title: Internal structure of the action and acceptance questionnaire II (AAQ-II): evidence for a three-factor and bifactor model in two samples of university students link: https://peerj.com/articles/19620 last-modified: 2025-07-09 description: BackgroundExperiential avoidance (EA), defined as an inflexible behavioral pattern by which a person tries to avoid contact with private unpleasant situations, is considered a transdiagnostic variable associated with various psychopathological disorders. The Acceptance and Action Questionnaire II (AAQ-II) is a broadly used measure of EA. However, inconsistencies in the methods employed for examining its internal structure and the need for culturally validated measures in diverse populations highlight the need for further study. We conducted two studies in Spanish-speaking university students (nStudy1 = 829; nStudy2 = 830) to determine the validity and reliability of the AAQ-II.MethodsIn the first study, we examined the questionnaire through exploratory factor analysis (EFA). In the second study, we conducted confirmatory factor analysis (CFA) to examine how well these factor structures fit our data.ResultsWe suggested a three-factor structure (namely: painful memories, emotional distress, and affective control), in contrast with the unidimensional model consistently reported in the literature. The three-factor model showed a better fit overall. Additionally, we tested a bifactor model to determine the feasibility of a general factor. Our results suggested that this general factor explained a high amount of the variance within the model when compared to the three independent factors. In terms of convergent validity, significant positive associations were found between EA and suicidal ideation, depressive and anxious symptoms, while negative associations were found with psychological well-being. The factor structures tested showed good internal consistency indices (ω = 0.853–0.918; α = 0.853–0.918).DiscussionWe discuss our results in terms of their methodological and practical implications for the use of the AAQ-II. creator: Daniel Núñez creator: César Villacura-Herrera creator: Javier Cubillos creator: Martín Donoso creator: Álvaro I. Langer uri: https://doi.org/10.7717/peerj.19620 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Núñez et al. title: Molecular evolution of TRPC4 regulatory sequences supports a role in mammalian thermoregulatory adaptation link: https://peerj.com/articles/19697 last-modified: 2025-07-08 description: BackgroundProteins encoded by the canonical transient receptor potential (Trpc) gene family form transmembrane channels involved in diverse signal-transduction pathways. Trpc4 has been shown necessary for the induction of nonshivering thermogenesis (NST) in mice, a key component of which is thermogenic brown adipose tissue (BAT). In bats, Trpc4 exhibited diversifying selection within exons encoding regulatory binding sites of TRPC4.MethodsTo assess whether diversification of these regulatory sequences mirrors the diversification of mammalian thermoregulatory strategies, the ratio of nonsynonymous to synonymous substitutions (ω) was estimated for multiple tetrapod outgroups and eutherian orders. Four questions were addressed: (1) Did the ancestral eutherian Trpc4 diverge under positive selection from nonplacental mammals that lack BAT? (2) Did Trpc4 subsequently become more constrained in descendant eutherian clades? (3) In eutherian clades that subsequently lost BAT by inactivation of the thermogenin gene Ucp1, did Trpc4 become less constrained? (4) Does the evolutionary rate of Trpc4 differ between quantitatively more heterothermic mammal orders (bats and rodents) relative to quantitatively less heterothermic outgroups (carnivores, artiodactylids, and primates)?ResultsCoincident with the advent of BAT, Trpc4 evolutionary rate increased significantly in ancestral eutheria after their divergence from nonplacental mammals but a branch-site model did not support a rate class ω > 1 along that branch. In descendant eutherian mammals, Trpc4 became far more constrained, with an evolutionary rate less than half that of tetrapod clades lacking NST, a pattern was not seen in other Trp channel genes. Intensifying selection in descendent eutherian mammals was further supported with the RELAX program, which also indicated reduced constraint on Trpc4 in clades that have secondarily lost BAT. However, no consistent pattern was identified within mammalian orders with strong variation in heterothermy: evidence of increased evolutionary rate was again found in bats for Trpc4 as well as homologs it directly binds in heteromeric membrane channels (Trpc5 and Trpc1), yet all rodent Trpc genes had low evolutionary rates. Evolutionary rates of Trpc4 and Trpc1 in bats were consistent with relaxed constraint whereas bat Trpc5 experienced diversifying selection. Most variation among tetrapod TRPC4 sequences lies within an  85 amino-acid window that is functionally uncharacterized. Sequence alignments demonstrated that the TRPC4 β isoform, which lacks a portion of the C-terminal regulatory region, originated in basal eutherians but appears to be lost in many tip lineages. Collectively, the data indicate that the C-terminal region of TRPC4 has responded to selection on NST thermoregulation during the diversification of eutherian mammals. The drivers of increased diversification of Trpc4 and interacting genes in bats remain to be determined. creator: Robert S. Cornman uri: https://doi.org/10.7717/peerj.19697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cornman title: The influence of cavity configuration and irrigation activation on root canal smear removal—an in vitro study link: https://peerj.com/articles/19678 last-modified: 2025-07-08 description: BackgroundEffective root canal therapy (RCT) depends on proper disinfection rather than complete sterilization of the root canal system. The smear layer created during instrumentation can inhibit disinfection, and its removal is crucial for successful treatment. Recently, various irrigant activation methods, including shock wave enhanced emission photoacoustic streaming (SWEEPS), passive ultrasonic irrigation (PUI), sonic activation (SA), and syringe irrigation (SI), have been developed to enhance cleaning efficacy. Sterilization of the root canal system is crucial for successful root canal therapy. Lasers have emerged as a popular choice for eliminating microorganisms from the root canal.AimThis in vitro study aimed to compare the effectiveness of different irrigant activation techniques—SWEEPS, PUI, SA, and SI—in removing the smear layer from root canals prepared with either a conventional access cavity (ConvAC) or an ultraincisal access cavity (UincAC) design. This study aimed to clarify and compare the effectiveness of various irrigant activation techniques in removing the smear layer from canals with conservative and conventional cavity designs.Materials and MethodsEighty extracted human maxillary incisors were prepared using a VDW 35/0.04 rotary system and randomly divided into eight groups (n = 10 per group), based on cavity configuration and activation technique: G1: SWEEPS–ConvAC, G2: SWEEPS–UincAC, G3: PUI–ConvAC, G4: PUI–UincAC, G5: SA–ConvAC, G6: SA–UincAC, G7: SI–ConvAC, G8: SI–UincAC. All samples were irrigated with 2.5% sodium hypochlorite (NaOCl) and 17% ethylenediaminetetraacetic acid (EDTA), followed by distilled water, and examined using scanning electron microscopy (SEM). Data were analyzed with Kruskal–Wallis and Bonferroni-adjusted Mann–Whitney U tests (α = 0.05).ResultsNo statistically significant difference was found in smear layer scores in the coronal and middle thirds among the groups. However, significant differences were observed in the apical third (p < 0.001). The SWEEPS–ConvAC group showed the least smear layer, while the SI–UincAC group exhibited the most. The effectiveness ranking was: SWEEPS, followed by PUI, SA, and SI.ConclusionsWhile access cavity design alone did not significantly affect smear layer removal, SWEEPS was the most effective activation method. The combination of SWEEPS with conventional cavity design yielded the most effective smear layer removal in the apical third. These results emphasize the importance of selecting not only an effective irrigant but also an appropriate cavity design to optimize apical disinfection in clinical endodontics. creator: Duygu Degirmencioglu creator: Şeyda Erşahan creator: Yelda Erdem Hepsenoglu creator: Erhan Erkan creator: Mustafa Gundogar creator: Kadir Sagir uri: https://doi.org/10.7717/peerj.19678 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Degirmencioglu et al. title: In vivo assessment of pharmacokinetic interactions of empagliflozin and henagliflozin with sorafenib: an animal-based study link: https://peerj.com/articles/19662 last-modified: 2025-07-08 description: BackgroundSorafenib is a multi-targeted tyrosine kinase inhibitor (TKI) used for the treatment of advanced renal cell carcinoma, hepatocellular carcinoma (HCC), and radioactive iodine-resistant thyroid carcinoma. Notably, glucose transporters sodium-glucose cotransporter 2 (SGLT2) and glucose transporter 1 are highly expressed in HCC and functionally promote tumorigenicity, which increase the possibility of coadministration of TKIs with SGLT2 inhibitors. Therefore, this study aimed to investigate the pharmacokinetic profiles of coadministration of sorafenib with novel SGLT2 inhibitors, either empagliflozin or henagliflozin and to explore their potential mechanisms.MethodsMale Sprague-Dawley (SD) rats were divided into seven groups (n = 6) that received: sorafenib (1), empagliflozin and sorafenib (2), henagliflozin and sorafenib (3), empagliflozin (4), sorafenib and empagliflozin (5), henagliflozin (6), sorafenib and henagliflozin (7). Blood samples were collected at multiple time points to measure plasma drug concentrations using UPLC-MS/MS, and pharmacokinetic parameters were calculated. In addition, messenger RNA (mRNA) expression was measured by quantitative polymerase chain reaction (RT-qPCR) to explore underlying mechanisms of interaction. Data analyses were conducted using DAS 2.1.1 software. A P-value of < 0.05 was used as the level of statistical significance.ResultsThe study revealed that sorafenib slightly increased the plasma concentration-time curves (AUC0–t and AUC0–∞) of empagliflozin, whereas the apparent clearance (CLz/F) and apparent volume of distribution (Vz/F) significantly decreased. Similarly, sorafenib increased the AUC0–t, AUC0–∞ and the maximum plasma concentrations (Cmax) of henagliflozin and decreased the CLz/F. Besides, coadministration of empagliflozin decreased the CLz/F, increased the AUC0–∞ and Cmax of sorafenib When coadministered with henagliflozin, the AUC0–t and AUC0–∞ of sorafenib significantly increased by 67% and 80%, respectively, accompanied by decrease in the CLz/F. Furthermore, PCR results demonstrated that sorafenib decreased the expression of Ugt2b7 in intestinal tissue. Empagliflozin and henagliflozin inhibited Oatp1b2 expression in the liver and P-gp expression in the liver and intestines.ConclusionsThese pharmacokinetic interactions provide valuable insights for future studies on optimizing the dosing regimens of sorafenib in combination with empagliflozin or henagliflozin, potentially reducing toxicity risks and improving the safety of coadministration in clinical settings. creator: Wenyu Du creator: Zihan Liu creator: Zhi Wang creator: Xin Zhou creator: Zhanjun Dong creator: Ying Li uri: https://doi.org/10.7717/peerj.19662 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Du et al. title: Validity and reliability of the Chinese version of the Jenkins