title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-08 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A mini-review of the relationship between intestinal microecology and acute respiratory distress syndrome link: https://peerj.com/articles/19995 last-modified: 2025-08-29 description: Acute respiratory distress syndrome (ARDS), a critical condition with high mortality, arises from dysregulated inflammation and lung injury. While evidence-based supportive care remains foundational, the lack of effective targeted therapies underscores the need for novel approaches. This review focuses on the emerging role of intestinal microecology in ARDS pathogenesis via the gut-lung axis. We discuss how ARDS disrupts gut barrier integrity, promotes dysbiosis and bacterial translocation, and highlight the significance of some gut microbiota-derived metabolites in modulating pulmonary immunity and inflammation. Furthermore, we explore how intestinal microecology influences ARDS progression through mechanisms like oxidative stress, apoptosis, autophagy, and pyroptosis. The review also examines the potential of microecology-based interventions and draws insights from failed immunomodulatory trials, emphasizing the critical interplay between the microbiome and host immunity. By synthesizing these links, this review identifies the gut microbiota as a source of potential early-warning biomarkers and novel therapeutic targets, aiming to inform future strategies for managing ARDS in the intensive care unit (ICU). creator: Lujia Chen creator: Hao He creator: Cheng Li creator: Sha Nie creator: Dong Liu creator: Qiwei Shi uri: https://doi.org/10.7717/peerj.19995 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Analysis of risk factors for poor prognosis in patients with renal insufficiency combined with Enterobacteriaceae bloodstream infection: a retrospective study link: https://peerj.com/articles/19993 last-modified: 2025-08-29 description: BackgroundThis study analyzed the risk factors for poor prognosis in patients with Enterobacteriaceae bloodstream infections and co-occurring renal insufficiency. A nomogram prediction model was constructed to aid in clinical diagnosis and treatment.MethodsData were retrospectively collected from patients admitted to the First People’s Hospital of Jiande with positive blood culture results of Enterobacteriaceae combined with renal insufficiency. Patients were divided into survival and death groups according to clinical outcome, and independent risk factors for poor prognosis were screened using a multifactorial logistic regression analysis. A nomogram was subsequently established and validated.ResultsThe following risk factors and conditions were significantly associated with a higher patient mortality rate: male sex; admission to the ICU; comorbidity with shock, respiratory failure, coma, pneumonia, or leukaemia; the presence of carbapenem-resistant enterobacteriaceae (CRE) organisms; anaemia; thrombocytopenia; elevated D-dimer; hypo-proteinaemia; and hypocalcaemia (P < 0.05). Multifactorial logistic regression analysis suggested that shock, respiratory failure, and CRE bacterial bloodstream infection were independent risk factors for mortality in these patients.ConclusionsThis study established a nomogram prediction model of risk factors for poor prognosis in patients with renal insufficiency combined with Enterobacteriaceae bloodstream infection. This tool can assist clinicians in assessing patient prognosis at an early stage and, therefore, allow for more efficient intervention measures to reduce patient morbidity and mortality. creator: Yunpeng Wang creator: Jijing Zhao uri: https://doi.org/10.7717/peerj.19993 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wang and Zhao title: Analysis of microbial diversity and functions in sediments and overlying water of the Shiliu River link: https://peerj.com/articles/19979 last-modified: 2025-08-29 description: BackgroundWith the acceleration of urbanization, urban rivers have become a significant component of the urban ecosystem, attracting considerable attention regarding their ecological status and biodiversity. This study focuses on the Shiliu River, aiming to analyze the microbial diversity and functions present in the overlying water and sediments of severely polluted areas.MethodsThis study investigated the Shiliu River. In August 2024, sediment and overlying water samples were collected from its severely polluted reaches. The NextSeq 2000 PE300 platform was employed for sequencing to detect bacterial and fungal taxa abundances. PICRUSt and FUNGuild predicted sample functional abundances using bacterial 16S rRNA and fungal internal transcribed spacer (ITS) gene sequences, respectively.ResultsThe findings demonstrate that sediments exhibit higher bacterial and fungal richness than overlying water, with significant discrepancies in bacterial and fungal community compositions. Dominant taxa differ at both phylum and genus levels: in sediments, the predominant bacterial phylum is Proteobacteria and genus norank_Anaerolineaceae, while the dominant fungal phylum is Rozellomycota and genus unclassified_Rozellomycota. In overlying water, the bacterial phylum remains Proteobacteria but the dominant genus shifts to Acinetobacter, whereas fungal phyla and genera (Rozellomycota and unclassified_Rozellomycota) are consistent with sediments. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation identifies 25 metabolic pathways, with amino acid metabolism-related genes showing the highest abundance in both environments. Clusters of Orthologous Genes (COG) annotation reveals the highest abundance of [R] General function prediction in both sample groups, and FUNGuild analysis indicates that Animal Endosymbiont-Animal Pathogen-Plant Pathogen-Undefined Saprotroph is the most prevalent functional category in both sediments and overlying water. This study provides a microbiological foundation by clarifying microbial community structures (dominant phyla, functional taxa), decoding pollutant-degrading metabolic potentials (N/C cycling pathways), and identifying river health ecological indicators. This enables targeted bioremediation strategies (e.g., sediment microbial consortia for nutrient removal) and integrates microbial ecological data into urban river restoration.ConclusionsThis study reveals the microbial community structures in the sediments and overlying water of the polluted Shiliu River, finding diverse patterns with higher richness in sediments, Proteobacteria and Ascomycota as dominants. Shared taxa have different abundances, indicating niche differentiation. Sediments have enriched nitrogen/carbon cycling pathways for pollutant degradation. These results offer a microbiological basis for urban river restoration, identify bioremediation-target taxa, and stress the integration of microbial ecology into pollution management. creator: Yazi Li creator: Shuhong Zhang creator: Yumei Guo creator: Ke Xu creator: Xiqing Zhang creator: Mengfei Pan creator: Qiaoping Sun creator: Yanfang Zhang creator: Yongshan Fan uri: https://doi.org/10.7717/peerj.19979 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Diagnostic value of Ep300 and FOXO4 proteins in acute ischemic stroke: preliminary findings from a case-control study link: https://peerj.com/articles/19970 last-modified: 2025-08-29 description: BackgroundStroke is a leading cause of death and disability worldwide, and there is still a lack of specific and sensitive biomarkers for its diagnosis.ObjectiveThis study aimed to investigate the diagnostic value of FOXO4 and Ep300 proteins in acute ischemic stroke patients who visited the emergency department.MethodsPatients were consecutively included in the study. The amount of Ep300 and FOXO4 proteins was determined using an enzyme-linked immunosorbent assay (ELISA). Receiver operator characteristic (ROC) analyses of FOXO4 and Ep300 proteins were performed.ResultsThe study was conducted on a total of 39 acute ischemic stroke patients, 17 females and 22 males, with a mean age of 66.9 ± 11 years. Seventeen females and 23 male control were also included. The discriminative ability of Ep300 protein was not statistically significant (p value = 0.380). FOXO4 protein had moderate discriminative ability (AUC value = 0.705 and p value = 0.002). When the cut-off value for FOXO4 protein was accepted as > 1.15, the sensitivity was 74.29%, the specificity was 64.52%, the positive predictive value was 70.3%, the negative predictive value was 69%, the positive likelihood ratio was 2.09, and the negative likelihood ratio was 0.4.ConclusionsThe study’s findings suggest that FOXO4 protein could potentially serve as a valuable biomarker in the diagnosis of stroke in acute ischemic stroke patients. creator: Emre Bülbül creator: İbrahim Toker creator: Halime Dana creator: Mehmet Doğan creator: İbrahim Mercan creator: Burcu Çoşkun Işık creator: Elif Funda Şener uri: https://doi.org/10.7717/peerj.19970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bülbül et al. title: Racialized bias in pediatric pain: the role of observers’ attentional processing and estimations of children’s pain link: https://peerj.com/articles/19969 last-modified: 2025-08-29 description: BackgroundResearch demonstrates racism in pediatric pain care. However, the mechanisms underlying these injustices are not well understood. This study examined White observers’ attentional processing of facial expressions of pain demonstrated by White vs. Black children and observers’ estimations of the pain expressiveness levels of these children. Furthermore, we assessed whether differences in observers’ attentional processing were influenced by observers’ pain beliefs and the pain expressiveness level.MethodEighty White adults (42 women; 38 men) performed the visual search task (VST), rated the levels of pain that the children expressed, and reported their beliefs concerning the pain experience of White vs. Black children.ResultsFindings revealed facilitated attentional engagement towards Black compared to White child pain faces, particularly at high pain expressiveness levels. No attentional disengagement effects were observed. Pain estimations increased with increasing pain expressiveness but, contrary to prior findings, did not differ for White vs. Black children. Observers’ false pain beliefs did not significantly impact their attentional processing nor pain estimations.ConclusionsThe results underscore the importance of understanding how racialized disparities in observers’ attentional processing of others’ pain may contribute to racialized inequities in pediatric pain care. creator: Ama Kissi creator: Dimitri Van Ryckeghem creator: Peter Mende-Siedlecki creator: Adam Hirsh creator: Ischa Van Alboom creator: Dries Debeer creator: Tine Vervoort uri: https://doi.org/10.7717/peerj.19969 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Kissi et al. title: Identification and validation of PSMB7 as a novel biomarker for prognosis and immune infiltrates of lung adenocarcinoma link: https://peerj.com/articles/19958 last-modified: 2025-08-29 description: BackgroundLung adenocarcinoma (LUAD) is one of the most prevalent types of lung cancer globally; it is characterized by high incidence and mortality rates and contributes to over 1.8 million deaths annually. PSMB7, a crucial component of the 20S proteasome involved in protein degradation and antigen presentation, has been implicated in various cancers; however, its specific function in LUAD remains inadequately explored.MethodsThis research aimed to investigate the expression of PSMB7 in LUAD and its clinical significance using real-time quantitative PCR, immunohistochemistry, differential expression analysis, pathway enrichment analysis, immune cell infiltration, and DNA methylation.ResultsPSMB7 expression levels in LUAD tissues were considerably higher than those in the surrounding normal lung tissues and were associated with advanced pathological stages and poorer clinical outcomes. High PSMB7 expression was correlated with reduced overall and disease-specific survival. Functional enrichment analysis indicated that the differentially expressed genes associated with PSMB7 were mainly involved in protein–DNA complex assembly and chromatin remodeling. Moreover, LUAD tissues showed lower DNA methylation in PSMB7 promoters than that in normal lung tissues, which was correlated with reduced survival rates. A negative correlation was observed between PSMB7 levels and immune cell infiltration, particularly for effector memory T, B, follicular helper T, and mast cells.ConclusionsWe identified PSMB7 as a promising biomarker for LUAD prognosis because of its strong association with tumor progression and immune microenvironment modulation. Future studies should explore therapeutic strategies targeting PSMB7 to improve patient outcomes for LUAD. creator: Yan Chen creator: Xin Ran creator: Ping Fu creator: Jie Ao creator: Guihua Zhu creator: Lianhua Zhao creator: HuaLiang Xiao uri: https://doi.org/10.7717/peerj.19958 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Chen et al. title: Seasonally frugivorous forest birds and window collision fatalities: novel integration of bird counts in fall improves assessment of species vulnerability to collisions link: https://peerj.com/articles/19943 last-modified: 2025-08-29 description: Bird-window collisions are a significant and growing threat to birds, but the issue is still understudied in many geographical areas and stages of the avian annual life cycle. The mountainous topography and numerous distinct biogeoclimatic zones along the Pacific coast of Canada and the United States may result in regional and seasonal differences in collision mortality and species vulnerability to collisions. We surveyed daily for evidence of bird-window collisions over six 21-day periods in fall, early winter, and late winter between 2019 and 2022 at a university campus in southwestern British Columbia, Canada, and assessed individual species’ vulnerability to collisions by examining whether species-specific collision rates were disproportionate to their local abundance. We accounted for poor detectability of some species in fall, by integrating point count data from our study site with mist net capture data from a nearby banding station to improve abundance estimates. Collision mortality peaked in fall, but early winter collision mortality was significantly higher than in the later winter months, potentially due to movements of altitudinal migrants into our low-elevation study area in early winter. We estimated that an average of 885–1,342 (median = 1,095) birds are killed at 51 buildings campus-wide each year between September 15 and February 10, the peak fall migration wintering period. Forest birds, particularly species that switch to highly frugivorous diets in fall and winter, were most vulnerable to collisions across the seasons studied. Non-breeding season mortality due to collisions may be substantial for these species, particularly when considering cumulative mortality across the entire non-breeding period. The potential role of collision mortality in species declines should be further explored by assessing collision frequency and species vulnerability across life cycle stages in other geographical locations, and through improved data on migratory connectivity and linkages between declining breeding populations and non-breeding season mortality. creator: Viviane Zulian creator: Louise K. Blight creator: Jon Osborne creator: Adam C. Smith creator: Andrea R. Norris creator: Rebecca Golat creator: Krista L. De Groot uri: https://doi.org/10.7717/peerj.19943 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zulian et al. title: Comparison of efficacy and costs between robotic-assisted and conventional thoracoscopic approaches for partial pulmonary resection: a systematic review and meta-analysis of propensity score-matched studies link: https://peerj.com/articles/19911 last-modified: 2025-08-29 description: BackgroundThis meta-analysis aimed to evaluate differences in perioperative outcomes and costs between robotic-assisted partial pulmonary resection (RAPPR) and video-assisted thoracoscopic partial pulmonary resection (VATPPR).MethodsWe systematically searched MEDLINE, PubMed, Google Scholar, and Cochrane databases for relevant studies published between March 2015 and March 2025. Propensity score-matched non-randomized controlled studies comparing RAPPR with VATPPR were included.ResultsEight propensity score-matched studies involving 3,104 patients were included: 1,528 patients underwent RAPPR and 1,576 underwent VATPPR. RAPPR was associated with longer operative time and higher medical costs, but patients had more lymph nodes dissected, shorter drainage tube duration, and shorter hospital length of stay. No significant differences were observed between the two groups in conversion to thoracotomy rates or complication rates, including persistent air leak, pneumonia, and chylothorax.ConclusionsRAPPR demonstrates comparable surgical efficacy to VATPPR with advantages including more thorough lymph node dissection, earlier drainage tube removal, and earlier patient discharge. However, RAPPR requires longer operative time and higher costs. The choice between surgical approaches should consider these clinical factors comprehensively. creator: Xinyang Huang creator: Haoxuan Li creator: Zihao Deng creator: Xinyuan Tian creator: Kunjiang Zhong creator: Xugang Zhang uri: https://doi.org/10.7717/peerj.19911 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Innovative utilization of argon plasma coagulation combined with endoclips for managing gastrointestinal bleeding attributed to colonic diverticular bleeding: a retrospective study link: https://peerj.com/articles/19910 last-modified: 2025-08-29 description: BackgroundColonic diverticular bleeding is one of the primary causes of lower gastrointestinal bleeding, with endoscopic hemostasis as the first-line treatment. However, the outcomes of endoscopic treatments remain suboptimal. This study utilized an innovative therapeutic method to manage colonic diverticular bleeding and evaluated its feasibility and safety in clinical settings.MethodsBetween July 2018 and July 2023, 35 patients with colonic divercular bleeding were treated through argon plasma coagulation combined with endoclips (APC-EC) at the Air Force Medical Center. The technical success rate, rebleeding rate, and complications associated with the therapeutic method over a 5-year period were retrospectively analyzed.ResultsThe technical success rate of the method was 100%, the early rebleeding rate of APC-EC was 8.57%. The incidence of late rebleeding at 1-year follow-up was 5.71%, it was 0% at the 2- and 3-year follow-up periods. Intraoperative perforation was observed only in two patients treated with APC-EC; however, delayed perforation was not observed in any patient, and none of them required surgical treatment.ConclusionsAPC-EC might be a viable, safe, and effective method for treating colonic divercular bleeding. creator: Zihan Huang creator: Xiaomeng Feng creator: Xin Yin creator: Tao Sun creator: Chongxi Fan creator: Hongyu Chen creator: Bairong Li creator: Shoubin Ning uri: https://doi.org/10.7717/peerj.19910 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Survival predictors of lung cancer patients in ICU: the importance of acute kidney injury prediction and prevention link: https://peerj.com/articles/19885 last-modified: 2025-08-29 description: BackgroundTo identify potential predictors of short-term survival among patients with lung cancer admitted to the intensive care unit (ICU).MethodsA multicenter longitudinal observational study of patients with lung cancer was conducted between May 10, 2021 and July 10, 2021, at the ICUs of 37 cancer-specialty hospitals in China. This study included patients with a primary diagnosis of lung cancer who were admitted to the ICU for ≥24 h. Predictive factors for ICU outcomes, with 90-day survival as the major outcome, were explored using single and multivariate analyses.ResultsA total of 269 patients were included in the final analysis. The 90-day mortality rate following ICU care was 45.4%. Patients with 90-day mortality exhibited more severe conditions before admission, a higher number of ICU-related complications, and underwent more intense treatment than survivors. Notably, despite the low recorded incidence, acute kidney injury (AKI) was independently associated with ICU, in-hospital, and 90-day mortality outcomes in the multivariate analysis. Furthermore, condition severity at admission and ICU treatment choices, especially anti-infection regimen, were identified as potential correlators of a higher AKI risk.ConclusionAKI prediction and prevention may require prioritization in patients with lung cancer admitted in the ICU. creator: Jue Shen creator: Changsong Wang creator: Gang Ma creator: Hong-Zhi Wang creator: Xuezhong Xing creator: Biao Zhu creator: Jianghong Zhao creator: Donghao Wang creator: Mingou Cui uri: https://doi.org/10.7717/peerj.19885 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shen et al. title: The effects of COVID-19 on semen parameter values in healthy males: a single-centre, retrospective study link: https://peerj.com/articles/19864 last-modified: 2025-08-29 description: BackgroundTo investigate the effects of the novel coronavirus disease 2019 (COVID-19) on spermatogenesis and the potential impact on patients with normal semen quality before a COVID-19 diagnosis.MethodsThis retrospective study included 22 male patients (aged 18–48 years) diagnosed with mild COVID-19 via reverse transcription polymerase chain reaction RT-PCR using combined oropharyngeal and nasopharyngeal swabs between April 2020 and June 2021. All participants had prior normal semen parameters (World Health Organization (WHO) standards) confirmed at our male infertility outpatient clinic before COVID-19 infection. Post-COVID-19 semen analyses were performed three months after diagnosis to evaluate subacute effects. Exclusion criteria included hospitalization for COVID-19, pre-existing abnormal semen parameters, or history of testicular surgery.ResultsThe mean age of the patients was 31.8 ± 5.9 years. An abnormality was detected in at least one parameter value in the post-COVID-19 semen analysis in nine patients (40.9%) whose semen quality was normal before COVID-19. When post-COVID-19 semen samples of the patients were divided into normal and abnormal groups, total sperm motility, progressive motility, and normal morphology were found to be significantly decreased, immotility significantly was increased, and semen pH tended to be more alkaline in the abnormal group.ConclusionEven though the effects of COVID-19 on spermatogenesis are not fully understood, COVID-19 infection may have negative effects on semen quality and impair fertilization. creator: Anil Erdik creator: Asli Merve Gokce creator: Ahmet Gokce uri: https://doi.org/10.7717/peerj.19864 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Erdik et al. title: Analysis of selected variables in body composition, upper limb strength, and resting energy expenditure among youth soccer players: insights based on field position link: https://peerj.com/articles/19860 last-modified: 2025-08-29 description: BackgroundThe study aimed to determine and compare selected variables of body composition, upper limb strength, and resting energy expenditure from the perspective of field position in youth soccer players.MethodsThe study group consisted of 189 boys aged 9 to 19 years ($\bar {x}$x ̄ = 14.7 ± 2.6 years) from the Sports Championship Schools. Body composition was determined using dual-energy X-ray absorptiometry (DXA), and resting energy expenditure (kcal/day) was measured using a Cosmed Quark RMR indirect calorimeter. Muscle strength was assessed using a handgrip dynamometer to measure grip strength.ResultsWe studied 189 boys (mean body mass 58.4 ± 16.1 kg; mean height 166.9 ± 14.5 cm) divided by field position: attackers (n = 43), defenders (n = 70), goalkeepers (n = 21), and midfielders (n = 55). Significant between-position differences were observed in age, body mass, height, body mass index (BMI), grip strength (GS), lean mass, fat mass, bone mineral content (BMC), bone mineral density (BMD), and resting energy expenditure (REE). Body mass differed between attackers and goalkeepers (51.3 vs. 73.3 kg) and defenders and goalkeepers (58.7 vs. 73.3 kg). Goalkeepers had the highest body mass. REE measured by indirect calorimetry differed between attackers and goalkeepers (1,729 vs. 2,088 kcal/day).ConclusionThese results allow for determining favorable parameters for each position on the field for young football players. creator: Edyta Łuszczki creator: Anna Bartosiewicz creator: Katarzyna Dereń creator: Paweł Jagielski creator: Andrzej Łukasik uri: https://doi.org/10.7717/peerj.19860 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Łuszczki et al. title: Surgery, radiotherapy and endocrine therapy for oligometastatic prostate cancer efficacy: a systematic review and network meta-analysis link: https://peerj.com/articles/19819 last-modified: 2025-08-29 description: In recent years, the treatment approach for metastatic prostate cancer has evolved, with early combination therapies increasingly being favored over androgen-deprivation therapy (ADT) alone. Despite the availability of various treatments, their relative effectiveness and safety trade-offs remain uncertain. Randomized controlled trials have explored a range of treatments for oligometastatic prostate cancer, but clear conclusions regarding their prognostic benefits and patient-centered outcomes have not been established. This network meta-analysis (NMA) aims to quantify the benefits of different treatments by analyzing data from a systematic search of Medline, EMBASE, and Cochrane databases, covering trials up to October 1, 2024. The primary outcomes evaluated in this study include overall survival (OS), progression-free survival (PFS), treatment-related adverse events (TRAEs), and quality of life (QoL). This study is registered with PROSPERO (CRD42022370203). We analyzed individual patient data from 13 eligible trials, involving a total of 2,524 patients. Our analysis revealed that ADT+ radiation therapy (RT) (hazard ratio (HR) = 0.39, 95% confidence interval (CI) [0.27–0.56]) and ADT+stereotactic body radiotherapy (SBRT) (HR = 0.35, 95% CI [0.21–0.58]) significantly improved progression-free survival (PFS) compared to ADT alone, while no treatment showed a significant overall survival (OS) benefit. Safety analysis revealed ADT monotherapy had the lowest risk of grade ≥3 adverse events (TRAEs), whereas ADT+abiraterone increased toxicity (OR = 1.54). Limited quality of life (QoL) data suggested ADT+RT may offer slight improvement (surface under the cumulative ranking curve (SUCRA) 74.3%). Most trials exhibited low bias risk, though heterogeneity and small sample sizes for some comparisons warrant cautious interpretation. These findings support ADT+RT/SBRT for PFS benefit but highlight the need for further research to optimize survival outcomes and treatment tolerability. creator: Wenwei Ying creator: Zhenshan Ding creator: Yuhui He creator: Jianfeng Wang creator: Xing Chen creator: Xuesong Li creator: Yanqing Gong uri: https://doi.org/10.7717/peerj.19819 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ying et al. title: Peanut oil is more environmentally sustainable than rapeseed oil from a carbon and nitrogen footprint perspective in China link: https://peerj.com/articles/19941 last-modified: 2025-08-28 description: Peanut and rapeseed oil, prominent edible oils in China, significantly contribute to greenhouse gas and reactive nitrogen emissions. A comprehensive examination of their environmental footprints is foundational for developing green and low-carbon products. Using a cradle-to-factory gate life cycle assessment, we quantified the carbon footprint (CF) and nitrogen footprint (NF) associated with the oil production of peanut and rapeseed from 2004 to 2023 in China. The results showed that peanut oil has a lower environmental impact than rapeseed oil, with a CF of 3,312.2 kg CO2eq t−1 oil and NF of 28.5 kg reactive nitrogen (Nr) t−1 oil, respectively, compared to 3,722.4 kg CO2eq t−1 oil and 43.3 kg Nr t−1 oil for rapeseed oil. It corresponded to less than 11.0% in CF and 34.2% in NF of peanut oil than that of rapeseed oil. The cropping phase was the primary source of disparity between the two oil products, with peanut exhibiting consistently lower yield-based CF and NF than rapeseed. Fertilizer application, primarily nitrogen (N) and compound fertilizers, accounted for 63.7% (peanut) and 91.4% (rapeseed) of CF, meanwhile N runoff and ammonia (NH3) volatilization were dominant in NF. Moreover, regions such as Jiangxi (peanut) and Yunnan, Shaanxi, and Gansu (rapeseed) exhibited high CF and NF but low productivity, suggesting the need for cropping layout optimization. Our findings highlight the environmental advantages of peanut oil, and recommend improved fertilizer management in agricultural stage and cleaner oil processing production to promote low-carbon, sustainable edible oil production in China. creator: Fen Ma creator: Mingbao He creator: Yingchun Li creator: Yanqun Wang creator: Zhengping Peng creator: Yinlong Xu creator: Bohan Zhao creator: Jingyu Zhang uri: https://doi.org/10.7717/peerj.19941 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ma et al. title: Nutrient and biomass dynamics for dual-organ yield in turmeric (Curcuma longa L.) link: https://peerj.com/articles/19933 last-modified: 2025-08-28 description: BackgroundIn China, Curcuma longa L. is primarily cultivated for its underground parts—rhizomes (commonly known as turmeric) and tubers (Yujin), with the latter holding greater market value. However, current cultivation practices in China remain largely traditional, lacking scientific optimization in nutrient management, growth cycle alignment, or soil fertility strategies. This study aims to establish a scientific foundation for precision fertilization by investigating the dynamic patterns of dry matter accumulation and nutrient distribution in multiple plant organs throughout the growth cycle.MethodsThe experiment was conducted in Shuangliu, Sichuan Province, a key production area for Curcuma longa in China. From 55 to 209 days after planting (DAP), nine sampling points representing different phenological stages were selected. At each stage, we systematically monitored the accumulation of dry matter and the distribution of nine essential nutrient elements—nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), iron (Fe), manganese (Mn), copper (Cu), and zinc (Zn)—across five plant organs: leaves, stems, rhizomes, tubers, and roots.ResultsThe total dry matter accumulation in Curcuma longa followed a typical S-shaped curve, reaching its peak at 195 DAP. Resource allocation patterns varied across four distinct growth stages. Before October (0–111 DAP), the aboveground parts dominated, with leaves and stems comprising 62.73% to 79.30% of the total dry mass. After October (111–195 DAP), underground development intensified, with priority given to the rhizomes and tubers. By late December (195 DAP), dry matter in the tubers peaked, and by early January (209 DAP), over 70% of the total dry mass was allocated below ground. Nutrient uptake also showed distinct temporal patterns. Total accumulation of nutrients in mature plants was as follows: K (1,492.39 mg), N (1,198.81 mg), P (396.98 mg), Ca (339.51 mg), Mg (210.63 mg), Fe (15.17 mg), Zn (1.15 mg), Mn (0.69 mg), and Cu (0.25 mg). The relative nutrient demand ranked as follows: K > N > P (macronutrients), Ca > Mg (secondary nutrients), and Fe > Zn > Mn > Cu (micronutrients).ConclusionThe growth and development of Curcuma longa depend on sufficient uptake of potassium and nitrogen, moderate amounts of phosphorus, calcium, and magnesium, and trace amounts of iron, zinc, manganese, and copper—of which potassium is required in the greatest quantity. These findings highlight the importance of adopting a stage-specific fertilization strategy to align with the plant’s shifting nutrient demands throughout its life cycle. creator: Wenxin Liao creator: Haohan Wang creator: Heling Fan creator: Jie Chen creator: Lili Yin creator: Xiaoyang Cai creator: Min Li uri: https://doi.org/10.7717/peerj.19933 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liao et al. title: Preoperative serum lipids as novel predictors for concomitant thyroid carcinoma in Graves’ disease link: https://peerj.com/articles/19915 last-modified: 2025-08-28 description: BackgroundThe occurrence of thyroid carcinoma in patients with Graves’ disease (GD) has been rising recently. However, the linkage between lipids and the incidence of thyroid carcinoma among GD patients is still not well-established.ObjectiveThe research aims to explore the relationship between serum lipid concentrations and the occurrence of thyroid cancer in patients diagnosed with GD.MethodsWe conducted a retrospective analysis of data from 512 patients with GD who underwent surgical procedures at our institution between 2015 and 2024. Our study focused on examining the correlations between various patient characteristics and the occurrence of thyroid cancer. Logistic regression models were developed to analyze the predictive factors. Ultimately, we constructed a predictive nomogram to estimate the potential of thyroid cancer in GD patients.ResultsAmong the 512 patients with GD, 299 patients were pathologically confirmed as differentiated thyroid carcinoma (DTC) (58.4%). Multivariate analysis revealed that high triglyceride (TAG > 1.185 mmol/L), low high-density lipoprotein (HDL < 1.325 mmol/L), and overweight (body mass index (BMI) ≥ 25) were risk factors for malignancy. In addition, ultrasound characteristics, including nodules in the thyroid, aspect ratio imbalance, hypoechogenicity, irregular borders, and microcalcifications, were risk factors for malignancy. The predictive nomogram demonstrated significant clinical utility, exhibiting an area under the curve (AUC) of 0.91 (95% CI [0.88–0.94]) and 0.91 (95% CI [0.87–0.96]) in the training set and validation set. Moreover, a high level of TAG was a risk factor for central lymph node metastasis and high AJCC staging in GD patients with thyroid carcinoma.ConclusionsOur study presents initial findings suggesting that elevated TAG levels, reduced HDL cholesterol levels, and overweight status are individually linked to the incidence of thyroid carcinoma in patients with GD. These results indicate that preoperative serum lipid profiles and BMI can serve as valuable predictors for the occurrence of thyroid carcinoma in this patient population. creator: Xingxing Gao creator: Mi Liu creator: Yijun Wu uri: https://doi.org/10.7717/peerj.19915 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gao et al. title: Outcomes of stereotactic body radiotherapy for unresectable cholangiocarcinoma: a meta-analysis and systematic review link: https://peerj.com/articles/19909 last-modified: 2025-08-28 description: BackgroundStereotactic body radiotherapy (SBRT) is an effective treatment for various malignancies. This meta-analysis aimed to determine the prognostic outcomes and toxicities of SBRT for unresectable cholangiocarcinoma (CC) using the most recent evidence.MethodsThe review protocol was registered on PROSPERO (CRD42023393642). We searched PubMed, EMBASE, and the Cochrane Library for studies involving SBRT and CC. Study endpoints included median overall survival (OS), 1- and 2-year OS rates, 1- and 2-year disease control rates (DCR), and the incidence of grade 3 or higher toxicities.ResultsThirteen studies (366 patients) were included. Of these, 138 patients (37.7%) had extrahepatic CC and 228 patients (62.3%) had intrahepatic CC. The median total SBRT dose was 45 Gy, and the median biologically effective dose (BED10) was 72.0 Gy. The pooled median OS was 13.4 months (95% confidence interval (CI) [10.9–15.8]). Pooled 1-year and 2-year OS rates were 58.7% (95% CI [53.8–63.7%]) and 33.2% (95% CI [28.3–38.2%]), respectively. Pooled 1-year and 2-year DCR rates were 84.7% (95% CI [81.0–88.3%]) and 70.5% (95% CI [65.2–75.8%]), respectively. Pooled incidence rates for grade ≥3 acute, late, and overall toxicity were 6.4% (95% CI [2.6–10.1%]), 16.4% (95% CI [1.9–31.0%]), and 16.9% (95% CI [9.3–24.6%]), respectively. No factor was significantly associated with improved OS or DCR.ConclusionsThis meta-analysis demonstrates that SBRT may be an efficacious and safe therapeutic option for unresectable CC. Further prospective studies comparing SBRT with alternative treatment approaches are required to define its definitive role in managing CC. creator: Peng Liu creator: Haiyan Ye creator: Lijun Song creator: Hua Li creator: Mingna Fu creator: Zhichao Dong uri: https://doi.org/10.7717/peerj.19909 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Development of simple sequence repeat markers and genetic diversity of Sipunculus nudus in the Beibu Gulf of China link: https://peerj.com/articles/19903 last-modified: 2025-08-28 description: BackgroundThe marine species Sipunculus nudus, valued for its medicinal and commercial significance, faces critical research gaps due to a lack of molecular markers (notably simple sequence repeats (SSRs)) and insufficient genetic diversity data, hindering genetic studies and evidence-based breeding initiatives.MethodsThe software of Misa and Primer3 were adopted to detect SSRs and develop primer pairs, and then some primers of highly polymorphic loci in the genome were used to reveal the genetic diversity of S. nudus along the Beibu Gulf in China.ResultsFrom the genome, 277,264 SSRs were detected an d 198,902 primers were designed. Ninety-five of the synthesized 100 primers could amplify across samples, with 93 showing polymorphism. Thirty highly polymorphic primers were chosen to disclose the genetic diversity of 219 materials from Beibu Gulf, China. We detected 370 alleles with high genetic diversity: observed heterozygosity (Ho) = 0.905, expected heterozygosity (He) = 0.833, Shannon’s index (I) = 2.042, and polymorphism information content (PIC) = 0.811. The study also revealed varying levels of genetic differentiation and gene flow among different provenances. Structure analysis partitioned all samples into seven distinct genetic clusters.ConclusionsWe identified 277,264 SSRs in S. nudus and developed primers for 198,902 SSRs. Subsequently, 100 primers were validated for assessing genetic diversity and population differentiation. These will establish a critical foundation for advancing germplasm conservation and targeted breeding strategies in this species. creator: Chunli Han creator: Yuzhu Ni creator: Guohao Yang creator: Jialin Yang creator: Jie Zou creator: Huijing Peng creator: Pengliang Wang uri: https://doi.org/10.7717/peerj.19903 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Han et al. title: Age and growth of chum salmon from the Tumen River link: https://peerj.com/articles/19902 last-modified: 2025-08-28 description: To investigate the age structure and growth characteristics of the chum salmon (Oncorhynchus keta) population in the Tumen River, this study conducted age determination and measured basic biological indicators including fork length (FL) and body weight (BW) for 331 specimens collected between 2020 and 2023. Results revealed that the spawning population comprised four age groups (2+, 3+, 4+, and 5+), dominated by age-2+ and age-3+ individuals (96.37% of the total). FL ranged from 51.0 to 74.6 cm and BW ranged from 1,400 to 5,200 g. The relationship between BW and FL was expressed as: BW = 0.0159×FL2.8969, indicating isometric growth. Von Bertalanffy growth equations (VBGF) were applied to examine growth patterns among age groups and between sexes, with parameters estimated via maximum likelihood. Analysis of the residual sum of squares (ARSS) indicated no significant growth differences between sexes but revealed significant differences between the age-2+ and age-3+ groups. The size at maturity (FL50%) for females and males was 45.87 cm and 43.93 cm, respectively, with corresponding ages at maturity (T50%) of 2.00 and 1.87 years, respectively. These findings provide essential biological data for science-based management and conservation of Tumen River chum salmon. creator: Anqi Wang creator: Peilun Li creator: Fujiang Tang creator: Shuhan Xiong creator: Jiaoyang Yu creator: Jilong Wang uri: https://doi.org/10.7717/peerj.19902 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Market-approved convolutional neural network tasked with classifying skin lesions under suspicion of melanoma: performance across primary care clinics within Australia link: https://peerj.com/articles/19876 last-modified: 2025-08-28 description: BackgroundArtificial intelligence (AI) is poised to revolutionise how melanoma is detected in clinical practice, yet few studies have been published with patient data at the forefront.ObjectiveThe primary aim of this study was to investigate the clinical performance of a market-approved convolutional neural network (CNN) to better differentiate skin lesions suspicious of being malignant melanoma (MM). A secondary aim of this study was to compare the diagnostic performance of the CNN across two separate general practices, that are skin cancer focused clinics.MethodsMulticentre, cross-sectional study using a commercially available CNN on 373 melanocytic lesions (114 melanoma, 259 non-melanoma) from participants attending a skin examination within two Australian specialised, general practice clinics. Performance metrics included sensitivity, specificity, predictive values, diagnostic odds ratios, accuracy and area under the curve (AUC) of receiver operating characteristics (ROC) used for classification of images.ResultsThe CNN average sensitivity [Gold Coast vs Townsville] was calculated as 63.2% [61.5% vs 68.6%], specificity as 53.9% [52.5% vs 55.1%], positive predictive value as 37.8% [28.9% vs 44.0%] and negative predictive value as 76.8% [71.4% vs 84.2%]. Likelihood ratios were 1.4 for positive likelihood ratio, 0.7 for negative likelihood ratio and a diagnostic odds ratio of 2.0 across both clinics. Accuracy was calculated as 56.6% [56.1% vs 57.5%] and the AUC of ROC for both clinics was 0.602 and 0.615 for Townsville and Gold Coast, respectively.ConclusionsImprovement of the performance of this CNN for the classification of images, particularly when suspecting MM is necessary before it may be used in a clinical setting in Australia. Other validated AI systems used internationally may also require review for use in an Australian setting. creator: Ian J. Miller creator: Michael Stapelberg creator: Jeremy Hudson creator: Paul Coxon creator: Nathaniel Milani creator: Nedeljka Rosic creator: James Furness creator: Joe Walsh creator: Mike Climstein uri: https://doi.org/10.7717/peerj.19876 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Miller et al. title: Effect of pasture and feeding systems on hematological traits of ewes and lambs link: https://peerj.com/articles/19846 last-modified: 2025-08-28 description: ContextSustainable livestock production depends on efficient pasture management and the continuous monitoring of the health of grazing animals.ObjectivesThis study investigated the effects of pasture types and sheep production systems on the hematological traits of Karacabey Merino (German Mutton Merino × Kıvırcık) ewes and lambs grazing on different pasture types throughout the year and reared in a semi-intensive system (control group).MethodsIn this twenty-six-month study, the hematological characteristics of ewes and lambs grazing on natural pastures and in spring (triticale and oat grass pasture), summer (sorghum Sudangrass and wheat stubble pasture), and autumn (triticale and oat grass pasture) were compared with ewes and lambs reared in a semi-intensive system (no pasture for lambs). A total of 36 ewes (aged 3–4 and 65.2 ± 0.55 kg) and 98 lambs were used. There were 12 ewes in total in each treatment group and four ewes in subgroups. Each subgroup in the pasture was separated by fences. The 12 ewes tagged in the control group were within the unit sheep flock. Blood samples were taken from the jugular vein of ewes and lambs at three to four-week intervals during live weight weighing using 3–4 mL edged tubes and transported in the cold chain to the laboratory for analysis.ResultsPregnant ewes grazing on natural autumn pasture had significantly lower red blood cell (RBC), hemoglobin (HGB), and platelet (PLT) counts (P < 0.05). Animals grazing on wheat stubble pasture exhibited higher hematological values compared to those grazing on Sorghum-Sudangrass pasture (P < 0.05). Lambs in the control group had lower hemoglobin (HGB) and hematocrit (HCT) levels during the post-weaning period than those in the pasture group (P < 0.05).ConclusionsThe hematological parameters of pregnant Karacabey Merino ewes grazing on natural pastures during the autumn season, as well as those of lambs raised in a semi-intensive system during the post-weaning period, should be carefully monitored. Additionally, appropriate feed supplementation, along with vitamin and mineral support, should be provided to maintain animal health and physiological balance. creator: Cemil Tölü creator: Hülya Hanoğlu Oral creator: Fırat Alatürk creator: Ahmet Gökkuş uri: https://doi.org/10.7717/peerj.19846 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tölü et al. title: Resistance of mature and elderly bodybuilders to anaerobic energy supply load link: https://peerj.com/articles/19844 last-modified: 2025-08-28 description: BackgroundThis study aims to assess the resistance level of beginner bodybuilders of mature and elderly age to strength training performed under anaerobic energy supply modes (creatine phosphokinase and glycolysis).MethodsThe study involved 60 men who had been engaged in bodybuilding for only 12 months. Group A included men aged 24 ± 1.5 years (early mature age), group B consisted of men aged 40 ± 2.1 years (late mature age), and group C comprised men aged 58 ± 1.6 years (elderly). An integral method of quantitative assessment of power loads was used to determine 1 repetitions maximum (RM) and load parameters for each anaerobic energy supply mode. Resistance levels were evaluated based on adaptive-compensatory responses to training stimuli, using heart rate variability (HRV) and biochemical blood markers (creatine phosphokinase (CPK), lactate dehydrogenase (LDH), testosterone, cortisol).ResultsPre-exercise results showed that participants in groups A and C exhibited more tense heart rhythm regulation, with autonomic balance shifted toward sympathetic dominance. Group B showed creatine phosphokinase activity in the blood that was twice as high as in the other groups. Cortisol levels in group C were on average 17.6% higher than in groups A and B. Post-exercise results under the creatine phosphokinase energy supply mode revealed increased autonomic regulation and decreased sympathetic tone in groups B and C. In contrast, Group A showed heightened heart rate regulation tension (standard deviation of RR intervals (SDNN) −38.5%) and increased central sinus rhythm regulation (very low frequency (VLF) +34.3%). In groups B and C, creatine phosphate was the primary energy source, while in group A, due to insufficient creatine phosphate reserves, muscle glycogen was additionally utilized, leading to increased blood LDH (+94.7%) and cortisol (+133.2%). Under the anaerobic glycolysis mode, groups A and B showed increased vagal influence on the sinus node, while group C exhibited increased sympathetic tone (low frequency (LF) +11.4%) and reduced autonomic regulation (high frequency (HF) −5.9%). In group A, only LDH activity increased (+90.2%) compared to rest. Cortisol levels decreased significantly in groups A (−21.0%) and C (−12.4%), indicating activation of compensatory mechanisms.ConclusionsThe findings underscore the need to develop tailored load adjustment strategies for mature and elderly individuals beginning bodybuilding. Load regimes should consider individual strength capacities and adaptive reserves. The use of heart rate variability (HRV) and blood biochemical markers is validated as an informative approach for assessing resistance to training-induced stress. creator: Andrii Chernozub creator: Alla Aloshyna creator: Georgiy Korobeynikov creator: Vadym Koval creator: Yurii Havrylov creator: Liudmyla