title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2025-01 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Fructose 1,6-bisphosphatase 1 is a potential biomarker affecting the malignant phenotype and aerobic glycolysis in glioblastoma link: https://peerj.com/articles/18926 last-modified: 2025-01-31 description: BackgroundFructose 1,6-bisphosphatase 1 (FBP1) has been considered as a potential prognostic biomarker in glioblastoma (GBM), and this study explored the underlying mechanism.MethodsThe expression and effect of FBP1 expression on the prognosis of GBM patients were examined applying bioinformatics analyses. After measuring the expression of FBP1 in normal glial cell line HEB and GBM cells, cell counting kit-8 (CCK-8), 5-ethynyl-2-deoxyuridine (EdU), colony formation, transwell, and wound healing assay were carried out to examine the effects of silencing FBP1 on the proliferation and invasion of GBM cells. Aerobic glycolysis was measured by calculating the extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) of FBP1-silenced GBM cells. Furthermore, the protein levels of the mediators related to PI3K/AKT pathway and BCL2 protein family were detected via immunoblotting. Additionally, the effects of FBP1 silencing on the macrophage M2 polarization were assessed based on the fluorescence intensity of CD206 and the phosphorylation of STAT6 quantified by immunofluorescence and immunoblotting, respectively.ResultsHigh-expressed FBP1 was indicative of a worse prognosis of GBM. FBP1 knockdown in GBM cells suppressed the proliferation, invasion, migration, and aerobic glycolysis of GBM cells, lowered the phosphorylation levels of AKT and PI3K and the protein expression of BCL2 but promoted BAX protein expression. Moreover, FBP1 knockdown reduced CD206 fluorescence intensity and the phosphorylation of STAT6.ConclusionTo conclude, FBP1 could be considered as a biomarker that affected the malignant phenotypes and aerobic glycolysis in GBM, contributing to the diagnosis and treatment of GBM. creator: Weihong Lu creator: Guozheng Huang creator: Yihan Yu creator: Xia Zhai creator: Xiangfeng Zhou uri: https://doi.org/10.7717/peerj.18926 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lu et al. title: Optimizing in vitro fertilization in four Caribbean coral species link: https://peerj.com/articles/18918 last-modified: 2025-01-31 description: BackgroundLarval propagation and seeding of scleractinian corals for restoration is a rapidly expanding field, with demonstrated applications to assist the recovery of declining populations on reefs. The process typically involves collecting coral reproductive material, facilitating in vitro fertilization (IVF), and settling and outplanting the resulting coral offspring. Optimizing IVF can reduce gamete wastage and increase larval yields for propagation, therefore improving the efficiency of this intervention.MethodsIn this study we tested three IVF conditions in four Caribbean broadcast-spawning coral species (i.e., Diploria labyrinthiformis, Colpophyllia natans, Pseudodiploria strigosa, Orbicella faveolata) to determine sperm concentration, gamete age, and co-incubation time resulting in the highest fertilization success. For each species, we exposed eggs from a single dam to pooled sperm samples from three sires (1) at concentrations ranging from zero to 109 cell mL−1, (2) after letting gametes age for 2 to 6 h, and (3) for a period of 15 to 120 min.ResultsThese experiments revealed a gamete longevity of at least 4 h and clear minimum sperm concentration thresholds (>105 to 106 cell mL−1) in all four species. Fertilization took place much faster than expected (≤15 min) in the three brain corals under study, whereas O. faveolata gametes required a co-incubation period of 60 to 120 min to achieve maximum IVF success.DiscussionWe present these results in the context of IVF data available for other hermaphroditic broadcast-spawning scleractinians. We then provide recommendations for coral breeding practitioners to maximize larval production from gamete collections, and finally, we discuss our findings’ potential implications on fertilization dynamics during natural coral spawning events. creator: Valérie F. Chamberland creator: Matthew-James Bennett creator: Tania Doblado Speck creator: Kelly R. W. Latijnhouwers creator: Margaret W. Miller uri: https://doi.org/10.7717/peerj.18918 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Chamberland et al. title: Integrated analysis of ATAC-seq and RNA-seq reveals ADSCP2 regulates oxidative phosphorylation pathway in hypertrophic scar fibroblasts link: https://peerj.com/articles/18902 last-modified: 2025-01-31 description: The primary effector cells involved in the formation of hypertrophic scars are fibroblasts. A potential peptide, ADSCP2 (adipose-derived stem cell peptide 2, the peptide fragment of ALCAM protein), derived from adipose-derived stem cell-conditioned medium, has been identified as having the potential to mitigate hypertrophic scar formation by targeting pyruvate carboxylase. However, the underlying mechanisms remain incompletely understood. Whether ADSCP2 attenuates hypertrophic scar fibrosis at the transcription level remains unclear. Consequently, this study sought to elucidate the potential mechanism associated with ADSCP2 by examining genome-wide transcriptional alterations and changes in chromatin accessibility in fibroblasts. This was achieved through the integrated analysis of assay for transposase accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq). In the ADSCP2 treatment group, ATAC-seq identified a total of 7,805 differential peaks associated with 3,176 genes. RNA-seq analysis revealed 345 upregulated and 399 downregulated transcripts in the same group. A combined Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of both downregulated genes and close-ACRs (accessible chromatin regions) genes within the ADSCP2 treatment group indicated regulation of the oxidative phosphorylation pathway (OXPHOS) by ADSCP2. The amalgamation of ATAC-seq and RNA-seq data elucidates that two OXPHOS associated genes, namely COX6B1 (cytochrome c oxidase subunit 6B1) and NDUFA1 (NADH dehydrogenase (ubiquinone) alpha subcomplex-1), demonstrate significant downregulation in the presence of ADSCP2. Further analysis using the integrative genomics viewer indicates that the promoter regions of both COX6B1 and NDUFA1 exhibit a higher degree of closure in the ADSCP2 treatment group. Quantitative PCR analysis demonstrated that ADSCP2 treatment resulted in a reduction of COX6B1 and NDUFA1 mRNA expression levels. Furthermore, cellular ATP and lactic acid concentrations were diminished in the ADSCP2-treated group. Collectively, these findings suggest potential avenues for future research into the therapeutic application of the peptide ADSCP2 in the treatment of hypertrophic scars. creator: Qian Li creator: Zhe Quan creator: Ling Chen creator: Yiliang Yin creator: Xin Chen creator: Jingyun Li uri: https://doi.org/10.7717/peerj.18902 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: The influence of gender stereotypes on gender judgement and impression evaluation based on face and voice link: https://peerj.com/articles/18900 last-modified: 2025-01-31 description: The present study examined the influence of gender stereotype information on cognitive judgments and impression evaluations of faces and voices. A 2 × 2 × 2 design was employed, with Perceptual Target (Face vs. Voice), Gender Stereotype Information (Consistent vs. Inconsistent) and Gender of Perceptual Targets (Male and Female) serving as within-subject factors. The results demonstrated that when gender stereotype information was consistent with the perceptual target’s gender, response times for face gender judgments were shorter than for voice gender judgments. Nevertheless, the accuracy of gender judgments was higher for voices than faces. Furthermore, likability ratings for targets were significantly higher when gender stereotype information was consistent with the target than when it was inconsistent, for both face and voice judgments. These findings indicate that visual and auditory cues are processed differently in the context of gender judgments, thereby highlighting the distinct roles of facial and vocal information in gender perception. The current study contributes to understanding the complex interplay between gender stereotypes and multimodal social information processing. creator: Jingyu Li creator: Chunye Fu creator: Yunrui Sun uri: https://doi.org/10.7717/peerj.18900 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: Investigation of geographic disparities and temporal changes of non-gestational diabetes-related emergency department visits in Florida: a retrospective ecological study link: https://peerj.com/articles/18897 last-modified: 2025-01-31 description: BackgroundRates of diabetes-related Emergency Department (ED) visits in Florida increased by 54% between 2011 and 2016. However, little information is available on geographic disparities of ED visit rates and how these disparities changed over time in Florida and yet this information is important for guiding resource allocation for diabetes control programs. Therefore, the objectives of this study were to (a) investigate geographic disparities and temporal changes in non-gestational diabetes-related ED visit rates in Florida and (b) identify predictors of geographic disparities in non-gestational diabetes-related ED visit rates.MethodsThe ED data for the period between 2016 and 2019 were obtained from the Florida Agency for Healthcare Administration. Records of non-gestational diabetes-related ED visits were extracted using the International Classification of Diseases (ICD)-10 codes. Monthly non-gestational diabetes-related ED visit rates were computed and temporal changes were investigated using the Cochran-Armitage trend test. County-level non-gestational diabetes-related ED visit rates per 100,000 person-years were calculated and their geographic distributions were visualized using choropleth maps. Clusters of counties with high non-gestational diabetes-related ED visit rates were identified using Kulldorff’s circular and Tango’s flexible spatial scan statistics. Predictors of non-gestational diabetes-related ED visit rates were investigated using negative binomial model. The geographic distributions of significant (p ≤ 0.05) high-rate clusters and predictors of ED visit rates were displayed on maps.ResultsThere was a significant (p < 0.001) increase in non-gestational diabetes-related ED visit rates from 266 visits per 100,000 person-months in January 2016 to 332 visits per 100,000 person-months in December 2019. Clusters of high non-gestational diabetes-related ED visit rates were identified in the northern and south-central parts of Florida. Counties with high percentages of non-Hispanic Black, current smokers, uninsured, and populations with diabetes had significantly higher non-gestational diabetes-related ED visit rates, while counties with high percentages of married populations had significantly lower ED visit rates.ConclusionsThe study findings confirm geographic disparities of non-gestational diabetes-related ED visit rates in Florida with high-rate areas observed in the rural northern and south-central parts of the state. Specific attention is required to address disparities in counties with high diabetes prevalence, high percentages of non-Hispanic Black, and uninsured populations. These findings are useful for guiding public health efforts geared at reducing disparities and improving diabetes outcomes in Florida. creator: Md Marufuzzaman Khan creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.18897 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Khan and Odoi title: A systematic review and meta-analysis of randomized controlled trials for physical activity among colorectal cancer survivors: directions for future research link: https://peerj.com/articles/18892 last-modified: 2025-01-31 description: BackgroundPhysical activity (PA) is critically important to cancer rehabilitation. However, PA levels are generally lower in colorectal cancer (CRC) survivors compared to other cancer survivors. The purpose of this study was to examine the effectiveness of PA interventions in increasing PA levels and to provide recommendations for developing PA interventions in CRC survivors.MethodsA systematic literature search was conducted in Cochrane Library, Embase, PubMed, Scopus, Web of Science, China National Knowledge Infrastructure, and Wan Fang Data from January 2010 to March 1, 2024. The Physiotherapy Evidence Database (PEDro) scale was used to assess the methodological quality of eligible studies, and the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) method was used to evaluate the certainty of evidence. The random-effects model was used in meta-analysis, and data were analyzed using standardized mean differences and 95% confidence intervals.ResultsA total of 22 studies were included in this review, all of which were rated as having good methodological quality based on the PEDro scale. In the meta-analysis, nine of these studies involving 684 participants were included, and results showed that PA interventions have a positive effect on increasing total PA levels in CRC survivors (Z = 2.79, p = 0.005). Results of subgroup analysis revealed that supervised PA interventions (Z = 2.82, p = 0.005) and PA interventions with multiple intervention components (Z = 3.06, p = 0.002) effectively increased total PA levels for CRC survivors. In addition, research evidence suggests that daily as the frequency (Z = 4.28, p < 0.001), Moderate-to-vigorous physical activity (MVPA) as the intensity (Z = 2.29, p = 0.022), aerobic combined with resistance exercise as the type of PA (Z = 4.19, p < 0.001) is appropriate for increasing total PA levels in CRC survivors.ConclusionsThe findings of this review provide strong evidence supporting the positive role of PA interventions in improving total PA levels among CRC survivors. This study offers preliminary insights into the appropriate patterns of PA interventions (e.g., frequency, intensity, type) for enhancing total PA levels in CRC survivors. However, further high-quality clinical trials are needed to determine the optimal timing, duration, and delivery methods of PA interventions to maximize their effectiveness in this population. creator: Jiayu Mao creator: Xiaoke Qiu creator: Yi Zhang creator: Can Wang creator: Xueli Yang creator: Qiuping Li uri: https://doi.org/10.7717/peerj.18892 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mao et al. title: Effect of exercise intervention on health-related quality of life in middle-aged and older people with osteoporosis: a systematic review and meta-analysis link: https://peerj.com/articles/18889 last-modified: 2025-01-31 description: BackgroundOsteoporosis is a common condition affecting middle-aged and older people, posing a serious threat to their health-related quality of life (HRQOL). In recent years, multiple studies have investigated the impact of exercise interventions on HRQOL in middle-aged and older individuals with osteoporosis, but the conclusions have been inconsistent. The aim of this study was to determine the true significance of exercise interventions on HRQOL in middle-aged and older individuals with osteoporosis and to identify optimal exercise prescriptions.MethodsSix databases were searched for RCTs on the impact of exercise interventions on HRQOL in middle-aged and older individuals with osteoporosis. The methodological quality of the study was evaluated with Cochrane risk assessment tool. The effect size pooling, heterogeneity testing, and publication bias were analyzed using Review Manager 5.4 software.ResultA total of 14 RCTs involving 1,214 participants were included, published between 2007 and 2022. The pooled results demonstrated that exercise interventions significantly improved general HRQOL (SMD = 0.79, 95% CI [0.34–1.24], p = 0.0006). In terms of physical HRQOL, significant improvements were observed in bodily pain (SMD = 0.51, 95% CI [0.24–0.78], p= 0.0002), physical function (SMD = 0.56, 95% CI [0.21–0.91], p = 0.002), role physical (SMD = 0.39, 95% CI [0.14–0.64], p = 0.003), and general health (SMD = 0.68, 95% CI [0.25–1.11], p = 0.002). Regarding mental HRQOL, significant improvements were found in vitality (SMD = 0.58, 95% CI [0.15–1.01], p = 0.008), social function (SMD = 0.37, 95% CI [0.17–0.58], p = 0.0004), and mental health (SMD = 0.50, 95% CI [0.25–0.74], p < 0.0001). Subgroup analysis results indicated that resistance training (SMD = 1.01, 95% CI [0.50–1.52], p = 0.0001), intervention frequency of at least three times per week (SMD = 0.80, 95% CI [0.22–1.38], p = 0.007), and intervention duration of 13–24 weeks (SMD = 0.85, 95% CI [0.37–1.33], p = 0.0005) had large and significant effects on general HRQOL improvements.ConclusionExercise interventions improved HRQOL in middle-aged and older individuals with osteoporosis. Resistance training has shown greater benefits than mixed exercises. The optimal frequency is at least three per week, yielding the greatest improvement. Exercise interventions lasting 13–24 weeks had the most pronounced effect compared to other durations.RegistrationPROSPERO (No. CRD42023438771). creator: Di Geng creator: Xiaogang Li creator: Yan Shi uri: https://doi.org/10.7717/peerj.18889 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Geng et al. title: Bidirectional association between breast cancer and dementia: a systematic review and meta-analysis of observational studies link: https://peerj.com/articles/18888 last-modified: 2025-01-31 description: BackgroundCognitive decline following cancer treatment can vary from mild cognitive impairment to severe dementia. However, there is inconsistent evidence regarding the relationship between breast cancer survivors and their risk of developing dementia. This meta-analysis aims to consolidate observational studies to explore the bidirectional association between breast cancer and dementia risk.MethodsWe conducted a comprehensive search using medical subject headings (MeSH) and keywords across PubMed, Cochrane Library, and Embase databases to identify cohort, case-control, and cross-sectional studies examining the link between breast cancer and dementia risk. Statistical analysis was performed using Stata version 14.0, with a random effects model employed to account for heterogeneity. Publication bias was assessed using funnel plots and Egger’s test.ResultsThis meta-analysis included 13 studies with a total of 346,051 participants, up to June 20, 2024. Of these, seven studies investigated the risk of dementia among patients with breast cancer, revealing a lower risk [OR = 0.56, 95% CI [0.27–1.18], I2 = 99.1%, P = 0.128]. Similarly, seven studies explored the risk of breast cancer in individuals with dementia, showing a lower risk as well [OR = 0.79, 95% CI [0.51–1.22], I2 = 94.5%, P = 0.290].ConclusionOur findings indicate that breast cancer is less likely to lead to dementia and that dementia is similarly low associated with risk of breast cancer. These insights are crucial for clinicians in guiding the prevention and monitoring of neurodegenerative conditions in patients with breast cancer. creator: Fuxing Bao creator: Liang Yu creator: Xiaolei Zhang creator: Qier Mu uri: https://doi.org/10.7717/peerj.18888 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bao et al. title: Associations of PM2.5 and its components with term preterm rupture of membranes: a retrospective study link: https://peerj.com/articles/18886 last-modified: 2025-01-31 description: BackgroundThere is evidence that fine particulate matter (PM2.5) exposure is associated with premature rupture of membranes (PROM); however, studies of its effect on term PROM (TPROM) are limited, and the results are inconsistent.ObjectiveThis study aimed to investigate the association between exposure to PM2.5 and its components and the risk of TPROM.MethodsFrom 2018 to 2022, we collected delivery data from pregnant women in Guangzhou. Using 1:1 case matching, we included 1,216 TPROM cases and 1,216 controls. PM2.5 and its component concentrations were obtained from Tracking Air Pollution in China. The time-varying mean concentration method was used to estimate exposure to PM2.5 and its components during different trimesters. Cox proportional hazards models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) to evaluate the associations of exposure to PM2.5 and its components with the risk of TPROM.ResultsThe incidence of TPROM in this study was 19.66%. After adjusting for potential confounders, statistically significant associations were found between TPROM and exposure to PM2.5, nitrate (${\mathrm{NO}}_{3}^{-}$NO3−), ammonium (${\mathrm{NH}}_{4}^{+}$NH4+), and black carbon (BC) during the second trimester and between TPROM and exposure to PM2.5, sulphate (${\mathrm{SO}}_{4}^{2-}$SO42−), and BC during the third trimester. Specifically, the interquartile range (IQR) 3 (IQR3) and IQR4 of ${\mathrm{SO}}_{4}^{2-}$SO42− exposure during the third trimester increased the risk of TPROM by 18% (95% CIs [1.01–1.39]) and 18% (95% CIs [1.01–1.39]), respectively. A nonlinear relationship was observed between exposure to PM2.5, ${\mathrm{SO}}_{4}^{2-}$SO42−, ${\mathrm{NH}}_{4}^{+}$NH4+, and OM during the second trimester and the risk of TPROM. No significant interactions were found between PM2.5 and its components with TPROM across various subgroups.ConclusionOur findings indicate significant associations between the risk of TPROM and exposure to PM2.5 and several of its components during pregnancy. Contribute to the literature on the associations of PM2.5 and its components with TPROM. creator: Jiangxia Qin creator: Weiling Liu creator: Haidong Zou creator: Chong Zeng creator: Cifeng Gao creator: Weiqi Liu uri: https://doi.org/10.7717/peerj.18886 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Qin et al. title: Nutrient cycling characteristics along a chronosequence of forest primary succession in the Hailuogou Glacier retreat area, eastern Tibetan Plateau link: https://peerj.com/articles/18867 last-modified: 2025-01-31 description: BackgroundThe Hailuogou Glacier has been continuously retreating since the end of the Little Ice Age, resulting in a 125-year soil chronosequence and a complete primary forest succession sequence. Nutrient cycling and utilization are the foundation to forest succession processes and dynamic changes, directly influencing the structure and stability of ecosystems. However, our understandings on the characteristics of ecosystem nutrient accumulation and recycling during succession, especially in the context of primary succession within glacier retreat areas, remain limited. To address this, we investigated nutrient characteristics across six forest primary succession sites in the Hailuogou Glacier retreat area.MethodsSix sites representing three forest stages: the pioneer plant stage (S1), the broad-leaved forest stage (S2–S4), and the coniferous forest stage (S5–S6). Three quadrats were established at each site, and measurements of biomass as well as soil characteristics were documented within each quadrat. Subsequently, we collected samples of vegetation, soil and litter. By measuring the concentrations of N, P, K, Ca, and Mg in vegetation and soil and combining with the data of the quadrat survey, the pools and nutrient characteristics of N, P, K, Ca, and Mg in various components of the ecosystem were calculated at each site.ResultsOur findings indicated that: (1) Nutrient pools, excluding the soil C layer, increased with forest primary succession, reaching 5,995.71 kg hm−2 N, 461.83 kg hm−2 P, 3,798.09 kg hm−2 K, 7,559.81 kg hm−2 Ca and 1,948.13 kg hm−2 Mg at site S6; however, the pools of P, K, and Mg in the Oa layer, and Ca and Mg in the tree layer, attained their peak levels at sites S3 to S4. (2) The pools of N, Ca, and Mg in the organic soil were significantly greater than vegetation. Although over 60% of the P and K were stored in the organic soil at site S1, these proportions shifted, with vegetation holding 60.71% of P and 56.86% of K at site S5. (3) Broad-leaved forests exhibited higher nutrient return, cycling, and absorption, thereby accelerating nutrient circulation and depleting soil nutrients to maintain growth. In contrast, coniferous forests were more efficient at nutrient utilization and storage, retaining nutrients and maintaining high biomass and productivity in nutrient-poor environments. Overall, these findings highlighted that the nutrients in each component of the ecosystem continue to accumulate with forest primary succession. Coniferous forests’ nutrient cycling mechanisms offer a competitive edge in nutrient-poor environments, enhancing ecosystem stability. creator: Danli Yang creator: Ji Luo creator: Shumiao Shu creator: Yan Hu creator: Hongsong Tang creator: Xuemei Li uri: https://doi.org/10.7717/peerj.18867 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yang et al. title: A narrative review on the role of cognition, nutrition and energy availability in athletes of competitive sports to combat RED-S link: https://peerj.com/articles/18849 last-modified: 2025-01-31 description: BackgroundIn the present scenario, competitive sports require athletes to achieve a phenomenal balance between cognitive abilities, motor skills, nutritional intake, and energy deficiencies. Such stability would enable the athletes to excel in their sporting field. Evidence shows that athletes develop specific cognitive abilities based on their sporting field. Nutrition is vital in creating an athlete’s cognitive ability and physical needs required to participate in competitive sports. The reduction in the intake of nutrients required before, after and during sports participation could result in relative energy deficiency in sports (RED-S), affecting the parts of the body.MethodsThe rationale behind the survey is to understand the role of nutrition and energy deficiency on the athletes’ cognitive abilities. The review’s research areas were identified as athletes’ cognition and nutrition in the context of RED-S. Search keywords were found based on the research area, such as “cognitive”, “nutrition”, and “energy deficiency/availability” in athletes. The search keywords were combined to form search queries (SQs). SQs were used to carry out the search on the Web of Science and Scopus databases.ResultsSports play an important role in athletes’ cognitive abilities, such as decision-making, attention, memory, etc. Nutritional intakes, such as caffeinated, carbohydrate, alkaline, and protein-based supplements and diets, also significantly affect athletes’ cognitive and motor abilities. Low energy availability (LEA) causes cognitive and physical health problems in both female and male athletes.ConclusionThe review identified that nutrition and LEA play crucial roles in athletes’ cognitive performance. Deficits in nutritional intake and energy availability lead to RED-S. Hence, cognitive performance could be used as an early indication to identify the nutritional and energy deficits in advance, enabling athletes to combat RED-S. creator: Subalatha M. creator: Dhanush Rachaveti creator: Amutha S. creator: Ponpandi M. uri: https://doi.org/10.7717/peerj.18849 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 M et al. title: Relationships among COVID-19 causal factors perceived by children, basic psychological needs and social anxiety link: https://peerj.com/articles/18828 last-modified: 2025-01-31 description: BackgroundThe pandemic caused by COVID-19 had a great impact on our society as the lives of children have been affected, as well as their psychological health and social anxiety.ObjectiveTo examine whether COVID-19 causal factors perceived by children predicted basic psychological needs and social anxiety, and if basic psychological needs predicted social anxiety.MethodsA sample of 58 schoolchildren (Mage = 10.18; SD = 0.77; 36 boys, 22 girls) participated in the study and completed a series of self-report measures. The relationship between the study variables was examined using partial least square path modelling (PLS-PM).ResultsSocial distancing and protection were found to significantly reduce competence satisfaction. Perceived psychological impact significantly negatively predicted relatedness satisfaction and significantly positively autonomy frustration and competence frustration. Perceived psychological impact significantly negatively predicted anxiety in the interaction with the opposite sex. Autonomy satisfaction significantly positively predicted anxiety in the interaction with the opposite sex. Autonomy frustration significantly positively predicted anxiety in public speaking interaction with teachers, significantly positively anxiety in the interaction with the opposite sex, significantly positively anxiety of being embarrassed or ridiculed and significantly positively anxiety in the interaction with strangers.ConclusionPerceived psychological impact was the causal factor that revealed a higher impact on basic psychological needs. As such, it is important to take measures with children in pandemic situations to minimize this variable. On the other hand, Autonomy frustration revealed a higher impact on social anxiety. Thus, it is necessary to emphasize autonomy in children respecting the restrictions imposed to minimize the impact of social anxiety. creator: Higinio González-García creator: Leandro Álvarez-Kurogi creator: Joel Prieto Andreu creator: Javier Tierno Cordón creator: Rosario Castro López creator: Jesús Salas Sánchez uri: https://doi.org/10.7717/peerj.18828 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 González-García et al. title: Effects of drought stress and Morchella inoculation on the physicochemical properties, enzymatic activities, and bacterial community of Poa pratensis L. rhizosphere soil link: https://peerj.com/articles/18793 last-modified: 2025-01-31 description: BackgroundSoil microorganisms are crucial for plant growth, and both plants and their associated rhizosphere microbes are impacted by changes in soil moisture. Inoculation with beneficial fungi can improve bacterial community structure and soil parameters.AimUnder drought stress conditions, the effects of inoculation with Morchella on the physicochemical properties, enzyme activity, and bacterial community structure of the rhizosphere soil of Poa pratensis were studied.MethodsHigh-throughput sequencing was employed to study rhizosphere soil bacterial communities in both Morchella-inoculated and uninoculated Poa pratensis rhizosphere soil subjected to moderate (50% soil moisture) and severe (30% soil moisture) drought stress, as well as under normal water conditions (70% soil moisture).ResultsMorchella inoculation significantly increased the alkaline nitrogen (AN) and available phosphorus (AP) contents, protease activity (PA), and alkaline phosphatase activity (APA) of Poa pratensis rhizosphere soil. Both Morchella inoculation and drought stress significantly altered the abundance and diversity of the P. pratensis rhizosphere community. The Chao1, Shannon, and Pielou diversity indices decreased with increasing drought stress. The effect of Morchella inoculation was improved under moderate drought stress and unstressed conditions. In addition, Morchella inoculation may help to stabilize the rhizosphere bacterial community under various levels of soil moisture. creator: Wei Yin creator: Le Wang creator: Qian Han Shang creator: Yi Xin Li creator: Wei Sa creator: Quan Min Dong creator: Jian Liang uri: https://doi.org/10.7717/peerj.18793 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Yin et al. title: Three new species of the spider genus Naphrys Edwards (Araneae, Salticidae) under morphology and molecular data with notes in the distribution of Naphrys acerba (Peckham & Peckham) from Mexico link: https://peerj.com/articles/18775 last-modified: 2025-01-31 description: Herein, we describe three new species of the spider genus Naphrys Edwards, 2003 from Mexico: Naphrys echerisp. nov., Naphrys tecoxquinsp. nov., and Naphrys tuucasp. nov. An integrative taxonomic approach was applied, utilizing data from morphology, ultra-morphology, the mitochondrial gene COI, and distribution records. Four molecular methods for species delimitation were implemented under the corrected p-distance Neighbor-Joining (NJ) criteria: (1) Assemble Species by Automatic Partitioning (ASAP); (2) general mixed Yule coalescent (GMYC); (3) Bayesian Poisson tree process (bPTP); and (4) multi-rate Poisson tree process (mPTP). Both morphological and molecular data supported the delimitation and recognition of the three new species. The average interspecific genetic distance (p-distance) within the genus Naphrys is 14%, while the intraspecific genetic distances (p-distance) is <2% for most species. We demonstrate that the natural distribution of Naphrys is not restricted to the Nearctic region. Furthermore, the reported localities herein represent the first with precise locations in the country for Naphrys acerba. In addition, a taxonomic identification key is provided for the species in the genus. creator: Juan Maldonado-Carrizales creator: Alejandro Valdez-Mondragón creator: María L. Jiménez-Jiménez creator: Javier Ponce-Saavedra uri: https://doi.org/10.7717/peerj.18775 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Maldonado-Carrizales et al. title: Harnessing the potential of chloroplast-derived expression elements for enhanced production of cellulases in Escherichia coli link: https://peerj.com/articles/18616 last-modified: 2025-01-31 description: Thermophilic cellulases can play a crucial part in the efficient breakdown of cellulose—a major component of lignocellulosic plant biomass, however, their commercial production needs simple and robust biomanufacturing biosystems. In this study, two cellulases (β-glucosidase and endoglucanase) were heterologously expressed in Escherichia coli under a chloroplast-derived constitutive promoter and expression-enhancing terminator. The genes encoding the cellulases were sourced from a thermophilic bacterium Thermotoga maritima to exploit their industrially needed thermotolerance potential. The codon-optimized gene sequences were synthesized and placed under a tobacco chloroplast 16S rRNA promoter (Prrn), along with the 5′ UTR (untranslated region) from gene 10 of phage T7 (T7g10). A six-residue long histidine tag (His6-tag) was attached to the N-terminus for protein detection. A high-level of expression of β-glucosidase and endoglucanase in E. coli was recorded from the chloroplast promoter and terminator. Furthermore, the activity assays confirmed that the recombinant enzymes maintained their activity at elevated temperatures. Thermostability analysis showed that recombinant enzymes retained their thermotolerance even after being expressed in a non-native host. Where, β-glucosidase and endoglucanase showed their optimum activities at 90 °C and 100 °C, respectively. Examination of the 3D structures of T. maritima cellulases revealed differential ionic interactions contributing to this high degree of thermotolerance. The study highlights the feasibility of producing thermostable versions of recombinant enzymes in E. coli at high levels. Our finding underscores the potential of this approach to meet industrial demands for efficient enzyme production employing E. coli as a robust biomanufacturing platform. creator: Ayesha Siddiqui creator: Muhammad Mudassar Iqbal creator: Asad Ali creator: Iqra Fatima creator: Hazrat Ali creator: Aamir Shehzad creator: Sameer H. Qari creator: Ghulam Raza creator: Muhammad Aamer Mehmood creator: Peter J. Nixon creator: Niaz Ahmad uri: https://doi.org/10.7717/peerj.18616 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Siddiqui et al. title: Life expectancy of cats in Britain: moggies and mollies live longer link: https://peerj.com/articles/18869 last-modified: 2025-01-30 description: The domestic cat (Felis catus) has been a popular companion animal for about 12,000 years, initially valued for rodent control before evolving into pets that provide affection and companionship. Unlike dogs, cats were not selectively bred for specific roles until the late 1800s, resulting in breeds defined primarily by appearance, which sometimes leads to genetic disorders. Modern animal welfare concerns emphasize longevity and health, prompting research into factors affecting cat lifespans, including sex, reproductive status, and breed. This study aims to expand on previous UK research by analyzing these interactions and highlighting the potential negative impacts of pure breeding on cat health. Data from 7,708 cats receiving veterinary care in the UK during 2019 were analyzed, focusing on reproductive status, breeding status, age at death, and sex. Data were analyzed using ANOVA and Cox proportional hazards models to assess survival differences. The overall mean lifespan of cats in the UK is 11.83 years. Analysis indicates that male cats live shorter lives than females, attributed to higher trauma rates and health issues among males. Neutered/spayed cats generally exhibit longer lifespans compared to entire cats. Tom cats have the shortest lifespan, while spayed females (mollies) live the longest. Moggies tend to outlive both pure and cross-bred cats, suggesting that genetic diversity may contribute to greater longevity. The results of this study emphasize the influence of sex, reproductive status, and cat type on feline lifespan, highlighting the need for targeted health interventions, particularly for male cats. The findings underscore the complex interplay of genetic and environmental factors in determining the health and longevity of domestic cats. This research not only contributes to existing knowledge but also advocates for the consideration of these variables in future studies and veterinary practices. creator: Fernando Mata uri: https://doi.org/10.7717/peerj.18869 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mata title: Prediction of influenza A virus-human protein-protein interactions using XGBoost with continuous and discontinuous amino acids information link: https://peerj.com/articles/18863 last-modified: 2025-01-30 description: Influenza A virus (IAV) has the characteristics of high infectivity and high pathogenicity, which makes IAV infection a serious public health threat. Identifying protein-protein interactions (PPIs) between IAV and human proteins is beneficial for understanding the mechanism of viral infection and designing antiviral drugs. In this article, we developed a sequence-based machine learning method for predicting PPI. First, we applied a new negative sample construction method to establish a high-quality IAV-human PPI dataset. Then we used conjoint triad (CT) and Moran autocorrelation (Moran) to encode biologically relevant features. The joint consideration utilizing the complementary information between contiguous and discontinuous amino acids provides a more comprehensive description of PPI information. After comparing different machine learning models, the eXtreme Gradient Boosting (XGBoost) model was determined as the final model for the prediction. The model achieved an accuracy of 96.89%, precision of 98.79%, recall of 94.85%, F1-score of 96.78%. Finally, we successfully identified 3,269 potential target proteins. Gene ontology (GO) and pathway analysis showed that these genes were highly associated with IAV infection. The analysis of the PPI network further revealed that the predicted proteins were classified as core proteins within the human protein interaction network. This study may encourage the identification of potential targets for the discovery of more effective anti-influenza drugs. The source codes and datasets are available at https://github.com/HVPPIlab/IVA-Human-PPI/. creator: Binghua Li creator: Xin Li creator: Xiaoyu Li creator: Li Wang creator: Jun Lu creator: Jia Wang uri: https://doi.org/10.7717/peerj.18863 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Serum salusin levels in diarrhea- and constipation-predominant irritable bowel syndrome link: https://peerj.com/articles/18859 last-modified: 2025-01-30 description: ObjectiveInflammation and immunity play major roles in the etiopathogenesis of functional intestinal disorders. The salusins that were identified in this study are important because of their ease of collection, sensitivity and reliability. For that reason, the aim of this study was to analyze the importance of the levels of salusin in the blood, an inflammation-related parameter, in the diagnosis and prediction of irritable bowel disease.MethodologyThe study participants included 28 diagnosed with constipation-predominant IBS, 29 (34.1%) diagnosed with diarrhea-predominant IBS (D-IBS), and 28 (32.9%) controls. Enzyme-linked immune-sorbent assay (ELISA) method has been used for the measurement of salusin levels.ResultsParticipants were 50 (58.8%) female and 35 (41.2%) male. The serum levels of salusin-α were substantially reduced in the diarrhea-predominant IBS group vs controls. There was also no major difference in the levels of salusin between the constipation-predominant-IBS and the diarrhea-predominant IBS group.ConclusionA major prognostic relationship was found between the level of salusins and the subgroup of D-IBS. It is well known that salusins have been related to inflammatory processes and oxidative injury in previous studies. The relationship between salusin and gastrointestinal diseases should be further investigated. Low-grade submucosal intestinal inflammation is also associated with irritable bowel syndrome. It is our belief that salusins may be useful in diagnosing, predicting or treating IBS. creator: Elif Tugba Tuncel creator: Seda Sabah Ozcan creator: Mehmet Korkmaz creator: Elif Börekci uri: https://doi.org/10.7717/peerj.18859 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Tuncel et al. title: Acidity, sugar, and alcohol contents during the fermentation of Osmanthus-flavored