Sleep Scale among university students in China link: https://peerj.com/articles/19657 last-modified: 2025-07-08 description: BackgroundThe Chinese version of the Jenkins Sleep Scale (JSS-C) is widely used; however, it lacks formal validation, and its applicability to Chinese university students has not been examined. This study evaluated the validity and reliability of the JSS-C in this population, with a focus on gender differences.MethodsA cross-sectional study was conducted with 1,534 Chinese university students (29.6% male, 70.4% female; mean age = 19.83 ± 1.54 years) recruited through convenience sampling. Participants completed the JSS-C, which assesses sleep disturbances across four key domains. Confirmatory factor analysis was used to examine construct validity. Internal consistency (Cronbach’s alpha) and composite reliability (CR) were calculated to assess reliability. Measurement invariance testing across gender groups was conducted to evaluate the scale’s robustness.ResultsConfirmatory factor analysis supported a strong one-factor structure for the JSS-C, with excellent model fit indices (χ2/df = 1.82, Tucker-Lewis index (TLI) = 0.997, comparative fit index (CFI) = 0.999, standardized root mean square residual (SRMR) = 0.007, root mean square error of approximation (RMSEA) = 0.023), exceeding conventional thresholds. Reliability analysis showed high internal consistency (Cronbach’s alpha = 0.840) and composite reliability (CR = 0.844), indicating strong scale stability. The JSS-C also demonstrated full measurement and structural invariance across genders, confirming its unbiased applicability for both male and female students.ConclusionThe JSS-C is a brief, valid, and reliable instrument for assessing sleep disturbances among Chinese university students. Its standardized scores support meaningful gender-based comparisons. creator: Mengyuan Zhao creator: Garry Kuan creator: Ke Zhou creator: Yee Cheng Kueh uri: https://doi.org/10.7717/peerj.19657 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Effectiveness of Schroth exercises for adolescent idiopathic scoliosis: a meta-analysis link: https://peerj.com/articles/19639 last-modified: 2025-07-08 description: BackgroundAdolescent idiopathic scoliosis (AIS) affects 2–3% of children aged 10 to 18 and can lead to both physical and psychological challenges. This review aims to evaluate the impact of Schroth exercises on Cobb angle, angle of trunk rotation, and quality of life in patients with AIS.MethodsA comprehensive search was conducted across Scopus, PubMed, CINAHL, Chinese National Knowledge Infrastructure, Cochrane Central, and ClinicalTrials.gov databases, identifying 11 randomized controlled trials (RCTs) with a total of 446 participants. These studies, primarily conducted in Asia and North America, compared the effects of Schroth exercises with either no treatment or alternative physical exercise interventions (standard physiotherapy regimens or non-specific exercise-based rehabilitation programs). Data were pooled using a random-effects model, and the quality of evidence was assessed using the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) approach.ResultsMeta-analysis showed that Schroth exercises were associated with a significant reduction in Cobb angle (standardized mean difference (SMD): −0.54; 95% confidence interval (CI) [−0.81 to −0.27]; p < 0.001). However, no significant effect was observed on the angle of trunk rotation (SMD: −0.90; 95% CI [−2.45 to 0.65]; p = 0.254). A significant improvement in quality of life was also noted (SMD: 0.67; 95% CI [0.33–1.01]; p < 0.001). The quality of evidence ranged from moderate to low.ConclusionsAlthough Schroth exercises were associated with a reduction in Cobb angle, the average change did not meet the conventional five-degree threshold considered clinically significant, and the analysis did not account for the natural progression of spinal curvature. Rather than asserting a definitive benefit, this review highlights significant methodological limitations in the current literature.PROSPERO registration number: CRD42024505289. creator: Yinfang Zhu creator: Caiying Zhu creator: Haiping Song creator: Manyan Zhang uri: https://doi.org/10.7717/peerj.19639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhu et al. title: Research on the application of biomaterial-based responsive hydrogels in the tumor microenvironment link: https://peerj.com/articles/19609 last-modified: 2025-07-08 description: The tumor microenvironment (TME) is a critical factor influencing the initiation, growth, and spread of solid tumors. Recent advancements highlight biomaterial-based responsive hydrogels as promising smart materials within the TME owing to their high biocompatibility, biodegradability, and sensitivity to various stimuli. This review details the fundamental properties, preparation techniques, and diverse applications of responsive hydrogels, specifically within the TME. Key applications include their use in targeted tumor therapy, controlled drug delivery, and modulation of the complex TME. Recent studies have shown how these hydrogels, by responding to environmental factors such as pH, temperature, or specific biomolecules, can enhance treatment efficacy while minimizing systemic toxicity. Additionally, challenges are identified in terms of hydrogel design, safety, and clinical translation, with future directions aimed at optimizing hydrogel interactions with tumor-specific conditions. This review provides a comprehensive assessment of the current landscape, shedding light on the potential and ongoing research in the field of hydrogel-mediated cancer therapy. creator: Wanrong Yue creator: Xiaoyu Zhu creator: Ming Wu creator: Wenyue Qiang creator: Yixin Yang creator: Ziyun Zhang creator: Youwei Wang creator: Yuanyin Teng creator: Mi Zhou uri: https://doi.org/10.7717/peerj.19609 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yue et al. title: The effect of yoga and aerobic exercise on children’s physical activity in rural India: a randomized controlled trial link: https://peerj.com/articles/19604 last-modified: 2025-07-08 description: PurposeThis study aimed to assess the impact of yoga and aerobic exercise on moderate-to-vigorous (MVPA) levels of children in rural India.MethodsThe study utilized secondary data from a randomized, controlled, open-labelled, single-center, two-site, parallel-group trial. The study was conducted in rural India over a 6-month period between 2018–2019. Children aged 6 to 11 years were randomized into three groups: aerobic exercise (30 minutes, 5 days/week), control (no intervention), and yoga (30 minutes, 5 days/week). MVPA was measured at baseline and at six months using the Quantification of Physical Activity in School Children and Adolescents survey adapted and validated for Indian children. Overall sample and gender-segregated data were analyzed using paired sample t-tests and one-way analysis of variance with post-hoc analyses.FindingsIn the overall sample (N = 151), mean MVPA (minutes/day) increased significantly in both yoga (n = 50; p < 0.001) and aerobic exercise (n = 49; p < 0.001) groups from baseline to endline. Among males, mean MVPA increased significantly from baseline to endline in all three groups, including the control group (n = 23; p = 0.005). Among females, mean MVPA increased only in the yoga group, with baseline to endline change being significant across the three groups (p = 0.005), and with the yoga group depicting greater change in comparison to the control group (p = 0.004).ConclusionsOur findings suggest that both yoga and aerobic exercise can increase MVPA among rural children, with yoga being particularly beneficial for girls—a significant finding to inform culturally-appropriate active living policies to minimize the current physical activity gender gap in India. These findings can have implications for public health programs and policies not only in India but across other rural areas worldwide, where similar challenges in promoting physical activity among children may exist. creator: Tarun Reddy Katapally creator: Jamin Patel creator: Sheriff Tolulope Ibrahim creator: Sonal Kasture creator: Anuradha Khadilkar creator: Jasmin Bhawra uri: https://doi.org/10.7717/peerj.19604 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Katapally et al. title: Potentially inappropriate medication and its associated factors in older people living in nursing homes: a cross-sectional study link: https://peerj.com/articles/19570 last-modified: 2025-07-08 description: BackgroundInstitutionalized residents tend to use more drugs and in larger doses. Potentially inappropriate medications (PIM) use is highly prevalent among them. In addition, they are more likely to be prescribed multiple medications (polypharmacy). Moreover, many drugs considered PIM have increased anticholinergic burden (ACB), responsible for adverse drug events (ADE).ObjectiveIdentifying PIM, polypharmacy and ACB among older people’s prescriptions as well as their associated factors.MethodsCross-sectional observational multicentre study. Drug information was collected from the nursing homes, medical registers. PIM exposure was assessed using Beers Criteria 2023. ACB was calculated using the Anticholinergic Risk Scale. Other sociodemographic, as well as health-related data were also collected.Results130 residents (83.8% women) mean age 85.1 (±7.4). Over 80% (111) of residents have prescriptions including at least one PIM. Polypharmacy (≥5 drugs) occurred in 69.1% (94), while extensive polypharmacy (≥10 drugs) occurred in 18.4% (25). The most prevalent PIMs were benzodiazepines (57.3%; 73), antipsychotics (48.5%; 66) and proton pump inhibitors (39.7%; 54). Regarding ACB, 63.1% (82) of the residents have prescriptions including at least one anticholinergic drug. In the multivariate analysis, ACB (p = 0.018; OR 3.52) and polypharmacy (p=0.015; OR 3.58) were associated with PIM.ConclusionsThe prevalence of PIM, polypharmacy and ACB was very high (84%, 69%, and 63% respectively) in this sample of nursing home residents. ACB and polypharmacy were significantly associated with PIM. Anticholinergic drugs should be carefully assessed and gradually withdrawn when not needed. Balancing treatment with other biopsychosocial interventions may contribute to reducing polypharmacy. creator: Ester Goutan-Roura creator: Geovanna O. Carneiro creator: Francisca S.M. Moreira creator: Montse Masó-Aguado creator: Pau Moreno-Martin creator: Eduard Minobes-Molina creator: Dawn A. Skelton creator: Javier Jerez-Roig uri: https://doi.org/10.7717/peerj.19570 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Goutan-Roura et al. title: Psittacosaurus houi, a longer snouted psittacosaurid from the Lower Cretaceous Lujiatun Unit of Yixian Formation, China, with the synonymy of the unresolved genus Hongshanosaurus revisited link: https://peerj.com/articles/19547 last-modified: 2025-07-08 description: The taxonomic validity of some genera and species within Psittacosauridae has been disputed, including that of Hongshanosaurus houi, which has been synonymized with Psittacosaurus lujiatunensis previously. To assess the validity of the former genus and species and elucidate the taxonomy and diversity in Psittacosauridae, we describe a nearly complete psittacosaurid skull (ZMNH M12414) with the aid of computed-tomography techniques. The specimen comes from the Lujiatun Unit of the Lower Cretaceous Yixian Formation, Liaoning, northeastern China, which has also produced Psittacosaurus major, P. lujiatunensis, and H. houi. ZMNH M12414 exhibits a series of unique features that are also present in the adult referred skull of H. houi (IVPP V12617), indicating that both