Sherstiuk creator: Vladimir Potop creator: Consuela Andreea Timnea-Florescu creator: Olivia Carmen Timnea uri: https://doi.org/10.7717/peerj.19844 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chernozub et al. title: Thermography analysis as a tool for assessing thermal asymmetries and temperature changes after therapy in patients with stroke: a pilot study link: https://peerj.com/articles/19843 last-modified: 2025-08-28 description: This pilot quasi-experimental study investigates the potential of infrared thermography as a non-invasive tool for assessing thermal asymmetries in patients with hemiplegia following stroke. Ten participants underwent thermographic imaging using a FLIR C5 camera before and after a lower-limb muscle-strength intervention. Thermal data were processed and analyzed with ThermImageJ software, following the TISEM protocol to ensure the precision of temperature measurements within predefined regions of interest (ROI). The primary aim was to evaluate whether thermography could reliably detect thermal discrepancies between the affected and unaffected sides of the body and whether these differences respond to targeted physical therapy. The results demonstrated significant baseline asymmetries between both sides of the body, which were notably reduced after the strength intervention. These findings suggest that muscle-strength training may contribute to improved thermal symmetry and that thermography is sensitive enough to detect such changes. While the outcomes are promising, larger-scale studies with extended follow-up are necessary to confirm these preliminary findings. Nonetheless, infrared thermography is an effective complementary method for monitoring physiological responses to rehabilitation in stroke patients. creator: Luis Augusto Silva Zendron creator: Marta Gómez Mateos creator: Beatriz María Bermejo Gil creator: Andrea Calleja Caballero creator: Vanesa Santos Rodríguez creator: Fátima Pérez-Robledo creator: Ana María Martín Nogueras uri: https://doi.org/10.7717/peerj.19843 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Silva Zendron et al. title: The effect of peer support on HbA1c levels in middle-aged and elderly patients with type 2 diabetes: a systematic review and meta-analysis link: https://peerj.com/articles/19803 last-modified: 2025-08-28 description: BackgroundPeer support is increasingly recognized as a valuable method for managing blood glucose levels and reducing the risk of chronic complications in patients with diabetes. This systematic review and meta-analysis specifically evaluated the effect of peer support on HbA1c levels in middle-aged and elderly patients with type 2 diabetes and explored the potential benefits of peer interactions on glycemic control.MethodologyA comprehensive search was conducted across six databases from January 2018 to July 2023, with a focus on randomized controlled trials (RCTs) that compared peer support interventions to standard diabetic care in adults. Among the 3,395 articles identified, eleven studies involving 2,187 participants were included. The quality of each study was assessed using the Cochrane risk of bias tool. A random-effects model was employed to calculate the mean difference (MD) in HbA1c changes, with additional subgroup analyses for specific contexts.ResultsThe findings revealed a modest but statistically significant improvement in HbA1c levels in groups receiving peer support (MD: −0.20; 95% CI [−0.37 to −0.02]; p = 0.03). More pronounced benefits were observed in interventions conducted within formal medical settings, those involving high-frequency contact, and those in group sessions, particularly among elderly patients.ConclusionsThe results suggest that while peer support provides a slight improvement in HbA1c levels, other intervention strategies—such as frequent contact, group sessions, and formal medical settings—may offer greater glycemic control benefits in elderly patients with type 2 diabetes. These findings support incorporating peer support into diabetes care and underscore the need for further research with larger samples and standardized protocols. creator: Jiankun Luo creator: Jiyuan Shu creator: Weiqing Pan creator: Duanqin Guan creator: Congmin Liang creator: Dongyan Zheng creator: Kailun Huang creator: Yixi Lai creator: Bing Meng creator: Renjian Lu creator: Ziwei Cai creator: Lifei Xing creator: Jialong Chen creator: He Zhang uri: https://doi.org/10.7717/peerj.19803 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Luo et al. title: The effect of cumulative ecological risk on migrant children’s Internet game addiction: a moderated mediation model link: https://peerj.com/articles/19787 last-modified: 2025-08-28 description: BackgroundInternet games are becoming a popular form of entertainment. However, overindulgence in online games may lead to online game addiction, which may have a negative impact on the health of adolescents. As a special group of adolescents, migrant children’s Internet game addiction has also attracted much attention. This study aimed to explore the effects of cumulative ecological risk on migrant children’s Internet game addiction, and to investigate the mediating role of self-educational expectations and the moderating role of gender.MethodsA questionnaire survey method was employed in this study. Using convenience sampling, a total of 314 migrant children completed the cumulative ecological risks scale, self-education expectations scale, and Internet game addiction scale.ResultsThe findings showed that cumulative ecological risk had a significant effect on migrant children’s Internet game addiction, and self-education expectations partially mediating the relationship between cumulative ecological risk and Internet game addiction. The latter part of the mediating effect in the pathway “cumulative ecological risk → self-educational expectations → Internet game addiction” is moderated by gender. Specifically, the impact of self-educational expectations on game addiction is stronger for male students compared to female students.ConclusionComprehensive measures should be taken to address the problem of online game addiction among migrant children, including reducing the ecological risk faced by migrant children, raising self-education expectations and paying attention to gender differences. creator: Zhengzheng Lin creator: Ying Zha uri: https://doi.org/10.7717/peerj.19787 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lin and Zha title: Socioeconomic status and risk of gestational diabetes mellitus among pregnant women in Zunyi, China link: https://peerj.com/articles/19782 last-modified: 2025-08-28 description: BackgroundThe impact of socioeconomic status on disease is becoming increasingly apparent. However, the relationship between gestational diabetes mellitus (GDM) and socioeconomic status (SES) has been less studied and remains inconsistent. The aim of this study was to investigate the relationship between SES and GDM.MethodsAll participants were selected from a prospective study on maternal and infant health in Zunyi City, China, between 2020 and 2022. Data on educational attainment, occupation, and household income were collected through standard questionnaires administered during face-to-face interviews. Logistic regression models were used to calculate adjusted odds ratios (ORs) and 95% confidence intervals (CIs), evaluating the association between GDM and SES—a composite measure comprising educational attainment, occupational status, and household monthly income.ResultsAmong 5,868 participants, 690 women (11.8%) were diagnosed with GDM. After adjusting for potential confounders, no significant association was observed between educational attainment and GDM prevalence. Compared to public sector employees, women engaged in private sector occupations, freelancing, or farming exhibited a lower GDM risk. Household monthly income demonstrated a significant positive correlation with GDM incidence. Stratified analyses revealed distinct age-related patterns: higher education attainment was associated with reduced GDM risk in women aged >35 years, while occupational influences on GDM were more pronounced in this age group. Conversely, income effects were stronger among women aged ≤35 years. BMI stratification further indicated that occupational factors predominantly affected GDM risk in underweight women (BMI <18.5 kg/m2), whereas income exhibited stronger associations in women with BMI ≥18.5 kg/m2.ConclusionOur study revealed a significant association SES and GDM development. Among household income and occupation emerged as stronger predictor of GDM to educational attainment in Zunyi City, Guizhou province, China. creator: Yan Xie creator: Jing Jiang creator: Jing Yang creator: Shiyi Gao creator: Rong Zeng creator: Yijun Liu creator: LingLu Wang creator: Pei Xu creator: Kunming Tian creator: Shimin Xiong creator: Xingyan Liu creator: Xubo Shen creator: Hong Pan creator: YuanZhong Zhou uri: https://doi.org/10.7717/peerj.19782 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xie et al. title: Vitamin D supplementation in Saudi Arabia: mothers’ knowledge, practices, and attitudes link: https://peerj.com/articles/19781 last-modified: 2025-08-28 description: ObjectiveDespite abundant sunshine, vitamin D (VIT D) deficiency remains prevalent in tropical regions such as the Kingdom of Saudi Arabia (KSA), largely due to limited dietary intake and sun exposure restrictions. This study evaluated mothers’ perceptions of VIT D supplementation for them and their children in KSA.MethodsThis observational cross-sectional study was conducted in KSA among mothers aged 18 and older with children under five years old. A convenience sampling method was employed to recruit participants in the study in the period from 31 July to 2 October 2022. The data were collected by developed questionnaire which was distributed to participants via WhatsApp and Facebook. The data were analyzed using an SPSS program with both descriptive and inferential statistical methods.ResultsA total of 200 mothers participated, with a mean age (SD) of 35.48 (6.9) years. Among them, 66.40% had poor knowledge of VIT D and its supplementation, while 33.60% demonstrated good knowledge. Regarding practices, only 22.95% of mothers reported good practices, 43.85% reported fair practices, and 33.20% reported poor practices. However, most mothers (95%) demonstrated a favorable attitude toward VIT D and its supplementation, and only 5% of them showed a negative attitude. Notably, significant correlations were observed between mothers’ salaries and their familiarity with VIT D (p = 0.024); their age and practices towards VIT D and its supplements (p = 0.049); as well as their level of education, functional status, and attitudes towards VIT D (p = 0.037 and p = 0.008, respectively).ConclusionThe findings indicate that a significant proportion of mothers had poor knowledge and inadequate practices regarding VIT D and its supplementation, despite their generally positive attitudes. These results underscore the need for targeted interventions to enhance knowledge and practices, considering socio-economic factors and educational background. creator: Hanan F. Alharbi creator: Khulud Ahmad Rezq uri: https://doi.org/10.7717/peerj.19781 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alharbi and Rezq title: MultNAT HIV-1 Viral Load Assay: a simple, rapid and sensitive cross-primer amplification assay for detecting the HIV-1 virus in the field link: https://peerj.com/articles/19753 last-modified: 2025-08-28 description: BackgroundA large number of new human immunodeficiency virus (HIV) patients are diagnosed worldwide every year. This study aimed to design a rapid, efficient, and convenient kit for detecting HIV-1 viral load.MethodsThe sensitivity and specificity of the kit were determined, and serum samples were collected from HIV-negative and HIV-positive individuals who underwent medical checkups at Xixi Hospital in Hangzhou City, Zhejiang Province, China, between June and August 2023 for testing. The presence of HIV-1 in the clinical samples was assessed via a diagnostic PCR system and a conventional fluorescent quantitative PCR technique in this study.ResultsHIV-1 RNA was measured with a 100 copies/mL sensitivity via the MultNAT HIV-1 Viral Load Assay. The accuracy of the a ssay was as follows: The assay showed near-perfect agreement with compare kit (kappa = 0.9945), positive compliance rate of 99.45% (182/183), negative compliance rate of 100% (183/183). The linear correlation coefficient between MultNAT HIV-1 Viral Load Assay and DaAn kit was 0.95, and the R2 was 0.90.ConclusionDue to its simplicity, rapid response time, and high sensitivity and specificity, the MultNAT HIV-1 Viral Load Assay is suitable for primary care and epidemiological screening, facilitating rapid and accurate HIV-1 detection. creator: Lili Huang creator: Zhongbao Zuo creator: Lanlan Hu creator: Jing Wu creator: Qingting Bu creator: Yueping Li creator: Xiuhui Li creator: Yanqiong Zhou creator: Aifang Xu uri: https://doi.org/10.7717/peerj.19753 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach link: https://peerj.com/articles/19728 last-modified: 2025-08-28 description: The interaction of mangrove trees with endophytic microorganisms contributes to the successful establishment of these plants in the challenging intertidal environment. The red mangrove, Rhizophora mangle L. (Rhizophoraceae), is one of the dominant species in mangrove ecosystems and is characterized by the provision of several ecologically relevant services. In this work, we integrated metagenomics and metatranscriptomics to perform a robust characterization of the community of endophytic microorganisms associated with R. mangle leaf and root tissues. The microbiota were characterized at taxonomic and functional levels, and abundance and gene expression profiles were compared between these two plant tissues. We found that the endophyte community consisted mainly of bacteria and eukaryotes, which were the most active groups at the transcriptional level, while archaea and viral groups were identified in lower abundance and expression. In addition, the results show that the community of endophytic microorganisms changes depending on the tissue type, with root-associated microorganisms being the most abundant at the metagenome level and active at the metatranscriptome level. It was also found that R. mangle endophytes actively contribute to key functions for adaptation to an intertidal ecosystem with high human intervention, such as salinity tolerance and degradation of heavy metals and xenobiotic compounds. Thus, according to the functions found and contributed by the endophyte community of red mangrove leaf and root tissues, it can be concluded that these microbial communities are crucial for the survival of R. mangle in the extreme environment of mangrove forests. This study provides a solid basis for future research aimed at understanding the role of plant-endophyte interactions. creator: Valentina Cárdenas-Hernández creator: Cesar Lemos-Lucumi creator: Nelson Toro-Perea uri: https://doi.org/10.7717/peerj.19728 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cárdenas-Hernández et al. title: A retrospective analysis of neoadjuvant chemotherapy in pneumonectomy for locally advanced central non–small cell lung cancer link: https://peerj.com/articles/20007 last-modified: 2025-08-27 description: AimsThe treatment of patients with locally advanced central non–small cell lung cancer (NSCLC) remains controversial. This study aimed to evaluate the effects of neoadjuvant chemotherapy in patients undergoing pneumonectomy.MethodsA retrospective analysis was conducted on patients who underwent pneumonectomy with or without neoadjuvant chemotherapy for locally advanced central NSCLC between 2014 and 2019. Categorical variables were compared using the Chi-square or Fisher’s exact test. Survival analysis was performed using the Kaplan–Meier method, with comparisons made via the log-rank test. Multivariate analysis of independent prognostic factors was conducted using the Cox proportional hazards regression model. A p-value < 0.05 was considered statistically significant.ResultsBased on inclusion and exclusion criteria, 104 patients were selected from a total of 6,930, including 69 who received neoadjuvant chemotherapy and 35 who did not. Univariate analysis showed that the neoadjuvant chemotherapy group had significantly improved 5-year overall survival (OS: 29.1% vs. 12.8%, $\chi^2$χ2 = 4.089, p = 0.043) and disease-free survival (DFS: 22.3% vs. 8.8%, $\chi^2$χ2 = 3.941, p = 0.047). The downstaging rate in the neoadjuvant chemotherapy group was 29.0%. Subgroup analysis revealed that patients with downstaging had significantly better 5-year OS and DFS compared to those without downstaging (OS: 56.6% vs. 17.1%, $\chi^2$χ2 = 10.266, p = 0.001; DFS: 54.1% vs. 6.0%, $\chi^2$χ2 = 20.785, p < 0.001). Another subgroup analysis showed that although 5-year DFS was 0% in both groups, patients with stage cN2 disease who received neoadjuvant chemotherapy had better 5-year OS (16.3% vs. 7.8%, $\chi^2$χ2 = 5.603, p = 0.018) and a statistically significant difference in DFS ($\chi^2$χ2 = 7.328, p = 0.007).ConclusionsNeoadjuvant chemotherapy significantly improves prognosis in patients with locally advanced central NSCLC undergoing pneumonectomy. Multivariate analysis confirms its positive impact on survival. Patients who experience downstaging after neoadjuvant chemotherapy show notably better outcomes. For patients with stage cN2 disease, neoadjuvant chemotherapy is associated with improved survival. creator: Yuchen Wang creator: Zhihang Dang creator: Pu Jiang creator: Zhifeng Li creator: Jin Yang creator: Kun Gao creator: Xiaona Chen creator: Jifang Yao uri: https://doi.org/10.7717/peerj.20007 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Sex differences in association football: a scoping review link: https://peerj.com/articles/19976 last-modified: 2025-08-27 description: BackgroundDespite some reviews examining sex differences in football within specific themes, a comprehensive, integrated overview of sex differences in football is lacking. This scoping review aimed to: (1) synthesize existing evidence regarding sex differences in elite football players; (2) identify research gaps to provide direction for future studies.MethodologyThe protocol adhered to the PRISMA Extension for Scoping Reviews guidelines. The searches were conducted on October 17, 2024, in Scopus, PubMed, ScienceDirect, and Web of Science (Core Collection). The risk of bias was assessed using the Revised Risk of Bias Assessment Tool for Nonrandomized Studies of Interventions (RoBANS 2). A narrative synthesis was performed to summarize the main findings.ResultsA total of 80 studies met the eligibility criteria and were included in the review, encompassing 4,896 players (2,226 female, 2,670 male) and 234 matches (99 female, 135 male). Seventy-two studies (90%) did not report female participants’ menstrual cycles or contraceptive medication use. Only six studies exclusively used “sex”-related terminology, with not a single study using “gender”-related terminology alone. Seventy-four studies (93%) presented various degrees of mixed usage of the terms “sex” and “gender”. All included studies were categorized into eight themes according to their research focus: Anthropometrics, Muscle and Joint Movements, Physiological Response, Physical Performance, Technical Performance, Match Performance, Psychological and Behavioral Performance, and Nutrition/Recovery/Sleep.ConclusionsPerhaps due to a combination of innate biological factors and acquired dietary habits, female players, who typically have a higher body fat percentage and lower lean body mass, exhibit performance gaps compared to male players in terms of speed, strength, and endurance. These differences further affect their technical skills and match performance. However, while these absolute differences exist, they often diminish or even disappear when data are standardized against certain anthropometric or physiological metrics. This underscores the importance of developing individualized analytical methods and evaluation criteria tailored to female players. Future studies should carefully define sex-specific inclusion/exclusion criteria and select appropriate sex and gender terminology to minimize bias and enhance study quality. creator: Wangyang Xu creator: Diyan Zhang creator: Xinbi Zhang uri: https://doi.org/10.7717/peerj.19976 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xu et al. title: Association of dietary inflammatory index with serum asprosin and omentin levels in women with prediabetes link: https://peerj.com/articles/19957 last-modified: 2025-08-27 description: Background and ObjectivesThe objective of present study was to assess the relationship between the Dietary Inflammatory Index (DII) and the Glycemic Index (GI), serum TNF-α (tumor necrosis factor alpha), IL-6 (interleukin 6), serum asprosin, and omentin adipokines in prediabetic adult women.MethodsThe study included a total of 60 women: 30 women with prediabetes, aged 19–50 years, with a body mass index (BMI) ranging from 25 to 35 kg/m2, and 30 healthy women with similar age and BMI as the control group. Dietary data for calculating DII and GI were obtained from food frequency questionnaires and food consumption records, respectively. Serum levels of asprosin, omentin, IL-6, and TNF-α were analyzed using the enzyme-linked immuno sorbent assay (ELISA) method. Correlation and regression analyses were performed to evaluate the relationships between DII scores, glucose metabolism markers, inflammatory markers, the specified adipokines, and the glycemic index.ResultsIn the case group, DII scores, GI values, serum asprosin, IL-6, TNF-α, and C-reactive protein (CRP) levels were found to be significantly higher (p < 0.001, p = 0.001, p = 0.010, p = 0.005, p < 0.001, p < 0.001, respectively). No significant difference was found between the case and control groups for serum omentin levels (p = 0.779). In the case group, a significant positive correlation was found between DII and insulin, insulin resistance (HOMA-IR) and GI (r = 0.365, p = 0.047; r = 0.440, p = 0.015; r = 0.512, p = 0.004, respectively), but no significant correlation was found with asprosin and omentin (r = 0.292, p = 0.117; r = 0.337, p = 0.069, respectively). However, an increase of one unit in serum asprosin levels in the case group was associated with an increase of 0.421 units in the DII score (F = 6.031, p = 0.021, β = 0.421, 95% CI [0.008–0.088], adjusted R2 = 0.148), while an increase of one unit in CRP values in the control group was associated with a 0.472 unit increase in the DII score (F = 8.009, p = 0.009, β = 0.472, 95% CI [0.343–2.141], adjusted R2 = 0.195).ConclusionsThe observed association between increased serum asprosin levels and higher DII scores in prediabetic women may provide preliminary evidence on potential biomarkers for prediabetes, but due to the cross-sectional design of the study, further prospective studies are required to investigate their diagnostic or therapeutic utility. On the other hand, no significant difference was observed between the groups in terms of serum omentin levels; this may be due to the complexity of the regulation mechanism and requires more detailed investigations. creator: Gizem Taban creator: Nursel Çalık Başaran creator: Aylin Ayaz uri: https://doi.org/10.7717/peerj.19957 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Taban et al. title: The role of N6-methyladenosine (m6A) RNA methylation modification in kidney diseases: from mechanism to therapeutic potential link: https://peerj.com/articles/19940 last-modified: 2025-08-27 description: BackgroundKidney disease is a major global health issue, causing numerous deaths and a loss of life years. This prompts us to explore potential targets or mechanisms that may increase the likelihood of diagnosing and treating kidney diseases. N6-methyladenosine (m6A) modifications dynamically regulate RNA through “writer” enzymes, “eraser” enzymes, and “reader” proteins, influencing its processing, stability, and translation efficiency. In cases of kidney disease, there is a likelihood that m6A methylation is a significant contributor to the pathological mechanisms of acute kidney injury (AKI), chronic kidney disease (CKD), diabetic kidney disease (DKD), renal cell carcinoma (RCC), and lupus nephritis (LN). In this article, we explore the role and mechanisms of m6A methylation in kidney diseases and its applications in the treatment of kidney diseases.MethodologyThis review systematically evaluated the therapeutic relevance of m6A methylation in renal diseases using a targeted search strategy across multiple databases (Scopus, PubMed, Web of Science, Google Scholar, bioRxiv, medRxiv) from January 1970 to May 2025. Study quality was assessed, and critical data elements were cataloged to ensure rigor.ResultsThe current research investigates m6A methylation’s role in kidney diseases, highlighting its significant impact on regulating gene expression, affecting cell signaling pathways, and modulating inflammation. In AKI, changes in m6A modification levels are closely associated with the severity of kidney damage. Specifically, m6A regulators such as METTL3 and FTO influence the progression of AKI by affecting gene expression, oxidative stress, and inflammation. Regarding CKD, decreased m6A modification levels could potentially cause atypical gene expression in cells, thus impairing normal cellular functions. In diabetic nephropathy (DN), dysregulated expression of genes linked to m6A methylation is closely associated with renal hypertrophy, proteinuria, and glomerulosclerosis. In LN, alterations in m6A regulator expression are strongly linked to glomerular filtration rate (GFR).ConclusionsEmerging studies link dysregulated m6A machinery to diverse kidney diseases, including acute/chronic kidney injury (WTAP/METTL3/FTO in oxidative stress and fibrosis), and diabetic nephropathy (METTL14/FTO polymorphisms in susceptibility). Mechanistically, m6A modulates TGF-β signaling, inflammatory responses, and gene networks underlying disease progression. Despite therapeutic promise, challenges persist in methodological standardization and understanding systemic regulatory roles. Future research should prioritize multi-omics integration, isoform-specific inhibitors, and longitudinal clinical validation. Interdisciplinary efforts to decode m6A’s multifaceted regulation may advance precision diagnostics and mechanism-based therapies, ultimately improving renal disease management. creator: Shaowen Guo creator: Wenjun Wang creator: Gaopan Lv creator: Yun Ling creator: Meifeng Zhu uri: https://doi.org/10.7717/peerj.19940 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo et al. title: Exploration of prognostic genes associated with lymphangiogenesis in breast cancer based on transcriptomics and experimental verification link: https://peerj.com/articles/19890 last-modified: 2025-08-27 description: BackgroundBreast cancer (BC), a malignant neoplasm resulting from the uncontrolled proliferation of mammary epithelial cells, is predominantly driven by pathogenic breast cancer gene (BRCA) 1/2 mutations in hereditary cases. Previous studies have implicated lymphangiogenesis in the progression of BC. This research aimed to identify prognostic genes associated with lymphangiogenesis in BC and explore their underlying biological mechanisms.MethodsPublicly available datasets were utilized to identify differentially expressed genes (DEGs). Lymphangiogenesis-related genes (LRGs) were sourced from public databases, and candidate genes were determined through the intersection of DEGs and LRGs. Univariate Cox regression analysis and machine learning algorithms were employed to select prognostic genes and develop a prognostic model. Further analyses, including a nomogram, Gene Set Enrichment Analysis (GSEA), immune cell infiltration analysis, and drug sensitivity predictions, were conducted based on the identified prognostic genes. Finally, reverse transcription quantitative polymerase chain reaction (PCR) (RT-qPCR) was performed to evaluate the expression levels of these genes.ResultsBy intersecting 9,577 DEGs with 179 LRGs, 109 candidate genes were identified. Ultimately, four prognostic genes—ZIC2, CD24, CEBPD, and CCL19—were selected, and a prognostic model was established. The model demonstrated robust performance upon evaluation and validation, with the nomogram confirming its strong predictive ability. Notably, the prognostic genes were found to influence pathways such as the cell cycle and EGFR ligands, as well as immune cells like activated CD4 T cells. Additionally, drugs like AUY922 and AZ628 showed considerable potential in treating BC. RT-qPCR results for these four genes in clinical samples aligned with the bioinformatics findings.ConclusionThis study identified and validated four prognostic genes—ZIC2, CD24, CEBPD, and CCL19—that are associated with BC and may provide novel targets for diagnostic and therapeutic strategies. creator: Chen Liu creator: Tuo Zhang creator: Fushen Luo creator: Xiaofeng Yang creator: Yadong Li creator: Tonghui Yi creator: Shuang Wu creator: Yanbing Wang creator: Yueping Zhu creator: Kun Zhao uri: https://doi.org/10.7717/peerj.19890 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Role of pyroptosis in pregnancy-related diseases link: https://peerj.com/articles/19922 last-modified: 2025-08-26 description: Pyroptosis, a form of programmed cell death characterized by inflammasome-mediated cellular swelling and membrane perforation. This pathway is involved in diverse pathophysiological processes, including inflammatory diseases and tumors. Notably, the role of pyroptosis in pregnancy-related diseases such as preeclampsia, recurrent spontaneous abortion, neonatal developmental dysplasia, preterm birth, and gestational diabetes mellitus has not been elucidated yet. This review aims to systematically dissect the molecular basis of pyroptosis in pregnancy-related diseases and summarize emerging therapeutic strategies targeting pyroptosis and inflammasomes. We first outline the mechanistic link between pyroptosis, inflammasome activation, and maternal-fetal immune regulation. Subsequent sections focus on the putative roles of pyroptotic pathways in the pathogenesis of major pregnancy complications, integrating recent findings from preclinical and clinical studies. Elucidating pyroptosis-mediated mechanisms may pave the way for developing targeted therapies to improve outcomes in pregnancy-related diseases. creator: Wanlu Li creator: Rui Zheng creator: Chaoqun Shi creator: Deqing Chen creator: Yixin Sun creator: Bo Hu creator: Guangtao Xu uri: https://doi.org/10.7717/peerj.19922 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Li et al. title: Exploration of gray matter alterations and cognitive function impairment in adolescents with first-episode non-suicidal self-injury and the associations with self-injury characteristics link: https://peerj.com/articles/19914 last-modified: 2025-08-26 description: BackgroundIt remains unclear if there are potentially associated abnormalities in gray matter (GM) and cognitive function in adolescents with non-suicidal self-injury (NSSI), and if there are associations with self-injury characteristics. Therefore, exploring the alterations in GM and cognitive functions and their associations with self-injury characteristics in adolescents with first-episode NSSI can provide imaging and clinical evidence for understanding the pathogenesis of NSSI.MethodsIn this cross-sectional study, we prospectively collected 29 adolescents (NSSI group) with first-episode NSSI and 28 healthy controls (HC group). Participants were scanned using a 3.0T MRI scanner. GM measures were extracted and compared between the NSSI group and the HC group using covariance analysis with total intracranial volume, age, sex, and years of education as covariates. Evaluate the cognitive functions of two groups and perform covariance analysis with years of education, age, and sex as covariates. The assessment of self-injury function was conducted using the Beck Scale for Suicide Ideation and the Ottawa Self-Injury Inventory. With years of education as the control variable, partial correlation analysis is carried out between GM volume (GMV) and cognitive functions. A mediation effect analysis was conducted on GMV, cognitive function, and NSSI to explore the relationships among them.ResultsThe cognitive functions of the NSSI group are poorer than those of the HC group. Compared with the HC group, the NSSI group had decreased GMV in the left putamen and left nucleus accumbens and an increased GMV in the left rostral anterior cingulate cortex. In the NSSI group, the self-injury characteristics and poorer cognitive function are associated with abnormal alternations in GMV, and the poorer cognitive functions are also associated with the self-injury characteristics. The mediation analysis showed that the volume of the left rostral anterior cingulate cortex played a partial mediating role in the relationship between NSSI behavior and cognitive decline. creator: Rui Yu creator: Kaike Liao creator: Yuwei Chen creator: Xinyue Chen creator: Shiji Peng creator: Xianfu Li creator: Nian Liu uri: https://doi.org/10.7717/peerj.19914 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yu et al. title: Longitudinal changes in estimated glomerular filtration rates in chronic hepatitis B patients treated with Tenofovir Alafenamide vs Entecavir link: https://peerj.com/articles/19901 last-modified: 2025-08-26 description: BackgroundFor individuals with chronic hepatitis B (CHB) at higher risk of nephrotoxicity, entecavir (ETV) and tenofovir alafenamide (TAF) are recommended antiviral options. This study aimed to investigate kidney safety among treatment-naïve individuals with CHB receiving TAF versus ETV.MethodTreatment-naïve individuals with CHB receiving either TAF or ETV from July 2019 to December 2020 were included. Follow-up data on estimated glomerular filtration rates (eGFR) were collected. Factors related to chronic kidney disease (CKD) development were analyzed by Cox regression analysis. Generalized additive mixed model (GAMM) was employed to investigate temporal eGFR changes and the association between the extent of follow-up eGFR change and antiviral agents.Results466 treatment-naïve individuals with CHB were included, with 296 in the ETV group and 170 in the TAF group. In the subgroup of individuals with a baseline eGFR higher than 90 mL/min/1.73 m2, 13.9% in the ETV group developed CKD, compared to 9.8% in the TAF group (p = 0.304). Multivariable Cox analysis demonstrated that male (hazard ratio (HR) 2.72; 95% confidence interval (CI) [1.02–7.25]; p = 0.045) and baseline eGFR (HR 0.86; 95% CI [0.82–0.90]; p < 0.001) were significantly associate with the CKD development. GAMM revealed that eGFR initially decreased and then stabilized around week 40. Every 12 weeks, the TAF group exhibited an overall lower rate of eGFR decline compared to the ETV group, with an adjusted difference of 0.38 mL/min/1.73 m2 (95% CI [0.11–0.65], p = 0.006). The difference remained significant in males and patients over 35 years old.ConclusionThe kidney safety profile of TAF among treatment-naïve individuals with CHB was comparable to that of ETV, without significant difference in developing CKD. Stratified analyses further revealed that TAF demonstrated superior kidney benefits compared to ETV specifically in males or patients aged over 35 years. creator: Xuan Li creator: Qiang Wu creator: Fang Huang creator: Changxiang Lai creator: Fengjuan Chen creator: Juan Meng creator: Fang Wang creator: Hui Zeng creator: Lina Zhang uri: https://doi.org/10.7717/peerj.19901 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Li et al. title: A closer look at severe acute kidney injury: risk factors and outcomes in PD-1/PD-L1 antibody treatment from a retrospective study link: https://peerj.com/articles/19886 last-modified: 2025-08-26 description: BackgroundImmune checkpoint inhibitors (ICIs) have improved cancer survival but increase the risk of adverse events, including acute kidney injury (AKI). Severe AKI, though rare, can disrupt treatment and worsen outcomes. Yet, research on risk factors for severe AKI in patients on PD-1/PD-L1 therapies is limited. This study aimed to identify these risk factors.MethodsThis retrospective cohort study analyzed electronic medical records from Zhejiang Provincial People’s Hospital from January 2019 to July 2023. In total, 907 patients who met the inclusion criteria, with a median age of 64 years, were included in the analysis. Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression analyses were conducted to determine independent risk factors for severe AKI.ResultsSevere AKI was observed in 3.2% of patients with AKI, with a significantly higher mortality rate than in non-AKI patients (20.7% vs. 4.1%) during the follow-up period. Multivariate Cox regression analysis identified elevated gamma-glutamyl transferase (hazard ratio (HR): 1.17), diuretic use (HR: 3.61), nonsteroidal anti-inflammatory drug (NSAID) use (HR: 4.58), and cytotoxic drugs (HR: 5.04) as independent risk factors for severe AKI. Only 11 patients (37.5%) with severe AKI recovered.ConclusionsThis study highlights the importance of monitoring these factors to reduce the risk of severe AKI in patients receiving PD-1/PD-L1 antibody therapy. creator: Yuemeng Wu creator: Lingfan Luo creator: Xin Sun creator: Xiaolan Ye creator: Yan Ren creator: Wei Zhang creator: Shuangshan Bu creator: Yiwen Li creator: Bin Zhu creator: Lina Shao uri: https://doi.org/10.7717/peerj.19886 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wu et al. title: Intraocular pressure responses during maximal and submaximal handgrip strength tasks in primary open-angle glaucoma patients and healthy individuals link: https://peerj.com/articles/19845 last-modified: 2025-08-26 description: BackgroundThis study aimed to compare intraocular pressure (IOP) responses during isometric handgrip strength tasks between primary open-angle glaucoma patients and healthy individuals.MethodsForty older adults participated: 21 glaucoma patients and 19 controls. Participants randomly performed four trials at two intensities, maximal and submaximal (at 50% of self-perceived maximal effort), with two trials per hand (one for the left eye and one for the right eye). IOP was measured immediately before exercise, during exercise, and 5 seconds post-recovery. A four-factor mixed ANOVA was used to analyze IOP responses, with task intensity and time of measurement as within-subject factors, and group (glaucoma vs. control) and sex as the between-subjects factors.ResultsIOP responses were comparable between glaucoma patients and healthy individuals, as the main effect of group (p = 0.117) and its interactions did not reach statistical significance. The main effect of time reached statistical significance (p = 0.016) due to greater IOP values during the task (17.3 ± 3.7 mmHg) compared to pre-exercise (16.3 ± 3.2 mmHg: p < 0.001), but post-exercise IOP (16.9 ± 4.1 mmHg) was not significantly different from pre-exercise (p = 0.334) or during exercise (p = 0.727). Greater IOP values were observed for the maximal task compared to the submaximal task (p = 0.001), with no differences between men and women (p = 0.699).ConclusionSubmaximal isometric strength training is a safe option for glaucoma patients treated with hypotensive eye drops. creator: Cristina González-Hernández creator: Maria Dolores Morenas-Aguilar creator: Beatriz Redondo creator: Danica Janicijevic creator: María José López-Gómez creator: Jesus Vera creator: Amador García-Ramos uri: https://doi.org/10.7717/peerj.19845 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 González-Hernández et al. title: Diurnal moths have larger hearing organs: evidence from comparative 3D morphometric study on geometrid moths link: https://peerj.com/articles/19834 last-modified: 2025-08-26 description: Tympanal organs, crucial for anti-bat defence in moths and key for taxonomy, are often overlooked due to their fragility during dissection. Using micro-CT, we analyzed the tympanal organs of 19 geometrid species, comparing diurnal and nocturnal species to understand how predators, like bats and diurnal birds or lizards, influence tympanal morphology and its allometric relationship with body size. We hypothesized that diurnal moths, with reduced anti-bat function, would have smaller tympanal organs, irrespective of body size. Allometry was tested using phylogenetic linear regression and tympanal volume was compared across diurnal and nocturnal moths relative to the abdominal volume. We used 3D geometric morphometry, followed by comparative analysis of the shape and size of ansa, a unique “mechanical” structure for geometrids. Contrary to our hypothesis, diurnal moths had significantly larger tympanal organs, with no allometric relationship with body size. Although activity patterns had no significant effect on ansa shape and size, convergence in shape among nocturnal species, suggests a possible auditory function. This study explores how daily activity patterns and predator-prey interactions may influence sensory adaptations, with larger tympanal organs of diurnal species potentially reflecting adaptations to detect lower, “non-bat” frequencies. It also highlights non-invasive imaging techniques for studying delicate anatomical features in museum specimens. creator: Pritha Dey creator: Max Söderholm creator: Pasi Sihvonen uri: https://doi.org/10.7717/peerj.19834 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dey et al. title: Exploring telerehabilitation awareness, application, and future outlook in sports rehabilitation among physiotherapy students: a web-based survey link: https://peerj.com/articles/19829 last-modified: 2025-08-26 description: Telerehabilitation is rapidly transforming the landscape of sports rehabilitation, with benefits for both recreational and elite athletes. The present study explores physiotherapy students’ awareness, application, and perspectives on sports telerehabilitation. It also investigates the feasibility of incorporating telerehabilitation into physiotherapy education by examining infrastructure requirements, available resources, and student willingness. To gain insight, we conducted a global survey that yielded 524 responses from physiotherapy students. The study used a 42-item validated, self-designed questionnaire, focusing on four key aspects: screening, awareness, application, and future outlook. The results demonstrated that 65.3% of the students were familiar with the concept of telerehabilitation. However, only 19.3% had taken it as part of their formal curriculum. The most common sources of knowledge gained are social media (22.5%) and research articles (19.8%). Notably, 59.4% expressed a strong desire to include telerehabilitation in their studies, highlighting the demand for structured training. In terms of awareness, 50.3% demonstrated a moderate level, while 32.5% showed high understanding. Regarding practical implementation, 36.5% reported moderate competency, while 47.7% displayed high application knowledge. Looking ahead, 34.2% had a moderate outlook on the future of sports telerehabilitation. Meanwhile, 49.4% were highly optimistic about the role of sports telerehabilitation in physiotherapy. creator: Vinodhkumar Ramalingam creator: Jeevarathinam Thirumalai creator: Ling Shing Wong creator: Rajkumar Krishnan Vasanthi creator: Vinosh Kumar Purushothaman creator: Prathap Suganthirababu creator: Buvanesh Annadurai uri: https://doi.org/10.7717/peerj.19829 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ramalingam et al. title: Reverse transcription recombinase polymerase amplification-lateral flow assay for detection of pathogenic orthoflaviviruses in mosquito vectors link: https://peerj.com/articles/19820 last-modified: 2025-08-26 description: BackgroundThe genus Orthoflavivirus primarily consists of arthropod-borne viruses capable of infecting vertebrate hosts and causing serious human diseases such as dengue fever, Zika fever, Japanese encephalitis, West Nile fever, and yellow fever. This study describes the development of a simple and field-deployable detection system for multiple pathogenic orthoflavivirus species using the recombinase polymerase amplification (RPA) technique.MethodsSeveral previously published broad-specific primers targeting the genus Orthoflavivirus were evaluated. A new primer pair, FlaviPath-F and FlaviPath-R, was designed and tested for its applicability in an RPA assay. The RPA protocol was experimentally optimized, with a focus on determining the assay’s sensitivity and assessing the primers’ specificity against pathogenic orthoflaviviruses.ResultsThe primer FlaviPath-F and FlaviPath-R targeted 36% of the selected pathogenic orthoflavivirus species without cross-reacting with non-pathogenic strains based on in silico analysis. The RPA assay successfully amplified DNA oligonucleotides from dengue virus, Japanese encephalitis virus, Zika virus, and West Nile virus. Furthermore, positive amplification was observed in RNA samples extracted from mosquitoes infected with dengue and Zika viruses. The RPA assay demonstrated high sensitivity, with the potential to detect as few as a single viral RNA copy, although confirmation is needed for concentrations below the detection limit of 104 RNA copies.DiscussionThis is the first study to develop an RPA-based method for the detection of multiple orthoflavivirus pathogens in mosquito vectors. The reverse transcription recombinase polymerase amplification assays with lateral flow dipsticks (RT-RPA-LFD) platform offers a rapid, cost-effective tool for identifying regions at risk of arboviral transmission, supporting the targeting of individual viral diseases. This technique holds promise as an early warning system for emerging arboviral threats in public health. creator: Parinda Thayanukul creator: Ronald Enrique Morales Vargas creator: Konkamon Sujijun creator: Pimchanok Khumpeera creator: Kittiya Suksawat creator: Nahallage Dona Asha Dilrukshi Wijegunawardana creator: Patsamon Rijiravanich creator: Werasak Surareungchai creator: Pattamaporn Kittayapong uri: https://doi.org/10.7717/peerj.19820 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Thayanukul et al. title: No pump, no problem: evaluating passive eDNA sampling for marine biomonitoring of a nuisance macroalga link: https://peerj.com/articles/19939 last-modified: 2025-08-25 description: Efficient detection and management of non-indigenous species are critical for mitigating their ecological impacts. Environmental DNA (eDNA) techniques have transformed biodiversity monitoring by enabling sensitive and cost-effective surveys. This study compares the efficacy of passive eDNA samplers (PEDS) to conventional active filtration methods for detecting the cryptogenic macroalga Chondria tumulosa within the Papahānaumokuākea Marine National Monument, Hawaiʻi, USA. Three components of the species-specific eDNA assay were evaluated: clinical sensitivity, DNA yield, and overall performance. Site-level detection sensitivity of 15-minute PEDS deployments matched that of 2-L active filtration, with both methods detecting C. tumulosa in all cases where it was known to present. Site-occupancy models provided a robust framework for evaluating overall performance, offering critical insights into the tradeoffs of PEDS for detecting rare taxa. The success of PEDS is largely dependent on the increased number of qPCR replicates employed in this study compared to the previously developed eDNA assay for C. tumulosa. Passive method performance resulted in lower qPCR detection rates with higher probabilities of false-positives and false-negatives. Model estimates for C. tumulosa eDNA occupancy were similar between PEDS affixed to stationary buoys and PEDS attached to roving SCUBA divers. There was, however, a decrease in the eDNA capture rate among samples collected while on SCUBA. We also tested two passive membrane types—research-grade mixed cellulose ester filters and low-cost cotton rounds. The absorbent cotton rounds yielded greater target eDNA yields and were more reliable for inferring the presence of C. tumulosa. However, DNA yields from PEDS were consistently lower than actively filtered samples, indicating the importance of optimizing sampling and processing protocols to