sweet rice wine and microbial community dynamics link: https://peerj.com/articles/18826 last-modified: 2025-01-30 description: Sweet rice wine is a popular traditional Chinese rice wine widely loved by Chinese people for its high nutritional value. Osmanthus flower petals contain various nutrients and have good medicinal value. However, the dynamics of the sugar level, acidity, alcohol content, and microbial community during the fermentation of Osmanthus-flavored sweet rice wine have not been evaluated, which can lead to the unstable quality of Osmanthus flower sweet rice wine (OFSRW). In this study, the dynamic changes in sugar level, acidity, alcohol content, microbial community composition, and microbial metabolic pathways during traditional fermentation of OFSRW at four-time points—0 h (AG0), 24 h (AG24), 36 h (AG36), and 43 h (AG43)—were analyzed via direct titration, total acid assays, alcoholometry, and high-throughput macrogenomic techniques. First, we found that bacteria were the dominant microorganisms in the early stage of OFSRW fermentation (AG0), fungi were the dominant microorganisms in the middle and late stages of fermentation (AG24 and AG36), and Rhizopus was the main fungal genus throughout fermentation. Acidity and total sugars increased with fermentation time, and alcohol was not detected until the end of fermentation. Diversity analysis revealed that the dominant species at the beginning of natural fermentation was A. johnsonii, and R. delemar became the dominant species as natural fermentation progressed. Metabolic pathway analysis revealed that energy production and conversion, carbohydrate transport, amino acid transport, and metabolic pathways were the most active metabolic pathways in the fermenter. These results provide a reference basis for changes in the microbial community during the fermentation of cinnamon-flavored sweet rice wine. creator: Ping Tian creator: Jiaqiong Wan creator: Tuo Yin creator: Li Liu creator: Hongbing Ren creator: Hanbing Cai creator: Xiaozhen Liu creator: Hanyao Zhang uri: https://doi.org/10.7717/peerj.18826 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tian et al. title: Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors link: https://peerj.com/articles/18807 last-modified: 2025-01-30 description: Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities. creator: Jacqueline G. Keleher creator: Taylor A. Strope creator: Noah E. Estrada creator: Allison M. Griggs Mathis creator: Cole G. Easson creator: Cara Fiore uri: https://doi.org/10.7717/peerj.18807 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Keleher et al. title: An analysis of the 24-hour on-call experience and treatment decision of a dental resident, a retrospective study link: https://peerj.com/articles/18678 last-modified: 2025-01-30 description: ObjectivesTo analyze the 24-hour on-call experience and factors influencing the treatment decisions of a dental resident for dental emergencies, particularly pulpitis, during on-call hours.MethodsThis retrospective study was conducted at a public stomatology hospital from January 1 to December 30, 2023. Each consultation was documented, recording the date and time, patient age and gender, diagnosis, and any emergent interventions. Statistical analyses were conducted using univariate analysis to explore the association between various factors and the incidence of dental interventions for pulpitis, with significance set at p < 0.05.ResultsOver 1 year, 81 residents from seven specialties managed 2,717 consultations during 365 instances of 24-h call duty. The busiest months were October (n = 297). Most consultations occurred during extended hours (1,856 consultations) compared to normal hours (8:00–17:00) (861 consultations). The busiest consultation periods were between 20:00 and 22:00. Pulpitis was the most frequently diagnosed condition (n = 988). Univariate analysis showed no significant impact of patient gender (p = 0.896) or age (p = 0.632) on the likelihood of receiving a dental intervention. However, consultations during extended hours were twice as likely (OR = 2.028, 95% CI [1.510–2.723]) to result in no intervention compared to normal hours. Endodontics and pediatric dentistry residents were more likely to perform interventions compared to other specialties, with postgraduate year (PGY) six residents being less likely to perform interventions compared to PGY4 residents.ConclusionResidents exhibit lower willingness to perform dental interventions during extended working hours and in higher grade levels, with significant variability across different specialties. Enhanced training and fatigue risk management for residents may help to ensure effective patient care during on-call hours. creator: Jiaoer Zheng creator: Ji Xu creator: Denghui Zhang uri: https://doi.org/10.7717/peerj.18678 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zheng et al. title: A new species of parrot snake, Leptophis (Serpentes: Colubridae) from the Brazilian Cerrado link: https://peerj.com/articles/18528 last-modified: 2025-01-30 description: We describe a new species of Leptophis (parrot snake) from the Cerrado ecoregion of Brazil. The new species, L. mystacinus sp. nov., differs from all other congeners in the following unique character combination: two Spectrum Green (129) to Light Parrot Green (133) dorsolateral stripes separated by a Buff (5) vertebral stripe, usually continuous onto the tail; loreal scale absent; postocular stripe Jet Black (300), wide and long (up 11 scales long onto nuchal region); maxillary teeth 21–25; ventrals 158–173; subcaudals 141–164; black spots on head absent; supracephalic plates of head not edged with black pigment; adult color pattern lacking dark oblique bands; keels absent on first dorsal scale rows; hemipenis unilobed, noncapitate, with undivided sulcus spermaticus, and first row of hemipenial body with four spines. Phylogenetic analysis of 16S mtDNA sequences indicate the new species is the sister taxon of L. dibernardoi, a species occurring in the neighboring Caatinga ecoregion. creator: Nelson R. Albuquerque creator: Roullien H. Martins creator: Priscila S. Carvalho creator: Donald B. Shepard creator: Diego J. Santana uri: https://doi.org/10.7717/peerj.18528 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Albuquerque et al. title: Biocontrol efficacy of Bacillus licheniformis and Bacillus amyloliquefaciens against rice pathogens link: https://peerj.com/articles/18920 last-modified: 2025-01-29 description: Biocontrol is a cost-effective and eco-friendly approach to control plant pathogens using natural enemies. Antagonistic microorganisms or their derivatives specifically target the plant pathogens while minimizing the harm to non-target organisms. Bacterial blight and brown spot are the major rice diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Bipolaris oryzae (Bo), respectively. This study was conducted to assess the plant growth-promoting potential and biocontrol activity of root-associated bacteria against the rice pathogens, Xoo and Bo. A total of 98 bacteria were isolated from rice roots and characterized for plant growth-promoting properties including phosphate solubilization, indole-3-acetic acid production, nitrogen fixation and biofilm formation. Based on these properties, 36 bacteria were selected and tested for biocontrol potential against rice pathogens via co-culturing antagonism assay. LE7 exhibited the maximum inhibition of 79%, while FR8, PE2, LE7, LR22 and LR28 also significantly reduced the growth of Xoo. Likewise, FR2, LR22, LR35 and LE7 significantly inhibited the growth of Bo, in which LR22 exhibited the maximum inhibition of 81%. Under controlled-conditions, LE7 and LR22 significantly reduced the disease incidence of Xoo and Bo, respectively, and improved the growth of rice. Full-length 16S rRNA gene sequencing of most potential bacterial isolates, LE7 and LR22, revealed their maximum identity with Bacillus amyloliquefaciens and Bacillus licheniformis, respectively. Application of Bacillus spp. as biocontrol agent represents enormous potential in rice farming. The most promising bacterial isolates could be used as bioinoculants for rice disease management and improved production in a sustainable manner. creator: Mohsin Tariq creator: Mehvish Zahoor creator: Tahira Yasmeen creator: Tahir Naqqash creator: Muhammad Abdul Rehman Rashid creator: Muhammad Abdullah creator: Abdul Rafay Rafiq creator: Marriam Zafar creator: Iqra Irfan creator: Ijaz Rasul uri: https://doi.org/10.7717/peerj.18920 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tariq et al. title: Phosphodiesterase 4 inhibition as a novel treatment for stroke link: https://peerj.com/articles/18905 last-modified: 2025-01-29 description: The incidence of stroke ranks third among the leading causes of mortality worldwide. It has the characteristics of high morbidity, high disability rate and high recurrence rate. The current risk associated with stroke surgery is exceedingly high. It may potentially outweigh the benefits and fail to ameliorate the cerebral tissue damage following ischemia. Therefore, pharmacological intervention assumes paramount importance. The use of thrombolytic drugs is most common in the treatment of stroke; however, its efficacy is limited due to its time-sensitive nature and propensity for increased bleeding. Over the past few years, the treatment of stroke has witnessed a surge in interest towards neuroprotective drugs that possess the potential to enhance neurological function. The PDE4D gene has been demonstrated to have a positive correlation with the risk of ischemic stroke. Additionally, the utilization of phosphodiesterase 4 inhibitors can enhance synaptic plasticity within the neural circuitry, regulate cellular metabolism, and prevent secondary brain injury caused by impaired blood flow. These mechanisms collectively facilitate the recovery of functional neurons, thereby serving as potential therapeutic interventions. Therefore, the comprehensive investigation of phosphodiesterase 4 as an innovative pharmacological target for stroke injury provides valuable insights into the development of therapeutic interventions in stroke treatment. This review is intended for, but not limited to, pharmacological researchers, drug target researchers, neurologists, neuromedical researchers, and behavioral scientists. creator: Jiahong Zhong creator: Xihui Yu creator: Zhuomiao Lin uri: https://doi.org/10.7717/peerj.18905 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhong et al. title: Leveraging machine learning to uncover multi-pathogen infection dynamics across co-distributed frog families link: https://peerj.com/articles/18901 last-modified: 2025-01-29 description: BackgroundAmphibians are experiencing substantial declines attributed to emerging pathogens. Efforts to understand what drives patterns of pathogen prevalence and differential responses among species are challenging because numerous factors related to the host, pathogen, and their shared environment can influence infection dynamics. Furthermore, sampling across broad taxonomic and geographic scales to evaluate these factors poses logistical challenges, and interpreting the roles of multiple potentially correlated variables is difficult with traditional statistical approaches. In this study, we leverage frozen tissues stored in natural history collections and machine learning techniques to characterize infection dynamics of three generalist pathogens known to cause mortality in frogs.MethodsWe selected 12 widespread and abundant focal taxa within three ecologically distinct, co-distributed host families (Bufonidae, Hylidae, and Ranidae) and sampled them across the eastern two-thirds of the United States of America. We screened and quantified infection loads via quantitative PCR for three major pathogens: the fungal pathogen Batrachochytrium dendrobatidis (Bd), double-stranded viruses in the lineage Ranavirus (Rv), and the alveolate parasite currently referred to as Amphibian Perkinsea (Pr). We then built balanced random forests (RF) models to predict infection status and intensity based on host taxonomy, age, sex, geography, and environmental variables and to assess relative variable importance across pathogens. Lastly, we used one-way analyses to determine directional relationships and significance of identified predictors.ResultsWe found approximately 20% of individuals were infected with at least one pathogen (231 single infections and 25 coinfections). The most prevalent pathogen across all taxonomic groups was Bd (16.9%; 95% CI [14.9–19%]), followed by Rv (4.38%; 95% CI [3.35–5.7%]) and Pr (1.06%; 95% CI [0.618–1.82%]). The highest prevalence and intensity were found in the family Ranidae, which represented 74.3% of all infections, including the majority of Rv infection points, and had significantly higher Bd intensities compared to Bufonidae and Hylidae. Host species and environmental variables related to temperature were key predictors identified in RF models, with differences in importance among pathogens and host families. For Bd and Rv, infected individuals were associated with higher latitudes and cooler, more stable temperatures, while Pr showed trends in the opposite direction. We found no significant differences between sexes, but juvenile frogs had higher Rv prevalence and Bd infection intensity compared to adults. Overall, our study highlights the use of machine learning techniques and a broad sampling strategy for identifying important factors related to infection in multi-host, multi-pathogen systems. creator: Daniele L. F. Wiley creator: Kadie N. Omlor creator: Ariadna S. Torres López creator: Celina M. Eberle creator: Anna E. Savage creator: Matthew S. Atkinson creator: Lisa N. Barrow uri: https://doi.org/10.7717/peerj.18901 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wiley et al. title: Dihydromyricetin inhibits injury caused by ischemic stroke through the lncRNA SNHG17/miR-452-3p/CXCR4 axis link: https://peerj.com/articles/18876 last-modified: 2025-01-29 description: Ischemic stroke (IS) is an important cause of death worldwide. Dihydromyricetin (DHM) has been reported to have neuroprotective potential, but its role and mechanism in IS have not been fully elucidated. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay was used to determine the safe dose of DHM in BV2 microglia and its applicability in OGD/R-treated cells. The mechanism of action of DHM was explored by RT-qPCR, ELISA, luciferase reporter gene assay and western blotting. DHM dose-dependently enhanced BV2 cell viability post-OGD/R and attenuated inflammation and oxidative stress. The protective effects of DHM were found to be mediated through the downregulation of SNHG17, which in turn modulated miR-452-3p expression. miR-452-3p was identified as a negative regulator of pro-inflammatory CXCR4, a direct target whose expression was inversely affected by SNHG17. The interaction between SNHG17 and miR-452-3p was further confirmed by RNA pull-down assays. Furthermore, manipulation of the SNHG17/miR-452-3p/CXCR4 axis was shown to modulate the NF-κB signaling pathway as evidenced by changes in phosphorylation levels. In conclusion, our findings elucidate a novel DHM-mediated neuroprotective mechanism in microglial cells involving the SNHG17/miR-452-3p/CXCR4 regulatory axis. This axis attenuates OGD/R-induced inflammatory and oxidative stress, suggesting a therapeutic potential for DHM in conditions characterized by such pathological processes. creator: Jiacheng Xie creator: Qiuyue Yang creator: Xueliang Zeng creator: Qi Zeng creator: Hai Xiao uri: https://doi.org/10.7717/peerj.18876 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al. title: A realistic human head phantom for electromagnetic detection of brain diseases link: https://peerj.com/articles/18868 last-modified: 2025-01-29 description: The research on electromagnetic detection technology for brain diseases requires precise simulation of the human head. This article combines high-precision computed tomography (CT) images and magnetic resonance imaging (MRI) images to establish an electromagnetic numerical model of the human head with a real anatomical structure. (1) It had Asian characteristics and encompassed 14 different structures, including skin, muscles, cranial bones, cerebrospinal fluid, cerebral veins, cerebral arteries, gray matter, white matter of the brain, basal ganglia, thalamus, cerebellum, brainstem, eyeballs, and vertebrae. (2) The model used a combination of 0.625 mm-resolution CT and 1 mm-resolution MRI image data for reconstruction, with a smooth surface and high accuracy. (3) Within the simulation environment, this model enabled the generation of various brain disease scenarios, such as different types and degrees of cerebral hemorrhage and cerebral ischemia. It proved valuable for studying the distribution of electromagnetic fields in the human head and for investigating novel electromagnetic detection techniques exploiting brain tissue dielectric properties. (4) The created physical model and the numerical model were derived from the same person, which provided a good continuity between simulation experiments and physical experiments, and provided a realistic verification platform for the research of electromagnetic detection technology for brain diseases, such as differentiating the kind of stroke, monitoring brain edema, brain tumor microwave imaging, and diagnosis of Alzheimer’s disease. creator: Zelin Bai creator: Diyou Chen creator: Ke Ma creator: Gui Jin creator: Jinlong Qiu creator: Quanquan Li creator: Haocheng Li creator: Mingsheng Chen uri: https://doi.org/10.7717/peerj.18868 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bai et al. title: Hematopoietic stem cell discovery: unveiling the historical and future perspective of colony-forming units assay link: https://peerj.com/articles/18854 last-modified: 2025-01-29 description: Stem cells are special cells with the distinctive capability to self-renew, forming a new pool of undifferentiated stem cells. They are also able to differentiate into lineage-specific cell types that are specialized and matured. Thus, stem cells are considered as the building blocks of tissues and organs in which they reside. Among the many types of stem cells, hematopoietic stem cells (HSCs) are the most studied adult stem cells and are considered as a promising source of cells for applications in the clinical and basic sciences. Historically, research on HSCs was initiated in the 1940s, where in a groundbreaking experiment, intravenously injected bone marrow (BM) cells prevented the death of irradiated mice by restoring blood cell production. Since then, HSCs have been studied and utilized in medical therapies and research for over several decades. Over time, more sophisticated tools have been developed to evaluate the behaviour of specifically purified subsets of hematopoietic cells that have the capacity to produce blood cells. One of the established tools is the colony-forming units (CFUs) assay. This assay facilitates the identification, enumeration, and analysis of colonies formed by differentiated hematopoietic stem and progenitor cells (HSPCs) from myeloid, erythroid and lymphoid lineages. Hence, the CFUs assay is a fundamental in vitro platform that allows functional studies on the lineage potential of an individual HSPCs. The outcomes of such studies are crucial in providing critical insights into hematopoiesis. In this review, we explore the fundamental discoveries concerning the CFUs assay by covering the following aspects: (i) the historical overview of the CFUs assay for the study of clonal hematopoiesis involving multilineage potential of HSPCs, (ii) its use in various experimental models comprising humans, mice/rodents, zebrafish and induced pluripotent stem cells (iPSCs) and (iii) research gaps and future direction concerning the role of CFUs assay in clinical and basic sciences. Overall, the CFUs assay confers a transformative platform for a better understanding of HSPCs biology in governing hematopoiesis. creator: Nur Afizah Yusoff creator: Zariyantey Abd Hamid creator: Siti Balkis Budin creator: Izatus Shima Taib uri: https://doi.org/10.7717/peerj.18854 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yusoff et al. title: Evaluating the feasibility of automating dataset retrieval for biodiversity monitoring link: https://peerj.com/articles/18853 last-modified: 2025-01-29 description: AimEffective management strategies for conserving biodiversity and mitigating the impacts of global change rely on access to comprehensive and up-to-date biodiversity data. However, manual search, retrieval, evaluation, and integration of this information into databases present a significant challenge to keeping pace with the rapid influx of large amounts of data, hindering its utility in contemporary decision-making processes. Automating these tasks through advanced algorithms holds immense potential to revolutionize biodiversity monitoring.InnovationIn this