title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-03 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Triple negative breast cancer cells acquire lymphocyte proteins and genomic DNA during trogocytosis with T cells link: https://peerj.com/articles/19236 last-modified: 2025-03-31 description: Trogocytosis is the process by which a recipient cell siphons small membrane fragments and proteins from a donor cell and can be utilized by cancer cells to avoid immune detection. We observed lymphocyte specific protein expressed by triple negative breast cancer (TNBC) cells via immunofluorescence imaging of patient samples. Image analysis of Cluster of Differentiation 45RA (CD45RA) expression, a naïve T cell specific protein, revealed that all stages of TNBCs express CD45RA. Flow cytometry revealed TNBC cells trogocytose CD45 protein from T cells. We also showed that the acquisition of these lymphoid markers is contact dependent. Confocal and super-resolution imaging further revealed CD45+ spherical structures containing T cell genomic DNA inside TNBC cells after co-culture. Trogocytosis between T cells and TNBC cells altered tumor cell expression of PTPRC, the gene that encodes for CD45. Our results revealed that CD45 is obtained by TNBC cells from T cells via trogocytosis and that TNBC cells express CD45 intracellularly and on the membrane. creator: Anutr Sivakoses creator: Haley Q. Marcarian creator: Anika M. Arias creator: Alice R. Lam creator: Olivia C. Ihedioha creator: Juan A. Santamaria-Barria creator: Geoffrey C. Gurtner creator: Alfred L. M. Bothwell uri: https://doi.org/10.7717/peerj.19236 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sivakoses et al. title: Effects of different light intensities on lettuce growth, yield, and energy consumption optimization under uniform lighting conditions link: https://peerj.com/articles/19229 last-modified: 2025-03-31 description: Vertical farming is an advanced form of modern agriculture, but it involves high energy consumption when providing supplemental lighting for crops. The research designed an automated lighting detection device and explored its application in vertical farms. It comprehensively investigated the effects of different red-blue light intensities on two lettuces (Lactuca sativa L. cv. ‘Spanish green’ and ‘Butterhead’) varieties under highly uniform supplemental lighting conditions. The research encompasses investigations into lettuce morphological parameters, photosynthetic physiology, productivity, and energy consumption. The experimental light quality and photoperiod were set at (R/B = 4, 16 h/d), with light intensity ranging from 125 to 300 μmol/m2/s. The experiment indicates that with the increase in light intensity, the yield of both lettuce varieties also increases. Furthermore, lettuce exhibits a significant increase in leaf amplitude from day 20 to day 25 of growth. At 300 μmol/m2/s, Butterhead lettuce demonstrates optimal fresh weight and productivity ratio. As for Spanish green lettuce, the productivity ratio at 200 μmol/m2/s is only 2.11% lower than at 300 μmol/m2/s. Under the cultivation conditions of R/B = 4 and 16 h/d, a light intensity of 300 μmol/m2/s is suitable for the production of Butterhead lettuce, in comparison, a light intensity of 200 μmol/m2/s is suitable for the production of Spanish green lettuce. creator: Jun Zou creator: Shipeng Luo creator: Mingming Shi creator: Dawei Wang creator: Wenbin Liu creator: Yan Shen creator: Xiaotao Ding creator: Yuping Jiang uri: https://doi.org/10.7717/peerj.19229 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zou et al. title: Association of chromosomal aberrations in chromosomes 3 and 7, and P16 mutations with malignancy in salivary gland tumors link: https://peerj.com/articles/19217 last-modified: 2025-03-31 description: BackgroundSalivary gland tumors, a prevalent type of head and neck neoplasm, exhibit significant morphological diversity and overlapping features, complicating pathological diagnosis. Although fluorescence in situ hybridization (FISH) is widely used for tumor detection, its diagnostic utility in salivary gland tumors remains unclear. This study aimed to explore a novel FISH-based approach to differentiate benign from malignant salivary gland tumors.MethodsGene probes (CSP3, CSP7, and GSP P16) were designed to detect P16 gene deletion, and polysomies of chromosomes 3 and 7. The FISH analysis was conducted on 22 malignant and 12 benign salivary gland tumor samples with complete clinical data. The study was expanded to 78 samples for further validation.ResultsThe CSP3, CSP7, and GSP P16 probes exhibited high specificity for salivary gland tumors, though CSP7 exhibited lower sensitivity. The combination of CSP3 and GSP P16 probes outperformed single-probe analysis or other probe combinations.ConclusionThe CSP3 and GSP P16 probe combination provides a highly sensitive and specific method for distinguishing malignant from benign salivary gland tumors. creator: Yanxia Wu creator: Zhiyue Xie creator: Nan Peng creator: Rui Zhou creator: Liang Zhao uri: https://doi.org/10.7717/peerj.19217 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wu et al. title: Effectiveness of dexmedetomidine as a premedication for pediatric patients undergoing outpatient dental surgery under general anesthesia-systematic review and meta-analysis link: https://peerj.com/articles/19216 last-modified: 2025-03-31 description: Pediatric patients undergoing outpatient dental surgery often exhibit instinctive resistance and fear in face of the unknown, which in turn creates obstacles to subsequent treatment. Appropriate sedation can increase compliance, decrease the incidence of adverse events, and lead to improved treatment outcomes. To evaluate the effectiveness of dexmedetomidine as pre-medication in children undergoing tooth extraction with general anesthesia, we searched databases including the Medline, Embase and Cochrane library for eligible trials. Randomized controlled trials of dexmedetomidine for premedication vs. placebo or midazolam in pediatric patients were included, while trials involving children having dental treatment under local anesthesia were excluded. Two review authors independently participated in the inclusion of trials and assessment of bias. Decisions were made based on group discussion. We finally included seven trials in this review, with a total of 496 pediatric patients. Three of the included trials compared dexmedetomidine with placebo. A meta-analysis indicated that dexmedetomidine was effective for preoperative sedation and for preventing emergence delirium; two of these studies reported no incidences of bradycardia and hypoxemia during study observation period. Four trials compared dexmedetomidine with midazolam, meta-analysis of these four trials gave risk ratios (RR) for successful parental separation, satisfactory mask acceptance and emergence delirium rate of 1.26 (95% CI [0.86–1.84]); 1.07(95% CI [0.94–1.22]); −0.18(95% CI [−0.29 to −0.07]), respectively. Only one study reported complications arising from administration of premedication. Based on the current evidence, we can conclude that the dexmedetomidine appears to be an effective premedication, offering the advantage of reducing the incidence of postoperative delirium compared to midazolam. However, high-quality clinical trials with larger sample sizes are needed to determine the selection of different medication modes and doses, as well as to study perioperative adverse reactions. creator: Xiao Zhang creator: Ze Fan creator: Danyi He creator: Yang Liu creator: Xiaotong Shi creator: Haopeng Zhang uri: https://doi.org/10.7717/peerj.19216 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Temporal and spatial distribution of histone acetylation in mouse molar development link: https://peerj.com/articles/19215 last-modified: 2025-03-31 description: Histone acetylation is one of the most widely studied histone modification, regulating a variety of biological activities like organ development and tumorigenesis. However, the role of histone acetylation in tooth development is poorly understood. Using the mouse molar as a model, we mapped the distribution patterns of histone H3 and H4, as well as their corresponding acetylation sites during tooth formation in order to unveil the connection between histone acetylation modification and tooth development. Moreover, key histone acetyltransferases and histone deacetylases were detected in both epithelial and mesenchymal cells during tooth development by scRNA-seq and immunohistochemistry. These results suggest that histone acetylation modification functions as an important mechanism in tooth development at different stages. creator: Wen Du creator: Wanyi Luo creator: Liwei Zheng creator: Xuedong Zhou creator: Wei Du uri: https://doi.org/10.7717/peerj.19215 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Du et al. title: A novel simple immunoassay for quantification of blood anti-NMDAR1 autoantibodies link: https://peerj.com/articles/19212 last-modified: 2025-03-31 description: Low titers of blood circulating anti-NMDAR1 autoantibodies have been reported in a significant subset of the general human population. Currently, immunohistochemical staining and cell-based assays are the standard methods for their detection and semi-quantification. However, detection and quantification of these low titers of blood circulating anti-NMDAR1 autoantibodies are problematic because of high non-specific background. Development of a new method to more accurately quantify these low titers of blood anti-NMDAR1 autoantibodies will facilitate studies on their potential impacts on psychiatric symptoms and cognition. We previously reported a robust production of anti-NMDAR1 autoantibodies against the ligand binding domain of NMDAR1. As a proof of principle, we report the development of a novel simple immunoassay for quantification of cross-species blood anti-NMDAR1 autoantibodies and its validation with immunohistochemistry and cell-based assays in both humans and mice. Specificity of our quantification was also investigated. creator: Melonie Vaughn creator: Susan Powell creator: Victoria Risbrough creator: Xianjin Zhou uri: https://doi.org/10.7717/peerj.19212 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vaughn et al. title: Microecological recombination of Angelica sinensis driven by the transplanting of “alpine seedling–cellar planting–dam cultivation” link: https://peerj.com/articles/19208 last-modified: 2025-03-31 description: Transplanting is important for obtaining and maintaining excellent germplasm of cultivated plants. During plant transplantation, the endophytic microbial community regularly reorganizes, which may be crucial for plant germplasm rejuvenation. Angelica sinensis, a widely used medicinal and edible plant, relies on transplanting for its exceptional quality. To explore the microecological recombination of A. sinensis during the transplanting process of “alpine seedling–cellar planting–dam cultivation”, this study analyzed shifts in endophytic and soil microbial communities across the three transplanting stages in Min County, Gansu Province, China. High-throughput sequencing revealed significant changes, with 82.27% to 84.65% of bacteria and 93.19% to 93.49% of fungi species altering in transplanted Angelica. Main findings indicate that Mortierellomycota, Actinobacteriota, and Myxococcota were dominant in cellar planting root and cellar rhizosphere soil, contrasting with Firmicutes predominance in alpine and dam areas. Notably, potentially pathogenic endophytes like Fusarium and Xanthomonas decreased post-alpine seedling and cellar planting, favoring a healthier plant environment. Cellar planting root exhibited a rich accumulation of psychrophilic flora, including Tetracladium, Pseudomonas, and Flavobacterium, alongside a unique dominance of Mortierella fungi. Microbial co-occurrence network analysis highlighted cellar planting root as pivotal, suggesting its importance in microbial interactions. In conclusion, transplanting significantly reshaped A. sinensis’s endophytic flora, with fungi showing more pronounced recombination than bacteria. Soil microbial communities emerged as crucial drivers of this recombination, facilitating the overwintering of A. sinensis, reducing diseases, and rejuvenating the germplasm. Transplanting-driven microecological reorganization is an important scientific mechanism for the high-quality production of cultivated medicinal plants. creator: Dongmei He creator: Weiping Gao creator: Zhanling Zhang creator: Jinniu Xing creator: Guiqi Han creator: Hai Wang creator: Zhuyun Yan uri: https://doi.org/10.7717/peerj.19208 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 He et al. title: Predictive factors associated with acute radiation dermatitis in patients with breast cancer: a retrospective cohort study link: https://peerj.com/articles/19202 last-modified: 2025-03-31 description: BackgroundRadiation therapy (RT) is a primary postsurgical treatment for breast cancer; however, it can cause acute radiation dermatitis (ARD), which can severely impair quality of life. The aim of this study was to identify predictive factors associated with moderate to severe ARD.Materials and MethodsIn this retrospective analysis, we utilized data from Chulabhorn Hospital’s Health Information System that was collected between January 2017 and December 2022. A radiation oncology specialist assessed ARD in a cohort of 635 patients using the Radiation Therapy Oncology Group (RTOG) ARD grading scale. The patients were classified into two groups based on the maximum grade recorded: mild (grade < 2) and moderate to severe (grade ≥ 2). Various factors were examined, including demographic characteristics (age, body mass index (BMI), comorbidities) and treatment-related variables (surgical history, adjuvant chemotherapy, hormone therapy, targeted therapy, fractionation, boost treatments, and bolus application). Logistic regression was used to perform the statistical analysis.ResultsAmong the 635 patients, the average age was 54.2 ± 10.9 years, and 32% were classified as having moderate to severe ARD. Multiple logistic regression analysis identified BMI ≥ 30 kg/m2 (adjusted odds ratio (AOR) = 2.33; 95% confidence interval (CI) [1.36–3.98]; p-value = 0.002), localized boost treatments (AOR = 2.09; 95% CI [1.08–4.06]; p-value = 0.029), and bolus application (AOR = 2.08; 95% CI [1.02–4.24]; p-value = 0.044) as significant risk factors for moderate to severe ARD. Conversely, hypofractionated RT (AOR = 0.31; 95% CI [0.16–0.57]; p < 0.001) and hormonal therapy (AOR = 0.60; 95% CI [0.42–0.86]; p-value = 0.005) were associated with a decreased risk. However, radiation to both the primary site and regional lymph nodes (AOR = 0.81; 95% CI [0.41–1.59]; p-value = 0.538) and targeted therapy (AOR = 0.72; 95% CI [0.43–1.20]; p-value = 0.210) did not significantly affect the risk of moderate to severe ARD.ConclusionsWe have identified key risk factors for moderate to severe ARD, including obesity and treatment modalities such as localized boost treatments and bolus application. Hormone therapy and hypofractionated RT appear to reduce ARD severity. These findings have implications for the development of treatment plans and the mitigation of the risk of ARD in patients undergoing RT. creator: Rattanaporn Nanthong creator: Sunanta Tungfung creator: Kamonwan Soonklang creator: Wiriya Mahikul uri: https://doi.org/10.7717/peerj.19202 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nanthong et al. title: Evaluation of optic nerve sheath diameter in acute stroke: pre- and post-thrombolytic assessment link: https://peerj.com/articles/19197 last-modified: 2025-03-31 description: BackgroundIntracranial pressure increases due to ischemic infarction caused by stroke. This study aimed to evaluate the pre-thrombolytic and post-thrombolytic optic nerve sheath diameter (ONSD) measurements in predicting clinical outcomes and complications for stroke patients.MethodsONSD was measured on computed tomography (CT) scans. The average ONSD (aONSD) was calculated from the right and left eyes. Pre-thrombolytic (ONSD-0) and post-thrombolytic (ONSD-24) values were compared according to right vs left eye, stroke-affected side of the brain, presence of complications, and mortality.ResultsNinety-three patients were enrolled; 52.7% were female, and the mean age of all participants was 76 years. The aONSD-24 values were higher than the aONSD-0 values (5.5 ± 0.7 mm and 5.3 ± 0.7 mm, respectively, p < 0.001). There was no significant difference between right and left measurements (right ONSD-0 5.3 mm vs. left ONSD-0 5.3 mm, p = 0.257; right ONSD-24 5.6 mm vs. left ONSD-24 5.5 mm, p = 0.146; and ∆right ONSD 0.23 mm vs. ∆left ONSD 0.22, p = 0.717) and between the stroke-affected side and non-stroke-affected side measurements (stroke-affected ONSD-0 5.2 mm vs. non-stroke-affected ONSD-0 5.2 mm, p = 0.292; stroke-affected ONSD-24 5.5 mm vs. non-stroke-affected ONSD-24 5.4 mm, p = 0.124; and ∆stroke-affected ONSD 0.23 mm vs. non-∆stroke-affected ONSD 0.23 mm, p = 0.569). Intracranial complications occurred in 14 (15%) patients. There was no difference in ONSD values between patients with and without complications (p = 0.338 for aONSD-0, p = 0.216 for aONSD-24, and p = 0.902 for ∆a ONSD). There was no significant difference between the aONSD-0 and aONSD-24 values of surviving and non-surviving patients (aONSD-0: 5.3 ± 0.7 vs. 5.0 ± 0.5, p = 0.345; aONSD-24: 5.5 ± 0.7 vs. 5.3 ± 0.4, p = 0.522; and p = 0.386 for ∆ aONSD).ConclusionsONSD values on 24-h brain CT scans were higher than admission values in acute stroke patients receiving thrombolytic therapy, irrespective of the right or left side, stroke-affected side, presence of complications, and mortality. However, ONSD is not a sufficient parameter for predicting complications and death. creator: Erdem Sivas creator: Nese Colak creator: Basak Bayram creator: Muhammet Kursat Simsek creator: Nuri Karabay creator: Vesile Ozturk uri: https://doi.org/10.7717/peerj.19197 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sivas et al. title: Rapid detection and quantification of Nile Red-stained microplastic particles in sediment samples link: https://peerj.com/articles/19196 last-modified: 2025-03-31 description: The distribution and migration processes of microplastics (MPs) in the marine sediments have yet to be fully elucidated. To estimate the contamination levels and distribution patterns, and develop countermeasures, the amount of MPs must be understood. Rapid and efficient processing of numerous samples is also needed to detect and determine MP contamination. However, whatever the sample of interest, MP analysis is time consuming. This is especially the case for deep-sea sediments, where the particle sizes are small and pretreatment processes are complex and time-consuming. To address the need for rapid and efficient detection of MPs, we propose a novel method for automatically identifying and counting Nile Red (NR)-stained sedimentary MP particles captured under a stereoscopic fluorescence microscope. In this study, we demonstrated the utility of the developed system by comparing its recovery rate and analysis time with those of the conventional methods used for manual processing. The developed method can efficiently detect MPs of sizes between 18 and 500 µm and classify them as fibers or grains (or fragments). This means that our method can efficiently detect MPs as small as 100 µm found in deep-sea sediments. The semi-automated MP detection system gave a counting time of 4.2–8.8 s per particle—as the number of particles increases, the analysis time per particle decreases. Similarly, when the number of particles counted using a stereomicroscope and image analysis software was set at 100, the automatic measurement method using a flow cell could measure 50−80% of the total number of particles, depending on the type of MPs. By using artificial particulate and fibrous MPs as training data and combining them with a machine learning system, we were able to build a system that can classify both types with 98% accuracy (100% for fibers and 96% for grains). In natural samples, approximately 150 µm (20–350 µm in range) MPs were detected, and the number was consistent with previous studies. This demonstrates the effectiveness of the method we developed. We established a rapid detection method for the number and form of MPs using a continuous semi-automated method, combining NR staining and artificial intelligence. Although this method does not allow the identification of polymer types, it enables that rapid and reliable quantification of MPs numbers. The new method established in this study is expected to improve the accuracy of information on the distribution, destination, and quantity of MPs. It is also relatively easy to use and can transfer technology in various fields, from citizen science to rapid diagnosis on research vessels in the open ocean. creator: Masashi Tsuchiya creator: Tomo Kitahashi creator: Yosuke Taira creator: Hitoshi Saito creator: Kazumasa Oguri creator: Ryota Nakajima creator: Dhugal J. Lindsay creator: Katsunori Fujikura uri: https://doi.org/10.7717/peerj.19196 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tsuchiya et al. title: Performance comparison of QuantiFERON-TB Gold In-Tube and QuantiFERON-TB Gold Plus in detecting Mycobacterium tuberculosis infection among HIV patients in China link: https://peerj.com/articles/19195 last-modified: 2025-03-31 description: IntroductionNo direct comparative study assessing QuantiFERON-TB Gold In-Tube (QFT-GIT) and QuantiFERON-TB Gold Plus (QFT-Plus) for Mycobacterium tuberculosis infection among persons living with HIV (PLHIV) in China has been conducted.MethodsSimultaneous QFT-GIT and QFT-Plus tests were conducted on PLHIV in a prison hospital. Positivity and negativity results from both assays were compared, and their diagnostic agreement was assessed.ResultsA total of 232 PLHIV individuals were included in this study. Among them, 57 patients (24.6%) and 56 patients (24.1%) were diagnosed with Mycobacterium tuberculosis infection based on QFT-GIT results and QFT-Plus, respectively. The overall agreement between the two assays was 98.3%, with a Cohen’s kappa value of 0.954. Consistency rates were observed between QFT-GIT plus, QFT-Plus TB1 and TB2 with QFT-GIT were 98.3%, 97.4% and 97.8%. The IFN-γ levels measured in QFT-GIT were found to surpass those in QFT-Plus TB1 (P = 0.04), while the difference compared to QFT-Plus TB2 exhibited a marginal trend (P = 0.134). Among the subgroup of 52 individuals who underwent dual QFT-GIT tests, a significant proportion of 23.1% (12 individuals) experienced a change in their QFT-GIT results, transitioning from a positive to a negative outcome.ConclusionsThe diagnostic performance of QFT-GIT and QFT-Plus for Mycobacterium tuberculosis infection among PLHIV with relatively higher CD4 counts was found to be comparable. Additionally, our investigation revealed that irrespective of the treatment regimen, whether it involved chemotherapy or immunotherapy, preventive Mycobacterium tuberculosis infection interventions among PLHIV consistently led to a reduction in IFN-γ levels. creator: Peng Lu creator: Haitao Yang creator: Fang Ge creator: Kai Wu creator: Yilin Lian creator: Xiaoyan Ding creator: Jingjing Pan creator: Hui Ding creator: Wei Lu creator: Qiao Liu creator: Limei Zhu uri: https://doi.org/10.7717/peerj.19195 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lu et al. title: The relationship between MAPK signaling pathways and osteogenic differentiation of periodontal ligament stem cells: a literature review link: https://peerj.com/articles/19193 last-modified: 2025-03-31 description: Periodontitis is a common oral disease that can lead to gingival inflammation, development of periodontal pockets, resorption of the alveolar bone, and the loosening and eventual loss of teeth. The optimal outcome of periodontitis treatment is maximum regeneration and functional reconstruction of periodontal tissues after control of infection and elimination of inflammation. Since both the self-healing ability of alveolar bone and the efficacy of traditional treatment methods are very limited, stem cell-based tissue regeneration engineering has received more and more attention from scholars. The best cells for periodontal tissue regeneration have been well examined, and these are called periodontal ligament stem cells (PDLSCs). The MAPK signaling pathways, including the ERK1/2, p38 MAPK, JNK, and ERK5 signaling pathways, are very complex and highly conserved tertiary kinase signaling pathways. These pathways are closely related to the osteogenic differentiation of PDLSCs, and this paper provides an overview of the research on the MAPK signaling pathways and the osteogenic differentiation of PDLSCs. creator: Xuanning Liu creator: Wanqing Zhao creator: Yanhui Peng creator: Na Liu creator: Qing Liu uri: https://doi.org/10.7717/peerj.19193 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: A proof-of-concept point-of-care test for the serodiagnosis of human amebic liver abscess link: https://peerj.com/articles/19181 last-modified: 2025-03-31 description: BackgroundAmebic liver abscess (ALA), caused by an extraintestinal invasion of the virulent protozoan Entamoeba histolytica, is important among parasitic causes of morbidity and mortality, especially in the tropics. Clinical symptoms, medical-imaging abnormalities of the liver and serological tests are normally made for supportive diagnosis. Serum-based enzyme-linked immunosorbent assay (ELISA) has been conventionally used for diagnosing ALA but is time-consuming and sophisticated equipment is required. Therefore, we sought to develop a new and rapid innovative point-of-care immunochromatographic test (ICT) that can use whole blood as an alternative to serum-based ELISA. An ICT tool using simulated whole-blood samples was developed for immunoglobulin G antibody detection, and its diagnostic efficiency was evaluated in comparison with serum-based ELISA.MethodsBoth methods were tested to assess their diagnostic performance using a total of 253 serum samples. These came from ALA patients (n = 13), healthy individuals (n = 40), and patients with other diseases (n = 200).ResultsAmebiasis-ICT exhibited 100% (95% confidential interval (CI) [75.3–100.0]) sensitivity and 97.1% (95% CI [94.1–98.8]) specificity, whereas ELISA gave the same sensitivity (100% 95% CI [75.3 –100.0]) and slightly lower specificity (95.8% 95% CI [92.5–98.0]). There were no significant differences in sensitivity and specificity between the two tests (Exact McNemar’s test; p > 0.05), with Cohen’s kappa agreement 96.44% (κ-value = 0.771, p < 0.001) indicating substantial agreement.ConclusionThis ICT tool using simulated whole-blood samples has a high possibility of being used with real whole blood. Therefore, since there is no need to separate serum, this can be considered an innovative diagnostic tool to replace serum-based ELISA in clinics and field surveys in remote areas where medical facilities are limited. creator: Rutchanee Rodpai creator: Penchom Janwan creator: Lakkhana Sadaow creator: Patcharaporn Boonroumkaew creator: Oranuch Sanpool creator: Tongjit Thanchomnang creator: Hiroshi Yamasaki creator: Toshihiro Mita creator: Pewpan M. Intapan creator: Wanchai Maleewong uri: https://doi.org/10.7717/peerj.19181 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Rodpai et al. title: Metagenome analysis of viruses associated with Anopheles mosquitoes from Ramu Upazila, Cox’s Bazar District, Bangladesh link: https://peerj.com/articles/19180 last-modified: 2025-03-31 description: Bangladesh has a warm climate and landscapes favourable for the proliferation of mosquitoes. Mosquito-borne pathogens including malaria and arthropod-borne viruses (arboviruses) remain a serious threat to the public health requiring constant vector control and disease surveillance. From November 2018 to April 2019, Anopheles mosquitoes were collected in three unions in the Ramu Upazila (sub-district) of Cox’s Bazar District, Bangladesh. The mosquito specimens were combined into pools based on date of collection, household ID, and sex. Metagenome next-generation sequencing was conducted to elucidate diversity of virus sequences in each pool. Homology-based taxonomic classification and phylogenetic analyses identified a broad diversity of putative viruses from 12 known families, with additional unclassified viruses also likely present. Analysis of male mosquitoes showed some of these viruses are likely capable of being vertically transmitted. Moreover, many of the assembled virus sequences share homology and phylogenetic affinity with segments in sequenced Anopheles genomes, and may represent endogenous viral elements derived from a past evolutionary relationship between these putative viruses and their mosquito hosts. creator: Tao Li creator: Mohammad Shafiul Alam creator: Yu Yang creator: Hasan Mohammad Al-Amin creator: Mezanur Rahman creator: Farzana Islam creator: Matthew A. Conte creator: Dana C. Price creator: Jun Hang uri: https://doi.org/10.7717/peerj.19180 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Evaluating the role of post-harvest glyphosate application in enhancing weed control in winter wheat link: https://peerj.com/articles/19177 last-modified: 2025-03-31 description: Changes in the timing and intensity of spring rainfall have led to a significant increase in late-season weed emergence in Türkiye. These newly emerged weeds tend to grow more vigorously due to the absence of competition with crops and other weeds during their development. Two field experiments were conducted in continuous monoculture winter wheat over three growing seasons (2020–2023) in Türkiye. The first goal was to determine the impact of post-harvest herbicide (PHH) on the critical time for weed removal (CTWR) in winter wheat, and the second goal was to evaluate the effects of PHH combined with various weed control treatments on weed populations, the soil seed bank, and crop yield. The experiment followed a split-plot design, with the PHH regimes and weed removal timing or weed control treatments serving as the main and sub-plots, respectively. The herbicide regime included post-harvest glyphosate potassium salt (PHG) applied at 2.646 kg ai ha−1 and No PHG. Weed removal timings were set at 10-day intervals, from 0 to 110 days after wheat emergence (DAE). Weedy and weed-free controls were included for comparison. The weed control treatments involved post-emergence tribenuron-methyl at 7.5 g ai ha−1 and hand weeding. The application of the PHG delayed the CTWR from 416 growing degree days (GDD) to 516.5 GDD in 2022 and from 465.6 GDD to 661.2 GDD in 2023, effectively preventing yield loss. The combined use of PHG with post-emergence tribenuron-methyl or hand weeding maximized wheat yield while minimizing the weed flora and the size of the soil seed bank. creator: Ahmet Tansel Serim creator: Ünal Asav creator: Yalçın Kaya creator: Bülent Başaran creator: Eric L. Patterson uri: https://doi.org/10.7717/peerj.19177 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Serim et al. title: Evaluating exercise therapies in adolescent idiopathic scoliosis: a systematic review with Bayesian network meta-analysis link: https://peerj.com/articles/19175 last-modified: 2025-03-31 description: BackgroundExercise therapy represents a financially prudent and readily applicable intervention that has gained considerable traction in the treatment of adolescent idiopathic scoliosis (AIS) in recent years. Nevertheless, a definitive agreement on the superiority of one method over another remains elusive.MethodsA comprehensive search was performed across the PubMed, Cochrane Library, Embase, and Web of Science databases for randomized controlled trials pertaining to exercise and AIS, concluding on August 20, 2024. Four independent researchers conducted a thorough review of the literature, engaged in meticulous data extraction, and assessed the risk of bias. A Bayesian network meta-analysis was performed utilizing the R programming language (version 4.3.4) and MetaInsight tool (version V6.0.1).ResultsA total of 23 studies were incorporated into the analysis, encompassing 1,289 participants with AIS. Compared to the control group, the primary meta-analysis showed that both SchrothCo and physiotherapeutic scoliosis-specific exercises (PSSE) modalities significantly improved Cobb angle (MD = −4.79, 95% CI [−8.56 to −1.11] MD = −3.11, 95% CI [−5.27 to −0.9]), axial trunk rotation (ATR) (MD = −3.03, 95% CI [−4.68 to −1.46]; MD = −2.37, 95% CI [−3.59 to −1.14]), and SRS-22 scores (MD = 0.66, 95% CI [0.39–0.94]; MD = 0.44, 95% CI [0.22–0.66]). The secondary meta-analysis showed that within the PSSE modality, Schroth therapy significantly reduced Cobb angle (MD = −2.3, 95% CI [−5.45 to −0.66]), while in the SchrothCo modality, both Schroth + Core and Schroth + Hippotherapy significantly improved Cobb angle (MD = −5.27, 95% CI [−14.15 to −3.5]). For ATR, Schroth therapy within PSSE (MD = −2.79, 95% CI [−6.4 to −0.1]), and Schroth + Core (MD = −4.03, 95% CI [−9.37 to −0.98]), Schroth + Sling (MD = −3.12, 95% CI [−10.05 to −2.94]), and Schroth + Hippotherapy (MD = −3.39, 95% CI [−10.29 to −2.84]) within the SchrothCo modality all showed significant reductions. Significant differences in SRS-22 scores were found only in the PSSE modality with Schroth therapy (MD = 0.48, 95% CI [0.02–0.9]) and in the SchrothCo modality with Schroth + Core (MD = 0.79, 95% CI [0.13–1.43]).ConclusionsAccording to the latest findings, the integration of the Schroth method with core stabilization training (Schroth + Core) is regarded as the optimal strategy for addressing AIS. The integration of core stabilization training with the Schroth method reveals a markedly enhanced effectiveness. Future inquiries should encompass more rigorous studies to establish a more robust evidence foundation and facilitate progress in this domain. creator: Yang Jiang creator: Hao Peng creator: Yanping Song creator: Li Huang creator: Hongbo Chen creator: Pengcheng Li creator: Guoshun Yang creator: Yueyu Song creator: Qigang Chen creator: Na Yao uri: https://doi.org/10.7717/peerj.19175 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Jiang et al. title: The urinary bladder wall is remodeled by undulatory resistance training in female Wistar rats link: https://peerj.com/articles/19172 last-modified: 2025-03-31 description: Urinary stress incontinence has a high prevalence in women, with many associated risk factors, such as high impact and intensity sports due to increased intra-abdominal pressure causing stretching and weakening of the pelvic floor muscles. No previous study has investigated the effects of undulatory resistance training (URT), deemed as high impact sports’s modality, on urinary bladder (UB) and tissue remodeling. Healing of tissue depends on the equilibrium of metalloproteinases (MMPs) and their inhibitors (TIMPS). We aimed to investigate the histomorphological effects of URT on UB wall. Twelve female Wistar rats were randomly divided in two groups: sedentary (SED, n = 5) and URT (n = 7). URT was performed with a ladder climbing equipment after the maximum loaded carrying test (MLCT) was carried out. The training sessions were organized in three blocks increasing the MLCT’s weight each block. New MLCT were set at the end of each block. The day after the last training, the rat was euthanized and the UB was harvested and stored in formalin for later histological analysis stained with hematoxylin-eosin (HE), Masson’s trichrome (MT), picrosirius-hematoxylin (PH) and resorcin-fuchsin (RF), and immunohistochemistry for metalloproteinase-1 (MMP1) and tissue inhibitor of metalloproteinase (TIMP1). UB slices of URT rats stained with HE showed changes in all UB layers, with increased thickeness of the urothelium. MT staining allowed to observe an increased collagen concentration on the lamina propria layer (LP) of URT rats. PH staining demonstrated a higher luminous intensity for collagen type I and III in lamina propria and smooth muscle layers of the UB wall in the URT group than in SED. RF staining demonstrated an increase of elastic fiber concentration on the LP and smooth muscle layer of the bladder wall in the URT group. Immunohistochemistry of UB slices showed that MMP1 and TIMP1 were immunolabeled on the LP the UB wall in URT rats, with TIMP1 showing a lighter labeling than MMP1. Therefore, the findings suggest that URT induces remodeling of the urinary bladder wall characterized by imbalance between MMP1 and TIMP1 and evoking an alteration in the connective tissue from loose to dense. creator: Amyr Braverman creator: Nuha A. Dsouki creator: Juliana M. Veridiano creator: Marcos R. R. Paunksnis creator: Laura B. M. Maifrino creator: Roberta L. Rica creator: Danilo S. Bocalini creator: Bruno F. Pereira creator: Dimitrius L. Pitol creator: Eduardo M. Cafarchio creator: Russ Chess-Williams creator: Patrik Aronsson creator: Monica A. Sato uri: https://doi.org/10.7717/peerj.19172 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Braverman et al. title: Adoption of a biologically-enhanced agricultural management (BEAM) approach in agroecosystems for regenerating soil fertility, improving farm profitability and achieving productive utilization of atmospheric CO2 link: https://peerj.com/articles/19167 last-modified: 2025-03-31 description: BackgroundA 4-year field study, on the adoption of a Biologically-Enhanced Agricultural Management (BEAM) protocol, in a cotton/cover-crop rotation in Turkey, was designed to observe “change-over-time” of soil organic carbon (SOC%) and total soil nitrogen (TSN%) at three soil profile depths (0–15 cm, 15–30 cm and 30–45 cm) while tracking farm productivity and profitability.MethodsBEAM systems employ regenerative practices: (a) no-till, (b) no, or reduced synthetic nutrient amendments, (c) continuous roots in the ground (commodity/cover), accompanied with an injection (in-furrow at planting) of an extract of beneficial microbes, from a Johnson-Su bioreactor. Three field nitrogen treatments: (1) BEAM+100% N (203 kg N ha−1); (2) BEAM+15% N (30.53 kg N ha−1); and (3) BEAM-0% N (No N applied), were implemented, on a 5.22-hectare plot, to assess the influence of BEAM protocols and nitrogen amendments, on SOC%, TSN%, cotton production, and profitability.ResultsThe SOC%, in the 0–15 cm soil profile demonstrated a significant increase from 0.39% SOC to 1.83% SOC, for a total increase of 1.44%, over the 4-year study period, (y = 0.3136x + 0.1206; r2 = 0.96; F(1,2) = 45.1616, p = 0.02143); The 15–30 cm soil profile demonstrated a non-significant loss of −0.23% SOC (y = −0.3161x + 0.156; r2 = 0.3183; F(1,2) = 0.9339, p = 0.4358), and the 30–45 cm soil profile exhibited a significant increase of 0.28% SOC; (y = 0.0477x + 0.4743; r2 = 0.9363; F(1,2) = 29.4005, p = 0.03237). Annual SOC cumulative increases of ~6.59 metric tons (t) carbon (C) ha−1yr−1, were observed, from 2019 to 2023, in the top 45 cm of the soil profile along with annual TSN increases of ~0.68 t N ha−1yr−1 in all three treatments. Cover-crop aboveground biomass increased annually in 2021, 2022 and 2023 from ~400 g, to ~692 g, to ~925 g dry biomass m−2yr−1 providing annual agroecosystem surface carbon accumulation of ~1.78 t C, ~3.08 t C and ~4.11 t C ha−1. Earthworm populations increased from zero earthworms m−2 in 2019 to ~100 earthworms m−2 in 2023. BEAM protocols also promoted: (a) farm input reductions of: 100% for herbicide, 56% for insecticide, 61% for diesel fuel, 85% for synthetic nitrogen fertilizer, and 100% for phosphorus fertilizer applications, reducing farm input costs ~$470 ha−1yr−1. Adoption of a BEAM regenerative agricultural management system, increased: (a) SOC (~6.59 t C ha−1yr−1); (b) C in the annual growth of cover-crop biomass (~4.12 t of C ha−1yr−1); (c) carbon in residual surface cover-crop plant residues from previous annual cover crops (~0.82 t C ha−1yr−1); and (d) C exported in cotton lint (~0.77 t C ha−1yr−1). Total C avoidance included: (a) reductions in fertilizer, pesticides and diesel inputs (~0.33 t C ha−1yr−1); and (b) reduction of C respiration from adoption of zero-till (~0.64 t C ha−1yr−1). Adoption of BEAM management, in this cotton/cover-crop agroecosystem, provided productive utilization, or avoidance of ~13.27 t of atmospheric C ha−1yr−1. creator: David C. Johnson creator: Hui-Chun Su Johnson uri: https://doi.org/10.7717/peerj.19167 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Johnson and Johnson title: Modulatory mechanisms of long-term volleyball practice on visuospatial working memory capacity: an fNIRS study link: https://peerj.com/articles/19153 last-modified: 2025-03-31 description: ObjectiveVisuospatial working memory capacity is crucial for daily life and various cognitive processes. Previous studies have shown that physical training not only improves physical fitness but also visual visuospatial working memory capacity. However, few studies have explored visuospatial working memory improvement and brain plasticity changes with long-term volleyball exercise. Therefore, the purpose of this study was to gain insight into whether there is a relationship between long-term volleyball practice and visuospatial working memory and the effects on the prefrontal lobes of the brain.MethodsNeural correlates of visuospatial working memory in elite (n = 23; raining age mean: 8.27 ± 1.75 years; age: 21.07 ± 1.58 years) and novice (n = 23; raining age mean: 1.81 ± 0.56 years; age: 20.53 ± 1.36 years) volleyball athletes are examined to uncover potential skill-based differences. Functional near-infrared spectroscopy (fNIRS) data from 46 participants performing visuospatial working memory test reveal compelling results.ResultsCompared with the novice group, the experts showed a higher accuracy rate (ACC) (p = 0.021) and shorter reaction time (RT) (p = 0.019) in the visuospatial working memory test. fNIRS data showed increased oxygen activation in the right dorsolateral prefrontal lobe (p < 0.05) and the right frontal region (p < 0.05).ConclusionsStudies have shown that long-term volleyball training can significantly enhance individuals’ visuospatial working memory capacity. This enhancement was mainly reflected in the fact that athletes who participated in long-term volleyball training demonstrated faster operational processing speed and higher accuracy in visuospatial working memory tasks, and plasticity changes in dorsolateral prefrontal and prefrontal pole regions. We also found no significant linear relationship between specific brain activation and behavioral performance in expert athletes. creator: Wen Zhang creator: Jingru Liu creator: Fangfang Hu creator: Yang Liu creator: Chao Kan uri: https://doi.org/10.7717/peerj.19153 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Computed tomography-based radiomic features combined with clinical parameters for predicting post-infectious bronchiolitis obliterans in children with adenovirus pneumonia: a retrospective study link: https://peerj.com/articles/19145 last-modified: 2025-03-31 description: ObjectivesTo develop a model incorporating computed tomography (CT) radiomic features and clinical parameters for predicting bronchiolitis obliterans (BO) with adenovirus pneumonia in children.MethodsA total of 165 children with adenovirus pneumonia between October 2013 and February 2020 were enrolled retrospectively. Among them, BO occurred in 70 patients, and the remaining 95 patients did not have BO. These children