specimens are attributable to the same species within Psittacosauridae. The proportionally large length of the snout used to diagnose H. houi cannot be used for taxonomic distinction of Psittacosaurus because this character is also found in P. amitabha, supporting that the genus Hongshanosaurus is a junior synonym of Psittacosaurus. On the other hand, ZMNH M12414 and IVPP V12617 exhibit a set of features that are not observed in any other species of Psittacosaurus, including P. lujiatunensis. Because of these features, the specimen in question better fits as its own species within Psittacosaurus: P. houi. A phylogenetic analysis supports the validity of P. houi, where the specimens form an independent species within Psittacosaurus. The computed-tomography techniques employed in the present study facilitated re-assessment of the taxonomy and morphological diversity of Psittacosaurus, and its application is encouraged for previously described dinosaur taxa whose validities are in question. By utilizing such techniques, the detailed evaluation of ontogenetic, intraspecific, and interspecific variations will be crucial to understand the true taxonomy and diversity of Psittacosaurus in future studies. creator: Asato Ishikawa creator: Wenjie Zheng creator: Takuya Imai creator: Soki Hattori creator: Masateru Shibata creator: Soichiro Kawabe creator: Xingsheng Jin uri: https://doi.org/10.7717/peerj.19547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ishikawa et al. title: Reliability and validity of the six-minute step test in assessing the functional capacity of hemodialysis patients link: https://peerj.com/articles/19157 last-modified: 2025-07-08 description: PurposeHemodialysis patients often experience functional limitations that are challenging to assess due to equipment and space constraints. The 6-min step test (6MST) requires little space and a small standardized ergometer, making it more accessible and feasible in various healthcare settings, when compared to the cardiopulmonary exercise test (CPET) and the 6-min walk test (6MWT). Thus, the aim of this study is to evaluate the test-retest reliability and concurrent validity of the 6MST for assessing the functional capacity of hemodialysis patients.MethodsAssessments conducted included anthropometry, spirometry, 6MWT, and 6MST. These two tests were randomized and performed on alternate days. Two 6MSTs and two 6MWTs were conducted with a minimum interval of 30 min between them.ResultsThe study involved 32 participants, 67% men (n = 22) and 33% women (n = 10), with an average age of 57 ± 13 years and body mass index (BMI) of 28.6 ± 5.2 kg/m2. The 6MST demonstrated high test-retest reliability (ICC = 0.94 (95% CI [0.85–0.97]; p < 0.001)) and a strong correlation between the number of steps performed in the 6MST and the distance covered in the 6MWT (r = 0.87; p < 0.001). A learning effect was observed, with a 7% improvement on retesting.ConclusionThe 6MST provides a feasible, reliable assessment option for hemodialysis patients and could be easily implemented in clinics lacking space and specialized equipment. Limitation of the present study are being a single-center investigation with a small sample size, thus limiting generalizability, and the variability of patient conditions, which may have influenced the results. Future research should explore the 6’ long-term stability, responsiveness, and impact on patient-centered outcomes, as well as its applicability across different hemodialysis populations and clinical settings, to improve its clinical usefulness. creator: Carla Cristina Lima creator: Maria Eduarda Godoy creator: Débora Kellen Ferreira Fratoni creator: Elaine Paulin uri: https://doi.org/10.7717/peerj.19157 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lima et al. title: Utilizing loop-mediated isothermal amplification (LAMP) for detecting hemoglobin Constant Spring and hemoglobin Pakse mutations amidst the high prevalence and genetic heterogeneity of thalassemia in Thailand link: https://peerj.com/articles/19687 last-modified: 2025-07-07 description: Thalassemia is a genetic disorder with significant prevalence in Southeast Asia, particularly in Thailand, where hemoglobin (Hb) Constant Spring (Hb CS) and hemoglobin Pakse (Hb PS) mutations are common. These mutations, resulting from stop codon alterations in the α2-globin gene, can lead to severe phenotypes such as non-deletional Hb H disease. This study aimed to develop and evaluate a novel colorimetric loop-mediated isothermal amplification (LAMP) assay for detecting Hb CS and Hb PS mutations. A total of 282 samples with several genotypes were recruited in the study. We developed LAMP assay, using a phenol red pH indicator, which provided visual detection of DNA amplification within 35 minutes at 65 °C. Both assays demonstrated a lower limit of detection of 0.625 ng/reaction and achieved 100% sensitivity and specificity across 282 DNA samples, validated against standard allele-specific polymerase chain reaction (PCR). Additionally, the assay’s minimal equipment requirements and cost-effectiveness make it suitable for use in community hospitals and large-scale screenings. The LAMP assay offers a rapid, accurate, and affordable alternative for Hb CS and Hb PS detection, addressing the challenges of managing thalassemia in genetically diverse and resource-limited regions like Thailand. creator: Kasama Wongprachum creator: Nichakan Thitipoomdecha creator: Phakkamon Ananratanakit creator: Wattanakit Prakobkul creator: Unchasa Angkuranak creator: Nitchagan Sawangkul creator: Prapaporn Panichchob creator: Rossarin Karnpean creator: Wittaya Jomoui uri: https://doi.org/10.7717/peerj.19687 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wongprachum et al. title: Adaptation analysis of two Asteraceae invasive plants in Lhasa, Tibet link: https://peerj.com/articles/19667 last-modified: 2025-07-07 description: Invasive plants pose a major threat to global ecosystems, especially in ecologically fragile high-altitude regions. Due to its unique geographical and climatic conditions, the Tibetan Plateau is considered highly susceptible to biological invasions. This study investigates the germination capacity and early growth performance of two invasive species, Bidens pilosa and Tagetes minuta, under the natural climatic conditions of Lhasa, Tibet. We assessed how seed burial depth, geographical provenance, and climatic variables affect their establishment potential. The results showed that B. pilosa exhibited the highest germination rate in shallow soil layers, especially for seeds originating from Kunming (KM). However, seeds from the same source that matured in Lhasa following one local growing season (LS), showed a significant reduction in germination capacity, indicating the negative effects of high-altitude stress on maternal seed quality. Seeds from different altitudes displayed varied adaptive performance, with high-altitude provenances showing greater plant height in Lhasa’s cold, dry environment. Although T. minuta exhibited generally low germination rates across all burial depths, the individuals that successfully emerged demonstrated vigorous early growth, particularly under deeper burial conditions. This suggests that once established, the species may possess strong potential for rapid population expansion and severe invasion. Climate data over the past three years showed that the growing season from May to October in Lhasa—characterized by increased temperature and precipitation—provided a favorable climate window for both species. Our findings suggest that the ongoing warming and humidification trend on the Tibetan Plateau, driven by global climate change, may further facilitate the expansion and establishment of these invasive species. This study provides essential insights for risk assessment and management of invasive plants in Lhasa and other high-altitude regions, emphasizing the importance of long-term monitoring and targeted early-warning strategies in response to shifting environmental conditions. creator: Zhefei Zeng creator: Ziyi Liang creator: Yan Chen creator: Qi Shu creator: Junru Li creator: Norzin Tso creator: Mengyan Chen creator: Shutong Zhang creator: Xin Tan creator: La Qiong creator: Junwei Wang uri: https://doi.org/10.7717/peerj.19667 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zeng et al. title: The quality and reliability of YouTube video content about gingival recession on different time periods link: https://peerj.com/articles/19653 last-modified: 2025-07-07 description: BackgroundGingival recession is a mucogingival problem that can cause esthetic concerns and sensitivity. While some patients remain unaware of it, others seek solutions through various means. The COVID-19 pandemic has increased the role of social media in accessing health information. The frequent use of YouTube has prompted researchers to evaluate its contents quality and reliability. This study aims to examine this issue by comparing two periods: before and after COVID-19.MethodsThe first 100 videos for the keyword ‘receding gums’ shared in 2019 and 2024 were analyzed. A total of 23 and 35 videos were included, respectively. Quality was evaluated using Video Quality Index (VIQI) and Global Quality Scale (GQS), reliability with DISCERN and Modified DISCERN and content through an approach developed by the authors. Videos were also assessed based on their characteristics and sources. Data were analyzed using IBM SPSS 26.0. For two-group comparisons, independent sample t-tests were applied to normally distributed data, while the Mann–Whitney U test was used for non-normally distributed data. Categorical variables were analyzed with the Chi-square test. Correlations between variables were examined using Spearman’s correlation analysis.ResultsAccording to content analysis, useful videos were found to have higher scores of quality and reliability indices in both the 2019 and 2024 groups (p < 0.001). In 2024, the amount of videos uploaded by dental professionals was significantly more ‘useful’ compared to those from other sources (p = 0.45). There was a tendency of increase in sharing videos by healthcare professionals following the COVID-19 pandemic. creator: Beyza Bozoklu creator: Nülüfer Demir creator: Merve Akbaş creator: Hatice Sena Öner creator: Duygu Yaman uri: https://doi.org/10.7717/peerj.19653 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bozoklu et al. title: Inter-colony and inter-annual behavioural plasticity in the foraging strategies of a fjord-dwelling penguin—good news in the face of environmental change? link: https://peerj.com/articles/19650 last-modified: 2025-07-07 description: The Fiordland penguin or tawaki (Eudyptes pachyrhynchus) breeds in the complex fjord systems of New Zealand/Aotearoa’s southwest, with penguin colonies distributed from fjord entrances to fjord heads, up to 40 km from the ocean. Until recently, little was known about the marine ecology of fjord-breeding tawaki and how access to the fjord environment may impact the species’ foraging strategies. We conducted a comparative study of foraging behaviour in chick-rearing tawaki from colonies located at the entrance and further inside Piopiotahi/Milford Sound, one of New Zealand’s 14 fjords. Through the attachment of GPS/dive data loggers, dive parameters were examined to determine behavioural differences between the inner fjord colony (Harrison Cove) and the outer fjord colony (Moraine) during 2019 and 2020. Although situated only eight km from each other, the two colonies showed markedly different foraging preferences, with Moraine birds almost exclusively foraging outside the fjord in both years, while Harrison Cove birds primarily foraged within