balance erroneous detections. Despite these limitations, passive sampling successfully detected C. tumulosa at low abundances (<1%), demonstrating its utility for uncovering cryptic taxa. PEDS are a cost-effective, versatile, and scalable alternative to active filtration, particularly in remote or resource-limited settings. creator: Patrick K. Nichols creator: Peter B. Marko uri: https://doi.org/10.7717/peerj.19939 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nichols and Marko title: Utilizing E-nose for detection of mealybug infestation and ripeness of durian link: https://peerj.com/articles/19936 last-modified: 2025-08-25 description: BackgroundMealybugs are major pests that cause sap loss and can significantly reduce the quality and market value of durian fruits. Early detection is essential for effective pest management. This study explores the impact of mealybug infestation on volatile emissions and evaluates the application of a low-cost electronic nose (E-nose) system for early infestation detection and ripeness monitoring.MethodsA prototype electronic nose (E-nose), equipped with four Grove Multichannel Gas Sensor V2 (GM) series sensors selected from a sensitivity survey of 13 sensors, was developed and tested on “Monthong” and “Kradum Thong” durians under outdoor and indoor conditions. Fruit odor signals were analyzed, and linear discriminant analysis (LDA) was used to assess classification performance.ResultsThe E-nose effectively differentiated odor profiles between infested and uninfested fruits and ripeness stages. Infested fruits exhibited a different trend of odor changes during ripening, likely due to stress-induced physiological responses.DiscussionThis is the first study demonstrating the use of an E-nose for durian pest detection and ripeness monitoring. The E-nose shows strong potential as a cost-effective, non-destructive tool for early pest detection and postharvest quality control. Future work will focus on scaling the technology with robotic platforms for large-scale monitoring in farms and storage facilities. creator: Chun-I Chiu creator: Thanchanok Yosen creator: Supatchaya Nampila creator: Jetsada Posom creator: Piyawan Suttiprapan creator: Yuwatida Sripontan uri: https://doi.org/10.7717/peerj.19936 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chiu et al. title: Ultra-processed food consumption is linked to quality of life and mental distress among university students link: https://peerj.com/articles/19931 last-modified: 2025-08-25 description: BackgroundUltra-processed foods (UPFs) are industrial formulations that typically contain little or no whole foods and are often high in added sugars, unhealthy fats, and sodium. Research indicates that higher intake of UPFs correlates with lower overall diet quality, which can exacerbate mental health issues such as anxiety and depression. This study aimed to assess the associations between UPF consumption with health-related quality of life, and mental distress in university students.MethodThis cross-sectional study consisted of 595 students resident in Samsun/Türkiye. The data were collected face-to-face with a questionnaire. Linear regression analysis was conducted to examine the relationship between the UPFs (% energy), health-related quality of life components and mental distress score (MDS). Receiver operating characteristic (ROC) analysis was conducted to establish the optimal threshold levels regarding physical component summary (PCS12), mental component summary (MCS12) and MDS.ResultsThe UPF ratios were negatively related to PCS12 (β = −0.112, p = 0.005) and positively associated with MDS (β = 0.102, p = 0.002) after adjusting for age, sex, physical activity, smoking duration, number of cigarettes and chronic disease. ROC analysis showed that those with UPF consumption above 45.096% had low physical quality of life, those above 50.999% had low mental quality of life, and those above 40.250% had moderate-to-high mental distress.ConclusionIncreased consumption of UPFs is associated with a decrease in physical quality of life and an increase in mental distress. Consuming more than 40% from UPFs can lead to mental and physical problems. There is a need for strategies to decrease the intake of UPFs to enhance both physical and mental wellbeing. creator: Yasemin Ertaş Öztürk creator: Zeynep Uzdil uri: https://doi.org/10.7717/peerj.19931 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ertaş Öztürk and Uzdil title: Impact of fructooligosaccharides on gut microbiota composition and metabolite production: implications for childhood obesity link: https://peerj.com/articles/19894 last-modified: 2025-08-25 description: BackgroundContemporary dietary habits in children have been linked to various health issues, particularly the increasing prevalence of childhood obesity. However, the complex relationship between children’s diets, gut microbiota, and health outcomes remains incompletely understood. This study investigates the effects of fructooligosaccharides (FOS) on gut microbiota composition and metabolic processes in children, and explores their potential impact on pediatric health outcomes such as obesity and metabolic disorders.MethodsFecal samples from 39 children (19 boys, 20 girls) aged 6–15 were subjected to in vitro fermentation with or without FOS supplementation. Bacterial composition, short-chain fatty acid (SCFA) production, and gas generation were analyzed. Potential biomarkers and associations between gut microbiota, metabolites, and metabolic pathways were identified using Random Forest algorithms and the MetOrigin cloud platform.ResultsFOS supplementation significantly altered the β-diversity of the gut microbiota, increasing the abundance of Bifidobacterium and Lactobacillus, while decreasing Escherichia-Shigella and Bacteroides. FOS also led to a significant increase in SCFA levels, particularly acetic acid, which correlated positively with Bifidobacterium and negatively with Streptococcus. Conversely, gas production (NH3, H2, and H2S) decreased significantly and showed a positive correlation with Escherichia-Shigella and a negative correlation with Bifidobacterium.ConclusionsThis study highlights changes in microbial structure, metabolite production, potential biomarkers, and altered metabolic pathways following FOS intervention. These findings provide valuable insights into the complex relationship between diet and gut microbiota in obese children and suggest that dietary interventions may influence pediatric health through modulation of the gut microbiome. creator: CanFeng Mo creator: Shan Zhou creator: Zhi Du creator: Xiangxin Huang uri: https://doi.org/10.7717/peerj.19894 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mo et al. title: Antimicrobial resistance and plasmid-associated virulence genes in Salmonella isolated from pigs, pork, and humans in border provinces of Thailand and neighboring countries link: https://peerj.com/articles/19884 last-modified: 2025-08-25 description: In Southeast Asia, most antimicrobial resistance (AMR) data on Salmonella have been generated at the phenotypic level, while insights into the genetic characteristics of AMR and virulence genes remain limited. This study aimed to further characterize AMR Salmonella isolates carrying plasmid-associated virulence genes in Thailand and neighboring countries. A total of 366 Salmonella isolates were collected from pigs (n = 265), pork (n = 69), and humans (n = 32) across Thailand, Lao People’s Democratic Republic, Cambodia, and Myanmar. Overall, 69.40% (n = 254/366) were multidrug resistant, including resistance to medically important antimicrobials tigecycline, azithromycin, colistin and ciprofloxacin. Whole genome sequencing analysis revealed that five Salmonella Enteritidis ST11 clinical isolates from different patients in different provinces carried IncFIB/IncFII plasmids with plasmid-associated virulence genes (spvBCD, pefABCD, rck, and mig-5), of which three of them (SA615, SA616 and SA617) additionally harbored IncX1 plasmid carrying blaTEM-135. Virulence plasmids (pSEVTs) exhibited a close relationship with the pSLT of Salmonella Typhimurium LT2 except for two absent segments (PSLT056-PSLT057-PSLT059 PSLT060-PSLT061-PSLT062-PSLT063-064-ssB-PSLT067) and (traR-traC-trabI-traW-traU trbC-traN-trbE-traF-traQ-traQ-trbB-traH-traD-traH-traI-traX) as well as two invert regions, R1 (locus tag PSLT001 to repA2) and R2 (PSLT025 to finO with deleted tra) in pSEVTs. None of the plasmids were horizontally transferred under ampicillin selective pressure. Phylogenetic analysis of whole genome sequence and virulence plasmids revealed the clonal dissemination of the isolates. The co-existence of virulence and resistance plasmids may complicate antibiotic therapy, highlighting the need to monitor plasmid-associated virulence genes alongside AMR genes in surveillance programs for humans and animals. creator: Siraphatson Wetchasirigul creator: Jiratchaya Puangseree creator: Sunpetch Angkititrakul creator: Rangsiya Prathan creator: Songsak Srisanga creator: Rungtip Chuanchuen uri: https://doi.org/10.7717/peerj.19884 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wetchasirigul et al. title: Internal and marginal fit of digitally fabricated all-ceramic crowns with auxiliary retentive features on short clinical abutments: a micro-CT study link: https://peerj.com/articles/19813 last-modified: 2025-08-25 description: BackgroundShort clinical crowns/abutments (SCC) pose a challenge in achieving adequate retention. Auxiliary retentive features (ARF), such as grooves, are commonly employed to enhance retention. The marginal gap (MG) and internal fit (IF) of restorations are critical factors influencing clinical success. This study aimed to evaluate the MG, IF, and cement volume of digitally fabricated (computer-aided design (CAD) and computer-aided manufacturing (CAM)) all-ceramic crowns with and without grooves on SCC using micro-computed tomography (micro-CT).MethodsA mandibular second molar typodont tooth was prepared to simulate SCC. Four groups of crowns (n = 30 per group) were fabricated: Group 1: CAD/CAM zirconia without grooves, Group 2: CAD/CAM zirconia with grooves, Group 3: CAD/CAM lithium disilicate with grooves, Group 4: Conventional lithium disilicate with grooves. Crowns were cemented using resin cement. MG, IF, and cement volume were evaluated using micro-CT. Gap measurements were taken in two planes across seven zones (Z1 to Z7). Statistical analysis was performed using one-way ANOVA and post hoc Tukey tests.ResultsSignificant differences in MG and IF were observed among the groups (p < 0.001). Group 1 exhibited the lowest MG and IF, followed by Group 3, Group 2, and Group 4. Group 4 showed the highest average marginal discrepancy (AMD) and average wall discrepancy (AWD) ((AMD: Z1 = 197.36 ± 10.56 µm; Z7 = 226.5 ± 8.24 µm), (AWD: Z2 = 150.05 ± 10.89 µm; Z6 = 169.38 ± 10.57 µm)), followed by Group 2 > Group 3 > Group 1. The greatest discrepancy at the cuspal area was observed in Group 2, followed by Group 3 > Group 1 > Group 4. In the central fossa, the maximum discrepancy was also noted in Group 2 (CFD = 194.48 ± 13.71 µm). No significant differences were found in total cement space volume among the groups.ConclusionCAD/CAM crowns with grooves demonstrated clinically acceptable MG and IF values, with lithium disilicate crowns showing superior performance. These findings support the use of CAD/CAM technology for SCC restorations and underscore the importance of material selection and crown design for optimal clinical outcomes. creator: Saeed M. Alqahtani creator: Saurabh Chaturvedi creator: Mohamed Khaled Addas creator: Nasser M. Alqahtani creator: Mohammad A. Zarbah creator: Mohammed Hussain Dafer Al Wadei creator: Feras Ali Alsaeed creator: Yasir Saad AlJaadan creator: Ali Abdullah Ali Alqahtani creator: Mohammed Abdullah Al Mansooi creator: Mudita Chaturvedi uri: https://doi.org/10.7717/peerj.19813 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alqahtani et al. title: Growth, mortality, and exploitation of Saurida lessepsianus Russell, Golani & Tikochinski, 2015, from a southern Aegean Sea small-scale fishery: a stock assessment for sustainable fisheries link: https://peerj.com/articles/19955 last-modified: 2025-08-22 description: This study aimed to determine the stock assessment and growth parameters of Saurida lessepsianus in the southern Aegean Sea. The length frequency distribution of the specimens varied between 11.1 and 38.5 cm. It was determined that females, males, and all individuals had positive allometric growth. The estimated growth parameters L, K, t0, and growth performance index (Ø′) were 58.6 cm, 0.141 year −1, −1.01 years, and 2.68, respectively. The reproduction period continued from April to August. The length at which 50% of the fish population reaches sexual maturity (Lm50) for females was calculated as 19.04 cm. The total mortality (Z), natural mortality (M), and fishing mortality (F) of S. lessepsianus in the southern Aegean Sea were determined to be 0.39, 0.24, and 0.15, respectively. The exploitation rate (E) was estimated at 0.37. The present biomass was calculated to be 183.24 tons for Fcurr (0.15). Maximum sustainable yield (MSY) was 820.07 tons, corresponding to F 2.2. It has been concluded that the stocks of S. lessepsianus are not overexploited. Fcurr may be increased to 2/3 (F = 0.6, yield = 546.6 tons) of the fishing level of 2.2 for MSY. creator: İsmail Reis creator: Celal Ateş uri: https://doi.org/10.7717/peerj.19955 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Reis and Ateş title: Significance of the inflammatory-immune-nutritional (IINS) score on postoperative survival and recurrence in breast cancer patients: a retrospective study link: https://peerj.com/articles/19950 last-modified: 2025-08-22 description: PurposeInflammation, immune system and nutritional status contribute significantly to tumorigenesis, progression and metastasis. The aim of this study was to evaluate the significance of the inflammation-immune-nutritional score (IINS) on postoperative survival and recurrence in breast cancer patients and to analyze and compare the IINS, platelet-to-lymphocyte ratio (PLR), and the prognostic nutritional index (PNI) in terms of progression-free survival (PFS) and overall survival (OS) in patients with breast cancer (BC) who underwent surgical treatment prognostic value.MethodsWe executed a retrospective investigation of the clinical information and related materials of 200 female breast cancer patients who had their first breast cancer operation at the Affiliated Hospital of Jiangnan University between January 2017 and December 2018, and the IINS was built using the sum of preoperative categorical scores for high-sensitivity C-reactive protein (hs-CRP), lymphocytes (LYM), and albumin (ALB). In our survival analysis, we graphed the survival curves employing the Kaplan-Meier method. The effectiveness of pre-operative IINS, PLR, and PNI in PFS and OS of breast cancer patients were evaluated with receiver operating characteristic (ROC) curves and Cox proportional risk regression analyses.ResultsThe median age of the patients was 55.5 years (range 34–75 years). In progression-free survival, the areas under the IINS, PLR, and PNI curves were as follows: IINS: 0.735, HR (95% CI) 0.037 [0.662–0.809], PLR: 0.724, HR (95% CI) 0.036 [0.655–0.794], PNI: 0.694, HR (95% CI) 0.038 [0.619–0.769]. In overall survival, the areas under the curves of IINS, PLR, and PNI were as follows: IINS: 0.738, HR (95% CI) 0.049 [0.642–0.834], PLR: 0.700, HR (95% CI) 0.039 [0.623–0.777], and PNI: 0.713 with HR (95% CI) 0.050 [0.615–0.811]. According to the findings, among patients with resectable breast cancer, preoperative IINS may be the most accurate indicator of both overall survival and progression-free survival.ConclusionIINS may be a dependable marker for predicting postoperative survival in patients with breast cancer, and its prognostic value may be higher than that of traditional markers. creator: Yuan Wang creator: Wenxin Gao creator: Shan Wang creator: Jiajia Zhang creator: Jiaru Zhuang creator: Yibo Wu creator: Xiaoyan Huang creator: Jing He uri: https://doi.org/10.7717/peerj.19950 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Analysis of novel therapeutic targets and construction of a prognostic model for hepatocellular carcinoma link: https://peerj.com/articles/19899 last-modified: 2025-08-22 description: BackgroundThe prognosis of patients with hepatocellular carcinoma (HCC) remains suboptimal due to limited biomarkers. Although ferroptosis and cuproptosis have emerged as promising therapeutic targets, their prognostic significance in HCC remains unclear.MethodsThis study analyzed the expression of ferroptosis- and cuproptosis-related genes associated with survival in HCC, utilizing datasets from The Cancer Genome Atlas and the Gene Expression Omnibus. The impact of clinical factors on patient prognosis was also analyzed. The key findings were validated using the Human Protein Atlas database, quantitative real-time PCR, and Western blot (WB) analyses.ResultsPrognostic modeling identified six ferroptosis-related genes (SLC1A5, SLC7A11, CBS, GABARAPL1, FLT3, and MT3) and three cuproptosis-related genes (ADM, CDKN2A, and GLS) significantly associated with HCC prognosis. A robust risk assessment model was developed with strong predictive power. The inflammatory cell apoptotic process is an immune-related pathway that is commonly enriched by ferroptosis and cuproptosis genes. Immune cell profiling using CIBERSORT revealed significant differences in macrophages, naive B cells, mast cells, monocytes, memory CD4+ T cells, and CD8+ T cells.ConclusionsThis study, for the first time, integrated multi-omics data and experimental verification to establish a prognostic model of HCC based on the ferroptosis gene. It can be used to dynamically monitor HCC using blood tests and provide a new target for personalized immunotherapy. creator: Pengyuan Lei creator: Wenfeng Li creator: Dafei Xie creator: Hua Guan creator: Xin Huang creator: Bo Huang uri: https://doi.org/10.7717/peerj.19899 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lei et al. title: Assessment of upper limb motor control: establishing normative benchmarks for clinical applications link: https://peerj.com/articles/19859 last-modified: 2025-08-22 description: BackgroundThis study presents and validates a methodology for assessing upper limb motor control using quantitative metrics derived from biomechanics and surface electromyography (sEMG). By combining kinematic and neurophysiological measurements, the study establishes normative benchmarks in healthy adults, which can offer a foundation for future clinical applications in populations with neuromotor impairments, which are commonly characterized by spasticity, involuntary coactivation, and restricted range of motion (ROM). A combination of clinical functional scales with the quantitative metrics presented here is expected to enable better evaluation of motor control.Materials and MethodsTwenty healthy adults performed elbow flexion-extension (FE) movements at three controlled speeds (42, 60, and 78 beats per minute (bpm)). The protocol involved recording sEMG signals of the biceps brachii and triceps brachii, with an inertial measurement unit (IMU) sensor, to compute four metrics: the range of motion (ROM), a derived angular velocity, the coactivation coefficient (CC), and muscle synergy. Movements were segmented into acceleration and deceleration phases to enable a phase-specific analysis, with a focus on both agonist and antagonist muscle activity during flexion and extension.ResultsThe results established normative values for each metric, showing alignment with previous results in the literature for healthy motor patterns. ROM values were consistent with the expected ranges for healthy adults ranging between normative values, with the angular velocity increasing proportionally to the speed of movement but showing greater variability at higher speeds. The CC analysis demonstrated distinct phase-dependent activation patterns, with higher values during flexion deceleration due to antagonist muscle stabilization requirements. The muscle synergy metric highlighted a balanced activation of the biceps and triceps, with minor secondary activation of the triceps during flexion to counteract gravitational forces.DiscussionThe results validate the feasibility of this approach for quantifying motor control based on the quantitative metrics presented here. Normative values and the ability to detect changes in ROM, CC, and muscle synergy enhance the diagnostic potential of this approach in terms of identifying spasticity, coordination deficits, or abnormal neuromuscular patterns in clinical populations. This study establishes a comprehensive methodology for evaluating upper limb motor control, based on a combination of kinematic and neurophysiological data. These findings offer a solid foundation for developing advanced diagnostic tools and personalized rehabilitation strategies, with potential applications to conditions such as stroke, cerebral palsy, and other neuromotor impairments. creator: Pablo Martín-Sierra creator: Cristina Sanchez creator: Eloy Urendes creator: Rafael Raya uri: https://doi.org/10.7717/peerj.19859 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Martín-Sierra et al. title: Between a rock and a hard place: experimental assessment of recruitment patterns in a bathyal environment of the Low Arctic link: https://peerj.com/articles/19850 last-modified: 2025-08-22 description: The study of larval transport and recruitment in the deep sea is crucial to the understanding of species distributions, community assembly, and the potential effects of anthropogenic activity and climate change on the maintenance of biodiversity. This study sought to better understand the role of substratum features in deep-sea larval recruitment at high latitudes. Four settlement frames composed of blocks of different substrata (mesh, plastic, stone, and wood) were deployed for 9 to 13 months at bathyal depths in the Labrador Sea (northeastern Canada). Colonial hydrozoans dominated as recruits, with one taxon (family Campanulariidae) colonizing all substratum types across all geographic sites. Other taxa, including arthropods, octocorals, and other anthozoans recruited only onto specific substrata and consistent microhabitats within them. Overall, higher morphospecies and phylum richness characterized the three-dimensional mesh substratum relative to other substratum types, whereas the complex surface area offered by projections in the plastic substratum had higher densities of individuals or colonies for all morphospecies combined. Wood, offered as a single elongated panel, was the most heavily colonized, whereas both mesh and stone hosted morphospecies not found on any other substratum type. Factors such as geographic location, depth, altitude above the sea floor, and orientation/obstruction of the frame, may have modulated recruitment patterns. These results provide foundational knowledge on larval recruitment patterns and early colonization by opportunistic hard-bottom benthic taxa in a poorly-studied region of the Eastern Canadian deep sea. creator: Sophie Wolvin creator: Jean-François Hamel creator: Annie Mercier uri: https://doi.org/10.7717/peerj.19850 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wolvin et al. title: Comparative genome analysis of patulin-producing Penicillium paneum OM1 isolated from pears link: https://peerj.com/articles/19848 last-modified: 2025-08-22 description: BackgroundThe filamentous fungus Penicillium paneum (P. paneum) produces patulin as a toxic secondary metabolite (SM) on apples and pears. Little is known about the biosynthetic gene clusters (BGCs) of SMs, including patulin in P. paneum.MethodsIn this study, we sequenced the whole genome of P. paneum (isolate OM1), a patulin producer isolated from pears, and analyzed the genome sequence to identify its SM BGCs and compare its patulin BGC with those in other patulin-producing strains. In addition, we investigated the genes that encode carbohydrate-active enzymes (CAZymes) in P. paneum OM1, which play important roles in the degradation of plant cell walls, and analyzed the phylogenetic relationships among P. paneum OM1 and other closely related Penicillium species.ResultsThe genome of P. paneum OM1 was estimated to be approximately 27.16 Mb with four chromosomes. Gene Ontology analysis using 7,098 functionally annotated proteins showed that genes involved in fungal defense mechanisms, such as SM biosynthesis, are enriched in the genome of P. paneum OM1. Of the 7,098 functionally annotated proteins from the genome, we identified 370 putative CAZymes. A phylogenetic analysis revealed that P. paneum OM1 has an evolutionarily close relationship with Penicillium chrysogenum (isolate Wisconsin 54-1255, a penicillin-producing strain) and Penicillium digitatum (isolate Pd1, a citrus fruit pathogen). We also identified a total of 33 SM BGCs, including a patulin BGC in P. paneum OM1. Moreover, the functional conservation analyses on all 15 patulin biosynthetic genes showed that each gene in P. paneum OM1 shares a high degree of sequence identity (above 73% identity) at both nucleotide and amino acid levels with the corresponding genes in four other patulin-producing Penicillium strains, while it shares a relatively low degree of identity (0-93%, identity, 0 and 60% as medians for amino acid sequence identity) with those in two non-patulin producing Penicillium species.ConclusionsOur study improves understanding about BGCs of SMs, including patulin in P. paneum OM1, which causes blue mold rot on pome fruits. These data could provide the genetic basis of patulin biosynthesis in P. paneum OM1 to develop effective strategies for reducing patulin contamination on pome fruits. creator: Wencai Zhao creator: Sung-Yong Hong creator: Ae-Son Om uri: https://doi.org/10.7717/peerj.19848 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhao et al. title: Feeding challenges in early infancy: the role of reflexes, muscle tone, and developmental milestones link: https://peerj.com/articles/19777 last-modified: 2025-08-22 description: BackgroundProblems with feeding are widespread in pre-term infants, but they also occur in full-term infants. Feeding skill is the first coordinated function a child acquires, providing him with nutrients and sensory stimulation needed for further proper development. The aim of the retrospective observational case-control study was to observe factors that may influence feeding problems in infants aged 0–3 months. The observed factors included the presence of oral reflexes, the differences in muscle tension, the advancement of motor development, the spontaneous movements, as well as the gestational age, and the pH value of the umbilical cord arterial.MethodsThe study involved 60 infants. The study and the control groups included 30 infants each. Feeding problems were the major inclusion criteria for the study group. The infants’ reflexes were checked, the muscle tone was palpated, the presence of general movements was visually assessed using Prechtl’s method, then the Sensitivity Assessment of the Stomatognathic Complex (SOWKUT) questionnaire and Albert Infant Motor Scale (AIMS) scale were evaluated. Through the perinatal interview with the patient’s parent, information regarding the pH of the umbilical cord arterial value was obtained.ResultsThe study involved 60 infants born between 24 and 41 gestational age (median and standard deviation: 35 ± 4.81). At the time of the study, their postconceptual age was 44 ± 7 weeks. The results showed that infants with problems regarding eating performance have their oral reflexes more often impaired, and their muscles more often show increased symmetrical tension, especially the frontal, orbicularis oris, and masseter muscles. The influence of delayed motor development, sensory hypersensitivity, and early gestational age on the occurrence of feeding problems was observed. No correlation was observed between the umbilical cord arterial’s pH values and the feeding issues.ConclusionsFeeding problems are multifactorial, which implies that infants should be provided with quick intervention and necessary therapy. It will allow the babies to develop correctly and reduce the risk of future problems. creator: Wiktoria Kowalska creator: Maria Tuczyńska creator: Jacek Kwiatkowski creator: Oskar Komisarek creator: Ewa Mojs creator: Mirosław Andrusiewicz creator: Tomasz Szczapa creator: Włodzimierz Samborski creator: Dorota Sikorska creator: Ewa Baum creator: Roksana Malak uri: https://doi.org/10.7717/peerj.19777 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kowalska et al. title: Kinetics of anti-SARS-CoV-2 antibodies and hematological parameters in hospitalized pre-vaccination COVID-19 patients in Peru link: https://peerj.com/articles/19771 last-modified: 2025-08-22 description: BackgroundThe COVID-19 pandemic exposed vulnerabilities in health systems and revealed variations in immune responses across populations worldwide. This study examined the kinetics of IgG and IgM antibodies against S1 and receptor-binding domain (RBD) proteins in hospitalized Peruvian patients prior to vaccination.MethodA total of 157 serological samples were collected from 44 hospitalized COVID-19 patients during Peru’s first wave (August–October 2020) and stored at −80 °C. Anti-SARS-CoV-2 IgG and IgM antibodies were quantified using an in-house ELISA with recombinant Spike S1 and RBD proteins. Statistical analyses—including linear regression, Kaplan-Meier curves, and receiver operating characteristic (ROC) curves—were conducted to evaluate antibody kinetics, clinical correlations, and predictive accuracy.ResultsIgG levels stabilized between days 10 and 15 of hospitalization, while IgM levels declined after day 10, with greater variability observed in severe acute respiratory distress syndrome (ARDS) cases. A significant positive correlation was found between IgG levels and lymphocyte counts (R = 0.37, p < 0.001), and a negative correlation with neutrophil counts (R =  − 0.33, p < 0.01), particularly in severe ARDS non-ICU patients (R =  − 0.34, p < 0.01). Severe ARDS cases also exhibited elevated neutrophil-to-lymphocyte ratios and increased inflammatory biomarkers, such as C-reactive protein and D-dimer, indicating an exacerbated inflammatory response associated with poorer prognosis. Risk factors, including sex and obesity, were linked to higher mortality and increased need for mechanical ventilation. This study contributes to a better understanding of the immune response in COVID-19 and supports the development of predictive models based on immunological and hematological biomarkers. creator: Salyoc Tapia-Rojas creator: Alexis Germán Murillo Carrasco creator: Maria J. Pons creator: Manuel Ugarte-Gil creator: Ana Mayanga-Herrera uri: https://doi.org/10.7717/peerj.19771 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tapia-Rojas et al. title: Prepollination barriers prevent gene flow between co-occurring bat-pollinated bromeliads in a montane forest link: https://peerj.com/articles/19652 last-modified: 2025-08-22 description: BackgroundReproductive isolation mechanisms in flowering plants are fundamental to preserving species’ evolutionary independence and to enabling the local coexistence of closely related species. These reproductive barriers are expected to contribute to maintaining local diversity of highly diverse plant guilds, such as bromeliads in neotropical ecosystems. We evaluated how strong and effective these barriers are by analyzing different mechanisms that act before and after pollination in a guild of four epiphytic bromeliads from the genus Werauhia (Tillandsioideae) pollinated by bats in a Costa Rican montane forest.MethodsWe employed several reproductive isolation indices proposed in the literature to estimate the effect of flowering phenology, floral morphology, interspecific compatibility, production, and viability of hybrid seeds as barriers to gene flow between species pairs.ResultsThe overall reproductive isolation between species was complete or nearly so. We found that temporal isolation due to different flowering schedules between species significantly contributed to preventing interspecific gene flow. However, flowering data from four reproductive seasons showed interannual variation in the intensity of this temporal barrier due to fluctuations in the species’ blooming patterns. For species with overlapping flowering, mechanical isolation caused by differences in flower size and position of reproductive organs was significant, and such differences in flower architecture are thought to influence pollen deposition on different areas of the pollinator’s body. Postpollination barriers showed varying intensity, from full to partial interspecific incompatibility. When hybrid progeny was produced, the number of seeds and their germination capacity were lower compared to progeny from intraspecific crosses.ConclusionsOverall, prepollination mechanisms (phenology and floral design) were of great importance to eliminate pollen transfer between species and, when present, postpollination barriers had a redundant effect. Our results contradict previous reports that suggested a weak effect of premating barriers among bromeliad species. Additional studies involving other pollination guilds are required to gain a better understanding of the prevalence of different reproductive isolation mechanisms in the highly diverse Bromeliaceae family. creator: Stephanie Núñez-Hidalgo creator: Alfredo Cascante-Marín uri: https://doi.org/10.7717/peerj.19652 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Núñez-Hidalgo and Cascante-Marín title: Early radiological adjacent segment changes following L4/5 fusion: a retrospective comparative study of oblique lateral interbody fusion and minimally invasive transforaminal lumbar interbody fusion link: https://peerj.com/articles/19918 last-modified: 2025-08-21 description: BackgroundAdjacent segment disease (ASD) has become one of the most common complications after lumbar interbody fusion. To date, there have been few reports on the radiological effects between oblique lateral interbody fusion (OLIF) and minimally invasive transforaminal lumbar interbody fusion (MIS-TLIF) in lumbar degenerative diseases adjacent to the superior and inferior segments.MethodThe data of patients treated with OLIF or MIS-TLIF due to L4/5 degenerative lumbar diseases from October 2018 to March 2022 were retrospectively analyzed. The anterior disc height (ADH), posterior disc height (PDH), intervertebral foramen height (FH), canal anteroposterior diameter (APD), foraminal area (FA), dural sac area (DSA), disc angle (DA), segmental lordosis angle (SLA), and lumbar lordosis (LL) were compared. The incidences of adjacent segment intervertebral disc degeneration (ADD), adjacent articular facet degeneration (AFD), and adjacent segment disease (ASD) were analyzed. Multiple linear regression analysis was performed on DSA of L3/4, L5/S1, and DA of L5/S1. Clinical assessments were performed using the visual analogue scale (VAS) and Oswestry disability index (ODI).ResultsAt the final follow-up, the Δ SLA, Δ ADH, Δ PDH, Δ FH, Δ FA, and Δ LL of L4/5 in the OLIF group were significantly improved compared with those in the MIS-TLIF group (P < 0.05). The Δ DSA and Δ APD of L3/4 and L5/S1 segments and L5/S1 Δ DA in the OLIF group were improved significantly (P < 0.05). Meanwhile, multiple linear regression analysis showed that Δ L5/S1DA increased with the increase of Δ LL, and decreased with the increment of Δ L5/S1DA (Pre). The incidence of ADD and AFD in L3/4 of the OLIF group was higher than that of the MIS-TLIF group (P < 0.05). The incidence of ASD in the L5/S1 was lower than in the L3/4 level (P < 0.05).ConclusionCompared with MIS-TLIF, OLIF has advantages in improving lumbar sagittal balance, significantly decreasing degeneration of intervertebral discs and facet joints in adjacent segments in the early stage. creator: Lantao Liu creator: Chicheng Ma creator: Lianghai Jiang creator: Longwei Chen creator: Xinpeng Zhou creator: Dechun Wang uri: https://doi.org/10.7717/peerj.19918 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: The relationship between disease activity and quality of life in rheumatoid arthritis patients: a network analysis link: https://peerj.com/articles/19907 last-modified: 2025-08-21 description: BackgroundThe relationship between disease activity and quality of life (QoL) in rheumatoid arthritis (RA) patients was explored using network analysis. The focus of network analysis has recently shifted from studying individual groups to comparing the network structures of different subgroups. RA patients with depressive symptoms generally have lower QoL scores, so we compared the QoL networks of RA patients with and without depressive symptoms to test for differences.MethodsQoL, depressive symptoms, and disease activity were measured using the 36-item Short-Form Health Survey (SF-36), Hospital Anxiety and Depression Scale (HADS), and Disease Activity Score 28 joints (DAS28). A flowchart was drawn to explore the relationship between disease activity and QoL. The RA patients were divided into groups with and without depressive symptoms for network comparison.ResultsA total of 424 patients with RA were included in this study. Disease activity was strongly associated with the PF (physical function) domain (edge weight = 0.237). The results of the network comparisons showed differences between the QoL network structures (M = 0.274, P = 0.029) and some specific edge strengths.ConclusionDisease activity is strongly associated with QoL in RA patients, especially in the domain of PF, and the structure of the QoL network changes in the presence of depressive symptoms in RA patients. creator: Ruo-Wei Ma creator: Lin Zhu creator: Ming-Hui Zhang creator: Cui-E Li creator: Yu-Xuan Zhang creator: Bin-Bin Feng creator: Guo-Cui Wu uri: https://doi.org/10.7717/peerj.19907 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ma et al. title: Evaluating COI and ITS2 dual barcoding for molecular delimitation and taxonomic insights in Arenosetella Wilson, 1932 (Harpacticoida: Ectinosomatidae) along Turkish Coasts link: https://peerj.com/articles/19870 last-modified: 2025-08-21 description: BackgroundAccurate species delimitation is essential in morphologically conservative taxa such as harpacticoid copepods, in which cryptic diversity may go unnoticed without molecular data. The genus Arenosetella, common along the Turkish coastline, comprises two species: Arenosetella germanica and A. lanceorostrata, with overlapping ranges and subtle morphological differences. This study aimed to assess species boundaries and uncover potential hidden diversity within Arenosetella using the dual-marker DNA barcoding approach.MethodsSpecimens of Arenosetella were collected from the Mediterranean, Aegean, and Black Sea coasts of Türkiye. Nuclear DNA from a total of 46 individuals were amplified and sequenced for both mitochondrial cytochrome oxidase I (COI) and nuclear internal transcribed spacer 2 (ITS2) markers. COI sequences were analysed for haplotype diversity, phylogenetic relationship, and species delimitations. ITS2 sequences were subjected to evaluation with regard to nucleotide diversity, secondary structure, and compensatory base changes (CBCs), using both sequence- and structure-based approaches. The concatenated dataset and species tree reconstruction (StarBEAST2) were employed to test gene tree-species tree congruence.ResultsThe COI analyses revealed a high level of haplotype diversity (21 haplotypes) and the presence of three molecular operational taxonomic units (MOTUs) within A. germanica and one MOTU within A. lanceorostrata, consistent with the geographic distribution patterns. ITS2 sequences exhibited relatively more conservation with nine haplotypes. These sequences revealed informative structural variation, including CBCs among candidate species. The species delimitation approaches reliably supported the identification of four to seven MOTUs, which corresponded to geographic populations. The analyses of the concatenated dataset supported four well-supported candidate species, and yielded congruent species trees, with high posterior probabilities. Morphological comparisons among MOTUs revealed subtle differences in female P5 structure and anal somite ornamentation among A. germanica lineages, while A. lanceorostrata MOTUs were morphologically indistinguishable.ConclusionThis study provides the first integrative application of COI and ITS2 barcoding in Arenosetella and within Harpacticoida overall, combining DNA sequences and structure, and morphological data for species delimitation. The results demonstrate that COI is effective for detecting geographic differentiation and haplotype diversity, whereas ITS2 contributes structural resolution and potential markers of reproductive isolation through CBCs. These findings suggest the presence of a species complex within A. germanica and confirm the distinct status of A. lanceorostrata. Dual-marker barcoding, particularly incorporating ITS2 secondary structure, represents a valuable tool for taxonomic studies in morphologically conservative copepod groups. creator: Dilara Bakmaz creator: Serdar Sönmez creator: Ertan Mahir Korkmaz uri: https://doi.org/10.7717/peerj.19870 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bakmaz et al. title: Effect of temperatures on some biological parameters of Aphis craccivora Koch (Hemiptera: Aphididae) on lentil link: https://peerj.com/articles/19865 last-modified: 2025-08-21 description: Aphis craccivora Koch (Hemiptera: Aphididae) is one of the aphid species known to cause economically important damage in lentil fields. Temperature effects on the developmental period, age stage, stage-specific survival, and reproductive capacity of A. craccivora were studied on lentil under laboratory conditions at four fixed temperatures (22.5, 25, 27.5, and 30 °C). As a result of the study, the developmental periods of nymphal stages of A. craccivora were determined as 26.04, 17.24, 23.98 and 26.74 degree days, respectively. A. craccivora had the longest pre-adult developmental period at 22.5 °C, the shortest developmental period at 27.5 °C, the highest productivity value was found as 62.74 at 25 °C, and the lowest value was found as 11.28 at 30 °C. In the study, the shortest preimaginal phases of development period, the longest individual lifespan, and the highest productivity were observed at 25 °C. In the study, the highest intrinsic rate of increase (r) of A. craccivora was 0.36 (day−1), the net reproductive rate (R0) was 63.67 (female/female), finite rate of increase (λ) was 1.43 day−1 and gross reproductive rate (GRR) was 80.88 at 25 °C. The shortest mean generation time (T) value was 8.63 days at 30 °C, while the shortest population doubling time (DT) was observed at 25 °C with 1.93 days. The most suitable temperature for population development was 25 °C for A. craccivora. The role of temperature as a key factor in determining the A. craccivora population on lentil is discussed. creator: Muhlis Sezgin creator: Merve Akyıldız creator: Selime Olmez Bayhan creator: Erol Bayhan uri: https://doi.org/10.7717/peerj.19865 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sezgin et al. title: The effects of soleus fascicle length on muscle fatigability link: https://peerj.com/articles/19842 last-modified: 2025-08-21 description: BackgroundAge-related deficits in Achilles tendon stiffness have been linked to shorter calf muscle operating lengths. These shorter lengths have the potential to precipitate higher requisite excitations and thereby an earlier onset of local fatigability in older adults. However, the connection between calf muscle operating lengths and muscle fatigability has yet to be systematically explored, even in healthy younger adults. Thus, the goal of this study was to establish a mechanistic pathway between soleus fascicle length, prescribed herein using changes in ankle joint angle, and muscle fatigue in a cohort of younger adults.MethodsParticipants performed repeated fixed-end calf muscle contractions to task failure in a computerized robotic dynamometer at two ankle joint angles to prescribe relatively shorter (i.e., 15° plantarflexion (PF15)) and longer (i.e., 15° dorsiflexion (DF15)) soleus fascicle lengths.ResultsOn average, moving from DF15 to PF15 elicited 14% shorter muscle fascicle lengths, a roughly two-fold higher EMG rms amplitude, significant but modest reductions in EMG median frequency, and a 60% reduction in time to task failure (p-values < 0.05). These findings may have clinical relevance for mechanisms associated with higher metabolic costs and increased fatigability among older adults, who often operate their calf muscles at shorter fascicle lengths due to lesser Achilles tendon stiffness. As a roadmap for comparison and hypothesis generation, this study sets the stage for future work in older adults. creator: Anh D. Nguyen creator: Aubrey Gray creator: Gregory Sawicki creator: Jason R. Franz uri: https://doi.org/10.7717/peerj.19842 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Nguyen et al. title: The effects of dance intervention on clinical symptoms and cognitive deficits in hospitalized patients with chronic schizophrenia: a randomized controlled trial link: https://peerj.com/articles/19840 last-modified: 2025-08-21 description: BackgroundSchizophrenia is a severe mental disorder that imposes significant social burdens. Traditional treatmens, however, have limited effectiveness in addressing negative symptoms and cognitive deficits. Recent studies have indicated interventions promoting sensorimotor integration may offer potential benefits for schizophrenia treatment. The current study aimes to investigate the effects of dance training as an intervention for patients with chronic schizophrenia.MethodsThis study recruited 34 individuals with schizophrenia, who were randomly allocated to either a dance intervention group (n = 18) or an aerobic exercise group (n = 14) for a 3-month program including fifty-minute sessions three times per week. Clinical symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS) and Nurses’ Observation Scale for Inpatient Evaluation (NOISE). Cognitive function was evaluated using the MATRICS Consensus Cognitive Battery (MCCB). Meanwhile, physiological indicators were also collected to explore the underlying physiological effects of the dance intervention. All measurements were taken before and after the interventions.ResultsThe PANSS total scores (P < 0.01**), PANSS negative scores (p < 0.001**), NOISE score (p < 0.001**), MCCB cognitive scores, and physiological indicators were significantly changed after the intervention in both groups compared with baseline. Post-hoc analysis revealed notable improvements in the specific cognitive subscales, including the Continuous Operation Test-identical pairs (CPT-IP, p = 0.026*), Hopkins Verbal Learning Test-Revised (HVLT-R, p = 0.019*) and the physiological indicators Cystatin C (CYS-C, p = 0.037*) in the dance intervention group. Additionally, significant correlation were found between PANSS positive score and Total Bilirubin (TBIL) (r = 0.449, p = 0.028*), as well as between CPT-IP and Cystatin C (CYS-C) (r = 0.501, p = 0.008**) were found in both groups.ConclusionWhile both interventions resulted in improvements in clinical symptoms and cognitive function, the dance intervention specifically enhanced attention and verbal memory. Dance and aerobic exercise induced different changes in physiological indicators, which might be the physiological basis for improvements in clinical symptoms and cognitive function. creator: Gujing Li creator: Hui He creator: Kexin Gao creator: Yuanyuan Yu creator: Yayun Liu creator: Tianhuan Li creator: Ping Xi creator: Frank Pollick creator: Jing Lu creator: Lixue Yin creator: Dezhong Yao creator: Mingjun Duan creator: Li Mi creator: Cheng Luo uri: https://doi.org/10.7717/peerj.19840 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Li et al. title: The effects of exercise on oxidative stress MDA and SOD in patients with type 2 diabetes: a systematic review and meta-analysis link: https://peerj.com/articles/19814 last-modified: 2025-08-21 description: ObjectiveSystematic review of the effect of exercise intervention on oxidative stress in patients with type 2 diabetes mellitus (T2DM).MethodsDatabases such as Embase, Web of Science, PubMed, The Cochrane Library, Wanfang, VIP, and China National Knowledge Infrastructure were searched from their inception to June 2024. PEDro was used to assess the quality of the literature, RevMan 5.4.1 and Stata 17.0 were used to perform meta-analysis and publication bias tests, respectively, and GRADEPro was used to evaluate the quality of the evidence for outcome indicators. Standardized mean difference (SMD) and 95% confidence interval (CI) were used as effect measures.ResultsThis study included 11 articles (1,111 patients). The results of the meta-analysis showed that exercise can improve malondialdehyde (MDA), standardized mean difference (SMD) = −1.29, 95% CI [−1.87 to −0.71], P < 0.0001 in patients with T2DM; and improve superoxide dismutase (SOD), SMD = 0.59, 95% CI [0.17–1.01], P = 0.006 in patients with T2DM. Subgroup analysis showed that exercise can improve MDA and SOD in patients aged >60 years. The effect is significant when the intervention method is aerobic exercise and combined exercise. The intervention period should be >12 weeks and intervention frequency <3 days/week. Exercise is more effective in improving MDA, an indicator of oxidative stress, when the intervention method is aerobic exercise, the period is >12 weeks and the frequency is <5 days/week, which improves oxidative stress indicators SOD.DiscussionThis study included 11 articles with an average PEDro score of 6.5, indicating good quality. Subgroup and sensitivity analyses of the oxidative stress indicators MDA and SOD failed to identify sources of heterogeneity, which is a limitation. Publication bias tests for the oxidative stress indicators MDA and SOD suggest that there is no significant publication bias. Therefore, moderate-quality evidence is given to the oxidative stress indicator MDA, and high-quality evidence is given to the oxidative stress indicator SOD. Exercise has a significant effect on improving oxidative stress indicators MDA and SOD in patients with type 2 diabetes. It is affected by the patient’s age, the method, duration, and frequency of the intervention. It can provide evidence-based medical evidence for the clinical rehabilitation of patients with type 2 diabetes. creator: Chen Qiu creator: Shufan Li creator: Shuqi Jia creator: Fen Yu creator: Chen Wei creator: Xing Wang creator: Bo Guo uri: https://doi.org/10.7717/peerj.19814 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Qiu et al. title: Inoculation with Pseudomonas spp. in Solanum lycopersicum increases yield and fruit quality under nutrient shortage conditions link: https://peerj.com/articles/19796 last-modified: 2025-08-21 description: BackgroundGreenhouse tomato cultivation has experienced significant growth in recent years. However, this production system requires high fertilization levels, relying mainly on synthetic agro-inputs. While their use meets the crop’s nutritional demand, they present major limitations. Excessive application reduces absorption efficiency, increases soil salinity, and can contaminate water sources. Additionally, rising global fertilizer costs have made it necessary to seek efficient alternatives with lower contamination risks. In this context, plant growth-promoting rhizobacteria (PGPR) are a viable option to reduce inorganic fertilizer use. These microorganisms enhance nutrient availability and stimulate crop development. For this reason, the ability of five Pseudomonas strains to reduce nitrogen, phosphorus, and calcium-based fertilizers by up to 50% was evaluated in ‘El Cid F1’ tomato cultivation under a hydroponic greenhouse production system. Their performance was analyzed both individually and in consortium.MethodsPreliminary in vitro tests demonstrated that Pseudomonas sp. isolates C13, C14, and C15, Pseudomonas fluorescens C30, and P. putida ACJ14, both individually and consortium could fix nitrogen, solubilize phosphate and biosynthesize indole-3-acetic acid. Greenhouse trials revealed the potential of the Pseudomonas spp. isolates to stimulate vegetative growth while improving fruit quality parameters including firmness, total soluble solids, titratable acidity, and lycopene concentration.ResultsThe P. putida ACJ14 and Pseudomonas sp. C14 isolates significantly increased fruit yield by 54% and 73%, respectively. Lycopene content increased to 132.9 mg/kg of fruit with Pseudomonas ACJ14 and 130.22 mg/kg of fruit with Pseudomonas sp. C14. The consortium showed no significant difference in any parameters compared to individual isolates. All isolates demonstrated rhizosphere persistence for 30 days post-root inoculation.ConclusionsThe results position Pseudomonas spp. isolates C13, C14, C15, P. fluorescens C30, and P. putida ACJ14 as sustainable PGPR alternatives enabling 50% reduction of nitrogen, phosphorus, and calcium fertilization in greenhouse tomatoes. The strain Pseudomonas sp. C14 emerged as particularly effective, demonstrating the highest nitrogen fixation capacity, second highest IAA production, and superior performance in seed germination rates, fruit firmness, and lycopene enhancement. creator: Patricia Torres-Solórzano creator: Homero Reyes-De la Cruz creator: Josué Altamirano-Hernández creator: Lourdes Macías-Rodríguez creator: Jesús Campos-García creator: Alfonso Luna-Cruz uri: https://doi.org/10.7717/peerj.19796 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Torres-Solórzano et al. title: Inflammatory and nutritional indexes as predictors of acute kidney injury in patients with Immunoglobulin A nephropathy: a retrospective study link: https://peerj.com/articles/19917 last-modified: 2025-08-20 description: BackgroundImmunoglobulin A nephropathy (IgAN) patients with acute kidney injury (AKI) have an elevated risk of adverse events and mortality. However, there is currently a lack of convenient and effective clinical tools to predict AKI risk in this population. The present study was conducted to create such tools containing inflammatory and nutritional indexes.MethodData from 720 adults diagnosed with IgAN by renal biopsy at the First Hospital of Jilin University were collected. They were randomly divided into a training set (n = 503) and a test set (n = 217) in a 7:3 ratio. Univariate and multivariate logistic regression analyses with backward selection were used to identify risk factors, resulting in multiple prediction models. The least absolute shrinkage and selection operator (LASSO) regression was used to simplify the model. The models were presented using nomograms, and their performances were evaluated through receiver operating characteristic (ROC) curves, area under the curve (AUC), Hosmer-Lemeshow test, net reclassification improvement (NRI), integrated discrimination improvement (IDI), calibration curves, and clinical decision curve analysis (DCA).ResultsEleven risk factors related to IgAN with AKI were identified, including nephrotic syndrome (NS), T score from the Oxford histological classification, estimated glomerular filtration rate (eGFR), blood urea nitrogen (BUN), 24-hour urinary protein quantification (24h-UPRO), C-reactive protein (CRP), systemic inflammatory response index (SIRI), lymphocyte-to-monocyte ratio (LMR), platelet-to-lymphocyte ratio (PLR), lymphocyte-to-CRP ratio (LCR), and prognostic nutritional index (PNI). These factors contributed to the development of seven prediction models. ROC curves indicated good predictive performance for all models, with the full model performing best. The Hosmer-Lemeshow test showed that six models fit well in the test set. DCA results demonstrated significant clinical benefits for all models.ConclusionCRP, SIRI, LMR, PLR, LCR, and PNI were identified as novel AKI predictors in patients with IgAN. A series of prediction models incorporating these factors were developed for better clinical applicability, with the full model performing the best. creator: Huimin Li creator: Chuyue Qian creator: Jingda Huang creator: Mindan Sun uri: https://doi.org/10.7717/peerj.19917 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Physical and mental effects of different radical prostatectomy techniques on urologic surgeons link: https://peerj.com/articles/19908 last-modified: 2025-08-20 description: ObjectiveIn this web-based international survey study, we aimed to show an association between physical exhaustion and patient, relatives, and employer-related mental stress for surgeons performing open radical prostatectomy (ORP), laparoscopic radical prostatectomy (LRP), and robot-assisted laparoscopic prostatectomy (RALP). Additionally, we also aimed to compare the outcomes of three approaches.MethodsWe sent a ten-question survey to the urologists performing ORP, LRP, and RALP via e-mail and social media. Only fully completed surveys were included in the study analysis. We asked questions about age, the preferred surgical approach for radical prostatectomy, frequency of weekly exercise, and their possible associations with physical exhaustion and musculoskeletal complaints.ResultsA total of 160 urologists completed the survey. The RALP group showed a lower physical exhaustion rate and increased eye strain (p < 0.001) and p = 0.002, respectively). Although walking was the most preferred sports activity, no correlation was found between regular sport or exercise and musculoskeletal complaints (p > 0.05).ConclusionCompared to ORP and LRP, physical exhaustion was lower in the RALP technique. Although the number of participants was limited, regular exercise weakly improved physical exhaustion and musculoskeletal complaints. We believe that regular sports activities by urologists dealing with LRP and RALP will help relieve physical discomfort. creator: Mahmut T. Olcucu creator: Mustafa S. Bolat creator: Kadir Yildirim creator: Yasar Ozgok creator: Theodoros Tokas creator: Ali Gözen uri: https://doi.org/10.7717/peerj.19908 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Olcucu et al. title: Survival prediction in gliomas based on MRI radiomics combined with clinical factors and molecular biomarkers link: https://peerj.com/articles/19906 last-modified: 2025-08-20 description: BackgroundTo investigate the practicability of a radiomics signature combined with clinical factors and molecular biomarkers for predicting overall survival (OS) in glioma patients.MethodsTraining (n = 331) and internal validation (n = 83) sets were retrospectively collected from the Cancer Image Archive/The Cancer Genome Atlas (TCIA/TCGA), and 165 patients from our hospital for an external validation set. The least absolute shrinkage and selection operator (LASSO) was developed to select features. A radiomics model was established for predicting OS based on contrast-enhanced T1-weighted imaging (CE-T1WI) and T2 fluid attenuated inversion recovery (T2FLAIR) images. The risk stratification value of the radiomics signature was explored using Kaplan-Meier survival analysis and the log-rank test. The integrated prediction model with selected clinical factors, molecular biomarkers, and radiomics features was constructed through multivariate Cox regression analysis. Radiomics prognostic performance and benefit were assessed for all cohorts.ResultsThe radiomics signature based on the combined sequences indicated exceptional predictive ability for OS in three cohorts and stratified glioma patients significantly into high-risk and low-risk groups (P < 0.0001). A nomogram incorporating O6-methylguanine-DNA-methyltransferase (MGMT), isocitrate dehydrogenase (IDH), pathological grade, age, and radiomics signature showed excellent evaluation performance and good calibration for predicting OS in the training (C-index = 0.774), internal (C-index = 0.750), and external (C-index = 0.776) validation cohorts.ConclusionThe radiomics signature demonstrates superior predictive performance for OS in glioma patients and significant subgroup risk stratification efficiency. Moreover, the comprehensive model combining clinical factors, molecular biomarkers, and radiomics features further achieves a robust assessment of survival prognosis. creator: Min Hao creator: Junyu Yan creator: Xiaochun Wang creator: Yan Tan creator: Hui Zhang creator: Guoqiang Yang uri: https://doi.org/10.7717/peerj.19906 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hao et al. title: Genome-wide discovery of circulating cell-free DNA methylation signatures for the differential diagnosis of triple-negative breast cancer link: https://peerj.com/articles/19888 last-modified: 2025-08-20 description: BackgroundPreoperative identification of breast cancer (BC) subtypes is essential for optimizing treatment strategies and improving patient outcomes. This study aimed to identify circulating cell-free DNA (cfDNA) methylation signatures to differentiate triple-negative breast cancer (TNBC) from other BC subtypes (non-TNBC).MethodsWe initially performed a genome-wide analysis to identify differentially methylated CpG sites (DMCs; |Δβ| > 0.10 and P < 0.05) between five TNBC and nine non-TNBC tissues using the Infinium HumanMethylationEPIC BeadChip. These DMCs were further validated using large-scale data from the Cancer Genome Atlas (TCGA, n = 774; |Δβ| > 0. 25 and P < 0.05), and only CpG sites with average β values > 0.90 or < 0.10 in white blood cells (GSE50132, n = 233) were retained to minimize potential background methylation interference. Least absolute shrinkage and selection operator (LASSO) regression was applied to select optimal markers. Diagnostic performance was assessed by the area under the receiver operating characteristic curve (AUC), and prognostic value was evaluated using Cox regression analysis. A multiplex digital droplet PCR (mddPCR) assay was developed to simultaneously detect cg06268921 and cg23247845 in cfDNA from TNBC (n = 33) and non-TNBC (n = 80) patients.ResultsWe identified 113 DMCs, of which eight were selected as optimal markers. They effectively discriminated TNBC from non-TNBC tissues. Then an eight-marker diagnostic panel was developed with an AUC of 0.922 in TCGA and 0.875 in GSE69914. Among them, cg06268921 was significantly associated with overall survival (hazard ratio = 0.249, P = 0.044) and disease-free survival (hazard ratio = 0.194, P = 0.015) in the TCGA-TNBC cohort. In the cfDNA cohort, cg06268921 significantly differentiated TNBC from non-TNBC (P < 0.001), and the combination of both markers yielded an AUC of 0.728. The findings demonstrated the potential of methylation signatures as non-invasive diagnostic tools for TNBC. Future research with larger cohorts is warranted. creator: Lijing Gao creator: Yanbing Li creator: Chao Qu creator: Yan Dong creator: Qingzhen Fu creator: Haibo Zhou creator: Ning Zhao creator: Xianyu Zhang creator: Da Pang creator: Yashuang Zhao uri: https://doi.org/10.7717/peerj.19888 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gao et al. title: Transformative insights from transcriptome analysis of colorectal cancer patient tissues: identification of four key prognostic genes link: https://peerj.com/articles/19852 last-modified: 2025-08-20 description: Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide, necessitating accurate and robust predictive approaches to assist oncologists with prognosis prediction and therapeutic decision-making in clinical practice. Here, we aimed to identify key genes involved in colorectal cancer pathology and develop a model for prognosis prediction and guide therapeutic decisions in CRC patients. We profiled 49 matched tumour and normal formalin-fixed paraffin-embedded (FFPE) samples using Affymetrix HGU133-X3P arrays and identified 845 differentially expressed genes (FDR ≤ 0.001, fold change ≥2), predominantly enriched in the extracellular matrix (ECM)-receptor interaction pathway. The integrative analysis of our data with publicly available mRNA and miRNA datasets, including their differentially expressed gene analyses, identified four overexpressed genes in the ECM-receptor interaction pathway as key regulators of human CRC development and progression. These four genes were independently validated for their differential expression and association with prognosis in a newly collected CRC cohort and publicly available datasets. A prognostic risk score was developed using these genes, with patient stages weighted by multivariate Cox regression coefficients to stratify patients into low-risk and high-risk groups, showing significantly poorer overall survival (OS) in the high-risk group. In conclusion, our risk assessment model exhibits strong potential for predicting poor survival and unfavorable clinicopathological features in CRC patients, offering valuable insights for personalised management strategies. creator: Nevin Belder creator: Sulgun Charyyeva creator: Edibe Ece Abaci Oruc creator: Hakiimu Kawalya creator: Namood-e Sahar creator: Nader Omidvar creator: Berna Savas creator: Arzu Ensari creator: Hilal Ozdag uri: https://doi.org/10.7717/peerj.19852 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Belder et al. title: Mechanisms of NLRP3 inflammasome in pathogenesis and progression of inflammation-related gastrointestinal diseases link: https://peerj.com/articles/19828 last-modified: 2025-08-20 description: The inflammasome is a novel component of the innate immune response. It plays a crucial role in the pathogenesis and progression of inflammation-related gastrointestinal diseases. Among various inflammasomes, the NLR family pyrin domain containing 3 (NLRP3) inflammasome is one of the most extensively studied. Increasingly, researchers are exploring its roles and mechanisms, particularly in inflammation-immune-related diseases. As a result, a review paper is demanded to review and summarize the previous and latest studies on the role and mechanisms of NLRP3 inflammasome in pathogenesis and progression of inflammation-related gastrointestinal diseases. This review comprehensively elaborates on the biological characteristics of the NLRP3 inflammasome, including its assembly and activation mechanisms. Additionally, it emphasizes the roles and mechanisms of the NLRP3 inflammasome in common inflammation-related gastrointestinal diseases such as ulcerative colitis, Crohn’s disease, pancreatitis, and non-alcoholic fatty liver disease (NAFLD). Furthermore, the application of NLRP3 inflammasome inhibitors in treating these diseases is discussed. Articles from PubMed and Web of Science on NLRP3 inflammasome, ulcerative colitis, Crohn’s disease, pancreatitis, and NAFLD were summarized to analyze the data and conclusions carefully to ensure the comprehensiveness, completeness, and accuracy of the review. This study aims to provide scholars engaged in research on gastrointestinal diseases with new directions for developing more effective therapeutics for inflammation-related gastrointestinal diseases by investigating the NLRP3 inflammasome’s role in these conditions. creator: Fengmei Liu creator: Bozong Shao creator: Yaqin Zhu creator: Xiaochun Xue creator: Xiaoyan Wu uri: https://doi.org/10.7717/peerj.19828 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Systematic review of electron transfer study in DNA relevant to Parkinson’s disease and scanning tunneling microscopy link: https://peerj.com/articles/19807 last-modified: 2025-08-20 description: BackgroundParkinson’s disease (PD) is the most typical neurological disorder associated with aging in humans. Since PD has much to do with the medical field, most research studies focus on the biological, chemical, and medical aspects of the investigations, in addition to epidemiological studies, drug intervention studies, and much more. The lack of studies using scanning tunneling microscopy (STM) to investigate the electron transfer properties of DNA in PD opens up a new opportunity to look at electron transfer, which is fundamental to understanding the biological processes of the damage-repair mechanism of DNA in this disease, from a physical perspective. Hence, this systematic review was conducted to identify the methods or techniques currently used in the medical-related fields to study electron transfer in PD. related to electron transfer and PD.MethodologyScopus, ScienceDirect, and EBSCOhost MEDLINE databases were used to search for literature related to electron transfer and PD.ResultsFrom the thirty studies identified, PD appears to be caused by various causes, including increased levels of cytochrome c, reactive oxygen species produced by the mitochondria, dysfunction of complex I that interferes with the electron transfer process, and mitochondrial dysfunction triggered by PINK1 mutation. 6.7% of prior research has focused on utilizing DNA as a specific sample for investigating electron transfer in synthetic DNA through the use of STM. This highlights a notable lack of research into the potential of DNA in PD, despite the theoretical advantages that STM offers.ConclusionsWe propose using STM as a new technique to study electron transfer in the DNA of PD from the physics perspective. creator: Muhammad Hanif Che Lah creator: Mohammed Faruque Reza creator: Shaharum Shamsuddin creator: Isao Watanabe creator: Jafri M. Abdullah uri: https://doi.org/10.7717/peerj.19807 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Che Lah et al. title: Prediabetes in adult Saudis: a systematic review & meta-analysis of prevalence studies (2000–2024) link: https://peerj.com/articles/19778 last-modified: 2025-08-20 description: BackgroundThere is a lack of national data on the pooled prevalence of prediabetes among adult Saudis. This study aimed to provide a comprehensive estimate of the prevalence of prediabetes among Saudi adults.MethodsWe searched databases for cross-sectional studies conducted between January 2000 and September 2024. We included studies written in English and conducted in Saudi Arabia. The studies had to report the prevalence of prediabetes among adults (≥18 years) using American Diabetes Association (ADA) or the World Health Organization (WHO) criteria. We excluded studies that involved non-adult or non-Saudi populations. We also excluded studies published before 2000 or those without clear diagnostic criteria or prevalence data. The review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement guidelines. Pooled prevalence was calculated using a random-effects model. Subgroup and sensitivity analyses were performed. We assessed the quality of the included studies using the Joanna Briggs Institute (JBI) checklist for prevalence studies. We used Comprehensive Meta-Analysis software version 4.0 to perform the statistical calculations.ResultsEighteen cross-sectional studies were analyzed, including 47,718 adult Saudis from the general population. The pooled national prevalence of prediabetes among Saudi adults was estimated at 24.1% (95% CI [19.5%–29.4%]). Sensitivity analysis confirmed this pooled prevalence. Funnel plot inspection and Egger’s test indicated no substantial publication bias. Subgroup analyses revealed a higher prevalence in fasting blood glucose (FBG) studies compared to glycated hemoglobin (HbA1c) studies: 25.7% (95% CI [16.6%–37.6%]) vs. 23.7% (95% CI [16.7%–32.5%]); males had a higher prevalence than females 34.8% (95% CI [25.4%–45.5%]) vs. 18.7% (95% CI [10.9%–30.2%]). Meta-regression analysis indicated a slight upward trend in prevalence over time, with a positive coefficient for ‘Year’ (0.027).DiscussionA high pooled prevalence of prediabetes was documented among the adult Saudi population, with a markedly higher prevalence among males. These findings emphasize the need for early lifestyle interventions, optimized screening programs, and effective resource allocation to prevent the progression to type 2 diabetes. We acknowledge the high level of heterogeneity among the included studies. Additionally, we note that no eligible studies specifically from the northern region of Saudi Arabia were included in the meta-analysis. creator: Abdelmarouf Mohieldein creator: Habeeb Ali Baig creator: Mahmoud Elhabiby creator: Abdullah Almushawwah creator: Mohamed Salih Mahfouz creator: Atif H. Khirelsied creator: Nour Abdelmarouf creator: GadAllah Modawe uri: https://doi.org/10.7717/peerj.19778 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mohieldein et al. title: Robotic evaluation of a 3D-printed scaffold for reconstruction of scapholunate interosseous ligament rupture: a biomechanical cadaveric study link: https://peerj.com/articles/19766 last-modified: 2025-08-20 description: BackgroundRupture of the scapholunate (SL) interosseous ligament (SLIL) is a challenging injury to treat surgically due to the small and complex nature of the SL linkage. This study was a preliminary robotic assessment of the immediate biomechanical effects of a novel 3D-printed scaffold used to reconstruct the ruptured SLIL.MethodsNine minimally loaded cadaveric wrists underwent robotically manipulated flexion-extension and radial-ulnar deviation under conditions of intact, transected, and reconstructed SLIL. Simulated radiographic measures (i.e., SL angle and SL gap) and three-dimensional SL gap across wrist motions were used to assess static and dynamic stability of the reconstructed SLIL.ResultsThree cadaveric specimens produced complete results across all experimental conditions. Intact SL linkage had a SL angle comparable (but slightly lower) than normative literature values. Once the native SLIL was transected, SL angle disruption was evident, and largely restored once the scaffold was surgically installed. Similar results were seen for SL gap. Results of the dynamic three-dimensional SL gap indicated the scaffold restored dynamic stability to a limited extent.ConclusionStatic and dynamic stability of the SL linkage was not compromised by surgical installation of the scaffold. Scaffold installation provided limited restoration of SL linkage towards native values; however, the small number of cadaveric specimens and minimal articular loading applied to the radiocarpal joint limits generalization. Overall, the scaffold may provide adequate mechanical fixation of the SL linkage and enable biological ingrowth of ligament. creator: Alastair R.J. Quinn creator: Jayishni N. Maharaj creator: Randy Bindra creator: Amelia Carr creator: Natividad Gomez creator: Kaecee Fitzgerald creator: Nataliya Perevoshchikova creator: Cedryck Vaquette creator: Claudio Pizzolato creator: Minghao Zheng creator: David Lloyd creator: David J. Saxby uri: https://doi.org/10.7717/peerj.19766 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Quinn et al. title: Effects of Undaria pinnatifida-derived brown algae polysaccharide (UPS) on the nutritional composition, digestive capacity, immune performance and intestinal microbiota of juvenile sea cucumber (Apostichopus japonicus) link: https://peerj.com/articles/19944 last-modified: 2025-08-19 description: BackgroundBrown algae polysaccharides (BAPs), derived from marine brown algae, represent bioactive macromolecules with potential functional feed applications as novel feed additives for improving the health and nutritional quality of aquatic animals. Previous studies have shown that BAPs possess antioxidant, anti-inflammatory, immunomodulatory, antimicrobial, and antiviral activities. BAPs extracted from Undaria pinnatifida (UPS) contain kinds of BAPs such as alginate, mannitol, fucoidan and fucoheterosaccharides but there are few studies on the combined effects of these BAPs.MethodsThis study investigated the effects of UPS by supplementing juvenile sea cucumbers with 0%, 0.5%, 1%, 1.5%, 2%, and 3% UPS (polysaccharide/sea cucumber biomass, W/W). After 60 days feeding, the nutritional composition of body wall, digestive capacity and immune performance were analyzed. The diversity of intestinal microbiota in sea cucumber was analyzed using 16S rRNA gene sequence amplification technology to elucidate the effects of UPS supplementation on the composition and function of intestinal microorganisms.ResultsIt was demonstrated that UPS supplementation significantly increased the nutritional content of the juvenile sea cucumber body wall although growth performance remained unchanged. The polysaccharide content peaked at 1% supplementation of UPS, which was 1.6-fold higher than that of the control group. Moreover, UPS also enhanced intestinal digestive enzyme activity such as cellulase or lipase activity, which was maximized at 1% or 3% supplementation with 5.8-fold and 1.6-fold higher than that of the control group. Additionally, UPS could improve immune performance of juvenile sea cucumber by significantly elevating superoxide dismutase activity (T-SOD). It was worth noting that low UPS concentrations (1% and 1.5%) reduced malondialdehyde (MDA) content while high concentrations (2% and 3%) increased it, indicating that low UPS supplementation may had a better effect on immune performance. 16S rRNA gene sequencing revealed that UPS supplementation reduced pathogenic Ralstonia populations. Function analysis showd that UPS may modulate metabolic pathways related to nitrotoluene and carbon source utilization. In summary, Undaria pinnatifida-derived BAP especially at low concentrations (1%) could enhance the nutritional composition, digestive and immune functions, and intestinal microbial community and metabolic profiles of juvenile sea cucumber. These findings provide a preliminary theoretical foundation for applying polysaccharides in aquaculture practices for sea cucumbers and other marine species. creator: Jinghao Dong creator: Hailong Ma creator: Kuimei Liu creator: Wei Zhou creator: Suya Liu creator: Yongjun Sun creator: Wenming Ju creator: Shanshan Wang uri: https://doi.org/10.7717/peerj.19944 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dong et al. title: An account of Korthalsia (Arecaceae) rattans and their uses in Thailand link: https://peerj.com/articles/19935 last-modified: 2025-08-19 description: Four species of Korthalsia are found in Thailand: K. flagellaris, K. laciniosa, K. rigida, and K. scortechinii. We present the comparative vegetative morphology, a key to the species, distribution, ecology, preliminary conservation assessments, utilization, and specimens examined. Korthalsia flagellaris is lectotypified here in a second-step. Three Thai Korthalsia species are confined to the peninsular region: K. flagellaris, K. scortechinii and K. rigida. The first, K. flagellaris, is known only from Narathiwat province and is restricted to peat swamp forests. The second, K. scortechinii, is myrmecophilous and found only in Narathiwat in lowland tropical evergreen rainforests. The third, K. rigida has a wider distribution and is known from Ranong, Trang and Narathiwat provinces in lowland tropical evergreen rainforests. Lastly, Korthalsia laciniosa is the most widespread species of the genus in both the south-eastern and peninsular regions of Thailand in lowland tropical evergreen rainforests. All Thai Korthalsia species are currently assessed as Least Concern (LC) under the IUCN conservation status. In Thailand, Korthalsia is used for traditional tools, furniture components, and fishery equipment. Its stems are valued in local crafts, while the young shoots are occasionally consumed as food. creator: Chatchai Ngernsaengsaruay creator: Nittaya Mianmit creator: Nisa Leksungnoen creator: Phruet Racharak creator: Suwimon Uthairatsamee creator: Pichet Chanton creator: Tushar Andriyas creator: Wirongrong Duangjai uri: https://doi.org/10.7717/peerj.19935 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ngernsaengsaruay et al. title: Mechanical response microRNA-145a-5p alleviates osteoarthritis by inhibiting inflammation and promoting chondrogenesis link: https://peerj.com/articles/19905 last-modified: 2025-08-19 description: BackgroundOsteoarthritis is characterized by cartilage wear or absence and is usually initiated by inflammation and abnormal mechanical stimulation. MicroRNAs have been identified as the main regulators of osteoarthritis, but the influence of miR-145a-5p on osteoarthritis has not been elucidated. In this study, we focused on the role of miR-145a-5p in cartilage.MethodsDestabilization of the medial meniscus surgery (DMM) and RNA fluorescence in situ hybridization (RNA FISH) were performed to detect the expression level of miR-145a-5p in osteoarthritis. Interleukin-1β was used to simulate the inflammatory environment in vitro. The Flexcell device was used for mechanical stimulation. Agomir-145a-5p was injected intra-articularly into the DMM-induced osteoarthritis mouse model. Histopathological examinations, and molecular biology techniques were used to investigate the underlying mechanisms.ResultsThe expression of miR-145a-5p was decreased in osteoarthritis mice, whereas its expression increased with prolonged chondrogenesis. Then, studies in vitro also confirmed the pro-chondrogenesis and interleukin-1β inhibitory ability of miR-145a-5p. Additionally, miR-145a-5p can be regulated by cyclic stretch stress, with physiological mechanical stimulation promotes, but excessive mechanical stimulation suppresses its expression. In addition, miR-145a-5p rescues DMM-induced osteoarthritis progression, which was observed through the intra-articular injection of agomiR-145a-5p.ConclusionsMiR-145a-5p, a mechanical responder, alleviates osteoarthritis progression through promoting chondrogenesis and alleviating inflammation response. And intra-articular injection of miR-145a-5p alleviates osteoarthritis progression. These findings suggest that miR-145a-5p is a promising target for the treatment of osteoarthritis. creator: Jingke Du creator: Zhen Zhang creator: Danyang Bai creator: Ting Zhu creator: Dong Jiang uri: https://doi.org/10.7717/peerj.19905 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Du et al. title: Avian biodiversity in central California vineyards link: https://peerj.com/articles/19904 last-modified: 2025-08-19 description: Avian biodiversity is declining globally, and conservation lands alone will likely not be able to support vibrant avian communities long-term. However, the integration of wildlife friendly practices into agricultural lands could support many birds that have lost habitat to agricultural and urban development. Here, we assessed how structural, natural, and anthropic vineyard characteristics in Edna Valley, California influence avian species occupancy, taxonomic diversity, and functional diversity from 31 point counts that, collectively, captured large gradients in environmental variation that exist in and around Edna Valley vineyards. Although we found the occupancy of relatively few species to covary with structural, natural, and anthropic vineyard characteristics, increasing canopy cover was associated with higher taxonomic and functional bird diversity in vineyards, and canopy cover and sound level were associated with shifts in bird community composition. We also found some evidence that proximity to surface water and agricultural cover variation surrounding vineyards could increase functional bird diversity; however this requires further investigation. Additionally, vineyard cover was negatively associated with functional evenness, but we did not find evidence that it was related to any other taxonomic or functional diversity metrics. This research could help guide wildlife friendly vineyard management throughout California to help increase the number of birds that can utilize these modified lands for foraging, shelter, and to connect larger areas of protected land. creator: Lindsay Peria creator: Clinton D. Francis uri: https://doi.org/10.7717/peerj.19904 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Peria and Francis title: Effect of acid-suppressive drugs on endoscopic transmural drainage of peripancreatic fluid collections—a randomized controlled trial link: https://peerj.com/articles/19872 last-modified: 2025-08-19 description: BackgroundAcid-suppressing drugs affect intestinal microbes by inhibiting the secretion of stomach acid. However, it is not clear whether acid suppressive drugs affect the microorganisms in the peripancreatic effusion and affect the postoperative complications.MethodsThis study was a prospective randomized controlled trial. A total of 45 patients were enrolled in the trial, and all patients were divided into acid-inhibited and non-inhibited groups. The primary endpoint of our study was to observe the difference in microbiota between the two groups of cyst fluid.ResultsA total of 25 patients were included in the acid-inhibited group, and 20 patients were included in the non-acid-inhibited group. There were no significant differences between the two groups in terms of postoperative infection, bleeding, and recurrence rates (p > 0.05). In terms of postoperative C-reactive protein levels, the acid-suppressing group was significantly higher than the non-acid-suppressing group (p < 0.05). In the 16S microbial sequencing analysis, we found no significant difference in α diversity between the acid-suppressing group and the non-acid-suppressing group, but there was a statistically significant difference in β diversity between the two groups.ConclusionAcid-suppressing drugs can change the microbial composition of pancreatic effusions and increase markers of postoperative inflammation. Acid-suppressive drugs may increase the risk of infection after endoscopic drainage. creator: Yaoting Li creator: Tingting Yu creator: Senlin Hou creator: Wei Zhang creator: Haiming Du creator: Yankun Hou creator: Jiao Tian creator: Lichao Zhang uri: https://doi.org/10.7717/peerj.19872 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Gram staining reveals diverse bacterial associations in coral cell-associated microbial aggregates in the Pacific Ocean link: https://peerj.com/articles/19867 last-modified: 2025-08-19 description: Cell-associated microbial aggregates (CAMAs) (also referred to as coral-associated microbial aggregates) have been observed in 24 coral species from the Pacific Ocean, and studies indicate most contain gram-negative bacilli from the genus Endozoicomonas. Here, we used histology with Gram staining to evaluate the morphology and distribution of CAMAs in six species of scleractinian corals from Hawaii and Palmyra. Within CAMAs, we observed the coexistence of bacteria with differing morphologies and Gram-staining properties both within and among coral species. Pocillopora and Acropora had mostly gram-negative bacilli, whereas gram-negative cocci dominated in Porites. Acropora had the highest abundance of gram-positive CAMAs. The anatomical distribution of CAMAs varied by coral species. CAMAs dominated in the tentacles of Pocillopora meandrina, Pocillopora grandis, and Porites evermanni, were mostly in the coenenchyme of Acropora cytherea, and were found equally between tentacles and coenenchyme in Porites compressa and Porites lobata. Tissue-layer distribution also varied, with CAMAs mainly in the epidermis of Pocillopora but in the gastrodermis of Porites and Acropora. The diversity of bacteria in CAMAs and their anatomic distribution in Pacific corals may be more complex than previously understood. This indicates other bacterial species, in addition to Endozoicomonas, are colonizing CAMAs in corals from the Pacific Ocean. creator: Chutimon Singhakarn creator: Robert J. Toonen creator: Thierry M. Work uri: https://doi.org/10.7717/peerj.19867 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Singhakarn et al. title: Multifactorial analysis of temperature, solute-to-solvent ratio, and ultrasound amplitude on the extraction of phenolic and antioxidant compounds from Aloysia citriodora Palau leaves link: https://peerj.com/articles/19821 last-modified: 2025-08-19 description: Ultrasonic-assisted extraction was applied to Aloysia citriodora Palau leaves. To achieve this, a set of extraction parameters—temperature, amplitude, and solute-to-solvent ratio—was evaluated. A 33 factorial design was implemented, generating 27 treatments, from which total phenolic content, total flavonoid content, and antioxidant capacity against 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS•+), 2,2-diphenyl-1-picrylhydrazyl (DPPH•), and hydroxyl (OH•) radicals were assessed. The extract showing the highest free radical scavenging capacity was obtained at 75 °C, a solute-to-solvent ratio of 1:15, and a wave amplitude of 25%. This extract contained 87.74 mg gallic acid equivalent (GAE)/g extract and 76.82 ± 6.21 mg quercetin equivalent (QE)/g extract. Antioxidant capacity was expressed as the half-maximal inhibitory concentration (IC50, µg/mL), with values of 9.08 ± 0.08 µg/mL for ABTS•+, 35.58 ± 0.50 µg/mL for DPPH•, and 0.72 ± 0.007 mg/mL for OH•. The A. citriodora leaf extract demonstrated strong potential for use in the development of new products containing bioactive molecules capable of preventing degenerative diseases. creator: Osvaldo Alvarez Cortes creator: Héctor Eduardo Martinez Flores creator: Martha-Estrella García-Pérez creator: Juan Carlos González-Hernández creator: Martha Eva Viveros-Sandoval creator: Mariano Martinez-Vazquez creator: Noemi Silva Jimenez creator: María Carmen Bartolomé-Camacho uri: https://doi.org/10.7717/peerj.19821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alvarez Cortes et al. title: Assessing the carbon footprint of the 15th International Coral Reef Symposium (ICRS) in Bremen, Germany link: https://peerj.com/articles/19811 last-modified: 2025-08-19 description: International scientific conferences serve as vital platforms for networking, knowledge exchange, and collaborative responses to global challenges. To exemplify sustainable practices, it is essential to organize these events in a climate-friendly manner, particularly for topics directly tied to environmental conservation, such as coral reef research. The 15th International Coral Reef Symposium (ICRS), held in Bremen, Germany, in July 2022, aimed to minimize its environmental impact through a comprehensive green strategy. This included reducing CO2 emissions and offsetting unavoidable emissions via investments in climate protection projects. This study presents a detailed assessment of the symposium’s carbon footprint over its five-day duration, accounting for both travel-related and local emissions. Total CO2 emissions were estimated at approximately 1,491 tons, with transportation contributing 84% and local activities 16%. Local emissions were reduced through measures such as the use of renewable energy, sustainable catering, and waste reduction. The hybrid format of the conference, which enabled online participation, significantly lowered per-capita emissions compared to full in-person attendance. The findings highlight the importance of integrating green strategies and virtual participation options to reduce the environmental impact of scientific gatherings. By offsetting all unavoidable emissions, the 15th ICRS successfully achieved carbon neutrality, setting a benchmark for future conferences to prioritize sustainability and environmental responsibility. creator: Sophie Littke creator: Jennifer Bogun creator: Christian Wild uri: https://doi.org/10.7717/peerj.19811 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Littke et al. title: Prognostic role and functional impact of cadherin genes in non-small cell lung cancer tumorigenesis: mechanistic insights from in silico and in vitro analyses link: https://peerj.com/articles/19785 last-modified: 2025-08-19 description: Non-small cell lung cancer (NSCLC) is a leading cause of cancer-related mortality worldwide, with poor prognosis and limited treatment options for advanced stages. Dysregulation of cadherin expression has been implicated in various cancers, but their exact roles and diagnostic potential of these genes in NSCLC remain unclear. The aim of this study is to investigate the diagnostic and prognostic significance of cadherin family genes (CDH1, CDH2, and CDH3) in NSCLC. This study follows an experimental design, involving both in vitro analyses of cell lines and survival data analysis from public databases. Nine NSCLC cell lines and five normal lung tissue-derived cell lines were cultured and CDH1, CDH2, and CDH3 expression was analyzed via RT-qPCR. Protein expression was validated using the Human Protein Atlas and survival analysis was conducted with the Kaplan-Meier database. Functional roles and regulatory mechanisms of cadherin genes were explored through mutational analysis, PPI networks, and miRNA interactions. The results revealed that all three cadherin genes were significantly upregulated in NSCLC cell lines and tissue samples compared to normal controls. Mutational and copy number variation analyses revealed frequent alterations in CDH2, CDH3, and CDH1 in NSCLC. Additionally, we identified hsa-miR-217, hsa-miR-203a-3p.2, and hsa-miR-6766-3p as potential regulatory miRNAs. The results of functional assays indicate that the silencing of CDH1 and CDH2 inhibits cell proliferation, colony formation, and migration in A549 cells, highlighting their potential roles in promoting tumorigenic and migratory properties in NSCLC. Collectively, our findings suggest that cadherin family genes (CDH1, CDH2, and CDH3) play critical roles in NSCLC tumorigenesis and progression, highlighting their significance as diagnostic markers. creator: Quanzhong Yang creator: Nan Feng creator: Feifei Shen creator: Lin Bai creator: Rihui Li creator: Shuang Li creator: Weikai Zhang uri: https://doi.org/10.7717/peerj.19785 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yang et al. title: How long is too long? Examining waiting times and stress in human-elevator interaction link: https://peerj.com/articles/19913 last-modified: 2025-08-18 description: Elevators have become an indispensable infrastructure in modern societies. Our use of them involves two distinct waiting periods: the waiting time (before the elevator arrives) and the transit time (riding to a destination). Reducing both is crucial for enhancing the user experience. For this purpose, researchers have focused on two approaches: such technological schemes as sophisticated elevator control algorithms for minimizing the actual waiting times, and such cognitive approaches as positioning mirrors that divert users’ attention for reducing the perceived waiting times. However, past studies failed to sufficiently examine the relationship between the actual and perceived waiting times in real elevator usage conditions; nor have they investigated how these waiting times are related to user stress. In this study we addressed these relationships by conducting an experiment that replicated real-world elevator usage scenarios and gathered both self-reported perceived waiting times and stress data from participants and objectively measured the actual waiting times by video analysis. Investigation of these data clarified the discrepancy between actual and perceived waiting times and more deeply explored how waiting times influence user stress. creator: Masahiro Shiomi creator: Masayuki Kakio creator: Takahiro Miyashita uri: https://doi.org/10.7717/peerj.19913 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shiomi et al. title: Impact of maternal iron and zinc intake on low birth weight risk: a nested case—control study link: https://peerj.com/articles/19896 last-modified: 2025-08-18 description: BackgroundThe association between maternal iron/zinc intake and the risk of low birth weight (LBW) in infants is still unclear. This study aimed to investigate the effects of iron and zinc daily intake preconception and during pregnancy on the risk of delivering LBW babies and to assess whether there is an interaction between iron and zinc intake on the risk of LBW.MethodsA nested case–control study was performed, including 565 cases and 7,510 controls in Lanzhou City, China. Eligible participants were interviewed about their diets and characteristics during pregnancy. Unconditional logistic regression was used to determine the association between dietary iron/zinc intake and the risk of LBW and its clinical subtypes. Multivariate-adjusted restricted cubic spline (RCS) models were applied to explore the nonlinear association between dietary iron/zinc intake levels and the risk of LBW.ResultsLower intake of iron/zinc preconception and during pregnancy was associated with a higher risk of LBW and some subtypes, and there was a nonlinear trend between iron/zinc intake and the occurrence risk of LBW (PNonlinear < 0.05). Moreover, the synergistic effects of low iron and low zinc intake on the risk of LBW were found.ConclusionEfforts to promote iron and zinc intake preconception and during pregnancy need to be strengthened to reduce the local incidence of LBW. creator: Liping Yang creator: Zifu Wang