were stratified into training and testing groups at a ratio of 7:3. Manual segmentation of lesions in baseline CT images during acute pneumonia was performed to extract radiomic features. Multiple statistical methods were used to determine the best radiomic features. Combined models based on radiomic and clinical features were established via logistic regression (LR), random forest (RF), and support vector machine (SVM) algorithms. Model performance was evaluated via the area under the receiver operating characteristic curve (AUC).ResultsA total of 2,264 radiomic features were extracted from the lesions, from which 10 optimal radiomic features were ultimately selected. The length of hospitalization, number of pneumonia lobes, and optimal radiomic features were incorporated into the combined models. In the training group, the AUCs of the combined LR, RF and SVM models were 0.946, 0.977, and 0.971, respectively; while in the testing group, they yielded AUCs of 0.890, 0.859, and 0.885, respectively. The predictive performance of these combined models surpassed that of the radiomic and clinical models.ConclusionCombining CT-based radiomic features with clinical parameters can offer an effective noninvasive model to predict BO in children with adenovirus pneumonia. creator: Li Zhang creator: Ling He creator: Guangli Zhang creator: Xiaoyin Tian creator: Haoru Wang creator: Fang Wang creator: Xin Chen creator: Yinglan Zheng creator: Man Li creator: Yang Li creator: Zhengxiu Luo uri: https://doi.org/10.7717/peerj.19145 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Comparative transcriptome analysis identified candidate genes associated with kernel row number in maize link: https://peerj.com/articles/19143 last-modified: 2025-03-31 description: Kernel row number (KRN) is a crucial trait in maize that has a high impact on yield. However, KRN is a typical quantitative trait with only a few genes being verified so far. Here, two maize inbred lines with contrasting KRN were used to perform transcriptome analysis at five early ear developmental stages. Pairwise differential gene expression analyses were performed, and a total of 11,897 line-specific differentially expressed genes (DEGs) were detected between the two lines across the five development stages. Clustering analysis of line-specific DEGs revealed that the trends of gene expression changed significantly in the five stages, thus the five stages were further divided into two development phases: Phase I (V6-V8) and Phase II (V9-V10). Gene ontology enrichment analysis revealed that different transcriptional pathways were activated in the two phases. DEGs in Phase I were significantly enriched in morphogenesis and differentiation processes and hormone regulation. Of the 5,850 line-specific DEGs in Phase I, 2,132 genes were in known quantitative trait loci (QTLs) or flanking regions of quantitative trait nucleotides (QTNs), of which 92 were repeatedly detected in QTLs where QTNs also exist. The 92 high-probability candidate genes included development-related transcription factors (SBP-box and AP2/EREBP TFs) as well as genes involved in hormone homeostasis and signaling. Our study provides genetic resources for the elucidation of the molecular mechanisms of KRN development and reference for the cloning of candidate genes. creator: Shukai Wang creator: Yancui Wang creator: Xitong Xu creator: Dusheng Lu creator: Baokun Li creator: Yuxin Zhao creator: Senan Cheng creator: Zhenhong Li creator: Cuixia Chen uri: https://doi.org/10.7717/peerj.19143 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Comparative analysis of rhizosphere soil between three plantation types in Karst Rocky Desertification area by widely targeted metabolomics link: https://peerj.com/articles/19131 last-modified: 2025-03-31 description: Understanding the differences in rhizosphere soil microbial metabolites between severely and mildly rocky desertified areas is crucial for developing ecological restoration strategies and land management measures in rocky desertification regions. This study systematically analyzed the differences in rhizosphere soil microbial metabolites of Toona sinensis, Vernicia fordii, and Cornus wilsoniana in severely and mildly rocky desertified areas of Western Hunan using untargeted metabolomics. The results showed that the types and quantities of primary and secondary metabolites in the rhizosphere soil of severely rocky desertified areas were significantly lower than those in mildly rocky desertified areas. Additionally, under severe rocky desertification conditions, 15 common compounds (e.g., 17a-estradiol, adenine, all-trans-retinoic acid) were significantly increased in the rhizosphere soil microbial metabolites of the three tree species. These compounds may provide defense mechanisms for plants to adapt to harsh environments. KEGG metabolic pathway analysis revealed that under severe rocky desertification conditions, Toona sinensis, Vernicia fordii, and Cornus wilsoniana shared six enriched pathways, which play an important role in the biosynthesis of compounds such as phenylpropanoids and unsaturated fatty acids. By revealing the differences in rhizosphere soil microbial metabolites, this study not only deepens the understanding of rocky desertification ecosystems but also provides valuable scientific evidence for ecological restoration and sustainable land management. creator: Tongtong Guo creator: Ninghua Zhu creator: Ziqian Pan creator: Peng Dang uri: https://doi.org/10.7717/peerj.19131 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Guo et al. title: Knowledge and attitude of dental school faculties towards stem cell therapies and their applications link: https://peerj.com/articles/19127 last-modified: 2025-03-31 description: BackgroundStem cells are characterized by their ability to self-renew and differentiate across multiple lineages. Knowledge about these cells and their potential is an important factor driving people to support their use. Therefore, we aimed to evaluate the knowledge and attitudes regarding stem cell therapies, education, and donation among faculty members of the College of Dentistry at King Saud University, Saudi Arabia.MethodsA self-completed questionnaire was distributed among the faculty members, in which questions about demographic data, basic knowledge of stem cells as well as attitudes towards education and participation in stem cell-related research, and tissue donation were raised.ResultsA total of 102 participants responded to the questionnaire. Most participants (62.7%) ranked their stem cell knowledge as basic, despite correctly answering most of the knowledge questions. More than half of faculty mentioned a lack of stem cell-related activities in their courses (59.8%), and most showed strong support for including related education in postgraduate programs (71.6%). Noteworthy, 64% of participants reported interest in stem cell research and 74.5% were willing to donate their tissue for research purposes. The mean ranks of knowledge scores were significantly higher in subjects who have related lectures in undergraduate courses (p < 0.05), and those with high interest in research participation and tissue donation (p < 0.0001), and (p < 0.05) respectively. Most participants (>60%) were not aware about the current applications of stem cell research and therapy in Saudi Arabia.ConclusionMost participants had an acceptable degree of knowledge about stem cells and showed a positive attitude to their education and participation in research. Additionally, knowledge scores have significantly and positively influenced those attitudes. More effort is required to promote the presence of local facilities for researchers to participate in stem cell-related research. The results of this study can be used as a foundation for evidence-informed policymaking within dental schools and research institutions. creator: Sumaiah Ajlan creator: Nahid Ashri uri: https://doi.org/10.7717/peerj.19127 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ajlan and Ashri title: Vertical assemblage of the holoplanktonic mollusks (Pteropoda and Pterotracheoidea: Carinaiidae, Pterotracheidae) in the Campeche Canyon, southern Gulf of Mexico, during a “Nortes” season link: https://peerj.com/articles/19118 last-modified: 2025-03-31 description: This study examines the vertical assemblages of the holoplanktonic mollusks (Pteropoda and Pterotracheoidea) in the Campeche Canyon, southern Gulf of Mexico, during a “Nortes” season (February 21–28, 2011) and explores their relationship with the hydrography and the geostrophic circulation pattern. High-resolution hydrographic data were acquired during a multidisciplinary research cruise of 48 hydrographic stations. Zooplankton samples were collected at 24 stations from four depths (10, 50, 100, and 200 m) using a multiple open/closed net system. The results revealed a deep thermocline at a depth of 90 m and a circulation pattern dominated by cyclonic and anticyclonic eddies that induced cold and warm cores. Thirty-three Pteropoda and three Pterotracheoidea species were identified, with the highest richness at a depth of 100 m (just below the thermocline). The highest organism densities were observed at a depth of 10 m. The diversity index (H’) showed variations depending on the sampling depth, with the highest values (1.9 bits ind−1) at 100 and 200 m, while at 10 m depth the lowest values (1.45 bits ind−1) were observed. Multivariate analyses showed that dissolved oxygen, and temperature were the main environmental factors determining organism density. creator: Zayra López-Cabello creator: Erik Coria-Monter creator: María Adela Monreal-Gómez creator: David Alberto Salas de León creator: Elizabeth Durán-Campos creator: Adolfo Gracia uri: https://doi.org/10.7717/peerj.19118 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 López-Cabello et al. title: Chaetoglobosin A induces apoptosis in T-24 human bladder cancer cells through oxidative stress and MAPK/PI3K-AKT-mTOR pathway link: https://peerj.com/articles/19085 last-modified: 2025-03-31 description: Chaetoglobosin A (ChA) is an antitumor compound produced by Chaetomium globosum. However, the mechanism of its antitumor effect has been rarely reported. In this study, we evaluated the anti-proliferative effect of ChA on T-24 human bladder cancer cells and explored its mechanism of action. ChA was found to have a good inhibitory effect on T-24 cells by MTT assay with an IC50 value of 48.14 ± 10.25 μΜ. Moreover, it was found to have a migration inhibitory ability and a sustained proliferation inhibitory effect on tumor cells by cell aggregation assay and cell migration assay. The cells morphological changes were determined by Hoechst33342 assay. While Annexin V-FITC/PI double-staining assay also demonstrated that the number of apoptotic cells increased with the increase of drug concentration. Flow cytometry results showed that ChA treatment increased reactive oxygen species (ROS) and decreased mitochondrial membrane potential (MMP) in T-24 cells and inhibited cell mitosis, resulting in an increase in the number of sub-G1 phase cells. Further western blot experiments demonstrated that MAPK and PI3K-AKT-mTOR pathways were activated after drug treatment in addition to endogenous and exogenous apoptotic pathways. The addition of the ROS inhibitor N-acetylcysteine (NAC) upregulated the expression level of Bcl-2 protein, decreased p38 phosphorylation, increased ERK phosphorylation and restored the levels of PI3K and p-mTOR after ChA treatment. These suggest that ChA induces apoptosis by regulating oxidative stress, MAPK, and PI3K-AKT-mTOR signaling pathways in T-24 cells. creator: Jia Song creator: Jinyu Qiao creator: Mingxue Chen creator: Jiahui Li creator: Jixia Wang creator: Dayong Yu creator: Huachuan Zheng creator: Liying Shi uri: https://doi.org/10.7717/peerj.19085 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Song et al. title: New digital anatomical data of Keichousaurus hui (Reptilia: Sauropterygia) and its phylogenetic implication link: https://peerj.com/articles/19012 last-modified: 2025-03-31 description: Three complete skulls of Keichousaurus hui from the Middle Triassic Xingyi Fauna of southwestern China were examined using high-resolution computed tomography (CT) scanning. The CT images allow a few refinements and supplements in cranial anatomy. Some previously ambiguous anatomical characters were identified, including the presence of an L-shaped ectopterygoid that extends from the lateral side of the pterygoid and bends ventrally, the wedge-shaped posterolateral process of the frontal, the trapezoidal pterygoid for articulating with the palatine, and a rodlike basioccipital tuber that extends posterolaterally. These new features provide new detailed anatomical information for taxonomy. The new phylogenetic analysis of Sauropterygiformes places Keichousaurus as an eosauropterygian that is more basal than the monophyly which includes Nothosauridae and Pistosauroidea. Moreover, the result also suggests that Keichousaurus is more closely related to Chinese pachypleurosaurs-like eosauropterygians than to European pachypleurosaurs and more derived than other Chinese pachypleurosaurs-like forms. creator: Jiayu Xu creator: Yu Guo creator: Yucong Ma creator: Wei Wang creator: Long Cheng creator: Fenglu Han uri: https://doi.org/10.7717/peerj.19012 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xu et al. title: Construction and validation of a risk prediction model for postoperative pulmonary infection in patients with brain tumor: a retrospective study link: https://peerj.com/articles/18996 last-modified: 2025-03-31 description: ObjectivesThis study aimed to investigate the influencing factors and construct a risk prediction model for postoperative pulmonary infection in patients with brain tumor.MethodsThis investigation encompassed a cohort of 636 individuals who were diagnosed with brain tumors and underwent surgical treatment between October 2019 and October 2023. According to the ratio of 7:3, the patients were randomly divided into training set and validation set. Univariate analysis and multivariate Logistic regression analysis were performed on the data in the training set. Finally, the independent risk factors of postoperative pulmonary infection in patients with brain tumor were screened out. R software was used to establish a nomogram model for predicting the risk of postoperative pulmonary infection. Receiver operating characteristic (ROC) curve, calibration curve and Hosmer-Lemeshow test were used to evaluate the discrimination and calibration of the model. Decision curve analysis was used to evaluate the clinical benefit of the model.ResultsThe prevalence of postoperative pulmonary infection in patients with brain tumors was 17.9%. The nomogram contained several independent risk factors: age ≥ 60 years, diabetes mellitus, GCS score < 13 points, postoperative bedtime, and postoperative D-Dimer. The prediction model yielded an area under the curve (AUC) of 0.814 (95% confidence interval CI [0.756–0.873]) in the training set, and an AUC of 0.752 (95% CI [0.653–0.850]) in the validation set. The P-values for the Hosmer-Lemeshow test in the training set are 0.629, while in the validation set, they are 0.128. Decision curve analysis demonstrated that the model’s clinical effectiveness is satisfactory.ConclusionsAge ≥ 60 years, diabetes mellitus, GCS score < 13 points, postoperative bedtime and postoperative D-Dimer are risk factors for postoperative pulmonary infection in patients with brain tumor. The developed prediction model demonstrates substantial predictive value and clinical applicability, serving as a valuable reference for medical professionals in recognizing postoperative pulmonary infections in patients with brain tumors and facilitating preventive nursing measures. creator: Jiangling Lan creator: Xing Liu creator: Ligen Mo creator: Dandan Wei creator: Shizhen Zhang creator: Yujiao Zhang creator: Yin Zhu creator: Yi Lei uri: https://doi.org/10.7717/peerj.18996 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Lan et al. title: Understanding uremic cardiomyopathy: from pathogenesis to diagnosis and the horizon of therapeutic innovations link: https://peerj.com/articles/18978 last-modified: 2025-03-31 description: Uremic cardiomyopathy (UC) is a significant cardiovascular complication in individuals with end-stage renal disease. This review aims to explore the multifaceted landscape of UC, including the key pathophysiological mechanisms, diagnostic challenges, and current therapeutic approaches. The prevalence of cardiac hypertrophy, as a hallmark of UC, is highlighted and some new insights to its intricate pathogenesis, involving uremic toxins, oxidative stress, and inflammatory responses is elucidated. Diagnostic complexities, including the absence of specific biomarkers, are discussed, and the need for advanced imaging modalities and emerging diagnostic strategies are emphasized. Current therapeutic interventions, although lacking specificity, are addressed, paving its way to the potential future directions in targeted therapies. The review concludes new insights into the critical importance of ongoing research and technological advancements which will enhance early detection, precision treatment, and ultimately improve outcomes for individuals with UC. creator: Qiong Song creator: Pengbo Wang creator: Yunfang Wu creator: Zhuan’e Yao creator: Wei Wang creator: Guangbo Tang creator: Peng Zhang uri: https://doi.org/10.7717/peerj.18978 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Song et al. title: A new specimen of Plesiopterys wildi reveals the diversification of cryptoclidian precursors and possible endemism within European Early Jurassic plesiosaur assemblages link: https://peerj.com/articles/18960 last-modified: 2025-03-31 description: BackgroundA virtually complete and articulated plesiosaur skeleton (MH 7) is described from the Lower Jurassic (Toarcian) Posidonienschiefer Formation near Holzmaden in southern Germany. Plesiosaur remains are rare in this rock unit compared to those of other marine reptiles, such as ichthyosaurs and thalattosuchian crocodylomorphs. The new specimen offers an opportunity to assess the biodiversity of Early Jurassic plesiosaurs documented from what is now Central Europe.MethodsThe osteology of MH 7 is described and compared with other Early Jurassic plesiosaurs based on first-hand observations. Phylogenetic analyses using both equal weighting and weighted parsimony determined phylogenetic placement within Plesiosauria.ResultsPlesiopterys wildi is an early-diverging plesiosauroid and a sister taxon to Franconiasaurus brevispinus and Cryptoclidia. MH 7 represents a subadult individual, providing an updated character state diagnosis of Plesiopterys wildi, which has hitherto only been known from the osteologically immature holotype SMNS 16812. The presence of multiple regionally distinct plesiosaur genera and species within the European epicontinental marine basins suggests possible paleobiogeographical segregation during the Toarcian. creator: Miguel Marx creator: Sven Sachs creator: Benjamin P. Kear creator: Mats E. Eriksson creator: Klaus Nilkens creator: Johan Lindgren uri: https://doi.org/10.7717/peerj.18960 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Marx et al. title: Fisetin may protect early porcine embryos from oxidative stress by down-regulating GRP78 levels link: https://peerj.com/articles/19198 last-modified: 2025-03-28 description: Fisetin is a natural flavonol with a variety of biological activities, including anti-inflammatory and antitumor activities. However, the effect of fisetin on mammalian oocyte and embryo development is unknown, so in this study, we used porcine oocytes as an experimental model, and added optimal concentrations of fisetin to the in vitro culture medium after parthenogenetic activated to investigate the effect of fisetin on porcine embryo development. It was found that 0.1 µM fisetin significantly increased the cleavage rate and blastocyst formation rate, and the quality of blastocysts was also improved. Staining results showed that the levels of reactive oxygen species (ROS), autophagy, endoplasmic reticulum stress and apoptosis were significantly reduced, while glutathione levels and mitochondrial function were significantly increased in the 0.1 µM fisetin-treated group of early porcine embryos compared with the control group. Meanwhile, fisetin decreased the expression level of the endoplasmic reticulum stress marker protein GRP78 (0.71 ± 0.19). In addition, fisetin decreased the expression of genes related to pro-apoptosis, autophagy and endoplasmic reticulum stress and increased the expression of genes related to antioxidant, pluripotency and mitochondrial. According to our results, fisetin promotes early embryonic development in porcine, and this effect may be realized by down-regulating the expression level of GRP78. creator: Xiu-Wen Yuan creator: Hao Guo creator: ChaoRui Wang creator: HeWei Ji creator: YongNan Xu creator: Xue Rui Yao creator: Lin Wang creator: QiLong Cao creator: Nam-Hyung Kim creator: Ying-Hua Li uri: https://doi.org/10.7717/peerj.19198 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yuan et al. title: The role of endoplasmic reticulum stress in type 2 diabetes mellitus mechanisms and impact on islet function link: https://peerj.com/articles/19192 last-modified: 2025-03-28 description: Type 2 diabetes mellitus (T2DM) is a globally prevalent metabolic disorder characterized by insulin resistance and dysfunction of islet cells. Endoplasmic reticulum (ER) stress plays a crucial role in the pathogenesis and progression of T2DM, especially in the function and survival of β-cells. β-cells are particularly sensitive to ER stress because they require substantial insulin synthesis and secretion energy. In the early stages of T2DM, the increased demand for insulin exacerbates β-cell ER stress. Although the unfolded protein response (UPR) can temporarily alleviate this stress, prolonged or excessive stress leads to pancreatic cell dysfunction and apoptosis, resulting in insufficient insulin secretion. This review explores the mechanisms of ER stress in T2DM, particularly its impact on islet cells. We discuss how ER stress activates UPR signaling pathways to regulate protein folding and degradation, but when stress becomes excessive, these pathways may contribute to β-cell death. A deeper understanding of how ER stress impacts islet cells could lead to the development of novel T2DM treatment strategies aimed at improving islet function and slowing disease progression. creator: Zhaxicao He creator: Qian Liu creator: Yan Wang creator: Bing Zhao creator: Lumei Zhang creator: Xia Yang creator: Zhigang Wang uri: https://doi.org/10.7717/peerj.19192 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 He et al. title: A retrospective analysis of anti-osteoporosis medication trends among patients under 50 years old in nine major regions of China from 2016 to 2019 link: https://peerj.com/articles/19187 last-modified: 2025-03-28 description: PurposeThis study aimed to assess the national trends in osteoporosis prescriptions among Chinese adult outpatients aged less than 50 years with osteoporosis, from 2016 to 2019.Patients and methodsPrescriptions for adult outpatients with osteoporosis from hospitals in nine major areas were extracted from the database of the Hospitals Prescription Analysis Cooperative Project. Trends in the annual prescriptions and expenditure of osteoporosis were analyzed.ResultsThe number of osteoporosis hospital visits showed an increasing trend year by year from 18,412 in 2016 to 23,447 in 2019 (P = 0.029), and the corresponding cost increased from 2,083,872.94 Chinese yuan (CNY) to 2,643,508.59 CNY in 2019 (P = 0.032). The result showed that the share of newer osteoporotic use of medicines increased continuously, accounting for 34.3% of prescriptions and 26.8% of expenditures in 2019. The study found that in osteoporosis hospital visits under 50 years of age, the use of medicine increased year by year. However, bone resorption inhibitors and bone formation promoters in this group did not change significantly, accounting for only small proportion.ConclusionThe development of osteoporosis prescription in this study reflected the current situation of research in China. Meanwhile, in this study, we also investigated the epidemiology of osteoporosis in China in patients under 50 years of age, for whom the incidence of osteoporosis showed an increasing trend, which reminded us to accelerate the prevention of osteoporosis. creator: Bo Chen creator: Liying Chen creator: Zhenwei Yu creator: Yanting Sun creator: Yuzhen Wang creator: Chen Wang creator: Siqi Wang creator: Yan Hu creator: Lian-Di Kan creator: Liu-Cheng Li uri: https://doi.org/10.7717/peerj.19187 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chen et al. title: A comparative analysis of the rhizosphere microbial communities among three species of the Salix genus link: https://peerj.com/articles/19182 last-modified: 2025-03-28 description: Rhizosphere microorganisms exert a significant influence in counteracting diverse external stresses and facilitating plant nutrient uptake. While certain rhizosphere microorganisms associated with Salix species have been investigated, numerous rhizosphere microorganisms from various Salix species remain underexplored. In this study, we employed high-throughput sequencing to examine the rhizosphere bacterial and fungal communities composition and diversity of three Salix species: Salix zangica (SZ), Salix myrtilllacea (SM), and Salix cheilophila (SC). Furthermore, the BugBase and FUNGuild were utilized to predict the functional roles of bacterial and fungal microorganisms. The findings revealed notable variations in the alpha and beta diversities of bacterial and fungal communities among the three Salix species exhibited significant differences (p < 0.05). The relative abundance of Flavobacterium was highest in the SZ samples, while Microvirga exhibited significant enrichment in the SM samples. Microvirga and Vishniacozyma demonstrate the highest number of nodes within their respective bacterial and fungal community network structures. The functions of bacterial microorganisms, including Gram-positive, potentially pathogenic, Gram-negative, and stress-tolerant types, exhibited significant variation among the three Salix species (p < 0.05). Furthermore, for the function of fungal microbe, the ectomycorrhizal guild had the highest abundance of symbiotic modes. This results demonstrated the critical role of ectomycorrhizal fungi in enhancing nutrient absorption and metabolism during the growth of Salix plants. Additionally, this findings also suggested that S. zangica plant was better well-suited for cultivation in stressful environments. These findings guide future questions about plant-microbe interactions, greatly enhancing our understanding of microbial communities for the healthy development of Salix plants. creator: Tianqing Feng creator: Juan Li creator: Xiaoning Mao creator: Xionglian Jin creator: Liang Cheng creator: Huichun Xie creator: Yonggui Ma uri: https://doi.org/10.7717/peerj.19182 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Feng et al. title: EcoNicheS: enhancing ecological niche modeling, niche overlap and connectivity analysis using the shiny dashboard and R package link: https://peerj.com/articles/19136 last-modified: 2025-03-28 description: EcoNicheS (https://github.com/armandosunny/EcoNicheS) is a comprehensive R package built on a Shiny dashboard that offers an intuitive and streamlined workflow for creating ecological niche models (ENMs) and landscape connectivity models. It incorporates tools for niche modeling, overlap analysis, and connectivity modeling, leveraging robust algorithms from the biomod2 suite. EcoNicheS is designed to simplify the technical complexities of ENMs, bridging the gap between advanced modeling techniques and user accessibility. The package offers an interactive interface for streamlined data input, model parameterization, and result visualization. Its comprehensive toolset includes occurrence data processing, pseudoabsence point generation, urbanization filters, and ecological connectivity modeling, distinguishing it from other platforms. EcoNicheS integrates innovative workflows with dynamic output visualizations while emphasizing reproducibility and comparability across statistical methods. Its practical applications span diverse research fields, including biogeography, epidemiology, evolutionary studies, climate change impacts, landscape connectivity, and biodiversity conservation. This versatility makes EcoNicheS a valuable resource for advancing in ecological and conservation science. creator: Armando Sunny creator: Clere Marmolejo creator: Rodrigo Vidal-López creator: Fredy A. Falconi-Briones creator: Ángela P. Cuervo-Robayo creator: René Bolom-Huet uri: https://doi.org/10.7717/peerj.19136 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sunny et al. title: Is there hidden genetic variability in the species of Steindachneridion Garavello, 2005 (Siluriformes: Pimelodidae)? link: https://peerj.com/articles/18193 last-modified: 2025-03-28 description: BackgroundThe genus Steindachneridion, which includes large-sized freshwater pimelodid species, is endemic to the southeastern coastal drainages of South America, specifically the Paraná River and Uruguay River basins.MethodsIn this study, genetic analyses of mitochondrial DNA (mtDNA) D-loop were conducted on four species within this genus across their respective distributions: Steindachneridion scriptum (from the Tibagi and Uruguay rivers), S. melanodermatum (from the Iguaçu River), S. doceanum (from the Doce River), and S. parahybae (from the Paraíba do Sul River). Zungaro zungaro and Brachyplatystoma rousseauxii were employed as outgroups, and the topology was inferred using Bayesian Inference (BI) and maximum likelihood (ML) phylogenetic reconstruction techniques. Additionally, the sequences were analyzed to assess genetic diversity levels.ResultsIn contrast to the remaining species, which exhibited distinct species-specific clades, our data suggests that S. scriptum formed two sister clades, potentially representing distinct operational taxonomic units. Novel haplotypes were identified for each of the four species, further supporting the conclusions derived from the phylogenetic analysis. Overall, Steindachneridion species displayed high haplotype diversity paired with low nucleotide diversity, indicating a demographic expansion event after reduced effective population size. Nevertheless, genetic structure indexes were notably high. These findings suggest that the genetic diversity within these species may be underestimated, which has implications for both taxonomic classification and biological conservation strategies.ConclusionIn conclusion, the study of genetic diversity in four Steindachneridion species has revealed distinct molecular operational taxonomic units (MOTUs), which highlights the necessity for conservation efforts. The detection of new haplotypes and intraspecific variability emphasizes the urgency of implementing systematic conservation measures in the face of looming extinction threats. creator: Daniele Aparecida Matoso creator: Hallana Cristina Menezes da Silva creator: Augusto Luiz Ferreira Júnior creator: Fábio Porto-Foresti creator: Ricardo Utsunomia creator: Fernanda Dotti do Prado creator: Roberto Ferreira Artoni uri: https://doi.org/10.7717/peerj.18193 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Matoso et al. title: Assessment of liquid media requirements for storing and evaluating respiratory cilia motility link: https://peerj.com/articles/19191 last-modified: 2025-03-27 description: Mucociliary clearance is critical for maintaining normal lung function. Respiratory cilia which drive mucociliary clearance are commonly studied by measuring cilia beat frequency (CBF). There is currently significant variation within the literature regarding what is a normal value for CBF, this may be due in part to the large variety of liquid media used to suspend, maintain, and image ciliated cells. This study aimed to conduct a thorough examination to assess how media choice influences respiratory cilia motility. To accomplish this, Adult C57/BL6 mouse trachea samples were incubated in eight commonly used liquid media including: Saline, Dulbecco’s Phosphate-Buffered Saline (DPBS), Hanks’ Balanced Salt Solution (HBSS), Medium 199 (M199), Dulbecco’s Modified Eagle’s Medium (DMEM), Roswell Park Memorial Institute Medium (RPMI), Minimum Essential Medium (MEM), and Leibovitz’s L-15 Medium (L-15); with or without 10% FBS supplementation. The effects of storage time (0–12 hours) and storage temperature (4 °C or room temperature) were also assessed. All media except saline were found to be equally effective in maintaining cilia function in airway samples that were freshly harvested and immediately imaged. Saline, however, significantly reduced the number of cells with motile cilia. A more complex pattern emerged when samples were stored before imaging. In saline, cilia function was significantly impaired after just one hour of storage. Samples stored in all other media showed strong maintenance of motile cilia function, with only minor changes. Notably, cilia function was better preserved with storage at 4 °C, while room temperature storage generally led to significant increases in CBF, especially in media containing FBS. Lastly, FBS supplementation was essential for maintaining cilia motility in L-15 media, as L-15 without FBS resulted in significant decreases in cilia motility following storage at either 4 °C or room temperature. In conclusion, saline should only be used if cilia are to be imaged immediately, as cilia stored in saline quickly lose motile function. All other commonly used media appear equally capable of maintaining motile cilia function for up to 12 hours when stored at 4 °C. Surprisingly, DPBS was just as effective as more expensive media in preserving ciliated samples. Storing ciliated tissue at room temperature generally leads to increased CBF, particularly in media containing FBS. Finally, L-15 media alone specifically requires the addition of 10% FBS to maintain cilia motility. These findings provide a valuable foundation for standardizing the handling, collection, and transport of ciliated samples for motile cilia assessment. creator: Richard Francis uri: https://doi.org/10.7717/peerj.19191 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Francis title: MicroRNA-99 family in cancer: molecular mechanisms for clinical applications link: https://peerj.com/articles/19188 last-modified: 2025-03-27 description: MicroRNAs (miRNAs) are a class of non-coding RNA sequences that regulate gene expression post-transcriptionally. The miR-99 family, which is highly evolutionarily conserved, comprises three homologs: miR-99a, miR-99b, and miR-100. Its members are under-expressed in most cancerous tissues, suggesting their cancer-repressing properties in multiple cancers; however, in some contexts, they also promote malignant lesion progression. MiR-99 family members target numerous genes involved in various tumor-related processes such as tumorigenesis, proliferation, cell-cycle regulation, apoptosis, invasion, and metastasis. We review the recent research on this family, summarize its implications in cancer, and explore its potential as a biomarker and cancer therapeutic target. This review contributes to the clinical translation of the miR-99 family members. creator: Yueyuan Wang creator: Dan Huang creator: Mingxi Li creator: Ming Yang uri: https://doi.org/10.7717/peerj.19188 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Assessment tools for attention deficits in patients with stroke: a scoping review across components and recovery phases link: https://peerj.com/articles/19163 last-modified: 2025-03-27 description: BackgroundAttention deficits are common in patients with stroke, making the assessment of attention functions crucial for improvement. A previous review reported on attention deficit assessments using specific components in patients with stroke. However, this study only included randomized controlled trials (RCTs) and did not encompass the attention assessments included in the observational study. Therefore, we reviewed and categorized the assessments used for attention deficits in patients with stroke according to specific attention components including RCTs and observational studies.MethodIn this study, we adhered to the scoping review guidelines. The population, concept, and context of this study were stroke; attention deficits, RCTs, observational studies, and assessments; and components (focused, selective, sustained, spatial, divided, visual, and auditory attention) and phase (acute, subacute, and chronic), respectively. Two reviewers independently screened articles at the title, abstract, and full-text levels based on inclusion and exclusion criteria using four databases and the Rayyan software. Furthermore, we identified the study design, sample size, duration since stroke onset, and assessment tools were identified.ResultsOut of 1,423 articles, we selected 35. The study designs included observational studies (80%) and RCTs (20%) and a total of 2,987 patients. The age range was 40.0 ± 7.7 to 83.6 ± 9.7 years. Twenty-four assessment tools were identified, mainly including the Trail Making Test Part A, Test of Everyday Attention, and other assessments (40%, 11.4%, and 62.8%, respectively). Regarding the five components of attention, there were 10 assessments were used each for sustained and selective attention (28.6%), and six each for alertness and divided attention (17.1%). Spatial attention was assessed using only one tool (2.9%).ConclusionsWe identified various assessment tools for analyzing attention deficit in patients with stroke and mapped them by component. This scoping review would be useful for selecting assessment methods for patients with stroke with attention deficits. creator: Katsuya Sakai creator: Takayuki Miyauchi creator: Junpei Tanabe uri: https://doi.org/10.7717/peerj.19163 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sakai et al. title: Enhancing drought resilience in durum wheat: effect of root architecture and genotypic performance in semi-arid rainfed regions link: https://peerj.com/articles/19096 last-modified: 2025-03-27 description: BackgroundDeveloping drought-adapted genotypes is a primary goal for achieving resilient agriculture in the Mediterranean region. Durum wheat, a widely grown crop in the drylands of the Mediterranean basin, would significantly benefit from increased drought resistance.MethodsWe investigated a diverse set of 30 durum wheat varieties, including both local landraces and modern cultivars that have proven successful in Algeria. These varieties were evaluated in field trials over two consecutive years with contrasting rainfall patterns (one very dry, the other quite wet). Grain yield (PGY), yield components, and flag leaf characteristics such as area, canopy temperature, or rolling index were evaluated. Data from previous studies of root traits recorded on the same set of genotypes at seedling and adult growth stages were used to search for possible associations with grain yield and other agronomic traits measured in the current work.ResultsGenotypic variation was found for all traits measured under both conditions. Grain yield and aerial biomass were reduced by 76% (from 5.28 to 1.97 Mg ha−1) and 66% (from 15.94 to 3.80 Mg ha−1), respectively in the dry year, whereas the harvest index increased by 32%. The breeding history of the germplasm (cultivar vs. landrace) had a significant effect on the traits studied. Landraces showed higher biomass only under drought (4.27 vs. 3.63 Mg ha−1), whereas modern cultivars out-yielded landraces only under non-drought conditions (5.56 vs. 4.49 Mg ha−1). Promising associations were found between root and agronomic traits, especially with grain yield, indicating that a profuse (large root length) and shallow (wide root angle) root system was related to increased yield of modern cultivars only in the dry year, without penalizing yield in the wet year.ConclusionBreeding programs could improve grain yield under Algerian, semi-arid conditions, by making crosses between selected landraces with good growth potential under drought and modern cultivars, with high efficiency of biomass conversion into grain, and searching for lines with acceptable agronomic performance, which combine these desirable traits from landraces and modern cultivars, with the presence of shallow and profuse root systems. creator: Ridha Boudiar creator: Abdelhamid Mekhlouf creator: Yacine Bekkar creator: Meriem Yessaadi creator: Adel Bachir creator: Larbi Karkour creator: Ana Maria Casas creator: Ernesto Igartua uri: https://doi.org/10.7717/peerj.19096 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Boudiar et al. title: Bacterial community composition is an important predictor of surface soil fertility across different land use types: a case study in the Three Gorges Reservoir area link: https://peerj.com/articles/18959 last-modified: 2025-03-27 description: BackgroundSurface soil is a vital component of terrestrial ecosystems and is of great importance for primary productivity. In Zhangjiachong, a small watershed in Zigui County, central China, human activity and erosion cause extensive surface soil degradation. It is still unclear as to what extent human activity influences soil fertility and soil microorganisms in this area.MethodsSoil samples were collected, during spring and autumn, across a series of land use types with different levels of human activity. We assessed soil fertility and microbial communities using 16S rRNA gene sequencing and Biolog ECO-plates.ResultsThe results showed that higher levels of human activity were associated with lower soil fertility and microbial metabolic activity, in addition to higher bacterial diversity. Moreover, human activity had negative effects on the relative abundances of Proteobacteria and Acidobacteriota, which were the key drivers of surface soil fertility. Conversely, stronger human activity was associated with lower abundance of Actinobacteriota. This study suggested that human activity had a negative influence on surface soil fertility, and bacterial community composition could be a good predictor of surface soil fertility. creator: Lin Xu creator: Dandan Cheng creator: Liang Feng creator: Xuetian Lu creator: Sarah Ruffell creator: Hongmei Wang uri: https://doi.org/10.7717/peerj.18959 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xu et al. title: Distribution, characteristics, and importance of particulate and mineral-associated organic carbon in China forest: a meta-analysis link: https://peerj.com/articles/19189 last-modified: 2025-03-26 description: BackgroundForest soil organic carbon (SOC) plays a critical role in the global carbon cycle, and increasing long-term forest carbon storage is essential for carbon sequestration. However, the distribution and drivers of mineral-associated (MAOC) and particulate organic carbon (POC) in forest soils at a continental scale remain poorly understood.MethodsUsing 540 data points from 59 studies related to POC, MAOC, and total SOC in China’s forests, we analyzed the distribution of POC and MAOC across forest type, soil depth and soil type, and further investigated their influencing factors.ResultsMAOC accounted for more than 63% of total SOC in forest