the fjord in 2020 but not in 2019. Tawaki from each colony also displayed contrasting dive behaviour across years, either adopting a strategy of deeper dives with fast velocities, (Harrison Cove in 2019, Moraine in 2020) or shallower dives with slower velocities (Moraine in 2019, Harrison Cove in 2020). Foraging activity and efficiency for both colonies appeared to be greater in 2020 than 2019, although birds foraged differently to achieve this: Harrison Cove birds dived primarily to depths of 0–20 m whereas Moraine birds switched between shallow dives, and deeper dives to 60–120 m of the water column. Notably different environmental conditions in both the ocean and fjord in 2019 versus 2020 may have contributed to the behavioural differences across years. Although replication across multiple fjords is necessary in future, these findings highlight that tawaki possess considerable plasticity in their foraging behaviours which could be advantageous for their future survival in a changing climate. creator: Myrene Otis creator: Thomas Mattern creator: Ursula Ellenberg creator: Robin Long creator: Pablo Garcia Borboroglu creator: Philip J. Seddon creator: Yolanda van Heezik uri: https://doi.org/10.7717/peerj.19650 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Otis et al. title: Stock assessment and management implications of sailfin sandfish (Arctoscopus japonicus) caught by multiple fishing gears with different selectivity in Korean waters link: https://peerj.com/articles/19602 last-modified: 2025-07-07 description: The yield per recruit (YPR) model developed by Berverton & Holt in 1957 is widely used to determine the optimal age at first capture (tc) and optimal fishing intensity (F0.1) for the sustainable use of fish stocks. The YPR model is mainly applied to fishing gears, including trawlers and Danish seines, as individual gear types. In practice, fishery resources are predominantly harvested using multiple fishing gears rather than using a single fishing gear, with selectivity differing among the various gears employed. Therefore, management reference points, such as F0.1 or F40%, should be derived from stock assessments that account for multiple fishing gears and their respective selectivity. In this study, the traditional (single-gear) YPR and spawning biomass per recruit (SBPR) models were modified into multi-gear YPR and SBPR models to assess the stock status of fish species caught using multiple fishing gears with different selectivities. The modified models were applied to sailfin sandfish (Arctoscopus japonicus) stocks, primarily caught by the East Sea mid-sized Danish seine and coastal gillnet fisheries in Korean waters. The results showed that the optimal fishing intensities (F0.1, F40%) were higher for the multi-gear model than those for the single-gear model. The optimal fishing intensities of the multi-gear model considered the different selectivities and fishing intensities of multiple fishing gears; therefore, the estimation results of this model provided a more accurate assessment of the stock status of the sandfish. The optimal fishing intensity derived from the traditional (single-gear) model was underestimated because it considered only one fishing gear. Consequently, employing this fishing intensity for resource management poses a risk of overfishing. In the sensitivity analysis of the main parameters used in the multi-gear models, the natural mortality (M) and growth (K) coefficients resulted in YPR exhibiting greater sensitivity than SBPR in response to variations in M and K. Furthermore, YPR demonstrated a greater sensitivity to variations in K than those in M. creator: Sung Il Lee creator: Eun-Gyu Kim creator: Jae-Hyeong Yang creator: Chang-Ik Zhang uri: https://doi.org/10.7717/peerj.19602 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Lee et al. title: Predicting and testing a gene network regulating seed germination in Arabidopsis link: https://peerj.com/articles/19599 last-modified: 2025-07-07 description: Maternal auxin signaling inhibits seed germination in Arabidopsis, but little is known about the gene network that mediates the inhibition of seed germination by auxin. Based on publicly available data, we first determined the expression patterns of AUXIN SIGNALING F-BOX (AFB) genes in the funiculus (FUN)-chalazal seed coat (CSC) continuum. We found that TIR1, AFB1, and AFB4 exhibited a down-expression gradient and AFB2, AFB3, and AFB5 an up-expression gradient from FUN to CSC, and members in each of the two AFB groups were linearly correlated in expression in FUN, CSC, and the distal seed coat (DSC). We then searched for auxin-regulated genes that exhibited one of the two expression gradients. We found 118 such genes that were assigned into four groups based on their response mode to auxin and expression gradient direction. The four groups were further broken down into 12 subgroups based on the linear correlation coefficient values. Only three of the 12 subgroups, including a total of 30 genes with 21 of them being known or highly likely to function in the seed germination process. To explore whether additional genes of the remaining nine play roles in seed germination, we tested mutants of five of them in a germination assay and found all of them exhibited either delayed or hastened germination. The experimental results support the validity of our approach for predicting the involvement of these genes in seed germination. Based on publicly available data and data from this investigation, we constructed a gene network, which should provide a valuable framework and new clues for future studies of the molecular mechanism controlling seed germination. creator: Ming Yang creator: Yixing Wang uri: https://doi.org/10.7717/peerj.19599 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yang and Wang title: Global stock structure of the Silky shark (Carcharhinus falciformis, Carcharhinidae) assessed with high-throughput DNA sequencing link: https://peerj.com/articles/19493 last-modified: 2025-07-07 description: Silky shark (Carcharhinus falciformis, Carcharhinidae) numbers have declined steeply in recent decades due to the fin fishery and bycatch in pelagic fisheries. Due to a lack of data on stock delineations, this species is currently managed in ocean-spanning jurisdictions defined by regional fisheries management organizations (RFMOs). Here we investigate the global stock structure of silky sharks and compare population structure to the four RFMO boundaries. Using high-throughput sequencing from pooled individuals (pool-seq) based on 628 specimens collected opportunistically across 11 circumglobal regions, yielding 854 nuclear single nucleotide polymorphisms (SNPs) and 23 mtDNA SNPs. Results indicate significant population genetic structure between all 11 regional sampling locations, with discriminant analysis of principal components (DAPC) identifying seven discrete groups. Within the Atlantic and Indo-Pacific Oceans, FST values ranged from 0.014 to 0.035 for nuclear (nDNA) markers, and from 0.012 to 0.160 for whole mtDNA genomes, with much higher values between than within oceans (mtDNA: 0.383–0.844, nDNA: 0.042–0.078). Using an analysis of molecular variance (AMOVA) framework, 22.24% of the observed population variance is explained by RFMOs, 32.1% is explained among ocean basins, and 34.81% is explained by the DAPC-identified groups. We find significant population genetic structure within the jurisdiction of every RFMO, from which we have more than a single sampling site. Our genomic-scale results indicate discordance between population genetic structure and RFMOs, highlighting the need for a detailed study to accurately identify stock boundaries. creator: Derek W. Kraft creator: Emily E. Conklin creator: Evan B. Freel creator: Melanie Hutchinson creator: Julia L.Y. Spaet creator: Robert J. Toonen creator: Zac H. Forsman creator: Michael I. Grant creator: John David Filmalter creator: John R. Hyde creator: Simon J.B. Gulak creator: Brian W. Bowen uri: https://doi.org/10.7717/peerj.19493 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kraft et al. title: Was Hupehsuchus a baleen whale-style filter feeder in the Early Triassic? A re-examination of the evidence link: https://peerj.com/articles/19666 last-modified: 2025-07-04 description: One of the recurring paleobiological questions over the last three decades has been whether there were any filter feeding tetrapods before whales evolved. Recently, a study proposed that a small marine reptile from the Early Triassic, Hupehsuchus nanchangensis, filter-fed in a mode similar to living right and bowhead whales (Balaenidae). The case for filter feeding was largely based on perceived similarities in dorsal-view cranial morphology between Hupehsuchus and Balaenidae, analyzed through geometric morphometrics of 2D landmarks. Here, we show that this similarity was an artifact of multiple errors, including the use of a dataset of extant cetaceans that does not match the morphology of respective species. Notably, 15 of the cetacean species examined were represented by narrow skulls reminiscent of Hupehsuchus­; without these unrealistic data points, Hupehsuchus has no morphospace overlap with any cetaceans, invalidating the proposed inference for Triassic filter-feeding. We collected a new set of landmarks using the published definitions to see how the result changes when using more accurate data along the original authors’ intention. We determined that odontocetes and mysticetes do not overlap in morphospace with Hupehsuchus, which plots outside any living cetacean species. We conclude that there is insufficient evidence to suggest that Hupehsuchus was a filter feeder, in concordance with: energetic studies suggesting balaenid-style feeding would be unsustainable at the small body sizes of Hupehsuchus; the lack of an intraoral space for the baleen; and the long neck and comparatively small head that are unsuitable for continuous ram feeding to filter prey-laden volumes of water. This re-examination of Hupehsuchus highlights the challenges for inferring filter-feeding in other extinct tetrapods. creator: Ryosuke Motani creator: Nicholas D. Pyenson creator: Da-yong Jiang uri: https://doi.org/10.7717/peerj.19666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Motani et al. title: Role of glycoproteins in hepatic lipid metabolism: emerging diagnostic markers and therapeutic targets link: https://peerj.com/articles/19627 last-modified: 2025-07-04 description: The liver is an important metabolic organ in the human body, and abnormal hepatic lipid metabolism may lead to a variety of diseases such as metabolic dysfunction-associated fatty liver disease, cirrhosis, and hepatocellular carcinoma. These diseases are often closely associated with chronic diseases, including obesity, hypertension, high cholesterol and diabetes, and have become major factors increasing the global disease burden. Currently, the diagnosis of diseases related to hepatic lipid metabolism relies mainly on imaging findings and serologic markers. In terms of treatment, lifestyle interventions such as dietary changes and increased exercise remain the mainstay of the fight against the diseases. However, effective therapies to control the progression of these diseases are still lacking. Glycoproteins are complex biomolecules consisting of sugar chains and proteins bound covalently, which are widely found in cell membranes and secretory fluids. In recent years, researchers have found that glycoproteins have potential application value in the diagnosis and treatment of diseases related to hepatic lipid metabolism. But there are currently no articles summarizing and analyzing the pathways and mechanisms