creator: Lei Cao creator: Yuqing Li creator: Jingyan Wang creator: Shuyu Ding creator: Baohong Mao uri: https://doi.org/10.7717/peerj.19896 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: Relationship between heart rate variability parameters and inflammatory activity in patients with Crohn’s disease: a retrospective study link: https://peerj.com/articles/19893 last-modified: 2025-08-18 description: BackgroundIt is widely recognized that individuals with Crohn’s disease (CD) often experience impaired autonomic nervous system (ANS) function. However, the specific relationship between autonomic activity and inflammatory processes in CD remains uncertain. The objective of this study was to investigate the association between autonomic nervous function, as assessed through heart rate variability (HRV) parameters, and the Crohn’s disease activity index (CDAI).MethodsThis cross-sectional study involved 82 CD patients. Demographic and medical history data were gathered, and disease activity was evaluated using the CDAI. Short-term HRV measurements were obtained from all participants.ResultsVarious adjustments to the model and trend analysis indicate that the HRV parameters are significantly negatively correlated with CDAI. After controlling for potential confounding factors, the smooth curve fitting shows that high-frequency (HF) power is negatively linearly correlated with CDAI. As the HF value increases, CDAI shows a decreasing trend. In contrast, total power (TP), low-frequency power (LF), and standard deviation of the R-R interval (SDNN) exhibit a nonlinear relationship with CDAI. To the left of the inflection point, as the values of TP, LF, and SDNN increase, CDAI shows a decreasing trend. However, to the right of the inflection point, there is no relationship between TP, LF, SDNN values, and CDAI.ConclusionIn patients with CD, autonomic dysfunction correlates with active inflammation. Among the HRV parameters, HF, which reflects vagal-mediated activity, displayed the strongest and most consistent negative correlation with inflammatory activity. creator: Beibei Wang creator: Shanying Liao creator: Linlin Huang creator: Zhongwen Zheng creator: Can Cui uri: https://doi.org/10.7717/peerj.19893 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Correlation of serum apolipoprotein B with the Framingham Risk Score among a group of Iraqi subjects: a cross-sectional study link: https://peerj.com/articles/19883 last-modified: 2025-08-18 description: BackgroundApolipoprotein B (apoB) is the primary structural protein in low-density lipoprotein (LDL) and plays a crucial role in atherogenesis. The Framingham Risk Score (FRS) is a widely used tool for assessing cardiovascular disease (CVD) risk. However, the correlation between apoB and FRS in Iraqi individuals remains underexplored.ObjectivesThis study aims to evaluate the association between serum apoB levels and FRS, establishing its potential utility as a predictive biomarker for coronary artery disease (CAD) risk.MethodsA cross-sectional study was conducted on 201 individuals aged ≥30 years attending a clinical laboratory in Baghdad between November 2022 and October 2023. Serum apoB and lipid profiles were measured, and FRS was calculated for all participants. Correlation analysis between apoB and FRS was performed using Spearman’s test, while group comparisons were conducted via Kruskal–Wallis and Mann–Whitney tests. The predictive performance of apoB for high FRS was assessed using receiver operating characteristic (ROC) analysis, determining an optimal cutoff value.ResultsThe median age of participants was 48 years, with males constituting 51.2% of the cohort. Median apoB and FRS values were 130 mg/dL and 4, respectively. A strong positive correlation was observed between serum apoB and FRS (R = 0.8, P = 0.0001). ROC analysis identified a cutoff value of 97.75 mg/dL for apoB in predicting high CAD risk.ConclusionsThese findings suggest that apoB may serve as a reliable biomarker for CAD risk assessment in the Iraqi population, where its predictive value has been underexplored. The identified cutoff value (97.75 mg/dL) highlights its potential role in refining risk stratification beyond traditional lipid markers. Further prospective studies are needed to validate these findings and assess their clinical impact. creator: Israa Nather Ahmed creator: Fatimatuzzahra’ Abd Aziz creator: Raid Dhia Hashim uri: https://doi.org/10.7717/peerj.19883 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ahmed et al. title: The urea-creatinine ratio on the seventh day predicts the short-term prognosis of spontaneous intracerebral hemorrhage: a retrospective study link: https://peerj.com/articles/19874 last-modified: 2025-08-18 description: Background and ObjectivesThis study aimed to investigate the association between hydration status and 90-day functional outcomes in patients with spontaneous intracerebral hemorrhage (SICH).MethodsWe conducted a retrospective analysis of 215 SICH patients admitted to the Neurology Department of the First Affiliated Hospital of Chongqing Medical University between January 2021 and September 2023. Demographic characteristics, imaging findings, and laboratory parameters were collected. Patients were stratified into good (modified Rankin Scale [mRS] ≤ 2) and poor (mRS > 2) prognosis groups based on 90-day outcomes.ResultsUnivariate analysis revealed that poor prognosis was associated with advanced age, prolonged hospitalization, and elevated urea nitrogen/creatinine ratio (UCR) on day 7 (p < 0.05). Multivariate logistic regression identified three independent predictors of poor outcome: age (OR = 1.059, 95% CI [1.025–1.094], p < 0.01), Glasgow Coma Scale score (OR = 0.420, 95% CI [0.308–0.571], p < 0.01), and day-7 UCR (OR = 1.095, 95% CI [1.045–1.148], p < 0.01). Receiver operating characteristic (ROC) analysis demonstrated that day-7 UCR predicted poor outcomes with an area under the curve (AUC) of 0.72 (95% CI [0.643–0.789]), with an optimal cutoff value of 30.68. Patients with UCR ≤ 30.68 had significantly higher rates of favorable outcomes (75.2%) compared to those with UCR > 30.68 (37.9%).ConclusionElevated blood UCR (>30.68) on day 7 post-SICH is an independent predictor of unfavorable short-term prognosis. creator: Xingguo Wu creator: Ningxiang Qin creator: Yiqi Zhang creator: Fahang Yi creator: Xi Peng creator: Liang Wang uri: https://doi.org/10.7717/peerj.19874 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: ALDOB is a prognostic biomarker and a potential immunotherapy target for clear cell renal cell carcinoma link: https://peerj.com/articles/19869 last-modified: 2025-08-18 description: BackgroundAldolase B (ALDOB), functioning as a glycolytic enzyme, exhibits a controversial role in malignancies and demonstrates dual potential as both a tumor suppressor and cancer-promoting enzyme. Nevertheless, it is still uncertain if there is a relationship between ALDOB levels, prognosis, and tumor-infiltrating lymphocytes in clear cell renal cell carcinoma (ccRCC).ObjectiveThis study aims to investigate the prognostic significance of ALDOB in ccRCC and its potential association with clinicopathological features and tumor immune microenvironment. By integrating multi-database bioinformatics analysis and experimental validation, we seek to elucidate the role of ALDOB in ccRCC progression and its potential as a predictive biomarker.MethodsTo ascertain the potential link between ALDOB level, clinical parameters, and overall survival (OS) in individuals with ccRCC, we employed diverse databases, which include The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), the Human Protein Atlas (HPA) and The University of Alabama at Birmingham Cancer data analysis Portal (UALCAN). Furthermore, an in-depth analysis of the link between tumor-infiltrating immune cells (TIIC) and ALDOB was carried out using the TIMER database. Immunohistochemistry (IHC) was applied to identify the ALDOB level in a tissue microarray.ResultsThe expression of ALDOB demonstrated a strong association with pathologic T stage, pathologic N stage, pathologic M stage, histologic grade, and gender. Decreased ALDOB level was linked to unfavorable disease-specific survival (DSS), progress free interval (PFI), and OS outcomes (p < 0.001). Subsequently, a marked link was observed between ALDOB level and a heightened presence of infiltrating Treg, Th17 cells, and neutrophils in ccRCC. IHC showed that the ALDOB level in ccRCC samples was notably diminished relative to that in the adjacent normal tissues.ConclusionsAs a prospective predictive indicator for individuals with ccRCC, reduced ALDOB level exhibited strong correlations with clinical characteristics, unfavorable outcomes, and immune infiltration in individuals with ccRCC. creator: Wu Xu creator: Dali Wu creator: Cuilian Li creator: Lingfei Yan creator: Bo Peng creator: Yang Luo creator: Dawei Liu creator: Qing Li creator: Tao Wang uri: https://doi.org/10.7717/peerj.19869 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xu et al. title: Impact of paternal hepatitis B on pregnancy outcomes in couples undergoing assisted reproductive technology treatment: a systematic review and meta-analysis link: https://peerj.com/articles/19824 last-modified: 2025-08-18 description: BackgroundThis study intends to evaluate the influence of hepatitis B virus (HBV) infection on clinical pregnancy rate (CPR) and live birth rate (LBR) per woman and cycle in couples who achieved pregnancy through assisted reproductive technology (ART).MethodsPubMed, Embase, CNKI, Scopus, Web of Science, and Wangfang databases were comprehensively searched for articles reporting data on pregnancies achieved through ATR and providing information on the paternal HBV status and CPR and LBR. A random-effects model was used for the meta-analyses to pool odds ratios (OR) with corresponding confidence intervals (CI). Subgroup analyses were done based on the matching status.ResultsThe analysis included 10 studies (4,848 participants) for CPR per woman, 10 studies (28,951 participants) for CPR per cycle, four studies (2,327 participants) for LBR per woman, and seven studies (26,324 participants) for LBR per cycle. The analysis showed no considerable association between the HBV status and the CPR or LBR, with the pooled OR of 1.015 (95% CI [0.860–1.199], p = 0.857) for CPR per woman and of 1.051 (95% CI [0.870–1.271], p = 0.603) for CPR per cycle. Pooled OR for LBR per woman was 0.852 (95% CI [0.717–1.012], p = 0.068), and for LBR per cycle was 0.999 (95% CI [0.851–1.172], p = 0.987).ConclusionsPaternal HBV infection does not significantly affect clinical pregnancy or live birth rates in ART pregnancies. Our findings inform clinical practice and provide reassurance to couples undergoing ART that paternal HBV infection should not be a major concern in terms of pregnancy outcomes. creator: Juanting Gao creator: Qiyin Dong creator: Liping Shen creator: Xiuping Zhu uri: https://doi.org/10.7717/peerj.19824 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gao et al. title: Functional characterization of antennae-enriched chemosensory protein 4 in emerald ash borer, Agrilus planipennis link: https://peerj.com/articles/19812 last-modified: 2025-08-18 description: Agrilus planipennis is an invasive species that inflicts substantial harm on ash trees (Fraxinus spp.) globally. Elucidating its olfactory mechanisms is essential for devising effective pest management approaches. In this research, we identified chemosensory protein 4 (AplaCSP4) in A. planipennis, which is highly expressed in the antennae of both male and female individuals. Notably, the mRNA expression level of AplaCSP4 in females is 1.9 times higher than that in males. Fluorescence competition binding assays revealed that recombinant AplaCSP4 has a broad binding spectrum, capable of interacting with 11 compounds from various chemical classes such as esters, alkanes, terpenes, terpenoids, and terpenols. The dissociation constants (KD) for these binding affinities range from 0.25 to 11.47 µM. AplaCSP4 shows binding affinity for volatiles from Fraxinus species, including dodecane, myrcene, ocimene, farnesene, (+)-limonene, and nerolidol, with the highest affinity observed for farnesene (KD = 0.25 µM). Molecular docking and dynamics simulation were employed to elucidate the binding mode of farnesene, which exhibited the strongest binding affinity with AplaCSP4. The results indicated that farnesene binds within the hydrophobic pocket of AplaCSP4, with a binding energy of −31.830 ± 2.015 kcal/mol and −32.585 ± 2.011 kcal/mol in dual-replicate molecular dynamics simulations, and primarily driven by van der Waals interactions. Importantly, during the two molecular dynamics simulations, the centroid distances between farnesene and the key residues in the binding pocket of AplaCSP4 were maintained relatively stable. The combined results from in vitro experiments and computational modeling suggest that AplaCSP4 is critically involved in plant volatile detection. This study offers insights into the molecular basis of olfactory perception in A. planipennis and may provide a foundation for developing novel olfactory-based pest control strategies targeting chemosensory proteins. creator: Ren Li creator: Zehua Wang creator: Fan Yang creator: Guanghang Qiao creator: Jingjing Tu creator: Ang Sun creator: Shanning Wang uri: https://doi.org/10.7717/peerj.19812 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Femoral metadiaphyseal and nutrient foramen perfusion suggests comparable maximal metabolic rates in a pterosaur and in a semi-aquatic maniraptoran dinosaur link: https://peerj.com/articles/19806 last-modified: 2025-08-18 description: Ornithodirans represent a diverse and highly successful clade that encompasses a wide array of morphologies and ecological adaptations. This group includes volant forms such as Rhamphorhynchus, a medium-sized, non-pterodactyloid long-tailed pterosaur from the Jurassic Solnhofen lagoons, characterized by prow-shaped lower jaw and forward-pointing teeth consistent with a piscivorous diet. In addition, the ornithodiran group included theropod dinosaurs such as Halszkaraptor escuilliei, a dromaeosaurid from Mongolia that exhibit morphological traits indicative of a semi-aquatic lifestyle. In this study, we retrodicted the aerobic performance of these two extinct ornithodirans by using femoral metadiaphyseal nutrient foramina dimensions as a proxy for maximal metabolic rate (MMR), based on an extant-amniote dataset of reference. We estimated femoral blood flow ($\dot {\mathrm{}Q}$Q ̇) through the femoral nutrient canal areas and retrodicted mass-independent MMR for immature specimens of Halszkaraptor and Rhamphorhynchus of 5.68 mLO2 h−1 g−0.87 and 5.55 mLO2 h−1 g−0.87 (p < 0.001), respectively. Our findings revealed that femoral blood flow rates and mass-independent MMR values were similar in the two taxa, despite their extreme differences in phylogenetic affinity, locomotory behavior and ecology. The predicted mass-independent MMR for H. escuilliei aligned with values observed in extant ground-dwelling emus and migratory shorebirds such as gulls and terns, but fall below the high MMR value of ducks. Further investigation into adult specimens is needed to refine our understanding of aerobic capacity in mature individuals, particularly with regards to the ability of Rhamphorhynchus for achieving the energetic demands of flight. Our research enhances understanding of the physiological strategies of extinct taxa and helps address key gaps in paleophysiological reconstructions. creator: Mariana V.A. Sena creator: Dennis F.A.E. Voeten creator: Esaú Araújo creator: Jorge Cubo uri: https://doi.org/10.7717/peerj.19806 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sena et al. title: Exploring ethical monitoring of physical activity behaviors among adults: a Smart Platform study operationalizing digital citizen science link: https://peerj.com/articles/19793 last-modified: 2025-08-18 description: BackgroundAccording to the World Health Organization, 27% of adults do not meet the recommended daily levels of physical activity (PA), making accurate PA measurement essential for informing evidence-based policies. This study explores ethical engagement with citizens through their ubiquitous digital tools (i.e., smartphones) to examine variations between retrospectively and prospectively reported PA behaviors within the same cohort.MethodsThis study is part of the Smart Platform, a digital citizen science initiative for ethical monitoring and real-time intervention. Data were collected from 118 adults who participated over eight consecutive days, including both weekdays and weekends. Prospective PA was assessed using time-triggered ecological assessments, while retrospective PA was measured using a modified, time-triggered, smartphone-based validated tool. Paired sample t-tests were used to compare retrospective and prospective PA. Linear regression models examined associations between socio-demographic and contextual factors and both types of PA reporting. Analyses were conducted for the overall sample and by gender (male vs. female).ResultsParticipants consistently reported higher PA through retrospective measures compared to prospective ones (p < 0.001). In the overall sample, one significant association was found in the retrospective model, while three were identified in the prospective model. Among males, those who engaged in PA for fun or to maintain physical health reported higher retrospective PA, though this was not significant in the prospective model. In contrast, female participants who engaged in PA for fun reported higher PA in both retrospective and prospective models.ConclusionsAlthough exploratory, early findings suggest that repeated, prospective assessments via ubiquitous digital devices may enhance the validity and reliability of PA measurement. As citizen-owned digital tools become increasingly widespread, ethically leveraging big data through digital citizen science offers a promising approach to improve PA monitoring and support public health efforts. creator: Caitlin Hung creator: Sheriff Tolulope Ibrahim creator: Tarun Reddy Katapally uri: https://doi.org/10.7717/peerj.19793 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hung et al. title: Genomewide analysis of the Class III peroxidase gene family in apple (Malus domestica) link: https://peerj.com/articles/19741 last-modified: 2025-08-18 description: Class III peroxidases (PRXs) play a crucial role in maintaining reactive oxygen species (ROS) homeostasis, thereby influencing plant growth, development, and defense responses. To date, the roles of PRXs in apple branch development and the control of rootstock growth vigor remain poorly understood. This research aimed to exhaustively annotate and analyze the Class III PRX family in the apple genome. Ninety-nine PRX proteins were identified from the Malus domestica genome. Phylogenetic analysis revealed that the PRXs from Malus domestica and Arabidopsis thaliana were classified into six groups. McSCAN analysis indicated that tandem duplication events played a dominant role in the expansion of Malus domestica peroxidases (MdPRXs), thus purifying selection maintained their function. Most MdPRX genes contained cis-elements responsive to light and plant hormones such as abscisic acid (ABA) and methyl jasmonate (MeJA), as well as various stress factors. Although most MdPRXs possess N-terminal signal peptides, in contrast to the majority of Arabidopsis PRX gene family members that are primarily localized in the apoplast, 50 MdPRXs are localized in the chloroplasts, with only one-third predicted to be apoplastic. Analysis of their spatiotemporal expression patterns, based on transcriptome data, revealed extensive involvement in apple tissue and organ development, demonstrating distinct and specialized expression profiles. These variations are primarily attributed to differences in cis-elements within the promoter regions and their three-dimensional structural variations, rather than to their phylogenetic relationships. In rootstock-scion composite trees, the expression patterns of MdPRXs were influenced by both rootstock species and scion varieties. Unlike previous studies relying on zymogram analysis, our findings reveal that the transcriptional expression of MdPRXs is not inherently negatively correlated with the dwarfing capacity of apple rootstocks. Notably, we identified that high expression of MdPRX59 is specifically associated with vigorous rootstocks. A set of MdPRXs such as MdPRX27, MdPRX59, and MdPRX90 may affect the ROS status in stem cell niche of the axillary buds and promote the differentiation of branches. This systematic analysis provides a foundation for the further functional characterization of MdPRX genes, with the aim of improving apple rootstock dwarfing ability and branching characteristics. creator: Yao Lu creator: Rongqun Ma creator: Kunhao Wu creator: Jilu Sun creator: Yutong Li creator: Jiawei Zhao creator: Zhenbao Qi creator: Guangli Sha creator: Hongjuan Ge creator: Yanjing Shi uri: https://doi.org/10.7717/peerj.19741 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lu et al. title: NLRP3 inflammasome and pyroptosis: implications in inflammation and multisystem disorders link: https://peerj.com/articles/19887 last-modified: 2025-08-15 description: The NLRP3 inflammasome is a multiprotein complex that senses diverse pathogen-associated molecular patterns (PAMPs) and danger-associated molecular patterns (DAMPs), activating the pyroptosis pathway. Pyroptosis is a form of programmed cell death that plays a crucial role in immune responses and inflammatory processes. The NLRP3 inflammasome-gasdermin D (GSDMD) axis has emerged as a critical therapeutic target in inflammatory diseases. Oligomerization of NLRP3 triggers caspase-1 activation, which subsequently induces GSDMD palmitoylation—an essential event that facilitates pyroptosis. Clinically, NLRP3 inhibitors, such as MCC950, demonstrate protective effects in NLRP3-mediated inflammatory diseases. GSDMD holds substantial potential as a diagnostic, monitoring, and therapeutic target across diverse diseases, underscoring its utility as a pan-biomarker. This review aims to synthesize current knowledge regarding the structure and function of the NLRP3 inflammasome and the regulatory mechanisms governing pyroptosis. Additionally, integrating findings from multiple physiological systems highlights the key roles of the NLRP3 inflammasome and pyroptosis in disease pathogenesis, offering novel perspectives for targeting inflammatory responses and associated disorders. creator: Xiaodi Li creator: Zhiyuan Zhang creator: Yang Han creator: Mianzhi Zhang uri: https://doi.org/10.7717/peerj.19887 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Epidemiology and genetic characteristics of Clostridioides difficile isolates in Northwest China link: https://peerj.com/articles/19877 last-modified: 2025-08-15 description: Clostridioides difficile (C. difficile) is a significant hospital-acquired pathogen that can cause antibiotic-associated diarrhea. In this study, we investigate the epidemiological and genetic characteristics of C. difficile isolates from a tertiary hospital in Northwest China. We prospectively collected fecal samples from 212 patients with diarrhea between January 2023 and May 2024 at the First Hospital of Lanzhou University. Twenty-five (11.8%, 25/212) strains of C. difficile were isolated, and twenty (9.4%, 20/212) were identified as toxigenic C. difficile (TCD). The dominant toxin gene profiles were tcdA+ B+ (80%, 20/25). Furthermore, twelve different sequence types (STs) belonging to three clades were identified, and the most prevalent types were ST3 followed by ST2 and ST35. Toxin variant analysis revealed the presence of eight types of tcdA variants and seven types of tcdB variants, most tcdA/B variants corresponded to specific ST types. Phylogenetic analysis based on single nucleotide polymorphisms (SNPs) further confirmed the genetic diversity and relationships among isolates. We identified 13 resistance genes, including mutations in gyrA/gyrB (96% of strains) and rpoB (72%), conferring resistance to fluoroquinolones and rifamycins, respectively. The study provides valuable insights into the epidemiological and genetic features of C. difficile in Northwest China, guiding future prevention and control measures. creator: Yang Li creator: Shujuan An creator: Hongjia Sun creator: Meimei Hu creator: Yanmei Xu creator: Yaming Xi uri: https://doi.org/10.7717/peerj.19877 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Li et al. title: UQCRC1 downregulation impairs cognitive function in mice via AMPK inactivation link: https://peerj.com/articles/19873 last-modified: 2025-08-15 description: BackgroundUbiquinol-cytochrome c reductase core protein 1 (UQCRC1) is an essential subunit of complex III in the mitochondrial respiratory chain. Although earlier studies have indicated that UQCRC1 downregulation causes cognitive impairment, the underlying mechanisms remain unclear.MethodsTo investigate its pathophysiological effects, we developed a mouse model with downregulated UQCRC1 expression. Hippocampus-dependent cognitive performance was evaluated using a series of behavioral paradigms. Mitochondrial bioenergetic status was assessed by measuring adenosine triphosphate (ATP) levels, while oxidative stress was quantified through detection of reactive oxygen species (ROS). Molecular analyses were performed to assess AMP-activated protein kinase (AMPK) signaling dynamics and autophagic flux. Additionally, pharmacological interventions aimed at activating AMPK and enhancing lysosomal function were employed to elucidate mechanistic pathways.ResultsDownregulation of UQCRC1 resulted in significant deficits in hippocampus-dependent cognitive performance, accompanied by impaired mitochondrial bioenergetics (lower ATP synthesis) and elevated oxidative stress (increased ROS levels). Mechanistically, these phenotypes were associated with diminished AMPK activation and disrupted autophagic flux. Importantly, pharmacological activation of AMPK or enhancement of lysosomal activity in UQCRC1-deficient mice effectively ameliorated cognitive deficits and restored mitochondrial redox homeostasis .ConclusionsThis study identifies AMPK as a pivotal metabolic orchestrator of mitochondrial-lysosomal functional crosstalk and reveals its non-canonical function in maintaining neuronal homeostasis via coordinated regulation of autophagic flux and redox balance. Our findings propose AMPK-driven interorganelle communication as a modifiable therapeutic target for addressing cognitive decline resulting from mitochondrial dysfunction. creator: Jing Zhang creator: Zuoxi Wu creator: Zonghong Long creator: Feng Ceng creator: Fuhai Bai creator: Hong Li uri: https://doi.org/10.7717/peerj.19873 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhang et al. title: Impact of foliar application using amino acids, yeast extract, and algae extract in different concentrations on growth parameters, yield traits, grain quality, and nitrogen-related parameters of wheat in arid environments link: https://peerj.com/articles/19802 last-modified: 2025-08-15 description: Wheat cultivation in arid environments faces significant challenges, necessitating innovative approaches to enhance productivity under current climate change conditions. Foliar application with bio-stimulants, such as amino acids, yeast extract, and algae extract, offers a sustainable solution to improve wheat growth, yield, and physiological efficiency under these conditions. A field trial was carried out over two winter growing seasons to assess the comparative effects of these bio-stimulants applied at varying concentrations on growth parameters, yield traits, grain quality, and nitrogen-related parameters. Treatments included an untreated control (sprayed with distilled water) and foliar applications at different concentrations: amino acids (1.5 and 3 ml/L), yeast extract (50 and 100 ml/L), and algae extract (5 and 10 ml/L). The results demonstrated that all bio-stimulant treatments significantly enhanced all studied parameters compared to the untreated control. The highest concentrations of each treatment (3 ml/L for amino acids, 10 ml/L for algae extract, and 100 ml/L for yeast extract) produced the greatest improvements, with amino acids at 3 ml/L exhibiting the strongest effects. Specifically, amino acids at 3 ml/L improved plant height by 12.46% and 21.56%, chlorophyll content by 22.32% and 19.12%, and plant dry weight by 63.30% and 70.38% in the first and the second seasons, respectively. Yield traits, including number of spikes, spike length, spike weight, number of spikelets per spike, number of grains per spike, and 1,000-grain weight, were also significantly improved, with amino acids at 3 ml/L producing the highest values. Grain yield, straw yield, and biological yield increased by 44.74% and 43.92%, 35.34% and 42.37%, and 36.29% and 43.95%, respectively, in the first and second seasons. Nitrogen content in both grains and straw was higher in treated plants, with amino acids at 3 ml/L enhancing grain nitrogen content by 25.52% and 22.50% and straw nitrogen content by 41.03% and 56.45% in the first and second seasons. The improvement resulted from amino acids at 3 ml/L followed by the application of algae extract at 10 ml/L and yeast extract at 100 ml/L, with all treatments showing significant improvements over the untreated control. Principal component analysis and heatmap analyses confirmed that higher concentrations of amino acids, algae extract, and yeast extract had the most positive effects on wheat growth and nitrogen-related parameters, while the untreated control and lower concentrations showed weaker results. These findings demonstrated that foliar application of amino acids, particularly at 3 ml/L, is a highly effective strategy for improving wheat productivity, grain quality, and nitrogen use efficiency in arid environments. creator: Mohamed Ebaid creator: Mohamed E. El-Temsah creator: Mohamed A. Abd El-Hady creator: Amirah S. Alahmari creator: Ahmed S. M. El-Kholy creator: Diaa Abd El-Moneim creator: Ahmed M. Saad uri: https://doi.org/10.7717/peerj.19802 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ebaid et al. title: Exercise type, training load, velocity loss threshold, and sets affect the relationship between lifting velocity and perceived repetitions in reserve in strength-trained individuals link: https://peerj.com/articles/19797 last-modified: 2025-08-15 description: PurposeTo explore the relationship between bar velocity and perceived repetitions in reserve (pRIR) for the bench press and the squat exercises during multiple training sessions in strength-trained individuals.MethodsNineteen well-trained individuals (9♀ and 10♂, 26 ± 4 yr, 174 ± 8 cm, 74 ± 9 kg (mean ± standard deviation)) trained squats and bench press for six weeks. Within each week, they conducted three sessions with different loads, corresponding to ∼77–79%, ∼82–84%, and ∼87–89% of one repetition maximum (1RM). The mean velocity was measured at the bar for all lifts, and the participants terminated each set based on a pre-set velocity loss threshold (20–60%). After every set termination, the participants reported pRIR.ResultsBased on 2,972 unique measurements, we observed trivial to very large individual correlations between the objectively measured mean velocity and the pRIR (average r2 = 0.3 for both squat and bench press). Type of exercise (squat or bench press), velocity loss threshold, load, and sets affected the pRIR for a given mean velocity. Sex (females vs. males) and training weeks were unrelated to pRIR.Discussion and conclusionOur findings indicate that mean bar velocity and pRIR offer complementary—but not interchangeable—perspectives on strength training performance. Because pRIR was systematically influenced by exercise type, external load, proximity to failure, and set number, practitioners and researchers should interpret pRIR with caution and in the context of these variables. creator: Gøran Paulsen creator: Roger Myrholt creator: Fredrik Mentzoni creator: Paul Andre Solberg uri: https://doi.org/10.7717/peerj.19797 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Paulsen et al. title: The effect of rotenone contamination on high-resolution mitochondrial respiration experiments link: https://peerj.com/articles/19879 last-modified: 2025-08-14 description: BackgroundHigh-resolution respirometry is commonly used in skeletal muscle research and exercise science to measure mitochondrial respiratory function in both permeabilized muscle fibers and isolated mitochondria. Due to the low throughput and high cost of the most used respirometer, the Oroboros 2k (O2k), multiple experiments are often conducted within the same chamber in short succession. Despite this, no methodological consideration has been given for the potential contamination of inhibitors, used to investigate the contribution of specific complexes within the electron transport chain, between experiments.MethodsWe first assessed the potential effect of inhibitor contamination on mitochondrial respiration experiments by evaluating the ability of the currently recommended wash protocol to remove rotenone and compared its efficacy against a simplified wash protocol of sequential rinses. Secondly, we assessed the potential effect of inhibitor contamination on mitochondrial respiration measured before and after a single session of high-intensity interval exercise, with and without the use of rotenone between experiments.ResultsThe currently recommended protocol for washing chambers was insufficient for removing rotenone. Following exercise, a decrease in mitochondrial respiration was observed exclusively in chambers exposed to rotenone between experiments.DiscussionOur findings highlight an important methodological consideration regarding the measurement of mitochondrial respiratory function using high-resolution respirometry, with inhibitor contamination potentially affecting the conclusions derived from experiments conducted in close succession. Future studies investigating mitochondrial respiratory function should assess the necessity of using inhibitors such as rotenone, ensure thorough wash procedures between experiments, and explicitly report the washing protocols used. creator: Dale F. Taylor creator: Jia Li creator: Nicholas J. Saner creator: Jia Wei creator: Xu Yan creator: Elizabeth G. Reisman creator: Hanzhe Li creator: Matthew J-C Lee creator: Navabeh Zare creator: Andrew Garnham creator: Jujiao Kuang creator: David J. Bishop uri: https://doi.org/10.7717/peerj.19879 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Taylor et al. title: The role of T cells in the treatment of Parkinson’s disease link: https://peerj.com/articles/19818 last-modified: 2025-08-14 description: Current pharmacological treatment of Parkinson’s disease (PD) predominantly employs dopaminergic agents aimed at enhancing cerebral dopamine levels. While these therapeutic strategies provide symptomatic relief, their palliative nature is frequently associated with dose-dependent complications, including gastrointestinal disturbances, emetic symptoms, and motor complications such as dyskinesia. Moreover, the honeymoon period of drugs has greatly limited their clinical application. The multifactorial etiology of PD continues to challenge researchers, yet substantial evidence implicates α-synuclein as a critical pathogenic mediator. Emerging findings suggest that dysregulated neuroimmune interactions constitute a fundamental mechanism in PD progression, where chronic immune activation appears particularly detrimental to neuronal survival. Notably, neuroinflammatory cascades coupled with compromised blood-brain barrier (BBB) integrity create a self-perpetuating cycle of neural degeneration, wherein α-synuclein-specific T cells exacerbate disease pathology while regulatory T cell populations demonstrate potential immunomodulatory capacities. This review systematically examines the mechanistic interplay involving neuroinflammatory cascades, BBB compromise, central nervous system (CNS) immunoregulation, and T lymphocyte subpopulations (including regulatory T cells) in the pathogenesis of PD. By synthesizing current evidence, we aim to establish a conceptual framework supporting the investigation of cellular immunity-based therapies for PD. creator: Zhuomiao Lin creator: Xihui Yu creator: Yunming Zhong creator: Guozhu Tan creator: Jiahong Zhong uri: https://doi.org/10.7717/peerj.19818 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lin et al. title: The interactive influence of gender and ergonomic factors, alongside psychosocial associations, on work-related musculoskeletal disorders in Saudi dental students: a cross-sectional study link: https://peerj.com/articles/19798 last-modified: 2025-08-14 description: BackgroundWork-related musculoskeletal disorders (WMSDs) among dental students have been documented, with female gender frequently identified as a contributing factor. Yet there is a lack of studies that have investigated the underlying factors between gender and WMSDs.ObjectivesThe primary aim of this study was to examine the interaction of gender with two specific ergonomic risk factors—academic level and weekly training hours—on WMSDs. Additionally, the associations of psychosocial factors, namely perceived stress and social support, with WMSDs were explored separately.MethodologyA self-reported questionnaire was distributed among a convenience sample of 409 undergraduate dental students at a dental school in Western Saudi Arabia. The questionnaire comprised socio-demographic characteristics, WMSDs using validated questionnaire (Nordic Musculoskeletal Questionnaire), the Perceived Stress Scale, and the Perceived Social Support Scale. Descriptive, bivariate and logistic regression analyses were performed.ResultsThe median/interquartile range age of the participants was 21 (2) years, and 59% were males. Of the participants, 71% (95% confidence interval (CI) [64.3–76.7]) self-reported WMSDs in at least one area of body over the past 12 months, with the most reported WMSDs being in the lower back, followed by the neck, wrists/hands, and shoulders at 48%, 45%, 31% and 30%, respectively. In fully adjusted logistic regression, being a female and the synergy between gender (female), academic levels and assigned training hours per week were significantly associated with self-reported WMSDs (adjusted odd ratio (AOR): 0.05, 95% CI [0.02–0.17], p < .001; AOR: 1.33, 95% CI [1.07–1.65], p = .011).ConclusionIn this study sample, psychosocial factors were not associated with WMSDs. However, the results suggest that female student were more likely to self-report WMSDs than counterparts. Notably, the interaction between gender, academic level and number of hours training assigned per week contributed significantly and positively in self-reported WMSDs specifically among female students. Intervention may consider female students at higher academic levels with training demands. creator: Saba Kassim creator: Hawazin Mohammad Alblehshi creator: Hala Bakeer creator: Manuel Barbosa Almeida creator: Doaa S. Al-Harkan creator: Safa Jambi creator: Doaa Felemban creator: Wafa Alaajam creator: Nebras Althagafi creator: Hani T. Fadel creator: Alla Alsharif uri: https://doi.org/10.7717/peerj.19798 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kassim et al. title: Topology-aware pathway analysis of spatial transcriptomics link: https://peerj.com/articles/19729 last-modified: 2025-08-14 description: Spatial transcriptomics (ST) has transformed genomics by mapping gene expression onto intact tissue architecture, uncovering intricate cellular interactions that bulk and single-cell RNA sequencing often overlook. Traditional ST workflows typically involve clustering spots, performing differential expression analyses, and annotating results via gene-set methods such as overrepresentation analysis (ORA) or gene set enrichment analysis (GSEA). More recent spatially-aware techniques extend these approaches by incorporating tissue organization into gene-set scoring. However, because they operate primarily at the level of individual genes, they may overlook the connectivity and topology of biological pathways, limiting their capacity to trace the propagation of signaling events within tissue regions. In this study, we address that gap by translating gene expression into pathway-level activity using the Pathway Signal Flow (PSF) algorithm. PSF integrates expression data with curated interaction networks to compute numeric activity scores for each branch of a biological pathway, producing a functionally annotated feature space that captures downstream signaling effects as branch-specific activity values. We applied PSF to two public 10x Genomics Visium datasets (human melanoma and mouse brain) and compared clustering based on PSF-derived pathway activities from 40 curated Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways and gene expression with standard Seurat Louvain clustering and spatially aware methods (Vesalius, spatialGE). We observed good correspondence between PSF-based and expression-based clustering when spatially aware clustering methods were used. This suggests that branch-level pathway activities can themselves drive clustering and pinpoint spatially deregulated processes. To assess cluster-specific functional annotation, we compared PSF results to conventional ORA (based on marker genes) and GSDensity (based on cluster-specific gene sets). PSF identified a broader set of significant pathways with substantial overlap with both ORA and GSDensity, providing increased sensitivity due to its branch-level resolution. We further demonstrated that PSF-derived activity values can be used to detect spatially deregulated pathway branches, yielding results comparable to those obtained with spatially aware gene set analysis approaches such as GSDensity and spatialGE. The availability of pathway topology and branch-specific information also enabled the identification of potential intercellular communication via ligand-receptor interactions between deregulated pathways in adjacent tumor regions. To support interactive exploration of results, we developed the PSF Spatial Browser, an R Shiny application for visualizing pathway activities, gene expression patterns, and deregulated pathway networks. creator: Siras Hakobyan creator: Maria Schmidt creator: Hans Binder creator: Arsen Arakelyan uri: https://doi.org/10.7717/peerj.19729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hakobyan et al. title: Effect of proprioceptive neuromuscular facilitation (PNF) technique on posture, balance and gait characteristics of older adults with scapular dyskinesis: a randomized controlled trial link: https://peerj.com/articles/19718 last-modified: 2025-08-14 description: BackgroundProprioceptive neuromuscular facilitation (PNF) techniques are being utilized among rehabilitation protocols for older adults because they are based on proprioception and coordination activities. The main purpose of this study was to analyze whether including scapular PNF in an intervention improves the posture, balance, and gait characteristics of older adults with scapular dyskinesis.MethodsForty-eight older adults (26 females; 22 males; mean ± SD age, 69.17 ± 4.36) with scapular dyskinesis were randomized into two groups: PNF and conventional exercise group (PNF+Ex) (n = 23) and conventional exercise group (Ex) (n = 25). Both groups received treatment three times a week for eight weeks and each session lasted 60 min. Outcome measurements included the Lateral Scapular Slide Test (LSST), Dynamic Gait Index (DGI), Walking Speed Test, Timed Up and Go Test (TUG), Functional Reach Test (FRT), and PostureScreen Mobile (PSM) iOS application, which were collected at baseline, after treatment, and three months after the last session.ResultsBoth groups showed improvements in scapular dyskinesis, gait characteristics, and posture. When the two groups were compared, the PNF+Ex group had significantly different LSST results in three positions (0°, 45°, and 90°) (P < 0.000, F = 5.414, F = 11.440 and F = 31.234) and postural results for head tilt (F = 4.116, P = 0.045), vertical displacement of head (F = 5.790, P < 0.000) and shoulder tilt (F = 6.959, P < 0.008). There were no statistically significant differences in the improvement in balance and gait characteristics between the groups (P > 0.05).ConclusionScapular PNF can be added to the rehabilitation of older adults with scapular dyskinesis to improve their scapular disposition and posture. A longer treatment duration is suggested to improve the gait and balance. creator: Hasan Cellatoğlu creator: Beliz Belgen Kaygısız uri: https://doi.org/10.7717/peerj.19718 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cellatoğlu and Belgen Kaygısız title: Biomechanical determinants of high ball speed during instep soccer kick by prepubescent male athletes: the importance of muscle elasticity link: https://peerj.com/articles/19923 last-modified: 2025-08-13 description: BackgroundThe purpose of this study was to determine whether muscle viscoelastic properties, muscle activation and thigh rotational velocity and rotational acceleration are significantly associated with high ball speed during instep soccer kick by prepubescent male athletes.MethodologyThis study included 31 prepubescent male soccer players. Maximal ball speed during the instep kick was measured using a radar gun. Viscoelastic properties such as tone, elasticity, and stiffness of the superficial abdominal and leg muscles were measured at rest using myotonometry. The activation of the rectus abdominis (RA) and rectus femoris (RF), as well as the thigh’s three-dimensional rotational velocity and acceleration, were evaluated using surface electromyography and an inertial measurement unit.ResultsSignificant negative correlations were found between the maximum ball speed and the hamstring medialis (HM) and gastrocnemius medialis (GM) elasticity (r = −0.656 and −0.680; power > 0.95; p < 0.05 for all). Significant positive correlations existed between maximum ball speed and RA–RF activation (r = 0.494 and 0.579), maximum thigh rotational velocity in the sagittal plane (r = 0.619), and maximum thigh rotational acceleration in the sagittal (r = 0.435) and horizontal (r = 0.380) planes (power > 0.95; p < 0.05 for all). The multiple linear regression analysis demonstrated that significant parameters for maximum ball speed were HM (B = −36.84) and GM (B = −26.83) elasticity along with thigh rotational velocity in sagittal plane (B = 0.01) (adjusted R2 = 0.56, delta R2 = 0.17).ConclusionsThe elasticity of the GM and HM muscles, the activation levels of the RA and RF muscles, and the rotational velocity-acceleration of the thigh in the sagittal and horizontal planes were significant factors associated with high ball speed during the instep kick. To enhance ball speed during the instep kick, training methods that focus on improving the elasticity of the GM and HM muscles, as well as increasing activation of the core and rectus femoris, should be prioritized for prepubescent male soccer players. creator: Volkan Deniz creator: Abdullah Kılcı uri: https://doi.org/10.7717/peerj.19923 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Deniz and Kılcı title: The effects of biotic stress on the sexual reproduction process of flowering plants link: https://peerj.com/articles/19880 last-modified: 2025-08-13 description: The sexual reproduction phase of flowering plants encompasses a multitude of physiological processes, including floral induction, floral organ morphogenesis, fertilization, and the maturation of seeds and fruits. In addition to being vital to the successful reproduction of the plants, these processes are also crucial to their adaptation to diverse environmental conditions. However, this phase is extremely complex and vulnerable to environmental impacts and constraints, with both biotic and abiotic stresses playing a significant role. Accumulating evidence has demonstrated that environmental stress has multifaceted impacts on plant sexual reproduction, leading to substantial losses in seed production and crop yield. Although several excellent reviews have explored the regulatory mechanisms of abiotic stresses (such as light and temperature stress) on the plant sexual reproduction process, particularly flowering time and gametophyte development, a comprehensive