soils. Both POC and MAOC increase with forest age, with mixed forests showing faster growth compared to monoculture forests. The MAOC/SOC ratio decreases with forest age but increases with soil depth, demonstrating the dominance of MAOC in deeper soils. Importantly, MAOC content continuously increases with SOC, and exhibits no upper limit, suggesting the potential for persistent soil carbon accumulation. MAOC is closely associated to microbial biomass carbon, and POC is mainly related with plant litter biomass.ConclusionMAOC and POC are influenced by different environmental factors and display distinct distribution patterns across forest types and soil depths. Thus, differentiating their respective responses to climate change is essential. The carbon sequestration potential of forests in China remains far from saturation. creator: Hao Cheng creator: Yangui Su creator: Zhengyi Huang creator: Sinuo Lin creator: Jingyi Yan creator: Guopeng Wu creator: Gang Huang uri: https://doi.org/10.7717/peerj.19189 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cheng et al. title: Effects of pH, temperature and hydraulic disturbance on nitrogen release from sediments in the Sunxi River, Three Gorges Reservoir Area, China link: https://peerj.com/articles/19161 last-modified: 2025-03-26 description: To clarify the influence of changes in the overlying water environment on internal nitrogen release from reservoir sediments, we collected surface sediments at a depth of approximately 10 cm from the Sunxi River in the tail area of the Three Gorges Reservoir area for simulation experiments. By using orthogonal simulation experiments in the laboratory, we studied the effects of water pH, temperature and hydraulic disturbance on nitrogen release in the sediment and established a quantitative linear relationship between the nitrogen release rate from the sediment and the environmental factors of the overlying water. The results indicated that the average concentrations of total nitrogen (TN) and total phosphorus (TP) in the sediment were 430 mg/kg and 200 mg/kg, respectively. The sediment TN concentration had a very significant positive correlation with the sediment organic matter content (P < 0.001). The sediment TN, NO3-N and NH4-N release intensities gradually increased with increasing incubation time, with maximum release rates of 29.24 mg/((m2⋅d), 23.11 mg/(m2⋅d) and 4.32 mg/((m2⋅d), respectively. Range analysis revealed that the significance of the effects of environmental factors on sediment TN and NH4-N release were ranked as follows: temperature > pH > disturbance, and that of NO3-N release was ranked as pH > temperature > disturbance. Temperature plays the most important role in the behavior of different forms of nitrogen release from sediments. The capacity and potential for nitrogen release from sediments offer crucial insights for assessing the risks posed to the overlying water and highlighting the importance of these factors in water quality management and prediction in the reservoir area. creator: Yihong Ning creator: Bin Gao creator: Haiyan Wang creator: Wenning Hou uri: https://doi.org/10.7717/peerj.19161 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ning et al. title: Intermittent horizontal mattress suture in proximal anastomosis for acute type A aortic dissection: a retrospective study link: https://peerj.com/articles/19159 last-modified: 2025-03-26 description: ObjectiveTo compare intermittent horizontal mattress suture (IHMS) technique and conventional sandwich technique for proximal anastomosis in acute type A aortic dissection (ATAAD) surgery.MethodsPatients who underwent ATAAD repair in our hospital between December 2020 and February 2023 were selected for inclusion in the study. The number of patients treated with the IHMS technique for aortic root repair were matched with those who received the conventional sandwich technique by the same surgeon. Perioperative and postoperative outcomes were analyzed and compared between the two groups.ResultsThis study compared 44 patients in each group. The IHMS group had a shorter operation time than the sandwich group (6.07 h vs. 7.02 h, p = 0.018). The proximal anastomosis time (35.50 min vs. 40.00 min, p = 0.013), and extracorporeal circulation assistance time (70.00 min vs. 92.00 min, p < 0.001) were significantly reduced compared to the sandwich group. IHMS patients sustained less intraoperative blood loss (900 .00 mL vs. 1,500.00 mL, p = 0.005) and blood transfusion need (0 U vs. 0.75 U, p = 0.028) than patients in the sandwich group. Multivariate analysis revealed the IHMS technique to be independently associated with shorter suture time, less blood loss, and higher spontaneous heartbeat recovery. The IHMS group also had shorter durations of mechanical ventilation use, delirium, and hospital stay than the sandwich technique group. No statistically significant differences were found in postoperative morbidities during the follow-up period.ConclusionThe IHMS technique for the aortic root anastomosis is simple, feasible and effective, particularly in ATAAD surgery with intimal rupture near the sinus-tubular junction to preserve the aortic valve during anastomosis of the ascending aorta. creator: Jiajun Li creator: Yongzhi Zhou creator: Yucong Zhang creator: Xuegui Chen creator: Jing Wang creator: Xiang Wei creator: Min Hu uri: https://doi.org/10.7717/peerj.19159 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: A cost-effective predictive tool for AFP-negative focal hepatic lesions of retrospective study: enhancing clinical triage and decision-making link: https://peerj.com/articles/19150 last-modified: 2025-03-26 description: BackgroundIdentifying alpha-fetal protein (AFP)-negative focal hepatic lesions presents a significant challenge, particularly in China. We sought to develop an economically portable tool for the diagnosis of benign and malignant liver lesions with AFP-negative status, and explore its clinical diagnostic efficiency.MethodsA retrospective study was conducted at Peking University Shenzhen Hospital from January 2017 to February 2023, including a total of 348 inpatients with AFP-negative liver space-occupying lesions. The study used a training set of 252 inpatients from January 2017 to September 2021 to establish a diagnostic model for differentiating benign and malignant AFP-negative liver space-occupying lesions. Additionally, a validation cohort of 96 inpatients from October 2021 to February 2023 was used to confirm the diagnostic performance of the model. From January 2017 to February 2023, patients at JingNing People’s Hospital, Gansu Province were assigned to the external cohort (n = 78).ResultsA predictive tool was established by screening age, gender, hepatitis B virus (HBV)/hepatitis C virus (HCV) infected, single lesion, alanine amino transferase (ALT), and lymphocyte-to-monocyte ratio (LMR) using multivariate logistic regression analysis and clinical practice. The area under the curve (AUC) of the model was 0.911 (95% CI [0.873–0.949]) in the training set and 0.882 (95% CI [0.815–0.949]) in the validation cohort. In addition, the model achieved an area under the curve of 0.811 (95% CI [0.687–0.935]) in the external validation cohort.ConclusionOur results demonstrated that the predictive tool has the characteristics of good diagnostic efficiency, economy and convenience, which is helpful for the clinical triage and decision-making of AFP-negative liver space-occupying lesions. creator: Yu Lin creator: Qianyi Wang creator: Minxuan Feng creator: Jize Lao creator: Changmeng Wu creator: Houlong Luo creator: Ling Ji creator: Yong Xia uri: https://doi.org/10.7717/peerj.19150 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lin et al. title: Electroencephalographic power spectrum patterns related to the intelligence of children with learning disorders link: https://peerj.com/articles/19138 last-modified: 2025-03-26 description: Children with learning disorders (LD) perform below average in tests of academic abilities and intelligence. These children also have a significantly abnormal resting-state electroencephalogram (EEG) compared to children with typical development (TD), i.e., an excess of slow brain oscillations such as delta and theta that may be markers of inefficient cognitive processing. We aimed to explore the relationship between the performance in an intelligence test and the resting-state EEG power spectrum of children with LD. Ninety-one children with LD and 45 control children with TD were evaluated with the Wechsler Intelligence Scale for Children 4th Edition (WISC-IV) test of intelligence and a 19-channel EEG during an eyes-closed resting-state condition. The EEG dimensionality was reduced with a principal component analysis that yielded several components representing EEG bands with functional meaning. The first seven EEG components and the intelligence values were analyzed with multiple linear regression and a between-group discriminant analysis. The EEG power spectrum was significantly related to children’s intelligence, predicting 13.1% of the IQ variance. Generalized delta and theta power were inversely related to IQ, whereas frontoparietal gamma activity was directly related. The intelligence test and the resting state EEG had a combined 82.4% success rate to discriminate between children with TD and those with LDs. creator: Benito Javier Martínez-Briones creator: Thalía Fernández creator: Juan Silva-Pereyra uri: https://doi.org/10.7717/peerj.19138 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Martínez-Briones et al. title: EGCG’s anticancer potential unveiled: triggering apoptosis in lung cancer cell lines through in vitro investigation link: https://peerj.com/articles/19135 last-modified: 2025-03-26 description: BackgroundNovel treatment techniques are needed since lung cancer is still a major worldwide health concern. Green tea contains a component called epigallocatechin-3-gallate (EGCG), which has demonstrated potential anticancer properties. This work sought to understand how EGCG affects the phosphatidylinositol-3-kinase protein kinase B (PI3K/Akt) signaling pathway, which in turn causes apoptosis in H1299 lung cancer cells.MethodsIn this experiment, multiple dosages of EGCG were applied to five H1299 cells and five A549 cell lines for a duration of 72 h. Apoptotic pathways, cellular responses, and protein expression levels were investigated in relation to EGCG by morphological, biochemical, and proliferation/migration investigations.ResultsIn H1299 and A549 cells, EGCG raised apoptosis rates and, in a dose-dependent way, hindered cell growth. The levels of phosphorylated Akt (p-Akt) and PI3K (p-PI3K) dramatically reduced following EGCG administration, despite no significant alterations in Akt and PI3K expressions. These results imply that EGCG inhibits the activation of the PI3K/Akt signaling pathway, which in turn causes apoptosis in H1299 and A549 cells.ConclusionThe research provides insights into the effects of EGCG on proliferation and migratory inhibition, as well as highlighting its potential to induce apoptosis in lung cancer cells. These results support EGCG’s promise as a therapeutic agent in the treatment of lung cancer and further our understanding of the processes underlying its anticancer activities. creator: Al Moutassem Billah Khair creator: Alexander Maniangat Luke creator: Rajashree Patnaik creator: Luca Testarelli uri: https://doi.org/10.7717/peerj.19135 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Khair et al. title: Enhancing the classification of isolated theropod teeth using machine learning: a comparative study link: https://peerj.com/articles/19116 last-modified: 2025-03-26 description: Classifying objects, such as taxonomic identification of fossils based on morphometric variables, is a time-consuming process. This task is further complicated by intra-class variability, which makes it ideal for automation via machine learning (ML) techniques. In this study, we compared six different ML techniques based on datasets with morphometric features used to classify isolated theropod teeth at both genus and higher taxonomic levels. Our model also intends to differentiate teeth from different positions on the tooth row (e.g., lateral, mesial). These datasets present different challenges like over-representation of certain classes and missing measurements. Given the class imbalance, we evaluate the effect of different standardization and oversampling techniques on the classification process for different classification models. The obtained results show that some classification models are more sensitive to class imbalance than others. This study presents a novel comparative analysis of multi-class classification methods for theropod teeth, evaluating their performance across varying taxonomic levels and dataset balancing techniques. The aim of this study is to evaluate which ML methods are more suitable for the classification of isolated theropod teeth, providing recommendations on how to deal with imbalanced datasets using different standardization, oversampling, and classification tools. The trained models and applied standardizations are made publicly available, providing a resource for future studies to classify isolated theropod teeth. This open-access methodology will enable more reliable cross-study comparisons of fossil records. creator: Carolina S. Marques creator: Emmanuel Dufourq creator: Soraia Pereira creator: Vanda F. Santos creator: Elisabete Malafaia uri: https://doi.org/10.7717/peerj.19116 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Marques et al. title: Back pain in the midwifery profession in northern Poland link: https://peerj.com/articles/19079 last-modified: 2025-03-26 description: BackgroundNeck pain (NP) and low back pain (LBP) are increasingly significant medical, social, and economic concerns. The midwifery profession, similar to other healthcare occupations, is particularly predisposed to these issues.MethodsThis study aimed to analyze the prevalence of back pain among midwives and evaluate the associated disability levels using the Neck Disability Index (NDI) and the Oswestry Disability Index (ODI). The study group included 208 actively practicing midwives aged 23 to 67 years (mean ± SD: 48.1 ± 10.7 years). Participants completed an anonymous survey comprising a custom-designed questionnaire, the Polish language versions of the NDI and ODI, and the Visual Analog Scale (VAS) for pain intensity.ResultsThe analysis revealed a statistically significant correlation between VAS pain intensity and both age (r = 0.2476) and work experience (r = 0.2758), indicating higher pain scores with increasing age and seniority. No significant association was found between BMI and VAS scores (r = 0.0011). Additionally, NDI and ODI scores correlated significantly with age (r = 0.1731; r = 0.3338), BMI (r = 0.1685; r = 0.2718), and work experience (r = 0.1987; r = 0.4074). Higher values for age, BMI, and seniority were associated with increased disability levels.ConclusionsNeck and low back pain represent prevalent and impactful issues for midwives in Poland, contributing to mild to moderate disability, absenteeism, reliance on pain medication, and limited physical activity. Key contributing factors include age, professional experience, BMI, and low levels of physical activity. creator: Aleksandra Bryndal creator: Sebastian Glowinski creator: Kazimiera Hebel creator: Agnieszka Grochulska uri: https://doi.org/10.7717/peerj.19079 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bryndal et al. title: Association of gender and metabolic factors with thyroid nodules in T2DM: a retrospective study link: https://peerj.com/articles/19068 last-modified: 2025-03-26 description: AimsSex differences in the incidence of thyroid nodules (TNs) are broadly recognized, but further analysis is lacking. Thus, the aim of this study was to evaluate the association between TNs and anthropometric parameters in type 2 diabetic males and females.Materials and MethodsThis cross-sectional study included 747 patients with type 2 diabetes mellitus (T2DM). All patients underwent clinical examination, thyroid ultrasound, laboratory tests, anthropometrics and body composition. Multivariable logistic regression assessed factors associated with TNs, and a simple nomogram was finally developed.ResultsIn total, the incidence of TNs was 36.95% (276/747) and was significantly higher in females (52.75%) than in males (27.85%). Age was positively correlated with TNs risk in patients with T2DM (males: OR = 4.141, 95% CI [1.999–8.577], females: OR = 4.630, 95% CI [1.845–11.618]). Obesity (OR = 2.655, 95% CI [1.257–5.607]) and hyperuricemia (OR = 1.997, 95% CI [1.030–3.873]) were only associated with the risk of TNs independent of other risk factors in type 2 diabetic females, as well as other obesity factors such as weight, BMI, waist-hip ratio, percent body fat, visceral curve area, and upper arm circumference, but not in type 2 diabetic males. However, the diameter of the largest thyroid nodule was only related to age (R = 0.226, p < 0.01). Finally, the nomogram for evaluating TNs in female T2DM patients was established, and the C-index of the nomogram was 0.704 (95% CI [0.89–0.94]).ConclusionTNs occur with a significantly higher frequency in type 2 diabetic females than in males, especially those with hyperuricemia and obesity. Modifiable metabolic factors, such as obesity and hyperuricemia, are a major focus for improving TNs risk in women. creator: Xi Yuan creator: Xin Wang creator: Xinwen Yu creator: Yuxin Jin creator: Aili Yang creator: Xiaorui Jing creator: Shengru Liang creator: Chunni Heng creator: Na Zhang creator: Lijuan Chao creator: Langlang Liu creator: Meiying Wang creator: Yufei Liu creator: Guohong Zhao creator: Bin Gao uri: https://doi.org/10.7717/peerj.19068 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yuan et al. title: Effects of different proportions of organic substitution for mineral fertilizers on soil methanogenic and methanotrophic communities in paddy fields link: https://peerj.com/articles/19000 last-modified: 2025-03-26 description: Mineral fertilizers are widely used to improve rice yields, but their overuse has caused severe environmental problems. Replacing mineral fertilizers with organic alternatives might be an effective practice for enhancing agro-ecosystems. This study investigated treatments with varying proportions of organic substitution to determine the optimal approach for increasing soil fertility and rice yield. In addition, the relationship between soil methane emission characteristics and associated microbial communities was studied by microcosm experiments and high-throughput sequencing to assess greenhouse gas emissions. Compared with mineral fertilizers alone, treatment with organic substitution, especially at high proportions, increased soil pH, fertility, and crop yield. Treatment with a medium proportion of organic substitution increased cumulative methane (CH4) emissions by 44.8% relative to mineral fertilization alone, but that with low and high proportions showed similar emissions compared with mineral fertilization alone. Organic substitution treatment significantly increased the gene copy numbers of soil methanogens and methanotrophs, with the highest increases observed under high proportions of organic substitution. The gene copy number of methanogens increased by 4.87 times, and that of methanophiles increased by 13.11 times. Additionally, organic substitution treatment significantly changed their community compositions. High organic substitution was associated with an exceptionally high abundance of methanotrophs. Treatment with a high proportion of organic substitution enhanced the relative abundance of Type I taxa of methanotrophs and increased soil pH to trigger higher pmoA abundance, thus strengthening methane oxidation capacity without additional cumulative CH4 emissions compared with mineral fertilizers alone. Besides, treatment with a high proportion of organic substitution increased crop yield and reduced the amount of mineral fertilizers needed, resulting in less environmental pollution. This study comprehensively evaluated the effects of organic substitution for mineral fertilizers, providing an essential theoretical basis for the sustainable development of agriculture. creator: Dandan Yuan creator: Keke Dang creator: Jing Yin creator: Han Liu creator: Tingting Ma creator: Jia Liu creator: Xingjia Xiang uri: https://doi.org/10.7717/peerj.19000 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yuan et al. title: Molecular profiling and phenotypic evaluation of thermo-sensitive genic male sterility genes for high-yielding rice hybrids (Oryza sativa L.) link: https://peerj.com/articles/18803 last-modified: 2025-03-26 description: Temperature-sensitive genic male sterility (TGMS) is crucial for boosting rice productivity and ensuring food security. In this study, we evaluated the morphological traits and genetic diversity of 57 rice TGMS lines under fertility-inducing (Gudalur) and sterility-inducing (Coimbatore) environments. Significant variations were observed in yield and floral characteristics, with flowering times ranging from 62.3 to 152.0 days. Lines such as TNAU 16S and TNAU 93S exhibited shorter plant heights and durations, along with higher numbers of productive tillers, making them promising candidates for hybrid breeding. Molecular profiling revealed that the tms8 gene was the most prevalent across the lines, with some carrying combinations of two or more TGMS genes. TNAU 38S and TNAU 60S possessed all four TGMS genes, ensuring stable sterility. These lines showed low fertility temperatures at Gudalur and low sterility temperatures at Coimbatore, indicating optimal conditions for hybrid seed production. Floral characteristics in lines like TNAU 19S, TNAU 126S-1 and TNAU 126S-2 were favorable, with total sterility under sterility-inducing conditions and increased fertility under fertility-inducing conditions, making them ideal for hybridization. For short-duration, semi-dwarf hybrids, TNAU 93S and TNAU 16S were identified as suitable female parents. Overall, this study highlights the significance of TGMS gene combinations for stable male sterility expression and identifies lines such as TNAU 37S, TNAU 60S and TNAU 85S as optimal for high-yielding two-line rice hybrids. The findings emphasize the potential for developing diverse, stable hybrids that can contribute to improved rice productivity and global food security. creator: B. Nagendra Naidu creator: Manonmani Swaminathan creator: Nivedha Rakkimuthu creator: Pushpam Ramamoorthy creator: Kumaresan Dharmalingam creator: Raveendran Muthurajan creator: Selvi Duraisamy creator: Tushar Arun Mohanty creator: Bonipas Antony John uri: https://doi.org/10.7717/peerj.18803 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Naidu et al. title: Psychometric evaluation of the Chinese version of Risky Loot Box Index (RLI) and cross-sectional investigation among gamers of China link: https://peerj.com/articles/19164 last-modified: 2025-03-25 description: Nowadays, many of the top-selling video games include options to purchase loot boxes as paid virtual items. As research progressed, loot boxes have been found to have similar characteristics to gambling, and there has been an ongoing debate as to whether loot boxes can be defined as gambling. In order to better study loot boxes, psychometrically meaningful scales are necessary. The Risky Loot Box Index (RLI) was developed by Brooks and Clark, which is the most commonly used tool to assess the use of loot boxes. This study aimed to translate the original RLI into Chinese and evaluate its psychometric properties. Two samples were recruited through online gaming forums (n = 143) and offline internet cafes (n = 236). An exploratory factor analysis of the online sample yielded a one-dimensional nine-item model, with the factor focused on risky behaviors associated with loot boxes. The confirmatory factor analysis carried out on the offline sample corroborated the results obtained from the exploratory factor analysis, and the Chinese version of the RLI displays satisfactory psychometric properties. Furthermore, the Problem Gambling Severity Index (r = 0.57, P < 0.001) and the Internet Gaming Disorder Scale-Short Form (r = 0.67, P < 0.001) were found to be significantly associated with the RLI. We also found that players with high RLI scores may have higher levels of anxiety and depression, and they were more willing to spend money on loot boxes, with some spending nearly all their earnings. Interestingly, no significant correlations between age, gender, education, or income level, and the RLI were found. creator: Peidong Guo creator: Yueheng Liu creator: Luyin Tan creator: Yifan Xu creator: Haolin Huang creator: Qijian Deng uri: https://doi.org/10.7717/peerj.19164 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo et al. title: Physiological traits underlying sodicity tolerance in Jamun (Syzygium cumini L. Skeels) cultivars link: https://peerj.com/articles/19132 last-modified: 2025-03-25 description: BackgroundThere is a lack of research on how sodicity stress affects tree growth and physiological relations in jamun (Syzygium cumini L. Skeels). An understanding of cultivar-specific morpho-physiological changes under sodic conditions might aid in the development of more sodicity-tolerant cultivars through genetic improvement, and help identify cultivars suitable for degraded sodic soils.MethodsWe assessed the effects of sodicity stress on tree growth, physiological relations, and ion uptake in four cultivars of jamun including CISH J-37 (J-37), CISH J-42 (J-42), Konkan Bahadoli (KB), and Goma Priyanka (GP).ResultsJamun cultivars exhibited varying degrees of reduction in tree growth, leaf area, and gas exchange properties under sodic conditions. Elevated soil pH caused relatively larger declines in trunk cross sectional area (TCSA; >30%) and canopy volume (CV; >25%) in J-42 and KB. Reductions brought on by sodicity stress in leaf area were rather modest (<10%) across cultivars, suggesting that maintaining leaf area may be a key adaptive trait in jamun to cope with sodic conditions. In addition to displaying a notable increase in water use efficiency (WUE), cultivar J-37 also exhibited largely intact levels of relative chlorophyll and photosynthetic rate (Pn) under sodic conditions. Despite a high intrinsic Pn under control treatment, cultivar GP displayed a large drop in Pn (37.16%) when exposed to sodicity stress. Comparatively greater increases in leaf phenolics in KB and GP seemed to be at the expense of growth and photosynthesis under sodic conditions. While superoxide dismutase (SOD) and catalase (CAT) activities showed notable spikes in both J-37 and GP, proline accumulation increased substantially only in cultivar J-37 in response to sodicity stress. Despite significant increases in leaf Na+ and Cl− concentrations, J-37 was found to be comparatively efficient in Na+ and Cl− exclusion from leaves when compared to other cultivars. Surprisingly, sodicity stress did not alter leaf K+, Ca2+ and Mg2+ levels noticeably across cultivars. Correlation analysis suggested that elevated leaf Cl− likely inhibited tree growth more than leaf Na+. Principal component analysis was reasonably efficient in discerning the shared and divergent responses to sodicity stress of the studied cultivars.ConclusionsMembership function analysis revealed a reasonable resilience to sodicity stress only in cultivar J-37. Maintenance of photosynthesis, reduced uptake of Na+ and Cl− ions, increased and synergistic activities of SOD and CAT, and a higher leaf K+/Na+ ratio likely accounted for better performance of J-37 trees in sodic soils. Further investigations are needed to elucidate the molecular underpinnings of sodicity tolerance. creator: Anshuman Singh creator: Ashwani Kumar creator: Jai Prakash creator: Daya Shankar Mishra uri: https://doi.org/10.7717/peerj.19132 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Singh et al. title: A new species and new generic synonymy in the family Vietnamellidae (Insecta: Ephemeroptera) from mid-Cretaceous Burmese amber with notes on ancient dispersal across East Gondwana link: https://peerj.com/articles/19048 last-modified: 2025-03-25 description: The monophyletic mayfly family Vietnamellidae has been introduced for a few extant species from the Indomalayan Realm. All these species belong to the genus Vietnamella and have been described in adult and larval stages. Recently, the fossil genus Burmella was established for male and female imagines of two new species from mid-Cretaceous Burmese amber and assigned to the family Vietnamellidae. In this contribution, we describe another species in the genus Burmella, namely B. inconspicuasp. nov. based on a female imago. It clearly differs from the previously described female of B. clypeata by the absence of an extension of the clypeus and by a different venation in fore and hind wings. Furthermore, we discuss here in detail the systematic position of the monotypic species Burmaheptagenia zhouchangfai originally assigned to the family Heptageniidae and provide arguments for the synonymy of the genus Burmaheptagenia syn. nov. with Burmella. We propose the new combination Burmella zhouchangfaicomb. nov., together with a modified generic diagnosis for the genus Burmella and discuss the adult characters of Vietnamellidae. Systematic placement of the genus Burmella in Vietnamellidae and the phylogenetic position of this family within Ephemerelloidea are discussed. We also consider the geographic origin of the family and the role of the Cretaceous Burma Terrane migration as a key event that facilitated the transfer of Gondwanan fauna to Asia. creator: Roman J. Godunko creator: Nadhira Benhadji creator: Alexander Martynov creator: Zhi-Teng Chen creator: Xuhongyi Zheng creator: Arnold H. Staniczek uri: https://doi.org/10.7717/peerj.19048 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Godunko et al. title: Strain differences between C57Bl/6 and DBA/2 mice (Mus musculus) in delayed matching and nonmatching-to-position tasks: impact of sample responses and delay intervals link: https://peerj.com/articles/19200 last-modified: 2025-03-24 description: BackgroundSpatial working memory is commonly assessed in rodents using delayed matching-to-position (DMTP) and delayed nonmatching-to-position (DNMTP) tasks. Although these tasks are widely used to examine memory function, particularly in relation to delay intervals and response requirements, strain differences in task performance remain underexplored. This study investigates spatial working memory in two widely used mouse strains, C57BL/6 and DBA/2, using these tasks.MethodsMice were trained and tested on the DNMTP task first, followed by the DMTP task. Both tasks were conducted with varying delay intervals and response requirements, allowing for the assessment of spatial working memory across different conditions.ResultsBoth strains acquired the tasks. However, DBA/2 mice exhibited a smaller decline in accuracy with increasing delay intervals in the DNMTP task compared to C57BL/6 mice. DBA/2 mice also demonstrated more stable performance across both tasks, whereas C57BL/6 mice showed a more pronounced accuracy decline in the DNMTP task than in the DMTP task. In addition, enhancing response requirements during sample trials improved performance in DBA/2 mice for both tasks, a trend that was not observed in C57BL/6 mice. These findings suggest that task-specific variables, such as response modality (e.g., lever pressing vs. nose poking) and prior training history, can significantly influence strain performance. Overall, these results emphasize the need for considering strain-specific traits and experimental conditions when interpreting behavioral data, particularly for DBA/2 mice, frequently used as models for hippocampal dysfunction. creator: Kazuhiro Goto uri: https://doi.org/10.7717/peerj.19200 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Goto title: Effect of atrial fibrosis on clot burden score and physicochemical properties of thrombus in patients with ischaemic stroke occurring in non-valvular atrial fibrillation link: https://peerj.com/articles/19173 last-modified: 2025-03-24 description: BackgroundTo investigate the effect of the degree of atrial fibrosis on the clot burden score (CBS) and physicochemical properties in patients with acute ischaemic stroke (AIS) due to non-valvular atrial fibrillation (NVAF).MethodsA total of 117 patients with AIS in NVAF attending the Department of Cardiovascular Medicine and the Cerebrovascular Diagnostic and Treatment Centre between August 2021 and May 2024 were included in the study. Baseline clinical data, biochemical indexes, and imaging data of the patients were collected, and the patients were divided into 93 cases of the CBS (score of 0–6) group and 24 cases of the CBS (score of 7–10) group according to the CBS. CBS (score of 0–6) signifies higher clot burden. The enzyme-linked immunosorbent assay was used to measure the concentration of galactaglutinin-3 (gal-3) and transforming growth factor (TGF-β1) in the serum of the patients, and the PTFV1 were collected by 12-lead electrocardiogram, and the differences in the degree of atrial fibrosis between different groups and the risk factors of CBS (score of 0–6) were analysed. To analyse the effect of atrial fibrosis on the collateral circulation of stroke, the patients were divided into 31 cases with good collateral circulation (grade 3–4) and 86 cases with poor collateral circulation (grade 0–2) according to the digital subtraction angiography (DSA) images. The cerebral thrombus was collected from 60 AIS patients who underwent mechanical thrombectomy. The content of erythrocyte, fibrin/platelets and leukocytes in the thrombus was analysed by Mathew’s scarlet blue staining, and the density of thrombus was measured by computed tomography (CT).ResultsA total of 117 patients were included in this study, and the proportion of hypertensive patients, proportion of chronic atrial fibrillation (CAF), B-type natriuretic peptide (BNP), neutrophil/lymphocyte ratio (NLR), D-dimer, uric acid concentration, proportion of patients with PTFV1 < −0.03 mm s, gal-3, and TGF-β1 were higher in the CBS (score of 0–6) group as compared to the CBS (score of 7–10) group (P-value < 0.05). Hypertension, proportion of CAF, homocysteine, NLR, D-dimer, uric acid, PTFV1 < −0.03 mm s, gal-3, and TGF-β1, were risk factors for the development of high CBS in atrial fibrillation (AF), and hypertension and CAF were the most important factors for the occurrence of AF in the independent risk factors for stroke combined with high clot burden. gal-3 and TGF-β1 were risk factors for poor collateral circulation, atrial fibrosis indexes were not associated with thrombus pathological composition and thrombus density.ConclusionsAtrial fibrosis increases clot burden in patients with AIS due to NVAF but does not significantly correlate with the physicochemical properties and density of the thrombus. creator: Juan Zhao creator: Guangjun Deng creator: Weijing Wang creator: Peng Wang creator: Xinyu Shen creator: Xiaoxiao Yuan creator: Haifei Jiang creator: Zhong-bao Ruan uri: https://doi.org/10.7717/peerj.19173 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Identification and biological characterization of pathogen causing sooty blotch of Ardisia crispa (Thunb.) A.DC. link: https://peerj.com/articles/19130 last-modified: 2025-03-24 description: Sooty blotch, a primary leaf disease affecting Ardisia crispa (Thunb.) A.DC. (A. crispa, AC), significantly impacts both the yield and quality of this medicinal plant. However, the specific species of pathogenic fungi responsible for this disease and their mechanisms of pathogenesis remain unclear. To elucidate the etiology of sooty blotch, it is essential to investigate effective prevention and treatment methods, and provide a theoretical basis for the effective protection of AC. Initially, the alterations in internal organelles that result in sooty blotch were examined using transmission electron microscopy (TEM) and scanning electron microscopy (SEM). Additionally, differential genes were analyzed using differential display reverse transcriptase-PCR (DDRT-PCR) in both healthy and diseased leaves of AC. Moreover, the pathogenic fungi were separated, purified and identified from leaves infected with sooty blotch of AC, and subsequently, their pathogenicity and biological characteristics were tested. Furthermore, the inhibitory effect of pathogens was measured using the water extract of traditional Chinese medicine, based on the growth rate of the mycelium. The findings indicated that the photosynthesis rate of diseased leaves was slower than that of healthy leaves, as revealed by TEM and SEM analyses. Additionally, DDRT-PCR results demonstrated that the differentially expressed genes primarily included those related to zinc finger proteins, acyl-CoA-transferases, and chloroplasts. The phylogenetic tree and pathogenicity test results showed that the pathogens causing sooty blotch of AC were Annulohypoxylon stygium and Diaporthe angelicae. Microscopic observation revealed that Annulohypoxylon stygium and Diaporthe angelicae exhibited distinct microscopic characteristics, and a pH range of 7–10 along with a subdued light environment were more conducive to the growth of pathogens. Additionally, the water extract of Lonicera fulvotomentosa Hsu et S. C. Cheng and A. crispa (Thunb.) A.DC. had a strong antifungal action on the two pathogens of sooty blotch, and the water extract of Ardisia crenate Sims had a better antifungal action on the Diaportheangelicae. In this study, Annulohypoxylon stygium and Diaportheangelicae were reported as pathogenic fungi causing sooty blotch for the first time, and affected the photosynthesis of AC leaf, and these study provides a theoretical basis for the diagnosis and prevention of A. crispa (Thunb.) A.DC. sooty blotch. creator: Demei Yang creator: Jiangli Luo creator: Ying Zhou creator: Sixuan Zhou creator: Xiongwei Liu creator: Chang Liu uri: https://doi.org/10.7717/peerj.19130 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yang et al. title: Polyunsaturated fatty acids and their endocannabinoid-related metabolites activity at human TRPV1 and TRPA1 ion channels expressed in HEK-293 cells link: https://peerj.com/articles/19125 last-modified: 2025-03-24 description: BackgroundPolyunsaturated fatty acids (PUFAs), particularly Omega-3 (ω-3) and Omega-6 (ω-6) PUFAs, may exert neuroprotective effects via the endocannabinoid system (ECS) and are promoted as brain health supplements. However, despite their potential role in endocannabinoid biosynthesis, the impact of PUFAs on ion channels such as TRPV1 and TRPA1, which are modulated by endocannabinoids, remains incompletely understood. Furthermore, the potential in vitro actions of ω-6 and ω-3 PUFA combined in the ratios available in supplements remains uncertain. Therefore, the objective of this study is to evaluate the functional activity of individual PUFAs, their combination in a specific ratio, and their endocannabinoid-related derivatives on TRPV1 and TRPA1 ion channels.MethodologyWe employed a fluorescent calcium-sensitive dye in HEK-293 Flp-In T-REx cells expressing human TRPV1, TRPA1, or an empty vector to measure changes in intracellular calcium concentration ([Ca]i).ResultsCapsaicin and PUFA derivatives such as docosahexaenoyl ethanolamide (DHEA), γ-linolenoyl ethanolamide (γ-LEA) and anandamide (AEA) stimulate TRPV1 activity directly, whereas eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), γ-linolenic acid (γ-LA), and their 9:3:1 ratio triggered TRPV1 response only after prior exposure to phorbol ester. Cinnamaldehyde and PUFA derivatives such as eicosapentaenoyl ethanolamide (EPEA), DHEA, γ-LEA, 2-arachidonoylglycerol (2-AG), 2-arachidonoylglycerol ether (2-AG ether) and AEA triggered TRPA1 response, with EPA, DHA, γ-LA, and the 9:3:1 ratio showing significant effects at higher concentrations.ConclusionsPUFAs alone and their combined form in 9:3:1 ratio stimulate TRPA1 activity, whereas their metabolites trigger both TRPV1 and TRPA1 response. These findings suggest new avenues to explore for research into potential mechanisms underlying the neurological benefits of PUFAs and their metabolites. creator: Atnaf Abate creator: Marina Santiago creator: Alfonso Garcia-Bennett creator: Mark Connor uri: https://doi.org/10.7717/peerj.19125 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Abate et al. title: Differential effects of multiplex and uniplex affiliative relationships on biomarkers of inflammation link: https://peerj.com/articles/19113 last-modified: 2025-03-24 description: Social relationships profoundly impact health in social species. Much of what we know regarding the impact of affiliative social relationships on health in nonhuman primates (NHPs) has focused on the structure of connections or the quality of relationships. These relationships are often quantified by comparing different types of affiliative behaviors (e.g., contact sitting, grooming, proximity) or pooling affiliative behaviors into an overall measure of affiliation. However, it is unclear how the breadth of affiliative behaviors (e.g., how many different types or which ones) a dyad engages in impact health and fitness outcomes. We used a novel social network approach to quantify the breadth of affiliative relationships based on two behaviors: grooming and sitting in contact. Dyadic relationships were filtered into separate networks depending on whether the pair engaged in multiple affiliative behaviors (multiplex networks) or just one (uniplex networks). Typically, in social network analysis, the edges in the network represent the presence of a single behavior (e.g., grooming) regardless of the presence or absence of other behaviors (e.g., contact sitting, proximity). Therefore, to validate this method, we first compared the overall structure of the standard network for each affiliative behavior: all grooming interactions regardless of contact sitting, and all contact sitting interactions regardless of grooming. We then similarly compared the structure of our filtered multiplex vs. uniplex networks. Results indicated that multiplex networks were more modular, reciprocal, and kin-based while connections in uniplex networks were more strongly associated with social status. These differences were not replicated when comparing networks based on a single behavior alone (i.e., all grooming networks vs. all contact sitting networks). Next, we evaluated whether individual network position in multiplex vs. uniplex (novel approach) or grooming vs. contact sitting (traditional approach) networks differentially impact inflammatory biomarkers in a commonly studied non-human primate model system, the rhesus macaque (Macaca mulatta). Being well connected in multiplex networks (networks where individuals both contact sat and groomed) was associated with lower inflammation (IL-6, TNF-alpha). In contrast, being well connected in uniplex grooming networks (dyad engaged only in grooming and not in contact sitting) was associated with greater inflammation. Altogether, these results suggest that multiplex relationships may function as supportive relationships (e.g., those between kin or strong bonds) that promote health. In contrast, the function of uniplex grooming relationships may be more transactional (e.g., based on social tolerance or social status) and may incur physiological costs. This complexity is important