involved. This review provides an overview of the progress of research on glycoproteins involved in diseases related to hepatic lipid metabolism as well as new insights into glycoproteins as potential diagnostic markers and therapeutic targets for lipid metabolism diseases. creator: Bo Lan creator: Sixing Huang creator: Jinping Luo creator: Ping Shi creator: Zhe Qiang uri: https://doi.org/10.7717/peerj.19627 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lan et al. title: Clinical diagnosis, treatment, and survival analysis of 61 cases of salivary duct carcinoma: a retrospective study link: https://peerj.com/articles/19626 last-modified: 2025-07-04 description: ObjectiveThis study aims to investigate the clinicopathological features, treatment modalities, and prognostic factors associated with salivary duct carcinoma (SDC).MethodsA retrospective analysis was conducted on the clinicopathological data of 61 patients with SDC admitted to Shanxi Cancer Hospital from January 2010 to February 2024. This study focused on their demographic information, treatment regimens, clinical outcomes, and overall prognosis.ResultsA total of 61 patients with SDC were included in this study, of whom 45 (73.77%) had primary tumors in the parotid gland, 44 (72.13%) were in stage IV at the initial visit, 35 (57.38%) had cervical lymph node metastases, and two (3.28%) had distant metastasis at the first visit. Immunohistochemical (IHC) staining showed that 54 cases (88.52%) were positive for androgen receptor (AR), and 25 cases (40.98%) were positive for human epidermal growth factor receptor 2 (HER-2). Two patients did not undergo surgical treatment due to distant metastasis and received palliative chemoradiotherapy. Fifty-nine patients underwent radical surgery, and of these, 52 (88.14%) received postoperative adjuvant treatment, including chemoradiotherapy or radiotherapy alone. The median overall survival (OS) time was 20 months for the non-surgery group (n = 2), 79 months (95% CI [72.60–85.40]) for the surgery and chemoradiotherapy group (n = 22), 61 months (95% CI [49.11–72.90]) for the surgery and radiotherapy group (n = 30), 20 months (95% CI [13.60–26.40]) for the surgery-only group (n = 7). The median OS was significantly higher in the adjuvant treatment groups (radiotherapy or chemoradiotherapy) compared with the surgery only or non-surgery groups (P < 0.05).ConclusionSDC is a rare and highly aggressive malignancy with a poor prognosis. Surgical margins, American Joint Committee on Cancer (AJCC) stage, and treatment method were identified as adverse prognostic factors affecting the OS of patients with SDC. Radical surgery remains the primary treatment for salivary duct carcinoma while adjuvant therapy significantly reduces recurrence rates and improves survival. However, the overall prognosis remains challenging, highlighting the need for novel therapeutic strategies. creator: Shubin Dong creator: Mengru Li creator: Zhiwei Zhang creator: Bowei Feng creator: Wei Ding creator: Jiang Chang creator: Feng Liu uri: https://doi.org/10.7717/peerj.19626 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dong et al. title: Metabolomic and transcriptomic analyses of drought resistance mechanisms in sorghum varieties link: https://peerj.com/articles/19596 last-modified: 2025-07-04 description: For a long time, sorghum breeding has focused on improving yield and quality traits, whereas little research has been conducted on drought resistance. To this end, this study evaluated the phenotypes of two sorghum varieties (GL98 and GL220) under drought stress and normal conditions, and sequenced their transcriptomes and metabolomes. After drought stress, the growth rates of the roots and shoots of GL220 exceeded those of GL98 at 72 h. A total of 6,344 differentially expressed genes (DEGs) were identified via RNA-seq differential expression analysis; these genes were significantly annotated in the phenylpropanoid biosynthesis, starch and sucrose metabolism, amino acid metabolism, and flavonoid biosynthesis pathways. The 6,344 DEGs were clustered into four clusters by K-means, and the pathways of each cluster were annotated. A total of 3,913 metabolites were identified by ultrahigh-performance liquid chromatography–MS (UPLC–MS), and a total of 1,942 differentially accumulated metabolites (DAMs), including five common DAMs, were identified. Through combined RNA-seq and metabolomics analyses, we determined that the flavonoid biosynthesis pathway is an important regulatory pathway in the sorghum response to drought stress and that Sobic.007G058600 was significantly correlated with 10 metabolites of the flavonoid pathway. In summary, our results provide a theoretical basis for a deeper understanding of the molecular mechanism of sorghum drought resistance and new genetic resources for subsequent research. creator: Li Yue creator: Hui Wang creator: Qimike Shan creator: Zaituniguli Kuerban creator: Hongyan Mao creator: Ming Yu uri: https://doi.org/10.7717/peerj.19596 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yue et al. title: Thymines opposite to bulky aristolactam-DNA adducts in duplex DNA are not targeted by human thymine-DNA glycosylase link: https://peerj.com/articles/19577 last-modified: 2025-07-04 description: BackgroundConsumption of aristolochic acids (AA) from the plant Aristolochia results in the formation of bulky aristolactam-dA (dA-AL) and aristolactam-dG (dG-AL) adducts in cellular DNA ultimately leading to the development of urothelial cancer. Intriguingly, the dA-AL adducts induce A•T→T•A transversions in tumor cells preferentially in CpA*→TpG context. The human mismatch-specific thymine-DNA glycosylase (TDG) protects cells against mutagenesis induced by spontaneous deamination of 5-methylcytosine (5mC) by removing thymine opposite to guanine in a CpG context in the base excision repair (BER) pathway. Nevertheless, challenges for DNA glycosylases to the faithful discrimination between non-damaged and damaged DNA strands do exist, such as mismatched pairs between two canonical bases, which may result due to DNA polymerase errors during replication. Previously, we demonstrated that TDG is prone to aberrant excision of T opposite to damaged adenine in duplex DNA in CpA*/TpG context.MethodsIn the present work, using in vitro reconstitution assays, we investigated whether TDG participates in the aberrant removal of thymine opposite to dA-AL adducts in duplex DNA.ResultsWe have demonstrated that TDG either does not excise thymine or does so with extremely low efficiency when it is paired with dA-AL or dG-ALII adducts in duplex DNA. At the same time, TDG excises with high efficiency thymine opposite to guanine and hypoxanthine in T•G and T•Hx mispairs.DiscussionThese findings strongly suggest that the human TDG is not involved in the aberrant DNA repair of AA-induced DNA damage. creator: Diana Manapkyzy creator: Gulzhan Zhamanbayeva creator: Viktoriya Sidorenko creator: Radha Bonala creator: Francis Johnson creator: Bakhyt T. Matkarimov creator: Dmitry Zharkov creator: Murat K. Saparbaev creator: Sabira Taipakova uri: https://doi.org/10.7717/peerj.19577 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Manapkyzy et al. title: In-hospital cardiac arrest (IHCA): survival status and its determinants in Malaysian public healthcare link: https://peerj.com/articles/19509 last-modified: 2025-07-04 description: BackgroundIn-hospital cardiac arrest (IHCA) remains a significant clinical challenge despite advances in resuscitation and critical care. Enhanced inpatient monitoring and post-IHCA management have improved survival rates and better neurological outcomes at discharge. This study aims to evaluate the IHCA survival rate and analyse key determinants influencing survival status.MethodsA cross-sectional study was conducted using retrospective secondary data from a northern referral tertiary public hospital’s cardiac arrest registry, encompassing IHCA cases in patients aged 18 and above between February 1, 2018, and January 31, 2019. The data included patient demographics, clinical characteristics, IHCA event timing, return of spontaneous circulation (ROSC), survival status, and post-arrest neurological outcomes. Patient survival was measured from the initiation of resuscitation to discharge or death, with survival analysis performed. Factors associated with IHCA survival were explored using logistic regression.ResultsA total of 934 IHCA cases were analyzed. The mean patient age was 60.8 years, with most being male (63.9%) and of Chinese ethnicity (45.5%). IHCA commonly occurred in non-critical care areas (61.0%), with 79.6% admitted for medical conditions. Successful ROSC was achieved in 43.5% of cases, and 8.2% had a shockable first rhythm. Only 6.4% survived to discharge or 30-day, with 45% having good neurological outcomes.ConclusionThe IHCA survival rate remains low despite advances in resuscitation. Key survival factors include arrest location, shockable rhythms, and CPR-adrenaline dosage ratio. Strengthening early recognition, prompt intervention, and optimized post-arrest care may enhance IHCA outcomes, particularly in non-critical care areas. creator: Marhaini Mostapha creator: Mohd Shahri Bahari creator: Min Fui Wong creator: Sivaraj Raman creator: Farhana Aminuddin creator: Shaiful Jefri creator: Nur Amalina Zaimi creator: Nor Zam Azihan Mohd Hassan creator: Hin Kwang Goh creator: Chee Kin Yoon creator: Eric Tang creator: Meng Li Lee creator: Lean Wah Luah uri: https://doi.org/10.7717/peerj.19509 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mostapha et al. title: Phosphoproteomic insights into the regulation of root length in rice (Oryza sativa L. cv. KDML 105): uncovering key events and pathways involving phosphorylated proteins link: https://peerj.com/articles/19361 last-modified: 2025-07-04 description: Root is a crucial organ in terrestrial plants, with the maximum root length (MRL) trait of the root system positively correlated with both plant growth and adaptation. However, the mechanisms regulating root length remain inadequately understood due to the dynamics of root growth. Protein phosphorylation precisely regulates various biological processes, providing a pathway to investigate the complex regulatory mechanisms of roots. This study aims to identify key events and pathways that are positively involved in regulating MRL in rice. Using liquid chromatography tandem mass spectrometry (LC-MS/MS), the phosphoprotein profiles of roots exhibiting different MRL phenotypes across three cultivating systems: deep water cultivation (DWC), water agar (WA), and vermiculite-based hydroponics (VBH) were examined. The results showed that the MRL trait of rice is strongly influenced by protein phosphorylation events. Further analysis indicated a clear convergence between phosphorylation signaling and phytohormone signaling in the regulation of MRL. The identified potential phosphoprotein promoters may enhance MRL by promoting root adaptation, optimizing hormonal crosstalk, and facilitating the synthesis of beneficial components. However, given the complexity and dose-dependent nature of hormonal networks, additional quantitative studies were necessary to fully elucidate the mechanisms underlying MRL regulation in rice. creator: Rui Li creator: Narumon Phaonakrop creator: Karan Lohmaneeratana creator: Sittiruk Roytrakul creator: Arinthip Thamchaipenet uri: https://doi.org/10.7717/peerj.19361 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Gibberellic acid-mediated transcriptional divergence underlies cold stress adaptation in two diploid cotton species link: https://peerj.com/articles/19721 last-modified: 2025-07-03 description: BackgroundThe diploid cotton