study, we investigate the potential for automating the retrieval and evaluation of biodiversity data from Dryad and Zenodo repositories. We have designed an evaluation system based on various criteria, including the type of data provided and its spatio-temporal range, and applied it to manually assess the relevance for biodiversity monitoring of datasets retrieved through an application programming interface (API). We evaluated a supervised classification to identify potentially relevant datasets and investigate the feasibility of automatically ranking the relevance. Additionally, we applied the same appraoch on a scientific literature source, using data from Semantic Scholar for reference. Our evaluation centers on the database utilized by a national biodiversity monitoring system in Quebec, Canada.Main conclusionsWe retrieved 89 (55%) relevant datasets for our database, showing the value of automated dataset search in repositories. Additionally, we find that scientific publication sources offer broader temporal coverage and can serve as conduits guiding researchers toward other valuable data sources. Our automated classification system showed moderate performance in detecting relevant datasets (with an F-score up to 0.68) and signs of overfitting, emphasizing the need for further refinement. A key challenge identified in our manual evaluation is the scarcity and uneven distribution of metadata in the texts, especially pertaining to spatial and temporal extents. Our evaluative framework, based on predefined criteria, can be adopted by automated algorithms for streamlined prioritization, and we make our manually evaluated data publicly available, serving as a benchmark for improving classification techniques. creator: Alexandre Fuster-Calvo creator: Sarah Valentin creator: William C. Tamayo creator: Dominique Gravel uri: https://doi.org/10.7717/peerj.18853 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Fuster-Calvo et al. title: Application of the flipped classroom model based on Bloom’s Taxonomy of Educational Objectives in endodontics education for undergraduate dental students link: https://peerj.com/articles/18843 last-modified: 2025-01-29 description: IntroductionThe current study was conducted to compare the effects of the lecture method of teaching and the flipped classroom model based on Bloom’s Taxonomy of Educational Objectives on the teaching of endodontics curriculum to undergraduate students majoring in stomatology, and to develop a standardized teaching process based on the flipped classroom model.Materials and MethodsA standardized flipped classroom model based on Bloom’s Taxonomy of Educational Objectives was established. Two groups of undergraduate students majoring in stomatology received instruction in a portion of the endodontics curriculum using either the lecture method or flipped classroom model of teaching. A teaching questionnaire was administered to evaluate the students’ mastery of theoretical knowledge, understanding of learning objectives, satisfaction of teaching method, and learning interest. The SPSS 26.0 software was used for statistical analysis, and the t-test was used to compare the differences between the two groups.ResultsBoth learning model cohorts filled out assessment questionnaires upon completion of the pilot curriculum. Compared with the responses from students in the lecture-based group, the self-rating of theoretical knowledge reported by students in the flipped classroom cohort increased by 10.9%, from 7.1 ± 0.8 to 7.9 ± 0.7 (t = 2.912, p < 0.006). Students’ test scores in the flipped classroom group increased by 17.1%, from 7.0 ± 0.8 to 8.2 ± 0.7 (t = 4.284, p < 0.001). Students’ understanding of ideological and humanistic objectives as well as medical ethics were both significantly improved by 11.4% (t = 2.267, p = 0.009) and 13.9% (t = 2.600, p = 0.014), respectively. Students’ satisfaction with the teaching model and class duration increased significantly, by 11.1% (t = 2.782, p = 0.009) and 14.3% (t = 2.449, p < 0.020), respectively. Students’ learning interest increased by 17.1% (t = 3.101, p = 0.004). The length of study time prior to class under the flipped classroom model was longer than when using the traditional lecture method (t = 3.165, p = 0.003), but the flipped classroom model shortened review time after class (t = 4.038, p = 0.001). Students’ self-reported understanding of teaching objectives improved by 8.3% (t = 1.762, p = 0.083), and satisfaction with the preview method and curriculum increased by 8.1% (t = 1.804, p = 0.081) and 11.1% (t = 1.861, p = 0.072), respectively. There was no statistically significant difference between the two groups.ConclusionsThe flipped classroom teaching model based on Bloom’s Taxonomy of Educational Objectives, combined with humanistic teaching objectives, can improve the efficacy of instruction, and merits popularizing and applying in the teaching of undergraduate students majoring in stomatology. creator: Yaru Wei creator: Zhengjun Peng uri: https://doi.org/10.7717/peerj.18843 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wei and Peng title: High speciation in the cryptic Pristimantis celator clade (Anura: Strabomantidae) of the Mira river basin, Ecuador-Colombia link: https://peerj.com/articles/18680 last-modified: 2025-01-29 description: Over the past decade, research in the montane forests of the Mira River basin, spanning Ecuador and Colombia, has identified it as crucial for the adaptive radiation of flora and fauna, shaped by its complex geological and climatic history. This study focuses on the phylogenetic and systematic revision of a frog clade initially labeled as Pristimantis verecundus, revealing significant cryptic diversity. Through detailed analyses of type material and expanded molecular sampling, we found that the original description actually included specimens representing two additional species, which are described herein. In this work, we discovered and formally described four new species within montane forests at elevations from 1,600 to 2,300 meters. Genetic distances of 3.34% to 14% and clear morphological differences underscore the clade’s hidden diversity. We propose renaming the group Pristimantis celator clade within Pristimantis myersi species group and subgenus Trachyphrynus, aligning with phylogenetic evidence and resolving taxonomic ambiguities using the oldest available name, Pristimantis celator (Lynch, 1976). This reclassification includes 14 species, seven formally described, and seven as candidates, distributed across northwestern Ecuador and southwestern Colombia, particularly in Mira and Esmeraldas River basins. The study highlights the Andean orogeny’s role in species diversification within Pristimantis celator clade, with geographic barriers like Cerro Golondrinas influencing genetic isolation. Genetic divergences exceeding 3.34% indicate evolutionary isolation across these landscapes. Our findings provide insights into montane ecosystem speciation, emphasizing vicariance, niche adaptation, and altitudinal gradients in shaping biodiversity. A polytomy among three well-supported clades within Pristimantis myersi species group is noted due to incomplete genetic data, yet distinctiveness and evolutionary relationships are affirmed. Cryptic diversity within Pristimantis celator clade links to unique orogenic and climatic conditions, highlighting conservation needs. Lastly, we provide a redescription of Pristimantis verecundus and species identification key to aid future research and conservation in this biogeographically influential region. creator: Mario H. Yánez-Muñoz creator: Juan P. Reyes-Puig creator: Carolina Reyes-Puig creator: Gabriela Lagla-Chimba creator: Christian Paucar-Veintimilla creator: Miguel A. Urgiles-Merchán creator: Julio C. Carrión-Olmedo uri: https://doi.org/10.7717/peerj.18680 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yánez-Muñoz et al. title: Age-related effects on dynamic postural stability and prefrontal cortex activation during precision fitting tasks link: https://peerj.com/articles/18548 last-modified: 2025-01-29 description: BackgroundDynamic postural control is impaired in older adults, as evidenced from worse dynamic postural stability compared to young adults during upright stance while concurrent goal-directed tasks. Prefrontal cortex (PFC) is considered to play an important role in goal-directed tasks. This study aimed to investigate the age effects on dynamic postural stability and PFC activation during precision fitting tasks.MethodsParticipant performed precision fitting tasks under four different conditions: large opening size with their arm’s length (close-large), small opening size with their arm’s length (close-small), large opening size with 1.3 times arm’s length (far-large), and small opening size with 1.3 times arm’s length (far-small). We analyzed the center of pressure-related outcomes representing dynamic postural stability and PFC activation at the six different subregions from healthy older adults (n = 15, 68.0 ± 3.5 years), and gender-matched middle-aged (n = 15, 48.73 ± 3.06 years) and young (n = 15, 19.47 ± 0.64 years) adults.ResultsThe dynamic postural stability presented the young > middle-aged > older groups across the conditions. Specifically, the young group presented better dynamic postural stability than the older group in the close-large, far-large, and far-small conditions (p < .05), while showed better dynamic postural stability than the middle-aged group in the close-large condition (p < .05). Additionally, the older group had greater PFC activation at all PFC subregions than the young group (p < .05), while had greater activation at left dorsolateral and ventrolateral PFC than the middle-aged group (p < .05). The middle-aged group presented greater activation at left dorsomedial PFC than the young group (p < .05).ConclusionHeightened dorsomedial PFC activation in middle-aged adults compared to young adults may reflect a deficit in processing the visuomotor information during the precision fitting tasks. Degeneration of the ability in automatic coordination of dynamic postural control may begin to occur at midlife. creator: Jiahao Pan creator: Hui Tang uri: https://doi.org/10.7717/peerj.18548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pan and Tang title: Different immunological characteristics of asymptomatic and symptomatic COVID-19 patients without vaccination in the acute and convalescence stages link: https://peerj.com/articles/18451 last-modified: 2025-01-29 description: The immune status of Coronavirus disease 2019 (COVID-19) patients in different stages of infection remains difficult to determine. In this study, we performed high-throughput single-cell mass cytometry on peripheral blood samples from 10 COVID-19 patients and four healthy donors to analyze their immune status at acute and convalescence phases. During the acute stage, the proportion of neutrophils increased significantly while natural killer (NK) cells decreased. In contrast, during the convalescence phase, the proportion of plasma cells decreased from the acute stage of disease onset and was lower than normal. The proportions of B, mast and plasma cell subsets decreased significantly with the process of disease recovery. Further analysis of the subsets of major immune cell types in COVID-19 patients with different clinical presentations in different stages showed that in the acute stages of disease progression, the T helper cell 1 (Th1), IgD+ B and neutrophil subsets increased in COVID-19 patients, especially in symptomatic patients, while the central memory CD4+T cells (CD4 TCM), mucosa-associated invariant T (MAIT) and NK cell subsets decreased significantly, especially in symptomatic patients. Then CD4 TCM and MAIT returned to normal levels at the recovery phase. Dynamic assessment displayed that the immune imbalance at the onset of COVID-19 could be corrected during recovery. Our study provides additional information on the immune status of COVID-19 patients with different clinical manifestations in different stages. These findings may provide new insights into COVID-19 immunotherapy and immune intervention. creator: Li Li creator: Xin Zhang creator: Huimin Yan creator: Muwei Dai creator: Huixia Gao creator: Yuling Wang creator: Ping Jiang creator: Erhei Dai uri: https://doi.org/10.7717/peerj.18451 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Li et al. title: In-vitro comparative thermo-chemical aging and penetration analyses of bioactive glass-based dental resin infiltrates link: https://peerj.com/articles/18831 last-modified: 2025-01-28 description: BackgroundTeeth with small to moderate cavities can be repaired with enamel resin infiltrants, a form of dental restorative material. In dental materials, it is standard practice to include several filler particles for experimental use in dental resin infiltrates. The resin’s BG particles penetrate the lesion and release ions that combine with saliva to provide a mineral-rich environment that can strengthen enamel and heal. This study aimed to compare resin infiltrants based on three types of bioactive glass materials and investigate the penetration depth, microleakage, and the effect of thermal and chemical aging.MethodologyA triethylene glycol dimethacrylate (TEGDMA) and urethane dimethacrylate (UDMA)-based experimental resin infiltrate was prepared. Initial mixing was done manually for 1 h at room temperature, followed by another mix for 30 min on a magnetic stirrer. This prepared resin, called “PURE RESIN” was then further incorporated with three different types of bioactive glasses, i.e., Bioglass (45S5), boron-substituted (B-BG), and fluoride-substituted (F-BG). Initial manual mixing for 1 h, followed by ultrasonic mixing for 3 min and then proceeded for the final mixing on a magnetic stirrer for 24 h in a dark room at ambient temperature. Human-extracted teeth were demineralized, and the experimental resins were infiltrated on the demineralized surface. The surface area, pore size, and volume of the demineralized surface were measured. The microleakage and penetration depth were analyzed with the stereomicroscope and micro-CT, respectively. The samples were challenged with the pH cycle for 14 days, followed by a scanning electron microscope (SEM). Thermocycling (5,000 cycles) and chemical aging (4 weeks) were conducted, followed by microhardness, surface roughness, and SEM analyses. Statistical analyses were conducted after each test.ResultsThe F-BG group achieved the highest initial and day 14 penetration coefficients. There was a superior dye penetration with the microleakage analysis in the F-BG group. The 45S5 group had the highest average penetration depth via micro-CT analysis. After thermocycling and chemical aging, the micro-hardness was reduced (non-significantly) among all samples except the F-BG group in post-chemical aging analysis, whereas the surface roughness was significantly increased. SEM images showed the presence of micro-pits on the surfaces after the thermal and chemical aging.ConclusionThe F-BG group achieved the highest initial and day 14 penetration coefficients. There was a superior dye penetration with the microleakage analysis in the F-BG group. The 45S5 group had the highest average penetration depth via micro-CT analysis. After thermocycling and chemical aging, the micro-hardness was reduced (non-significantly) among all samples except the F-BG group in post-chemical aging analysis, whereas the surface roughness was significantly increased. SEM images showed the presence of micro-pits on the surfaces after the thermal and chemical aging. creator: Syed Zubairuddin Ahmed creator: Abdul Samad Khan creator: Maram Alshehri creator: Fatimah Alsebaa creator: Fadak Almutawah creator: Moayad Mohammed Aljeshi creator: Asma Tufail Shah creator: Budi Aslinie Md Sabri creator: Sultan Akhtar creator: Mohamed Ibrahim Abu Hassan uri: https://doi.org/10.7717/peerj.18831 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ahmed et al. title: Clinical considerations on antimicrobial resistance potential of complex microbiological samples link: https://peerj.com/articles/18802 last-modified: 2025-01-28 description: Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample. creator: Norbert Solymosi creator: Adrienn Gréta Tóth creator: Sára Ágnes Nagy creator: István Csabai creator: Csongor Feczkó creator: Tamás Reibling creator: Tibor Németh uri: https://doi.org/10.7717/peerj.18802 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Solymosi et al. title: Correction factors for prey size estimation from PenguCams link: https://peerj.com/articles/18598 last-modified: 2025-01-28 description: The use of animal-borne cameras enables scientists to observe behaviours and interactions that have until now, gone unseen or rarely documented. Researchers can now analyse prey preferences and predator-prey interactions with a new level of detail. New technology allows researchers to analyse prey features before they are captured, adding a new dimension to existing prey analysis techniques, which have primarily relied on examining partially or fully digested prey through stomach flushing. To determine prey size, the video footage captured needs a correction factor (pixel:mm ratio) that allows researchers to measure prey dimensions using image measuring software and convert the pixels to actual measurements. This in turn will help estimating the prey energy content. This method requires a reference object with known dimensions (such as beak measurements) to ground truth your distance. Using PenguCams we determined the correction factor by measuring a 2 cm section of 1 mm grid paper from video footage taken at known distances (10, 20, 30, 40, 50, 60 cm) in different salinities ranging from air and fresh water, up to 35 psu in 5 psu increments while controlling for temperature and pressure. We found no significant difference between correction factors of water at different salinities. However, due to their considerable differences in refraction index, correction factors contrast between water and air. Linear equations modelled from correction factors at tested distances help predict correction factors between tested distances and, therefore, enable a wider application of this research. We provide examples from PenguCam footage taken of Humboldt (Spheniscus humboldti), Tawaki (Eudyptes pachyrhynchus) and King (Aptenodytes patagonicus) penguins to illustrate the use of identified correction factors. This study provides a tool for researchers to further enhance their understanding of predator-prey interactions. creator: Owen Dabkowski creator: Ursula Ellenberg creator: Thomas Mattern creator: Klemens Pütz creator: Pablo Garcia Borboroglu uri: https://doi.org/10.7717/peerj.18598 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dabkowski et al. title: Surgical outcomes in patients with Achilles tendon rupture—a retrospective study link: https://peerj.com/articles/18890 last-modified: 2025-01-27 description: BackgroundThere are two main methods used to treat Achilles tendon rupture (ATR): conservative treatment and surgical intervention. Surgical techniques are divided into three main categories: open surgical repair, mini-open surgical repair, and percutaneous repair (PR). We aimed to compare clinical outcomes in individuals with ATR who were treated with PR, primary repair, and flexor hallucis longus augmentation (FHL-A) with those treated with V-Y plasty and FHL-A.MethodsThe study involved 54 patients who underwent ATR surgical intervention retrospectively. Thirty-two of these were identified as acute and 22 were chronic rupture patients. PR was performed in 32 patients, primary repair and FHL-A in 14 patients, and V-Y plasty and FHL-A in eight patients.ResultsThe mean forward jump was 142.69 ± 7.14 cm in individuals who received PR, 137.71 ± 4.51 cm in those who received primary repair + FHL-A, and 123.88 ± 3.09 cm in those who received V-Y plasty + FHL-A (p < 0.001). The decrease in the mean vertical jump distance on the operated side compared to the contralateral extremity was 0.97 ± 0.93, 2.07 ± 0.99, and 3.00 ± 1.69 cm in individuals who underwent PR, primary repair + FHL-A, and V-Y plasty + FHL-A, respectively (p < 0.001). The decrease in the mean dorsiflexion of the operated side ankle compared to the contralateral extremity was found to be 4.34 ± 1.18, 1.93 ± 1.07, and 2.38 ± 0.92 degrees in individuals who underwent PR, primary repair + FHL-A, and V-Y plasty + FHL-A, respectively (p < 0.001).ConclusionAlthough no surgical technique is completely superior to another, better performance tests were observed after PR repair compared to open surgery in individuals involved in sports, but rerupture, dorsiflexion restriction, and painful ankle were disadvantages. FHL-A, which has gained popularity in recent years, showed better performance in tests by contributing to more stable and stronger ankles in sporting individuals with chronic ruptures who had undergone open surgery. FHL-A can be utilized in