to consider for understanding the mechanisms underlying the association of social relationships on human and animal health. creator: Jessica J. Vandeleest creator: Lauren J. Wooddell creator: Amy C. Nathman creator: Brianne Beisner creator: Brenda McCowan uri: https://doi.org/10.7717/peerj.19113 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vandeleest et al. title: Serum ferritin associated with atherogenic lipid profiles in a high-altitude living general population link: https://peerj.com/articles/19104 last-modified: 2025-03-24 description: BackgroundSerum ferritin (SF) levels are associated with metabolic syndrome and dyslipidemia. However, the association between SF and atherogenic lipid profiles in high-altitude living populations remains unclear.MethodsIn 2021, a cross-sectional study was conducted on adult Tajik individuals residing in Tashkurgan Tajik Autonomous County (average altitude 3,100 meters). Demographic information and anthropometric measurements were collected in local clinics. Fasting blood samples were analyzed using a Beckman AU-680 Automatic Biochemical analyzer at the biochemical laboratory of Fuwai Hospital. Univariate linear regression analyses were used to explore the association between SF and atherogenic lipid levels. Subgroup analysis was used based on gender and different high-sensitivity C-reactive protein (hs-CRP) and serum amyloid A (SAA) levels. The association between higher SF quartiles and different kinds of dyslipidemia were analyzed by logistic regression.ResultsThere were 1,703 participants in total, among which 866 (50.9%) being men. The mean ages of male and female participants were similar (41.50 vs. 42.38 years; P = 0.224). SF levels were significantly correlated with total cholesterol (TC) (Beta = 0.225, P < 0.001), low-density lipoprotein cholesterol (LDL-C) (Beta = 0.197, P < 0.001), high-density lipoprotein cholesterol (HDL-C) (Beta = −0.218, P < 0.001), triglycerides (TG) (Beta = 0.332, P < 0.001), and small dense LDL-C (sdLDL-C) (Beta = 0.316, P < 0.001), with the exception of lipoprotein (a) (Lp(a)) (Beta = 0.018, P = 0.475). SF was significantly correlated with LDL-C and HDL-C in women, and correlated with TC, TG, and sdLDL-C levels in both men and women in different inflammatory conditions. Elevated SF levels was significantly correlated with high TC (OR: 1.413, 95% CI [1.010–1.978]), high TG (OR: 1.602, 95% CI [1.299–1.976]), and high sdLDL-C (OR: 1.631, 95% CI [1.370–1.942]) in men and high TC (OR: 1.461, 95% CI [1.061–2.014]), high LDL-C (OR: 2.104, 95% CI [1.481–2.990]), low HDL-C (OR: 1.447, 95% CI [1.195–1.752]), high TG (OR: 2.106, 95% CI [1.454–3.050]), and high sdLDL-C (OR: 2.000, 95% CI [1.589–2.516]) in women. After adjusting for potential confounders, elevated SF levels continue to be correlated with high TG in male (OR: 1.382, 95% CI [1.100–1.737]) and female (OR: 1.677, 95% CI [1.070–2.628]) participants. In both young and middle-aged subgroups, the associations between SF and TG, TC, HDL-C, LDL-C, and sdLDL-C were still significant.ConclusionsSF was closely related to atherogenic lipid profiles, especially with regard to TG in high-altitude populations. This association cannot be attributed to its role as an inflammation marker. creator: Menglong Jin creator: Mawusumu Mamute creator: Hebali Shapaermaimaiti creator: Hongyu Ji creator: Zichen Cao creator: Sifu Luo creator: Mayire Abudula creator: Abuduhalike Aigaixi creator: Zhenyan Fu uri: https://doi.org/10.7717/peerj.19104 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jin et al. title: The spatial and temporal evolution of habitat quality and driving factors in nature reserves: a case study of 33 forest ecosystem reserves in Guizhou Province link: https://peerj.com/articles/19098 last-modified: 2025-03-24 description: BackgroundBiodiversity plays a crucial role for humanity, serving as a foundation for human survival and development. Habitat quality serves as a critical indicator for assessing biodiversity and holds significant importance in both theoretical and practical domains. The unique natural geographical environment of Guizhou Province has fostered rich biodiversity and facilitated the establishment of numerous nature reserves, predominantly centered on forest ecosystems. Analyzing the habitat quality of nature reserves and its influencing factors is of great significance for maintaining the regional ecosystem stability, promoting sustainable development, and improving the ecological environment.MethodTherefore, taking the 33 nature reserves of forest ecosystem in Guizhou Province as the study area, we first quantified habitat quality using the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model to analyze changes in the nature reserve from 2000 to 2020. Then, we explored the effects of natural and social factors on the spatiotemporal evolution of habitat quality using the optimal parameters-based geographical detector (OPGD).ResultsForests were identified as the primary land-use type in the study area. However, the nature reserves saw an increase area in cropland, and impervious land by 5,001.39 ha and 102.15 ha; a significant decrease in forests and grasslands; and a slight decrease in watersheds. Rapid urbanization, therefore, negatively affected the overall habitat quality of the reserve. Although there is a declining trend in the habitat quality of the nature reserve, the magnitude of change from 2010 to 2020 (−0.04) is smaller than that from 2000 to 2010 (−0.17), indicating that the management of the reserve has been somewhat effective. In national-level nature reserves, interactions between natural geographic factors and socio-economic factors were greater than interactions between natural geographic factors. Similarly, in local-level nature reserves, interactions between natural geographic factors and socio-economic factors outweighed interactions among social factors.ConclusionThe spatiotemporal variability of habitat quality in the study area was shaped by the combined effects of natural and social factors. The habitat quality of local-level protected areas is, furthermore, more significantly affected by human activities, which are the primary cause of their degradation. creator: Xuemeng Mei creator: Yi Liu creator: Li Yue creator: Mingming Zhang uri: https://doi.org/10.7717/peerj.19098 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mei et al. title: Physiological responses of wild birds to artificial grass during introduction to laboratory housing link: https://peerj.com/articles/19095 last-modified: 2025-03-24 description: Introduction of wild animals to captivity induces chronic stress often leading to weight loss, increases in baseline corticosterone, and increased DNA damage. To mitigate these effects, providing enrichment to the captive environment has been proposed. Yet, studies investigating the physiological effects of captive environment enrichments are rare in wild birds. Here, we test the potential of a single enrichment factor by monitoring weight, baseline corticosterone, and DNA damage in two groups of house sparrows (Passer domesticus) during introduction to captivity: (1) birds in standard laboratory cages with food dishes and (2) birds in cages where food is spread across artificial grass to simulate a more natural foraging environment. After 3 weeks, all birds switched environments for 3 additional weeks. Weight was monitored bi-weekly while baseline corticosterone and DNA damage were measured weekly. Initially, both groups lost significant weight and weight plateaued by about 2 weeks of captivity. However, after switching housing environments, only initially grass-caged birds continued to lose weight. After one week of captivity, grass-caged birds had lower DNA damage compared to standard-caged birds. Over time, standard-caged birds remained unchanged and initially grass-caged birds increased damage after switching housing environments. There were no significant differences in baseline corticosterone across groups or over time. Our findings provide limited support for artificial grass as a substantial enrichment in mitigating the physiological consequences associated with introduction to captivity. Furthermore, given the challenges to husbandry of using artificial grass, the data are insufficiently strong to recommend the use of artificial grass as a stress-reducing enrichment to laboratory housing. creator: Bradley P. Pedro creator: L. Michael Romero uri: https://doi.org/10.7717/peerj.19095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pedro and Romero title: Isolation and in silico analysis of a new subclass of parasporin 4 from Bacillus thuringiensis coreanensis link: https://peerj.com/articles/19061 last-modified: 2025-03-24 description: BackgroundBacillus thuringiensis (Bt) is a Gram-positive bacterium whose strains have been studied mainly for the control of insect pests, due to the insecticidal capacity of its Cry and Vip proteins. However, recent studies indicate the presence of other proteins with no known insecticidal action. These proteins denominated “parasporins” (PS) have cytotoxic activity and are divided into six classes, namely PS1, PS2, PS3, PS4, PS5, and PS6. Among these, parasporins 4 (PS4) has only one described subclass, present in the Bacillus thuringiensis shandongiensis strain. Given the importance and limited knowledge about the actions of PS4 proteins and the existence of only one described subclass, the present work aimed to characterize the Bacillus thuringiensis coreanensis strain as a potential source of PS4 protein.MethodsA preliminary screening to detect the ps4 gene was conducted in a bank of standard strains and isolates of Bacillus thuringiensis from the Laboratory of Bacterial Genetics and Applied Biotechnology, FCAV/UNESP. The positive strain for this gene had its genomic DNA extracted, the ps4 gene was isolated, cloned and in silico analyses of its sequence were performed. Tools such as Bioedit, BLAST, Clustal Omega, Geneious, IQ-Tree, and iTOL were used in these analyses. For the structural analysis of the PS4 detected, in comparison to the database PS4 (BAD22577), the tools Alphafold2, Pymol, and InterPro were used. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel analyses allowed the visualization of the inactive and active PS4 protein from the positive strain, after solubilization and activation with Proteinase K.ResultsPrevious screening of Bt standard strains revealed the presence of a partial ps4 gene in Bacillus thuringiensis coreanensis strain. The alignment obtained by the BLAST tool revealed 100% identity between the fragment detected in this work with a hypothetical protein (ANN35810.1) from the genome of that same strain. Considering this, the isolation of the complete gene present in this strain was performed by applying the polymer chain reaction (PCR) technique, using the hypothetical sequence as a basis for the primers elaboration. The in silico analysis of the obtained sequence revealed 92.03% similarity with the ps4 sequence presented in the database (AB180980). Protein modeling studies and comparison of their structures revealed that the B. thuringiensis coreanensis has a new subclass of PS4, denominated PS4Ab1, being an important source of parasporin to be explored in biotechnological applications. creator: Thais N. F. Santos creator: Raquel O. Moreira creator: Jardel D. B. Rodrigues creator: Luis A. C. Rojas creator: Jackson A. M. Souza creator: Janete A. Desidério uri: https://doi.org/10.7717/peerj.19061 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Santos et al. title: Mitigative effect of sodium alginate on streptozotocin (STZ)-induced diabetic neuropathy through regulation of redox status and miR-146a in the rat sciatic nerve link: https://peerj.com/articles/19046 last-modified: 2025-03-24 description: Diabetic peripheral neuropathy (DPN) is a significant complication of diabetes with limited effective therapeutic options. Sodium alginate (SA), a natural polysaccharide from brown algae, has demonstrated health benefits, however, whether it can treat streptozotocin (STZ)-induced DPN remains unclear. The present experiment aimed to test the preventive role of SA on STZ-induced DPN in rats and explored the possible mechanisms. The DPN rat model was established in rats by intraperitoneal injection of a single dose of 40 mg/kg b.w. STZ, and SA (200 mg/kg b.w./day) was orally administered for 28 days after type 2 diabetes mellitus (T2DM) induction. The obtained findings revealed that STZ significantly increased serum levels of FBG, HOMA-IR, TC, TG, VLDL-C, and LDL-C, while decreased serum insulin, incretin GLP-1, HDL-C, and lipase activity. In the sciatic nerves, STZ significantly increased proinflammatory cytokine levels (IL-1β, IL-6, and TNF-α), caspase-3 (a pro-apoptotic protein), markers of oxidative stress (MDA and NO), and AGEs. In parallel, STZ induced a significant decline in the activities of enzymatic antioxidants, viz., SOD, CAT, and GPx, and non-enzymatic GSH. These changes were accompanied by a low expression of miR-146a in the sciatic nerves of DPN rats. Except for HOMA-IR, SA treatment to STZ injected rats significantly improved these parameters and helped to rescue the neurological morphology of the sciatic nerve fibers. In conclusion, SA mitigated experimental DPN, and this might be due to its ability to suppress hyperglycemic-hyperlipidemic effects, counteract the overactivation of inflammatory molecules, increase miR-146a expression, modulate oxidative dysregulation, and reduce cell apoptosis. creator: Nema A. Mohamed creator: Naeimah M. Shouran creator: Amina E. Essawy creator: Ashraf M. Abdel-Moneim creator: Sherine Abdel Salam uri: https://doi.org/10.7717/peerj.19046 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mohamed et al. title: Demographics and physical and mental health of clients at a sports center with and without exercise addiction link: https://peerj.com/articles/19002 last-modified: 2025-03-24 description: BackgroundWhile exercise is widely recognized for its health benefits, excessive engagement can lead to exercise addiction (EA), a behavioral condition characterized by compulsive and harmful physical activity. Limited research exists on the demographic, physical, and mental health profiles of individuals with EA. This descriptive cross-sectional study examines demographic factors and related health outcomes among clients at a university sports center with and without EA.MethodsA total of 386 participants were randomly recruited through convenience sampling at the Chulalongkorn University Sports Center in Bangkok, Thailand. EA, physical well-being, and mental well-being were assessed using the Exercise Addiction Inventory (EAI), the Knee and Osteoarthritis Outcome Score (KOOS), and the Questionnaire for Eudaimonic Well-Being (QEWB), respectively. Demographic and exercise-related variables, psychological well-being, and knee outcomes were compared between participants with and without EA using Chi-square tests. Logistic regression analysis was performed to identify predictors of EA.ResultsThe majority of participants were male (55.2%), with a mean age of 27.5 years (SD = 10.9). Among the 386 participants, 322 (83.4%) exhibited partial symptoms, and 35 (9.1%) exhibited full symptoms of EA. Full symptoms of EA were significantly associated with gender, exercise frequency, smoking status, hours spent walking, hours spent in other sports, cognitive focus on metabolism during exercise, and poor knee outcomes (P < 0.05). Logistic regression revealed that being male was the sole significant predictor of EA (OR = 2.65, P = 0.024).ConclusionsEA was prevalent among clients at the sports center and was associated with adverse knee outcomes. Being male was identified as a key predictor of EA. Future research should explore additional factors associated with EA and its effects on physical and mental health. creator: Rasmon Kalayasiri creator: Chayamon Rattanawijarn uri: https://doi.org/10.7717/peerj.19002 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kalayasiri and Rattanawijarn title: Moving beyond the physical impervious surface impact and urban habitat fragmentation of Alaska: quantitative human footprint inference from the first large scale 30 m high-resolution Landscape metrics big data quantification in R and the cloud link: https://peerj.com/articles/18894 last-modified: 2025-03-24 description: With increased globalization, man-made climate change, and urbanization, the landscape–embedded within the Anthropocene-becomes increasingly fragmented. With wilderness habitats transitioning and getting lost, globally relevant regions considered ‘pristine’, such as Alaska, are no exception. Alaska holds 60% of the U.S. National Park system’s area and is of national and international importance, considering the U.S. is one of the wealthiest nations on earth. These characteristics tie into densities and quantities of human features, e.g., roads, houses, mines, wind parks, agriculture, trails, etc., that can be summarized as ‘impervious surfaces.’ Those are physical impacts and actively affecting urban-driven landscape fragmentation. Using the remote sensing data of the National Land Cover Database (NLCD), here we attempt to create the first quantification of this physical human impact on the Alaskan landscape and its fragmentation. We quantified these impacts using the well-established landscape metrics tool ‘Fragstats’, implemented as the R package “landscapemetrics” in the desktop software and through the interface of a Linux Cloud-computing environment. This workflow allows for the first time to overcome the computational limitations of the conventional Fragstats software within a reasonably quick timeframe. Thereby, we are able to analyze a land area as large as approx. 1,517,733 km2 (state of Alaska) while maintaining a high assessment resolution of 30 m. Based on this traditional methodology, we found that Alaska has a reported physical human impact of c. 0.067%. We additionally overlaid other features that were not included in the input data to highlight the overall true human impact (e.g., roads, trails, airports, governance boundaries in game management and park units, mines, etc.). We found that using remote sensing (human impact layers), Alaska’s human impact is considerably underestimated to a meaningless estimate. The state is more seriously fragmented and affected by humans than commonly assumed. Very few areas are truly untouched and display a high patch density with corresponding low mean patch sizes throughout the study area. Instead, the true human impact is likely close to 100% throughout Alaska for several metrics. With these newly created insights, we provide the first state-wide landscape data and inference that are likely of considerable importance for land management entities in the state of Alaska, and for the U.S. National Park systems overall, especially in the changing climate. Likewise, the methodological framework presented here shows an Open Access workflow and can be used as a reference to be reproduced virtually anywhere else on the planet to assess more realistic large-scale landscape metrics. It can also be used to assess human impacts on the landscape for more sustainable landscape stewardship and mitigation in policy. creator: Moriz Steiner creator: Falk Huettmann uri: https://doi.org/10.7717/peerj.18894 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Steiner and Huettmann title: The prognostic model of low-grade glioma based on m6A-associated immune genes and functional study of FBXO4 in the tumor microenvironment link: https://peerj.com/articles/19194 last-modified: 2025-03-21 description: Backgroundm6A plays a dual role in regulating the expression of oncogenes and tumor suppressor genes, and is crucial in tumorigenesis and progression. The immune system is closely involved in tumorigenesis and development, playing a key role in tumor therapy and resistance. However, research on m6A-related immune markers in low-grade gliomas is still limited and requires further investigation.MethodsAll data was obtained from the Chinese Glioma Genome Atlas database and The Cancer Genome Atlas. The construction of the prognostic model and the online application of the dynamic nomogram relied on univariate Cox analysis, LASSO regression, and multivariate Cox analysis. Two different clustering analyses were performed on all samples, resulting in high, medium, and low expression groups of m6A regulatory and immune genes, followed by an analysis of the correlations between these scores. Finally, the biological role of FBXO4 in glioma cells was determined through quantitative reverse transcription polymerase chain reaction, cell proliferation assays, and cell migration experiments.ResultsThe prognostic model for low-grade glioma demonstrated strong performance, with an AUC over 0.9 in the training group. In the internal validation group, AUC values ranged from 0.831 to 0.894, while in the external validation group, the AUC ranged from 0.623 to 0.813. Additionally, the online application of the dynamic nomogram allowed for relatively accurate predictions of LGG patients’ survival time. Further analysis revealed that the high-expression groups of m6A regulatory genes and m6A-related immune genes exhibited higher levels of immune cells and stromal cells, lower tumor purity, and poorer survival rates. GSEA enrichment analysis suggested that these findings might be related to the activation of multiple signaling pathways. This may explain the lower survival rates observed in this group. Furthermore, the m6A score was significantly associated with moderate to high expression of immune genes and high expression of m6A regulatory genes, and it showed a positive correlation with most immune cell types. Finally, in vitro experiments confirmed that silencing FBXO4 significantly inhibited proliferation and migration in glioma cell lines, further supporting the biological relevance of our model.ConclusionBased on multi-dimensional clustering analysis and experimental validation, the prognostic model developed in this study can effectively assess the prognosis of LGG patients and their relationship with the immune microenvironment. Furthermore, the correlation analysis between m6A scores and the tumor microenvironment provides a foundation for further exploration of the disease’s pathophysiology. Additionally, we suggest that FBXO4 may serve as an important biomarker for the diagnosis and prognosis of LGG. creator: Yiling Zhang creator: Na Luo creator: Xiaoyu Li creator: Chuanfei Zeng creator: Xin Chen creator: Xiaohong Peng creator: Yuanyuan Zhang creator: Guangyuan Hu uri: https://doi.org/10.7717/peerj.19194 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Classification of red beet and sugar beet for drought tolerance using morpho-physiological and stomatal traits link: https://peerj.com/articles/19133 last-modified: 2025-03-21 description: Drought is a global phenomenon that endangers agricultural production by creating water scarcity. Selecting drought-tolerant cultivars, varieties, and species is essential for maintaining the food supply and advancing breeding efforts. The study aimed to compare red beet (Beta vulgaris L. var. cruenta) and sugar beet (B. vulgaris L. var. altissima Döll.) for drought tolerance at the early growth stage considering morpho-physiological and stomatal parameters. Three red beet cultivars (Bicores, BT Pancina, and Yakut) and three sugar beet cultivars (Mohican, Orthega KWS, and Valentina) were subjected to various drought stress (Control, 10%, and 20% PEG-6000) for 30 days at the four-leaf stage. Fresh and dry plant weight, leaf area, dry matter, chlorophyll content (SPAD), leaf temperature, relative water content, membrane stability index, stomatal density, and size were investigated. The results revealed that the cultivars exhibited different responses to drought stress, and a greater percentage reduction in morphological parameters was observed in red beet cultivars. Drought markedly reduced the fresh and dry weights, leaf area, relative water content, membrane stability, and stomatal size. Enhanced dry matter and stomatal density were identified. The stomatal density increased from 158 to 215 mm−2 while the stomatal size decreased from 433 to 342 µm2 in the plants subjected to 20% PEG. Moderate drought stress effectively distinguished drought-tolerant sugar beet and red beet genotypes. It was concluded that sugar beet appeared to be more drought-tolerant than red beet and that the membrane stability index, relative water content, and stomatal density could be effectively used for selecting drought-tolerant beet genotypes. creator: Gamze Kaya creator: Nurgül Ergin uri: https://doi.org/10.7717/peerj.19133 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kaya and Ergin title: Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta link: https://peerj.com/articles/19081 last-modified: 2025-03-21 description: BackgroundHaemophilus influenzae is a Gram-negative bacterium that can exist as a commensal organism or cause a range of diseases, from ear infections to invasive conditions like meningitis. While encapsulated H. influenzae strains have historically been linked to severe diseases, non-typeable Haemophilus influenzae (NTHi) strains, lacking an intact capsule locus, have emerged as the leading cause of invasive H. influenzae infections, particularly following the widespread use of the H. influenzae serotype b (Hib) vaccine.MethodsIn response to a significant increase in invasive NTHi infections among persons living with HIV in metropolitan Atlanta during 2017–2018, we conducted a comparative genomic analysis of two predominant NTHi clones, C1 and C2, identified during this period. These clones correspond to multilocus sequence types ST164 and ST1714, respectively. We analyzed the genomic characteristics of C1 and C2 using whole genome sequencing data and compared them to a broader pangenome of H. influenzae strains to identify potential virulence factors and genetic adaptations.ResultsBoth C1 and C2 isolates were highly related within their clusters, with C1 showing a maximum of 132 SNPs and C2 showing 149 SNPs within their respective core genomes. Genomic analysis revealed significant deletions in known virulence genes, surprisingly suggesting possible attenuation of virulence. No unique accessory genes were identified that distinguished C1 and C2 from other H. influenzae strains, although both clusters exhibited a consistent loss of the pxpB gene (encoding 5-oxoprolinase subunit), replaced by a mobile cassette containing genes potentially involved in sugar metabolism. All C1 and C2 isolates showed potential enrichment in accessory genes associated with systemic infections.ConclusionsOur study suggests that while C1 and C2 clones possess some genetic markers potentially linked to systemic infections, there are no definitive unique genetic factors that distinguish these clones as more virulent than other H. influenzae strains. The expansion of these clones in a vulnerable population may reflect both chance introduction and potential adaptations to the host environment. Further research is needed to understand the implications of these genetic findings on the clinical management and prevention of invasive NTHi infections. creator: Brianna J. Bixler creator: Charlotte J. Royer creator: Robert A. Petit III creator: Abraham G. Moller creator: Samantha Sefton creator: Stepy Thomas creator: Amy Tunali creator: Lauren F. Collins creator: Monica M. Farley creator: Sarah W. Satola creator: Timothy D. Read uri: https://doi.org/10.7717/peerj.19081 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bixler et al. title: Construction of an immunoinformatics-based multi-epitope vaccine candidate targeting Kyasanur forest disease virus link: https://peerj.com/articles/18982 last-modified: 2025-03-21 description: Kyasanur forest disease (KFD) is one of the neglected tick-borne viral zoonoses. KFD virus (KFDV) was initially considered endemic to the Western Ghats region of Karnataka state in India. Over the years, there have been reports of its spread to newer areas within and outside Karnataka. The absence of an effective treatment for KFD mandates the need for further research and development of novel vaccines. The present study was designed to develop a multi-epitope vaccine candidate against KFDV using immunoinformatics approaches. A total of 74 complete KFDV genome sequences were analysed for genetic recombination followed by phylogeny. Computational prediction of B- and T-cell epitopes belonging to envelope protein was performed and epitopes were prioritised based on IFN-Gamma, IL-4, IL-10 stimulation and checked for allergenicity and toxicity. The eight short-listed epitopes (three MHC-Class 1, three MHC-Class 2 and two B-cell) were then combined using various linkers to construct the vaccine candidate. Molecular docking followed by molecular simulations revealed stable interactions of the vaccine candidate with immune receptor complex namely Toll-like receptors (TLR2-TLR6). Codon optimization followed by in-silico cloning of the designed multi-epitope vaccine construct into the pET30b (+) expression vector was carried out. Immunoinformatics analysis of the multi-epitope vaccine candidate in the current study has potential to significantly accelerate the initial stages of vaccine development. Experimental validation of the potential multi-epitope vaccine candidate remains crucial to confirm effectiveness and safety in real-world conditions. creator: Sunitha Manjari Kasibhatla creator: Lekshmi Rajan creator: Anita Shete creator: Vinod Jani creator: Savita Yadav creator: Yash Joshi creator: Rima Sahay creator: Deepak Y. Patil creator: Sreelekshmy Mohandas creator: Triparna Majumdar creator: Uddhavesh Sonavane creator: Rajendra Joshi creator: Pragya Yadav uri: https://doi.org/10.7717/peerj.18982 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kasibhatla et al. title: Quantitative MRI reveals infrapatellar fat pad changes after running a marathon link: https://peerj.com/articles/19123 last-modified: 2025-03-20 description: BackgroundMarathon running, while offering health benefits, is associated with a high incidence of knee injuries. The infrapatellar fat pad (IFP) plays a critical role in knee joint homeostasis and injury mitigation. This study investigated IFP adaptations to the acute stress of marathon running using quantitative magnetic resonance imaging (MRI).MethodsFourteen amateur marathon runners (12 male, two female) were prospectively enrolled and underwent 3.0T MRI (GE SIGNA Architect) one week before and after the marathon. Left knee imaging included MAGiC and IDEAL-IQ sequences. MAGiC sequences provide T1, T2, and proton density (PD) maps. IDEAL-IQ sequences yield fat fraction (FF), representing the relative amount of fat within the IFP, and the transverse relaxation rate (R2*) within the IFP. IFP volume and maximum cross-sectional area were quantified. Two experienced radiologists independently analyzed the images using dedicated software. Inter-observer reliability for quantitative MRI measurements was assessed using intraclass correlation coefficients (ICCs). Paired t-tests were used to compare pre- and post-marathon measurements of T1, T2, FF, R2* values, IFP volume and maximum cross-sectional area. Pearson correlation analysis explored relationships between changes in IFP parameter changes and participant characteristics. P < 0.05 was considered statistically significant for all analyses.ResultsPost-marathon, IFP FF significantly increased (p < 0.05), while IFP volume significantly decreased (p < 0.05), T1 and T2 values showed a decreasing trend. IFP appeared morphologically compressed post-marathon. A significant negative correlation was found between FF change and both body weight and body mass index (BMI) (p < 0.05).ConclusionsThis study provides novel evidence of robust IFP adaptation to marathon running, characterized by increased FF and potential fluid shifts, suggesting enhanced cushioning and load dissipation. These findings highlight the importance of considering individual biomechanics in understanding IFP function and injury susceptibility. Future research should clarify the clinical implications of these adaptations for runner injury prevention and rehabilitation. creator: Xiang Bo Zhao creator: Haifeng Zhao creator: Wen Juan Du creator: Hao Zhang uri: https://doi.org/10.7717/peerj.19123 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhao et al. title: Fatty acid profiles of highly migratory resources from the Southeastern Pacific Ocean, Chile: a potential tool for biochemical and nutritional traceability link: https://peerj.com/articles/19101 last-modified: 2025-03-20 description: The traceability of fish species and their resulting food products is essential to maintain the global supply of these goods, allowing us to distinguish and reconstruct the origin and history of their production chain. One way to trace food is through biochemical determinations, which aid in identifying their geographical origin quickly. This study analyzed the fatty acid (FA) profiles of highly migratory fishery resource species (HMRS) from the Southeastern Pacific Ocean (SEPO), and their use as potential tools to determine the geographic origin and nutritional condition of these marine resources. The fatty acids (FAs) presented in fillet or muscle tissue of 18 HMRS were measured as FA methyl esters by gas chromatography. Our results reveal that the swordfish Xiphias gladius presented the greatest variety of FAs, strongly characterized by the presence of saturated, monounsaturated, and polyunsaturated FAs. A similar trend of high diversity in all classes of FAs was observed in tuna species (i.e., Thunnus alalunga; T. albacares; T. obesus), oilfish (Ruvettus pretiosus) and escolar fish (Lepidocybium flavobrunneum). In turn, Lampris guttatus, Makaira indica, and Tetrapturus audax presented an intermediate variety of FAs and the highest amount of saturated and monounsaturated FAs of the evaluated species. Finally, Luvarus imperialis, Coryphaena hippurus and the sharks (Lamna nasus; Alopias vulpinus; Prionace glauca; Isurus oxyrinchus; Sphyrna zygaena) presented a low diversity of FAs, with only saturated FAs strongly predominating. Regarding the total concentration of FAs, the highest average values were recorded in X. gladius, L. flavobrunneum and R. pretiosus. The present study revealed notable differences in the FA compositions of the muscle of diverse HMRS from the SEPO off the coast of Chile, with the swordfish showing the healthiest FAs (i.e., mono and polyunsaturated) for human consumption. The data on FAs collected for HMRS could be used as a reference to characterize the FA profiles of other fisheries in the SEPO (e.g., coastal pelagic fishes). In an ecosystem approach, our findings help us to understand how essential nutrients (i.e., FA biomolecules) are transferred through the marine food web in the SEPO, revealing the diet type and/or feeding habits of HMRS considered as top predators. Furthermore, identifying the FA profiles of fishery resources at a spatial level provides crucial information for their management and conservation, particularly in those resources that are overexploited and also have a critical nutritional importance for human consumption. creator: Fabián Guzmán-Rivas creator: Marco Quispe-Machaca creator: Jorge Lazo creator: Juan Carlos Ortega creator: Sergio Mora creator: Patricio Barría Martínez creator: Ángel Urzúa uri: https://doi.org/10.7717/peerj.19101 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Guzmán-Rivas et al. title: NCBP2 predicts the prognosis and the immunotherapy response of cancers: a pan-cancer analysis link: https://peerj.com/articles/19050 last-modified: 2025-03-20 description: BackgroundThe cap-binding complex (CBC) plays a crucial role in facilitating gene expression by safeguarding mRNA from nonsense-mediated decay, promoting mRNA splicing, 3′-end processing, and facilitating nuclear export. Nevertheless, the precise biological functions and clinical implications of CBC in cancer remain ambiguous, necessitating further investigation for clarification.MethodsThe present study utilized the cBioPortal database to investigate the genetic alterations of nuclear cap binding protein subunit 2 (NCBP2) in pan-cancer. The Cancer Genome Atlas (TCGA) and online web tools were employed to analyze the correlation between NCBP2 and prognosis, genome instability, immune infiltration, immune response, cancer stemness, and chemotherapeutic efficacy in pan-cancer. Furthermore, the expression of NCBP2 was confirmed by immunohistochemistry (IHC) and functional analysis at the single-cell level was conducted using the CancerSEA database.ResultsNCBP2 exhibited distinct genetic alterations in pan-cancer with an increased expression in 24/32, while decreased expression in 3/32, types of cancers. IHC confirmed the aberrant expression of NCBP2 in lung squamous cell carcinoma (LUSC), pancreatic adenocarcinoma (PAAD), kidney renal papillary cell carcinoma (KIRP) and kidney renal clear cell carcinoma (KIRC). NCBP2 was correlated with overall survival (OS), disease-specific survival (DSS), and progression-free survival (PFS) in various cancers. Importantly, it was identified as a risk factor for OS, DSS and PFS in PAAD and uterine corpus endometrial carcinoma (UCEC). Gene Set Enrichment Analysis (GSEA) demonstrated that elevated NCBP2 was linked to immune and proliferation related pathways across multiple cancer types. Furthermore, a negative association between NCBP2 and stromal score, immune score, and ESTIMATE score was detected, and a positive correlation was observed between NCBP2 and diverse immune cells as well as stemness-indexes in the majority of cancer types. Drug sensitivity analysis revealed that drugs associated with NCBP2 primarily targeted DNA replication, chromatin histone methylation, ABL signaling, cell cycle, and PI3K signaling. Additionally, an examination at the single-cell level indicated that NCBP2 was positively correlated with cell cycle progression, DNA damage, DNA repair, invasion, and stemness in most cancer types, while negatively correlated with apoptosis, inflammation, and hypoxia in certain cancers.ConclusionIn this study, we revealed the correlation of NCBP2 with prognosis, microenvironment and stemness, indicating that NCBP2 might be a potential therapeutic target for more effective and personalized therapy strategies in pan-cancer. creator: Shichao Li creator: Yulan Wang creator: Xi Yang creator: Miao Li creator: Guoxiang Li creator: Qiangqiang Song creator: Junyu Liu uri: https://doi.org/10.7717/peerj.19050 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Applications and prospects of phosphoproteomics in renal disease research link: https://peerj.com/articles/18950 last-modified: 2025-03-20 description: IntroductionPhosphoproteomics, an advanced branch of molecular biology, utilizes specific techniques such as mass spectrometry, affinity chromatography, and bioinformatics analysis to explore protein phosphorylation, shedding light on the cellular mechanisms that drive various biological processes. This field has become instrumental in advancing our understanding of renal diseases, from identifying underlying mechanisms to pinpointing new therapeutic targets.Areas coveredThis review will discuss the evolution of phosphoproteomics from its early experimental observations to its current application in renal disease research using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We will explore its role in the identification of disease biomarkers, the elucidation of pathogenic mechanisms, and the development of novel therapeutic strategies. Additionally, the potential of phosphoproteomics in enhancing drug discovery and improving treatment outcomes for renal diseases will be highlighted.Expert opinionPhosphoproteomics is rapidly transforming renal disease research by offering unprecedented insights into cellular processes. Utilizing techniques such as LC-MS/MS, it enables the identification of novel biomarkers and therapeutic targets, enhancing our understanding of drug mechanisms. This field promises significant advancements in the diagnosis and treatment of renal diseases, shifting towards more personalized and effective therapeutic strategies. As the technology evolves, its integration into clinical practice is pivotal for revolutionizing renal healthcare. creator: XueJia Zheng creator: LingLing Zhou creator: TianTian Xu creator: GuoYing Wang creator: YaLi Peng creator: ChunMei Wen creator: MengYao Wu creator: HuiHui Tao creator: Yong Dai uri: https://doi.org/10.7717/peerj.18950 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zheng et al. title: Phylogeny of Cassieae based on seed morphological and ITS evidence link: https://peerj.com/articles/18947 last-modified: 2025-03-20 description: The Cassieae tribe, comprising economically significant species, is understudied in terms of phylogenetics within China. This study aimed to elucidate the taxonomic status and systematic relationships among Cassieae species by integrating seed coat micro-morphological characteristics with molecular data from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. (1) The results indicate that the tribe is classified into seven distinct clades; Clade V consists of Chamaecrista, which is characterized by primarily monosymmetric flowers with occasional asymmetry, the presence of extrafloral nectaries (EFNs), five or ten stamens, and pods that dehisce elastically. Clade VI is associated with Senna, which displays polysymmetric or monosymmetric flowers, uniformly ten stamens or occasionally three staminodes, variable presence of EFNs, and predominantly indehiscent pods, with rare instances of slit dehiscence. Clade VII is characterized by the presence of Cassia, which exhibits polysymmetric flowers, consistently ten stamens—three of which are elongated and curved, typically exceeding the length of the petals—and indehiscent pods. (2) The monophyly of Cassia and Senna was strongly supported, with Cassia grouping closely with Senna, but distantly from Chamaecrista. (3) It is noteworthy that Senna occidentail and Senna sophera are confirmed as sister taxa, while Senna corymbosa and S. bicapsularis are confirmed as sister taxa. By integrating molecular biology and morphological taxonomy, this research enhances our comprehension of the phylogenetic relationships and evolutionary history within the Cassieae tribe in China. creator: Jing Cai creator: Chuang Yang creator: Leyang Wang creator: Jiaqing He creator: Qiang Wang uri: https://doi.org/10.7717/peerj.18947 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cai et al. title: Female philopatry may influence antipredatory behavior in a solitary mammal link: https://peerj.com/articles/18933 last-modified: 2025-03-20 description: Whether neighboring individuals are related or not has a number of important ecological & evolutionary ramifications. Kin selection resulting from philopatry can play an important role in social and antipredatory behavior. Ground squirrels exhibit alarm vocalizations in the presence of predators; however, the degree to which kin selection shapes alarm calling behavior varies with species ecology and the degree of relatedness between neighbors. We studied a solitary ground squirrel species that exhibits sex-biased calling propensity to determine if female philopatry may be responsible for sex differences in antipredatory behavior observed in our population. We used double digest restriction-site