species Gossypium thurberi (D1) and Gossypium trilobum (D8) exhibit significant divergence in cold stress tolerance despite their close phylogenetic relationship.MethodsTo explore the genetic basis of this difference, we conducted a comparative transcriptomic analysis under cold stress at 4 °C, identifying 697 and 311 species-specific differentially expressed genes (DEGs) in G. thurberi and G. trilobum, respectively. Functional enrichment analysis was performed to investigate the biological pathways associated with these DEGs. Additionally, hormone levels, particularly gibberellic acid (GA), were measured to assess their role in cold stress responses.ResultsThe DEGs in both species were significantly enriched in the “hormone signal transduction” pathway, highlighting the importance of hormonal regulation in cold adaptation. Distinct trends in GA levels were observed between G. thurberi and G. trilobum, with GA strongly correlated with species-specific DEGs. G. thurberi demonstrated greater cold tolerance than G. trilobum, likely due to a more robust GA-regulated response.ConclusionThese findings indicate that expression divergence in GA-mediated pathways between sister species has driven adaptive evolution in cold stress tolerance. This study not only advances our understanding of cold adaptation mechanisms in cotton but also provides genetic insights for improving cold tolerance in cultivated varieties through targeted breeding and genetic engineering. creator: Dong Wang creator: Juyun Zheng creator: Ke Liu creator: Yanchao Xu creator: Dingsha Jin uri: https://doi.org/10.7717/peerj.19721 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Drought and rewatering effects on soybean photosynthesis, physiology and yield link: https://peerj.com/articles/19658 last-modified: 2025-07-03 description: Drought stress is a common environmental stress factor for soybeans (Glycine max L.), significantly impeding the growth and yield. Therefore, studying the photosynthetic and physiological characteristics during two crucial growth and development periods, namely the flowering and grain-filling stages, under drought stress and rewatering conditions is of great significance for clarifying the physiological and photosynthetic regulatory response mechanisms of soybeans to drought stress. In this study, the cultivar ‘Liaodou 15’ was subjected to mild drought (L, 65% field capacity) and severe drought (H, 50% field capacity) treatments during the flowering and grain-filling stages for 7, 14, and 21 days respectively. At the conclusion of the stress period, rewatering (R) was carried out. Results showed that the stomatal limit value increased and intercellular CO2 concentration decreased with the increase in drought stress intensity, and the decrease in net photosynthetic rate was dominated by stomatal factors at the flowering stage. At the grain-filling stage, the stomatal limit value decreased and intercellular CO2 concentration increased with the increase in drought stress intensity, and the decrease in net photosynthetic rate changed from stomatal factors to non-stomatal factors. Drought stress led to peroxidation damage. In this study, it significantly increased the contents of soluble protein and malondialdehyde (MDA), as well as the activities of peroxidase (POD) and superoxide dismutase (SOD). On the other hand, rewatering had a compensatory effect on various physiological indices of soybean leaves. Under drought stress, the yield indices of soybeans were affected during both the flowering and grain-filling stages. Specifically, the yield during the flowering stage decreased by 15.63%–55.47%, and the yield during the grain-filling stage decreased by 24.17%–59.63%. This indicates that drought has a greater impact on the yield of soybeans during the grain-filling stage. Moreover, as the duration and intensity of drought increase, the reduction in yield becomes more significant, and the yield is the lowest when there is severe drought stress for 21 days. Our study elucidates the complex physiological and photosynthetic responses of soybeans to drought stress and rewatering, which provides valuable insights for improving soybean cultivation strategies under drought environments. creator: Cheng Wang creator: Anni Sun creator: Li jie Zhu creator: Min Liu creator: Qi Zhang creator: Liwei Wang creator: Xining Gao uri: https://doi.org/10.7717/peerj.19658 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wang et al. title: MDDeep-Ace: species-specific acetylation site prediction based on multi-domain adaptation link: https://peerj.com/articles/19649 last-modified: 2025-07-03 description: BackgroundLysine post-translational modification (PTM) is pivotal in regulating diverse cellular processes, profoundly impacting protein structure and function. Over recent decades, numerous experimental techniques have advanced PTM site identification, significantly contributing to research progress. However, these methods are time-intensive and labor-intensive. Deep learning technologies have shown promise in predicting PTM sites, yet current approaches struggle with species-specific PTM site prediction.MethodsWe introduce MDDeep-Ace, a novel deep learning method based on multi-domain adaptation for predicting lysine acetylation sites. By integrating data from multiple species, MDDeep-Ace enhances the generalization of species-specific prediction models, improving predictive performance.ResultsExperimental findings illustrate that our proposed multi-domain adaptation approach significantly enhances prediction accuracy across multiple species, surpassing existing lysine acetylation site prediction tools. creator: Yu Liu creator: Chaofan Ye creator: Can Lin creator: Kangkang Mao creator: Ming Zhu uri: https://doi.org/10.7717/peerj.19649 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: A novel evaluation approach for functional impairment in subacromial impingement syndrome: focus on Temporal Summation of Activity-related Pain (TSAP) link: https://peerj.com/articles/19638 last-modified: 2025-07-03 description: BackgroundPatients with subacromial impingement syndrome (SIS) often experience increased pain during repetitive upper-extremity movements in their daily life. However, conventional assessments of movement-evoked pain are mostly limited to single movement pain (SMP) and may not fully capture the effects of pain during repetitive activities. In this study, we developed the Temporal Summation of Activity-related Pain (TSAP) as a novel method for assessing increases in pain intensity during repetitive movements, and investigated its clinical usefulness.MethodsThirty patients with SIS were included in this cross-sectional study. Movement-evoked pain was assessed using patient-reported outcome measures, SMP and TSAP scores, which were evaluated by the increase in pain intensity after 10 repetitions of a shoulder abduction task. Additionally, the conventional temporal summation of pain (cTSP) was assessed using pinprick stimulation. We analyzed the association between the parameters and the impact of movement-evoked pain on upper extremity dysfunction assessed using Quick Disabilities of the Arm, Shoulder, and Hand (QuickDASH).ResultsThe TSAP score significantly correlated with the cTSP and QuickDASH scores (p <  0.05). Regression analyses revealed that the TSAP score was the only significant factor explaining the impact on upper extremity dysfunction, even after controlling for confounding factors [B (95% CI) = 0.461 (0.099–0.824), p = 0.015].ConclusionsTSAP provides valuable insights into the functional impact of pain in patients with SIS. Our findings suggest that TSAP may offer a more sensitive evaluation of movement-evoked pain compared to conventional assessments, although further validation is needed. creator: Katsuyoshi Tanaka creator: Shota Oda creator: Masashi Izumi uri: https://doi.org/10.7717/peerj.19638 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Tanaka et al. title: Molecular and hematological characteristics of two different δ-globin promoter variants, δ−276(A>G) and δ−77(T >C) among Thai, Burmese, and Laotian subjects link: https://peerj.com/articles/19636 last-modified: 2025-07-03 description: BackgroundWe described molecular characteristics, phenotypic expression, and genetic origins of known δ−77(T >C) and hitherto undescribed δ−276(A>G) variants in both heterozygotes and homozygotes found in Thai, Burmese, and Laotian subjects.MethodsA family and 19 unrelated subjects with absent or decreased hemoglobin (Hb) A2 levels referred to three thalassemia diagnostic centers in the north, northeast, and south of Thailand were recruited. Hematological parameters were recorded, and Hb analysis was done using capillary electrophoresis. Molecular analysis of globin genes was carried out by PCR-based methods. β-Globin gene haplotype analysis, including seven DNA polymorphic sites, was done using the PCR-RFLP assay, and the results were compared with those described in the Japanese subject.ResultsA proband with Hb E trait and decreased Hb A2 was identified. DNA sequencing of the δ-globin gene revealed a heterozygosity for a hitherto undescribed δ−276(A>G) transition. However, unusually decreased Hb A2 was not observed in her family members with this δ−276(A>G) mutation in both heterozygote and homozygote states. Further screening of this variant in unrelated Thai individuals revealed a high allele frequency of δ−276(A>G) in the Thai population, the data indicating a non-pathological DNA polymorphism. In contrast, many Thai, Burmese, and Laotian subjects were encountered with another δ-globin promoter variant, the δ−77(T >C) mutation in both heterozygote and homozygote. Most of them had normal hematological features, but decreased Hb A2 in heterozygotes and absent Hb A2 in homozygotes. β-Globin gene haplotype analysis points to different origins of this pathologic variant among Thai, Laotian, Burmese, and Japanese populations.ConclusionsThis study described the molecular characteristics and phenotype-genotype correlation of two different δ-globin promoter variants, δ−77(T >C) and δ−276(A>G), found in the Southeast Asian population. Since the level of Hb A2 is useful for the diagnosis of several forms of thalassemia and hemoglobinopathies, the study of the δ-globin gene in areas endemic for thalassemia and hemoglobinopathies should facilitate a prevention and control program of the diseases in the region. creator: Sitthichai Panyasai creator: Patcharawadee Prayalaw creator: Kritsada Singha creator: Supan Fucharoen uri: https://doi.org/10.7717/peerj.19636 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Panyasai et al. title: Serum miR-15a-5p may predict recurrence of atrial fibrillation after catheter ablation: a single center retrospective study link: https://peerj.com/articles/19618 last-modified: 2025-07-03 description: BackgroundThere is still a lack of an easily obtainable, sensitive, and specific biomarker for predicting the recurrence of atrial fibrillation (AF) after radiofrequency catheter ablation (RFCA). In the present study, we aimed to investigate the predictive value of serum miR-15a-5p as a biomarker of recurrence in AF patients undergoing RFCA.MethodsForty-three consecutive AF patients indicated for RFCA and 20 non-AF subjects were enrolled. The levels of serum miR-15a-5p and PICP, PIIINP, MMP-9, and sST2 were detected. Then, linear regression analysis, binary logistic regression analysis, and receiver operating characteristic (ROC) analysis were used to investigate the correlation between the expression level of serum miR-15a-5p and the degree of myocardial fibrosis and assess the value of serum miR-15a-5p for predicting postoperative recurrence of