addition to primary surgical intervention in individuals with high performance expectations before and after injury. creator: Hüseyin Kürüm creator: Hacı Bayram Tosun creator: Faruk Aydemir creator: Orhan Ayas creator: Kübra Orhan Kürüm creator: Funda İpekten uri: https://doi.org/10.7717/peerj.18890 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kürüm et al. title: Safety profile of EZH2 inhibitors for cancer: a systematic review and meta-analysis link: https://peerj.com/articles/18871 last-modified: 2025-01-27 description: ObjectiveTo evaluate the safety profiles of EZH2-targeted inhibitors in cancer treatment, focusing on treatment-related adverse events (TRAEs) across various clinical trials.MethodsWe conducted a systematic review and meta-analysis using data from clinical trials involving EZH2 inhibitors reported up to May 31, 2024. Databases searched included PubMed, Embase, CENTRAL (Cochrane Central Register of Controlled Trials), and ClinicalTrials.gov. Studies included were those involving patients treated with EZH2 inhibitors as monotherapy or in combination, specifically detailing the incidence of TRAEs. Data on all-grade TRAEs, grade 3 or higher TRAEs, and severe TRAEs were extracted and analyzed using random-effects models.ResultsOur systematic review and meta-analysis included 22 studies encompassing 1,002 patients who met the inclusion criteria. TRAEs were commonly observed during EZH2 inhibitor therapy, affecting 86% of patients (95% CI [79–94%]%; I2 = 89.5%). The incidence of grade 3 or higher TRAEs was 33% (95% CI [21–44%]; I2 = 93.5%), while severe TRAEs occurred in 15% of the cases (95% CI [9–22%]; I2 = 87.5%). The most frequently reported grade 3 or higher TRAEs in the pooled analysis were neutropenia (8%), thrombocytopenia (8%), and anemia (6%). Specifically, for tazemetostat, the most common grade 3 or higher TRAE was neutropenia (5%). For SHR2554, the most prevalent grade 3 or higher TRAEs were thrombocytopenia (17%), neutropenia (8%), and anemia (7%). Notably, treatment-related fatalities were rare, with only 0.9% of patients experiencing potentially fatal outcomes due to therapy.ConclusionEZH2 inhibitors demonstrate a manageable safety profile with a low incidence of severe TRAEs, emphasizing their potential as safe therapeutic options in cancer treatment. The low rate of severe TRAEs and the rare occurrences of treatment-related deaths support the continued clinical use and further investigation of EZH2 inhibitors. creator: Zhou Zhao creator: Xiufeng Chen creator: Huayang Pang creator: Yan Shi creator: Hao Sun uri: https://doi.org/10.7717/peerj.18871 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zhao et al. title: Correlation of diabetes and adverse outcomes in hospitalized COVID-19 patients admitted to a tertiary hospital in China during a small-scale COVID-19 outbreak link: https://peerj.com/articles/18865 last-modified: 2025-01-27 description: BackgroundThe aim of this study was to investigate the impact of diabetes on mortality and adverse outcomes in COVID-19 patients and to analyse the associated risk factors.MethodsThis is a retrospective cohort study in 500 hospitalized patients with COVID-19 infection (214 with diabetes and 286 without diabetes) admitted to a tertiary hospital in China from December 2022 to February 2023. Demographic information, clinical characteristics and outcomes were collected. Survival status was investigated at discharge and at 6 months after discharge.ResultsThe mortality rate of COVID-19 patients with diabetes was higher than the rate of non-diabetic COVID-19 patients, both at discharge, and at 6 months after discharge. Body mass index (BMI), C-reactive protein (CRP), pH, D-dimer, blood osmotic pressure, serum creatinine, white blood cell count, creatine kinase and hospitalization expenses were significantly different between diabetic group and non-diabetic group (p < 0.05). Compared with the survivors, non-survived COVID-19 patients with diabetes had worse diabetes control indicators, with random blood glucose increased by 3.58 mmol/L (p < 0.05), and fasting blood glucose increased by 2.77 mmol/L (p < 0.01). In addition, there were significant differences in age, heart rate, CRP, pH, potassium (K+), serum creatinine, white blood cell count, creatine kinase, the proportion with diabetic complications, treatment in ICU and mechanical ventilation between survivors and non-survivors of COVID-19 patients with diabetes. By multivariate logistic regression analysis, the death of COVID-19 patients with diabetes is positively correlated with age and CRP (p < 0.05), and has a trend towards significance with fasting blood glucose (p < 0.1).ConclusionInfection with COVID-19 on the basis of diabetes can significantly increase mortality, which was further associated with diabetes control indicators. creator: Yu Li creator: Guanni Li creator: Jiahong Li creator: Zirui Luo creator: Yaxuan Lin creator: Ning Lan creator: Xiaodan Zhang uri: https://doi.org/10.7717/peerj.18865 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Clusters explaining the relation between menopause and self-reported periodontal disease: a cross-sectional study link: https://peerj.com/articles/18861 last-modified: 2025-01-27 description: BackgroundMenopause is an important milestone in the women’s life continuum and is associated with potentially adverse effects, including those related to oral health. This study assessed self-reported periodontal disease in relation to menopausal status.MethodsA cross-sectional study involving a convenience sample of female university dental hospital attendees was conducted using a validated, self-administered, self-reported periodontal disease questionnaire. A two-step cluster analysis was used to categorize the participants based on menstrual period (MP) continuity, systemic diseases and age. Differences between clusters were analyzed using chi-square test.ResultsFrom 112 included participants, three clusters resulted from the analysis: Cluster #1 (37 ± 8 years, no systemic diseases and continued MP), Cluster #2 (40 ± 10, with systemic diseases and continued MP) and Cluster #3 (54 ± 9, with systemic diseases and discontinued MP). Cluster #3 tended to have less optimal oral hygiene habits and more missing teeth (p > 0.05). Clusters #1 and #2 insignificantly reported more gingival bleeding, tooth sensitivity and calculus (p > 0.05). Cluster #3, on the other hand, presented with more self-reported oral dryness (p ≤ 0.05).ConclusionsWithin study limits, clusters of menopausal women with systemic diseases reported high symptoms of periodontal disease that were not significantly different from younger individuals, with the exception of oral dryness. creator: Hani T. Fadel creator: Lujain A. Qarah creator: Manal O. Alharbi creator: Alla Al-Sharif creator: Doaa S. Al-Harkan creator: Saba Kassim creator: Osama Abu-Hammad creator: Najla Dar-Odeh uri: https://doi.org/10.7717/peerj.18861 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Fadel et al. title: A novel ddPCR™ assay for eDNA detection and quantification of Greater Amberjack Seriola dumerilli and three congeners in US waters: challenges and application to fisheries independent surveys link: https://peerj.com/articles/18778 last-modified: 2025-01-27 description: BackgroundFour Seriola species support recreational and commercial fisheries along the U.S. Atlantic Ocean and the Gulf of Mexico, with the S. dumerili Gulf of Mexico stock being overfished for over three decades. The study presented here is part of a fisheries-independent project initiated to determine an absolute abundance of S. dumerili, to expand biological knowledge of the species and to develop novel tools for fisheries management. Environmental DNA (eDNA) tools aimed at the detection and quantification of target species are starting to emerge in support of marine fisheries surveys. Key to progressing the field is Droplet Digital™ PCR (ddPCR™), a highly sensitive technique with advanced multiplexing and direct quantification capabilities that can provide fisheries scientists with improved interpretation of eDNA data.MethodsWe developed and validated a novel tetraplex ddPCR™ assay able to detect and distinguish between S. dumerili, S. fasciata, S. rivoliana, and S. zonata from seawater eDNA samples. In order to groundtruth ddPCR™ data, and explore its capacity to provide abundance estimates, we compared ddPCR™ detections and quantifications to abundance data inferred from multiple camera (ROV, S-BRUV, chevron trap) and acoustic (VPS array) gears deployed during a fisheries research gear-calibration cruise.ResultsWe demonstrated that with eDNA contamination controls and best practice protocols, it is viable to conduct eDNA research as part of a fisheries survey cruise. eDNA sampling was completed in less time than camera gears (15 min vs 2 h). Both eDNA and camera gears detected the presence of S. dumerili and S. rivoliana at both sites and all sampling days, but not S. fasciata and S. zonata. eDNA concentration data was higher for S. dumerili than S. rivoliana at both sites for all sampling days, in line with abundance patterns obtained from camera gears. The highest correlation (r = 0.97) was obtained between the measures of eDNA between gear deployments and ROV.DiscussionIncorporating eDNA in fisheries surveys would not require additional days at sea and could improve precision in fish detection and abundance. eDNA can be a valuable complement to camera gears deployed in geographic areas or seasons with poor visibility conditions, where fish may be present but cannot be confidently identified to the species level. The high correlation obtained between ROV and eDNA data collected between gear deployments adds to a growing number of studies demonstrating the potential of eDNA as an indicator of abundance for fisheries stock assessments. Time-series data from a carefully designed eDNA survey, that estimates relative abundance, could be used as an index of relative abundance for the S. dumerili stock assessment. To achieve this, investment into follow-up studies with increased sample sizes and spatial and temporal replication would be necessary to allow for year-to-year comparisons and validate the robustness of the correlation observed. creator: P. Joana Dias creator: Ryan Lehman creator: Bryan L. Huerta-Beltrán creator: Ana Wheeler creator: Crystal L. Hightower creator: Jessica Heise creator: Theodore Switzer creator: Clint Rhode creator: J. Marcus Drymon creator: Lynne Stokes creator: Mark A. Albins creator: Sean Powers creator: Nicole Phillips uri: https://doi.org/10.7717/peerj.18778 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dias et al. title: Super Partition: fast, flexible, and interpretable large-scale data reduction in R link: https://peerj.com/articles/18580 last-modified: 2025-01-27 description: MotivationAs data sets increase in size and complexity with advancing technology, flexible and interpretable data reduction methods that quantify information preservation become increasingly important.ResultsSuper Partition is a large-scale approximation of the original Partition data reduction algorithm that allows the user to flexibly specify the minimum amount of information captured for each input feature. In an initial step, Genie, a fast, hierarchical clustering algorithm, forms a super-partition, thereby increasing the computational tractability by allowing Partition to be applied to the subsets. Applications to high dimensional data sets show scalability to hundreds of thousands of features with reasonable computation times.Availability and implementationSuper Partition is a new function within the partition R package, available on the CRAN repository (https://cran.r-project.org/web/packages/partition/index.html). creator: Katelyn J. Queen creator: Malcolm Barrett creator: Joshua Millstein uri: https://doi.org/10.7717/peerj.18580 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Queen et al. title: Beyond support: exploring the dynamic and static biomechanical changes induced by preventive ankle taping: a novel cross-sectional study link: https://peerj.com/articles/18472 last-modified: 2025-01-27 description: IntroductionIn sports, 80% of all ankle injuries are sprains of the external compartment. Functional bandages are usually used preventively, specially in individuals with a history of lateral ankle injuries. To this day, the actual benefits of such taping remain unknown as important modifications are introduced in the ankle biomechanics.ObjectiveThe aim of the present study is to describe the biomechanical processes underlying these effects, such as modification during stance times, balance, contact surface and maximum and average pressures in the rearfoot, forefoot and midfoot, using a sprain preventive taping for the external ankle compartment.MethodsAn observational, analytic, cross-sectional study was designed. Data from static and dynamic plantar pressures with a pressure platform and balance data assessed with the Y Balance Test (YBT) were analysed in 50 participants (age = 21.00 ± 2.34 years, weight = 71.11 ± 13.12 kg, height = 1.75 ± 00.9 m, BMI = 22.94 ± 2.50 kg/m2, foot size = 41.60 ± 3.00) with and without preventive functional taping for lateral ankle sprain (LAS).ResultsA statistically significant decrease in YBT was observed in the taped participants toward anterior (p = 0.001) and posterolateral (p = 0.005) motion. On the static measures at the pressure platform, an increase in peak pressure at the midfoot (p = 0.001), a decrease in the maximum pressure in the forefoot (p = 0.003) and a decrease in the contact surface in the rearfoot (p = 0.003) were recorded. Dynamic measures at the pressure platform analysis showed a statistically significant decrease in contact surface at the rearfoot (p = 0.001), an increase in mean pressure in both the midfoot (p = 0.044) and forefoot (p = 0.001) and a significant decrease in velocity in the forefoot (p = 0.003).ConclusionsIn conclusion, we observed that ankle taping led to increased peak pressures in the midfoot and decreased maximum pressures in the forefoot, indicating a shift in load distribution within the plantar surface. Simultaneously, a significant reduction in the velocity at the forefoot during dynamic tasks suggests that taping may alter natural gait dynamics, potentially affecting movement efficiency and stride characteristics. In addition, the application of ankle taping significantly altered balance, as evidenced by a decrease of YBT scores anterior and posterolateral directions. Prophylactic taping in patients with no prior history of LAS is not recommended. creator: María Bravo-Aguilar creator: Vanesa Abuín-Porras creator: María Blanco-Morales creator: Carlos Romero Morales creator: Jaime Almazán-Polo creator: Jorge Hugo Villafañe creator: Lorena Canosa-Carro uri: https://doi.org/10.7717/peerj.18472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bravo-Aguilar et al. title: The correlation of region-specific lifestyle and subjective perception of oral health with oral health-related quality of life among Tibetan early adolescents in Ganzi: a cross-sectional study link: https://peerj.com/articles/18842 last-modified: 2025-01-24 description: BackgroundThe oral health-related quality of life (OHRQoL) of Tibetan adolescents has been largely overlooked.AimThis cross-sectional study examined the association of region-specific lifestyle, subjective perception, and clinician conditions of oral health with Tibetan adolescents’ OHRQoL in Ganzi, Sichuan.MethodsThe OHRQoL was measured using standardized Child Oral Impacts on Daily Performances (sC-OIDP) scores. Binary logistic regression was used to explore the association between region-specific lifestyle, subjective perception of oral health, clinician oral health conditions (gingival bleeding on probing (BOP), dental calculus (DC), and decayed, missing, and filled teeth (DMFT)), and OHRQoL.ResultsIn total, 485 Tibetan adolescents were included. In relation to region-specific lifestyle, the factors associated with poorer OHRQoL were residence altitude of 3,300 m (compared to 1,400 m), buttered tea consumption by adolescents or mother, and being a boarding student. Regarding the subjective perception of oral health, adolescents that rated bad or very bad oral health or self-reported dental pain had poorer OHRQoL. Interestingly, clinician oral health conditions were not related to OHRQoL.ConclusionsThis study underscores the relationship between region-specific lifestyle, subjective oral health perceptions, and OHRQoL among Tibetan adolescents. Addressing these factors through tailored health initiatives can play a pivotal role in improving oral health outcomes and overall quality of life in remote regions like Ganzi. Future research should focus on longitudinal studies to better understand the causality and long-term impact of targeted interventions. creator: Shaoying Duan creator: Renjie Tang creator: Chenchen Zhang creator: Qianqian Su creator: Huiyu Yang creator: He Cai creator: Tao Hu uri: https://doi.org/10.7717/peerj.18842 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Duan et al. title: Single-cell analysis of Mycobacterium tuberculosis with diverse drug resistance using surface-enhanced Raman spectroscopy (SERS) link: https://peerj.com/articles/18830 last-modified: 2025-01-24 description: In this work, we investigated individual bacteria M. tuberculosis belonging to strains of the Beijing family with different drug sensitivity (sensitive, multi and extensive drug-resistant) by surface-enhanced Raman spectroscopy (SERS) in the fingerprint region. The latter is focused on the spectral bands, which correspond to a set of glutathione bands and DNA methylation patterns revealed due to 5-methylcytosine spectral biomarkers. It is shown that these spectral features can be correlated with drug sensitivity and DNA methylation. Thus, since this kind of diagnostics is fast and operates with individual cells, it can be considered a promising tool, which significantly shortens the time required for a strain’s type identification necessary to prescribe adequate therapy. creator: Andrey Zyubin creator: Anastasia Lavrova creator: Marine Dogonadze creator: Evgenii Borisov creator: Eugene B. Postnikov uri: https://doi.org/10.7717/peerj.18830 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zyubin et al. title: A plant-derived biostimulant Aminolom Enzimatico® application stimulates chlorophyll content, electrolyte leakage, stomata density and root yield of radishes under salinity stress link: https://peerj.com/articles/18804 last-modified: 2025-01-24 description: Biostimulants stimulate plant growth and tolerance to salinity stress, which creates unfavorable conditions for plant growth from emergence to harvest; however, little is known about their roles in triggering salt tolerance. Therefore, the study aimed to determine how applying a foliar plant-derived biostimulant (Aminolom Enzimatico® 24%) affects the growth (leaf area, biomass weight, root diameter, root fresh weight, and water-soluble dry matter), physiology (chlorophyll content, electrolyte leakage, cell membrane stability, and relative water content), and stomata of the lower and upper parts of leaves in radish plants (Raphanus sativus L.) under salinity stress. Radish plantlets at 7 d old were irrigated with saline water (i.e., 50, 100, 150, and 200 mM NaCl), and the biostimulant was sprayed twice at 7 d intervals. Under salinity stress, increased water-soluble dry matter content was detected, along with reduced plant biomass weight, root fresh weight, and root diameter. Meanwhile, the foliar biostimulant increased the mean root fresh weight, biomass fresh weight, and leaf area by 12%, 13.6%, and 24% compared to the control, respectively. Increasing NaCl dramatically reduced leaf area and relative water content, whereas chlorophyll content and stomata densities on both sides of the leaves improved. By regulating physiological parameters and thereby promoting root and leaf growth, the biostimulant application improved the radish plants’ tolerance to salinity stress up to 100 mM NaCl. Spraying the biostimulant can also boost plant growth, root yield, and radish quality under moderate salinity stress. creator: Gamze Kaya uri: https://doi.org/10.7717/peerj.18804 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kaya title: Chitosan-DNA nanoparticles: synthesis and optimization for long-term storage and effective delivery link: https://peerj.com/articles/18750 last-modified: 2025-01-24 description: BackgroundChitosan nanoparticles (CsNPs) are an effective and inexpensive approach for DNA delivery into live cells. However, most CsNP synthesis protocols are not optimized to allow long-term storage of CsNPs without loss of function. Here, we describe a protocol for CsNP synthesis, lyophilization, and sonication, to store CsNPs and maintain transfection efficiency.MethodsThe size and zeta potential of CsNPs were analyzed by dynamic light scattering (DLS) and the morphology of CsNPs was