associated DNA sequencing (ddRADseq) to sample the genomes of Harris’s antelope squirrel (Ammospermophilus harrisii) to determine the relatedness between individuals and test whether genetic and geographic distance were correlated. We found that geographic distance had a positive relationship with genetic distance, and that this relationship was sex-dependent, suggesting male-biased dispersal. Our results provide supporting evidence that female philopatry may be responsible for higher calling propensity observed in female squirrels, potentially influencing antipredatory behavior in this species via kin selection. Our findings add to a growing body of evidence that philopatry is an important ecological driver influencing sociospatial organization in solitary species. creator: Alexandra Burnett creator: Michelle Hein creator: Natalie Payne creator: Karla L. Vargas creator: Melanie Culver creator: John L. Koprowski uri: https://doi.org/10.7717/peerj.18933 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Burnett et al. title: Assessment of YouTube videos on post-dural puncture headache: a cross-sectional study link: https://peerj.com/articles/19151 last-modified: 2025-03-19 description: BackgroundPost-dural puncture headache (PDPH) is a common complication of central neuroaxis anesthesia or analgesia, causing severe headaches. YouTube is widely used for health information, but the reliability and quality of PDPH-related content are unclear. This study evaluates the content adequacy, reliability, and quality of YouTube videos on PDPH.MethodsThis cross-sectional study analyzed English-language YouTube videos on PDPH with good audiovisual quality. Two independent reviewers assessed the videos using the DISCERN instrument, Journal of American Medical Association (JAMA) benchmark criteria, and Global Quality Scale (GQS). Correlations between video characteristics and their reliability, content adequacy, and quality scores were examined.ResultsOut of 71 videos, 42.3% were uploaded by health-related websites, 36.6% by physicians, and 21.1% by patients. Strong correlations were found between DISCERN, JAMA, and GQS scores (p < 0.001). Videos from physicians and health-related websites had significantly higher scores than those from patients (p < 0.001). No significant correlations were observed between descriptive characteristics and scores (p > 0.05).ConclusionYouTube videos on PDPH uploaded by health-related websites or physicians are more reliable, adequate, and higher in quality than those uploaded by patients. Source credibility is crucial for evaluating medical information on YouTube. creator: Seher İlhan creator: Turan Evran uri: https://doi.org/10.7717/peerj.19151 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 İlhan and Evran title: Epidemiology of kerosene poisoning in Saudi Arabia: a retrospective analysis link: https://peerj.com/articles/19094 last-modified: 2025-03-19 description: BackgroundLimited national studies exist on the epidemiology of kerosene poisoning in Saudi Arabia. This study aimed to determine the frequency, demographic distribution, geographic patterns, and seasonal variations of kerosene poisoning incidents in Saudi Arabia from January 2019 to December 2021.MethodsThis retrospective cross-sectional study utilized data on all reported kerosene poisoning cases from the National Poisoning Surveillance System. Cross-tabulation with chi-square tests assessed the relationships between poisoning cases and key variables such as gender, age group, and region.ResultsA total of 460 kerosene poisoning cases were documented: 32.2% in 2019, 37.2% in 2020, and 30.6% in 2021. Saudi nationals comprised 97.6% of cases, and the male populace felt more influenced (60.9%) than females (39.1%), although the variation that was found was not proven to be statistically significant (p = 0.912). Out of all age groups, kids between the ages of 1 and 5 were the ones to be primarily affected, accounting for 87.6% of cases (p = 0.029). Most incidents occurred in residential settings (83.7%) and involved oral ingestion (91.7%, p < 0.001). Regionally, the AlQrayat Region reported the highest number of cases (53%), followed by the Northern Borders (18%) and AlJouf (15.7%), with incidents peaking during the colder months. Hospital admissions accounted for 41.3% of cases, while discharges against medical advice (DAMA) increased notably from 8.1% in 2019 to 28.4% in 2021.ConclusionKerosene poisoning in Saudi Arabia predominantly affects young children and occurs in residential settings, with higher concentrations in northern regions during colder months. Public health interventions focusing on parental education, safe kerosene storage practices, and region-specific prevention strategies are essential to reduce the burden of kerosene poisoning and improve outcomes. creator: Bassam M. Hakami creator: Randa Mohammed Nooh creator: Ali Ahmed Asiri uri: https://doi.org/10.7717/peerj.19094 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hakami et al. title: Effects of different grazing intensities on plant species diversity at different spatial scales in a desert steppe in Inner Mongolia link: https://peerj.com/articles/19087 last-modified: 2025-03-19 description: The effect of grazing intensity on plant diversity has been widely studied. In this study, desert steppes with different grazing intensities (no grazing (CK), light grazing (LG), moderate grazing (MG), heavy grazing (HG), and extremely heavy grazing (EG)) in Inner Mongolia were selected to study the changes in species diversity at different spatial scales (α, β, and γ diversity) and the α diversity of different plant groups (dominant species, common species, and rare species).The results showed that the α, β, and γ diversity first decreased and then increased with increasing grazing intensity, and β diversity was observed to be the most sensitive index to the grazing intensity. Grazing had the greatest impact on the α diversity of rare species and the least impact on the α diversity of common species. Therefore, rare species are of great significance for the maintenance and assessment of biodiversity. We concluded that grazing leads to a sensitive response of β diversity, and this sensitive phenomenon is mainly affected by rare species. The results could provide scientific bases for the protection of plant diversity and sustainable grazing in desert steppes. creator: Changlin Xue creator: Shijie Lv creator: Yanling Wu creator: Jie Yun creator: Rui Dong creator: Wentao Wang uri: https://doi.org/10.7717/peerj.19087 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xue et al. title: A comprehensive prognostic and immunological analysis of hexokinase domain containing protein-1 (HKDC1) in pan-cancer link: https://peerj.com/articles/19083 last-modified: 2025-03-19 description: BackgroundCurrently, research on the role of hexokinase domain-containing protein-1 (HKDC1) in neoplasm metabolism remains sparse. This study seeks to conduct a thorough investigation of HKDC1’s potential functions across thirty-three different tumor types, utilizing data obtained from The Cancer Genome Atlas (TCGA).MethodWe conducted a thorough data extraction from the TCGA database, subsequently employing R (version 4.2.2) and its associated software packages for detailed analysis. Our investigation centered on evaluating the differential expression and prognostic significance of HKDC1, while also examining its connections to tumor heterogeneity, mutation profiles, and RNA modifications. Furthermore, we analyzed the relationship between HKDC1 expression and tumor immunity utilizing the TIMER analysis approach.ResultsA comprehensive analysis of various tumor types has revealed that HKDC1 is significantly upregulated in many malignant tumors. Importantly, patients with elevated HKDC1 levels in their tumor tissues often experience poorer prognoses. The association between HKDC1 expression, immune cell infiltration, and the existence of immune checkpoints suggests a possible connection between the tumor microenvironment and HKDC1, alongside tumor advancement. Gene set enrichment analysis (GSEA) further substantiates the idea that HKDC1 may play a role in several critical pathways and biological processes associated with neoplasm. Additionally, the overexpression of HKDC1 is influenced by promoter methylation and alterations in DNA copy number amplification. Furthermore, in vitro experiments demonstrated that silencing HKDC1 resulted in a marked reduction in the proliferation, migration, and invasion capabilities of neoplasm cells.ConclusionOur initial pan-cancer analysis provided a comprehensive understanding of the oncogenic roles of HKDC1 across diverse cancer types. Moreover, HKDC1 has the potential to serve as a significant prognostic biomarker. creator: Zhi Liang creator: Tianhao Zhang creator: Jiajia Huang creator: Zhixin Huang creator: Zeyu Zhao creator: Shirong Cai creator: Jinping Ma uri: https://doi.org/10.7717/peerj.19083 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liang et al. title: TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis link: https://peerj.com/articles/19072 last-modified: 2025-03-19 description: BackgroundCervical cancer (CC) is a prevalent female malignancy strongly influenced by the tumor microenvironment (TME). This study focuses on the role of TGF-β signaling in cancer-associated fibroblasts (CAFs) and its interaction with immune cells, aiming to elucidate its impact on CC progression.MethodsThe TME of CC patients was analyzed using scRNA-seq data and we identified the major cell types in the TME with a focus on the activation of the TGF-β signaling pathway in fibroblasts. Gene modules related to the TGF-β signaling pathway were identified by Weighted correlation network analysis (WGCNA). Using The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA-CESC) dataset, a prognostic gene model was constructed by univariate Cox, LASSO Cox and multivariate Cox regression analyses. For cellular validation, the mRNA level of prognostic model-related genes was tested via quantitative real-time real-time polymerase chain reaction (PCR). Thereafter, the following assays, including cell counting kit-8, scratch and wound healing assays, were applied to assess the viability, migration and invasion of CC cells.ResultsAnalysis at single-cell resolution identified nine major cell types in the TME, and significant activation of the TGF-β signaling pathway in fibroblasts was correlated with tumor proliferation and differentiation. Strong TGF-β signaling communication between fibroblasts and macrophages and NK/T cells suggested a crucial role in the shaping of the immunosuppressive microenvironment. WGCNA analysis identified gene modules significantly associated with the TGF-β signaling pathway. The prognostic model constructed based on three genes, ITGA5, SHF and SNRPN, demonstrated good predictive ability in multiple datasets, validating its potential for clinical application. Meanwhile, the cellular validation assays have revealed the higher expression of ITGA5 and SNRPN and lower expression of SHF in CC cells. Further, ITGA5 knockdown suppressed the viability, migration and invasion of CC cells.ConclusionThis study confirmed the important role of the TGF-β signaling pathway in CC, especially in fibroblasts on tumor microenvironment and tumor progression. The current model could effectively evaluate the prognosis of CC, providing a theoretical foundation for developing CC therapies according to the TGF-β signaling pathway. The present results provide new perspectives for further research on the pathological mechanisms and clinical management of CC. creator: Haina Qu creator: Jing Zhao creator: Xia Zuo creator: Hongyue He creator: Xiaohan Wang creator: Huiyan Li creator: Kun Zhang uri: https://doi.org/10.7717/peerj.19072 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Qu et al. title: Assessing morphological variations in the seagrass genus Halodule (Cymodoceaceae) along the Brazilian coast through genetic analyses link: https://peerj.com/articles/19038 last-modified: 2025-03-19 description: BackgroundSeagrass meadows are distributed globally and provide critical ecological functions and ecosystem services, but seagrasses are still poorly studied compared with other coastal and marine foundation species. Species taxonomy is uncertain in various seagrass genera, such as the genus Halodule. Until recently, the morphological characteristics of leaves were the major criteria for species identification. In Brazil, three species of Halodule are recognized and separated solely using leaf morphology criteria by some authors; however, the leaves present high variability and plasticity, resulting in great uncertainty about species diversity. A review of seagrass species validation using both morphological and phylogenetic methods is needed. This includes examining the genus Halodule with the aim of better understanding its diversity and spatial distribution and consequently supporting management and conservation goals.MethodsPlant samples with the morphological forms of H. beaudettei and H. wrightii were collected at five sites across three Brazilian marine ecoregions. Leaf tip format and leaf width and length were compared among all the sites and between the two populations with different leaf tip forms. Molecular diversity and divergence indices and analyses were used to estimate the genetic distance between H. wrightii and H. beaudettei populations. To determine the phylogenetic relationship between the two morphologies, we sequenced two molecular markers, the internal transcribed spacer (ITS) fragment and the rbcL gene, to construct phylogenetic trees using Bayesian inference.ResultsWe identified H. beaudettei morphology at two sites in Northeast Brazil, while H. wrightii was found in all the ecoregions in the remaining areas, distinguished by the leaf tip shape that occurred at each site. Leaf width and length varied across the five sites, and leaf length differed between H. wrightii and H. beaudettei, with higher values observed in H. beaudettei. Variations in morphological measurements may be related to habitat conditions at each site studied. No divergence was observed for the DNA sequences of two molecular markers, except for a single base in the ITS region, resulting in the Brazilian specimens merging at a single node in the phylogenetic trees. AMOVA and genetic distance analysis revealed low genetic variation but high structuring within populations. The ITS marker showed insufficient genetic variance to delineate the two morphologies as different species which indicating H. wrightii and H. beaudettei are closely related. A genomic approach is needed to fully resolve this issue. This study represents the first step toward the complete determination of the Halodule genus on the Brazilian coast. creator: Virgínia Eduarda de Sousa creator: Maria Cristina F. da Silva Cortinhas creator: Joel C. Creed creator: Maria Gardênia S. Batista creator: Maira C. Proietti creator: Margareth Copertino uri: https://doi.org/10.7717/peerj.19038 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sousa et al. title: Fatty acid biomarkers reveal the interaction between two highly migratory species in the Southern Humboldt System: the swordfish and its prey, the jumbo squid link: https://peerj.com/articles/19129 last-modified: 2025-03-18 description: Marine trophodynamics refer to the transfer of energy from prey to predators. In marine invertebrates and fishes, the nutrients obtained through the consumption of food and/or prey are stored as energy reserves in certain tissues and/or organs including the liver, muscle, or gonads, and that these are subsequently used as bioenergetic fuel for highly energy-demanding fundamental physiological processes. In the southern Humboldt Current System, the interaction between two highly migratory resources and top species has been observed: the swordfish (Xiphias gladius) and its prey the jumbo squid (Dosidicus gigas). Because of this trophic interaction, these species store large amounts of energy (as lipids and fatty acids) in their main organs. However, how the fatty acid profile varies in the various organs of the predator and its prey is still unknown, as is its potential use as trophic biomarkers and the ecophysiological role it plays. Our results showed a moderate similarity between the fatty acid profile of the digestive gland of D. gigas with the profiles of the liver, gonad, and muscle of X. gladius, particularly with fatty acids: palmitic (C16:0), stearic (C18:0), oleic (C18:1n9), gadoleic (C20:1), EPA (C20:5n3), and DHA (C22:6n3). Our findings on the use of fatty acids as biomarkers of the interaction between two highly migratory species in the southern Humboldt System may reveal the degree of preference swordfish have for preying on jumbo squid, particularly through the consumption of the digestive gland. In both species, a high bioenergetic fuel content characterized by a predominance of saturated, monounsaturated, and polyunsaturated fatty acids may be necessary to sustain the high energy costs involved in their migratory and reproductive processes in the Humboldt Current system. creator: Marco Quispe-Machaca creator: Fabián Guzmán-Rivas creator: Patricio Barría Martínez creator: Christian Ibáñez creator: Ángel Urzúa uri: https://doi.org/10.7717/peerj.19129 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Quispe-Machaca et al. title: Advancing the environmental DNA and RNA toolkit for aquatic ecosystem monitoring and management link: https://peerj.com/articles/19119 last-modified: 2025-03-18 description: The application of environmental DNA (eDNA) and RNA (eRNA) technologies to aquatic ecosystem monitoring and management has increased rapidly in the last decade. These methods are providing many new and exciting opportunities for enhanced biodiversity assessment, ecological health evaluation, and species detection. This special issue of PeerJ Life and Environment brings together 20 innovative studies that collectively advance the eDNA toolkit. Four key themes are covered: (i) Methodological advancements, (ii) Ecological health assessments and biomonitoring, (iii) Species detection, and (iv) Application and management. The studies cover a suite of topics including; optimizing sample collection, developing species-specific assays, evaluating bioindicator species, assessing microbial activity, and biodiversity monitoring in diverse freshwater and marine habitats. Emerging applications, such as the use of genome skimming to identify new fish markers, showcase the many new advancements in this field. The studies in this issue also highlight challenges, including the need for standardized protocols and ethical considerations that must be addressed before these tools can be implemented or adopted for decision making at national or global scales. Together, these contributions demonstrate the transformative potential of environmental nucleic acids’ technologies for advancing aquatic conservation and management. By bridging methodological rigor with applied research, the studies in this special issue provide an important resource for researchers, policymakers, and practitioners committed to sustainable aquatic ecosystem stewardship. creator: Xavier Pochon creator: Holly A. Bowers creator: Anastasija Zaiko creator: Susanna A. Wood uri: https://doi.org/10.7717/peerj.19119 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pochon et al. title: Correlation analysis of serum endothelial cell specific molecule-1, endothelial microparticles, hypoxia inducible factor-1α levels and acute myocardial infarction and their predictive value for major adverse cardiovascular events: a retrospective study link: https://peerj.com/articles/19111 last-modified: 2025-03-18 description: ObjectiveThis study aimed to analyse the correlation of endothelial cell specific molecule-1 (ESM-1), endothelial microparticles (EMPs) and hypoxia inducible factor-1α (HIF-1α) serum levels with the occurrence of acute myocardial infarction (AMI) and determine their short-term predictive value for major adverse cardiovascular events (MACE) following AMI treatment.MethodsRetrospective data analysis was performed on the medical records of 106 patients with AMI admitted to our hospital between October 2020 and October 2022. The control group consisted of 106 healthy volunteers that received a physical examination at our hospital’s physical examination centre within the same time frame. ESM-1, EMP and HIF-1α serum levels were compared between the two groups. Independent risk variables for AMI were examined. Furthermore, these individuals were separated into the poor prognosis group (n = 41) and good prognosis group (n = 65) according to the presence or absence of MACE. Finally, the ESM-1, EMPs and HIF-1α serum levels were correlated with the development of MACE in patients with AMI, and the predictive value of serum ESM-1, EMPs and HIF-1α for MACE was evaluated. The serum HIF-1α, EMP and ESM-1 levels were significantly different between the two groups (P < 0.05). Multivariate logistic regression analysis revealed the elevated serum levels of HIF-1α (odds ratio (OR) = 1.819), EMPs (OR = 1.071) and ESM-1 (OR = 14.655) as AMI risk variables. A substantially significant (P < 0.05) correlation was found between the elevated levels of serum HIF-1α (OR = 18.716), EMPs (OR = 26.185) and ESM-1 (OR = 13.992) and the development of MACE in patients with AMI. According to receiver operating characteristic (ROC) curve analysis, the combined evaluation value of HIF-1α, EMPs and ESM-1 serum levels in predicting MACE was high with an area under the curve (AUC) of 0.931.ConclusionPatients with AMI have abnormally high ESM-1, EMP and HIF-1α levels in their serum, all of which have been linked to the development of MACE. Together, these parameters have high sensitivity and specificity for early MACE identification. creator: Qiubing Zhang creator: Zhe Xu creator: Ping Shi creator: Jia Zeng creator: Xiaohong Yin creator: Fang Gou uri: https://doi.org/10.7717/peerj.19111 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Effect of blood-flow restricted vs heavy-load resistance training on strength, power, and speed for healthy volunteers: a systematic review and meta-analysis link: https://peerj.com/articles/19110 last-modified: 2025-03-18 description: BackgroundLow-load blood flow restriction (LL-BFR) training has been shown to enhance muscle strength, power, and speed, but its effectiveness compared to traditional high-load resistance (HLR) training remains unclear. This meta-analysis aimed to compare the effects of LL-BFR and HLR training on muscle strength, power, and speed.MethodologyStudies were identified by searching the SCOPUS, SPORTDiscus, PubMed, Web of Science, and CNKI databases up to May 13, 2024, using the following inclusion criteria: (a) healthy population; (b) comparison of LL-BFR vs HLR training; (c) pre- and post-training assessment of muscle strength (dynamic, isometric, and isokinetic), muscle power, jump, or speed performance; (d) PEDro scale score ≥4. The methodological quality of the included studies was assessed using the PEDro tool and the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach, with meta-analyses conducted using the R program.ResultsA total of 41 studies, involving 853 subjects, were included in the meta-analysis. Based on the PEDro scores and GRADE assessment, the overall quality of the included studies was assessed as moderate. LL-BFR training showed a slightly smaller effect on maximal strength compared to HLR training (ES = −0.19, 95% CI [−0.31 to −0.06], p < 0.01). There were no significant differences between LL-BFR and HLR training for muscle power (ES = −0.04, 95% CI [−0.33 to 0.24], p > 0.05), jump performance (ES = −0.08, 95% CI [−0.30 to 0.15], p > 0.05), and speed (ES = −0.28, 95% CI [−0.71 to 0.15], p > 0.05). Additionally, individual characteristics (i.e., age, gender, and training status) and training parameters (i.e., training duration, frequency, cuff pressure, and cuff width) did not significantly moderate the training effect.ConclusionsLL-BFR training showed slightly less improvement in maximal strength compared to HLR training but demonstrated comparable effects on muscle power, jump performance, and speed in healthy individuals in healthy individuals. These findings suggest that LL-BFR may be a practical and effective alternative for individuals seeking performance improvements with lower training loads. creator: Tao Wang creator: Yutong Liu creator: Xiaolin Wang creator: Saidon Amri creator: Tengku Fadilah Kamalden creator: Zhendong Gao creator: Yee Guan Ng uri: https://doi.org/10.7717/peerj.19110 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Multiplex vs. singleplex assay for the simultaneous identification of the three components of avian malaria vector-borne disease by DNA metabarcoding link: https://peerj.com/articles/19107 last-modified: 2025-03-18 description: Accurate detection and identification of vector-host-parasite systems are key to understanding their evolutionary dynamics and to design effective disease prevention strategies. Traditionally, microscopical and serological techniques were employed to analyse arthropod blood meals for host/parasite detection, but these were limited in taxonomic resolution and only to pre-selected taxa. In recent years, molecular techniques have emerged as a promising alternative, offering enhanced resolution and taxonomic range. While singleplex polymerase chain reaction (PCR) assays were used at first to identify host, vector and parasite components in separate reactions, today multiple primer pairs can be combined in a single reaction, i.e., multiplex, offering substantial time and cost savings. Nonetheless, despite the potential benefits of multiplex PCR, studies quantifying its efficacy compared to singleplex reactions are scarce. In this study, we used partially digested mosquito blood meals within an avian malaria framework to jointly identify the host, vector and parasite using multiplex DNA metabarcoding, and to compare it with separate singleplex PCRs. We aimed to compare the detection probabilities and taxonomic assignments between both approaches. We found both to have similar performances in terms of detection for the host and the vector, but singleplex clearly outperformed multiplex for the parasite component. We suggest adjusting the relative concentrations of the PCR primers used in the multiplex assay could increase the efficiency of multiplex in detecting all the components of the studied multi-species system. Overall, the results show that multiplex DNA metabarcoding can be an effective approach that could be applied to any vector-borne interaction involving blood-feeding arthropods. Our insights from this proof-of-concept study will help improve laboratory procedures for accurate and cost-efficient medical diagnosis of vector-borne diseases, the spread of which is globally exacerbated by current climate change. creator: Eduard Mas-Carrió creator: Judith Schneider creator: Victor Othenin-Girard creator: Romain Pigeault creator: Pierre Taberlet creator: Philippe Christe creator: Olivier Glaizot creator: Luca Fumagalli uri: https://doi.org/10.7717/peerj.19107 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mas-Carrió et al. title: Exploratory analysis of COVID-19 propagation using logistic model link: https://peerj.com/articles/19106 last-modified: 2025-03-18 description: Pandemics pose significant threats to social, economic, and public health. The novel coronavirus (COVID-19), which emerged in late 2019, quickly became a global public health crisis due to its high contagion and pathogenicity. Using data from the World Health Organization (WHO), this study applied the Logistic model to analyze the spread patterns of COVID-19 in 16 countries with over 10 million infections from 2020 to 2023. The findings reveal that as of December 31, 2023, global infections exceeded 772 million with over seven million deaths. The USA and China had the highest infection numbers, while Brazil had the highest mortality rate. The study identified three main outbreak patterns: initial, late, and gradual development, reflecting different stages of the pandemic. Countries with earlier outbreaks, such as India, Brazil, the USA, and Argentina, generally had higher mortality rates, while those with later outbreaks, such as China, Pakistan, Japan, and Australia, had lower mortality rates. Significant differences were observed in the duration and speed of the spread, with China showing the shortest average duration and Russia the longest. The Logistic model’s parameter k values revealed policy adjustments, with Australia, Vietnam, and China showing significant changes over time, while the USA, France, and Russia showed less impact on epidemic control. These results provide an important perspective for understanding global pandemic transmission patterns and assessing the effectiveness of quarantine strategies across countries. They also provide a scientific basis for future public health policy and pandemic response development, helping countries to develop more targeted prevention and control strategies according to the characteristics of virus transmission, rationally allocate medical resources, and reduce social harm. creator: Xing Zhang creator: Chunhe Da creator: Wenjuan Ye uri: https://doi.org/10.7717/peerj.19106 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhang et al. title: Which patients are more likely to experience compensatory hyperhidrosis after endoscopic thoracic sympathectomy: a meta-analysis and systematic review link: https://peerj.com/articles/19097 last-modified: 2025-03-18 description: BackgroundCompensatory hyperhidrosis (CH) is a common consequence of sympathectomy, which can adversely affect patients’ quality of life after surgery. Understanding the factors that influence the occurrence of CH and severe compensatory hyperhidrosis (SCH) is crucial for effective management and counseling of patients undergoing this procedure.Materials and MethodsWe registered the protocol in International Prospective Register of Systematic Reviews (CRD42024592389) and following PRISMA guidelines. We searched PubMed, EMBASE, and Web of Science databases for studies published up to September 11, 2024. A systematic literature search identified a total of 10 studies involving 3,117 patients. The primary outcome was the number of CH or SCH. The secondary outcome was the weighted mean difference calculated based on identified related factors. When pooling results or conducting a meta-analysis was not feasible, the study findings were presented in a narrative descriptive format.ResultsThe overall incidence of CH was found to be 0.62 (95% confidence interval CI [0.51–0.72]), and four studies totaling 1,618 patients regarding the occurrence of severe compensatory hyperhidrosis, the overall incidence of CH was found to be 0.23 (95% CI [0.12–0.34]). Older age, higher body mass index (BMI) and smoking history correlated positively with CH incidence. In addition, higher BMI level is also associated with the occurrence of SCH (1.20 95% CI [1.01–1.39], p < 0.0001).ConclusionThe findings of this meta-analysis highlight important demographic and lifestyle factors that contribute to the development of CH and SCH following sympathectomy. Older patients, smokers, and those with higher BMI may be at greater risk for these conditions. creator: Zhi-yi Lin creator: Min Lin uri: https://doi.org/10.7717/peerj.19097 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lin and Lin title: A combination of hepatic leukemia factor and circulating tumor cells serve as effective biomarkers for lung adenocarcinoma prognosis link: https://peerj.com/articles/19092 last-modified: 2025-03-18 description: BackgroundLung adenocarcinoma (LUAD) is a highly malignant tumor with the highest mortality rate among all cancers. Early diagnosis and prognosis are important factors in treatment. Hepatic leukemia factor (HLF) is thought to be closely associated with lung cancer metastasis. It is downregulated in lung cancer tissues and negatively correlated with the number of metastasis-activating circulating tumor cells (CTCs) in the peripheral blood of patients.Method and ResultsIn this study, we analyzed data from LUAD samples in TCGA and found that HLF was significantly upregulated in samples with EGFR mutations. Immunohistochemical (IHC) staining of 343 clinical samples also revealed a trend of HLF upregulation in patients with EGFR mutations. EGFR is one of the driver genes in non-small cell lung cancer (NSCLC), and the proportion in LUAD is as high as 50% in the East Asian population. In this study, EGFR mutation was not significantly correlated with the prognosis of LUAD patients and the number of CTC was also not related to EGFR mutation, but was closely related to HLF expression, with more CTCs being captured in the peripheral blood of patients with low expression of HLF (SI ≤ 4). By following up these 343 LUAD patients, high HLF expression (SI > 4) was found to be an independent protective factor for progression-free survival regardless of EGFR status (P < 0.001), whereas high CTC count (> 3) was an independent risk factor for recurrence or death in LUAD patients (P < 0.001). When low HLF and high CTCs coexisted, patients had the shortest median survival time. Patients with low HLF or high CTCs appeared alone had a moderate median survival time. Patients had the longest median survival time when HLF was high and CTCs were low.ConclusionIn summary, we believe that HLF expression in cancer tissues and the number of CTCs can be used as effective biomarkers for predicting the prognosis of LUAD, which plays an important role in clinical diagnosis and prognosis judgment. creator: Yaofeng Zhi creator: Jinhua Wu creator: Ronggang Li creator: Xuefei Chang creator: Silin Liu creator: Wenjie Lu creator: Mingzhu Zheng creator: Baoyi Liu creator: Jiarong Chen creator: Xin Zhang creator: Yanming Huang uri: https://doi.org/10.7717/peerj.19092 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhi et al. title: Analysis of the factors influencing the proximity and agreement between critical power and maximal lactate steady state: a systematic review and meta-analyses link: https://peerj.com/articles/19060 last-modified: 2025-03-18 description: Identifying the boundary between heavy and severe exercise domains is crucial since it demarcates the transition from sustainable to unsustainable exercise. This systematic review aimed to determine differences and agreement between two indices used to determine this boundary, namely critical power (CP) and maximal lactate steady state (MLSS), and how moderators may affect these differences. Ten out of 782 studies found were included in the meta analyses. Random effect meta-analyses were performed to evaluate the mean differences (MD) between CP and MLSS, and moderators’ effect on MD was assessed using meta-regression. CP and MLSS agreement was tested using Bland-Altman meta-analyses on the limits of agreements (LoA) of the MD. Power output (PO) at CP was higher (MD (95% LoA) = 12.42 [−19.23; 44.08] W, p = 0.005) than PO at MLSS, with no differences between CP and MLSS in terms of oxygen uptake (MD (95% LoA) = 0.09 [−0.34; 0.52] L⋅min−1, p = 0.097), heart rate (MD (95% LoA) = 0.61 [−15.84; 17.05] bpm, p = 0.784), and blood lactate concentration (MD (95% LoA) = 1.63 [−2.85; 6.11] mM, p = 0.240). Intensities at CP (p = 0.002) and MLSS (p = 0.010) influenced the MD expressed in W. In conclusion, solely when expressed in PO, CP was higher than MLSS, with larger differences in fitter and younger individuals, emphasizing the possible effect of the indicators used for assessing exercise intensity. Finally, the high interindividual variability observed in the differences between CP and MLSS could compromise their interchangeability in predicting the heavy to severe boundary regardless of the parameter used to assess exercise intensity. creator: Lorenzo Micheli creator: Francesco Lucertini creator: Tommaso Grossi creator: Silvia Pogliaghi creator: Daniel A. Keir creator: Carlo Ferri Marini uri: https://doi.org/10.7717/peerj.19060 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Micheli et al. title: Vertical jump performance in recreational runners with visual impairment: a cross-sectional study link: https://peerj.com/articles/19059 last-modified: 2025-03-18 description: BackgroundRunners with visual impairment (VI) may show changes in jump technique due to momentary loss of spatial reference specifically related to the base of support on the ground and rapid postural adjustment. The vertical jump performance and the analysis of the technique can provide information about the neuromuscular characteristics of the runners with VI, motor control and training strategies.ObjectiveThus, the purpose of this study was to analyze the relationship between vertical jump performance and lower limb joint angles in recreational runners with VI.MethodsEight recreational runners (age 33.9 ± 12.7 years and body mass 64.1 ± 13.6 kg) with VI (visual classification: 4 T1, 2 T2 and 2 T3) performed five consecutive squat jumps (SJ) and five consecutive countermovement jumps (CMJ) with 5 min of rest between them. The vertical jumps were recorded by one camera and the jump height and power were evaluated using accelerometer Myotest.ResultsNo difference was found between the SJ (16.8 ± 4.9 cm) and CMJ performances (13.6 ± 5.8 cm) (p = 0.056). Pearson’s correlation test identified a strong and negative correlation between SJ height and internal knee angle (r = −0.712; p = 0.047), while no correlation between CMJ height and internal knee angle was found (r = −0.226; p = 0.591).ConclusionWe concluded that recreational runners with VI reach higher jump heights in a deeper squat position during SJ. creator: Edson Soares da Silva creator: Pedro Henrique De Araújo creator: Veronica Mindrescu creator: Fabio Liedtke creator: Leonardo Alexandre Peyré-Tartaruga creator: Gabriela Fischer uri: https://doi.org/10.7717/peerj.19059 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 da Silva et al. title: Factors affecting molar root and periodontal hard tissue changes after orthodontic anterior molar closure of missing tooth spaces retrospective explored based on cone-beam computed tomography three-dimensional reconstruction link: https://peerj.com/articles/18875 last-modified: 2025-03-18 description: ObjectiveTo correlate the molar teeth and their periodontal conditions after orthodontic anterior removal of the molars to close the gap of missing teeth and to provide risk factor analysis and prognostic assessment for the treatment of such cases.MethodsTwenty-six orthodontic patients (five males and 21 females) with a total of 42 teeth were selected to undergo full-mouth orthodontic treatment due to the absence of the first/second molar and the molar bone volume was recorded by cone-beam computed tomography (CBCT) scanning before (T0) and after (T1) the treatment, and the root volume and the bone volume of the molar teeth were calculated by three-dimensional reconstruction of the CBCT. Afterwards, the correlation analysis was performed between the molar root volume change and bone volume condition and age, gender, density, width, height of the alveolar bone in the edentulous area, edentulous gap and root condition.ResultsThe amount of alveolar bone loss and root resorption in the anteriorly displaced molars after treatment was less than 20%. There was a statistically significant correlation between age and pre-treatment periodontal condition, distal mesial and buccal bone loss; there was a statistically significant correlation between alveolar bone width in the edentulous area and pre-treatment periodontal condition and buccal bone loss; there was a statistically significant correlation between edentulous gap and post-treatment periodontal changes and buccal bone loss; there was a statistically significant correlation between gender and lingual bone loss; and there was a statistically significant correlation between root resorption and pre-treatment There was a statistically significant correlation between the width of the alveolar bone in the edentulous area; there was no statistically significant correlation between the density and height of the alveolar bone in the edentulous area and the periodontal condition.ConclusionClosure of the missing gap by orthodontic proximal-medial movement of the molar is a feasible method, but we need to pay close attention to the width of the alveolar bone and the missing space in the edentulous area. creator: Yuhao Huang creator: Jinglan Zhang creator: Tianwei Lin creator: Hong Ai creator: Ding Bai creator: Zhihui Mai uri: https://doi.org/10.7717/peerj.18875 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Huang et al. title: Use and application of iNaturalist on land snails from Argentina link: https://peerj.com/articles/19152 last-modified: 2025-03-17 description: Gastropods are a large and diverse taxonomic group, and South America has an impressive diversity of land snails. However, there are no accurate and complete lists or estimates of native species’ richness in South America. The aim of this work is to evaluate the use of iNaturalist in Argentina for terrestrial gastropods and its potential to contribute to the knowledge of malacofauna. A search was performed for Argentina on 15 June 2024, filtering observations for terrestrial gastropods, yielding 3,758 records, of which about 10% were of interest for this work. Exotic species represented between 60–63% of the observations in iNaturalist, and native species represented between 37–40%, with post-validation and pre-validation respectively. The geographical distribution of exotic species was mostly concentrated in the urban areas of the capital cities, and the observations of native species were concentrated in a few provinces. It was possible to detect and expand the distribution area of exotic species such as Rumina decollata, Limacus flavus, Bradybaena similaris, Deroceras laeve, Deroceras reticulatum, Deroceras invadens, Arion intermedius, Milax gagates, Limax maximus, Vallonia pulchella, possibly Laevicaulis alte; native species such as Phyllocaulis soleiformis, Drymaeus poecilus, Drymaeus papyraceus. Potential species not recorded in Argentina were identified as Helix pomatia, Mesembrinus gereti. We also recorded species within the known range, potential new species not described by science, a possible case of accidental transfer of Mesembrinus interpunctus, and the prediction of the distribution of Megalobulimus lorentzianus was verified. Through the development of this study, we were able to demonstrate the relevance of citizen science in providing interesting contributions to the knowledge of terrestrial mollusks biodiversity in Argentina. creator: Ana Carolina Díaz creator: Stella M. Martin uri: https://doi.org/10.7717/peerj.19152 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Díaz and Martin title: Quantitative evaluation of muscle mass based on chest high-resolution CT and its prognostic value for tuberculosis: a retrospective study link: https://peerj.com/articles/19147 last-modified: 2025-03-17 description: ObjectiveThis study aims to explore the prognostic value of quantitatively evaluating muscle mass using chest high resolution computed tomography (HRCT) in patients with active tuberculosis (TB).MethodsThis retrospective cohort study collected data from 309 patients with active TB diagnosed at Ningbo No.2 Hospital from 2020 to 2023. Based on the skeletal muscle index (SMI) at