overview of the effects of biotic stresses is still lacking. Rather than comprehensively reviewing the massive amount of literature in this field, our review aims to leverage case studies to cover a wide range of mechanisms by which biotic stressors, including fungi, bacteria, viruses, parasitic plants, and herbivorous animals, affect the sexual reproduction process of flowering plants. creator: Zhenzhen Li creator: Shuo Wang creator: Yike Wang creator: Hongxia Zhang creator: Lu Liu creator: Shiwen Su creator: Sue Lin uri: https://doi.org/10.7717/peerj.19880 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Genetic variants of Toll-like receptor 9 are associated with susceptibility to systemic lupus erythematosus in Han Chinese female patients link: https://peerj.com/articles/19847 last-modified: 2025-08-13 description: BackgroundVariations in the TLR9 gene have been associated with several autoimmune disorders, but the relationship between TLR9 polymorphisms and systemic lupus erythematosus (SLE) remains controversial. This study aims to evaluate the potential association between three single-nucleotide polymorphisms (SNPs) within the TLR9 gene and susceptibility to SLE in the Han Chinese female population.MethodsA total of 150 SLE patients and 151 healthy controls of Han Chinese ethnicity were enrolled. Genotyping of TLR9 was performed using sequence-specific primer (SSP) polymerase chain reaction and validated by Sanger sequencing. Associations between the SNPs and SLE susceptibility were analyzed using the chi-square test or Fisher’s exact test. Additionally, correlations between the SNPs and clinical manifestations of SLE were assessed.ResultsThe TLR9 rs352139 polymorphism was significantly associated with increased SLE susceptibility in heterozygous (AG vs. AA, OR = 1.79, 95% CI [1.07–2.99], p =  0.025), homozygous (GG vs. AA, OR = 2.11, 95% CI [1.06–4.19], p =  0.033), dominant (GG+AG vs. AA, OR = 1.86, 95% CI [1.15–3.03], p =  0.012), and allele (G vs. A, OR = 1.49, 95% CI [1.07–2.06], p =  0.017) models. Similarly, rs352140 was significantly associated with SLE risk in homozygous (TT vs. CC, OR = 2.47, 95% CI [1.23–4.96], p =  0.010), recessive (TT vs. CC+CT, OR = 2.57, 95% CI [1.35–4.88], p =  0.003), and allele (T vs. C, OR = 1.43, 95% CI [1.03–1.99], p =  0.031) models. Haplotype analysis revealed that haplotype HT1 (C/A/T) had a protective effect against SLE (OR = 0.70, 95% CI [0.506–0.966], p =  0.030), while haplotype HT2 (T/G/T) was positively associated with increased susceptibility (OR = 1.505, 95% CI [1.068–2.121], p =  0.019).ConclusionsThese findings suggest that the TLR9 rs352139 and rs352140 polymorphisms are significantly associated with increased susceptibility to SLE in the Han Chinese population, indicating a potential role of TLR9 in the pathogenesis of SLE. creator: Lili Zhao creator: Shushu Du creator: Wenqi Xu creator: Xiaofei Shi creator: Rongzeng Liu uri: https://doi.org/10.7717/peerj.19847 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Use ATCCfinder to identify commercially available American Type Culture Collection strains based on sequence queries link: https://peerj.com/articles/19832 last-modified: 2025-08-13 description: Microbiology research was conducted for decades before widespread availability of sequencing resources and large culture collection sequence repositories, making it challenging to efficiently identify and validate strains used in historical studies. Similarly, finding commercially available microbe strains similar to strains of interest, or containing target genes of interest found during metagenomic experiments is challenging. Despite tremendous advances in sequencing data availability, database curation, and sequence-searching software capabilities, identifying commercially available microbe strains from sequence data remains complicated and tedious. The American Type Culture Collection (ATCC) is an organization selling a wide variety of microbes, uniquely providing strain-level taxonomy classification and associated sequenced reference genomes for over four thousand isolates, with more being added regularly. As researchers purchase and sequence isolates from ATCC, many sequences derived from ATCC isolates are deposited on public databases such as NCBI-Genome. Sequences uploaded to public databases will vary in laboratory, bioinformatics, and metadata quality and can also contain mutations derived from cultivation which are not representative of ATCC stocks. Using ATCC-sourced reference genomes ensures consistent quality and analysis methodologies are implemented to accurately represent strain sequences. Currently, ATCC does not provide methods to search for sequence similarity between many query sequences and ATCC genomes. While NCBI-BLAST could be used to search for queries against GenBank, with results filtered for “ATCC” tags, search result quality varies and requires time-consuming sorting. Here we present the software ATCCfinder (GitHub: https://github.com/lanl/ATCCfinder, Zenodo: https://doi.org/10.5281/zenodo.15178103), utilizing ATCC application interface software (API) to generate query-able databases from ATCC genome resources. The algorithm generates databases of the four ATCC data types: strain-specific genome assembly sequence data (sequence), information about how each strain was collected (metadata, catalogue), and structural/functional information about genome assemblies (annotation). Once ATCC sequences are retrieved by ATCCfinder, nucleotide queries are compared against ATCC reference genomes via sequence alignment tool minimap2, with results parsed and analyzed to produce summaries describing ATCC-available strain homologous sequence matches. ATCCfinder identifies and downloads new ATCC references, allowing users to maintain an updated target search database. ATCCfinder efficiently accesses, queries, and summarizes ATCC resources, identifying purchasable strains homologous to historical sequences, functional genes, operons, and other genetic components. creator: Samuel I. Koehler creator: Earl A. Middlebrook creator: Blake T. Hovde creator: Erik R. Hanschen uri: https://doi.org/10.7717/peerj.19832 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: ©2025 Koehler et al. title: Chaetomium globosum from Alisma orientale (Sam.) Juzep. enhances the antioxidative stress capacity of Caenorhabditis elegans link: https://peerj.com/articles/19827 last-modified: 2025-08-13 description: BackgroundMedicinal plant endophytic fungi hold significant potential for producing natural antioxidants, as they thrive in environments rich in bioactive antioxidant compounds.MethodsThis study focuses on Chaetomium globosum, an endophytic fungus isolated from Alisma orientale (Sam.) Juzep., to explore the in vivo antioxidant activity associated with the ethyl acetate extract (CGE) and to explore the underlying mechanisms.ResultsThe results indicated that CGE treatment enhances the stress resistance in Caenorhabditis elegans, stimulates the antioxidant protection mechanisms of C. elegans, and exhibits strong antioxidant activity in vivo. RNA-seq analysis showed that CGE regulates Fatty acid degradation, glutathione metabolism, longevity regulating pathway-multiple species and MAPK signaling pathway in C. elegans. This study offers an important reference to the utilization of CGE as an antioxidant in the food and medical sectors, while also establishing a theoretical framework for utilizing the C. globosum as a natural antioxidant source. creator: Nayu Shen creator: Zhao Chen creator: Siyu Wang creator: Mingqi Zhang creator: Yujie Jia creator: Xinyu Zhang creator: Yirong Xiao creator: Zizhong Tang creator: Qingfeng Li creator: Ming Yuan creator: Tongliang Bu uri: https://doi.org/10.7717/peerj.19827 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shen et al. title: Sampling strategies for digestive system flora studies: current research and perspectives link: https://peerj.com/articles/19810 last-modified: 2025-08-13 description: BackgroundThe digestive system is significantly associated with the incidence and progression of various diseases. Investigating its microbial community will aid in the diagnosis, treatment, and prognostication of digestive pathologies. Microbial composition varies not only between distinct organs but also within different regions of the same organ. Additionally, dynamic shifts in microbial composition occur throughout various phases of the disease, complicating research. This study systematically evaluated the biological samples and diverse collection methods employed in digestive system microbiota research, with the aim of guiding sample selection and collection strategies for future microbial studies.MethodologyWe conducted a comprehensive literature review using professional databases such as PubMed and Web of Science. The focus of this review is on microbial community research, particularly the use of high-throughput sequencing to compare different samples of the same organization, as well as the impact of different sampling methods on microbial community structure of the same sample.ResultsA diverse array of microbiological samples are available for study, including saliva, endoscopic biopsies, luminal mucosa, luminal fluid, feces, bile, and surgically excised tissues. Multiple techniques exist to obtain specimens from identical locations, each with a unique set of benefits and limitations.ConclusionsWhen selecting specimens and sampling methods for microbiota studies, it is essential to consider the characteristics of the microbiota population, research environment, and the objectives of the study. Despite the importance of appropriate sampling for microbial community studies, consensus on the optimal sample type and collection method remains elusive. creator: Xiaobo Liu creator: Xia Cheng creator: Ziye Gao creator: Jun Pan creator: Shizhen Luo creator: Pei Liu creator: Hui Wen creator: Shu Jin uri: https://doi.org/10.7717/peerj.19810 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Liu et al. title: Ultrasonographic evaluation of intrinsic foot muscle thickness in soccer and basketball players: an observational study link: https://peerj.com/articles/19773 last-modified: 2025-08-13 description: ObjectiveThis study aimed to assess and compare the thickness of specific intrinsic foot muscles (IFM)—abductor hallucis brevis (ABH), flexor hallucis brevis (FHB), flexor digitorum brevis (FDB), quadratus plantaris (QP)—and the plantar fascia (PF) in amateur soccer and basketball players using ultrasonography.MethodsA cross-sectional design was employed, involving 35 male amateur athletes, including 17 soccer players and 18 basketball players. Ultrasonographic imaging was performed to measure the thickness of the IFM and PF in a relaxed position for all participants.ResultsBasketball players demonstrated significantly greater thickness in the ABH and FHB compared to soccer players. However, no substantial differences were observed in the thickness of the FDB, QP, or PF between the two groups.ConclusionsThe study identified sport-specific differences in the thickness of certain intrinsic foot muscles between soccer and basketball players. These variations may be attributed to the unique movement patterns and biomechanical demands of each sport, highlighting the importance of targeted training and injury prevention programs tailored to the needs of these athletes. creator: Lorena Canosa-Carro creator: Jorge Hugo Villafañe creator: Unai Torres-Berra creator: Jaime Almazán-Polo creator: Helios Pareja-Galeano creator: Sergio Vázquez-González creator: Carlos Romero-Morales uri: https://doi.org/10.7717/peerj.19773 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Canosa-Carro et al. title: The concentration of single-stranded DNA-binding proteins is a critical factor in recombinase polymerase amplification (RPA), as revealed by insights from an open-source system link: https://peerj.com/articles/19758 last-modified: 2025-08-13 description: Recombinase polymerase amplification (RPA) facilitates rapid, exponential, isothermal nucleic acid amplification without the need for specialized equipment. Since its development in 2006, RPA has been widely applied to detect hundreds of RNA and DNA targets, spanning point-of-care diagnostics and agricultural uses. However, its reliance on pre-assembled commercial kits limits flexibility for customization. In this study, we introduce an open-source alternative to commercial RPA kits, utilizing purified, heterologously expressed proteins to circumvent the fixed molar ratios of proprietary systems. Our method incorporates enzymes from the bacteriophage T4 homologous recombination pathway—single-stranded binding protein (gp32), recombinase (UvsX), and mediator (UvsY)—along with Moloney murine leukemia virus (MMLV) reverse transcriptase with enhanced thermal stability, and Bst and Bsu DNA polymerases. We assessed the impact of buffer composition, reagent concentrations, and reaction temperature using synthetic SARS-CoV-2 genes. Notably, gp32 concentration and buffer composition emerged as critical factors in optimizing RPA performance. Using this tailored system, we demonstrated successful detection of the SARS-CoV-2 N gene on lateral flow devices (LFDs) with cDNA from eight clinical samples, achieving results consistent with RT-PCR. This open-source RPA platform provides an adaptable and cost-effective alternative for researchers, enabling the exploration of diverse experimental conditions and offering a viable solution for those without access to commercial kits. creator: Francisco Cordoba-Andrade creator: Antolin Peralta-Castro creator: Paola L. García-Medel creator: Eduardo Castro-Torres creator: Rogelio Gonzalez-Gonzalez creator: Atzimba Y. Castro-Lara creator: Josue D. Mora Garduño creator: Claudia D. Raygoza creator: Noe Baruch-Torres creator: Alejandro Peñafiel-Ayala creator: Corina Diaz-Quezada creator: Cesar S. Cardona-Felix creator: Fernando Guzman Chavez creator: Carlos H. Trasviña-Arenas creator: Rogerio R. Sotelo-Mundo creator: Beatriz Xoconostle-Cazares creator: Agustino Martínez-Antonio creator: Luis Gabriel Brieba de Castro uri: https://doi.org/10.7717/peerj.19758 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cordoba-Andrade et al. title: The importance of individuals of different sizes in the population maintenance of a palm species used by the Fulni-ô Indigenous People in northeast Brazil link: https://peerj.com/articles/19739 last-modified: 2025-08-13 description: Factors such as climate, soil characteristics, habitat type, and land management practices can influence the demography of plant populations harvested by Indigenous Peoples and local communities. Here, we assessed the demographic responses of the palm Syagrus coronata to varying leaf harvest frequencies by the Fulni-ô Indigenous People in sites with different environmental and anthropogenic conditions in Águas Belas, Pernambuco, northeast Brazil. The leaves of this species are primarily harvested for handicraft production. In collaboration with local artisans, we conducted a participatory workshop where they identified harvest locations on a regional map. Plots and subplots were established in six of these sites, and the total height of all S. coronata individuals was recorded. We monitored survival and growth over three consecutive years and counted infructescences on reproductive individuals every three months during the first two years. Newly recruited individuals were also recorded and measured. Environmental variables (light availability, air temperature, and humidity) were measured quarterly in the first year, and soil samples were collected for chemical and physical analysis. We performed a principal component analysis (PCA) to evaluate differences among sites based on environmental and anthropogenic variables. Using demographic data, we constructed integral projection models (IPMs) and conducted a life table response experiment (LTRE) analysis to estimate vital rates and deterministic population growth rates (λ) for each population and sampling interval. Our results showed that S. coronata populations under high harvest frequencies declined during the study period. In contrast, populations with lower harvest frequencies were more influenced by the growth of smaller individuals, though seedling recruitment was reduced, highlighting the need to preserve these younger plants. Higher air temperatures, nutrient availability, and soil pH likely contributed to low adult fecundity and reduced recruitment. Additionally, cattle and livestock presence may have further hindered recruitment by trampling and grazing on smaller plants. In populations subjected to intermediate and high harvest frequencies, larger individuals had the greatest impact on population growth rates. However, these individuals exhibited lower survival, suggesting that harvest pressure may negatively affect this vital rate, as the Fulni-ô harvesters preferentially target larger juveniles and adults for their more substantial leaves. Based on these findings, we recommend management strategies to support S. coronata conservation while ensuring sustainable harvesting and safeguarding Fulni-ô handicraft production. creator: Juliana Loureiro Almeida Campos creator: Elcida de Lima Araújo creator: Aldicir Scariot creator: Eduardo Teles Barbosa Mendes creator: Rita de Cássia Quitete Portela creator: Ulysses Paulino Albuquerque uri: https://doi.org/10.7717/peerj.19739 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Campos et al. title: Identification of hub genes and prediction of the ceRNA network in adult sepsis link: https://peerj.com/articles/19619 last-modified: 2025-08-13 description: BackgroundSepsis refers to a dysregulated host immune response to infection. It carries a high risk of morbidity and mortality, and its pathogenesis has yet to be fully elucidated. The main aim of this study was to identify prognostic hub genes for sepsis and to predict a competitive endogenous RNA (ceRNA) network that regulates the hub genes.MethodsSix transcriptome datasets from the peripheral blood of septic patients were retrieved from the Gene Expression Omnibus (GEO) database. The robust rank aggregation (RRA) method was used to screen differentially expressed genes (DEGs) across these datasets. A comprehensive bioinformatics investigation was conducted, encompassing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses using the “clusterProfiler” package in R, as well as gene set enrichment analysis (GSEA) to further elucidate the biological functions and pathways associated with the DEGs. Weighted gene co-expression network analysis (WGCNA) was performed to identify a module significantly associated with sepsis. Integration of this module with protein–protein interaction (PPI) network analysis facilitated the identification of five hub genes. These hub genes were subsequently validated using an independent dataset and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis of peripheral blood samples from septic patients. The prognostic values of these hub genes were assessed via receiver operating characteristic (ROC) curve analysis. Finally, a ceRNA network regulating the prognostic hub genes was constructed by integrating data from a literature review as well as five online databases.ResultsRRA analysis identified 164 DEGs across six training cohorts. Bioinformatics analyses revealed concurrent hyperinflammation and immunosuppression in sepsis patients. Five hub genes were identified via WGCNA and PPI network analysis, and their differential expression was verified by the validation dataset (GSE28750) and RT-qPCR analysis in the peripheral blood of septic patients. ROC analysis confirmed four hub genes with prognostic value, and a ceRNA network was predicted to elucidate their regulatory mechanisms.ConclusionThis study identified four hub genes (CLEC4D, GPR84, S100A12, and HK3) with significant prognostic value in sepsis and predicted a ceRNA network (NEAT1-hsa-miR-495-3p-ELF1) regulating their expression. The integrated analysis reconfirmed the concurrent presence of hyperinflammation and immunosuppression in hospitalized sepsis patients. These findings enhance the understanding of sepsis pathogenesis and identify potential therapeutic targets. creator: Kangyi Xue creator: Kan Wu creator: Haoxian Luo creator: Haihua Luo creator: Zhaoqian Zhong creator: Fen Li creator: Lei Li creator: Li Chen uri: https://doi.org/10.7717/peerj.19619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xue et al. title: Reliability of the use of foot pressure pain threshold in adults: a test-retest analysis link: https://peerj.com/articles/19875 last-modified: 2025-08-12 description: BackgroundFoot pain is very common, affecting 24% of the adult population over 45 years old. Mechanical stimulation devices, such as pressure algometers, are used for the precise and objective quantification of the pain threshold (minimum tolerable pain). The digital pressure algometer is a diagnostic tool for evaluating pain thresholds and pain tolerance related to musculoskeletal conditions in patients. Pressure pain thresholds (PPT) measured with a digital algometer have shown good to excellent intra-rater agreement and reliability for most body locations. However, no study has focused on evaluating specific locations on the foot. This study aimed to determine the intra- and inter-session agreement and reliability of pressure pain threshold measurements on the foot in a population of adults aged 55 to 75 years.MethodUsing a JTECH Commander digital algometer, an experienced podiatrist measured the pressure pain thresholds at four locations on the sole of the dominant and non-dominant foot (head of the first metatarsal, head of the fifth metatarsal, pulp of the first toe, and center of the heel) in 15 male and 16 female volunteers aged 55 to 75. In each session, three pressure pain thresholds measurements were taken at each location. Measurements were repeated over three different sessions; the first and second sessions were 30 min apart, and the third session was 1 week later. The standard error of measurement (SEM) and coefficient of variation (CV) were calculated to reflect within- and between-session agreement. Reliability was assessed using intraclass correlation coefficients (ICC).ResultsWithin-session agreement, expressed as SEM, ranged from 3Newtons (N) to 8N depending on the test location. Between session agreement, expressed as SEM, ranged from 5N to 10N, and the CV ranged from 7.9% to 13.7% per location. The ICC values ranged from 0.76 to 0.91.ConclusionsA digital algometer can be used to measure pressure pain thresholds on the foot. Specifically, this study used this technique to evaluate PPT at four points on the plantar surface (head of the first and fifth metatarsals, pulp of the first toe, and center of the heel), and the results showed good to excellent reliability for within- and between-session measurements. creator: Lidia Mayorga-Vega creator: Ana Maria Jimenez-Cebrian creator: Francisco Javier Barón-López creator: Alonso Montiel-Luque creator: Juan Carlos Benavente-Marín creator: Julia Warnberg uri: https://doi.org/10.7717/peerj.19875 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mayorga-Vega et al. title: Road ecology of a Chihuahuan Desert snake community: size-based mortality sets the stage for evolutionary change in a widespread pitviper link: https://peerj.com/articles/19871 last-modified: 2025-08-12 description: Snakes are significant predators in many ecosystems, but high rates of road mortality threaten to diminish their ecological contributions. Documenting species-specific and demographic patterns of road use is crucial for understanding potential impacts, information that can be leveraged for implementing mitigation measures. I investigated the road ecology of a snake community in the Chihuahuan Desert of southern New Mexico, USA. Nocturnal road-cruising surveys were performed three times per month from April to November 2017 along a 37-km stretch of road, which produced 101 snake encounters of 10 species. On average, 4.2 snakes were encountered per survey with no individuals recaptured, equating to a density of 0.057 snakes per kilometer. Seasonal activity patterns indicated a peak in snake encounters from August through October. Standardized data were combined with opportunistic surveys conducted along the same stretch of road from 2014 to 2016. Overall, road mortality was considerable, with 34% of all snakes found dead-on-road (DOR). Across all species, males and females exhibited similar proportions of DOR while juveniles had a lower DOR rate. The Western Diamondback Rattlesnake (Crotalus atrox) was the most frequently observed species across all surveys (48% of all encounters) and 33% of these observations were found DOR. Models for adult C. atrox revealed that longer body sizes were linked to road mortality, where every 1 cm increase in total length increased the probability of a vehicle collision by almost 10%. Preliminary simulations indicated that directional selection against larger body sizes could reduce the mean size in this population by nearly 12 cm in 50 generations (or about 165 years in this species). Road mortality may have set the stage for evolutionary change in a widespread and ecologically important pitviper. Because roads and vehicle traffic will continue to expand globally, efforts to mitigate road-based effects on snakes are essential to implement before major ecological and evolutionary impacts are felt. creator: Daniel F. Hughes uri: https://doi.org/10.7717/peerj.19871 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hughes title: Muscle contraction type-specific association of acceleration and deceleration performance with rates of force development link: https://peerj.com/articles/19862 last-modified: 2025-08-12 description: BackgroundMany sports require rapid acceleration and deceleration, particularly when changing direction. These movements require a large impulse, highlighting the importance of rates of force development (RFDs). However, the relationships between acceleration and deceleration performance and concentric and eccentric RFDs have remained uncertain. This study evaluated the correlation between RFDs in different muscle contraction types and acceleration and deceleration performances.MethodsThis study included 28 healthy subjects (13 males and 15 females; age: 21 ± 2 years; height: 1.66 ± 0.09 m; body mass: 65 ± 10 kg). Concentric, eccentric, and isometric RFDs were evaluated by having the subjects perform squat jumps, countermovement jumps, and isometric squats, respectively. Acceleration and deceleration performances were measured using a 10-yard (9.14 m) sprint and change of direction deficit (CODdeficit; calculated by subtracting the linear sprint time from the total time of the pro-agility test), respectively. Correlation analyses were performed to determine the relationship between the RFDs and the 10-yard sprint time and CODdeficit. The Pearson product-moment correlation coefficient (r) was used for normally distributed dependent variable combinations, whereas the Spearman rank correlation coefficient (r(s)) was applied when at least one variable was not normally distributed.ResultsA faster 10-yard sprint time was only correlated with greater concentric RFD (r(s) = −0.41, p = 0.03, 95% CI [−0.69 to −0.03]), whereas a smaller CODdeficit was only correlated with greater eccentric RFD (r(s) = −0.44, p = 0.02, 95% CI [−0.71 to −0.07]). The isometric RFD showed no correlation with any performance parameters.ConclusionsA faster 10-yard sprint time was only correlated with a greater concentric RFD, whereas a smaller CODdeficit was only correlated with a greater eccentric RFD. Overall, these results provide insights into the association between the acceleration and deceleration performance and RFDs according to muscle contraction type, which could help in the creation of effective training methods for improving acceleration and deceleration performance. creator: Hikaru Kurosaki creator: Ema Tsubota creator: Motoki Katsuge creator: Kosuke Hirata creator: Kuniaki Hirayama uri: https://doi.org/10.7717/peerj.19862 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kurosaki et al. title: RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data link: https://peerj.com/articles/19849 last-modified: 2025-08-12 description: BackgroundThe capacity of metagenomic sequencing-based diagnostics to fully identify infections have made them useful instruments in clinical practice. We introduce an interactive platform that runs on a local server-class hardware resource and implements a number of open-source programs.ResultsRpNGS integrates an interactive tabular interface for the management of experimental processes, patient metadata, and automated sequencing analysis. This technology optimizes clinical reporting by autonomously generating standardized reports in Word format. We have utilized the platform on an artificial microbial community reference panel and several clinical metagenomics datasets from public databases to demonstrate the efficacy of this workflow.ConclusionsRpNGS is an innovative, user-friendly standalone application designed to store laboratory data (including reagents, primers, contaminants and run configurations), manage clinical metadata, process FASTQ files and produce analytical and comparative reports (including Word documents) that can be readily reviewed and certified. Its interactive interface necessitates no programming expertise, rendering it an invaluable instrument for clinical metagenomic pathogen identification. creator: Jing Zhou creator: Yao Tian creator: Min Yang creator: Ting Hao creator: Jun Ma creator: Shengyu Wang uri: https://doi.org/10.7717/peerj.19849 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhou et al. title: Ecotoxicological effects of CuO and TiO2 nanoparticles dietary exposure on the marine gastropod Littorina brevicula link: https://peerj.com/articles/19838 last-modified: 2025-08-12 description: Contamination of the aquatic environment by nanoparticles is a threat to marine biota but remains poorly understood. Engineered nanoparticles tend to rapidly sediment in the aquatic environment. Once deposited on the bottom, they become less available to filter organisms, but become available to the bottom feeders and grazers, benthic organisms. In this context, the present study investigated the effects on the gastropod Littorina brevicula of a food substrate containing copper oxide and titanium dioxide nanoparticles (NPs) by evaluating metal accumulation in their tissues, cytotoxicity, lipid peroxidation products and genotoxicity. The results showed an increase in copper and titanium content in the soft tissues of L. brevicula after 14 days of exposure. Significant cytotoxicity and an increase in malondialdehyde concentration, an indicator of peroxidation of membrane lipid peroxidation, were observed. The results of the comet assay showed pronounced genotoxicity of both NPs, as reflected by an increase in the mean percentage of DNA in the comet tail, as well as an increase in the number of highly damaged comets. The results provided clear evidence that even though the nanoparticles penetrated the digestive system of the mollusk as part of the food substrate, they retained toxic properties. In addition, the food model used in the experiments may be a useful tool in ecotoxicological studies using gastropods and other organisms with similar feeding behavior. creator: Sergey Kukla creator: Victor Chelomin creator: Andrey Mazur creator: Nadezhda Dovzhenko creator: Valentina Slobodskova creator: Evgeniy Elovskiy uri: https://doi.org/10.7717/peerj.19838 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kukla et al. title: Antigenic and mutational insights into the Nipah virus G glycoprotein: implications for viral entry, host specificity, therapeutics, and vaccine development link: https://peerj.com/articles/19835 last-modified: 2025-08-12 description: Nipah virus (NiV), a highly lethal RNA virus from the Paramyxoviridae family, causes severe neurological and respiratory diseases in humans. First identified during the 1990s outbreak in Malaysia, NiV remains a significant global health threat due to the absence of approved vaccines or antiviral treatments. Since its discovery, more than 754 cases have been reported, with a mortality rate exceeding 50%. Despite its classification as a biosafety level 4 pathogen, the molecular mechanisms underlying NiV pathogenesis remain poorly understood. Two surface glycoproteins—the attachment (G) and fusion (F) proteins—play crucial roles in facilitating early stages of cell entry and determining host specificity. While naturally occurring mutations in the G glycoprotein are limited, experimental studies involving engineered mutations have provided critical insights into receptor binding, fusion activation, and immune evasion. This review summarizes current knowledge of these antigenic and mutational findings, highlighting their implications for viral entry and host specificity, and providing valuable insights for the development of vaccines and therapeutics. creator: Nur Syafiqah Mohamad Nasir creator: Yasmin Khairani Muhammad Ismadi creator: Noreafifah Semail creator: Wan Alif Syazwani Wan Alias creator: Nik Mohd Noor Nik Zuraina creator: Nik Yusnoraini Yusof creator: Zakuan Zainy Deris creator: Mohd Zulkifli Salleh uri: https://doi.org/10.7717/peerj.19835 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mohamad Nasir et al. title: Light use efficiency (LUE) based bimonthly gross primary productivity (GPP) for global grasslands at 30 m spatial resolution (2000–2022) link: https://peerj.com/articles/19774 last-modified: 2025-08-12 description: The article describes production of a high spatial resolution (30 m) bimonthly light use efficiency (LUE) based gross primary productivity (GPP) data set representing grasslands for the period 2000 to 2022. The data set is based on using reconstructed global complete consistent bimonthly Landsat archive (400TB of data), combined with 1 km MOD11A1 temperature data and 1° CERES Photosynthetically Active Radiation (PAR). First, the LUE model was implemented by taking the biome-specific productivity factor (maximum LUE parameter) as a global constant, producing a global bimonthly (uncalibrated) productivity data for the complete land mask. Second, the GPP 30 m bimonthly maps were derived for the global grassland annual predictions and calibrating the values based on the maximum LUE factor of 0.86 gCm−2d−1MJ−1. The results of validation of the produced GPP estimates based on 527 eddy covariance flux towers show an R-square between 0.48–0.71 and root mean square error (RMSE) below ~2.3 gCm−2d−1 for all land cover classes. Using a total of 92 flux towers located in grasslands, the validation of the GPP product calibrated for the grassland biome revealed an R-square between 0.51–0.70 and an RMSE smaller than ~2 gCm−2d−1. The final time-series of maps (uncalibrated and grassland GPP) are available as bimonthly (daily estimates in units of gCm−2d−1) and annual (daily average accumulated by 365 days in units of gCm−2yr−1) in Cloud-Optimized GeoTIFF (~23TB in size) as open data (CC-BY license). The recommended uses of data include: trend analysis e.g., to determine where are the largest losses in GPP and which could be an indicator of potential land degradation, crop yield mapping and for modeling GHG fluxes at finer spatial resolution. Produced maps are available via SpatioTemporal Asset Catalog (http://stac.openlandmap.org) and Google Earth Engine. creator: Mustafa Serkan Isik creator: Leandro Parente creator: Davide Consoli creator: Lindsey Sloat creator: Vinicius Vieira Mesquita creator: Laerte Guimaraes Ferreira creator: Simone Sabbatini creator: Radost Stanimirova creator: Nathalia Monteiro Teles creator: Nathaniel Robinson creator: Ciniro Costa Junior creator: Tomislav Hengl uri: https://doi.org/10.7717/peerj.19774 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Isik et al. title: A workflow of open-source tools for drone-based photogrammetry of marine megafauna link: https://peerj.com/articles/19768 last-modified: 2025-08-12 description: Drones have revolutionized researchers’ ability to obtain morphological data on megafauna, particularly cetaceans. The last decade has seen a surge in studies using drones to distinguish morphological differences among populations, calculate energetic reserves and body condition, and identify decreasing body sizes over generations. However, standardized workflows are needed to guide data collection, post-processing, and incorporation of measurement uncertainty, thereby ensuring that measurements are comparable within and across studies. Workflows containing free, open-source tools and methods that are accommodating to various research budgets and types of drones (consumer vs. professional) are more inclusive and equitable, which will foster increased knowledge in ecology and wildlife science. Here we present a workflow for collecting, processing, and analyzing morphological measurements of megafauna using drone-based photogrammetry. Our workflow connects several published open-source hardware and software tools (including automated tools) to maximize processing efficiency, data quality, and measurement accuracy. We also introduce Xcertainty, a novel R package for quantifying and incorporating photogrammetric uncertainty associated with different drones based on Bayesian statistical models. Stepping through this workflow, we discuss pre-flight setup and in-flight data collection, imagery post-processing (image selection, measuring, linking metadata with measurements, and incorporating uncertainty), and methods for including measurement uncertainty into analyses. We coalesce examples from these previously published tools and provide three detailed vignettes with code to demonstrate the ease and flexibility of using Xcertainty to estimate growth curves and body lengths, widths, and several body condition metrics with uncertainty. We also include three examples using published datasets to demonstrate how to include measurement uncertainty into analyses and provide code for researchers to adapt to their own datasets. Our workflow focuses on measuring the morphology of cetaceans but is adaptable to other taxa. Our goal is for this open-source workflow to be accessible and accommodating to research projects across a range of budgets and to facilitate collaborations and longitudinal data comparisons. This workflow serves as a guide that is easily adoptable and adaptable by researchers to fit various data and analysis needs, and emergent technology and tools. creator: K.C. Bierlich creator: Josh Hewitt creator: Clara N. Bird creator: David W. Johnston creator: Julian Dale creator: Enrico Pirotta creator: Robert S. Schick creator: Joshua D. Stewart creator: Leslie New creator: Elliott Chimienti creator: Jeremy A. Goldbogen creator: Ari S. Friedlaender creator: Mauricio Cantor creator: Leigh G. Torres uri: https://doi.org/10.7717/peerj.19768 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bierlich et al. title: Substrate type and light intensity determine lampenflora concentration on paleontological remains in show caves link: https://peerj.com/articles/19622 last-modified: 2025-08-12 description: Artificial lighting in show caves is responsible for the growth of nuisance photosynthetic organisms, the so-called lampenflora, causing aesthetic, chemical and physical damage to cave cultural heritage, including paleontological resources in situ. This study focuses on the role of substrate in determining the concentration of lampenflora on paleontological findings in show caves, using the bone deposit “Cimitero degli Orsi” in the Toirano show cave (NW-Italy) as a testing ground. Specifically, we investigated whether the concentration of three distinct photosynthetic microorganisms—cyanobacteria, diatoms, and green algae—varies on different substrates, i.e., bones, rock, and soil, also keeping into account the role of light intensity. Our findings revealed that, among the tested organisms, diatoms exhibited higher concentration on bones compared to other substrates and it was even higher at increasing light intensity. On the other hand, cyanobacteria increased their concentration at increasing light without a clear preference for a specific substrate, while the presence of green algae was higher on rock and soil substrates rather than bones. When modelling the concentration of photosynthetic microorganisms within the bone deposit under different scenarios of light intensity reduction, we predicted a general decrease of all groups, that was stronger in cyanobacteria and green algae and weaker in diatoms on bone substrates. These results provide valuable insights on the colonization of nuisance photosynthetic microorganisms on bone substrates exposed to artificial lighting, with management implications for the conservation of paleontological findings in show caves. creator: Elena Piano creator: Marta Zunino creator: Giuseppe Nicolosi creator: Isabella Nicole Pisoni creator: Alice Cimenti creator: Alberto Cina creator: Marco Isaia uri: https://doi.org/10.7717/peerj.19622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Piano et al. title: On Dracograllus miguelitus sp. nov. (Nematoda: Draconematidae) from an inactive structure: insights into its taxonomy, biodiversity and ecology at hydrothermal vents link: https://peerj.com/articles/19585 last-modified: 2025-08-12 description: BackgroundHydrothermal vent fields are habitats to a diverse array of benthic organisms, including several nematode species, which represent a significant portion of the biodiversity in these environments. Despite their ecological importance, most research on hydrothermal vents has focused on macro-invertebrates. As a result, vent nematode biodiversity remains largely unexplored, especially in peripheral and inactive structures, underscoring the need for further investigation. A sampling program conducted in 2017 and 2018 along a gradient of venting activity led to the collection of a number of Draconematidae species in various habitats. In this article, we introduce Dracograllus miguelitus sp. nov., the first species of the genus described at a hydrothermal vent field, sampled from a visually inactive sulphide structure.MethodsThe samples were collected at the Lucky Strike vent field, on the Mid-Atlantic Ridge, using the suction sampler of the Remotely Operated Vehicle Victor6000. Specimens were retrieved from an edifice covered by a black layer of manganese oxy-hydroxides, with no local visible hydrothermal activity, at a depth of 1.639 m. Samples were sieved on a 32 µm mesh onboard, sorted and, for nematodes, identified to species level back in the lab. Fluorescent images were obtained using the ApoTome Fluorescence Microscope Module, and 3D observations were possible through the depth change method.ResultsWe established D. miguelitus sp. nov. as a new species based on the combination of the following characters: four cephalic adhesive tubes (CATs), an elongated loop-shaped amphid with varying branch sizes between males and females, and a circular amphid in juveniles. Additionally, females display a minute setae emerging from the vulvar aperture. In males, the posterior adhesive tubes (PATs) are arranged in four longitudinal rows: two sublateral rows, each containing 10–12 PATs, and two subventral rows, consisting of 10 PATs in each. In females, sublateral and subventral rows with 13 PATs each. So far, D. miguelitus sp. nov. is the first species of the genus to be described from a hydrothermal environment and the deepest one. Beyond the formal description of this new species, we provide ecological and taxonomic backgrounds on Draconematidae at hydrothermal vents, with insights into the genus distribution, biogeography, and nomenclatural issues.ConclusionThis discovery contributes to the knowledge of Draconematidae biodiversity, and highlights the importance to investigate nematode communities at species-level, data that is often missing at vent studies. Additionally, it underscores the significance of preserving inactive hydrothermal habitats, which are threatened by deep-sea mining activities. creator: William Johnson da Silva creator: Daniela Zeppilli creator: Valentin Foulon creator: Pierre-Antoine Dessandier creator: Marjolaine Matabos creator: Jozee Sarrazin uri: https://doi.org/10.7717/peerj.19585 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Johnson da Silva et al. title: The impact of changes in LH levels in flexible antagonist protocols on the clinical outcomes of fresh IVF/ICSI cycles in populations of POSEIDON groups 1 and 2: a retrospective cohort study link: https://peerj.com/articles/19857 last-modified: 2025-08-11 description: ObjectiveTo investigate the impact of changes in luteinizing hormone (LH) levels during ovulation induction using flexible gonadotropin-releasing hormone antagonist (GnRH-A) regimens in POSEIDON groups 1 and 2 on the clinical outcomes of fresh in-vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) cycles.MethodA retrospective analysis was conducted on the clinical data of females in POSEIDON groups 1 and 2 who underwent IVF/ICSI using a flexible GnRH-A regimen at the Reproductive Medicine Center of Fujian Maternal and Child Health Hospital from January 2017 to December 2022. According to the values of change in LH [(LH level on the trigger day − baseline LH)/baseline LH] × 100%, the study subjects were divided into five groups. The general information, laboratory indicators, and clinical outcomes of each group were compared.ResultsIn POSEIDON group 1, a significant difference was observed in terms of the number of retrieved eggs, mature eggs, fertilization number (two pronuclei (2PN) number), and cleavage among all groups (all P values < 0.05). In POSEIDON group 2, a significant difference was observed in terms of the number of retrieved eggs, mature eggs, fertilization number (2PN number), cleavage, excellent embryos, and blastocysts (all P values < 0.05). The number of eggs retrieved in group A was significantly lower than that in groups D and E (P = 0.010 and 0.001, respectively). The number of mature eggs in group A was significantly lower than that in groups D and E (P = 0.008 and 0.000, respectively). The number of mature eggs in group E was significantly higher than that in groups B and C (P = 0.033 and 0.021, respectively). The 2PN number in group A was significantly lower than that in groups D and E (P = 0.042 and 0.002, respectively). The cleavage count of group E was significantly higher than that of groups A and C (P = 0.005 and 0.037, respectively). The excellent embryos in group B were significantly lower than those of group E (P = 0.038).ConclusionThe use of a flexible GnRH-A regimen to induce ovulation in the POSEIDON groups 1 and 2 can lead to better-controlled ovarian stimulation (COS) outcomes. This involves the LH level on trigger day decreasing within the range of 0–100% from baseline (with optimal range being ≥ −100% to −50%). This trend was more obvious in the POSEIDON group 2 population. creator: Yuan Zhou creator: Yanying Lin creator: Lili Chen creator: Lisheng Huang creator: Yizhen Yang creator: Beihong Zheng creator: Yan Sun uri: https://doi.org/10.7717/peerj.19857 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhou et al. title: Effects of chemical surface pretreatments on the surface roughness and shear bond strength of fiber post-resin cement interfaces: a preliminary in vitro study link: https://peerj.com/articles/19853 last-modified: 2025-08-11 description: BackgroundThis preliminary study evaluates the impact of different chemical surface pretreatments on the surface roughness (Ra) of fiber posts and the shear bond strength (SBS) at the interface between the horizontal surface of fiber posts and resin cement, highlighting an area that has not been extensively researched.MethodsFifty glass fiber posts (Cytec Blanco, Hahnenkratt) were used, and polishing discs were employed to create a horizontally flat surface. Their dimensions were standardized using a digital caliper and divided into two pieces from each post (n = 20). The experimental groups included different pretreatment protocols: Group I (Control) had no pretreatment, Group II used 4% hydrofluoric acid (HF) (Porcelain Etchant, Bisco), Group III used 9.6% HF (Porcelain Etch Gel, Pulpdent), Group IV used 20% hydrogen peroxide (HP) (Merck KGaA), and Group V used 35% HP (Whiteness HP, FGM). Ten