AF.ResultsThere was a significant difference in age, CK-MB, uric acid (UA), left atrial diameter (LAD), history of coronary heart disease (CAD), and left ventricular ejection fraction (LVEF) between the AF group and the control group (p < 0.05). Compared with the control group, the level of serum miR-15a-5p, MMP-9, PICP, PIIINP, and sST2 was higher in the AF group (p < 0.05 or p < 0.01). miR-15a-5p had a significant and positive relationship with the level of the four serum fibrosis biomarkers (p < 0.05). Compared with paroxysmal AF, persistent AF had a higher increase in serum miR-15a-5p expression level (p < 0.001). Compared with the non-recurrent, the expression level of serum miR-15a-5p in the recurrent patients was significantly increased (p < 0.01). ROC analysis showed that the AUC of serum miR-15a-5p for predicting AF recurrence was 0.823 (95% CI [0.668–0.979], p < 0.01), and the cutoff value was 1.5224, with a sensitivity of 71.4% and specificity of 86.1%.ConclusionsThe high expression of serum miR-15a-5p in AF patients was related to the degree of myocardial fibrosis and the recurrence of AF after RFCA, which indicated that serum miR-15a-5p could be used as a serum biomarker for predicting AF recurrence after RFCA. creator: Zhong-Bao Ruan creator: Qian Peng creator: Xiang-Jiang Sun creator: Fei Wang creator: Li Zhu uri: https://doi.org/10.7717/peerj.19618 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Ruan et al. title: EsoDetect: computational validation and algorithm development of a novel diagnostic and prognostic tool for dysplasia in Barrett’s esophagus link: https://peerj.com/articles/19613 last-modified: 2025-07-03 description: Barrett’s esophagus (BE) is the only known precursor to esophageal adenocarcinoma (EAC), a malignancy with increasing incidence and unfavorable prognosis. This study endeavors to identify BE biomarkers capable of diagnosing low-grade dysplasia (LGD) in BE, as well as biomarkers that can predict the progression from BE to EAC to be subsequently integrated into diagnostic and prognostic algorithms. Datasets containing gene expression data from metaplastic and dysplastic BE, as well as EAC tissue samples, were collected from public databases and used to explore gene expression patterns that differentiate between non-dysplastic (ND) and LGD BE (for diagnostic purposes) and between non-progressed and progressed BE (for prognostic purposes). Specifically, for the diagnostic application, three RNAseq datasets were employed, while for the prognostic application, nine microarray datasets were identified, and 25 previously described genes were validated. A thresholding function was applied to each gene to determine the optimal gene expression threshold for group differentiation. All analyzed genes were ranked based on the F1-score metrics. Following the identification of genes with superior performance, different classifiers were trained. Subsequently, the best algorithms for diagnostic and prognostic applications were selected. In evaluating the value of gene expression for diagnosis and prognosis, the analyzed datasets allowed for the ranking of biomarkers, resulting in eighteen diagnostic genes and fifteen prognostic genes that were used for further algorithm development. Ultimately, a linear support vector machine algorithm incorporating ten genes was identified for diagnostic application, while a radial basis function support vector machine algorithm, also utilizing ten genes, was selected for prognostic prediction. Notably, both classifiers achieved recall and specificity scores exceeding 0.90. The identified algorithms, along with their associated biomarkers, hold significant potential to aid in the early management of malignant progression of BE. Their strengths lie in their development using multiple independent datasets and their ability to demonstrate recall and specificity levels superior to those reported in the existing literature. Ongoing experimental and clinical validation is essential to further substantiate their utility and effectiveness, and to ensure that these tools can be reliably integrated into clinical practice to improve patient outcomes. creator: Migla Miskinyte creator: Benilde Pondeca creator: José B. Pereira-Leal creator: Joana Cardoso uri: https://doi.org/10.7717/peerj.19613 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Miskinyte et al. title: Exploring changes in family routines and family quality of life among Israeli families during the COVID-19 pandemic link: https://peerj.com/articles/19587 last-modified: 2025-07-03 description: BackgroundThe COVID-19 pandemic has significantly disrupted family life globally, altering daily routines and impacting family quality of life (FQOL). This study explores the changes in family routines during the pandemic lockdowns and their correlation with FQOL.MethodsParticipants included 253 families with children aged 3 to 18, recruited through an online survey. Families completed the Family Routines Inventory and the FQOL Scale, reporting on both pre-pandemic and during-pandemic conditions. Data analysis included principal component analysis and regression analysis to identify changes in routine frequency and importance and their predictive relationship with FQOL.ResultsThe principal component analysis resulted in three distinct factors of family routines, highlighting significant shifts in the frequency and importance of these routines from before and during COVID-19. Notably, routines involving within-family interactions increased, whereas those involving external interactions decreased. Regression analysis showed that the frequency of within-family interactions (Factor 1) and the importance of general morning and evening routines (Factor 3) significantly predicted FQOL, accounting for 24% of the variance in FQOL scores during the pandemic.ConclusionThe COVID-19 pandemic has underscored the critical role of family routines in maintaining FQOL in times of crisis. Interventions aimed at supporting families should consider enhancing the adaptability and resilience of family routines to foster well-being during unpredictable stressors. Future research should continue to explore the dynamics of family routines and their impact on FQOL across different types of crises. creator: Liat Hen-Herbst creator: Yael Fogel uri: https://doi.org/10.7717/peerj.19587 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hen-Herbst and Fogel title: High-frequency repetitive transcranial magnetic stimulation protects against 6-OHDA-induced Parkinson’s disease symptoms by modulating the proNGF-p75NTR-sortilin pathway link: https://peerj.com/articles/19633 last-modified: 2025-07-02 description: BackgroundHigh-frequency repetitive transcranial magnetic stimulation (HF rTMS) is a promising non-invasive treatment for Parkinson’s disease (PD) in clinical settings. However, the precise mechanisms are incompletely understood. The proNGF-p75NTR-sortilin signaling pathway is closely associated with nigrostriatal dopaminergic (DA) neuron degeneration, a hallmark feature of PD. This study aimed to evaluate the neuroprotective efficacy of HF rTMS on the proNGF-p75NTR-sortilin pathway in PD.MethodsUsing a PD rat model induced by 6-hydroxydopamine (6-OHDA), the rats were randomly divided into two groups: sham rTMS group and HF rTMS group. After a 4 w intervention, the rats’ motor function was assessed using a rotarod test. Additionally, immunofluorescence technology was used to analyze the DA neurons in the midbrain of PD rats, and immunohistochemistry and Western blot analysis were employed to evaluate the expression levels and effects of proNGF-p75NTR-sortilin in the midbrain following HF rTMS.ResultsOur research revealed a significant increase of proNGF expression in reactive astrocytes and upregulated sortilin and p75NTR in DA neurons in the substantia nigra of the hemisphere ipsilateral to the induced lesion, correlated with the degeneration of DA neurons and impaired motor functions. A four-week regimen of HF rTMS, as opposed to sham rTMS, significantly improved the above pathological conditions. The decrease in proNGF-p75NTR-sortilin expression following HF rTMS correlated with a significant increase in DA neuron survival and motor function improvement. HF rTMS exhibited no effects on proBDNF expression. Our study findings indicate that the targeted proNGF-p75NTR-sortilin complex modulation may be an essential mechanism through which HF rTMS exerts its neuroprotective effect. This insight offers a new therapeutic perspective for PD management, highlighting the potential of rTMS to modulate key neurodegenerative pathways. creator: Rui Zhao creator: Wanqing Du creator: Ke Tian creator: Kunlong Zhang creator: Hua Yuan creator: Fang Gao creator: Xin Kang creator: Xiaolong Sun uri: https://doi.org/10.7717/peerj.19633 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Integrating mindfulness and physical activity: a meta-analysis of mindful movement interventions for symptoms of anxiety and depression among university students link: https://peerj.com/articles/19640 last-modified: 2025-07-01 description: BackgroundUniversity students are increasingly vulnerable to mental health problems, such as anxiety and depression, which have been associated with academic stress, job market uncertainty, and lifestyle-related factors such as physical inactivity and poor sleep habits. Mindful movement, defined as structured programs integrating mindfulness practice with physical movement, offers a holistic approach to reducing anxiety and depression, though its effectiveness and specific intervention differences—such as duration, delivery mode, and behavior change techniques—remain underexplored. This study evaluated the effects of mindful movement interventions on anxiety and depression among university students.MethodsA systematic search of six databases up to August 2024 identified 19 randomized controlled trials involving a total of 1,697 participants. A random-effects model was employed to pool effect sizes; subgroup analyses were conducted to explore sources of heterogeneity, and sensitivity analyses were performed to test the robustness of the results.ResultsThe meta-analysis indicated that mindful movement interventions significantly reduced anxiety (standardized mean difference (SMD) = −0.42, 95% confidence interval (CI) [−0.52 to −0.31], p < 0.0001, I2 = 70%) and depression (Standardized Mean Difference (SMD) = −0.61, 95% CI [−1.01 to −0.20], p < 0.0001, I2 = 87%) compared to control groups. Subgroup analyses demonstrated no significant differences in effect sizes across different mindful movement types (yoga, tai chi, qigong). Meta-regression indicated that intervention type did not significantly explain heterogeneity (p = 0.495). Publication bias was not observed in most subgroups, except for potential bias in the tai chi group due to limited studies.ConclusionMindful movement interventions are associated with enhanced mental health among university students, with no significant differences in the effects of yoga, tai chi, and qigong on reducing symptoms of anxiety and depression. It supports treating mindful movement as a unified approach to analyzing its impact on mental health. Residual heterogeneity highlights the need for further research on specific intervention elements and intervention and participant-related factors. PROSPERO registration number (CRD42024569238). creator: Xinjian Xu creator: Borhannudin Bin Abdullah creator: Shamsulariffin Bin Samsudin creator: Yongneng Tan uri: https://doi.org/10.7717/peerj.19640 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xu et al. title: Establishment and validation of a risk prediction model for adverse drug reactions in patients