the T12 vertebra (with thresholds of <28.8 cm2/m2 for men and <20.8 cm2/m2 for women), patients were divided into a low muscle mass group and a normal muscle mass group. The study compared baseline characteristics, muscle mass-related indicators, body mass index (BMI), and imaging features between the two groups. The correlation between muscle mass-related indicators, BMI, and TB imaging features and prognosis was analyzed. Receiver operating characteristic (ROC) curve analysis and multivariate logistic regression were used to assess the prognostic value of muscle mass-related indicators and BMI in patients undergoing anti-TB treatment.ResultsA total of 309 patients were included in the study, divided into a normal muscle mass group (n = 229) and a low muscle mass group (n = 80). There was a significant difference in prognosis between the two groups (χ2 test, p < 0.05). Patients in the low muscle mass group were older, had a higher proportion of males, and had a lower BMI (p < 0.05). Additionally, these patients had a higher likelihood of developing pulmonary cavities (p < 0.05). In terms of imaging features, the two groups showed significant differences in the pre-treatment proportion of pulmonary fibrotic bands, ground-glass opacities, consolidation, lesion percentage, and lesion absorption ratio (all p < 0.05). Univariate analysis indicated that both the T12 skeletal muscle index (T12 SMI) and BMI were correlated with TB imaging characteristics (p < 0.05), with T12 SMI showing a stronger correlation than BMI. Multivariable linear regression analysis revealed that after adjusting for age, gender, and T12 skeletal muscle radiation attenuation (T12 SMRA), T12 SMI remained significantly correlated with the whole-lung lesion proportion (β: − 4.56, 95% CI [−5.45 to −3.67]) and lesion absorption ratio (β:0.036, 95% CI [0.031–0.041]). Multivariable logistic regression analysis demonstrated that after accounting for age, gender, T12 SMRA, T12 SMI was significantly associated with the prognosis of TB patients (OR: 20.10, 95% CI [8.81–51.56], p < 0.05), indicating that low T12 SMI is an independent risk factor associated with poor prognosis. ROC curve analysis indicated that T12 SMI may offer advantages over BMI, with an area under the ROC curve (AUC) of T12 SMI (0.761, 95% CI [0.690–0.832]) higher than the AUC of BMI (0.700, 95% CI [0.619–0.781].ConclusionQuantitative evaluation of muscle mass using chest HRCT, particularly the T12 SMI, may provide valuable prognostic information for tuberculosis patients, potentially offering advantages over BMI in assessing patient outcomes. creator: Ankang Huang creator: Yuyao Zhang creator: Qi Dai creator: Jingfeng Zhang creator: Jianjun Zheng uri: https://doi.org/10.7717/peerj.19147 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Diversity of lanternfish (Myctophidae) larvae along the Ninety East Ridge, Indian Ocean link: https://peerj.com/articles/19144 last-modified: 2025-03-17 description: Since the 19th century, the impact of seamounts on the distribution of plankton has been a topic of considerable interest. The influence of seamounts on the biogeographic patterns of marine organisms is complex, with some aspects still under debate. It is generally accepted that seamounts can drive the upwelling of nutrient-rich deep waters. Tidal amplification, flow acceleration, and internal waves can further enhance vertical mixing, leading to increased primary productivity near seamounts. Seamounts may also act as barriers to the migration of marine organisms, affecting gene flow. Research on Pacific seamounts suggests these features might serve as “stepping stones” for the dispersal of marine species across the ocean. However, investigations of seamounts in the eastern Indian Ocean remain limited. Focusing on the Ninety East Ridge region in the eastern Indian Ocean, this study collected zooplankton samples using horizontal (surface) and vertical (0–200 m) plankton nets and measured temperature and salinity profiles with a conductivity, temperature, and depth (CTD) sensor. A total of 544 fish larvae were identified, including 260 lanternfish larvae, representing 38 species across 12 genera, determined through COI DNA barcoding. Phylogenetic trees and haplotype networks were constructed to analyze genetic distances and population structures of lanternfish species. Among the samples, intra-specific genetic distances ranged from 0% to 2.99%, while inter-specific distances ranged from 1.88% to 25.71%. Except for Notolychnus valdiviae (Brauer, 1904), the maximum intra-specific distances were lower than the minimum inter-specific distances for all species. Haplotype analysis of nine species revealed significant variations in haplotype number, structure, and spatial distribution. Specifically, Ceratoscopelus warmingii (Lütken, 1892) and N. valdiviae exhibited a notable north-south divergence pattern, consistent with the temperature and salinity distribution of the region’s water masses. This conclusion was supported by analysis of molecular variance analysis, suggesting that larval stages of certain lanternfish species may struggle to cross boundaries between water masses. However, the remaining species showed no significant north-south distribution differences, possibly due to their adaptive capabilities, vertical migration patterns, or the duration of their planktonic larval stages. These findings suggest that seamounts and water mass distribution have varying implications for lanternfish species, potentially influencing gene flow and horizontal distribution patterns, which could contribute to speciation. Global climate change-induced alterations in ocean currents may profoundly impact the genetic diversity of fish species. This study provides new insights into the diversity of lanternfish in the Ninety East Ridge region and offers valuable data for understanding the biogeography of seamounts. creator: Qiong Wu creator: Peng Xiang creator: Chunguang Wang creator: Chunsheng Jing creator: Xinyu Lin creator: Yanguo Wang creator: Guangcheng Chen creator: Mao Lin creator: BingPeng Xing uri: https://doi.org/10.7717/peerj.19144 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: Effect of thermal cycling on the mechanical properties of conventional, milled, and 3D-printed base resin materials: a comparative in vitro study link: https://peerj.com/articles/19141 last-modified: 2025-03-17 description: PurposeThe purpose of this study is to evaluate the impact of thermal cycling on the mechanical properties of conventional, milled, and 3D-printed denture base materials.MethodsUnigraphics NX software was used to design the sample data, after which denture base resin samples were fabricated using conventional polymerization (conventional), milling, and 3D-printing techniques. Flexural strength, Vickers hardness, and impact strength of each group of samples were evaluated both before and after 10,000 thermal cycles in distilled water at 5 °C and 55 °C (n = 8/group). Statistical analysis of the data was conducted using the Kruskal-Wallis H test, Weibull analysis and Spearman correlation analysis.ResultsThe flexural strength and impact strength of the 3D-printed group significantly decreased after thermal cycling (P = 0.001), whereas no significant differences were observed before and after thermal cycling in the conventional or milled groups (P > 0.05). No significant correlation was found between flexural strength and impact strength for any of the groups. The Weibull modulus of 3D printed groups for both flexural and impact strength decreased after thermal cycling. The Vickers hardness of the conventional group increased significantly after thermal cycling, while Vickers hardness significantly decreased in the milled or 3D-printed groups (P < 0.05).ConclusionCompared with the conventional or milled groups, thermal cycling had a more pronounced effect on the flexural strength, Vickers hardness, and impact strength of the 3D-printed group. These findings indicate that further improvements (e.g., material composition, printing parameters and post-processing) in the mechanical properties of 3D-printed materials is necessary before clinical application. creator: Shuang Xiao creator: Ruo-Jin Zhang creator: Fa-Bing Tan uri: https://doi.org/10.7717/peerj.19141 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xiao et al. title: Gastroduodenal artery aneurysm/ pseudoaneurysm: a systematic review of reported cases link: https://peerj.com/articles/19115 last-modified: 2025-03-17 description: BackgroundThis systematic review and meta-analysis investigated the clinical characteristics of patients with gastroduodenal artery aneurysm (GDA), identified risk factors associated with poor clinical outcomes, and elucidated potential differences between various GDA etiologies.MethodsA systematic literature search was conducted from January 2000 to October 2023 in the PubMed, EMBASE, and Google Scholar databases. The analysis focused on extracting data regarding clinical presentations, diagnostic modalities, and patient outcomes.ResultsThis meta-analysis included data from 224 patients derived from 207 case reports spanning 47 countries over a 23-year period. The majority of patients presented with comorbidity (85.3%) and had a predisposing factor for GDA (71.9%). The diagnostic accuracy of the three most common diagnostic investigations—namely angiography, abdominal computed tomography, and ultrasound—was 100.0%, 86.2%, and 59.6%, respectively. Transarterial embolization (75.0%) and surgery (24.1%) were the two most common therapeutic approaches. Emergent treatment for GDA was necessary in 31.7% of patients. Notably, hemostasis was achieved after the initial treatment attempt in 82.6% of patients. The in-hospital mortality rate was 6.7%, with complications occurring in 16.1% of cases. A higher percentage of patients with a complicated hospital course were subjected to observation management and presented with shock during hospitalization.ConclusionsPatients with GDA often have comorbidities and predisposing factors. Clinical presentations of GDA were found to include abdominal pain, hemorrhage, and obstruction of peripheral structures in the vicinity of the gastroduodenal artery. Splanchnic artery angiography and abdominal computed tomography are recognized as the most accurate tools for diagnosing GDA. Endovascular management is the mainstay treatment approach for most patients and have a high rate of hemostasis success during the initial intervention. Surgical intervention is also a practical treatment. Conservative management with observation management may lead to a complicated hospital course, highlighting the potential benefit of aggressive treatment strategies for GDA. Patients with pancreatitis exhibited more comorbidities, predisposing factors, and a broader spectrum of clinical manifestations compared to those without pancreatitis. However, the in-hospital mortality rate was lower in the pancreatitis group, likely due to the younger age of the patients and the more prominent clinical presentations, which prompted earlier and more extensive diagnostic imaging studies. creator: Yi-Tzu Lee creator: Chien-Chin Hsu creator: Kuo-Tai Chen uri: https://doi.org/10.7717/peerj.19115 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Lee et al. title: Impact of phenytoin and valproic acid on cytotoxicity and inflammatory mediators in human mononuclear cells: with and without lipopolysaccharide stimulation link: https://peerj.com/articles/19102 last-modified: 2025-03-17 description: BackgroundValproic acid (VPA) is known for its broad-spectrum antiepileptic effects and is recommended for generalized epilepsy, in contrast to phenytoin, which has a more limited spectrum. This study investigated the cytotoxic and inflammatory responses to phenytoin and VPA in peripheral blood mononuclear cells (PBMCs), with and without bacterial lipopolysaccharide (LPS) stimulation.MethodsPBMCs from healthy donors were divided into 12 groups: control (Ctrl), phenytoin (Phy), and four concentrations of VPA (Val-50, Val-75, Val-100, Val-200), with and without LPS. Assessments were conducted on days 1 and 3, including total, live, and dead cell counts, cell viability, and lactic acid dehydrogenase (LDH) cytotoxicity assays. Inflammatory mediators (IL-6, IL-1β) and immune markers (IL-18, IgA) were measured using enzyme-linked immunosorbent assay (ELISA) on day 3. Statistical analysis involved two-way ANOVA, Tukey’s HSD tests, and paired t-tests.ResultsAll treatment groups showed significant declines in cell counts and viability from day 1 to day 3, which were exacerbated by LPS. Val-50 + LPS maintained higher cell counts compared to Ctrl + LPS and Phy + LPS. Elevated LDH levels were primarily observed in the Val-100 and Val-200 groups, with and without LPS. In the absence of LPS, the Val-75 and Val-100 groups showed notable reductions in IL-18 and IgA levels, while all VPA treatments reduced IL-6 levels compared to controls. This effect was enhanced under LPS exposure, although IL-1β reductions in the Val-75, Val-100, and Val-200 groups were reversed in the presence of LPS. Val-75 demonstrated lower cytotoxic and inflammatory responses compared to Phy and higher VPA doses, showing moderate LDH increases and reduced IL-18, IgA, IL-1β, and IL-6 levels, particularly under LPS challenge.ConclusionPhenytoin and VPA induced significant cytotoxic and inflammatory responses, influenced by dosage and LPS exposure. Val-75 exhibited a dose-specific immunomodulatory effect, reducing both pro-inflammatory and immune markers. creator: Aminah Alesawy creator: Norah Alotaibi creator: Marwa Alalshaikh creator: Faisal E. Aljofi creator: Nada Aldossary creator: Nada Al-Zahrani creator: Omar Omar creator: Marwa Madi uri: https://doi.org/10.7717/peerj.19102 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alesawy et al. title: Predicting mortality in geriatric patients with peptic ulcer bleeding: a retrospective comparative study of four scoring systems link: https://peerj.com/articles/19090 last-modified: 2025-03-17 description: BackgroundPeptic ulcer bleeding (PUB) is a significant cause of morbidity and mortality, especially in geriatric patients. Risk stratification tools such as AIMS65, Glasgow Blatchford Score (GBS), T-score, and Age, Blood tests, and Comorbidities (ABC) score are frequently used to predict outcomes in PUB patients. This study aims to compare the predictive performance of these four scoring systems in geriatric patients with PUB.MethodsThis retrospective cohort study included patients aged 65 years and older who were diagnosed with PUB between January 1, 2019, and January 1, 2024, in a tertiary care hospital. Data collected included demographic information, clinical presentation, laboratory results, and comorbidities. AIMS65, GBS, T-Score, and ABC score were calculated for each patient. The primary outcome was in-hospital mortality.ResultsA total of 315 patients were included in the study, with an overall in-hospital mortality rate of 7.9%. AIMS65 had the highest area under the curve (area under the receiver operating characteristic curve (AUROC): 0.829), followed by the ABC score (AUROC: 0.775). The GBS (AUROC: 0.694) and T-score (AUROC: 0.526) demonstrated lower predictive performance. Pairwise comparisons showed a statistically significant difference between the AIMS65 and GBS (p = 0.0214). AIMS65 was the most accurate predictor of in-hospital mortality in geriatric PUB patients.ConclusionThe AIMS65 and ABC scoring systems are more effective in predicting in-hospital mortality in geriatric patients with PUB compared to the GBS and T-Score. Implementing these tools in clinical practice could improve risk stratification and decision-making processes in managing high-risk elderly patients. creator: Omerul Faruk Aydin creator: Ali Cankut Tatlıparmak uri: https://doi.org/10.7717/peerj.19090 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Aydin and Tatlıparmak title: CD161, a promising prognostic biomarker in hepatocellular carcinoma, correlates with immune infiltration link: https://peerj.com/articles/19055 last-modified: 2025-03-17 description: BackgroundCD161, encoded by the killer cell lectin-like receptor B1 (KLRB1) gene, exhibits varied roles among different tumors. This study aimed to explore both the potential value of CD161 as a prognostic biomarker for hepatocellular carcinoma (HCC) and its association with immune cell infiltration.MethodsA total of 109 HCC patients who underwent surgery were retrospectively analyzed. Immunohistochemistry, bioinformatic analyses, and statistical measurements were used to investigate the associations between CD161 expression, immune cell infiltration, and clinical outcomes in both public databases and in-house cohorts.ResultsCD161 was highly expressed at both protein and mRNA levels in adjacent normal tissues compared to tumor tissues of HCC patients. Meanwhile, CD161 was enriched in HCC cases characterized by smaller tumor sizes (≤5 cm) and the absence of portal vein tumor thrombus. Individuals with high CD161 expression showed extended overall survival (OS) and relapse free survival (RFS) compared to those with lower CD161 levels. CD161 was identified as an independent prognostic indicator for both OS and RFS. In addition, the enrichment analysis indicated a close correlation between CD161 and immune response, as well as between CD161 and the signaling pathways of cytokines and chemokines, implying its role in immune regulation during cancer development. Specifically, CD161 expression was positively associated with immunomodulators and tumor-infiltrating immune cells, especially CD8+T cells, CD4+T cells, and dendritic cells. Multiple public databases showed that patients with high CD161 expression were more likely to derive benefits from immunotherapy.ConclusionCD161 was identified as a promising prognostic biomarker for HCC, as its expression indicates a favorable prognosis. Additionally, CD161 is closely linked to high infiltration of immune cells, participates in the regulation of the tumor immune microenvironment, and holds promise as a potential biomarker for predicting the efficacy of immunotherapy. creator: Jinfeng Wang creator: Xiaoxiao Wang creator: Jianfei Shi creator: Yongjun Wang creator: Lili Mi creator: Man Zhao creator: Guangjie Han creator: Fei Yin uri: https://doi.org/10.7717/peerj.19055 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Predictors of preterm births in North Dakota: a retrospective study of the North Dakota Pregnancy Risk Assessment Monitoring System (PRAMS) link: https://peerj.com/articles/19049 last-modified: 2025-03-17 description: BackgroundPreterm births represent approximately 10% of all births in the United States (US) annually. Although North Dakota (ND) has large rural and American Indian populations that experience disparities in health outcomes relative to the general population, few studies have investigated risk factors of preterm births in this state. Therefore, the objective of this study was to investigate predictors of preterm births in ND among women who had a live singleton birth and no prior history of preterm births.MethodsData on live births from 2017 to 2021 were obtained from the ND Pregnancy Risk Assessment Monitoring System. Potential predictors of preterm birth were identified using a conceptual model. Multivariable logistic regression was then used to investigate and identify significant predictors of preterm births.ResultsThe overall prevalence of preterm birth in North Dakota from 2017 to 2021 was 8.1%. However, among the population of interest in this study, which excluded births with multiple infants as well as women with a prior history of preterm birth, the preterm birth rate was 6.4%. Race, age, pregestational diabetes, and gestational hypertension were significantly associated with preterm birth in the final multivariable logistic model. The odds of preterm birth were higher among women who were American Indian (adjusted odds ratio (AOR) = 1.7, 95% confidence interval (CI) [1.3–2.4]), were aged 35 years or older (AOR = 1.6, 95% CI [1.01–2.5]), had pregestational diabetes (AOR = 4.3, 95% CI [2.0–9.3]), and had gestational hypertension (AOR = 4.5, 95% CI [3.1–6.7]) compared to women who were White, aged 20–34 years, and did not have pregestational diabetes or gestational hypertension.ConclusionsPreventing and controlling chronic diabetes and hypertensive disorders of pregnancy is critical for reducing the risk of preterm birth, especially among women of advanced maternal age. Further research is needed to understand the underlying causes of racial disparities of preterm birth in ND. creator: Grace Njau creator: Ramona Danielson creator: Corey Day creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.19049 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Njau et al. title: The association between non-high-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio (NHHR) and risk of prostate cancer: a retrospective study link: https://peerj.com/articles/19065 last-modified: 2025-03-14 description: BackgroundProstate cancer is one of the most frequent malignancies in the world, with significant morbidity and death rates. Identifying novel biomarkers is critical to reducing morbidity and mortality from the illness today. Although lipids have been linked to an increased risk of prostate cancer, it is unclear if the non-high-density lipoprotein cholesterol (NHDL-C) to high-density lipoprotein cholesterol (HDL-C) ratio (NHHR) is related to prostate cancer. Therefore, we assessed the relationship between NHHR and prostate cancer risk.MethodsThis study comprised 1,718 individuals who attended the First Affiliated Hospital of Xinjiang Medical University between March 2020 and March 2024. A pathological examination of a prostate puncture biopsy was utilized to confirm the diagnosis of prostate cancer. The study collected information on participants’ clinical and laboratory examinations, used propensity score matching to eliminate potential confounders, and analyzed the relationship between NHHR and prostate cancer, using logistic regression models combined with restricted cubic spline (RCS) and receiver operating characteristic (ROC) curve. Furthermore, sensitivity analyses were undertaken to assess the robustness of the results.Results(1) There were statistically significant differences in neutrophils, erythrocytes, triglycerides, alkaline phosphatase, and NHHR between the two groups; (2) after adjusting for all covariates, logistic regression revealed a negative association between NHHR and prostate cancer (0.91 (0.83∼0.99), P = 0.028). Participants in the second quartile had a significantly lower risk of prostate cancer after comprehensive adjustment (0.69 (0.50∼0.96), P = 0.026); (3) the restrictive cubic spline curve shows a non-linear relationship between NHHR and prostate cancer risk, with a turning point of 1.824; (4) the results of the ROC curve showed that the NHHR had an area under the curve (AUC) of 0.73; the results of the decision curve suggested that the model was able to provide a high benefit value for patients, with a threshold range of approximately 0.01–0.98 and a maximum net benefit of 0.52, and the calibration curve demonstrated that the model was accurate and reliable.ConclusionsThere is a non-linear dose-response relationship between NHHR and prostate cancer risk, which may be associated with a reduced risk of prostate cancer. The finding can be used to detect high-risk groups and prevent prostate cancer. creator: Ke Bu creator: Jinru Wang creator: Xiaojie Zheng creator: Kaige Zhang creator: Duolao Wang creator: Hengqing An creator: Ning Tao uri: https://doi.org/10.7717/peerj.19065 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bu et al. title: Susceptibility of lymnaeid snails to Fasciola hepatica and Fasciola gigantica (Digenea: Fasciolidae): a systematic review and meta-analysis link: https://peerj.com/articles/18976 last-modified: 2025-03-14 description: BackgroundFasciolosis is a food-borne disease that causes major economic losses, globally. This zoonotic disease is caused by Fasciola hepatica and Fasciola gigantica species which employ freshwater snails from the family Lymnaeidae as their intermediate hosts. Thus, a key aspect of understanding the epidemiology of the disease lies in understanding the transmission ecology of the parasite. Therefore, this systematic review and meta-analysis were conducted to assess the experimental susceptibility and prevalence of natural infections of F. hepatica and F. gigantica in lymnaeid snails.MethodsRelevant peer-reviewed articles published in the past 20 years (2004–2023) were searched and appraised. Prevalence and infection rate estimates were based on 41 studies that met the inclusion criteria.ResultsFive thousand five hundred and seventy-five (5,575) lymnaeid snails were subjected to experimental infections and 44,002 were screened for natural infections. The overall pooled infection rate was higher in experimental infections 50% (95% CI [42–58%]) compared to natural infections of field-collected snails 6% (95% CI [0–22%]). The highest pooled infection rate was recorded in South America at 64% (95% CI [48–78%]) for experimental infections while the lowest was recorded for natural infections at 2% (95% CI [0–6%]) in Europe and 2% (95% CI [0–17%]) in Asia. In experimental studies, F. gigantica recorded the highest pooled prevalence at 73% (95% CI [61–84%] compared to F. hepatica which recorded 47% (95% CI [38–56%]). For natural infections, however, F. hepatica had the highest prevalence (12% (95% CI [0–30%]) while the lowest was noted for naturally infected F. gigantica at 2% (95% CI [0–18%]). Based on the snail species, the highest pooled prevalence was recorded for Pseudosuccinea columella infected with F. hepatica and F. gigantica at 47% (95% CI [33–61%]) while the lowest was recorded for F. hepatica naturally infected Galba truncatula at 4% (95% CI [0–10%]). Natural Fasciola spp. infections in intermediate snail hosts decreased in prevalence while experimental infections have increased in prevalence over the past 20 years.ConclusionsWhile there seems to be a strong intermediate host specificity between the two Fasciola spp., experimental infection results showed that G. truncatula and R. natalensis are susceptible to F. hepatica and F. gigantica, respectively. creator: Philile Ignecious Ngcamphalala creator: Ignore Nyagura creator: Mokgadi Pulane Malatji creator: Samson Mukaratirwa uri: https://doi.org/10.7717/peerj.18976 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ngcamphalala et al. title: Relationship between salivary flow rate and dental caries in normal and underweight children: a comparative cross-sectional study from district Tharparkar link: https://peerj.com/articles/19128 last-modified: 2025-03-13 description: Background and ObjectivesThis study aims to explore the relationship between body mass index (BMI), salivary flow rate, and dental caries among children in Tharparkar.Materials and MethodsA comparative cross-sectional study was conducted over 6 months involving 179 children aged 8–12 years from Tharparkar and Hyderabad. Weight and height were recorded, BMI was computed using height and weight, and salivary flow rate was measured using the spitting method. Dental caries were assessed using the DMFT (decayed, missing, and filled teeth) index. Data were analyzed using SPSS, and independent t-tests were performed to assess group differences.ResultsUnderweight children (60.9% male, mean BMI 15.46 ± 2.45 kg/m2) showed higher mean DMFT scores for deciduous teeth (2.44 vs. 1.06, p = 0.009) compared to normal-weight peers. No significant differences were found in permanent teeth DMFT scores or salivary flow rates between BMI groups.ConclusionsUnderweight children exhibited a higher prevalence of dental caries in their primary teeth, underscoring the need for integrated nutritional and oral health interventions in vulnerable populations. However, salivary flow rate did not differ significantly between BMI groups, suggesting other factors may play a more critical role in caries prevention. creator: Abdul Qadir Khan Dall creator: Muhammad Adeel Ahmed creator: Fizza Zulfiqar creator: Sarwat Batool creator: Rizwan Jouhar creator: Muhammad Faheemuddin uri: https://doi.org/10.7717/peerj.19128 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dall et al. title: Evaluating moss diversity and biomass for sustainable harvesting methods in semi-arid forests of Turkey link: https://peerj.com/articles/19010 last-modified: 2025-03-13 description: In Turkey, it is legal to harvest moss from designated areas; however, the lack of comprehensive inventory studies in these harvested zones poses a significant threat to moss species. Harvesting without proper inventories can negatively impact rare, sensitive, and even endemic species in the region. Furthermore, research on the sustainable amount of moss harvestable per hectare in forested areas is severely lacking. The goal of this study, which covered 4,200 hectares on Eldivan Mountain, was to close the significant gap in moss inventory and sustainable harvesting methods. Sampling was conducted every 300-meters, measuring mosses in four m2 ground plots and 50 m2 tree plots. The total area covered by the identified moss species was approximately 97,216,557 m2, with a total dry weight of 44,640,972 kilograms. The most widespread ground species, Syntrichia ruralis (Hedw.) F. Weber & D. Mohr, covered 64,772,801 m2 with a dry weight of 623,268 kilograms, while the dominant tree species, Hypnum cupressiforme var. lacunosum Brid., covered 3,937,266 m2 with a dry weight of 1,448,533 kilograms. The research determines that the collection of epiphytic mosses is unsustainable, owing to insufficient rainfall in Turkey’s semi-arid areas. We recommend a sustainable harvest rate of 1–1.5 tons per hectare for ground mosses to balance ecological conservation with commercial objectives. These findings furnish critical information for conservation strategies and the formulation of sustainable moss harvesting methodologies. creator: Serhat Ursavaş creator: Recep Söyler uri: https://doi.org/10.7717/peerj.19010 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ursavaş and Söyler title: Effects of land use change on ecosystem services in freshwater wetlands in Bacalar, Mexico link: https://peerj.com/articles/18954 last-modified: 2025-03-13 description: Wetlands, such as those in Laguna Bacalar, Mexico, are highly productive and biodiverse ecosystems that provide a wide range of invaluable ecosystem services (ES). Despite their importance, these ecosystems are under significant threat from disturbances such as land-use changes, making them among the most endangered ecosystems worldwide. This study aimed to (1) assess the spatio-temporal variation of ecosystem services in Laguna Bacalar, Mexico, between 1999 and 2021 using medium-resolution satellite imagery from the Landsat sensor; and (2) estimate the monetary value of ES losses attributable to land-use changes by applying a unit value transfer method with global value coefficients based on data from Brander et al. (2024). Twenty-two key ESs were identified and associated with mangroves, inland wetlands, and the hydrological system. A total of 277 hectares of natural ecosystems were lost, leading to a reduction in the total value flow of ecosystem services (ES), which was estimated at 10,411,098 Int$/year over the study period. The loss of inland wetlands is particularly alarming due to their critical role in filtering agrochemicals and organic matter from the watershed. Increasing pressures from human activities, including urbanization and tourism, significantly contribute to the degradation of these ecosystems. This highlights the urgent need for responsible environmental management and the implementation of conservation strategies to protect their functionality and the invaluable ecosystem services they provide to local communities. creator: Erika Betzabeth Palafox–Juárez creator: Mariana E. Callejas–Jiménez creator: Jorge A. Herrera–Silveira creator: Claudia Teutli–Hernández creator: Vera Camacho–Valdez creator: Jorge Omar López–Martínez uri: https://doi.org/10.7717/peerj.18954 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Palafox–Juárez et al. title: Giants in the landscape: status, genetic diversity, habitat suitability and conservation implications for a fragmented Asian elephant (Elephas maximus) population in Cambodia link: https://peerj.com/articles/18932 last-modified: 2025-03-13 description: Asian elephant (Elephas maximus) populations are declining and increasingly fragmented across their range. In Cambodia, the Prey Lang Extended Landscape (PLEL) represents a vast expanse of lowland evergreen and semi-evergreen forest with potential to support Asian elephant population recovery in the country. To inform effective landscape-level conservation planning, this study provides the first robust population size estimate for Asian elephants in PLEL, based on non-invasive genetic sampling during the 2020–2021 dry season in three protected areas: Prey Lang, Preah Roka and Chhaeb Wildlife Sanctuaries. Further, it provides an assessment of the species’ range, habitat suitability and connectivity within the landscape using Maxent and Fuzzy suitability models. Thirty-five unique genotypes (individual elephants) were identified, of which six were detected in both Preah Roka and Chhaeb Wildlife Sanctuaries, providing evidence that elephants move readily between these neighbouring protected areas. However, no unique genotypes were shared between Preah Roka/Chhaeb and the less functionally connected southerly Prey Lang Wildlife Sanctuary. The estimated population size in the southern population was 31 (95% CI [24–41]) individuals. The northern population of Preah Roka/Chhaeb Wildlife Sanctuaries is estimated to number 20 (95% CI [13–22]) individuals. Habitat loss is prevalent across the landscape and connectivity outside of the protected areas is very limited; however, large swathes of suitable elephant habitat remain. As the landscape holds the potential to be restored to a national stronghold for this flagship species, in turn resulting in the protection of a vast array of biodiversity, we recommend protection of remaining suitable habitat and reduction of threats and disturbance to elephants within these areas as top priorities. Our study offers a model for integrated elephant population and landscape-level habitat modelling that can serve to guide similar research and management efforts in other landscapes. creator: Pablo Sinovas creator: Chelsea Smith creator: Sophorn Keath creator: Nasak Chantha creator: Jennifer Kaden creator: Saveng Ith creator: Alex Ball uri: https://doi.org/10.7717/peerj.18932 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sinovas et al. title: Psychometric properties of instruments for assessing adherence to oral antineoplastic agents: a COSMIN systematic review link: https://peerj.com/articles/19088 last-modified: 2025-03-12 description: IntroductionOral antineoplastic therapies have increasingly become a mainstay therapy for various cancers. Selecting the most suitable instrument for assessing adherence to oral antineoplastic agents (OAAs) in cancer patients is crucial to tracking patients’ medication compliance. This review is the first to identify available instruments for assessing adherence to OAAs and examine the quality of their psychometric properties.MethodsFollowing the Consensus-based Standards for the Selection of Health Measurement Instruments (COSMIN) guidelines and Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, eight electronic databases (PubMed, Embase, Web of Science, Cumulative Index to Nursing and Allied Health Literature (CINAHL), China National Knowledge Infrastructure (CNKI), Wanfang, Weipu, and Sinomed) were systematically searched for relevant studies published from inception until December 31, 2023. The study protocol received registration with the International Prospective Register of Systematic Reviews (CRD42024546402).ResultsEight studies assessing eight identified instruments were included. Four instruments were universal to cancer patients treated with any OAA; the other four instruments were only suitable for a specific type of OAA. None of the studies explored measurement error, cross-cultural validity/measurement invariance, and responsiveness of the instruments. All the instruments failed to meet the COSMIN criteria. Eventually, seven instruments were weakly recommended for use to assess OAA adherence, and one was not recommended for assessing OAA adherence due to high-quality evidence for insufficient internal consistency.ConclusionThe selection of the most appropriate instrument to assess adherence to OAAs depends on its psychometric properties and relevance to the type of OAA. Eight identified instruments for assessing adherence to OAAs demonstrated limited reliability and validity. Further thorough validation is required for all included instruments. Instruments with rigid measurement properties are urgently needed to be developed to assess OAA adherence in cancer patients. creator: Miaomiao Sun creator: Kanghui Huang creator: Suxiang Liu creator: Chuchu Fang creator: Lili Yang uri: https://doi.org/10.7717/peerj.19088 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Sun et al. title: The effect of mountaineering on the grit of college students: an empirical study link: https://peerj.com/articles/19086 last-modified: 2025-03-12 description: ObjectiveAlthough ample evidence in the literature suggests a correlation between general sports participation and resilience, information on the potential impact of specific sports activities on resilience is lacking. Therefore, we attempt to evaluate the effect of mountaineering on the grit of college students.MethodsThe study recruited 12 healthy college students for a three-day mountaineering activity. Then, the grit scores of the students before and after mountaineering were tested using the Chinese version of the original grit scale (Grit-O). During the mountaineering process, the oxygen saturation of the subjects was measured and recorded using a portable finger clipper. The scores of the Lake Louise Scale (2018 Lake Louise Acute Mountain Sickness Score, LLS) were used to distinguish whether the mountaineers had acute mountain sickness (AMS). Independent t-tests and paired t-tests were performed on the data separately.ResultsA significant correlation exists between the total score of grit among college students before and after mountaineering (r = 0.646, Sig < 0.05). However, the total score did not significantly improve after mountaineering (p = 0.054), the effort scores of all college students increased significantly before and after mountaineering (p = 0.045). A significant correlation is also observed between the total score of grit among college students who have not suffered from AMS (r = 0.764, Sig < 0.05). However, no significant improvement occurs (p = 0.075). Meanwhile, no significant correlation exists between the efforts (r = 0.499, Sig > 0.05) and interests (r = 0.562, Sig > 0.05) of college students before and after mountaineering. AMS has no significant correlation with the resilience of college students before and after mountaineering, in terms of effort (r = 0.456, Sig > 0.05) and interest (r = 0.601, Sig > 0.05), while no significant difference was observed between the total resilience score, effort and interest of mountaineering and non-mountaineering college students before and after mountaineering (all p >  0.05).ConclusionIn the short term, mountaineering has a certain enhancing effect on cultivating the grit of college students. However, the existing grit scale cannot fully reflect the resilience scores of mountaineers before and after. Hence, other situational dimensions should be added to the design of the grit scale. creator: Lun Li creator: ZuWang Chu creator: FuLin Li creator: JiaoJiao Li creator: Kang Wang creator: Yun Zhou uri: https://doi.org/10.7717/peerj.19086 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Ecological associations of the coastal marsh periwinkle snail Littoraria irrorata: field and laboratory evidence of vegetation habitat preferences link: https://peerj.com/articles/19071 last-modified: 2025-03-12 description: Coastal salt marshes serve as the margin between terrestrial and marine biomes, provide a variety of important services, and are dynamic ecosystems characterized by keystone species that shape trophic networks. In coastal salt marshes of the Atlantic and Gulf Coasts of the United States, marsh periwinkle snails (Littoraria irrorata) exhibit high abundance and form critical trophic pathways as important herbivores and detritivores. Specifically, snails forage on Spartina alterniflora and associated fungal growth, for which L. irrorata may act as a top-down control on plant growth. Yet, L. irrorata occupies other salt marsh plants, suggesting its habitat niche may be broader than previously reported. Here, we documented snail densities and size distributions in a Louisiana (USA) salt marsh composed of multiple marsh graminoids and report the results of behavioral choice experiments designed to test snail habitat preferences as a potential mechanism underlying their field distribution. We observed higher snail densities on S. alterniflora stalks (283 snails m−2) than other plant species, however, snails were highly abundant on S. patens (116 snails m−2), Juncus roemerianus (95 snails m−2), and Distichlis spicata (57 snails m−2) with densities comparable or higher on all species than reported on S. alterniflora in other studies along the U.S. Atlantic and Gulf coasts. Snails found on S. alterniflora and J. roemerianus, both plants with tall and rigid stalks, were also larger than snails found on other plant species. In species preference experiments, snails preferred S. alterniflora over S. patens and D. spicata, but no clear preferences were observed between S. alterniflora and J. roemerianus, nor between any combinations of S. patens, D. spicata, and J. roemerianus. Finally, we found that snails preferred senescing and dead S. alterniflora tissue over fresh S. alterniflora. Interpreting these results in tandem, this study suggests L. irrorata snails have consistent patterns of field distributions that match their habitat preferences, and future studies should test potential processes driving snail habitat selection, such as dietary habits and predator refugia (i.e., climbing sturdy stalks to avoid aquatic predators). Considering the abundance and trophic role of L. irrorata in coastal salt marshes, snail behavior may be a key modulator for salt marsh trophic networks. creator: David H. Klinges creator: Charles W. Martin creator: Brian J. Roberts uri: https://doi.org/10.7717/peerj.19071 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Klinges et al. title: Extracellular vesicles in endometrial-related diseases: role, potential and challenges link: https://peerj.com/articles/19041 last-modified: 2025-03-12 description: Endometrial dysfunction underlies many common gynecologic disorders, such as endometriosis, endometrial cancer, intrauterine adhesions, and endometritis, which affect many women around the world. Extracellular vesicles play an important role in the pathophysiologic process of endometrial-related diseases. Extracellular vesicles are released by cells, which usually act as a form of intercellular communication, affecting biological processes such as fibrosis, angiogenesis, cell proliferation, and inflammatory responses