assessed by transmission electron microscopy (TEM). HEK293 cells were transfected with CsNPs, and expression of H2B-CMV-mScarlet plasmid was assessed by flow cytometry. Confocal microscopy was used to visualize post-transfection gene expression. Time, volume, and effect of sonication were tested to optimize the lyophilization process.ResultsDLS and TEM analysis indicated amine groups on chitosan to phosphate groups on DNA (N:P) ratios yielded smaller CsNPs sizes. Transfection efficiency, measured by FACS and confocal microscopy, peaked at N:P ratios of 2:1 and 3:1 for both fresh and lyophilized CsNPs. Chitosan/DNA complexes remained stable in solution for at least 72 h at a ratio ≥2:1 as assessed by agarose gel electrophoresis. A lower surface charge with lower N:P ratios was indicated by zeta potential measurements. Lyophilized CsNPs lost 50% transfection efficiency compared to those freshly made. In contrast, sonication of lyophilized CsNPs restored their transfection efficiency to the level of fresh CsNPs. Sonicated CsNPs maintained spherical morphology, while unsonicated CsNPs showed aggregates. Cytotoxicity assays revealed high cell viability (>90%) after CsNPs transfection for a ratio of 2:1 or 3:1.ConclusionThis optimized CsNPs synthesis protocol opens the possibility of long-term storage for CsNPs, which would provide broader applications of this technology. creator: Aigul Raimbekova creator: Ulpan Kart creator: Akbayan Yerishova creator: Timur Elebessov creator: Sergey Yegorov creator: Tri Thanh Pham creator: Gonzalo Hortelano uri: https://doi.org/10.7717/peerj.18750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Raimbekova et al. title: Geochemical signatures and nanomechanical properties of echinoid tests from nearshore habitats of Florida: environmental and physiological controls on echinoid biomineralization link: https://peerj.com/articles/18688 last-modified: 2025-01-24 description: The mechanisms that regulate minor and trace element biomineralization in the echinoid skeleton can be primarily controlled biologically (i.e., by the organism and its vital effects) or by extrinsic environmental factors. Assessing the relative role of those controls is essential for understanding echinoid biomineralization, taphonomy, diagenesis, and their potential as geochemical archives. In this study, we (1) contrast geochemical signatures of specimens collected across multiple taxa and environmental settings to assess in situ the effects of environmental and physiological factors on skeletal biomineralogy; and (2) analyze the nanomechanical properties of the echinoid skeleton to assess potential linkages between magnesium/calcium (Mg/Ca) ratios and skeletal nanohardness. Live specimens of sand dollars and sea biscuits (Mellita tenuis, Encope spp., Leodia sexiesperforata, and Clypeaster subdepressus) were collected from three different salinity regimes: (1) a coastal region of Cedar Key influenced by freshwater input from Suwannee River, with low and fluctuating salinity; (2) St. James Bay with less fluctuating, higher salinity; and (3) Florida Keys with stable, fully marine salinity conditions. No clear relationship was found between the bulk skeletal barium/calcium (Ba/Ca), zinc/calcium (Zn/Ca), sodium/calcium (Na/Ca), cadmium/calcium (Cd/Ca), copper/calcium (Cu/Ca), phosphorous/calcium (P/Ca), lead/calcium (Pb/Ca), boron/calcium (B/Ca), manganese/calcium (Mn/Ca) ratios pooled across all taxa. In contrast, bulk Mg/Ca, strontium/calcium (Sr/Ca), sulfur/calcium (S/Ca) and lithium/calcium (Li/Ca) ratios exhibited notable differences between the three regions, indicating that distribution of these elements can be at least partly influenced by environmental factors such as salinity. However, such patterns were highly variable across taxa and regions, indicating that both environmental and physiological factors influenced geochemical signatures to varying degrees, depending on the species and environmental setting. In addition, regardless of species identity, different types of stereom within single tests were characterized by distinct skeletal Mg/Ca ratios and nanohardness. The inner galleried and coarse labyrinthic stereom typically exhibited a lower Mg/Ca ratio and nanohardness than the outer imperforate stereom layer that locally forms tubercles. Such heterogeneity in Mg distribution within single specimens cannot be ascribed solely to environmental changes, indicating that these echinoids actively regulate their intraskeletal Mg content: the higher magnesium concentration at the tubercles relative to that of the underlying stereom may be interpreted as a strategy for enhancing their mechanical strength to withstand surface friction and wear. The results suggest that the trace element composition of echinoid tests is a complex outcome of environmental and physiological factors. creator: Przemysław Gorzelak creator: Luis Torres Jr. creator: Dorota Kołbuk creator: Tobias B. Grun creator: Michał Kowalewski uri: https://doi.org/10.7717/peerj.18688 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Gorzelak et al. title: Tea cultivation: facilitating soil organic carbon accumulation and altering soil bacterial community—Leishan County, Guizhou Province, Southwest China link: https://peerj.com/articles/18683 last-modified: 2025-01-24 description: BackgroundCamellia sinensis is an important cash crop in southwestern China, with soil organic carbon playing a vital role in soil fertility, and microorganisms contributing significantly to nutrient cycling, thus both of them influencing tea tree growth and development. However, existing studies primarily focus on soil organic carbon, neglecting carbon fractions, and the relationship between soil organic carbon fractions and microbial communities is unclear. Consequently, this study aims to clarify the impact of different tea planting durations on soil organic carbon fractions and microbial communities and identify the main factors influencing microbial communities. It provides a theoretical basis for soil quality evaluation in the study area and scientific guidance for tea plantation management, thus fostering the region’s economic sustainability.MethodsThis study selected tea plantations with different tea planting durations of 3–5 years (Y5), 12–16 years (Y15), 18–22 years (Y20), 40–42 years (Y40), and 48–50 years (Y50), as research subjects and adjacent uncultivated forest without a history of tea planting (CK) served as controls. Soil organic carbon (SOC), particulate organic carbon (POC), easily oxidizable organic carbon (EOC), dissolved organic carbon (DOC), microbial biomass carbon (MBC), and bacterial diversity were measured in the 0–20 cm and 20–40 cm soil layers, respectively.ResultsCompared to the adjacent uncultivated forest (CK), the soil organic carbon (SOC), easily oxidizable carbon (EOC), particulate organic carbon (POC), and dissolved organic carbon (DOC) contents in a 40-year tea plantation significantly increased. Nonetheless, the microbial biomass carbon (MBC) content notably decreased. POC/SOC ratios rose with prolonged planting, signifying enhanced conversion of organic carbon into particulate forms. Bacterial community diversity peaked at 15 years and declined by 40 years post-planting and after tea planting dominated by Acidobacteriota, Chloroflexi, Proteobacteria, and Actinobacteriota in the tea garden. FAPROTAX analysis highlighted aerobic and anaerobic chemoheterotrophy, cellulolysis, and nitrogen fixation as key bacterial functions. POC and MBC significantly influenced bacterial community structure. In conclusion, tea plantation soil exhibited the highest organic carbon content at 40 years of tea planting, indicating strong carbon accumulation capacity. However, soil acidification in the tea plantation may affect changes in organic carbon and bacterial community. Therefore, in the tea planting process, it is necessary to improve the management system of tea plantations to ensure the maintenance of a good ecological environment in the tea plantation soil, thus achieving sustainable development of the tea industry in the region. creator: Yingge Shu creator: Shan Xie creator: Hong Fan creator: Chun Duan creator: Yuansheng Liu creator: Zuyong Chen uri: https://doi.org/10.7717/peerj.18683 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shu et al. title: The influence of physical activity levels on lactate production during squat training using a functional electromechanical dynamometer link: https://peerj.com/articles/18215 last-modified: 2025-01-24 description: ObjectiveThis study aimed to determine the association between changes in lactate production and levels of physical activity in a group of healthy young adults in response to two squat training protocols.Material and methodsTwenty-nine students majoring in Sports Science willingly participated in this study. Participants visited the lab four times within a two-week period, ensuring at least 48 h between visits. In each session, they completed three sets of 12 repetitions at 75% 1RM and three sets of 30 repetitions at 50% of maximum strength, with the order of protocols being randomized.ResultsIn the regression analysis, there was a significant positive association between lactate delta changes immediately post-squat at 50% of maximum strength at session 2 with the variable “sex: women” (β: 3.02, 95% CI [−0.18–0.30], p = 0.047) and BMI (kg/m2). Age exhibited a positive association (β: 0.19, 95% CI [0.02–0.36], p = 0.032) with lactate delta changes immediately post-squat at 75% of maximum strength at session 2. There was also a significant inverse association between lactate delta changes at 10 min post-squat test exercise at 75% of maximum strength at session 1 and 2, and vigorous physical activity (−0.01, 95% CI [−0.02–0.00], p = 0.046).ConclusionIn summary, this study provides valuable insights into the association between lactate production and physical activity levels in young, healthy adults undergoing different squat training protocols. These findings suggest that intense physical activity may be associated with lower lactate production, indicating greater metabolic efficiency. In addition, sex differences in metabolic responses were observed, emphasizing the importance of personalized approaches in program design. creator: Indya del-Cuerpo creator: Daniel Jerez-Mayorga creator: Luis Javier Chirosa-Ríos creator: Felipe Caamaño-Navarrete creator: Pedro Delgado-Floody uri: https://doi.org/10.7717/peerj.18215 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 del-Cuerpo et al. title: Analysing head and trunk motion in the judo osoto-gari technique: relationship to sweeping-leg velocity link: https://peerj.com/articles/18862 last-modified: 2025-01-23 description: BackgroundOsoto-gari is a leg throw technique that primarily relies on the hip extension to initiate the sweeping motion of the leg. A high sweep contact velocity is a crucial factor in efficiently executing this technique. While some literature emphasises whole-body coordination in the leg-sweeping action, the roles of trunk and head motion remain unclear. This study investigates head and trunk movements (including the pelvic and upper torso) contributing to higher leg-sweep velocities when executing the judo osoto-gari.MethodsKinematic data were collected from 17 male black-belt judokas using a motion capture system (250 Hz). Pearson product-moment correlation and stepwise linear regression were used to identify kinematic variables linked to the sweeping-leg velocity at sweep contact (SC).ResultsSix out of twenty-four variables correlated with sweeping-leg velocity at SC. A stepwise regression model (adjusted R2 = 0.53, p = 0.009) predicted sweeping-leg velocity based on head-tilt angle at maximum sweeping-leg height (MSH) and SC, head-tilt angular velocity at MSH, and trunk-tilt angular velocity at MSH.ConclusionsThe findings of this study indicate that (1) increasing the forward angle of the head aids the visual system in rapidly processing spatial information about the target position, thus facilitating the execution of the leg sweep, and (2) a greater forward-tilt rotation of the head, which leads to rapid trunk rotation, is conducive to enhancing sweeping-leg velocity. creator: Lingjun Liu creator: Tatsuya Deguchi creator: Mitsuhisa Shiokawa creator: Kazuto Hamaguchi creator: Masahiro Shinya uri: https://doi.org/10.7717/peerj.18862 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: The bacterial composition signatures of perianal abscess and origin of infecting microbes link: https://peerj.com/articles/18855 last-modified: 2025-01-23 description: BackgroundPerianal abscess is a common anal condition primarily caused by bacterial infections, yet the precise origins of these infecting bacteria remain unclear. Understanding the distinct microbial signatures associated with periaabscesses is crucial for provide fresh ideas for disease prevention.Materials and MethodsSamples of anal skin, feces, and abscesses were collected from a cohort of 75 patients diagnosed with perianal abscesses. The microbial composition at each site was analyzed using 16S rRNA gene sequencing to characterize the bacterial communities present.ResultsAnalysis using MaAslin2 revealed distinct bacterial compositional signatures among the anal skin, feces, and abscess samples. Alpha diversity analysis indicated significant differences in bacterial diversity between abscesses, anal skin, and feces, with abscesses showing lower diversity compared to higher richness in feces. Biomarker analysis highlighted key taxa such as Bacteroides and Escherichia-Shisgella in fecal samples, and Staphylococcus and Corynebacterium in anal skin samples. The analysis of abscess samples suggested that the bacterial composition may originate from the skin, feces, and potentially other sources. creator: Song Han creator: Wenya Su creator: Kefeng Fan creator: Zhen Xu creator: Hai Xu creator: Mingyu Wang creator: Ling Li creator: Wenlong Shen uri: https://doi.org/10.7717/peerj.18855 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Han et al. title: Evolutionary patterns of the SSU rRNA (V4 region) secondary structure in genus Euplotes (Ciliophora, Spirotrichea): insights into cryptic species and primitive traits link: https://peerj.com/articles/18852 last-modified: 2025-01-23 description: The genus Euplotes, a group of ciliated protists, has attracted attention as a model organism due to its widespread distribution and ease of cultivation. This study examines the evolutionary patterns of the SSU rRNA secondary structure within this genus, aiming to elucidate its role in supporting evolutionary relationships and uncovering cryptic species. By predicting the secondary structure of SSU rRNA and applying the CBC (Compensatory Base Change) concept analysis, we examined 69 species of the genus Euplotes, with 57 SSU rRNA gene sequences retrieved from GenBank and 12 newly sequenced specimens from South Korea. Our analysis revealed significant variations in the V4 region secondary structure, particularly in helix E23_8, across different clades of Euplotes. Reconstruction of the ancestral state indicated a transition from a simpler (Type I) to a more complex (Type II) secondary structure, with several species showing a reversal to Type I especially species in clade VI, suggesting of reverse evolution. In addition, our study identified cryptic species within Euplotes based on differences in the secondary structure of the V4 region, particularly evident in clade VI, where CBC analysis highlighted differences in E. minuta compared to E. vannus and E. crassus. These results highlight the utility of molecular data in refining species boundaries and evolutionary patterns within the genus Euplotes. creator: Ratih Kusuma Wardani creator: Ragib Ahsan creator: Mann Kyoon Shin uri: https://doi.org/10.7717/peerj.18852 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wardani et al. title: Re-evaluation of mastodon material from Oregon and Washington, USA, Alberta, Canada, and Hidalgo and Jalisco, Mexico link: https://peerj.com/articles/18848 last-modified: 2025-01-23 description: The presence of at least two contemporaneous Pleistocene mastodon taxa in North America (Mammut americanum and M. pacificus) invites re-examination of specimens at the geographic margins of each species in order to determine range boundaries, overlaps, and fluctuations. Third molars from Oregon in the United States, as well as from Hidalgo and Jalisco in Mexico, were found to be morphologically consistent with M. pacificus. Washington in the United States includes a number of specimens that could not be confidently assigned to either taxon. Alberta in Canada was found to have some specimens that were consistent with M. pacificus, but others that were identified as M. americanum. The Alberta specimen referred to M. pacificus is the same tooth found to have a Pliocene divergence time from M. americanum based on mitochondrial genome data from a previous study, suggesting a deep divergence time between the two taxa. The apparent presence of both mastodon taxa in close geographic proximity has interesting paleobiogeographic implications. It is not yet clear if both taxa were present simultaneously in a given location; if not, it suggests fluctuating ranges that may reflect shifting climates and/or biomes over time. Alternatively, if both taxa were simultaneously present in the same place, it may suggest a high degree of niche partitioning in mammutids. Additional accurately dated specimens will be required to resolve this question. creator: Alton C. Dooley creator: Chris Widga creator: Brittney E. Stoneburg creator: Christopher Jass creator: Victor M. Bravo-Cuevas creator: Andrew Boehm creator: Eric Scott creator: Andrew T. McDonald creator: Mark Volmut uri: https://doi.org/10.7717/peerj.18848 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dooley Jr et al. title: Deep water vetulicolians from the lower Cambrian of China link: https://peerj.com/articles/18864 last-modified: 2025-01-22 description: Vetulicolians are an enigmatic phylum of extinct Cambrian marine invertebrates. They are particularly diverse in the Chengjiang Biota of China, but representatives have been recovered from other Fossil-Lagerstätten (Cambrian Stage 3-Drumian). These organisms are characterized by a bipartite body, which is split into an anterior section and a posterior segmented section connected by a narrow constriction. Here we report new material of the genus Pomatrum from the Cambrian Balang Biota (Series 2, Stage 4) of Hunan, southern China. This is the first discovery of this vetulicolian outside of the Chengjiang Biota (Series 2, Stage 3) and the first report of vetulicolians from the Balang Biota. This finding not only suggests that this group had a wider spatial and temporal distribution than previously known, but also adds information to the overall biodiversity of the Balang Biota—one of the most important Stage 4 fossil deposits known from Gondwana. creator: Shuhan Ma creator: Julien Kimmig creator: James D. Schiffbauer creator: Ruibo Li creator: Shanchi Peng creator: Xianfeng Yang uri: https://doi.org/10.7717/peerj.18864 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ma et al. title: Altered expression of miRNA profile in peripheral blood mononuclear cells following the third dose of inactivated COVID-19 vaccine link: https://peerj.com/articles/18856 last-modified: 2025-01-22 description: COVID-19 vaccination is the most effective strategy for preventing severe disease and death. Inactivated vaccines are the most accessible type of COVID-19 vaccines in developing countries. Several studies, including work from our group, have demonstrated that the third dose (booster vaccination) of inactivated COVID-19 vaccine induces robust humoral and cellular immune responses. The present study aimed to examine miRNA expression profile in participants who received a homologous third dose of the CoronaVac vaccine. Samples of peripheral blood mononuclear cells (PBMCs) were collected from healthcare volunteers both before and 1–2 weeks after the booster dose. miRNA microarray analysis in a discovery cohort of six volunteers identified 67 miRNAs with differential expression. Subsequently, the expression of six miRNAs related to immune responses was examined in a validation cohort of 31 participants via qRT-PCR. Our results validated the differential expression of miR-25-5p, miR-34c-3p, and miR-206 post-booster, with a significant correlation to the receptor binding domain (RBD)-specific antibody. Bioinformatic analysis suggested that miR-25-5p, miR-34c-3p, and miR-206 may target multiple pathways involved in immune regulation and inflammation. Therefore, our study highlights miR-25-5p, miR-34c-3p, and miR-206 in PBMCs as promising biomarkers for assessing the immune response induced by the booster dose of the CoronaVac vaccine. creator: Guanguan Qiu creator: Ruoyang Zhang creator: Huifeng Qian creator: Ruoqiong Huang creator: Jie Xia creator: Ruoxi Zang creator: Zhenkai Le creator: Qiang Shu creator: Jianguo Xu creator: Guoping Zheng creator: Jiangmei Wang uri: https://doi.org/10.7717/peerj.18856 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Qiu et al. title: Assessing the readability, quality and reliability of responses produced by ChatGPT, Gemini, and Perplexity regarding most frequently asked keywords about low back pain link: https://peerj.com/articles/18847 last-modified: 2025-01-22 description: BackgroundPatients who are informed about the causes, pathophysiology, treatment and prevention of a disease are better able to participate in treatment procedures in the event of illness. Artificial intelligence (AI), which has gained popularity in recent years, is defined as the study of algorithms that provide machines with the ability to reason and perform cognitive functions, including object and word recognition, problem solving and decision making. This study aimed to examine the readability, reliability and quality of responses to frequently asked keywords about low back pain (LBP) given by three different AI-based chatbots (ChatGPT, Perplexity and Gemini), which are popular applications in online information presentation today.MethodsAll three AI chatbots were asked the 25 most frequently used keywords related to LBP determined with the help of Google Trend. In order to prevent possible bias that could be created by the sequential processing of keywords in the answers given by the chatbots, the study was designed by providing input from different users (EO, VH) for each keyword. The readability of the responses given was determined with the Simple Measure of Gobbledygook (SMOG), Flesch Reading Ease Score (FRES) and Gunning Fog (GFG) readability scores. Quality was assessed using the Global Quality Score (GQS) and the Ensuring Quality Information for Patients (EQIP) score. Reliability was assessed by determining with DISCERN and Journal of American Medical Association (JAMA) scales.ResultsThe first three keywords detected as a result of Google Trend search were “Lower Back Pain”, “ICD 10 Low Back Pain”, and “Low Back Pain Symptoms”. It was determined that the readability of the responses given by all AI chatbots was higher than the recommended 6th grade readability level (p < 0.001). In the EQIP, JAMA, modified DISCERN and GQS score evaluation, Perplexity was found to have significantly higher scores than other chatbots (p < 0.001).ConclusionIt has been determined that the answers given by AI chatbots to keywords about LBP are difficult to read and have low reliability and quality assessment. It is clear that when new chatbots are introduced, they can provide better guidance to patients with increased clarity and text quality. This study can provide inspiration for future studies on improving the algorithms and responses of AI chatbots. creator: Erkan Ozduran creator: Volkan Hancı creator: Yüksel Erkin creator: İlhan Celil Özbek creator: Vugar Abdulkerimov uri: https://doi.org/10.7717/peerj.18847 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ozduran et al. title: UPLC-MS metabolite profiling and antioxidant activity of Sanghuangporus sanghuang extract link: https://peerj.com/articles/18758 last-modified: 2025-01-22 description: BackgroundThe objective of the present study is to examine the total phenolic and flavonoid content of an ethanol extract of Sanghuangporus sanghuang and to evaluate its phytochemical properties, antioxidant activity, and capacity to protect DNA from damage. This pharmaceutical/food resource mushroom may serve as a novel substitute functional food for health-conscious consumers, given its promising source of phenolics and flavonoids.MethodsS. sanghuang ethanol extract (SEE) was evaluated for total phenolic and flavonoid contents, while UPLC-MS analysis was used for terpenoids, phenylpropanoid, flavonoids, steroidal, phenols identification, and function prediction. Antioxidant and anti-DNA damage activities were tested in vitro using ferric reducing antioxidant power (FRAP), 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2′-azino-bis-3-ethylbenzotiazolin-6-sulfonic acid (ABTS), and DNA damage protection assay.Results and ConclusionTotal phenolic content (TPC) in SEE was 385.38 ± 1.36 mg GA/g extract, while total flavonoid content (TFC) was 298.22 ± 2.38 mg QE/g extract. The extracts exhibited high antioxidant and free radical scavenging activities with relatively stronger free radical scavenging activity. A total of 491 metabolites were investigated by Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). Most of the top 20 compounds were predicted to have various functions like antioxidant, anti-cancer and anti-inflammatory. This study highlighted S. sanghuang was a beneficial source of phenolics and flavonoids. It contains potential natural antioxidant that could be used as a lead contender in the development of antioxidant medicines for the treatment of a wide range of oxidative stress-related illnesses. creator: Weike Wang creator: Na Lu creator: Cheng Jiang creator: Guanping Chen uri: https://doi.org/10.7717/peerj.18758 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Wang et al. title: A nomogram for predicting bladder dysfunction in patients with type 2 diabetes mellitus: a retrospective study link: https://peerj.com/articles/18872 last-modified: 2025-01-22 description: BackgroundDiabetic bladder dysfunction (DBD) is a common urinary complication in diabetic patients, significantly affecting their overall well-being and quality of life, and placing a considerable burden on healthcare resources. Early prevention is crucial; however, the absence of a simple and effective tool to predict DBD onset remains a significant challenge. This study aims to identify risk factors for DBD in patients with type 2 diabetes mellitus (T2DM) and to develop a predictive nomogram for clinical application.MethodsThis retrospective study included patients with T2DM treated at two hospitals. Data from patients treated at one hospital between January 2020 and August 2023 were used to create the training set, while data from patients treated at another hospital between March 2022 and October 2023 were used to create the validation set. Patients were classified into two groups based on the presence or absence of DBD: the DBD group and the non-DBD group. Significant factors identified via bivariate analysis (P < 0.05) were incorporated into multivariate logistic regression to construct a predictive model, and a corresponding nomogram was developed. The model’s performance was assessed using receiver operating characteristic (ROC) curves, calibration plots, decision curve analysis (DCA), and clinical impact plots (CIC), with validation performed through 1,000 bootstrap resamplings.ResultsA total of 1,010 participants were included in this study, with a DBD incidence rate of 38.81% (392/1,010). Multivariate logistic regression analysis identified HbA1c, PCP-2h, DPN, TCO2, PAB, T-Bil, I-Bil, IgE, URBC, UI and UR as independent risk factors for DBD. A nomogram was constructed based on these factors. Both internal and external validations demonstrated the good predictive performance of the nomogram. The area under the curve (AUC) for the training and validation datasets was 0.897 and 0.862, respectively. The calibration curve showed a high degree of consistency. Results from DCA and CIC indicated that the prediction model had high clinical utility.ConclusionsA predictive model and nomogram for DBD in T2DM patients were developed, demonstrating strong accuracy and clinical utility, aiding in early DBD risk assessment and intervention. creator: Yingjie Hu creator: Fengming Hao creator: Ying Wang creator: Ling Chen creator: Lihua Wen creator: Jue Li creator: Wei Ren creator: Wenzhi Cai uri: https://doi.org/10.7717/peerj.18872 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hu et al. title: Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome link: https://peerj.com/articles/18602 last-modified: 2025-01-21 description: BackgroundThe initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns’ gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.MethodologyWe analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.ResultsB. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.DiscussionOur results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being. creator: Nicholas Pucci creator: Joanne Ujčič-Voortman creator: Arnoud P. Verhoeff creator: Daniel R. Mende uri: https://doi.org/10.7717/peerj.18602 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pucci et al. title: Three-dimensional analysis of facial morphology in nine-year-old children with different unilateral orofacial clefts compared to normative data link: https://peerj.com/articles/18739 last-modified: 2025-01-21 description: AimTo compare three-dimensional (3D) facial morphology of various unilateral cleft subphenotypes at 9-years of age to normative data using a general face template and automatic landmarking. The secondary objective is to compare facial morphology of 9-year-old children with unilateral fusion to differentiation defects.Methods3D facial stereophotogrammetric images of 9-year-old unilateral cleft patients were imported into 3DMedX® for processing. All images of patients with a right sided cleft were mirrored. A regionalized general facial template was used for standardization. This template was pre-aligned to each face using five automatically determined landmarks and fitted using MeshMonk. All cleft patients were compared to an age-and gender matched normative face using distance maps and inter-surface distances (mm). Average faces were created for five groups (unilateral cleft lip, alveolus, and/or palate (UCL/A/P), fusion and differentiation defects). The selected regions for the evaluation of facial morphology were: complete face, nose, upper lip, lower lip, chin, forehead, and cheeks.ResultsA total of 86 consecutive 3D-stereophotogrammetry images were acquired for examination. No statistically significant differences were observed among the UCL, UCLA, and UCLP groups for the complete face, cheeks, chin, forehead, lower lip, and nose. However, in the upper lip region a significant difference was observed between the UCLP and UCL groups (P = 0.004, CI [−2.93 to −0.48]). Further visual examination of the distance maps indicated that more severe clefts corresponded to increased retrusion in the midface and the tip of the nose, though these differences were not statistically significant across groups. For fusion vs differentiation defects, no statistically significant differences were observed, neither for the complete face nor for any of the individual regions.ConclusionThe findings demonstrate statistically significant differences in the upper lip region between children with UCL and those with UCLP, particularly with greater upper lip retrusion in the UCLP group. The use of color-coded distance maps revealed local variations and a trend of asymmetry in the nasal region, with increasing retrusion of the nose tip, upper lip, and cheeks correlating with the severity of the cleft. Although these trends were not statistically significant, they suggest a progressive facial retrusion pattern as cleft severity increases. For the secondary objective, no statistical differences were found between the facial morphology of children with fusion and differentiation defects, although a similar progression of maxillary retrusion was observed in the distance maps. creator: Marjolein Crins-de Koning creator: Robin Bruggink creator: Marloes Nienhuijs creator: Till Wagner creator: Ewald M. Bronkhorst creator: Edwin M. Ongkosuwito uri: https://doi.org/10.7717/peerj.18739 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Crins-de Koning et al. title: Attaching artificial Achilles and tibialis cranialis tendons to bone using suture anchors in a rabbit model: assessment of outcomes link: https://peerj.com/articles/18756 last-modified: 2025-01-21 description: ObjectiveThe purpose of this study was to investigate the timing and mode of failure of metallic screw-type suture anchors used to attach artificial tendons to bone in an in vivo New Zealand White rabbit model.Study DesignMetal suture anchors with braided composite sutures of varying sizes (United States Pharmacopeia (USP) size 1, 2, or 5) were used to secure artificial tendons replacing both the Achilles and tibialis cranialis tendons in 12 female New Zealand White rabbits. Artificial tendons were implanted either at the time of (immediate replacement, n = 8), or four/five weeks after (delayed replacement, n = 4) resection of the biological tendon. Hindlimb radiographs of the rabbits were obtained immediately after surgery and approximately every other week until the study endpoint (16 weeks post-surgery).ResultsAll suture anchors used for the tibialis cranialis artificial tendons remained secure and did not fail during the study. The suture anchor used to attach the Achilles artificial tendon to the calcaneus bone failed in nine of 12 rabbits. In all cases of suture anchor failure, the suture broke away from the knot, while the metallic screw remained securely embedded in the bone. Based on radiographic analysis, the mean estimated failure timepoint was 5.3 ± 2.3 weeks post-surgery, with a range of 2–10 weeks. Statistical analyses (Mann–Whitney U test and Fisher’s exact test) revealed no significant effect of tendon implantation timing or suture size on either the timing or frequency of suture anchor failure.ConclusionFor the suture anchors used to attach artificial tendons in this study, suture anchor failure was most likely due to suture wear or cutting against the eyelet of the anchor screw. Future studies are needed to test the effect of suture-eyelet interaction on suture strength under different loading conditions. creator: Obinna P. Fidelis creator: Caleb Stubbs creator: Katrina L. Easton creator: Caroline Billings creator: Alisha P. Pedersen creator: David E. Anderson creator: Dustin L. Crouch uri: https://doi.org/10.7717/peerj.18756 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fidelis et al. title: Morphometric analysis revealed two different Mediterranean horse mackerel (Trachurus mediterraneus) stocks in the Adriatic Sea link: https://peerj.com/articles/18765 last-modified: 2025-01-21 description: Phenotypical differentiation among individuals of Mediterranean horse mackerel Trachurus mediterraneus in the Adriatic Sea was investigated through the analysis of several morphometric characters. Overall, 426 individuals of Mediterranean horse mackerels were sampled from the northern, central and southern Adriatic Sea during the summers of 2012 and 2013. Forty-six morphometric characters were measured for each individual and then compared using multivariate techniques (linear discriminant analysis). Based on the morphometric characteristics, at least two different Mediterranean horse mackerel were identified: one comprising the northern and central Adriatic, and the other formed by individuals from the southern Adriatic basin. The northern and central areas showed stable populations, overlapping both in space and time. The southern area seemed to be more variable over the years, with a low degree of overlapping both in space and time. A possible hypothesis for this, to be further investigated, could be the flow of individuals from the Ionian and Aegean Seas populations through the Otranto Channel. The main differences between the two stocks were associated with the head characters of the fish. In particular, the northern and central Adriatic Sea individuals had shorter and thicker heads than the southern ones. This could be due to different feeding habits: the former mainly feed on small fishes, the latter mainly on euphausiids. A short mouth could reduce the power of suction of bigger preys, while a long mouth could increase the volume of water to be filtered to feed on small planktonic crustaceans. From this study, it becomes clear that the Mediterranean horse mackerel should not be managed as a single stock in the Adriatic Sea as it was evident that at least two morphologically different stocks are present in the basin. creator: Claudio Vasapollo uri: https://doi.org/10.7717/peerj.18765 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vasapollo title: Geometrical determinants of cerebral artery fenestration for cerebral infarction link: https://peerj.com/articles/18774 last-modified: 2025-01-21 description: PurposeFew data are available on the causality of cerebral artery fenestration (CAF) triggering cerebral infarction (CI) and this study aims to identify representative morphological features that can indicate risks.MethodsA cohort comprising 89 patients diagnosed with CAF were enrolled from a total of 9,986 cranial MR angiographies. These patients were categorized into Infarction Group (n = 55) and Control Group (n = 34) according to infarction events. These two groups are divided into two subgroups depending on fenestration location (basilar artery or other cerebravascular location), respectively, i.e., BA Infarction Group (n = 37), BA Control Group (n = 23), Non_BA Infarction Group (n = 18), Non_BA Control Group (n = 11). This study firstly defined 12 indices to quantify the morphological characteristics of fenestration per se and its connecting arteries. The data were evaluated using either the independent sample t-test or the Mann–Whitney U test. Conducting univariate and multivariate logistic regression analyses to ascertain potential independent predictors of CI.ResultsThe initiation angle φ1 and confluence angle φ2 at the fenestration in the Infarction Group are both smaller compared to the Control Group, but only the Infarction Group and BA Infarction Group have significant difference (p < 0.05). The maximum left fenestration axis (fAL) and the left tortuosity index (TIL) were greater in the Infarction Group for CAFs than those in the Control Group (p < 0.05). In contrast, the maximum right fenestration axis (fAR) and the right tortuosity index (TIR) were smaller than those in Control Group (p < 0.05). The logistic regression analysis revealed that φ2 (AUC = 0.68, p = 0.02), fAL (AUC = 0.72, p < 0.01), and fAR (AUC = 0.70, p < 0.01) serve as independent risk factors influencing the occurrence of CI. The regression predictive model achieved an AUC of 0.83, enabling accurate classification of 77.5% of cases, indicating a robust predictive performance of the model.ConclusionMorphological results demonstrated a left-leaning type of fenestration with more narrow fenestration terminals indicating a higher risk of CI occurrence. Furthermore, the regression predictive model established in this study demonstrates a good predictive performance, enabling early prediction of CI occurrence in fenestrated patients and facilitating early diagnosis of CI. creator: Yuqian Mei creator: Xiaoqin Chen creator: Yao Zhang creator: Yanling Wang creator: Bo Wu creator: Mingcheng Hu creator: Quan Bao uri: https://doi.org/10.7717/peerj.18774 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mei et al. title: Development of metastasis and survival prediction model of luminal and non-luminal breast cancer with weakly supervised learning based on pathomics link: https://peerj.com/articles/18780 last-modified: 2025-01-21 description: ObjectiveBreast cancer stands as the most prevalent form of cancer among women globally. This heterogeneous disease exhibits varying clinical behaviors. The stratification of breast cancer patients into risk groups, determined by their metastasis and survival outcomes, is pivotal for tailoring personalized treatments and therapeutic interventions. The pathological sections of radical specimens encompass a diverse range of histological information pertinent to the metastasis and survival of patients. In this study, our objective is to develop a deep learning model utilizing pathological images to predict the metastasis and survival outcomes for breast cancer patients.MethodsThis study utilized pathological sections from 204 radical mastectomy specimens obtained between January 2013 and December 2014 at the Second Affiliated Hospital of the Medical College of Zhejiang University. The 204 pathological slices were scanned and transformed into whole slide imaging (WSI), with manual labeling of all tumor areas. The WSI was then partitioned into smaller tiles measuring 512 × 512 pixels. Three networks, namely Densely Connected Convolutional Network 121 (DenseNet121), Residual Network (ResNet50), and Inception_v3, were assessed. Subsequently, we combined patch-level predictions, probability histograms, and Term Frequency-Inverse Document Frequency (TF-IDF) features to create comprehensive participants representations. These features served as the foundational input for developing a machine learning algorithm for metastasis analysis and a Cox regression model for survival analysis.ResultOur results show that the Inception_v3 model shows a particularly robust patch recognition ability for estrogen receptor (ER) recognition. Our pathological model shows high accuracy in predicting tumor regions. The train area under the curve (AUC) of the Inception_v3 model based on supervised learning is 0.975, which is higher than the model established by weakly supervised learning. But the AUC of the metastasis prediction in training and testing sets is higher than value based on supervised learning. Furthermore, the C-index of the survival prediction model is 0.710 in the testing sets, which is also better than the value by supervised learning.ConclusionOur study demonstrates the significant potential of deep learning models in predicting breast cancer metastasis and prognosis, with the pathomic model showing high accuracy in identifying tumor areas and ER status. The integration of clinical features and pathomics signature into a nomogram further provides a valuable tool for clinicians to make individualized treatment decisions. creator: Hui Liu creator: Linlin Ying creator: Xing Song creator: Xueping Xiang creator: Shumei Wei uri: https://doi.org/10.7717/peerj.18780 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Melatonin attenuates MPP+-induced autophagy via heat shock protein in the Parkinson’s disease mouse model link: https://peerj.com/articles/18788 last-modified: 2025-01-21 description: BackgroundThis study investigates the protective properties of melatonin in an in vivo Parkinson’s disease (PD) model, focusing on the underlying mechanisms involving heat shock proteins (HSPs).MethodsTwelve adult male C57BL/6 mice were randomly divided into four groups (normal control, melatonin control, Parkinson’s model, and melatonin treatment; n = 3 per group) and housed in a single cage. 