specimens from each pretreatment group were used for Ra evaluation (Perthometer Mahr), while the other ten were prepared for SBS testing. Silane and primer were applied before dual-cure resin cement (Multilink N, Ivoclar Vivadent), and SBS was tested after 48 h using a universal testing machine (Instron). SBS and Ra data were analyzed with one-way ANOVA and Tukey’s post hoc tests (p < 0.05).ResultsStatistical analysis revealed no significant pairwise differences when evaluating SBS values (p = 0.055). However, Groups IV and V exhibited higher SBS values compared to Groups I, II, and III. While 20% HP and 4% HF did not significantly enhance SBS, higher concentrations of HP achieved clinically acceptable bond strength. The surface pretreatment methods significantly influenced Ra (p = 0.00003). Groups III and IV exhibited significantly higher Ra values than Groups I, II, and V.ConclusionThis preliminary study indicates that chemical surface pretreatments can be safely used to enhance the bond strength between fiber posts and resin cement, as they are not time-consuming, easy to use, and clinically applicable. creator: Elif Turkes Basaran creator: Magrur Kazak creator: Kagan Gokce creator: Yasemin Benderli Gokce uri: https://doi.org/10.7717/peerj.19853 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Turkes Basaran et al. title: Bioinformatics analysis of laryngeal squamous cell carcinoma based on the high infection rate of HPV in Northwest China link: https://peerj.com/articles/19851 last-modified: 2025-08-11 description: BackgroundAn increasing number of studies have demonstrated that human papillomavirus (HPV) plays a crucial role in the occurrence and development of laryngeal cancer. The present study aims to identify the differentially expressed genes and pathways in HPV-positive and HPV-negative laryngeal squamous cell carcinoma (LSCC) cells for the diagnosis and treatment of HPV-related LSCC, and to determine the prevalence rate of HPV in laryngeal cancer in Northwest China.MethodsPCR-reverse dot blot was used to detect HPV genotypes in 115 LSCC patients’ paraffin sections from Jan 2022 to Jun 2024.HPV-positive TU212 cells (TU212HPV) were constructed via lentiviral transfection. RT-qPCR and Western blot detected mRNA and protein levels. RNA-seq and TMT sequenced gene and protein differences. DAVID database was used for Gene Ontology and pathway enrichment analyses. STRING and Cytoscape screened key genes and further analyzed pathways.ResultsAmong 115 patients, 64 were HPV-positive (HPV16 being the most common, 57 cases). The TU212HPV cell line was successfully constructed. RNA-seq identified 1,336 differentially expressed genes (797 upregulated, 539 downregulated). TMT found 236 differentially expressed proteins (124 upregulated, 112 downregulated). The key genes were discovered to be EGFR, CDC42, PXN, SLC2A1, GAPDH, FGF2, ICAM1, ITGB1, SFN, PGK1, and ISG15. Pathway enrichment showed involvement in neuroactive ligand-receptor interaction, Cytoskeleton in muscle cell, transcriptional misregulation in cancer, etc. (P < 0.05).ConclusionHPV infection rate is 55.65% among laryngeal cancer patients in Northwest China. Ten key genes, namely EGFR, CDC42, PXN, SLC2A1, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), FGF2, ICAM1, ITGB1, PGK1 and ISG15, as well as pathways like proteoglycans in cancer, regulation of actin cytoskeleton and HIF-1 signaling pathway are demonstrated to be of significance in the occurrence and development of laryngeal squamous cell carcinoma. PXN, ITGB1, ISG15, SLC2A1 and ICAM1 are regarded as potential therapeutic targets for HPV-positive laryngeal cancer. PXN and PGK1 are considered as potential prognostic markers for HPV-positive laryngeal cancer. creator: Fan Guo creator: Shurong Li creator: Shiqi Yan creator: Yuqiao Zhang creator: Guangke Wang creator: Ruixia Ma uri: https://doi.org/10.7717/peerj.19851 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo et al. title: Comparison of the efficacy of 12 interventions in the treatment of diabetic foot ulcers: a network meta-analysis link: https://peerj.com/articles/19809 last-modified: 2025-08-11 description: ObjectiveThis study aimed to comprehensively compare the efficacy of 12 interventions for diabetic foot ulcer (DFU) using a network meta-analysis (NMA).MethodsThe NMA was conducted by PRISMA guidelines, and the protocol was registered in PROSPERO (CRD42023461811). PubMed, Web of Science, Cochrane Library, and Embase databases were systematically searched from inception to September 2023. Randomized controlled trials (RCTs) enrolling patients with DFU were included if they compared epidermal growth factor (EGF), platelet-derived growth factor (PDGF), platelet-rich plasma (PRP), stem cells (SC), low-frequency ultrasound (LFU), negative pressure wound therapy (NPWT), low-level laser therapy (LLLT), electric stimulation (ES), extracorporeal shockwave therapy (ESWT), amniotic membrane therapy (AMT), hyperbaric oxygen therapy (HBOT), and topical oxygen therapy (TOT) against standard of care (SOC) or placebo. The primary endpoint assessed was the wound healing rate. Secondary endpoints comprised wound healing time, percentage area reduction (PAR), and amputation rate. The surface under the cumulative ranking curve (SUCRA) was calculated to rank the efficacy of interventions.ResultsA total of 99 RCTs involving 7,356 patients were included. Among the 12 interventions analyzed, only LFU (OR = 2.20; 95% CI [0.99–4.91]) and ES (OR = 1.88; 95% CI [0.87–4.05]) did not demonstrate statistically significant improvements in ulcer healing rate compared with SOC. Based on SUCRA rankings, SC (SUCRA = 89.7%; OR = 5.71; 95% CI [2.64–12.34]) and AMT (SUCRA = 89.2%; OR = 5.11; 95% CI [3.12–8.37]) ranked highest in promoting ulcer healing, while LFU (29.4%) and SOC (10.4%) ranked lowest. Regarding wound healing time, AMT (MD = –26.91 days; 95% CI [−44.27 to −9.55]), PRP (MD = –21.65 days; 95% CI [−33.61 to −9.69]), and NPWT (MD = −16.79 days; 95% CI [−31.12 to −2.26]) significantly reduced healing durations compared to SOC. SUCRA rankings indicated that AMT (84.7%) and PRP (74.6%) ranked highest, while LFU (29.4%) and SOC (10.4%) remained lowest. Concerning PAR, LLLT (MD = 34.27; 95% CI [17.35–51.20]) and ESWT (MD = 27.50; 95% CI [11.00–44.00]) showed significant improvements over SOC, with LLLT (SUCRA = 93.9%) and ESWT (SUCRA = 84.0%) ranking highest, while SOC (21.0%) and TOT (18.3%) ranked lowest. For amputation rate, SC (OR = 0.12; 95% CI [0.03–0.55]) and HBOT (OR = 0.35; 95% CI [0.16–0.78]) significantly lowered the risk compared to SOC, with SUCRA rankings placing SC (79.9%) and PRP (73.2%) as most effective, while NPWT (26.4%) and SOC (9.9%) were least effective.ConclusionsSC and AMT emerged as highly effective, demonstrating superior efficacy in improving healing rate compared to PDGF, ES, and HBOT. AMT also showed significant effects in shortening ulcer healing time. LLLT exhibited considerable effectiveness in reducing ulcer areas, and SC therapy was associated with reduced amputation rate. creator: Xuyang Hu creator: Huixin Meng creator: Jiaru Liang creator: Hang An creator: Jiaqi Zhou creator: Yuling Gao creator: Chong You creator: Zhenni Zhang creator: Xiaoyang Gong creator: Yong Liu uri: https://doi.org/10.7717/peerj.19809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hu et al. title: 25-gauge vitrectomy with gas tamponade for uncomplicated rhegmatogenous retinal detachment: experienced vs. inexperienced surgeons link: https://peerj.com/articles/19795 last-modified: 2025-08-11 description: BackgroundRhegmatogenous retinal detachment (RRD) is a vision-threatening condition that requires prompt surgical intervention. With advancements in surgical techniques and equipment, pars plana vitrectomy (PPV) has become increasingly popular for the management of RRD. This, in turn, requires beginner vitreoretinal surgeons to be able to manage RRD early in their training.IntroductionComparison of the results and complication rates of a 25-gauge (25 g) PPV with gas tamponade for RRD between experienced and inexperienced surgeons.MethodsThis is a retrospective comparative consecutive case series study of patients with uncomplicated RRD treated with 25 g PPV with gas tamponade. Patients were divided into two groups: in the experienced surgeon group (ESG), the procedure was performed by an experienced vitreoretinal surgeon, in the inexperienced surgeon group (ISG), it was performed by two inexperienced surgeons. Anatomical and functional results and complication rates were compared between the two groups.ResultsA total of 216 eyes were included in the study. In the ESG (106 eyes), the single operation success rate was 94.3%, and the final success rate was 100%. In the ISG (110 eyes), the single operation success rate was 93.6%, and the final success rate was 100%. The difference in single surgery success rate between groups was not statistically significant (P = 0.828). The mean postoperative BCVA improvement was 0.348 decimal in the ESG and 0.405 decimal in the ISG (P = 0.234). The difference in complication rates between groups was not significant.ConclusionsA 25 g PPV with gas tamponade for the treatment of RRD yields excellent anatomical results and improvement in best-corrected visual acuity (BCVA). With good technique and the use of modern vitrectomy machines and instruments, some inexperienced surgeons can achieve a high single-surgery success rate, suggesting a short learning curve. The complication rate is comparable between experienced and inexperienced surgeons. creator: Martin Pencak creator: Zbynek Stranak creator: Jakub Dite creator: Jana Vranova creator: Pavel Studeny creator: Miroslav Veith uri: https://doi.org/10.7717/peerj.19795 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pencak et al. title: Psychopathological symptoms in soccer referees: the role of psychological inflexibility and perfectionism link: https://peerj.com/articles/19790 last-modified: 2025-08-11 description: BackgroundRefereeing is associated with a high prevalence of mental health issues. Mental health problems are quite common in sport and referees are no exception. In the case of referees, psychological disorders have been associated with a number of factors and lower league officials appear more likely to experience psychological distress compared to their higher league counterparts.AimThe aim is to analyze the relationship between psychological inflexibility, perfectionism, and psychopathological symptomatology in soccer officials.MethodA cross-sectional, anonymous, online study was conducted. Psychopathological symptoms were assessed using the Symptom Assessment-45 Questionnaire; the Acceptance and Action Questionnaire was used to assess psychological inflexibility; Perfectionism was assessed using the Multidimensional Perfectionism Scale. Participants are 156 active main referee (96.8% male), of whom 63.5% are at amateur level and 36.5% at semi-professional/professional level.ResultsNo significant differences were found between amateur and semi-professional/professional referees in psychological inflexibility and psychopathological symptoms, except for paranoid ideation, where amateurs scored higher. Significant differences were observed in the total scores of maladaptive perfectionism, particularly regarding external influences, with amateurs scoring higher. In adaptive perfectionism, significant differences were noted in both total scores and achievement expectations, with amateurs obtaining higher scores. Psychological inflexibility demonstrated a strong predictive capacity for psychopathological symptoms (β = .716). When maladaptive perfectionism was incorporated in the model, it significantly predicted 17.6% of the variance. Adaptive perfectionism, however, did not significantly predict psychopathological symptomatology.ConclusionThe results suggest that psychological inflexibility and maladaptive perfectionism are good predictors of psychopathological symptoms and mental health in referees. The status of amateur or semi-professional officials does not differentiate them from professional referees in terms of psychological disorders, but it does in terms of perfectionism. With a view to the future, it is important to intervene on these constructs, which are modifiable and facilitate their well-being. creator: Félix Arbinaga creator: Emilio Moreno San Pedro creator: María-Isabel Mendoza-Sierra uri: https://doi.org/10.7717/peerj.19790 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Arbinaga et al. title: Development of a relapse-related RiskScore model to predict the drug sensitivity and prognosis for patients with ovarian cancer link: https://peerj.com/articles/19764 last-modified: 2025-08-11 description: BackgroundOvarian cancer (OC) is a highly aggressive malignancy in the reproductive system of women, with a high recurrence rate. The present research was designed to establish a relapse-based RiskScore model to assess the drug sensitivity and prognosis for patients with OC.MethodsGene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were accessed to obtain relevant sample data. The single-cell atlas of primary and relapse OC was characterized using the “Seurat” package. Differentially expressed genes (DEGs) between primary and relapse samples were identified by FindMarkers function. Subsequently, univariate Cox, least absolute shrinkage and selection operator (LASSO) and stepwise regression analysis were employed to determine independent prognostic genes related to relapse in OC to establish a RiskScore model. Applying “timeROC” package, the predictive performance of RiskScore model was assessed. Drug sensitivity of different risk groups was evaluated using “pRRophetic” package. The effects of relapse-related prognostic genes on OC cells were detected with in vitro assays.ResultsThe single-cell atlas revealed that compared to primary OC, fibroblasts were reduced but epithelial cells were increased in relapse OC. Five prognostic genes (LDHA, NOP58, NMU, KRT19, and RPS23) independently linked to relapse in OC were identified to construct a RiskScore model, which showed high robustness in the prognostic prediction for OC patients. High-risk group tended to have worse outcomes in terms of different clinical features than the low-risk group. Further, six drugs (Vinorelbine, GW-2580, S-Trityl-L-cysteine, BI-2536, CP466722, NSC-87877) were found to be correlated with the RiskScore. While the high-risk group had higher IC50 values to these drugs, the low-risk group was more sensitive to the six drugs. In addition, KRT19 silencing markedly inhibited the invasion and migration of OC cells.ConclusionThis study established a relapse-related RiskScore model based on five prognostic genes (LDHA, NOP58, NMU, KRT19, and RPS23), offering novel insights into the recurrence mechanisms in OC and contributing to the development of individualized treatment strategies. creator: Zhixin Jin creator: Xuegu Wang creator: Xiang Li creator: Shasha Yang creator: Biao Ding creator: Jiaojiao Fei creator: Xiaojing Wang creator: Chengli Dou uri: https://doi.org/10.7717/peerj.19764 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jin et al. title: Urate-lowering effects of polyphenolic compounds in animal models: systematic review and meta-analysis link: https://peerj.com/articles/19731 last-modified: 2025-08-11 description: BackgroundRecent research underscores the critical role of uric acid (UA) in the pathogenesis and progression of various diseases. However, the effects of polyphenolic compounds on uric acid levels remain poorly defined.ObjectiveThis review aims to assess the impact of five specific polyphenolic compounds on uric acid levels in animal models.MethodologyWe performed an exhaustive literature search through October 30, 2024, utilizing databases including Wanfang, VIP, Cochrane Library, CNKI, Embase, and PubMed. The methodological quality of the included animal studies was evaluated using the SYRCLE (Systematic Review Centre for Laboratory animal Experimentation) risk of bias tool. Data analysis was conducted using R software, with meta-analyses performed via RevMan 5.3, adhering to the Cochrane Handbook for Systematic Reviews of Interventions.ResultsOur analysis integrated data from 49 studies, revealing that the selected polyphenolic compounds significantly lowered serum uric acid (SUA) levels across various animal models (standardized mean difference (SMD) = −2.33, 95% CI [−2.73, −1.93]) and increased urinary uric acid (UUA) levels (SMD = 2.53, 95% CI [1.38, 3.69]). Subgroup analyses demonstrated consistent SUA reduction across different disease models. Detailed meta-analyses for each polyphenol disclosed distinct contributions to SUA reduction: resveratrol (RES) (SMD = −1.86, 95% confidence interval (CI) [−2.28, −1.45]), chlorogenic acid (CGA) (SMD = −2.31, 95% CI [−2.89, −1.73]), ferulic acid (FA) (SMD = −2.82, 95% CI [−4.46, −1.19]), punicalagin (PU) (SMD = −3.87, 95% CI [−5.99, −1.75]), and bergenin (BER) (SMD = −8.51, 95% CI [−10.30, −6.73]).ConclusionThis meta-analysis supports the proposition that polyphenols such as RES, CGA, FA, PU, and BER effectively reduce serum uric acid in animal models. Notably, RES exhibited an inverted U-shaped nonlinear trend. However, the high heterogeneity and methodological constraints, including small sample sizes, ambiguous randomization practices, and potential publication bias, necessitate cautious interpretation. Further high-quality research is essential to substantiate these findings and facilitate their translation into clinical practice. creator: Jianhong Chen creator: Boye Zhang creator: Zhongzhi Cao creator: Li Yang creator: Ye Yuan uri: https://doi.org/10.7717/peerj.19731 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen et al. title: Influence of the Great Amazon Reef System and Pleistocene sea-level drops on the phylogeography of Haemulon aurolineatum (Haemulidae) link: https://peerj.com/articles/19415 last-modified: 2025-08-11 description: BackgroundPhylogeography is based on the principle that species exhibit genetic structure shaped by biogeographic, ecological or environmental barriers, using both genetic and geographic components, offering valuable insights into evolutionary processes. In marine organisms, gene structure is influenced by life histories, geological events, and oceanographic conditions. The Greater Caribbean (GC), is a biogeographic region spanning from North Carolina, United States to northern Guyana, comprising three provinces: Northern, Central and Southern Caribbean. South of the GC is the Brazilian biogeographic province. Bellow the Amazonas-Orinoco plume the Great Amazon Reef System is present having mesophotic reefs situated beneath the freshwater discharge of the river. Each province is defined by distinct oceanographic conditions and habitat types, which play a significant role in shaping the evolutionary history of fish species. Due to its life history traits and the habitat heterogeneity across the GC, Haemulon aurolineatum, a widespread species found from Chesapeake Bay to Southern Brazil serves as an excellent model for studying evolutionary history of reef fishes in the GC region.MethodsWe use three nuclear DNA (nDNA) and one mitochondrial DNA (mtDNA) markers to study the phylogeographic history of H. aurolineatum. We performed gene structure, diversity indexes, haplotype networks, isolation by distance test, divergence time analysis and species delimitation methods in populations distributed through the geographic range of the species to understand the relation between the evolutionary history of the species, geophysical and biological aspects and make some taxonomic annotations.ResultsAll four molecular markers revealed two distinct genetic groups: one predominantly distributed in the Northern province and the other mainly found in the Central, Southern Caribbean and Brazilian provinces. The divergence between these groups is estimated to have occurred around 800,000 years ago (Kya), this is attributed to the redirection of the Loop Current caused by climatic and oceanographic changes during the Pleistocene epoch. Our investigation has found genetic homogeneity among populations in the Central, Southern, and Brazilian provinces, which may be attributed to the ability of H. aurolineatum to migrate along the mesophotic reefs of the Great Amazon Reef System within the Amazonas-Orinoco plume region. creator: A. Karim Awhida-Robinson creator: Eloísa Torres-Hernández creator: Rodolfo Pérez-Rodríguez creator: Víctor Julio Piñeros creator: María Gloria Solís-Guzmán creator: Arturo Angulo creator: Nuno Simões creator: Oscar M. Lasso-Alcalá creator: Mario Monroy creator: Omar Domínguez-Domínguez uri: https://doi.org/10.7717/peerj.19415 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Awhida-Robinson et al. title: Kinetic parameters of Scenedesmus obliquus (Chlorophyceae) growth and yield under different cultivation conditions in vitro link: https://peerj.com/articles/17879 last-modified: 2025-08-11 description: The aim of the present study is to assess the kinetic growth and yield of microalgae belonging to the species Scenedesmus obliquus (Kützing, 1833) grown under different macronutrient concentrations (N:P:K), pH and temperature. A three-level three-variable Box-Behnken factorial design was developed to test the influence of environmental factors on the growth parameters applied to a microalgal crop, namely: maximum cell density (Nmax), specific growth rate (µ, d−1), doubling time (T2) and maximum yield (Pmax). A classical logistic growth model was applied to estimate the kinetic behavior of a S. obliquus culture in comparison to other studies in the literature. Maximum cell density (Nmax) significantly changed between 32.3 ± 0.84 and 101.5 ± 12.5 × 105 cells mL−1 (p = 0.004). Specific growth rates (µ) and Pmax showed significant mean variations between 0.28 ± 0.10 day−1 and 6.21 ± 4.57 cells mL−1 d−1, respectively. All growth curves were adjusted to the proposed logistic model and range variation was (0.65 ≤ r2 ≤ 0.99, p = 0.01). Maximum microalgae cell density per crop was found at temperature of 24 °C (Nmax = 49.0 × 105 cells mL−1) (p = 0.01), in 20 mL Nitrogen, Phosphorus, and Potassium (NPK) dilution (Nmax = 46.5 × 105 cells mL−1) (p = 0.02). Despite the significant variation in pH values (5.0 ≤ pH ≤ 9.0, p = 0.05), it did not have strong influence on plant growth responses. In conclusion, the kinetic study applied to S. obliquus growth and yield parameters emerged as reference for this species’ kinetic behavior and bioprospecting under controlled and experimentally standardized conditions, and as support for pilot projects on bioreactors. creator: Arialdo M. Silveira Júnior creator: Silvia Maria Mathes Faustino creator: Fabrício Holanda e Holanda creator: Irlon Maciel Ferreira creator: Alan Cavalcanti da Cunha uri: https://doi.org/10.7717/peerj.17879 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Silveira Júnior et al. title: Transcriptomic insights into grain size development in naked barley (Hordeum vulgare L. var. nudum Hook. f): based on weighted gene co-expression network analysis link: https://peerj.com/articles/19856 last-modified: 2025-08-08 description: BackgroundThis study investigated the molecular mechanisms underlying grain size variation between two distinct naked barley varieties using comprehensive phenotypic and transcriptomic (RNA-Seq) analyses.MethodsIn this study, we employed a comparative transcriptomics approach to analyze two naked barley varieties: the large-grained Shenglibai and the small-grained Lalu Qingke. Our investigation focused on three critical developmental periods of grain growth (early, mid, and late grain-filling periods). By integrating longitudinal three-dimensional phenotypic data with temporal expression profiles and applying weighted gene co-expression network analysis (WGCNA), we successfully identified gene modules that co-vary with morphological expansion.ResultsPhenotypic assessments revealed that grains underwent rapid expansion during the filling period, with significant differences in grain width (GW) and thickness (GT) across all three developmental periods. In contrast, grain length (GL) remained relatively consistent by the end of the filling period. Transcriptome sequencing identified a peak in differentially expressed genes (DEGs) during the mid-filling period, indicating that the regulation of grain size development is most active in the early and mid-filling phases. WGCNA identified a blue module strongly correlated with grain size, which was significantly enriched in key metabolic pathways, including starch and sucrose metabolism. Further analysis identified seven hub genes, among which HvENO1 exhibited pronounced upregulation in large-grain varieties during the mid-to-late filling periods, closely aligning with the observed phenotypic traits. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation confirmed the period-specific and variety-specific expression patterns of these genes, further supporting the potential of these genes as targets for improving grain size in breeding. creator: Yan Wang creator: Jiahao Zhou creator: Mingqi Yang creator: Youhua Yao creator: Yongmei Cui creator: Xin Li creator: Baojun Ding creator: Xiaohua Yao creator: Kunlun Wu uri: https://doi.org/10.7717/peerj.19856 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Effect of ecological restoration on carbon storage of damaged mountain slope in China’s East Ussuri River Basin link: https://peerj.com/articles/19854 last-modified: 2025-08-08 description: Ecological restoration techniques are extensively employed in the ecological restoration of damaged mountain ecosystems via effectively restoring the plant community and improving soil functions. Aggregate spray seeding technology as an effective ecological restoration method, can quickly restore the damaged slopes to their previous status and keep the ecosystem functions. However, the lack of understanding of the characteristic of carbon storage as well as its influencing factors limits the scientific management of carbon sink function of the rehabilitated damaged mountain ecosystem. In this study, relying on field surveys in the East Ussuri River Basin, we analyzed the carbon storage distribution and its influencing factors in damaged mountain slopes that had been restored through the spray seeding technology after an 8-year restoration phase. The results showed that the carbon storage distribution of the damaged slopes repaired by aggregate spray seeding is in the order of soil layer > tree layer > shrub layer > litter layer > herbaceous layer. Among them, the carbon storage of the vegetation layer is mainly distributed in the tree layer, and its size is similar to that of undisturbed natural slopes. Plants and soil are the main factors affecting the carbon storage of the repaired slopes, where the plant density has a significant positive correlation with carbon storage, accounting for 19% of the carbon storage variation, and the soil bulk density has a significant negative correlation with carbon storage, accounting for 23.7% of the carbon storage variation. This study reveals the mechanism of the aggregate spray seeding technology in restoring the carbon storage of damaged slopes and points out that regulating vegetation density and improving soil conditions are key to enhancing the carbon sink capacity of slopes. creator: Jianjun Zhu creator: Shilei Zhang creator: Chen Chen creator: Chunlin Li uri: https://doi.org/10.7717/peerj.19854 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhu et al. title: Effects of different exercise types on vascular endothelial function in individuals with abnormal glycaemic control: a systematic review and network meta-analysis link: https://peerj.com/articles/19839 last-modified: 2025-08-08 description: BackgroundBrachial artery flow-mediated dilation (FMD) is a key marker of endothelial function, often impaired in individuals with abnormal glycemic control. While exercise has been shown to improve brachial artery FMD, the relative efficacy of different exercise modalities remains unclear. This study employed a network meta-analysis (NMA) to compare the effects of various types of exercise on FMD.MethodsA comprehensive search of PubMed, Embase, Cochrane, Web of Science, and EBSCO databases identified randomized controlled trials evaluating the effects of exercise on brachial artery FMD up to January 2025. Two independent reviewers screened studies, extracted data, and assessed risk of bias. Eligible studies were assessed for bias using version 2 of the Cochrane Risk of Bias tool. Stata 16.0 was used for the NMA.ResultsSeventeen studies with 797 participants (prediabetes: 76; T2DM: 721) were included. Aerobic interval exercise (AIE) significantly improved FMD (MD = 2.23%, 95% CI [1.0 9%–3.37%], P < 0.05), followed by mind-body exercise (MBE) (MD = 1.97%, 95% CI [0.60%–3.33%], P < 0.05). Combined exercise (CE) (MD = 1.17%, 95% CI [0.13%–2.21%], P < 0.05) and aerobic continuous exercise (ACE) (MD = 1.20%, 95% CI [0.52%–1.87%], P < 0.05) also showed significant improvements. SUCRA values indicated that AIE (89.0) and MBE (80.1) were the most effective in improving FMD, followed by CE (51.0), ACE (50.9), and resistance exercise (RE) (20.1), all outperforming the control group (SUCRA = 9.2).ConclusionAIE was the most effective modality for improving FMD, with MBE serving as a viable alternative for individuals with lower fitness or cardiovascular concerns. CE and ACE also provided benefits, while RE was less effective. Future studies should focus on long-term outcomes and personalized exercise strategies. creator: Zongxiang Li creator: Shengyao Luo creator: Xuebing Bai creator: Lu Huang creator: Hongyan Guo creator: Song Chen creator: Dan Wang uri: https://doi.org/10.7717/peerj.19839 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Unveiling the mental state: validating the uBioMacpa Pro stress measurement tool among Chinese college students link: https://peerj.com/articles/19830 last-modified: 2025-08-08 description: Mental stress is a significant contributor to various health issues, including cardiovascular disease, anxiety, and depression. Scholars have developed many tools and methods to evaluate psychological stress states. uBioMacpa Pro is one of the measuring meters that evaluates accumulated stress by measuring heart rate variability (HRV). This study uses reliability and validity tests to validate uBioMacpa Pro among Chinese college students. A total of 260 students (females = 146, males = 114) with a mean age of 21 years (SD = 1.48, 1.51) were volunteers and recruited in the reliability and validity tests, respectively. The heart rate variability parameters showed satisfactory test-retest and inter-rater reliability, with the most intraclass correlation coefficient (ICC) values exceeding the acceptable threshold of 0.75. Validity assessment was done by exploring concurrent validity that measured the psychological stress of college students by using uBioMacpa Pro and using the validated Chinese version of the Stress Scales for College Students (C-SSCS) as a reference. The result showed a significant correlation between the uBioMacpa Pro stress index and C-SSCS questionnaire scores (r = 0.246, p < 0.001). The overall finding of our study implies that the uBioMacpa Pro has good reliability and validity, and it can be used for monitoring and assessing Chinese college students’ mental stress. creator: Mingzhu Pan creator: Xinxing Li creator: Liying Yao creator: Solomon Gbene Zaato creator: Yee Cheng Kueh creator: Garry Kuan uri: https://doi.org/10.7717/peerj.19830 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pan et al. title: A retrospective study on beta-blocker use and outcomes in hematopoietic stem cell transplant patients link: https://peerj.com/articles/19822 last-modified: 2025-08-08 description: Recent studies have linked beta-blocker (BB) use in critical care settings with improved survival outcomes, potentially due to beta-adrenergic receptor (β-AR) blockade and associated anti-inflammatory effects. Given the immune system’s role in the development of graft-versus-host disease (GVHD)—a major complication of allogeneic hematopoietic stem cell transplant (allo-HCT)—we conducted a single-center retrospective review to assess the impact of BB use on acute GVHD (aGVHD) and other survival outcomes in patients undergoing their first allo-HCT. We analyzed 10 years of data (January 2010 to May 2020), including 105 patients who received a BB for more than four days before and after HCT, and 669 control patients who did not receive a BB. Patients on BBs had a lower incidence of aGVHD (55.2% vs. 65.8%, p = 0.036); however, this difference was not statistically significant in multivariate analysis (p = 0.150). When stratified by BB mechanism, outcomes varied: non-selective BBs were associated with lower post-HCT weight (p = 0.034), and vasodilating BBs showed a borderline reduction in length of stay (LOS) (p = 0.054). While our findings confirm the pharmacological safety of BBs in this population, they do not support their routine use for modifying allo-HCT outcomes. Future prospective studies with larger cohorts are needed to further explore the role of BBs in peri-HCT management and to clarify their clinical implications and therapeutic potential. creator: Matthew A. Bergens creator: John T. Bokman creator: Ernaya J. Johnson creator: Matthew L. Braun creator: Yan Li creator: Amy T. Bush creator: Lauren Hill creator: Jolien Van Opstal creator: Alessandro Racioppi creator: Rebecca Fan creator: Sejal Kaushik creator: Edwin Alyea creator: Nelson Chao creator: Taewoong Choi creator: Cristina Gasparetto creator: Mitchell Horwitz creator: Richard Lopez creator: Sendhilnathan Ramalingam creator: Keith Sullivan creator: Paul Wischmeyer creator: Anthony D. Sung uri: https://doi.org/10.7717/peerj.19822 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bergens et al. title: Molecular profiling and sex determination of Cannabis sativa germplasm collection: Exploring microsatellite markers and high-resolution melting (HRM) analysis link: https://peerj.com/articles/19770 last-modified: 2025-08-08 description: Cannabis sativa L., a versatile plant grown for its seeds, fiber, and cannabinoids, has recently received significant scientific interest due to its wide range of industrial and pharmaceutical uses and economic prospects. The objective of this study is to assess the genetic variation of cannabis by examining its morphological and molecular characteristics in 83 different genotypes preserved at the Institute of Plant Breeding and Genetic Resources in Thessaloniki. Utilizing 10 microsatellite markers, important genetic variation was observed among the samples. Population structure analysis using STRUCTURE software indicated four distinct genetic subpopulations, which were further supported by the principal coordinate analysis (PCoA). The validity of these clusters was further confirmed through unweighted pair group method with arithmetic mean (UPGMA) phylogenetic analysis. The analysis of molecular variance (AMOVA) indicated that most of the genetic variation is present within individuals rather than among them or among populations (9% among populations, 53% within individuals). The expected heterozygosity (He or uHe) turned out to be 0.60–0.66, which supports moderate diversity. The fixation indices (Fst = 0.094, Fis = 0.417, Fit = 0.472) were statistically significant and suggested a moderate level of genetic differentiation between the two populations. Nei’s genetic distance between hemp and marijuana groups was calculated as D = 0.288, indicating a moderate level of genome-wide divergence between these two major use types. Additionally, high-resolution melting (HRM) analysis utilizing sex-linked markers successfully identified 73 female and 10 male plants, underscoring the value of early sex identification in enhancing breeding strategies. These findings contribute valuable insights into the genetic diversity and sex determination mechanisms of Cannabis sativa and support future breeding programs which aim at developing cultivars with favorable traits. creator: Anastasia Boutsika creator: Eleftheria Deligiannidou creator: Theodoros Moysiadis creator: Nikolaos Tourvas creator: Panagiotis Karnoutsos creator: Marios Karagiovanidis creator: Dimitrios Magalios creator: Christos Nanos creator: Vangelis Mitsis creator: Eleni Tsaliki creator: Eirini Sarrou creator: Apostolos Kalivas creator: Ioannis Ganopoulos uri: https://doi.org/10.7717/peerj.19770 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Boutsika et al. title: Variability of bulb morpho-geometrical properties in onion (Allium cepa L.) germplasm collections, using digital imaging tools link: https://peerj.com/articles/19583 last-modified: 2025-08-08 description: BackgroundPhenotypic characterization of onion germplasm is requisite for designing breeding programs, and for meeting industrial processing, and marketing demands. Onion bulb morphology, and geometrical properties, which are the physical and spatial dimensions and shape characteristics influence consumer and market demand, as well as suitability for processing and mechanizing post-harvest handling. Many previous studies employed manual tools such as Vernier calipers for measurement of onion bulb parameters, which is time-consuming. The emergence and application of phenomics tools such as digital cameras are more convenient for rapid phenotypic characterization.AimThis study aimed to investigate the phenotypic variability of 29 onion accessions based on ten qualitative and twelve quantitative bulb characteristics.MethodologyFreshly harvested onion bulbs (n = 10/accession) were obtained from the Allium Vegetable Research Institute (AVRI), at Muan-Gun, Republic of Korea. A digital camera was used to capture images of the bulbs. The images were saved in JPEG file format, and uploaded into ImageJ software for measurement of linear dimensions, including polar diameter, equatorial diameter, transverse diameter or thickness. To ensure accurate measurement, images were first calibrated, using the straight line tool and the “Set scale” function in the software. Results of the linear dimensions were then used for estimating other geometrical properties, such as aspect ratio, sphericity, and geometric and arithmetic mean diameters.ResultsOur findings revealed a broad range of phenotypic variation within the germplasm. Polar and equatorial diameters ranged from 4.731 to 11.998 cm, and from 4.54 to 10.196 cm, with mean values of 9.213 and 7.472 cm, respectively. Also, geometric and arithmetic mean diameters ranged from 4.224 to 10.484 cm, and from 4.257 to 10.569 cm, with corresponding mean of 7.901 and 7.980 cm, respectively. Principal component analysis grouped the accessions into three distinct clusters, with cluster three composing the highest number of accessions. Strong significant positive associations were observed among several traits. For instance, polar diameter correlated strongly with polar diameter and transverse diameter (r > 0.97), geometric and arithmetic mean diameters (r > 0.98), surface area (r > 0.96), frontal surface area (r > 0.94), cross sectional area (r > 0.96), equatorial diameter (r > 0.83), and thickness of neck (r > 0.84). High to moderate broad sense heritability and genetic gain were estimated for several traits.ConclusionOverall, the significant variability within the onion germplasm provides a potential for breeding new cultivars to meet consumer and industrial requirements. The results also provide information vital for future genomic and metabolite studies. creator: Seong-Hoon Kim creator: Kanivalan Iwar creator: JiWon Han creator: Inchan Choi creator: Jaesu Lee creator: Kingsley Ochar uri: https://doi.org/10.7717/peerj.19583 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Kim et al. title: Silver-spoon effect in agricultural crop consumers: crop consumption enhances skeletal growth in sika deer link: https://peerj.com/articles/19836 last-modified: 2025-08-07 description: Owing to agricultural expansion worldwide, agricultural crops can have major effects on the life history traits of wildlife. However, the functional role of crop consumption on the life history traits of long-lived mammals is seldom evaluated quantitatively. Body size is an important life history trait because it is directly related to fitness. In this study, we investigated the functional role of long-term crop consumption on skeletal growth of sika deer (Cervus nippon). Crop consumption accelerated skeletal growth of not only the consumer but also the next generation, and its effect differed by sex. In females, the degree of crop consumption produced maximum differences of about 1.4 years in the ages at which 98% asymptotic size was attained. Furthermore, there was a maximum difference of 1.5 times in the skeletal growth rate. On the other hand, crop consumption did not always affect skeletal growth in males. The degree of crop consumption by mothers generated a maximum difference of about 15% in the hind-foot length of their fetus. This study revealed that long-term crop consumption makes a difference in skeletal growth of deer at an individual level, even within the same population. Crop consumption by the mother has “a silver-spoon effect” on the next generation from the fetus stage. creator: Ayaka Hata creator: Midori Saeki creator: Chinatsu Kozakai creator: Rumiko Nakashita creator: Keita Fukasawa creator: Yasuhiro Nakajima creator: Ryodai Murata creator: Yuki Harada creator: Mayura B. Takada uri: https://doi.org/10.7717/peerj.19836 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hata et al. title: Exposure to Batrachochytrium dendrobatidis metabolites altered ghost shrimp behavior and reduced mortality link: https://peerj.com/articles/19815 last-modified: 2025-08-07 description: Batrachochytrium dendrobatidis, or Bd, is a waterborne, pathogenic chytrid fungus implicated in the decline and extinction of hundreds of amphibian species worldwide. Bd can infect multiple taxa, causing disease in susceptible species associated with epidermal degradation, lethargy, weight loss, gill damage, and disruption of osmoregulation and cardiac dysfunction, ultimately leading to mortality in many instances. Bd produces water soluble chemicals (Bd metabolites) that, while implicated in infection and Bd-related pathology, have also been shown to have prophylactic effects for amphibians. This study examined the impact of Bd metabolite exposure on critical non-target freshwater invertebrates to better understand how Bd metabolites might impact non-target species if used as a prophylaxis in the field. We examined the effects of Bd metabolites on the freshwater species, Palaemonetes paludosus, or ghost shrimp, focusing specifically on the effects on behavior, cardiac function, and mortality. Shrimp were randomly split into two treatment groups and on day 4, they were dosed with 1 ml of either an artificial spring water (ASW) control or Bd metabolite treatment. We found that ghost shrimp exposed to Bd metabolites experienced decreased heart rate, reduced threat response behaviors, and reduced mortality, when compared to those exposed to an ASW control. Our findings suggest that exposure to the Bd metabolites may actually provide some benefits to ghost shrimp as it decreased mortality compared to controls. While more research is needed to understand if there are indirect impacts of the metabolites associated with the behavioral and cardiac changes, this research highlights that exposure to Bd metabolites does not appear to be detrimental to these critical, keystone freshwater invertebrates. This is particularly important given that Bd metabolites may be used prophylactically in the field, which may lead to non-target organism exposure. creator: Ellisa Carla Parker-Athill creator: Liam C. Muldro creator: Aiza J. Malinias creator: Taegan A. McMahon uri: https://doi.org/10.7717/peerj.19815 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Parker-Athill et al. title: Insights into the molecular mechanisms underlying the function of lysyl oxidase like 1 in cancers link: https://peerj.com/articles/19628 last-modified: 2025-08-07 description: Cancer is one of the primary causes of human mortality and a significant barrier to increasing human life expectancy. The effective screening, early diagnosis, and treatment of cancer have long been clinical challenges, and thus new biomarkers or molecular targets must be identified to improve the diagnosis and treatment of cancer patients. Lysyl oxidase like 1 (LOXL1), a secreted copper-dependent amine oxidase, is commonly expressed in a variety of cell types. LOXL1 can maintain the steady state of elastin, engage in extracellular matrix (ECM) remodelling. LOXL1 has diverse biological functions, and its dysregulation is the basis of many clinical diseases. The abnormal expression or activation of LOXL1 can disrupt the cellular microenvironment, contributing to the development of various diseases, such as atherosclerosis, tissue damage, fibrosis, and cancer. Recent research has revealed that LOXL1 is often overexpressed in a majority of cancers, where it plays a role in regulating tumor growth and metastasis. However, some studies have also suggested that LOXL1 may have a tumor-suppressive function. Research has indicated that the LOXL1 protein is reduced in human renal cell carcinoma (RCC) and bladder cancer (BLCA), where it acts to suppress tumor growth. Conversely, it is upregulated in human salivary adenoid cystic carcinoma (SACC), non-small cell lung cancer (NSCLC), pleural mesothelioma (PM), brain glioma, prostate cancer (PRAD), gastric cancer (GC), breast cancer (BC), thyroid carcinoma (THCA), pancreatic adenocarcinoma (PAAD), and osteosarcoma (OS). The expression of LOXL1 in colorectal cancer (CRC) remains a topic of debate, as it may either be upregulated or downregulated. These findings imply that LOXL1 may have a dual role in cancer, either inhibiting or facilitating carcinogenesis. This article provides a comprehensive review of the structure and function of LOXL1, along with its associations with cancer. Additionally, it explores the role of LOXL1 in tumor microenvironment remodeling, tumorigenesis, metastasis, and the molecular mechanisms that underpin these processes. creator: Xinmeng Wang creator: Xiaoyi Wang creator: Yihan Li creator: Dan Zhao creator: Jintao He creator: Lin Wang creator: Zhengliang Li creator: Wei Xiong uri: https://doi.org/10.7717/peerj.19628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Compatibility of endoscopic examination using i-scan technology with histopathology results in laryngeal carcinoma: prospective observational study link: https://peerj.com/articles/19552 last-modified: 2025-08-07 description: IntroductionLaryngeal carcinoma is a type of cancer that occurs in the laryngeal tissue with a high mortality rate. Fiber optic laryngoscopy examination with i-scan is a non-invasive technology used to visualize changes in the structure of the mucosa and blood vessels, aiding in better identification of malignancies. Despite its promising potential, the routine use of i-scan technology in examinations is not yet established in Indonesia, especially West Java.ObjectiveTo compare endoscopic findings using i-scan with histopathological results in patients with laryngeal carcinoma.MethodsThis study is an analytical prospective observational research with a cross-sectional design, followed by a concordance test analysis using accuracy tests and the kappa index. The data collected include information from all laryngeal tumor patients at the ORLHNS outpatient clinic at Dr. Hasan Sadikin General Hospital from July to December 2023.ResultsThis prospective observational study evaluated i-scan endoscopy’s diagnostic accuracy versus histopathology in 29 laryngeal carcinoma patients, demonstrating 96% sensitivity (95% CI [80.4–99.3%]) and 100% specificity (95% CI [39.8–100%]) with substantial histopathological agreement (κ = 0.86, 95% CI [0.61–1.00]). The technology outperformed white light endoscopy (κ = 0.608) in detecting malignancies, correctly identifying vascular patterns in 24/25 malignant cases (eight poorly differentiated, six moderately differentiated, five well-differentiated squamous cell carcinomas) and all four benign lesions. One false-negative involved a well-differentiated carcinoma, potentially due to obscuring edema or tumor positioning. These findings underscore