by transferring their own proteins, lipids, RNA transcripts, and DNA for messaging, and play a key role in physiological dynamic homeostasis and disease development. This review combines the studies of the last decade, using the sub-description method to introduce the application of different sources of extracellular vesicles in the diagnosis and treatment of related diseases, and discusses the challenges faced by extracellular vesicles in the diagnostic and therapeutic application of endometriosis-related diseases, with the aim of contributing to our understanding of the mechanism of action of extracellular vesicles and their therapeutic roles, so as to provide a reference for the development of endometriosis-related diseases, as well as their prognosis and treatment. creator: Zilu Wang creator: Feng Li creator: Wenqiong Liu uri: https://doi.org/10.7717/peerj.19041 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Fairly flexible: brown-tufted capuchins and a squirrel monkey adjust their motor responses in a foraging task link: https://peerj.com/articles/19023 last-modified: 2025-03-12 description: Prior research on non-human primates has produced contradictory results regarding behavioral flexibility and habit formation. Most observational studies of wild primates show flexibility in foraging behavior, whereas experimental data suggest captive primates tend to form habits, thus displaying conservative tendencies. Jacobson and Hopper (2019) proposed and supported the hypothesis that captive apes’ conservatism resulted from causally-unclear experimental apparatuses rather than a lack of flexibility as previous studies concluded. We replicated the experiment conducted by Jacobson and Hopper (2019) on apes with 18 brown capuchin monkeys (Cebus [Sapajus] apella) and five squirrel monkeys (Saimiri sciureus). Our goal was to investigate if they showed a similar degree of flexibility to chimpanzees (Pan troglodytes) and western lowland gorillas (Gorilla gorilla gorilla) when presented with a causally-clear task. Thus, the primary aim of this study was to determine whether this task was causally clear to monkeys, and if so, to compare their performance to that of apes. Monkeys were presented with a baited, clear tube where the removal of rods would allow the reward to drop, thus enabling the subject to retrieve said reward. Phase 1 of the study allowed us to determine whether the monkeys had a causal understanding of the task and provided an opportunity for habits to develop. Phase 2 presented the monkeys with a new reward configuration, requiring the removal of fewer rods to retrieve the reward to test if their causal understanding of the task would result in a flexible, more efficient response. The capuchins demonstrated cognitive flexibility and possible causal understanding in a manner similar to that of the apes. However, only one of five squirrel monkeys was efficient, suggesting the majority may not have understood a causal relationship between removing the rods and receiving the reward. Our study supports Jacobson and Hopper’s (2019) conclusion that causally-clear tasks reduce habit formation and conservatism in capuchins, but more evidence is needed with respect to squirrel monkeys. creator: Renee C. Russell creator: Colleen M. Buckley creator: Carly B. Rovner creator: Peter G. Judge uri: https://doi.org/10.7717/peerj.19023 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Russell et al. title: Impact of a multicomponent physical exercise program on intrinsic capacity in community-dwelling older adults link: https://peerj.com/articles/19017 last-modified: 2025-03-12 description: IntroductionIn 2015, the World Health Organization introduced intrinsic capacity, a health indicator encompassing five domains aimed at promoting healthy aging. Multicomponent exercise programs are recommended to maintain and optimize intrinsic capacity; however, evidence on their effects in robust older adults is limited. This study aimed to evaluate the effects of a multicomponent exercise program on intrinsic capacity in older adults.MethodsOlder adults (≥60 years) enrolled in a multicomponent training program in Porto Alegre (RS) were evaluated for intrinsic capacity using specific tests for each domain. The total score, ranging from 0 to 10 points, was obtained by summing the scores of the five domains. Participants underwent a 12-week multicomponent exercise intervention and were reassessed.ResultsAfter the 12-week intervention, the composite intrinsic capacity score significantly increased. Significant improvements were found in the cognitive, vitality and locomotion domains. The practice of Chinese curative gymnastics contributed to a one-point increase in the composite intrinsic capacity score. No association was found between frequency, duration of training, or the number of exercise modalities and the composite intrinsic capacity score.ConclusionThe multicomponent exercise program positively influenced composite intrinsic capacity, with notable improvements in vitality, cognition, and mobility. Personalization and individualization of training, combined with health education and social integration, were crucial in promoting healthy aging in the studied sample. creator: Sarah Giulia Felipe creator: Clarissa Biehl Printes creator: Douglas Kazutoshi Sato creator: Rafael Reimann Baptista uri: https://doi.org/10.7717/peerj.19017 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Felipe et al. title: Contribution of metabolomics to the taxonomy and systematics of octocorals from the Tropical Eastern Pacific link: https://peerj.com/articles/19009 last-modified: 2025-03-12 description: Octocorals are sessile invertebrates that play a key role in marine habitats, with significant diversity in the Tropical Eastern Pacific, especially in Ecuador’s shallow waters. This study focuses on the most representative octocorals within the Marine Protected Area El Pelado, Santa Elena, Ecuador, as a part of a marine biodiscovery project employing an integrative approach. While molecular techniques have advanced, challenges persist in distinguishing closely related species. Octocorals produce a wide range of compounds, characterized by unique chemical structures and diverse biological properties. Therefore, the main objective of this study was to assess the potential of metabolomics and advanced analytical techniques to analyze the metabolome of these organisms, aiming to refine species classification and improve understanding of octocoral systematics in this region. Untargeted metabolomics effectively discriminates 12 octocoral species across five genera: Muricea, Leptogorgia, Pacifigorgia, Psammogorgia, and Heterogorgia, with notable differentiation between species within the genus Muricea, reinforcing its utility as an additional data set for species characterization. Secondary metabolites such as sterols, steroids, and terpenes (furanocembranolides and sesquiterpenes), were identified in Leptogorgia and Muricea. Overall, this method enabled the identification of 11 known species and a potentially new one, Leptogorgia cf. alba, confirming the extreme diversity of this group in the Tropical Eastern Pacific and within the Ecuadorian marine ecosystem. The study highlights the value of metabolomics in octocoral systematics and encourages for its broader application in marine biodiversity research. creator: Karla B. Jaramillo creator: Paúl O. Guillén creator: Rubén Abad creator: Jenny Antonia Rodríguez León creator: Grace McCormack uri: https://doi.org/10.7717/peerj.19009 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Jaramillo et al. title: Efficacy of novel activated bamboo charcoal in reducing uremic toxins and enhancing kidney function in chronic kidney disease patients: a pilot randomized controlled trial link: https://peerj.com/articles/19007 last-modified: 2025-03-12 description: BackgroundThe role of uremic toxins in the progression of chronic kidney disease (CKD) and novel treatments to mitigate their effects are critical areas of research. This pilot study investigated the efficacy of a novel activated bamboo charcoal and/or probiotics in reducing uremic toxins and improving renal function in CKD patients.MethodsThis prospective, randomized, open, blinded end-point (PROBE) study included patients with stage 3 CKD. Patients were randomly assigned to one of four groups: activated bamboo charcoal (ABC), probiotics, ABC with probiotics, or standard treatment for 3 months.ResultsA total of 46 patients were enrolled (mean age 66.7 ± 11.5 years, 71.7% male). The ABC and ABC with probiotics groups showed a significant reduction in serum levels of the uremic toxins trimethylamine N-oxide (TMAO), p-cresyl sulfate (PCS), indoxyl sulfate (IS), and phenyl sulfate (PS) after 3 months of treatment (all p < 0.05). There was a particularly pronounced decrease in the percentage of IS in both the ABC group (−23.9 ± 28.9% vs. 33.9 ± 63.4%, p = 0.005) and the ABC with probiotics group (−29.3 ± 30.6% vs. 33.9 ± 63.4%, p = 0.009). The eGFR change ratio also significantly improved in the ABC group compared to the control group (4.6 ± 10.2% vs. −8.6 ± 12.5%, p = 0.011). However, the probiotics group did not exhibit a similar reduction in uremic toxins or an improvement in the eGFR.ConclusionThis study suggested that ABC significantly reduced uremic toxins and might have potential in improving eGFR in CKD stage 3 patients over a 3-month period. These findings suggest a potential protective effect of ABC on kidney function, highlighting the need for further large-scale, long-term randomized controlled trials to confirm these results. creator: Kuo-Chin Hung creator: Mei-Yueh Lee creator: Shih-Yuan Hung creator: Chiao-Yin Sun creator: Chau-Chung Wu creator: Cheng-Jui Lin uri: https://doi.org/10.7717/peerj.19007 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Hung et al. title: Synergistic effects of foliar applied glycine betaine and proline in enhancing rice yield and stress resilience under salinity conditions link: https://peerj.com/articles/18993 last-modified: 2025-03-12 description: Soil salinity is one of the most challenging environmental factors affecting rice productivity, particularly in regions with high saline soils such as Egypt. The ability of rice to maintain high yield and quality under saline stress is often limited, leading to significant reductions in productivity. With the increasing salinization of agricultural lands, finding effective agronomic practices and treatments to mitigate salt-induced damage in rice crops is critical for ensuring food security. This study investigates the potential of exogenous glycine betaine (GB) and proline (Pro) applications to mitigate the adverse effects of salt stress on rice (cv. Sakha 108) over two consecutive growing seasons (2021–2022). Treatments of 30 mM GB and 30 mM Pro significantly enhanced dry weight (162.2 and 169.7 g in 2021 and 2022, respectively), plant height (88.94 and 99.00 cm), tiller number (10.58 and 10.33), and grain yield (4.22 and 4.30 t/ha) compared to control groups. Combined treatments of 30 mM GB and 30 mM Pro exhibited the greatest improvements across both years, with maximum dry weight (193.44 and 186.56 g), plant height (112.00 and 112.33 cm), tiller number (15.33 and 16.28), spikelet number per meter (264.00 and 264.05), thousand-kernel weight (70.00 and 73.2 g), and grain yield (6.17 and 6.64 t/ha). Additionally, the combined treatments resulted in the highest harvest index (53.22% in 2021 and 48.94% in 2022), amylose content (24.24% and 20.09%), and protein content (12.33% and 12.00%). Correlation analysis highlighted strong positive relationships among traits, such as plant height with grain yield (r = 0.94), biomass yield (r = 0.92), and harvest index (r = 0.90). Path analysis further demonstrated that thousand-kernel weight and biomass yield had the most significant direct effects on grain yield, with values of 0.43 and 0.42, respectively. Heatmap clustering and principal component analysis (PCA) confirmed the synergistic effects of combined GB and Pro treatments, with the 30P_30GB treatment consistently clustering with high-yield traits, enhancing nitrogen use efficiency and stress resilience. In conclusion, the combined application of glycine betaine and proline significantly enhances the agronomic and chemical traits of rice under salt stress. This study demonstrates that these osmoprotectants improve vegetative growth, grain yield, and quality, with synergistic effects observed at optimal concentrations. The findings highlight the potential of glycine betaine and proline as effective tools for improving salt tolerance in rice, offering practical solutions to address challenges in saline-affected agricultural regions. creator: Sobhi F. Lamlom creator: Aly A. A. El-Banna creator: Honglei Ren creator: Bassant A. M. El-Yamany creator: Ehab A. A. Salama creator: Gawhara A. El-Sorady creator: Mohamed M. Kamara creator: Amal Mohamed AlGarawi creator: Ashraf Atef Hatamleh creator: Abdelsalam A. Shehab creator: Ahmed M. Abdelghany uri: https://doi.org/10.7717/peerj.18993 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lamlom et al. title: A systematic review of fluralaner as a treatment for ectoparasitic infections in mammalian species link: https://peerj.com/articles/18882 last-modified: 2025-03-12 description: Fluralaner (Bravecto™) is a novel isoxazoline ectoparasiticide used for controlling ectoparasites of domestic mammals and is increasingly being used on wildlife. The aim of this systematic review was to evaluate the efficacy, pharmacokinetics, and safety of fluralaner on mammals given its increasing use. The search was performed in GoogleScholar and the SciFinder databases using the terms ‘fluralaner’ and ‘Bravecto™’, and was concluded on 30th August, 2024. A total of 250 references were initially saved and reduced to 121 peer-reviewed journal articles using PRISMA guidelines, based on the removal of duplicates, those published in low quality journals (ranked less than Q2), and limiting publications to clinical trials. Articles were then categorised and ranked using the level of evidence, Cochrane ‘risk of bias’ assessment tool, methodological quality, and study size. Overall, the efficacy of fluralaner has been assessed on 14 mammalian species, and pharmacokinetic investigations conducted on 15. Fluralaner was mostly effective at treating some ectoparasites on captive individuals when there was little chance of re-infection; however, it did not prevent bites from blood-sucking ectoparasites and could not prevent blood-borne pathogen transfer to host animals. Very few studies have investigated the pharmacokinetics of fluralaner, and hence were difficult to compare; however, wombats differed greatly from their eutherian counterparts in their Cmax and t½ values and require further investigation. Overall, fluralaner was deemed moderately safe; however, most studies were classified as fair in terms of quality and most studies were based on small or very small sample numbers. Nineteen studies reported side effects, one of which included signs of severe neurological toxicity, with most of the articles not reporting on safety either positively or negatively. Concerns were raised regarding the extended time fluralaner was detected in faeces and subsequently environmental contamination is a concern. No longer-term impacts of the use of fluralaner have been investigated, and wider implications of the use of this ectoparasiticide have not yet been assessed. creator: Yuanting Jiang creator: Julie M. Old uri: https://doi.org/10.7717/peerj.18882 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Jiang and Old title: The re-description of Liaoningotitan sinensis Zhou et al., 2018 link: https://peerj.com/articles/19154 last-modified: 2025-03-11 description: Liaoningotitan sinensis is one of three sauropod species found in the Jehol Biota. Liaoningotitan sinensis is from the Lower Cretaceous Yixian Formation in Liaoning, China. The discovery of Liaoningotitan sinensis was an important breakthrough for researching the diversity of giant herbivorous animals in the Jehol Biota. However, the research and analysis of Liaoningotitan sinensis are not yet complete. This study presents a comprehensive research and analysis of Liaoningotitan sinensis holotype. First, the skull, vertebrae, pelvic girdle, and appendicular elements of Liaoningotitan sinensis holotype were carefully reexamined, leading to the discovery of mosaic evolution occurring in the skull and the identification of one new autapomorphy of humerus of Liaoningotitan sinensis: the attachment point of coracobrachialis muscle on the anterior surface of the proximal end of the humerus is flat. Second, the characteristics of the Liaoningotitan sinensis holotype and other well-preserved sauropod dinosaurs were used to reconstruct the skull of Liaoningotitan sinensis. Next, Euhelopus zdanskyi was used to reconstruct the body type of Liaoningotitan sinensis holotype, the result indicating that Liaoningotitan sinensis was approximately 10 m in length. Finally, TNT software was utilized to analyze the phylogenetic position of Liaoningotitan sinensis, with the result indicating that Liaoningotitan sinensis can be classified into the Euhelopodidae. creator: Bingqing Shan uri: https://doi.org/10.7717/peerj.19154 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Shan title: Clinical, molecular, and resistance features of Listeria monocytogenes in non-perinatal patients with listeriosis: 8-year retrospective data from four tertiary hospitals in Shandong, China link: https://peerj.com/articles/19126 last-modified: 2025-03-11 description: BackgroundListeriosis, caused by Listeria monocytogenes (L. monocytogenes), is a severe infectious disease with high hospitalization and fatality rates. Urgent epidemiological studies on this disease with geographic variability are needed, particularly in developing countries.MethodsThis study included non-perinatal patients with listeriosis from four tertiary centers in Shandong, China. Data on demographics, clinical characteristics, and outcomes were collected retrospectively over 8 years (2015–2022).ResultsAmong 292,254 non-perinatal patients, 27 listeriosis cases were identified, resulting in an incidence of nine cases per 100,000 admissions. Patients had a median age of 56 years, with 66.7% having comorbidities. Fever was the most common symptom (88.9%), and 44.4% had central nervous system involvement. Most patients (26/24; 96.3%) received antibiotics, 37.0% received monotherapy and 59.3% combination therapy. The mortality rate was 22.2%. The antimicrobial susceptibility test showed that 25 strains were sensitive to most antibiotics. Multilocus sequence typing revealed nine sequence types (ST), predominantly ST8 (44.4%), and serogroup 1/2a is the most common serogroup (66.7%).ConclusionsThis study provides valuable insights into the clinical and molecular features of L. monocytogenes in non-perinatal patients with listeriosis. The findings demonstrated the predominance of serogroup 1/2a and ST8. Despite low resistance and appropriate treatment, listeriosis remains associated with a significant mortality rate, emphasizing the need for timely diagnosis and effective management strategies. creator: Yan Liu creator: Yuan Xie creator: Lei Liu creator: Jie Wang creator: Wenjing Li creator: Chengfan Yang creator: Shuhua Lu uri: https://doi.org/10.7717/peerj.19126 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Liu et al. title: Mining of co-expression genes in response to cold stress at maize (Zea mays L.) germination and sprouting stages by weighted gene co-expression networks analysis link: https://peerj.com/articles/19124 last-modified: 2025-03-11 description: BackgroundMaize (Zea mays L.) is one of the main agricultural crops with the largest yield and acreage worldwide. Maize at the germination and sprouting stages are highly sensitive to low-temperatures, especially in high-latitude and high-altitude regions. Low-temperature damage in early spring presents a major meteorological disaster in maize, severely affecting plant growth and maize yield. Therefore, mining genes tolerant to low temperatures is crucial. We aimed to analyze differential gene expression and construct co-expression networks in maize under low temperatures.MethodsInbred lines, Zhongxi 091/O2 and Chang 7-2, are tolerant and sensitive to low temperatures at the germination and sprouting stages, respectively. We grew these lines at 10 °C and 2 °C at the germination and sprouting stages, respectively. Samples were taken at five time points (0, 6, 12, 24, and 36 h) during the two stages, and transcriptome sequencing was performed. The analyses were conducted using weighted gene co-expression networks analysis (WGCNA), Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene co-expression networks.ResultsWGCNA was used to construct co-expression networks at two stages, resulting in six and nine co-expression modules, respectively. Two modules at the germination stage (blue and yellow) and two modules at the sprouting stage (turquoise and magenta) were identified. These were significantly associated (p < 0.01) with tolerance at low temperature. The differentially expressed genes (DEGs) in the four modules revealed entries related to hormone and oxygen-containing compound responses by GO functional enrichment. Among the four modules, DEGs from three modules were all significantly enriched in the MAPK signaling pathway. Based on the connectivity, the top 50 genes for each module were selected to construct a protein interaction network. Seven genes have been proven to be involved in the response to low-temperature stress.ConclusionWGCNA revealed the differences in the response patterns of genes to low-temperature stress between tolerant and sensitive lines at different time points. Seven genes involved in low-temperature stress were functionally annotated. This finding suggests that WGCNA is a viable approach for gene mining. The current findings provide experimental support for further investigation of the molecular mechanisms underlying tolerance to low temperatures in maize. creator: Chuangye Shi creator: Jing Dong creator: Chunxiao Zhang creator: Liquan Sun creator: Fengxue Jin creator: Xiaohui Zhou creator: Xueyan Liu creator: Weilin Wu creator: Xiaohui Li uri: https://doi.org/10.7717/peerj.19124 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shi et al. title: SplintR ligation-triggered in-situ rolling circle amplification on magnetic bead for accurate detection of circulating microRNAs link: https://peerj.com/articles/19082 last-modified: 2025-03-11 description: The circulating microRNAs (miRNAs), endogenous noncoding RNAs, post-transcriptionally participate in multiple processes during cell growth and development. Moreover, dysregulation of miRNAs expression is intricately associated with cancer. Currently, challenges of high homology, sequence similarity, and low abundance encountered in the detection of target miRNAs in complex samples need to be addressed. Biosensors established for miRNAs detection suffer from limitations in terms of sensitivity, specificity and high cost. Herein, a miRNA detection method based on in-situ RCA on magnetic bead catalyzed by SplintR ligase was proposed to achieve high sensitivity and high specificity. The following steps are included: (1) formation of P1-P2-miRNA double-stranded complex under catalyzation of SplintR ligase, and the release of P1-P2 single strand under denaturation; (2) enrichment of P1-P2 single chain by streptavidin-modified magnetic beads (SM-MB); (3) in situ RCA on surface of magnetic beads; (4) fluorescence detection. After optimization of experimental conditions, miRNA-155 detection with improved sensitivity and specificity was achieved. The detection limit was low to 36.39 fM, and one-base mismatch discrimination was demonstrated. Also, the clinical practicability for circulating miRNA-155 detection was preliminarily validated in human serum samples. creator: Sha Yang creator: Lijia Yuan creator: Xing Luo creator: Ting Xiao creator: Xiaoqing Sun creator: Liu Feng creator: Jiezhong Deng creator: Mei Zhan uri: https://doi.org/10.7717/peerj.19082 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: Tree height-diameter allometry and implications for biomass estimates in Northeastern Amazonian forests link: https://peerj.com/articles/18974 last-modified: 2025-03-11 description: The relationship between tree height and diameter varies across forest types, introducing uncertainties in height that can affect aboveground biomass estimates in tropical forests. Here, we used a four-step approach to assess whether incorporating height estimates from local height-diameter models, compared to two published equations, improves biomass estimates across spatial scales. First, we measured the diameter and height of 1,962 trees in two representative forest types in the Northeastern Amazon: non-flooded terra-firme and seasonally-flooded várzea forests. Second, we selected the best height-diameter models from a set of 10 candidates to establish local allometric equations. Third, we applied these best local models and two previously published height models (the regional Guyana shield, and the pantropical model) to estimate tree height, and compared these estimates to measured height. Finally, we computed tree biomass using equations that both included and excluded height, and compared these biomass estimates to those calculated using directly measured height. Asymptotic height-diameter models provided the best fit at local and regional scales. The Quadratic model was the best choice for terra-firme and várzea forests separately, while the Weibull and Michaelis-Menten models performed best for both forests. Local models closely matched measured heights, with deviations of only 0.1%, outperforming the regional and pantropical models within each forest type. The regional model underestimated height in terra-firme by 3% and overestimated it in várzea by 29%, while the pantropical model underestimated height in terra-firme by 19% and overestimated it in várzea by 6%. Using local asymptotic models to estimate height improved the accuracy of biomass estimates, with differences of around 1% between biomass computed using measured heights and estimated heights for terra-firme and várzea forests. In contrast, the biomass calculated using estimated heights from both the regional and pantropical models overestimated the biomass in várzea by 41% and 17%, respectively, while the pantropical model underestimated biomass in terra-firme by 17%. The estimated height and biomass of large trees using regional and pantropical models showed the highest deviations from the observed values. Our findings underscore the necessity for height-diameter modeling for different forest types, and highlight the need to increase sampling of large trees to improve biomass estimation accuracy in Northeastern Amazonia. creator: Aldine Luiza Pereira Baia creator: Henrique E. M. Nascimento creator: Marcelino Guedes creator: Renato Hilário creator: José Julio Toledo uri: https://doi.org/10.7717/peerj.18974 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Baia et al. title: Propofol-based deep sedation for colonoscopy: does sufentanil, alfentanil or ketamine help? A propensity score weighted retrospective study link: https://peerj.com/articles/19146 last-modified: 2025-03-10 description: IntroductionGastrointestinal endoscopy is a frequent procedure for diagnosing and following up on various digestive disorders. It is often conducted under propofol sedation. The aim of this work is, first, to determine whether the addition of sufentanil, alfentanil, or ketamine to propofol has a propofol-sparing effect and, secondarily, how these drugs affect the patients’ hemodynamic parameters and oxygenation as well as the duration of the procedure.MethodsData from patients who underwent colonoscopy were extracted from the anesthesia records database and divided into four groups. Patients received either propofol or a combination of propofol and sufentanil, alfentanil, or ketamine. After inverse propensity weighting, we determined the average treatment effects for each group for the primary and secondary endpoints.ResultsSufentanil was associated with a less than 10% decrease in propofol consumption. Alfentanil and ketamine showed no propofol-sparing effect. Sufentanil was associated with 2 min shorter procedures. Alfentanil was associated with more patients presenting hypoxemia and had no propofol-sparing effect.ConclusionShould a balanced sedation technique be chosen, sufentanil appears to be the adjuvant of choice, given its propofol-sparing effect and the absence of induced hypoxemia. A further prospective study is necessary to explain the lack of propofol-sparing effect of ketamine and alfentanil and confirm and explain the negative impact of alfentanil on patients’ oxygenation. creator: Michele Fostier creator: Quentin Delhez creator: Gintare Januleviciute creator: Laurent Bairy uri: https://doi.org/10.7717/peerj.19146 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Fostier et al. title: The impact of long COVID on quality of life and work performance among healthcare workers in Portugal link: https://peerj.com/articles/19089 last-modified: 2025-03-10 description: BackgroundCoronavirus disease 2019 (COVID-19) is a multisystem infectious disease which affected 5.7 million people in Portugal. A subgroup of patients experienced long-term effects from the infection, now referred to as long COVID. Long COVID can considerably reduce the quality of life (QoL) of affected patients. This study aimed to evaluate the impact of long COVID on QoL and work performance among healthcare workers (HCWs) in Portugal.MethodsA cross-sectional correlational survey was performed in 348 HCWs employed either in hospitals, or non-hospital health facilities in Portugal. Participants completed an online survey using Google Forms between May and June 2024, which consisted of multiple-choice questions and took less than 10 min to fill out. Long COVID was considered present if the defined symptoms started at least 3 months after the primary infection of COVID-19, and persisted for at least 2 months. The outcome measures were performance at work and QoL. Performance at work was measured using a seven-point Likert scale and QoL was evaluated using the Satisfaction with Life Scale (SWLS). Data was analyzed using SPSS.ResultsA total of 277 participants (79.6%) had history of SARS-CoV-2 infection, and 223 participants (64.1%) reported a history of long COVID. Extreme fatigue was reported by 158 participants (57.0%), cognitive dysfunction by 118 participants (42.6%), shortness of breath by 76 participants (27.4%), and persistent cough by 168 participants (60.6%). In the multivariate analysis, long COVID was significantly associated with lower SWLS scores indicating that long COVID negatively impacted QoL. Having two or more chronic diseases showed a trend towards lower performance, and extreme fatigue and cognitive dysfunction showed strong negative associations with performance.DiscussionBased on a national sample of HCWs (348 individuals), a high percentage of participants (64.1%) reported a history of long COVID. These results suggest that HCWs in Portugal have a prevalence of the disease similar to that of the worldwide population. Concerning performance at work, having two or more chronic diseases showed a trend towards lower performance, as well as extreme fatigue and cognitive dysfunction. Interestingly, we found a negative association between being a clinical secretary and SWLS. This might be explained by the specific challenges or stressors faced by clinical secretaries, which could negatively impact their QoL. In conclusion, long COVID was prevalent in the studied sample of HCWs and had a negative impact on their QoL. Extreme fatigue and cognitive dysfunction were strongly negatively associated with performance. This suggests the need for targeted care for HCWs as a group. The results of this study can guide healthcare authorities in addressing important long-term consequences that should be considered in rehabilitation programs for post-COVID-19 recovery. creator: Filipe Prazeres creator: Ana Paula Romualdo creator: Inês Campos Pinto creator: Joana Silva creator: Andreia M. Oliveira uri: https://doi.org/10.7717/peerj.19089 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Prazeres et al. title: Exploring the classical and numerical Delboeuf illusion: the impact of transcranial alternating current stimulation on magnitude processing link: https://peerj.com/articles/19064 last-modified: 2025-03-10 description: Understanding cognitive and neural mechanisms underlying quantity processing is crucial for unraveling human cognition. The existence of a single magnitude system, encompassing non-symbolic number estimation alongside other magnitudes like time and space, is still highly debated since clear evidence is limited. Recent research examined whether spatial biases also influence numerosity judgments, using visual illusions like the Delboeuf illusion. While findings support a generalized magnitude system, direct comparisons of spatial and numerical Delboeuf illusions are missing. This study explored whether perceptual biases similarly affect different magnitude processing and whether transcranial alternating current stimulation (tACS) modulates these processes. Participants underwent three tACS conditions (seven Hz, 18 Hz, placebo) while performing tasks involving the classic and numerical Delboeuf illusions. We hypothesized that theta-frequency tACS (seven Hz) would enhance visual integration and illusion strength, while beta tACS (18 Hz) would reduce it by promoting visual segregation. Results indicated higher discrimination accuracy in area-based tasks than numerical judgments. Nonetheless, a significant correlation between performances in spatial and numerical illusions supported the existence of a shared mechanism for magnitude processing. Contrary to expectations, seven Hz tACS reduced the perceptual illusion’s strength. No significant interaction emerged between tACS frequency and discrimination abilities. These findings deepen our understanding of the cognitive processes involved in magnitude perception, potentially supporting the hypothesis of a generalized magnitude system. They also highlight the potential and limitations of non-invasive brain stimulation techniques, such as tACS, in modulating perceptual processes, offering insights into the neural underpinnings of quantity perception. creator: Maria Santacà creator: Francesco Carabba creator: Achini Mihindukulasooriya Fernando creator: Enrico Pitocco creator: Luca Battaglini creator: Umberto Granziol uri: https://doi.org/10.7717/peerj.19064 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Santacà et al. title: Effectiveness of FIFA injury prevention programs in reducing ankle injuries among football players: a systematic review link: https://peerj.com/articles/18910 last-modified: 2025-03-10 description: BackgroundAnkle injuries are some of the most common injuries among footballers and can prevent players from participating in sport. The Fédération Internationale de Football Association (FIFA) developed FIFA injury prevention programs to reduce overall football injuries, but their effectiveness on a particular joint, such as the ankle, was not assessed. Therefore, this project aims to investigate if these FIFA injury prevention programs are particularly effective in reducing ankle injuries.MethodA systematic review was conducted with the following criteria for study selection: Randomized controlled trials (RTCs) comparing the FIFA programs (FIFA 11 the old version and FIFA 11+) with the usual training for the teams. Other studies that included the number or percentage of ankle injuries as an outcome. Sample: Male and female footballers aged between 13 and 40 years old and without any restriction on particular skill levels. The Physiotherapy Evidence Database scale (PEDro) was used to assess the methodological quality of the included studies.ResultsThe search strategy identified five RCTs that used the FIFA programs. The included studies had a good-to-excellent methodological quality according to the PEDro scale (ranging from 5 to 7 out of 10). The pooled data from all the included studies indicated that the FIFA 11 and FIFA 11+ programs were effective in reducing the ankle injury rate by 14%, while pooled results from the studies that used the FIFA 11+ program significantly reduced ankle injury rate by 32%. However, the FIFA 11 program was not effective in reducing the ankle injury rate.ConclusionThe FIFA programs, and especially the FIFA 11+ program, appear to be more effective than the usual training in preventing ankle injuries among footballers. creator: Mohammad Alhazmi creator: Emad Alhazmi creator: Wael Abdulghani Alghamdi creator: Mohammed Zalah creator: Shadab Uddin creator: Moattar Raza Rizvi creator: Fuzail Ahmad uri: https://doi.org/10.7717/peerj.18910 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alhazmi et al. title: Mapping desert shrub aboveground biomass in the Junggar Basin, Xinjiang, China using quantile regression forest (QRF) link: https://peerj.com/articles/19099 last-modified: 2025-03-07 description: Haloxylon ammodendron is an essential species within the Central Asian desert ecosystem, with its aboveground biomass (AGB) serving as a crucial marker of ecosystem health and desertification levels. Precise and effective methods for predicting AGB are vital for understanding the spatial distributions and ecological roles of desert regions. However, the low vegetation cover in these areas poses significant challenges for satellite-based research. In this study, aboveground biomass training and validation datasets were gathered using UAV LiDAR, covering an area of 50 square kilometers. These datasets were integrated with high-resolution, multi-temporal satellite images from Sentinel-1 (S1) and Sentinel-2 (S2). This study applied a spatial cross-validation method to develop a quantile regression forest (QRF) prediction model. This model was used to predict the AGB of Haloxylon ammodendron forest across a study area of 14,000 square kilometers. The findings suggest that, when supported by ground data, multi-source remote sensing technology can estimate the AGB distribution of Haloxylon ammodendron over large areas. Significant uncertainty exists within the model due to the low vegetation cover characteristic of arid regions and the uneven distribution of sampling points. This uncertainty can be reduced by using area of applicability (AOA) and uncertainty maps, which identify the regions where the model’s predictions are most accurate and guide further data collection to enhance precision. This study provides improved insight into the spatial distribution and extent of Haloxylon ammodendron AGB in the research area and offers essential geospatial information for ecosystem conservation strategies. The results also contribute to the understanding of how desert vegetation growth and carbon cycling respond to environmental changes, and for forecasting future vegetation dynamics in arid regions. creator: XueFeng Yang uri: https://doi.org/10.7717/peerj.19099 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang title: Self-reported history of head injury is associated with cognitive impulsivity on a delay discounting task link: https://peerj.com/articles/19057 last-modified: 2025-03-07 description: BackgroundHead injuries are a major health care concern that can produce many long lasting cognitive, mental, and physical problems. An emerging literature indicates increased impulsivity in patients with a history of traumatic brain injury (TBI). In a recent study, Veterans with clinically-assessed history of mild TBI had increased cognitive, but not motor, impulsivity. Cognitive impulsivity refers to a preference for smaller immediate rewards (i.e., less willing to wait for larger rewards) while motor impulsivity refers to difficulty inhibiting a motor response. This study extended this work to investigating cognitive and motor impulsivity in a non-clinical sample of putatively healthy undergraduates self-reporting a history of head injury.MethodsOne hundred and sixteen undergraduates, fifty reporting a history of head injury (HI+) and sixty-six reporting no head injury (HI-), participated in an online study via Qualtrics. They completed a series of demographic questionnaires, the UPPS Impulsive Behavior Scale, a computer-based Go/No-go task to assess motor impulsivity, and a computer-based version of the Monetary Choice Questionnaire (MCQ) to assess cognitive impulsivity.ResultsHI+ individuals exhibited cognitive impulsivity, measured as a reduced willingness to wait for a larger delayed reward in the MCQ, as compared to HI- individuals. There were no significant differences in performance on the Go/No-go task between the HI+ and HI- groups. Overall, these findings that a self-reported history of head injury in a non-clinical sample are related to cognitive impulsivity, but not motor impulsivity, are consistent with findings from Veterans with clinically-assessed mild TBI. Future work should assess more details on head injuries to further explore how a head injury relates to cognitive impulsivity. creator: M. Todd Allen creator: Alejandro Interian creator: Vibha Reddy creator: Kailyn Rodriguez creator: Catherine E. Myers uri: https://doi.org/10.7717/peerj.19057 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Allen et al. title: Changes in tooth size of Otaria byronia: an indicator of density-dependent effects? link: https://peerj.com/articles/18963 last-modified: 2025-03-07 description: Teeth provide valuable information about an individual’s life cycle and serve as a powerful tool for visualizing population-level changes associated with density-dependent processes. In pinnipeds, teeth are used to estimate the age of individuals based on the count of growth layer groups (GLG) in the dentine. In this study, we analyzed changes in tooth size and GLG widths in the canines of Otaria byronia throughout the past 100 years, linking these to fluctuations in population abundance. A total of 76 male individuals from Patagonia were analyzed, classified into two periods: harvest and postharvest. The length and diameter of each tooth were measured prior to sagittal sectioning. Only for the postharvest period body length was recorded. Longitudinal sections of the upper canine were prepared, age was determined and the width of each GLG was measured in the resulting half-tooth. Results indicated a positive correlation (F = 62.90; p < 0.001; n = 50; r2 = 0.59) between body length and tooth length in postharvest individuals, suggesting that tooth growth is a reliable indicator of body growth. Individuals from the harvest period had narrower GLGs (t = 3.75; p < 0.001) and smaller tooth size (t = 3.48; p < 0.001) compared to those from the postharvest period. These results indicate that somatic growth of individuals may vary with population numbers and resources available. Also, hard structures like teeth are excellent tools for visualizing density-dependence effects. creator: Ailin Sosa Drouville creator: Federico Heredia creator: Mariano A. Coscarella creator: Enrique Crespo creator: María Florencia Grandi uri: https://doi.org/10.7717/peerj.18963 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sosa Drouville et al. title: Effects of 440-Hz vs. 432-Hz preferred music frequencies, during warm-up, on intermittent