with coronary heart disease after taking statins: a retrospective study link: https://peerj.com/articles/19630 last-modified: 2025-07-01 description: ObjectiveThis study aims to develop and validate a nomogram-based predictive model for estimating the risk of adverse drug reactions (ADR) to statins in patients with coronary heart disease (CHD).MethodsA retrospective cohort study was conducted using clinical data from 351 patients with CHD who received statin therapy in the cardiology department of a tertiary hospital in Anhui Province, China, between February 2021 and January 2022. The dataset was randomly divided into a development cohort (n = 283) and a validation cohort (n = 68) in an 8:2 ratio. Logistic regression analysis was applied in the development cohort to identify independent risk factors for statin-induced ADR. A nomogram was subsequently constructed in R based on the selected predictors, and its clinical utility, discriminative performance, and calibration were evaluated.ResultsThe overall incidence of statin-associated ADR among the 351 subjects was 24.22%, classified into three categories according to the affected system: musculoskeletal toxicity, hepatic/renal dysfunction, and gastrointestinal reactions. Univariate and multivariate logistic regression analyses in the development cohort identified the following as significant independent risk factors (P < 0.05): age ≥60 years, body mass index ≥23 kg/m2, disease duration ≥5 years, presence of ≥3 comorbid conditions, dyslipidemia, history of cerebral infarction, high-dose statin use, and concomitant use of multiple medications. A nomogram model was constructed based on these predictors. The model demonstrated strong discriminative performance, with an area under the receiver operating characteristic (ROC) curve of 0.808 (95% CI [0.751–0.865]) in the development cohort and 0.852 (95% CI [0.752–0.951]) in the validation cohort.ConclusionA nomogram-based risk prediction model was successfully developed to estimate the probability of statin-induced ADR in patients with CHD, based on a set of statistically significant clinical risk factors. The model exhibited favorable predictive accuracy and discrimination. It offers a practical tool for clinicians to identify high-risk individuals and implement early preventive or interventional strategies accordingly. creator: Lixiang Zhang creator: Jiaoyu Cao creator: Xiaojuan Zhou uri: https://doi.org/10.7717/peerj.19630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Superoxide dismutase activity in tear fluid and blood of patients and mouse model of amyotrophic lateral sclerosis: a pilot study link: https://peerj.com/articles/19623 last-modified: 2025-07-01 description: Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease characterized by progressive degeneration of motor neurons and skeletal muscle atrophy. The heterogeneity of clinical symptoms and the lack of reliable biomarkers hamper diagnostics of ALS. The dysfunction of superoxide dismutase 1 (SOD1) protein is considered one of the molecular mechanisms underlying ALS pathology. We measured total SOD activity in the tear fluid and blood serum of ALS patients, healthy volunteers, and in the ALS mouse model, harboring the human truncated form of fused in sarcoma (FUS) protein—FUS (1–359). The average SOD activity in tear fluid did not differ between ALS patients and the control group. However, an increased proportion of patients with low SOD activity in tear fluid was observed compared to the control group. In contrast, SOD activity in blood serum was higher in the ALS group. Transgenic FUS (1–359) mice showed decreased SOD activity in tear fluid at both presymptomatic and symptomatic stages of ALS. SOD activity in blood serum did not differ between transgenic and control animals. These findings suggest that changes in SOD activity in the tear fluid of ALS patients and transgenic FUS (1–359) mice reflect local metabolic disturbances in the eyes associated with ALS. creator: Tatiana A. Pavlenko creator: Natalia B. Chesnokova creator: Olga V. Beznos creator: Natalia N. Shikareva creator: Marina R. Nodel creator: Ksenia V. Shevtsova creator: Uliana V. Panina creator: Daniil A. Shteinberg creator: Olga A. Kukharskaya creator: Iuliia S. Sukhanova creator: Nadezhda E. Pukaeva creator: Michail S. Kukharsky creator: Ruslan K. Ovchinnikov uri: https://doi.org/10.7717/peerj.19623 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pavlenko et al. title: Structural insights and biomedical potential of biosynthesized silver nanoparticles: antibacterial activity, anti-biofilm and cancer cell inhibition link: https://peerj.com/articles/19608 last-modified: 2025-07-01 description: BackgroundThe increasing threat of antimicrobial resistance and cancer has driven the search for new therapeutic agents, with plant-based biosynthesis of nanoparticles emerging as a promising approach. Silver nanoparticles (AgNPs) synthesized from plant extracts have gained attention for their potential biomedical applications.ObjectiveThis study aimed to synthesize, characterize, and evaluate the antimicrobial, anti-biofilm, and anticancer properties of AgNPs derived from Teucrium polium (Tp), Teucrium marum (Tm), and Punica granatum (Pg).MethodsAgNPs were synthesized using plant extracts and characterized by X-ray diffraction (XRD), dynamic light scattering (DLS), UV spectroscopy, and Fourier-transform infrared spectroscopy (FTIR). Antibacterial activity was assessed against Gram-negative and Gram-positive bacteria. The anti-biofilm efficacy was tested against Staphylococcus aureus and Pseudomonas aeruginosa. Cytotoxicity was evaluated on MCF-7 breast cancer cells.ResultsXRD confirmed the face-centered cubic (fcc) crystal structure of AgNPs, with peaks at (111), (200), (220), and (311) planes. Crystallite sizes were smaller than their hydrodynamic diameters, suggesting surface modifications affecting DLS measurements. DLS analysis indicated monodisperse size distributions for Tp-AgNPs and Tm-AgNPs, while Pg-AgNPs showed a broader range. The biosynthesized silver AgNPs from different plants exhibit unique physicochemical properties, as evidenced by their distinct UV-vis absorption spectra, and show potential for optical and optoelectronic applications. FTIR spectroscopy analysis confirmed the presence of specific functional groups on the surface of biosynthesized AgNPs, indicating the role of plant extracts as reducing and capping agents, and revealed variations in binding sites and molecular interactions. Among the synthesized nanoparticles, Tp-AgNPs exhibited the highest antibacterial efficacy, particularly against Staphylococcus epidermis and Pseudomonas aeruginosa, though slightly less potent than chloramphenicol. Tp-AgNPs also showed the strongest inhibition of biofilm formation, followed by Tm-AgNPs, with Pg-AgNPs being the least effective. Cytotoxicity assays demonstrated that Tm-AgNPs had the highest anticancer activity against MCF-7 cells, with Tp-AgNPs exhibiting comparable effects.ConclusionThe findings underscored the potent antimicrobial, anti-biofilm, and anticancer properties of Tp-AgNPs and Tm-AgNPs, making them promising candidates for biomedical applications. Further studies are needed to assess their clinical safety and therapeutic potential. creator: Ikram Jemel creator: Najeh Krayem creator: Hajer Jlidi creator: Abir Ben Bacha creator: Mona Alonazi creator: Raihane Charguia creator: Areej Ali Alzahrani creator: Sami Aifa creator: Sami Mnif uri: https://doi.org/10.7717/peerj.19608 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jemel et al. title: Effects of glycopyrronium bromide versus anisodamine hydrobromide in preventing nausea and vomiting and relieving spasm after ERCP: a randomized controlled trial link: https://peerj.com/articles/19582 last-modified: 2025-07-01 description: BackgroundPostoperative nausea and vomiting (PONV) frequently occur in patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) under general anesthesia. Glycopyrronium bromide, an anticholinergic medication, is believed to not only relieve gastrointestinal spasms but also effectively prevent PONV.ObjectiveTo compare the incidence of nausea and vomiting and the effect of relieving spasm between patients administered glycopyrronium bromide and those given anisodamine hydrobromide following endoscopic retrograde cholangiopancreatography (ERCP).DesignThis is a monocentric prospective study.MethodsPatients eligible for ERCP were randomly assigned to two groups. One group received 0.2 mg glycopyrronium bromide (Group G) intravenously, while the other group received 10 mg anisodamine hydrobromide (Group A) intramuscularly for anesthesia induction. The study assessed duodenal motility during ERCP and the incidence of PONV within 24 hours.ResultsThe study included 130 patients. Nausea and vomiting within 24 hours post-surgery occurred in nine patients (13.8%) in Group G and 19 patients (29.2%) in Group A, with statistical significance (relative risk (RR), 0.47; 95% confidence interval (CI) [0.02–0.29]; p = 0.033). Vomiting specifically was observed in three patients (4.6%) in Group G and 12 patients (18.5%) in Group A, showing statistical significance (RR 0.25; 95% CI [0.03–0.25]; p = 0.028). There was no significant difference in duodenal peristalsis between the groups (Group G: 10.9 ± 3.1 times/min; Group A: 11.6 ± 3.1 times/min; p = 0.174).ConclusionFor patients undergoing ERCP under general anesthesia, a subcutaneous injection of 0.2 mg glycopyrronium bromide significantly reduces PONV and provides similar anti-spasmodic effects to 10 mg intramuscular anisodamine hydrobromide. creator: Qingjing Ma creator: Dina Sun creator: Yan Rao creator: Yi Yang creator: Jie Liu creator: Chunmu Miao creator: Guangyou Duan creator: Guizhen Chen creator: Jie Chen uri: https://doi.org/10.7717/peerj.19582 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ma et al. title: Interictal neural fragility predicts seizure onset zone and surgical outcomes in drug-resistant epilepsy link: https://peerj.com/articles/19548 last-modified: 2025-07-01 description: Epilepsy is a chronic neurological disorder affecting approximately 70 million individuals worldwide, with a significant subset of patients exhibiting drug-resistant epilepsy (DRE). Accurate identification of the seizure onset zone (SOZ) is crucial for successful surgical intervention. This study investigates interictal neural fragility as a potential biomarker for predicting SOZ and guiding treatment outcomes in DRE patients. By applying dynamic mode decomposition (DMD) techniques to interictal stereoelectroencephalography (SEEG) data from 30 patients, we generated patient-specific dynamic network models and constructed fragility heatmaps. Our findings demonstrate that patients with favorable surgical outcomes exhibit significantly higher fragility in the SOZ during interictal periods. The fragility-based SOZ prediction model showed high sensitivity and specificity, with a strong concordance between the predicted SOZ and clinically identified treatment targets. This study highlights the clinical utility of interictal neural fragility in enhancing SOZ localization and improving treatment strategies for patients with low seizure frequency. Future research should focus on integrating this model into clinical workflows and exploring its potential in personalized treatment approaches. creator: Yue Pang creator: Yixuan Yang creator: Yunqing Lin creator: Jianyu Zhu creator: Penghui Liu creator: Yu Tian creator: Feng Wang creator: Zhen Mei creator: Dezhi Kang creator: Miao Cao creator: Yuanxiang Lin uri: https://doi.org/10.7717/peerj.19548 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pang et al.