i-scan’s utility for precise malignancy detection and biopsy guidance in laryngeal carcinoma evaluation.ConclusionOur findings demonstrate concordance between i-scan endoscopic examination and histopathological results in laryngeal carcinoma evaluation. While this study provides preliminary evidence supporting the potential utility of i-scan technology for early lesion identification and biopsy targeting, further validation through larger-scale multicenter studies is warranted to confirm its clinical applicability. creator: Gracia Cintia Massie creator: Agung Dinasti Permana creator: Shinta Fitri Boesoirie creator: Lina Lasminingrum creator: Melati Sudiro creator: Yussy Afriani Dewi uri: https://doi.org/10.7717/peerj.19552 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Massie et al. title: Acute effects of lower trapezius activation exercises on shoulder muscle activation during overhead functional tasks in symptomatic and asymptomatic adults link: https://peerj.com/articles/19861 last-modified: 2025-08-06 description: IntroductionShoulder musculoskeletal disorders are associated with atypical kinematics and muscle activity. Exercises to activate weakened muscles may reduce pain and disability. The objectives of this study were to test the effectiveness of exercises for activating the lower trapezius and to compare changes in shoulder muscle activity during functional tasks before and after the exercises in symptomatic and asymptomatic groups.MethodsEighteen adults, nine with subacromial pain syndrome and nine asymptomatic controls, participated in this study. A within-session repeated measures case-control design was employed. Participants performed overhead functional tasks before and after completing lower trapezius activation exercises. Electromyography (EMG) data of scapular muscles were captured during the tasks and exercises. One-way analysis of variance (ANOVA) compared muscle activations during the exercises. Paired t-test statistical parametric mapping assessed changes in muscle activity after the exercises.ResultsLower trapezius activation was highest during the Trapezius Muscle Exercise for both groups. Post-exercise, a transient increase in lower trapezius activation was observed in the pain group during the Comb Hair task (p = 0.0012, d = 1.55) and the no pain group in the Overhead Reach task (p < 0.001, d = 1.38) , but this effect did not persist in either group.DiscussionThe exercise protocol successfully increased lower trapezius activation immediately post-exercise, but the effects were short-lived. The findings suggest that while lower trapezius activation exercises can temporarily alter muscle activation, their efficacy for acute prevention or rehabilitation is limited. Further research is needed to explore the effects of longitudinal training programs on functional task performance. creator: Sophia Abiara creator: Vivian Heinrichs creator: Annaka Chorneyko creator: Angelica E. Lang uri: https://doi.org/10.7717/peerj.19861 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Abiara et al. title: Habituation but not classical conditioning of the disturbance hiss of the hissing cockroach (Gromphadorhina portentosa) link: https://peerj.com/articles/19805 last-modified: 2025-08-06 description: This article explores learned changes in the disturbance hiss of the hissing cockroach, Gromphadorhina portentosa. Compared to extensive research on learning in other cockroaches, studies with this species are rare. Of the natural behaviors of G. portentosa, the disturbance hiss is also seldom investigated. Two experiments were conducted to address these deficits. The first experiment investigated habituation to repeated tactical stimulus delivered near the cerci. The effect of sex and heat were also assessed in a group design. This experiment found typical habituation trends, with males showing higher rates of hissing, and heated cockroaches showing marginally higher rates of hissing. Similar, but less pronounced results were seen with probability of movement. The second experiment explored classical conditioning by presenting an olfactory stimulus prior to, and along with, tactile stimulation. After conditioning, the olfactory stimulus and a second novel olfactory stimulus were presented on opposite ends of the apparatus to determine if there was conditioned preference. No evidence of conditioned response was observed in this experiment. Hissing and movement were observed during and after tactile stimulation, but responses were not observed before trials or during olfactory stimulus presentations. No preference between novel and conditioned odor was observed in the preference test. These findings confirm habituation in G. portentosa but highlight challenges in eliciting conditioned responses, emphasizing the need for further research to enhance understanding of insect learning and behavior. creator: Christopher A. Varnon uri: https://doi.org/10.7717/peerj.19805 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Varnon title: High cyclic GMP-AMP synthase and stimulator of interferon genes in cholangiocarcinoma suggest their potential as targets for treatment link: https://peerj.com/articles/19800 last-modified: 2025-08-06 description: BackgroundCancer remains the leading cause of death worldwide. Chromosomal instability (CIN) is one hallmark of cancer. Micronuclei (MN) is an observable outcome of CIN. The role of cytosolic MNs or DNAs in activating an immune response via a cyclic guanosine monophosphate–adenosine monophosphate (GMP-AMP) synthase (cGAS)-a stimulator of interferon genes (STING) signaling cascade is established. However, the information regarding the cGAS-STING pathway in cholangiocarcinoma (CCA) is limited. This study aimed to determine cGAS-STING-related molecules in CCA and reveal their clinical importance.MethodsMNs in CCA cell lines were demonstrated by nuclear staining and cGAS, STING, nuclear factor kappa B (NF-κB) p65 were determined by Western blot analysis. Expressions of cGAS-STING-related mRNAs in gastrointestinal cancers were analyzed using Gene Expression Profiling Interactive Analysis (GEPIA) based on The Cancer Genome Atlas (TCGA) database. The expressions of cGAS, STING, and NF-κB p65 in clinical CCA samples were determined by immunohistochemistry (IHC) staining. The survival analyses were conducted using Kaplan-Meier survival analysis with a log-rank test, and the correlations between the targeted protein expression levels and clinical parameters were examined using Pearson’s Chi-square test. Furthermore, the Cox proportional hazard regression model was utilized for multivariate analysis. The expression levels of CGAS, STING, and RELA were analyzed using two public datasets of CCA. The relationship between key mRNAs and related immune cell infiltration was analyzed using the Tumor Immune Estimation Resource (TIMER).ResultsMNs generated during cytokinesis were demonstrated in the CCA cell lines and were positively correlated to STING level. GEPIA analysis revealed that members of the cGAS-STING pathway were significantly increased in GI cancers, particularly CCA and pancreatic cancer. IHC confirmed high cGAS and STING in CCA tissues, while NF-κB p65 showed variable expression. High NF-κB p65 was correlated with shorter patient survival, and larger tumor size. High NF-κB p65 contributed to an increased hazard ratio of 1.679 (95% confidence interval [1.074–2.626]). TIMER analysis demonstrated CGAS and STING were positively correlated with neutrophil, γδ T cell, and CD8+ T cell infiltration, while STING and RELA were associated with higher B cell infiltration. High CGAS, STING, and RELA were related to increased myeloid dendritic cell infiltration.ConclusionsThe high number of MNs in CCA cell lines emphasize their importance. Elevated cGAS, STING, and NF-κB p65 in CCA tissues highlight the significance of this pathway. While cGAS and STING showed no direct prognostic value, NF-κB p65 was identified as a prognostic predictor. Altogether, the opportunity of cGAS and STING targeting for CCA treatment and the predictive character of NF-κB p65 are proposed, and further exploration is recommended. creator: Han Ni Zin Myint creator: Paksiree Saranaruk creator: Natnicha Paungpan creator: Sakda Waraasawapati creator: Chawalit Pairojkul creator: Saowaluk Saisomboon creator: Nutsara Settha creator: Jatuporn Pattanachot creator: Seiji Okada creator: Wunchana Seubwai creator: Amnat Kitkhuandee creator: Kanlayanee Sawanyawisuth creator: Kulthida Vaeteewoottacharn uri: https://doi.org/10.7717/peerj.19800 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zin Myint et al. title: Serum β-klotho is a potential biomarker for diagnosing alcoholic liver disease and differentiating from nonalcoholic fatty liver disease link: https://peerj.com/articles/19779 last-modified: 2025-08-06 description: BackgroundAlcoholic liver disease (ALD), with the control of infectious liver disease and the improvement in living standards, is emerging as a significant liver disease posing a threat to public health. Besides, ALD often overlaps or coexists with nonalcoholic fatty liver disease (NAFLD), however, due to the lack of specific non-invasive biomarkers and the fact that drinkers’ self-reported alcohol consumption is often concealed, the identification of ALD and NAFLD is sometimes not easy. This study aims to explore a new specific serum biomarker to more easily diagnose ALD and differentiate it from NAFLD.Subjects and MethodsA total of 204 serum samples were collected, including 70 from ALD patients, 68 from NAFLD patients and 66 from healthy controls (HC). Serum β-klotho (sKLB) levels were measured using the enzyme-linked immunosorbent assay (ELISA). The diagnostic performance of potential biomarkers was evaluated using the area under the receive operating characteristic curve (AUROC).ResultsThe levels of sKLB were significantly elevated (1,332.12 (410.40, 2,687.00) pg/mL, p < 0.001) in ALD patients and significantly reduced in NAFLD patients (47.82 (32.76, 77.11) pg/mL, p = 0.018) compared to the healthy controls. The AUROC for sKLB in diagnosing ALD is 0.927, which was higher than that for the aspartate aminotransferase (AST)/alanine aminotransferase (ALT) ratio (0.672) and γ-glutamyl transpeptidase (GGT) (0.891). The combined AUROC for sKLB + AST/ALT, sKLB + GGT, and AST/ALT ratio + GGT in diagnosing ALD were 0.924, 0.967 and 0.917, respectively.ConclusionsKLB is a potential biomarker for diagnosing ALD, and may aid in differentiating between ALD and NAFLD, when combined with GGT, sKLB offers enhanced diagnostic sensitivity and specificity for ALD. creator: Chengmei Fang creator: Xin Miao creator: Chuyan Peng creator: Zhenguo Xie creator: Fuzhen Zhao creator: Tian Chen creator: Wenjin Zhang creator: Xiaofei Bi creator: Xuan An creator: Guicheng Wu uri: https://doi.org/10.7717/peerj.19779 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fang et al. title: Physiological effects and technical strategies of LED supplemental lighting for pitaya cultivation: a review link: https://peerj.com/articles/19720 last-modified: 2025-08-06 description: Pitaya is a high-value perennial tropical fruit known for its nutritional and health benefits. It is now widely cultivated in many tropical and subtropical countries, offering strong economic returns. China ranks first globally in pitaya cultivation, which includes both open-field production in tropical and subtropical regions and facility-based cultivation in temperate zones. As a long-day, light-loving plant, pitaya can be produced year-round. However, during off-season cultivation in winter and spring, weak light conditions and limited daylight hours lead to low flowering and fruit-setting rates, resulting in reduced yield and quality, factors that significantly constrain the industry’s development. The core technological challenge in achieving high-quality, high-yield, multi-cropping pitaya production lies in inducing abundant, high-quality blooms in a staged manner using LED artificial lighting. Based on current domestic and international research on the physiological mechanisms and technical strategies of light-induced flowering in pitaya, the effects of LED light supplementation on flowering and yield, along with relevant technical parameters, have been clarified. Practical applications have demonstrated the feasibility of using three-dimensional, precise LED supplemental lighting to regulate flowering and photosynthesis in both facility and open-field cultivation. This technology synergistically promotes both vegetative and reproductive growth, significantly improving flowering and fruit-setting rates, increasing single fruit weight, enhancing yield and quality, and boosting annual production efficiency. This article comprehensively summarizes the enhancement effects and physiological mechanisms of LED supplemental lighting on pitaya flowering regulation, focusing on light intensity, light quality, and photoperiod, within the context of international research. It also analyzes existing challenges and proposes strategies such as optimizing LED light source design, accurately planning supplemental light periods and durations, and establishing three-dimensional lighting methods. These strategies aim to improve the efficiency of LED lighting systems and provide a theoretical foundation for developing a precise and efficient pitaya LED supplemental lighting technology system. In conclusion, LED supplemental lighting promotes both the quantity and timing of pitaya flowering, as well as fruit yield and quality. Red, blue, and far-red light, combined with a photoperiod of 4–6 h, are recommended for effective application. creator: Ren Chen creator: Yiming Ding creator: Wenke Liu creator: Xianwei Zhan creator: Kexin Lin creator: Kaifeng Lian creator: Weilong Chen creator: Keyu Wang creator: Shangfei Lin uri: https://doi.org/10.7717/peerj.19720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chen et al. title: Lead and cadmium toxicity effects on the Pinus roxburghii seed germination and early seedling growth in different environments link: https://peerj.com/articles/19593 last-modified: 2025-08-06 description: Heavy metal toxicity affects germination, seedling growth, and other physiological processes in plants. To assess the toxic effects of heavy metals on the seed germination and seedling growth of Pinus roxburghii, we tested lead (Pb) and cadmium (Cd) at multiple concentrations ranging from 30–180 mg/L in both heterogeneous and homogeneous environments. The results showed that all seeds germinated regardless of Pb and Cd concentrations and environmental conditions, and the final germination percentage (GP) remained unchanged. Under different Pb and Cd stress levels, the seedlings grown under homogeneous conditions exhibited a higher stress tolerance index (STI) in morphological traits than those grown in heterogeneous environments. Pb and Cd also affected physiological indicators, their various concentrations promoted free proline in both environmental conditions. Sugar content in seedlings grown in heterogeneous environments ranged from 47.82% to 6.52% with Pb and 58.69 to 4.34% with Cd. In seedlings grown in homogenous environments, sugar content ranged from 45.71% to 5.71% with Pb and 37.14 to 2.85% with Cd. Chlorophyll a/b and carotenoids exhibited declining trends, with chlorophyll ‘a’ declining more than chlorophyll ‘b’. This research indicates that P. roxburghii can be successfully used for plant restoration. It provides insights into potential hyper-tolerance mechanisms and can be utilized as a potential tree for roadside plantations to alleviate air pollution. creator: Shabana Bibi creator: Tour Jan creator: Nasrullah Khan creator: Muhammad Wahab creator: Mohammad K. Okla creator: Bandar M. Almunqedhi creator: Ibrahim A. Saleh creator: Yasmeen A. Alwasel creator: Saud Alamri creator: Hayat Ullah creator: Mostafa A. Abdel-Maksoud uri: https://doi.org/10.7717/peerj.19593 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bibi et al. title: Characteristics of soil microbial phospholipid fatty acids in artificial, black-soil mountain degraded, and natural grasslands in the source region of the Three Rivers link: https://peerj.com/articles/19837 last-modified: 2025-08-05 description: BackgroundThe source region of the Three Rivers is a concentrated distribution area of alpine grassland. Due to intensified human interference and unsustainable land use, the vegetation and soil in these grasslands have undergone severe degradation, resulting in extensive areas of secondary bare land known as “black soil beach”. A specific form of this degradation is referred to as “black-soil mountain”. To address soil degradation in this region, the establishment of artificial grassland has been proposed. Recent research on grassland restoration has increasingly focused on belowground processes, particularly the role of soil microbial communities in soil recovery.MethodsThis study quantitatively analyzed vegetation characteristics, soil nutrients, microbial community structure, and influencing factors across three grassland types: artificial grassland (AG), black-soil mountain degraded grassland (BG), and natural grassland (NG). Standard laboratory analyses and the phospholipid fatty acid (PLFA) method were employed.ResultsThe establishment of artificial grassland significantly increased aboveground biomass and the contents of soil organic carbon, total nitrogen, and total phosphorus, while notably reducing species richness. A total of 29 PLFA biomarkers were detected across the three grassland types, with AG showing significantly higher biomarker content than BG and NG. Key PLFA biomarkers included 16:1 w7c, 18:1 w7c, 15:0 iso, 15:0 anteiso, 16:00, and 18:1 w9c. Among microbial groups, bacteria were most abundant, followed by fungi, actinomycetes (act), and arbuscular mycorrhizal fungi (AMF). Compared to BG, AG exhibited significantly lower G+/G−and saturated-to-monounsaturated fatty acid (Sat:mono) ratios. Correlation analysis revealed that total PLFA, bacterial (B), fungal (F), G+, and G−contents were significantly or highly significantly positively correlated with soil organic carbon, total nitrogen, and water content (P < 0.01; P < 0.001). Redundancy analysis (RDA) showed that two principal components explained 76.96% and 13.74% of the variation in microbial community structure, with soil organic carbon and total nitrogen identified as the main driving factors.ConclusionThe establishment of artificial grassland is an effective strategy for restoring black-soil mountain degraded grassland. Monitoring microbial PLFA diversity and composition provides a reliable index for assessing soil environmental changes and nutrient dynamics. However, even after five years of restoration, the soil functionality of artificial grassland does not fully recover to the level of natural grassland. creator: Lele Xie creator: Yushou Ma creator: Yanlong Wang creator: Yuan Ma creator: Xiaoli Wang creator: Ying Liu uri: https://doi.org/10.7717/peerj.19837 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xie et al. title: A retrospective study of automatic progressive optimization for lung cancer radiotherapy plans on the Halcyon and RayStation systems link: https://peerj.com/articles/19831 last-modified: 2025-08-05 description: This study aims to evaluate the feasibility of using RayStation’s scripting function to generate automated radiotherapy plans for non-small cell lung cancer (NSCLC) patients on a Varian Halcyon accelerator and to compare their dosimetric characteristics with those of retrospectively collected manual clinical plans. A total of 63 conventional fractionation plans for NSCLC, previously designed using RayStation 4.5 for a variety of linear accelerators—including Trilogy, TrueBeam, Halcyon, and Elekta Infinity—were compared with automated plans generated using RayStation 9.0 for Halcyon. This heterogeneous control group was chosen to reflect real-world clinical practice across multiple platforms. Target coverage, doses to organs at risk (OARs), monitor units, and plan complexity were assessed. The automated plans showed improved dose conformity and lower OAR exposure under the planning configuration used. However, these differences should be interpreted with caution, as the comparison involved different treatment planning systems (TPS) versions and hardware platforms. Further controlled studies using the same TPS and linac are needed to validate the observed improvements. creator: Kainan Shao creator: Fenglei Du creator: Lingyun Qiu creator: Yinghao Zhang creator: Yucheng Li creator: Jieni Ding creator: Wenming Zhan creator: Weijun Chen uri: https://doi.org/10.7717/peerj.19831 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shao et al. title: Risk factors for hypocalcemia after total thyroidectomy: a narrative review link: https://peerj.com/articles/19808 last-modified: 2025-08-05 description: Hypocalcemia is a frequent complication after total thyroidectomy and seriously affects patients’ postoperative quality of life and long-term prognosis. This article reviews the relationship between postoperative hypocalcemia and its suspected risk factors, including age, sex, serum magnesium, vitamin D, high-risk pathological subtype, parathyroid injury, and parathyroid hormone levels, and assesses the ability of preoperative and postoperative parathyroid hormone levels and changes therein at various time points to predict postoperative hypocalcemia. It also discusses the protection of the parathyroid glands in situ by tracer techniques during total thyroidectomy. The various studies that have concluded that parathyroid injury is the most important indicator of postoperative hypocalcemia among these risk factors are reviewed. It is important for general surgeons to know how to avoid intraoperative parathyroid injury, which will contribute to the prevention of hypocalcemia. creator: Bohan Cao creator: Guangzhe Wu uri: https://doi.org/10.7717/peerj.19808 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cao and Wu title: Harnessing citizen science for marine conservation in Malta: a comparative analysis of GAM and MaxEnt models in bottlenose dolphin habitat mapping link: https://peerj.com/articles/19804 last-modified: 2025-08-05 description: BackgroundSpecies distribution models (SDMs) are powerful tools for informing conservation, particularly for highly mobile marine species such as common bottlenose dolphins (Tursiops truncatus). In Maltese waters, the limited availability of data on this species has constrained the effectiveness of conservation efforts. Despite the designation of offshore Special Areas of Conservation (SACs), key coastal regions need more detailed spatial studies to support evidence-based management.MethodsIn this study, we analyzed and compared the outputs of a generalized additive model (GAM) and a maximum entropy (MaxEnt) model to assess summer habitat suitability for bottlenose dolphins within a coastal SAC in Malta. The models were informed by presence-only data collected through systematic surveys and a citizen science campaign, integrated with environmental and anthropogenic predictors including chlorophyll-a concentration, sea surface temperature anomaly, slope, and distance to aquaculture sites.ResultsBoth modeling approaches identified high habitat suitability in shallow, nearshore regions, with chlorophyll-a concentration and proximity to aquaculture sites emerging as the most important predictors. Slope and sea surface temperature anomaly contributed less substantially. The two models showed spatial agreement in highlighting these nearshore areas as core habitats, though GAM predicted a broader extent of suitable habitat, whereas MaxEnt results were more spatially restricted. Both models demonstrated strong predictive performance (AUC > 0.85), reinforcing the ecological relevance of the identified drivers.ConclusionThis study demonstrates the potential of integrating opportunistic data with SDMs to support habitat assessments in data-limited contexts. The use of complementary modeling approaches provides robust insights into species–environment relationships. These results aim to guide spatial planning and future assessments of conservation priorities in Maltese coastal waters. creator: Francesca Soster creator: Tim Awbery creator: Nina Vérité–Taulet creator: Timothy Zammit creator: Kimberly Terribile uri: https://doi.org/10.7717/peerj.19804 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Soster et al. title: Phosphite effects on sugarcane growth and biochemicals under in vitro osmotic stress link: https://peerj.com/articles/19763 last-modified: 2025-08-05 description: BackgroundBiostimulants positively impact plant growth, yield, and chemical composition while enhancing tolerance to biotic and abiotic stress. Phosphite (Phi), a phosphate analog, has been proposed as a biostimulant due to its advantages over traditional phosphate fertilizers and herbicides.MethodsThis study evaluated the effects of Phi on sugarcane seedlings (CP 72-2086) under conventional (non-stress) and osmotic stress conditions during in vitro multiplication. Seedlings were treated with Phi at 0.1, 0.3, and 0.5 mM (derived from H3PO3) for 30 days, followed by 7 days of osmotic stress induced with 10% polyethylene glycol 6000 (PEG).ResultsPhi significantly increased leaf length, width, and number, as well as shoot count. Additionally, it enhanced foliar concentrations of chlorophylls a and b, sugars, and amino acids under both conventional and osmotic stress conditions. In conclusion, Phi serves as an effective inorganic biostimulant for sugarcane (CP 72-2086) during in vitro multiplication, stimulating seedling growth and modulating essential biomolecule concentrations. creator: Jennifer Martínez-Ballesteros creator: Karina P. Bañuelos-Hernández creator: Daniel A. Rodríguez-Lagunes creator: Juan V. Hidalgo-Contreras creator: Miriam C. Pastelín-Solano creator: Guadalupe Vivar-Vera creator: Javier E. Bulbarela-Marini creator: Odon Castañeda-Castro uri: https://doi.org/10.7717/peerj.19763 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Martínez-Ballesteros et al. title: Measurement of bovine (Bos taurus) serum albumin by different methods and the comparison of protein fractions determined by capillary zone electrophoresis and agarose gel electrophoresis link: https://peerj.com/articles/19685 last-modified: 2025-08-05 description: Serum albumin measurement is an important parameter routinely evaluated in clinical biochemistry within the livestock industry. It plays a crucial role in assessing the nutritional and health status of animals, as well as in aiding the diagnosis of various pathological conditions as a complementary tool. Several laboratory methods are available for albumin measurement; however, some methods have been documented to overestimate the concentration of serum albumin versus the proposed gold standard of serum protein electrophoresis. The primary aim of the study was to analyze the agreement between albumin measurement in bovine serum samples by the capillary zone electrophoresis (CZE), agarose gel electrophoresis (AGE), bromocresol green (BCG), and purple (BCP) methods. In addition, AGE and CZE methods were also compared for quantitation of globulin fractions. Lastly, reference intervals were established using all methods using the American Society for Veterinary Clinical Pathology (ASVCP) guidelines. Serum samples from 55 clinically normal Brangus cattle (5 ± 1.5 years old) were examined by the four methods. For the albumin method comparison, all methods were significantly correlated (r = 0.55–0.91, p < 0.0001) and the bias between methods ranged from 0.01–0.22 g/dL. For AGE and CZE methods, all protein fractions were significantly correlated (r = 0.85–0.91, p < 0.0001) except for the alpha 1 fraction (r = 0.21, p = 0.12). Five fractions were quantitated using AGE method: albumin, alpha 1, alpha 2, beta, and gamma globulins. For the CZE method, six fractions were resolved with the sub fractionation of beta 1 and beta 2 globulin fractions. The evaluated methods showed good agreement in determining albumin levels in cattle. Although CZE offers higher resolution, it requires careful interpretation and precise definition of fractions. Therefore, methodological choice and consideration of analyzer-specific reference intervals are essential for accurate results. creator: Leandro Abreu da Fonseca creator: Fabiano Montiani-Ferreira creator: Marilyn Rodriguez creator: Joao Henrique Jabur Bittar creator: Fabricia Modolo Girardi creator: Theo Matos Arantes Moraes creator: Carolyn Cray uri: https://doi.org/10.7717/peerj.19685 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fonseca et al. title: Prediction of microbe-drug associations using a CNN-Bernoulli random forest model link: https://peerj.com/articles/19637 last-modified: 2025-08-05 description: BackgroundAntibiotics play a critical role in treating microbial infections. However, their widespread use has contributed to the growing problem of microbial resistance. Addressing this challenge requires the identification of new microbe-drug associations to support the development of novel therapeutic strategies. Since traditional wet-lab experiments are time-consuming and costly, computational models offer an efficient alternative for discovering potential applications of existing drugs against previously untested microbes. These models can facilitate the identification of novel microbe-drug associations and help counteract resistance mechanisms.MethodsThis study proposes a novel computational model: convolutional neural network with Bernoulli random forest for Microbe-Drug Association prediction (CNNBRFMDA). The model constructs feature vectors for all microbe-drug pairs based on known associations, microbe similarity, and drug similarity. A subset of these vectors is randomly selected to form the training set. A convolutional neural network (CNN) is then used to reduce the dimensionality of all feature vectors, including those in the training set. The reduced training set is subsequently used to train a Bernoulli random forest (BRF) to predict potential microbe-drug associations. The innovation of CNNBRFMDA lies in its integration of CNN for nonlinear feature extraction and BRF for robust prediction. This approach enhances computational efficiency and improves the model’s ability to capture complex patterns, thereby increasing the precision and interpretability of drug response predictions. The dual use of the Bernoulli distribution in BRF ensures algorithmic consistency and contributes to superior performance.ResultsThe model was evaluated using five-fold cross-validation on the Microbe-Drug Association Database (MDAD) and abiofilm datasets. CNNBRFMDA achieved mean AUC scores of 0.9017 ± 0.0032 (MDAD) and 0.9146 ± 0.0041 (abiofilm). Two case studies further validated the model’s reliability: 41 of the top 50 predicted microbes associated with ciprofloxacin and 38 of the top 50 associated with moxifloxacin were confirmed through literature review. creator: Zihao Song creator: Qingnuo Li creator: Jincheng Zhao creator: Qinggang Bu creator: Zekang Bian creator: Jia Qu uri: https://doi.org/10.7717/peerj.19637 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Song et al. title: Comparison of survival in patients with low vs. intermediate prostate-specific antigen concentrations and development of a nomogram: a surveillance, epidemiology and end results program database study with external validation on a Chinese cohort link: https://peerj.com/articles/19823 last-modified: 2025-08-04 description: BackgroundIn this study of patients with prostate cancer, we explored associations between low prostate-specific antigen (PSA) concentrations and disease progression as well as prognosis.MethodsWe retrospectively reviewed data of 233,554 prostate cancer patients in the Surveillance, Epidemiology and End Results (SEER) program and of 199 prostate cancer patients from the medical records of the Affiliated Hospital of Qingdao University with PSA ≤10 ng/mL at diagnosis. The patients were stratified into eight subgroups by T stage and Gleason score (GS) and survival curves for the resultant subgroups plotted using the Kaplan–Meier method. Multivariate Cox analyses were performed to investigate the effects of PSA concentrations in different subgroups. After randomly dividing patients into a training set and an internal validation set with a ratio of 7:3, a nomogram model to predict the survival of prostate cancer patients was subsequently established and validated.ResultsIn all prostate cancer patients with Gleason score (GS) 8–10, low PSA concentrations were significantly associated with advanced disease and poor prognosis, functioning as a statistically significant risk factor. Conversely, in patients with GS 6–7 and Stage T1 disease, low PSA concentrations acted as a protective factor. A nomogram model for predicting prognosis was established and validated. We obtained similar results with an external validation cohort.ConclusionsOur findings indicate that low PSA concentrations exert divergent impacts on prostate cancer patients stratified by T stage and GS. Specifically, in patients with high GS (8–10), low PSA concentrations represent a risk factor for disease progression to advanced stages and poor prognosis. Additionally, we developed a novel nomogram that effectively predicts survival outcomes in these patients. creator: Jingchang Mei creator: Guanqun Zhu creator: Yu Yao creator: Fengju Guan creator: Lijiang Sun creator: Guiming Zhang uri: https://doi.org/10.7717/peerj.19823 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mei et al. title: Effect of sleep quality on vision-related quality of life in a sample of Qassim University students: an ocular surface health approach link: https://peerj.com/articles/19801 last-modified: 2025-08-04 description: BackgroundOptimal sleep is essential for maintaining physiological homeostasis, and its disruption is associated with numerous physical and mental health issues. Previous studies have linked poor sleep quality to ocular conditions such as dry eye. However, the relationship between sleep quality and vision-related quality of life remains underexplored. This study aimed to investigate the association between ocular surface health and sleep quality, and how both factors relate to vision-related quality of life.MethodsEthical approval was granted by the Deanship of Graduate Studies and Scientific Research at Qassim University (reference no. 21-20-09), and the study was conducted in accordance with the Declaration of Helsinki. Young adult participants completed three questionnaires: the Pittsburgh Sleep Quality Index, the National Eye Institute Visual Function Questionnaire, and the Ocular Surface Disease Index. Ocular surface assessments were conducted using the Keratograph 5M and the Schirmer test to measure tear production.ResultsAnalysis revealed significant correlations between ocular symptoms and vision-related quality of life (Spearman’s r = 0.47, p < 0.0001, n = 93), sleep efficiency (r = 0.22, p < 0.05, n = 75), and sleep disturbances (r = 0.25, p < 0.05, n = 75). A significant negative correlation was also found between sleep quality and vision-related quality of life (r = −0.31, p < 0.005, n = 75). These findings highlight the impact of sleep quality on ocular health, particularly the ocular surface.ConclusionThe results suggest a meaningful link between sleep quality, ocular surface health, and vision-related quality of life. Further research is needed to clarify the causal mechanisms and risk factors contributing to ocular discomfort and its effects on visual well-being. creator: Hanan Awad Alkozi creator: Saleh Alshammeri uri: https://doi.org/10.7717/peerj.19801 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Awad Alkozi and Alshammeri title: Response surface optimization for cadmium biosorption onto the pre-treated biomass of red algae Digenia simplex as a sustainable indigenous biosorbent link: https://peerj.com/articles/19776 last-modified: 2025-08-04 description: BackgroundCadmium pollution from industrial effluent can cause major health concerns, so it must be removed from wastewater prior to disposal. The objective of this study was to remove cadmium (Cd2+) from aquatic environments using red macroalgae Digenia simplex pretreated with calcium chloride (CaCl2) (DSC).MethodsBatch adsorption studies were carried out to evaluate the individual impacts of adsorbent-metal contact time, cadmium concentration, and temperature on the cadmium removal efficiency and biosorption capacity. The Box-Benhken experimental design of response surface methodology was also used to investigate the relationship between different factors (pH, Cd2+ concentration and algal dose) and the cadmium removal efficiency of pretreated D. simplex.ResultsThe highest removal efficiency of 97.27% was achieved by combining different optimal parameters, including pH 5.78, initial Cd2+ concentration of 24.79 mg/L, and adsorbent dosage of 6.13 g/L. Moreover, cadmium removal from agricultural wastewater samples by pretreated D. simplex was evaluated under the optimal conditions, and the removal rate excessed 97%. Kinetic and isotherm investigations showed that the pseudo-second-order, Freundlich, Langmuir, and Dubinin–Radushkevich models of cadmium biosorption on pretreated algal biomass correlated well with the experimental biosorption data, implying that the biosorption of Cd2+ is a homogeneous monolayer and multilayer chemisorption process. The equilibrium isotherm data indicated that the biosorption capacity of the biosorbent was 11.16 mg/g as determined by the Langmuir model. Furthermore, the biosorption process was evaluated as an endothermic process with entropy and enthalpy values of 0.134 kJ/mol K and 38.01 kJ/mol, respectively. The functional groups, surface morphology, and elemental composition of the algal biomass were investigated, revealing the porous nature of the cell surface and the abundance of functional groups responsible for the Cd2+ biosorption process. These results suggest that DSC biomass can be used as a biosorbent for the effective removal of Cd2+ ions from effluent due to its availability and strong biosorption capability. creator: Sedky H.A. Hassan creator: Maryam M. Alomran creator: Nada I.A. Alsugiran creator: Mostafa Koutb creator: Hassan Ahmed creator: Mustafa A. Fawzy uri: https://doi.org/10.7717/peerj.19776 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hassan et al. title: Randomized clinical study of electrical impedance tomography-guided chest physiotherapy in difficult-to-wean patients: study protocol link: https://peerj.com/articles/19727 last-modified: 2025-08-04 description: BackgroundDiaphragm dysfunction and inadequate chest wall and respiratory muscle function are common in critically ill patients who face difficulties in weaning from mechanical ventilation (MV). This can lead to secretion retention and impaired airway clearance. Chest physiotherapy (CPT) in these patients can help reduce secretion retention. This study protocol outlines an investigation into the feasibility and effectiveness of CPT guided by electrical impedance tomography (EIT) in difficult-to-wean patients on lung function, duration of mechanical ventilation, functional performance, and intensive care unit (ICU) hospitalization expenses.MethodsThis single-center, single-blind, randomized pilot study employed a parallel-group design. Participants will be randomly assigned to either an intervention group receiving EIT-guided CPT or a control group receiving only experiential CPT Interventions, lasting 20 minutes each, were administered up to twice daily from ICU admission until discharge. The assessments will occur before interventions, after the 14 days, and after the 28 days. Outcome measures will be collected at before and after the intervention, peak expiratory flow, 30-day weaning success rate, maximum inspiratory pressure, diaphragm thickening rate, diaphragmatic excursion, ICU stay duration, and days from baseline to MV removal or Day 30. Adverse events will be documented.ConclusionThis study will evaluate the feasibility and effectiveness of EIT-guided CPT versus conventional CPT in difficult-to-wean patients. If successful, this approach could enhance the efficiency of CPT.Trial registrationThis study was prospectively registered at the National Library of Medicine (https://clinicaltrials.gov/; reference: NCT06677099; Date of registration: 5th November 2024). creator: Hao Wang creator: Jianing Xi creator: Hongying Jiang uri: https://doi.org/10.7717/peerj.19727 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wang et al. title: An unusual early-diverging plesiosauroid from the Lower Jurassic Posidonia Shale of Holzmaden, Germany link: https://peerj.com/articles/19665 last-modified: 2025-08-04 description: The lower Toarcian Posidonia Shale at Holzmaden, Southwest Germany, has yielded some of the most remarkable Lower Jurassic marine tetrapod specimens, including five plesiosaur taxa identified from nearly complete skeletons. This study provides a comprehensive description of an osteologically immature plesiosauroid skeleton found in a Holzmaden quarry in 1978. Despite that the specimen has been researched in the past, previous studies have been either brief or targeted some specific aspects of the specimen, such as its soft tissue preservation. The anatomy and taxonomy of the specimen have never been explored in detail. We reinterpret several of its osteological features and evaluate their taxonomic and phylogenetic significance. Our findings reveal that the specimen possesses an unusual combination of character states, which are not markedly affected by ontogenetic development, warranting the designation of a new taxon, Plesionectes longicollum gen. et sp. nov., thereby increasing the known plesiosaur diversity of both the Toarcian age and the Posidonia Shale. creator: Sven Sachs creator: Daniel Madzia uri: https://doi.org/10.7717/peerj.19665 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sachs and Madzia title: Intraoperative hypotension and postoperative pneumonia in patients after selective intracranial tumor resection: a retrospective cohort study link: https://peerj.com/articles/19514 last-modified: 2025-08-04 description: BackgroundPostoperative pneumonia is common and associated with increased postoperative mortality. Intraoperative hypotension is suggested to be associated with an increased risk of postoperative surgical infection. We aim to explore whether intraoperative hypotension could increase the risk of postoperative pneumonia in adult patients undergoing intracranial tumor resection.MethodsA total of 341 patients who received selective intracranial tumor resection under general anesthesia between January 2018, and December 2022 in a single university hospital were reviewed. Univariate and multivariate analyses were performed. The outcomes included the incidence of postoperative pneumonia and the association between intraoperative hypotension and postoperative pneumonia.ResultsThe incidence of postoperative pneumonia during hospitalization after intracranial tumor resection was 16.8%. Univariate analysis revealed a history of preoperative smoking, intraoperative mean arterial pressure (MAP) < 55 mmHg, American Society of Anesthesiologists classification (ASA) > 2, the duration of surgery > 4 hours, and the duration of controlled ventilation > 4 hours were identified as possible risk factors (P < 0.1). Multivariate analysis revealed a history of preoperative smoking (adjusted odds ratio: 5.205, 95% confidence interval [1.826–14.836], P = 0.003) and intraoperative MAP < 55 mmHg (adjusted odds ratio: 3.082, 95% confidence interval [1.447–6.432], P = 0.003) were independently associated with postoperative pneumonia.ConclusionsIntraoperative hypotension may be associated with postoperative pneumonia in patients who received selective intracranial tumor resection under general anesthesia. creator: Yuan Chang creator: Yanqiong Wang creator: Yinyan Zhou creator: Huamei Chen creator: Yuanhua Li creator: Ruhua Long creator: Jianlin Shao uri: https://doi.org/10.7717/peerj.19514 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chang et al. title: Diversity, antibacterial and antioxidant activities of fungi associated with Apis cerana link: https://peerj.com/articles/19762 last-modified: 2025-08-01 description: Insect-associated fungi are a treasure trove of natural active compounds. Nevertheless, the diversity and biological activities of fungi associated with Apis cerana have not been studied in depth. Here, we investigated fungal diversity in the A. cerana gut and honeycomb using a combination of culture-dependent and -independent methods. A total of 652 fungal operational taxonomic units belonging to five phyla and 334 genera were detected in the samples. Significant differences were found in the fungal communities of the honeybee gut and honeycomb—the genera Fusarium, Stenocarpella, and Botrytis were dominant in the gut, whereas Botrytis, Periconia, and Aspergillus were dominant in honeycomb. A total of 28 fungal strains were isolated from honeybee gut, head, and honeycomb, belonging to two phyla, four classes, and 10 genera. Most of these isolates were identified as Aspergillus, Penicillium, and Cladosporium spp. The antibacterial and antioxidant activities of crude extracts of their fermentation broths were investigated. Extract from A. subramanianii ZFCZ33 exhibited the best antibacterial activities against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and P. syringae pv. Actinidiae with the disc diameter of inhibition zone diameter (IZD) of 24.33, 15.33, 17.00, and 25.33 mm, respectively. Extract from P. adametzioides ZFCZ03 had a free radical scavenging rate of 89.71% in assay with 2,2-diphenyl-1-picrylhydrazyl, and that from strain ZFT07 had a free radical scavenging rate of 97.13% in assay with 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid). Our results preliminarily elucidate the fungal diversity of A. cerana gut and honeycomb and indicate that honeybee-associated fungi have antibacterial and antioxidant activities. This study provides a basis for further development and use of honeybee-associated fungi. creator: Pu Cui creator: Guanxiu Guan creator: Zhuoting Gan creator: Ting Yao uri: https://doi.org/10.7717/peerj.19762 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cui et al. title: Assessing an acoustic bioindicator of leisure boating disturbance on bottlenose dolphins link: https://peerj.com/articles/19726 last-modified: 2025-08-01 description: Growing concerns about the impact of leisure boating on marine ecosystems are particularly relevant for marine mammal species, given their dependence on sound and significant spatial overlap with human activities. Monitoring the effects of leisure boating disturbances on marine ecosystems presents considerable challenges, as it is resource-intensive and may require many years of data collection. However, since species can alter their behavior and daily routines in response to human disturbances, behaviors essential for individual fitness, reproduction, and parental care success—such as acoustic behavior—could serve as bioindicators for assessing the impact of leisure boating. Common bottlenose dolphins (Tursiops truncatus) emit acoustic signals, known as signature whistles (SWs), for individual identification, communication, and social bonding. This study aimed to examine how leisure boating influences SW characteristics (e.g., fundamental frequencies, frequency modulation, and duration) and whether these effects remain consistent across different social contexts (e.g., presence of calves), environmental conditions (e.g., seabed habitat type), and behavioral states in a population of bottlenose dolphins inhabiting the northwestern coast of Sardinia (Mediterranean Sea, Italy). The results demonstrate that certain SW characteristics were consistently affected by the presence of boats, regardless of ecological, behavioral, and social differences. These findings suggest that SWs have the potential to serve as reliable bioindicators for boating disturbances. Further research in diverse marine environments and with other dolphin populations is needed to validate and expand upon these findings. creator: Gabriella La Manna creator: Fabio Ronchetti creator: Francesco Perretti creator: Giulia Ceccherelli uri: https://doi.org/10.7717/peerj.19726 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 La Manna et al.