anaerobic speed test performance in men and women kickboxers: a double-blind crossover study link: https://peerj.com/articles/19084 last-modified: 2025-03-06 description: BackgroundPreferred music has been shown to enhance psychological and physiological parameters in order to increase physical performance in high intensity exercises. However, the effects of preferred music are less conclusive with different frequencies. The present study assessed the effects of listening to preferred music during warm-up at different frequencies on physical performance and psychophysiological responses specific in male and female kickboxers.MethodsIn a double-blind crossover study design, fifteen men and thirteen women kickboxers randomly performed the intermittent kickboxing anaerobic speed test (IKAST) after listening to preferred music around 440 Hz (PM44Hz), or 432 Hz (PM432Hz) frequencies or no music during warm-up. Physical performance indices, heart rate, blood lactate, rating of perceived exertion (RPE) and feeling scale (FS) were measured.ResultsWarm-up with PM440 Hz significantly improved IKAST performance indices with the highest impact velocity and FS, lowest mean heart rate and RPE, followed by PM432 Hz for both sexes compared to the control condition. For sex interaction, men had lower heart rate with PM440Hz, women the lowest with PM432Hz. In addition, women had higher positive feeling scale with PM440Hz, while men did not experience any significant change between the two musical conditions.ConclusionPM440Hz during warm-up was found to be more effective in improving specific performance, positive mood with a potential dissociation from discomfort during the test. Also, women were more affected by the music frequency difference compared to men. creator: Nidhal Jebabli creator: Manar Boujabli creator: Mariem Khlifi creator: Nejmeddine Ouerghi creator: Anissa Bouassida creator: Abderraouf Ben Abderrahman creator: Roland van den Tillaar uri: https://doi.org/10.7717/peerj.19084 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jebabli et al. title: Factors associated with post-stroke fatigue among stroke survivors: a cross-sectional study link: https://peerj.com/articles/19052 last-modified: 2025-03-06 description: BackgroundPost-stroke fatigue (PSF) is a common complication experienced by stroke survivors. These individuals often confront psychological challenges such as depression and anxiety, along with significant obstacles like reduced quality of life (QoL) and limitations in activities of daily living (ADLs). Such challenges can profoundly affect their overall recovery and well-being. Despite its prevalence, the associated factors contributing to PSF remain poorly understood. This study aims to primarily investigate these associated factors, while also examining the interrelationships among PSF, depression level, QoL, and ADLs, highlighting the need for a better understanding of these complex interactions.MethodsThis cross-sectional study involved 271 stroke survivors and was conducted at the Department of Neurology, Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, China, from September 2023 to January 2024. Participants independently completed the Fatigue Severity Scale (FSS), Patient Health Questionnaire-9 (PHQ-9), and the Short Version of the Stroke-Specific Quality of Life Scale (SV-SS-QoL) as part of a convenience sampling method, while medical professionals assessed the Barthel Index (BI) using the same sampling framework. Multivariable linear regression analyses were employed to determine the factors associated with the persistence of PSF.ResultsThe mean FSS score was 35.04 ± 11.60, while the average score for the SV-SS-QoL was 34.28 ± 9.51, and the BI score averaged 77.79 ± 25.90. Approximately 45.8% of participants (n = 124) experienced PSF. The mean score on the PHQ-9 was 7.63 ± 6.13. A significant negative correlation was identified between fatigue and both QoL and ADLs (P < 0.01). Furthermore, multiple linear regression analyses revealed that age, gender, income level, depression level, QoL, and ADLs were associated factors of fatigue severity among stroke survivors, all showing statistically significant differences (P < 0.01).ConclusionThis study emphasizes the critical factors associated with PSF and highlights the necessity of developing targeted interventions, such as depression management, QoL enhancement, and ADLs restoration, to alleviate fatigue in stroke survivors. Future research should focus on evaluating the effectiveness of these interventions to optimize rehabilitation outcomes and improve survivors’ overall recovery and well-being. creator: Yuan Dong creator: Linxi Tang creator: Salwismawati Badrin creator: Salziyan Badrin creator: Jiarun Wu uri: https://doi.org/10.7717/peerj.19052 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dong et al. title: Investigating passive eDNA samplers and submergence times for marine surveillance link: https://peerj.com/articles/19043 last-modified: 2025-03-06 description: Passive environmental DNA (eDNA) samplers offer a cost-effective and scalable approach to marine biodiversity monitoring, potentially aiding detections of non-indigenous species. This study explored the efficiency of passive eDNA samplers to detect a variety of globally problematic marine invasive species in field conditions: Sabella spallanzanii, Styela clava, Bugula neritina and Undaria pinnatifida. Four passive sampler substrates, nylon filters, positively charged nylon discs, nylon mesh, and artificial sponges, were tested across six submergence times, ranging from 10 to 720 min, against standard filtration-based approaches. Our results demonstrated that passive samplers could achieve comparable or even higher eDNA yields than traditional active filtration methods, indicating their potential for biosecurity surveillance. Species-specific droplet-digital PCR (ddPCR) assays provided sensitive and quantifiable eDNA signals, though assay validation remains crucial to avoid false negatives. Significant variation in eDNA signal detection highlighted the importance of considering both material selection and submersion time, depending on the targeted organisms. Furthermore, 18S rRNA metabarcoding was undertaken to assess how the overall detected biodiversity might interfere with species-specific detections. Certain sessile organisms, such as ascidians and polychaetes, dominated early representation on the passive filters but did not interfere with species-specific detection. By optimizing material selection, submersion time, and assay validation, passive eDNA sampling can enhance the sensitivity and reliability of eDNA-based monitoring, contributing to improved marine biosecurity and conservation efforts. creator: Ulla von Ammon creator: Gert-Jan Jeunen creator: Olivier Laroche creator: Xavier Pochon creator: Neil J. Gemmell creator: Jo-Ann L. Stanton creator: Anastasija Zaiko uri: https://doi.org/10.7717/peerj.19043 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 von Ammon et al. title: Optimal control simulations tracking wearable sensor signals provide comparable running gait kinematics to marker-based motion capture link: https://peerj.com/articles/19035 last-modified: 2025-03-06 description: ObjectiveInertial measurement units (IMUs) offer a method for assessing gait beyond the confines of a laboratory. Signal noise and calibration errors pose significant obstacles to accurately estimating joint angles, particularly during dynamic activities such as running. Advancements in dynamic optimisation tools could enable a more comprehensive analysis with fewer sensors and/or low-quality data. The objective of this study was to compare two IMU-based modelling approaches (inverse kinematics and optimal control simulations) with optical marker-based motion capture in reconstructing running gait kinematics.MethodsSix participants performed treadmill running at three speeds whilst marker trajectories and IMU signals were collected concurrently. The subject-specific biomechanical model consisted of a 3D representation of the lower body and torso, with contact spheres added to simulate ground contact in the optimal control simulations. The objective of the optimal control simulations was to track the accelerations, angular velocities, and orientations of eight sensors with simulated signals from the model sensors. Additional constraints were enforced, reflecting physiological and biomechanical principles and targeting dynamic consistency. The objective of the IMU-based inverse kinematics was to minimize the difference between the input and simulated sensor orientations. The joint kinematics derived from both methods were compared against optical marker-based motion capture across a range of running speeds, evaluating the absolute and normalized root mean square errors.ResultsCompared with motion-capture joint angles, optimal control simulations resulted in lower absolute errors (RMSE 8° ± 1) that were consistent across all speeds. IMU-based inverse kinematics exhibited greater differences with motion capture (RMSE 12° ± 1), which was more significant at faster speeds. The largest absolute inaccuracies were observed in the sagittal angles when not normalizing for the joint range of motion. The computational times for the optimal control were 46 ± 60 min, whereas they were 19.3 ± 3.7 s for the IMU-based inverse kinematics.ConclusionsCompared with traditional IMU-based inverse kinematics, the optimal control approach provides a more comparative representation of joint kinematics from optical motion capture. This method can mitigate errors associated with closely tracking IMU noise and drift, and it offers a dynamic analysis that considers the underlying forces and torques producing movement. However, these advantages come at the expense of challenges in parameter selection and computational cost.SignificanceThese findings highlight the potential of using IMUs with optimal control methods to provide a comprehensive understanding of gait dynamics across diverse applications. IMU-based inverse kinematics remains a viable option for faster computation and when model fidelity is less of a concern. creator: Grace McConnochie creator: Aaron S. Fox creator: Clint Bellenger creator: Dominic Thewlis uri: https://doi.org/10.7717/peerj.19035 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 McConnochie et al. title: Detection of O25B-ST131 clone and blaCTX-M-15 gene in Escherichia coli isolated from patients with COVID-19 link: https://peerj.com/articles/19011 last-modified: 2025-03-06 description: BackgroundIsolation of blaCTX-M family of extended-spectrum beta-lactamases (ESBL) is a challenge in the field of microbiology in our locality that makes treatment fail and disseminate quickly.ObjectivesTo determine the prevalence of blaCTX-M-15 ESBL gene in Escherichia coli clone O25B-ST131 isolated from COVID-19 patients with different infections.MethodsThis cross-sectional study was conducted on 528 patients hospitalized due to COVID-19 infection with various symptoms from April to September 2021. Using standard culturing techniques, E. coli were isolated from patients’ various samples (urine, catheter tip, sputum, blood, endotracheal tube aspiration, pleural/peritoneal fluids, and throat swab). After the antibiotic susceptibility test, E. coli isolates that were resistant to more than one of the three cephalosporins (cefotaxime, ceftriaxone and ceftazidime) were tested for ESBL production using the double disc synergy test and combined disc test, then confirmed by genotypic detection of blaCTX-M-15 gene among clones of O25B-ST131 E. coli. Finally, it was sequenced and its incision number was received from NCBI.ResultsA total of 234 E. coli isolates were detected from various patients’ samples, and all isolates showed multiple degrees of antibiotic resistance, especially ceftriaxone, ceftazidime, and cefepime. The phenotypic test showed that 63.2% of E. coli isolates were positive for ESBL, of which 58.1% were confirmed by double disc synergy test (DDST) (p = 0.002), 83.8% by combined disc test (CDT1) (p < 0.001) and 60.1% by CDT2 (p < 0.001). However, CDT1 has a better agreement as a phenotypic screening test (72.5% with a kappa value of 0.24) than DDST and CDT2. Most E. coli isolates were positive for the blaCTX-M-15 gene (68.4%), of which 75% were positive for the O25B- ST131 clone.ConclusionsMost E. coli isolates were ESBL producers, held blaCTX-M-15 gene and were positive for the O25B-ST131 clone. creator: Khanda Abdulateef Anwar uri: https://doi.org/10.7717/peerj.19011 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Anwar title: Antibacterial activity of the endophytic fungal extracts and synergistic effects of combinations of ethylenediaminetetraacetic acid (EDTA) against Pseudomonas aeruginosa and Escherichia coli link: https://peerj.com/articles/19074 last-modified: 2025-03-05 description: The growing threat of antibiotic resistance in bacteria is a critical public health concern. Combining natural compounds with antimicrobial agents is an alternative approach to improve the antibacterial efficacy and safety of these agents. The strategy is to restore the effectiveness of existing antibiotics while minimizing the required concentrations of antibiotics or antimicrobial agents. This study aimed to isolate the endophytic fungi from medicinal plants, including Lantana camara, Orthosiphon aristatus, Mansonia gagei, Terminalia bellirica, Oroxylum indicum, Elaeagnus latifolia, Talinum paniculatum, and Capsicum annuum, and evaluate the combined antibacterial efficacy with selected antibiotics or ethylenediaminetetraacetic acid (EDTA) against Pseudomonas aeruginosa. The antimicrobial activity of the extracts was assessed using agar well diffusion and broth microdilution methods. The minimum inhibitory concentration (MIC) values of the extracts were 32–64 µg/mL against Escherichia coli, and 512–2,048 µg/mL against P. aeruginosa, respectively. Time-kill assays demonstrated the bacteriostatic effect of the extracts. The checkerboard microbroth dilution method was performed to determine the synergistic effect between endophytic fungal extracts and antibiotics or EDTA. The synergistic effect was observed in the extractions of endophytic fungi isolated from M. gagei, T. bellirica, O. indicum, E. latifolia, T. paniculatum, and C. annuum combined with EDTA against P. aeruginosa. Combinations of endophytic fungi with EDTA, which exhibited a synergistic effect, demonstrated bactericidal action against Gram-negative bacteria. The present study suggests that combining endophytic fungal extracts and EDTA could be an essential strategy for combating pathogenic Gram-negative bacteria. creator: Sirirak Rosdee creator: Sueptrakool Wisessombat creator: Malatee Tayeh creator: Ramitanun Malakul creator: Teva Phanaksri creator: Wipawadee Sianglum uri: https://doi.org/10.7717/peerj.19074 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Rosdee et al. title: Outcomes of metabolic syndrome and anxiety levels in light and heavy smokers link: https://peerj.com/articles/19069 last-modified: 2025-03-05 description: BackgroundThis study aimed to assess the impact of smoking status, as measured by pack-years (PY), on components of metabolic syndrome while considering the influence of anxiety.DesignThis cross-sectional study was conducted at a smoking cessation clinic in Turkey, enrolling individuals who visited the clinic in 2022. The Fagerstrom Test for Nicotine Dependence and the State-Trait Anxiety Inventory were utilized as assessment tools, while metabolic syndrome parameters (body mass index, hypertension, hyperglycemia, dyslipidemia) were evaluated. Smoking status was classified based on pack-years.ResultsThe study revealed a dose-dependent relationship between smoking status and essential metabolic factors such as systolic blood pressure (SBP), diastolic blood pressure (DBP), hemoglobin A1c (HbA1c), and low-density lipoprotein (LDL). Notably, triglyceride (TG) levels exhibited a significant increase, particularly at 25 pack years. While anxiety levels did not exhibit a significant correlation with smoking status, they demonstrated an upward trend with increasing SBP and DBP values. Anxiety levels did not exhibit a significant correlation with smoking status.ConclusionsA significant association was identified between nicotine addiction, as indicated by PY, and both metabolic syndrome parameters and anxiety levels. Early smoking cessation is strongly recommended for current smokers, and former smokers are advised to abstain from smoking to mitigate its adverse effects on metabolic syndrome components. These findings underscore the interconnectedness of cigarette smoking’s effects on both physical and mental health, emphasizing the necessity of comprehensive approaches encompassing both metabolic disorder management and mental health support within cessation programs. creator: Musa Şahin creator: Didem Yüzügüllü uri: https://doi.org/10.7717/peerj.19069 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Şahin and Yüzügüllü title: Mass harvested per trunkload as a constraint to forage consumption by the African savanna elephant (Loxodonta africana) link: https://peerj.com/articles/19033 last-modified: 2025-03-05 description: BackgroundAfrican elephants can convert woodland to shrubland or grassland. Moderate conversion observed at low elephant densities may improve conditions for other animals, while extensive transformation at high densities may reduce plant and animal diversity. The threshold density separating facilitation from habitat destruction varies spatially and is partly determined by food choice, which differs between adult bulls and members of breeding herds. When elephants consume herbaceous forage, woodland damage is low but this increases when woody plants are the primary food source. Consequently, an understanding of diet selection by elephants is important for forecasting the degree of vegetation conversion. One hypothesis is that elephants select forage that provides the highest rate of intake. The mass harvested per trunkload is a constraint to intake and therefore this study sought to determine if trunkload mass changes seasonally; varies across common forage types utilised by elephants; and differs between adult bulls and members of breeding herds.MethodsMechanistic models were used to estimate the mass harvested per trunkload of green grass, mixed green and dry grass, forbs, and leaves and bark from woody plants across a heterogenous, semi-arid savanna at a daily time step for one annual cycle. Separate models were constructed for adult bulls and members of breeding herds.ResultsHarvestable mass changed seasonally for herbaceous forage and for leaves from woody plants but was constant for canopy bark. The maximum average trunkload mass of green grass was >75 times heavier than the bite mass reported for other grazers while trunkloads of leaves from woody plants were only eight times heavier than the bite mass reported for other browsers. This is attributed to the advantage provided by the trunk, which increases harvestable mass beyond the constraint of mouth volume, particularly when feeding on grass. Herbaceous forage yielded heavier trunkloads than leaves and bark from woody plants during the wet season, but this was reversed in the dry season. Adult bulls harvested heavier trunkloads than members of breeding herds for all forage types except forbs; and adult bulls harvested disproportionately large trunkloads of grass and bark.ConclusionThe strong correlation between the model outputs and well-established trends in the seasonal changes in elephants’ diet suggests that elephants are preferential foragers of the largest trunkload on offer. Consequently, they are grazers when suitable herbaceous forage is available, and browsers when it is scarce. Green grass provides adult bulls with disproportionately large trunkloads and, therefore, adult bulls are predicted to have a strong preference for green grass. Availability of suitable green grass during the dry season may therefore buffer woodlands from heavy impact by adult bulls. Consequently, where possible, protected areas with elephants should aim to include key grass resources. creator: Bruce W. Clegg creator: Timothy G. O’Connor uri: https://doi.org/10.7717/peerj.19033 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Clegg and O’Connor title: Characteristics of the retinal and choroidal thicknesses in myopic young adult males using swept-source optical coherence tomography link: https://peerj.com/articles/19030 last-modified: 2025-03-05 description: BackgroundChanges in retinal and choroidal structures are key biomarkers for predicting, diagnosing, and monitoring various ocular conditions, including myopia.ObjectiveTo assess the characteristics of the retinal and choroidal thicknesses in myopic young adult males using swept-source optical coherence tomography (SSOCT).MethodsThis cross-sectional comparative study included 198 young adults with a mean age of 21.87 ± 1.69 years, only male subjects were recruited for this study, comprising 102 diagnosed with myopia and 96 with emmetropia. Refraction was assessed using an autorefractometer, and comprehensive SSOCT scans were conducted to measure the thickness of the retina and choroid at nine predefined locations. Data analysis focused on identifying significant patterns and correlations between myopia and retinal and choroidal thickness.ResultsMyopic subjects with a mean of −2.66 ± 1.59D exhibited significantly decreased retinal thickness compared to emmetropic with a mean of 0.18 ± 0.39D, (p < 0.01). Similarly, their choroidal thickness was also significantly thinner (p < 0.01). The findings showed a weak but statistically significant inverse correlation between retinal thickness and the spherical equivalent of myopia (r = −0.257, p < 0.01). Correspondingly, a stronger inverse correlation was observed between choroidal thickness and the spherical equivalent of myopia (r = −0.306, p < 0.01). Choroidal thickness in all studied areas showed an inverse correlation with the degree of myopia (p < 0.05), except in the superior outer region, where the association was not statistically significant (p = 0.056).ConclusionThe study identified significant differences in the retinal and choroidal structures between myopic and emmetropic individuals. The use of SSOCT effectively detected these morphological changes in myopic young adults, offering valuable insights into myopia’s pathophysiology and potentially guiding targeted therapeutic strategies for myopia control. creator: Saif Hassan Alrasheed creator: Yazan Gammoh uri: https://doi.org/10.7717/peerj.19030 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alrasheed and Gammoh title: Soft anatomy and morphological variation in Daptomys peruviensis (Rodentia, Cricetidae), a rare ichthyomyine from the northwestern Amazonian forests link: https://peerj.com/articles/18997 last-modified: 2025-03-05 description: The recently resurrected genus Daptomys Anthony, 1929 includes poorly known small cricetid rodents that are widely distributed in tropical South America. Along with Neusticomys Anthony, 1921, these species are the most terrestrial members of the tribe, which is otherwise distinguished by adaptations that allow species to live in both aquatic and terrestrial environments. Newly collected Ecuadorean specimens provide complementary information of the craniodental and soft anatomy of Daptomys, focusing on rhinarium morphology, soft palate, stomach, caecum configuration, and other features. In addition, the phylogeny presented here, combined with species distribution models, suggests a simplified taxonomy indicating that Daptomys peruviensis (Musser & Gardner, 1974) has a wide distribution extending from Venezuela to Peru. In this novel scenario, Daptomys mussoi (Ochoa & Soriano, 1991) would be a junior synonym of D. peruviensis, and the application of a trinominal taxonomy appears premature. creator: Jorge Brito creator: Mateo A. Vega-Yánez creator: Jhandry P. Guaya-Ramos creator: Melanie Polo creator: Claudia Koch creator: Nicolás Tinoco creator: Ulyses F.J. Pardiñas uri: https://doi.org/10.7717/peerj.18997 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Brito et al. title: The extended impact of the COVID-19 pandemic on medical imaging case volumes: a retrospective study link: https://peerj.com/articles/18987 last-modified: 2025-03-05 description: ObjectiveThis study aims to investigate the long-term effects of the COVID-19 pandemic on medical imaging case volumes.MethodsThis retrospective study analyzed data from the Integrated Radiology Information System-Picture Archive and Communication System (RIS-PACS), including monthly medical imaging case volumes at a public hospital, spanning from January 2019 to December 2022. The study collected data on medical imaging examinations, comparing the pre COVID-19 period, which acted as a control group, with the periods following COVID-19, which were designated as cohort groups.ResultsThe total number of medical imaging procedures performed (n = 597,645) was found significantly different (F = 6.69, P < 0.001) between 2019 and 2022. Specifically, the bone mineral density/computed radiography (BMD/CR) modality experienced a significant decrease (P = 0.01) of the procedures performed in 2020 and 2021 compared to 2019. Conversely, the nuclear medicine/computed tomography (NM/CT) and computed tomography (CT) modalities demonstrated a significant increase of the procedures performed in 2021 (P = 0.04) and (P < 0.0001), respectively, and in 2022 (P = 0.0095) and (P < 0.0001), respectively, compared to the pre-pandemic year. The digital X-ray modality (DX) showed the highest volume (67.63%) of the performed procedures overall between 2019 and 2022. Meanwhile, magnetic resonance imaging (MR) and ultrasound (US) modalities experienced a slight drop in the number of procedures in 2020—4.47% for MR and 1.00% for US, which subsequently recovered by 22.15% and 19.74% in 2021, and 24.36% and 17.40% in 2022, respectively, compared to 2019.ConclusionThe COVID-19 pandemic initially led to a drop in the number of medical imaging procedures performed in 2020, with the most noticeable drop occurring during the early waves of the pandemic. However, this trend revealed a gradual recovery in the subsequent years, 2021 and 2022, as healthcare systems adapted, and pandemic-related restrictions were modified. creator: Fahad H. Alhazmi creator: Faisal A. Alrehily creator: Walaa Alsharif creator: Moawia Gameraddin creator: Kamal D. Alsultan creator: Hassan Ibrahim Alsaedi creator: Khalid M. Aloufi creator: Sultan Abdulwadoud Alshoabi creator: Osamah M. Abdulaal creator: Abdulaziz A. Qurashi uri: https://doi.org/10.7717/peerj.18987 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alhazmi et al. title: Determining population structure from k-mer frequencies link: https://peerj.com/articles/18939 last-modified: 2025-03-05 description: BackgroundUnderstanding population structure within species provides information on connections among different populations and how they evolve over time. This knowledge is important for studies ranging from evolutionary biology to large-scale variant-trait association studies. Current approaches to determining population structure include model-based approaches, statistical approaches, and distance-based ancestry inference approaches.MethodsIn this work, we identify population structure from DNA sequence data using an alignment-free approach. We use the frequencies of short DNA substrings from across the genome (k-mers) with principal component analysis (PCA). K-mer frequencies can be viewed as a summary statistic of a genome and have the advantage of being easily derived from a genome by counting the number of times a k-mer occurred in a sequence. In contrast, most population structure work employing PCA uses multi-locus genotype data (SNPs, microsatellites, or haplotypes). No genetic assumptions must be met to generate k-mers, whereas current population structure approaches often depend on several genetic assumptions and can require careful selection of ancestry informative markers to identify populations. We compare our k-mer based approach to population structure estimated using SNPs with both empirical and simulated data.ResultsIn this work, we show that PCA is able to determine population structure just from the frequency of k-mers found in the genome. The application of PCA and a clustering algorithm to k-mer profiles of genomes provides an easy approach to detecting the number and composition of populations (clusters) present in the dataset. Using simulations, we show that results are at least comparable to population structure estimates using SNPs. When using human genomes from populations identified by the 1000 Genomes Project, the results are better than population structure estimates using SNPs from the same samples, and comparable to those found by a model-based approach using genetic markers from larger numbers of samples.ConclusionsThis study shows that PCA, together with the clustering algorithm, is able to detect population structure from k-mer frequencies and can separate samples of admixed and non-admixed origin. Using k-mer frequencies to determine population structure has the potential to avoid some challenges of existing methods and may even improve on estimates from small samples. creator: Yana Hrytsenko creator: Noah M. Daniels creator: Rachel S. Schwartz uri: https://doi.org/10.7717/peerj.18939 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hrytsenko et al. title: Identifying leptospirosis hotspots in Selangor: uncovering climatic connections using remote sensing and developing a predictive model link: https://peerj.com/articles/18851 last-modified: 2025-03-05 description: BackgroundLeptospirosis is an endemic disease in countries with tropical climates such as South America, Southern Asia, and Southeast Asia. There has been an increase in leptospirosis incidence in Malaysia from 1.45 to 25.94 cases per 100,000 population between 2005 and 2014. With increasing incidence in Selangor, Malaysia, and frequent climate change dynamics, a study on the disease hotspot areas and their association with the hydroclimatic factors could enhance disease surveillance and public health interventions.MethodsThis ecological cross-sectional study utilised a geographic information system (GIS) and remote sensing techniques to analyse the spatiotemporal distribution of leptospirosis in Selangor from 2011 to 2019. Laboratory-confirmed leptospirosis cases (n = 1,045) were obtained from the Selangor State Health Department. Using ArcGIS Pro, spatial autocorrelation analysis (Moran’s I) and Getis-Ord Gi* (hotspot analysis) was conducted to identify hotspots based on the monthly aggregated cases for each subdistrict. Satellite-derived rainfall and land surface temperature (LST) data were acquired from NASA’s Giovanni EarthData website and processed into monthly averages. These data were integrated into ArcGIS Pro as thematic layers. Machine learning algorithms, including support vector machine (SVM), Random Forest (RF), and light gradient boosting machine (LGBM) were employed to develop predictive models for leptospirosis hotspot areas. Model performance was then evaluated using cross-validation and metrics such as accuracy, precision, sensitivity, and F1-score.ResultsMoran’s I analysis revealed a primarily random distribution of cases across Selangor, with only 20 out of 103 observed having a clustered distribution. Meanwhile, hotspot areas were mainly scattered in subdistricts throughout Selangor with clustering in the central region. Machine learning analysis revealed that the LGBM algorithm had the best performance scores compared to having a cross-validation score of 0.61, a precision score of 0.16, and an F1-score of 0.23. The feature importance score indicated river water level and rainfall contributes most to the model.ConclusionsThis GIS-based study identified a primarily sporadic occurrence of leptospirosis in Selangor with minimal spatial clustering. The LGBM algorithm effectively predicted leptospirosis hotspots based on the analysed hydroclimatic factors. The integration of GIS and machine learning offers a promising framework for disease surveillance, facilitating targeted public health interventions in areas at high risk for leptospirosis. creator: Muhammad Akram Ab Kadir creator: Rosliza Abdul Manaf creator: Siti Aisah Mokhtar creator: Luthffi Idzhar Ismail uri: https://doi.org/10.7717/peerj.18851 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ab Kadir et al. title: Effects of time, anticoagulant and detection channel on platelet count in ethylenediaminetetraacetic acid (EDTA)-dependent pseudothrombocytopenia link: https://peerj.com/articles/19103 last-modified: 2025-03-04 description: BackgroundEDTA-dependent pseudothrombocytopenia (EDTA-PTCP) is an in vitro phenomenon that may lead to expensive, time-consuming, and invasive diagnostic procedures as well as unnecessary patient treatment. The purpose of this study was to explore the effects of time, anticoagulant and detection channel on the platelet (PLT) count of EDTA-PTCP samples, and to suggest a better method for correcting spurious low PLT counts.MethodsIn this study, 43 identified EDTA-PTCP samples were collected. The Sysmex XN-9100, Mindray BC-6900 and Mindray BC-5390 haematology analysers were used to test these EDTA-PTCP samples on the following detection channels at different time points: PLT count by impedance method (PLT-I), PLT count by optical method (PLT-O) and PLT count by fluorescent staining (PLT-F).ResultsEDTA-PTCP was time-dependent and small PLT agglutination occurred in most of the corresponding citrate-treated samples. Our results further demonstrated that the detection channel significantly affected the PLT count of the EDTA-PTCP samples. The XN-9100 PLT-F channel exhibited a greater dissociative effect than the XN-9100 PLT-I and PLT-O channels. Moreover, blood samples processed in the PLT-O channel of the Mindray hematology analyzer showed the highest PLT count in EDTA-K2 tubes compared to the other detection channels.ConclusionOur data showed that time, anticoagulant and detection channel significantly affected the PLT count in the EDTA-PTCP samples. For the EDTA-PTCP samples, the simplest retest method was to use the PLT-O channel of the Mindray automatic blood analyser within 30 min. In addition, changing the sodium citrate anticoagulant and using the XN-9100 PLT-F channel within 15 min were also suitable for correcting the spurious low PLT of the EDTA-PTCP samples. creator: Yu Zhang creator: Bei Chen creator: Jiaoying Feng creator: Wen Yu creator: Wei Liang creator: Meifen Li creator: Guanghua Zhai creator: Meina Yan uri: https://doi.org/10.7717/peerj.19103 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zhang et al. title: Genome-wide association studies reveal potential candidate genes associated with amino acid in tea plants link: https://peerj.com/articles/18969 last-modified: 2025-03-04 description: BackgroundAmino acids, as the main flavor substances of umami in tea, are also the primary components determining the taste of tea, which is positively correlated with the quality and grade of tea. The Guizhou Plateau is located in the core area of the origin of the tea plant and has abundant tea germplasm. However, there are relatively few studies using genome-wide association studies (GWAS) to mine genes related to amino acid content in tea plants in the Guizhou Plateau.ResultsIn this study, 78,819 high-quality single nucleotide polymorphisms (SNPs) markers were identified from 212 tea accessions composed by our group in the previous study by genotyping sequencing technology (GBS), and the population structure, genetic diversity, and GWAS of 212 tea accessions resources of tea were analysed. Phylogenetic tree and population structure analysis divided all germplasm into four inferred groups (Q1, Q2, Q3, Q4). By analysing the eight SNPs associated with amino acids obtained by GWAS, four candidate genes that may be related to amino acids were identified. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to verify the expression levels of four candidate genes, suggesting that there may be a potential gene that is important for the accumulation of amino acid content.ConclusionsThis study provides new information for the in-depth analysis of the genetic mechanism of amino acid content in tea plants and provides important genetic resources for accelerating the cultivation of new tea varieties with suitable amino acid content. creator: Qidi Wu creator: Li Song creator: Dingchen Bai creator: Yihan Wang creator: Yuting OuYang creator: Kaixin Rao creator: Qinfei Song creator: Juanying Wang creator: Suzhen Niu creator: Yujie Ai uri: https://doi.org/10.7717/peerj.18969 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wu et al. title: Assay of cardiopulmonary bypass system for porcine alveolar macrophages removing GFP-E. coli from erythrocyte surfaces link: https://peerj.com/articles/18934 last-modified: 2025-03-04 description: While it is established that complement receptor molecules on the surface of erythrocytes are crucial for the clearance of immune complexes in the body, the molecular mechanisms underlying the interaction between macrophages and erythrocytes in pigs remain inadequately understood. Consequently, we built a detection system with a closed-circulation flow chamber and a constant flow pump. Additionally, we optimized parameters including system flow velocity and fluid shear force. In the circulatory system, our study measured the fluorescence intensity of erythrocyte and pulmonary alveolar macrophages (PAMs) surfaces before and after the blockade of complement receptor 1 (CR1)-like receptors and Fc receptors. The results indicated that porcine erythrocytes and PAMs exhibited a diminished rate of change in fluorescence intensity under the blocked condition. Through transmission electron microscopy, it was observed that PAMs effectively removed sensitized GFP-E. coli adhering immunologically to porcine erythrocytes. The findings indicate that PAMs effectively removed sensitized GFP-E. coli from the surface immunoadhesion of porcine erythrocytes, facilitated by the mediation of surface CR1-like receptors and Fc receptors. creator: Yongqiang Liu creator: Nan Wang creator: Qing Ru creator: Kuohai Fan creator: Na Sun creator: Panpan Sun creator: Hongquan Li creator: Wei Yin uri: https://doi.org/10.7717/peerj.18934 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: The efficacy comparison on femoral vein hemodynamics and morphology between two types of graduated elastic compression stockings among patients undergoing knee replacement: a single center, double-blind, randomized trial link: https://peerj.com/articles/19070 last-modified: 2025-03-03 description: BackgroundVenous thromboembolism is a significant complication after knee replacement. The short-term efficacy disparities between different types of graduated elastic compression stockings (GCS) among patients undergoing total/unicompartmental knee replacement remain unclear.ObjectiveThe aim of the trial was to compare the efficacies on hemodynamics and morphology of femoral vein between two types of GCS, providing more evidence on GCS prophylaxis among patients undergoing total/unicompartmental knee replacement.MethodsIn this single center, double-blind, parallel design, randomized trial, 141 adult patients who underwent selective, unilateral total/unicompartmental knee replacement operation for the first time were enrolled, with 71 were assigned to type A GCS and 70 to type B GCS, respectively. Compressed ultrasound of the lower extremity was conducted before the operation (without GCS, as preoperative baseline) and within 24 hours post operation (postoperative baseline , with GCS, and with GCS + ankle pump). The relative changes in TV and PV, as well as the diameter of the femoral vein in the healthy leg, were assessed both before and after GCS application following the knee replacement surgery.ResultsThe median ages were 67.0 years in type A group and 68.0 years in type B group. All parameters of femoral vein were comparable between type A and type B GCSs. Compared with postoperative baseline, GCS + ankle pump significantly reduced femoral vein diameter and improved the TV in both GCS types; GCS and GCS + ankle pump also significantly increased the TV (median 1.2%, IQR −21.4% to 58.6%, P = 0.0384; median 14.0%, IQR −24.3% to 93.0%, P = 0.0019, respectively) in left leg, while not significant in right leg.ConclusionThe efficacies of two GCSs were comparable, and both were effective in improving velocity and morphology of femoral veins of the healthy legs among patients undergoing knee replacement, especially in improving TVs of femoral veins for left leg. creator: Yaping Xu creator: Ruping Liu creator: Feiya Xu creator: Yibo Feng creator: Shuang Li creator: Dingyi Wang creator: Guohui Fan uri: https://doi.org/10.7717/peerj.19070 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Xu et al. title: Effect of high glucose on the gene expression profiling in cardiac fibroblasts from rats at different ages link: https://peerj.com/articles/19040 last-modified: 2025-03-03 description: BackgroundCardiac fibroblasts (CFs) play a vital role in the physiological and pathological processes of the heart. Previous studies have demonstrated that high glucose stimulation induces the transformation of CFs into myofibroblasts, contributing to cardiac fibrogenesis. However, in vivo experiments have predominantly utilized adult animals, whereas most in vitro studies have focused on CFs derived from neonatal animals. The responses of CFs from different age groups to high glucose levels remain unclear. This study aimed to investigate transcriptional alterations in CFs at distinct developmental stages in response to high glucose exposure.MethodsCFs were isolated from neonatal (S1, 0–3 days), juvenile (S2, 3–4 weeks), adult (S3, 10–13 weeks), and aged (S4, 20 months) rats. CFs were exposed to normal (5.5 mM, NG) or high glucose (33 mM, HG). The cellular RNA was extracted for sequencing and analysis. Differentially expressed genes (DEGs) were validated by quantitative real-time PCR.ResultsAfter NG treatment, fibrosis and inflammation-related gene expression in CFs (e.g., Col8a1, Col8a2, IL-6, Ccl2, Ccl20, Mmp2 and Mmp9) increased with age, while proliferation-related genes (MCM family, Sox10, Sox11) decreased. HG treatment most affected S3-CFs, showing 228 DEGs; it suppressed growth-related genes (Adra1d, Htr2b) and enhanced inflammatory genes (IL-6, Olr1). In S1-CFs, 197 inflammation-rich genes were upregulated under HG. S4-CFs displayed 166 DEGs, mostly metabolic downregulation (G6pc). S2-CFs had the fewest DEGs (112), focusing on cell metabolism.ConclusionsFibrosis- and inflammation-associated gene expression in CFs showed an age-dependent stepwise elevation. CFs from distinct developmental stages responded differently to HG stimulation, with S3-CFs exhibiting the most pronounced response. These findings highlight the developmental characteristics of CFs and provide implications for the selection of appropriate CFs to investigate diabetes-associated cardiac fibrosis. creator: Quqian Mo creator: Angyu Zhan creator: Ruining Bai creator: Shaoling Lin creator: Jiaojiao Feng creator: Tongjun Li creator: Zijian Lao creator: Xiao Yang creator: Keke Wang creator: Xianglu Rong creator: Lexun Wang uri: https://doi.org/10.7717/peerj.19040 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Mo et al.