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was injected intraperitoneally in the Parkinson’s model and treatment groups to establish a subacute PD model, while controls received saline. Limb motor ability was assessed 1 h after the final injection using behavioral tests, including the open field test to evaluate central zone entries and average movement. Dopamine transporter (DAT) expression in the striatum was analyzed by immunohistochemistry, and Western blot was used to measure autophagy proteins and HSP70 levels.ResultsThe PD mouse model was successfully established through MPTP stimulation. Compared to the normal control group, the model group showed a significant reduction in the frequency of entering the central zone and average movement. The number of DAT-positive cells in the brain also decreased significantly. The expression levels of HSP70 and CDK5 were significantly lower, while the expression levels of LC3 II /LC3I and p62 increased significantly. In the MT treatment group, both the frequency of entering the central zone and the average movement were significantly higher compared to the model group. DAT-positive cells in the midbrain also increased significantly. The expression levels of HSP70 and CDK5 were significantly elevated, while the expression levels of LC3 II /LC3I and p62 protein were significantly decreased.ConclusionMelatonin exerts a protective effect against MPP+-induced damage to dopaminergic neurons, presumably by upregulating HSP70, which inhibits neuronal autophagy. creator: Yinli Guo creator: Chengbo Liu uri: https://doi.org/10.7717/peerj.18788 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo and Liu title: Controlled temperature contrasts of three native and one highly invasive annual plant species in California link: https://peerj.com/articles/18794 last-modified: 2025-01-21 description: Plant responses to changes in temperature can be a key factor in predicting the presence and managing invasive plant species while conserving resident native plant species in dryland ecosystems. Climate can influence germination, establishment, and seedling biomass of both native and invasive plant species. We tested the hypothesis that common and widely distributed native and an invasive plant species in dryland ecosystems in California respond differently to increasing temperatures. To test this, we examined the effects of temperature variation on germination, establishment, and per capita seedling biomass of three native and one invasive plant species (Bromus rubens) in independent 6 week growth trial experiments in a controlled greenhouse. Higher relative temperatures reduced the germination and establishment of the tested invasive species and two tested native species, however, per capita biomass was not significantly affected. Specifically, germination and establishment of the invasive species B. rubens and the native species Phacelia tanacetifolia was significantly reduced. This invasive species can often outcompete natives, but increasing temperature could potentially shift the balance between the germination and establishment of natives. A warming climate will likely have negative impacts on native annual plant species in California tested here because increasing temperatures can co-occur with drought. This study shows that our tested native annual plant species tested here have some resilience to relatively significant increases in temperature, and this can favor at least one native species relative to at least one highly noxious invasive plant species. creator: Mario Zuliani creator: Stephanie Haas-Desmarais creator: Laura Brussa creator: Jessica Cunsolo creator: Angela Zuliani creator: Christopher J. Lortie uri: https://doi.org/10.7717/peerj.18794 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zuliani et al. title: Turkish validation of a resilience scale from older people’s perspectives: resilience scale for older adults link: https://peerj.com/articles/18837 last-modified: 2025-01-21 description: BackgroundAs the global population ages and life expectancy increases, older adults encounter challenges like chronic illnesses and losing loved ones; resilience is crucial for adapting to these difficulties. This study aims to culturally and linguistically adapt the psychological resilience scale designed for older adults to the Turkish context.MethodsThis methodological study included 566 individuals aged 65 and older. All participants completed the Resilience Scale for Older Adults, the Perceived Stress Scale, the Geriatric Depression Scale, and the Quality of Life in Older Adults Scale—Short Form. Construct validity was assessed through confirmatory and exploratory factor analyses, while convergent and discriminant validity were evaluated through the correlation of the scales. Reliability was determined using internal consistency and the split-half method.ResultsThe scale retains its original structure with 33 items and four sub-dimensions (Intrapersonal, Interpersonal, Spiritual, and Experiential). The content validity index of the scale is 0.98, with item loadings ranging from 0.406 to 0.947, according to exploratory factor analysis. Confirmatory factor analysis indicates good fit indices. Convergent validity is supported by a strong positive correlation (r = 0.657, p < 0.001) between the Resilience Scale for Older Adults and the Quality of Life in Older Adults Scale—Short Form. Reliability measures include a Cronbach’s alpha internal consistency coefficient of 0.93 and a Guttman split-half reliability coefficient of 0.723.ConclusionThe results show that the Turkish version of the Resilience Scale for Older Adults is a valid and reliable measurement tool. creator: Seher Palanbek Yavaş creator: Caner Baysan uri: https://doi.org/10.7717/peerj.18837 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Palanbek Yavaş and Baysan title: SSR marker-based genetic diversity and structure analyses of Camellia nitidissima var. phaeopubisperma from different populations link: https://peerj.com/articles/18845 last-modified: 2025-01-21 description: BackgroundCamellia nitidissima var. phaeopubisperma is a variety in the section Chrysantha of the genus Camellia of the family Theaceae which is native to Fangchenggang, Guangxi, China. To date, the genetic diversity and structure of this variety remains to be understood.MethodsIn the present study, eight simple sequence repeat (SSR) molecular markers previously screened were used to analyze the genetic diversity and structure of C. nitidissima var. phaeopubisperma natural populations from 14 growing areas in China, so as to determine the influence of environmental changes on genetic variations and provide the basis for introduction and selection of suitable growing sites of that variety.ResultsOur results show that, for the eight SSR loci, the observed numbers of alleles per locus (Na) and the effective numbers of alleles per locus (Ne) were nine and 3.206, respectively on average, and the Ne was lower than the Na for all loci; the observed heterozygosity (Ho) was lower than the expected heterozygosity (He). For all the eight loci, the fixation index (F) was greater than 0, and the intra-population inbreeding coefficient (Fis) for seven loci was positive. Three loci were moderately polymorphic (0.25 < polymorphism information content (PIC) <0.5), and five loci were highly polymorphic (PIC > 0.5); all eight loci had a moderate genetic differentiation level (0.05 < genetic differentiation coefficient (Fst) <0.25). As shown by the genetic diversity analysis, the He was bigger than the Ho for 10 populations, indicating the presence of a certain degree of intra-population inbreeding. The F had a negative value for four populations, suggesting that excessive random mating was present within each of them. Results of the analysis of molecular variance show that 19% of the total variation was attributed to among-individuals and 78% of the total variation originated from within-individuals. The adjusted Fst (F’st) was 0.073, indicative of a moderate level of genetic differentiation among the populations. The value of gene flow was greater than 1 (7.367), suggesting that genetic differentiation among populations was not caused by genetic drift. Results of the STRUCTURE analysis show that all the samples tested could be clustered into five ancestor groups. Results of the Unweighted Pair Group Method using Arithmetic Averages (UPGMA) clustering analyses show that the 84 plant samples could be divided into three clusters and natural populations from the 14 growing areas could be divided into two clusters. Clustering results of the populations were not affected by geographic distances, and gene flow occurred frequently among the populations, suggesting that the genetic variation among the natural populations of C. nitidissima var. phaeopubisperma from 14 growing areas was not influenced by environmental changes of these areas but mainly derived from the genetic variation present in pre-introduction populations. creator: Yang-Jiao Xie creator: Meng-Xue Su creator: Hui Gao creator: Guo-Yue Yan creator: Shuang-Shuang Li creator: Jin-Mei Chen creator: Yan-Yuan Bai creator: Jia-Gang Deng uri: https://doi.org/10.7717/peerj.18845 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al. title: A nociceptor-specific RNAi screen in Drosophila larvae identifies RNA-binding proteins that regulate thermal nociception link: https://peerj.com/articles/18857 last-modified: 2025-01-21 description: Nociception is the process by which sensory neurons detect and encode potentially harmful environmental stimuli to generate behavioral responses. Nociceptor neurons exhibit plasticity in which their sensitivity to noxious stimuli and subsequent ability to drive behavior may be altered by environmental conditions, injury, infection, and inflammation. In some cases, nociceptor sensitization requires regulated changes in gene expression, and recent studies have indicated roles for post-transcriptional mechanisms in regulating these changes as an aspect of nociceptor plasticity. The larvae of Drosophila melanogaster have been developed as a powerful model for studying mechanisms of nociception, nociceptor plasticity, and nociceptor development. Diverse RNA-binding proteins regulate the development and morphology of larval nociceptors, implying important roles for post-transcriptional regulation of gene expression in these neurons, but the importance of these mechanisms for nociceptive behavior has not been investigated systematically. In this study, we conducted a nociceptor-specific RNAi screen of 112 candidate RNA-binding protein genes to identify those that are required for normal sensitivity to noxious thermal stimuli. The screen and subsequent validation experiments identified nine candidate genes (eIF2α, eIF4A, eIF4AIII, eIF4G2, mbl, SC35, snf, Larp4B and CG10445) that produce defects in nociceptive response latency when knocked down in larval nociceptors. Some of the genes identified have well-understood roles in the regulation of translation initiation and regulation of nociceptor sensitization in vertebrate and invertebrate animal models, suggesting an evolutionarily conserved role for these mechanisms in regulating nociceptor sensitivity. Other screen isolates have previously described roles in regulating nociceptor morphology and mRNA processing, but less clear roles in regulating nociceptor function. Further studies will be necessary to identify the mechanisms by which the identified RNA-binding proteins regulate sensory neuron function and the identities of the mRNAs that they target. creator: Amber Dyson creator: Gita Gajjar creator: Katherine C. Hoffman creator: Dakota Lewis creator: Sara Palega creator: Erik Rangel Silva creator: James Auwn creator: Andrew Bellemer uri: https://doi.org/10.7717/peerj.18857 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dyson et al. title: Photogrammetric determination of movement speed of invasive Indo-Pacific lionfish in the Florida Keys link: https://peerj.com/articles/18474 last-modified: 2025-01-20 description: As a key determinant of how efficiently lionfish (Pterois sp.) locate and capture prey, swimming speed plays a crucial role in shaping the predator-prey interactions and broader ecological dynamics within the invaded ecosystems. Swimming speed on a small temporal and spatial scale is difficult to measure because of the need for precise measurements of both distance and duration of the behavior. Using photogrammetry by way of stereo-camera setups is ideal for analyzing the minutiae of lionfish behaviors because it can include the benefits of remote video traps coupled with precise measurements of movements in three-dimensional space and time. The primary objective of this study was to identify and characterize lionfish behavior associated with different movement speeds, and then to quantify small-scale swimming speeds of lionfish associated with those behaviors. Swimming speeds were classified under three different observed behaviors: relaxed swimming, traverse swimming, and striking at prey. The differences between these behaviors were primarily distinguished based on body and fin positioning, as well as the apparent intent of the motion if any was evident. The mean lionfish swimming speed from stereoscopic camera footage was 44.75 mm s−1 for relaxed swimming, 138.99 mm s−1 for traverse swimming, and 625.44 mm s−1 for striking at prey. Swimming speed can be used to quantify how much habitat area a lionfish may cover in a day, and therefore the amount of prey that may be encountered by a predator. Lionfish feeding success under different environmental conditions could be an important factor in understanding their survival and growth in areas where they are found. creator: Neal Kolonay creator: Cassandra N. Glaspie uri: https://doi.org/10.7717/peerj.18474 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kolonay and Glaspie al. title: Genetic determinants of COVID-19 severity and mortality: ACE1 Alu 287 bp polymorphism and ACE1, ACE2, TMPRSS2 expression in hospitalized patients link: https://peerj.com/articles/18508 last-modified: 2025-01-20 description: BackgroundThe angiotensin-converting enzyme 2 (ACE2) and the transmembrane serine protease 2 (TMPRSS2) are central human molecules in the SARS-CoV-2 virus-host interaction. Evidence indicates that ACE1 may influence ACE2 expression. This study aims to determine whether ACE1, ACE2, and TMPRSS2 mRNA expression levels, along with the ACE1 Alu 287 bp polymorphism (rs4646994), contribute to the severity and mortality of COVID-19.MethodsSwabs were collected in two Brazilian cities in 2020: Belo Horizonte (n = 134) and Rio de Janeiro (n = 41). A swab of mild patients in Rio de Janeiro who were not hospitalized (n = 172) was also collected. All analyzed biological material was obtained from residual diagnostic samples in 2020, prior to the emergence of SARS-CoV-2 variants of concern. ACE1, ACE2, TMPRSS2, and B2M (reference gene) expression levels were evaluated in 40 cycles of quantitative PCR. ACE1 Alu 287 bp polymorphism was genotyped using the FastStart Universal SYBR Green Master kit.ResultsThe median age differed between clinical sites (p = 0.016), but no difference in median days of hospitalization was observed (p = 0.329). Age was associated with severity (p = 0.014) and mortality (p = 0.014) in the Belo Horizonte cohort. No alteration in ACE1, ACE2 and TMPRSS2 expression was associated with severity or mortality. ACE1 polymorphism rs4646994 did not influence the likelihood of either outcome. A meta-analysis including available data from the literature showed significant effects: the D-allele conferred risk (OR = 1.39; 95% CI [1.12–1.72]). creator: João Locke Ferreira de Araújo creator: Átila Duque Rossi creator: Jessica Maciel de Almeida creator: Hugo José Alves creator: Isabela de Carvalho Leitão creator: Renata Eliane de Ávila creator: Anna Carla Pinto Castiñeiras creator: Jéssica da Silva Oliveira creator: Rafael Mello Galliez creator: Marlon Daniel Lima Tonini creator: Débora Souza Faffe creator: Shana Priscila Coutinho Barroso Barroso creator: Gustavo Gomes Resende creator: Cássia Cristina Alves Gonçalves creator: Terezinha Marta Pereira Pinto Castiñeiras creator: Amilcar Tanuri creator: Mauro Martins Teixeira creator: Renato Santana Aguiar creator: Cynthia Chester Cardoso creator: Renan Pedra de Souza uri: https://doi.org/10.7717/peerj.18508 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 de Araújo et al. title: Targeted correction of megabase-scale CNTN6 duplication in induced pluripotent stem cells and impacts on gene expression link: https://peerj.com/articles/18567 last-modified: 2025-01-20 description: Copy number variations of the human CNTN6 gene, resulting from megabase-scale microdeletions or microduplications in the 3p26.3 region, are frequently implicated in neurodevelopmental disorders such as intellectual disability and developmental delay. However, duplication of the full-length human CNTN6 gene presents with variable penetrance, resulting in phenotypes that range from neurodevelopmental disorders to no visible pathologies, even within the same family. Previously, we obtained a set of induced pluripotent stem cell lines derived from a patient with a CNTN6 gene duplication and from two healthy donors. Our findings demonstrated that CNTN6 expression in neurons carrying the duplication was significantly reduced. Additionally, the expression from the CNTN6 duplicated allele was markedly lower compared to the wild-type allele. Here, we first introduce a system for correcting megabase-scale duplications in induced pluripotent stem cells and secondly analyze the impact of this correction on CNTN6 gene expression. We showed that the deletion of one copy of the CNTN6 duplication did not affect the expression levels of the remaining allele in the neuronal cells. creator: Maria Gridina creator: Polina Orlova creator: Oleg Serov uri: https://doi.org/10.7717/peerj.18567 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Gridina et al. title: Assessment of physical education teachers’ use of distance teaching behavior under the influence of the COVID-19 pandemic link: https://peerj.com/articles/18743 last-modified: 2025-01-20 description: BackgroundFor many physical education teachers, being suddenly forced to switch from traditional face-to-face teaching to online teaching without adequate mental preparation posed numerous challenges and difficulties. Therefore, the purpose of this study is to validate the use of distance teaching behavior models for physical education teachers under the influence of the COVID-19 pandemic.MethodThe unified theory of acceptance and use of technology (UTAUT) model was employed to explore the use intention and use behavior of distance teaching. The model contains four independent variables: performance expectancy (PE), effort expectancy (EE), social influence (SI), and facilitating conditions (FC), two dependent variables: behavioral intention (BI) and use behavior (UB) and three moderating variables: gender, age, and experience. A total of 400 questionnaires were distributed to elementary and junior high school physical education teachers with 364 valid responses. Partial least squares structural equation modeling (PLS-SEM) was used to test the relationships among variables.ResultsThe results found PE, EE and SI had significant influences on BI and FC and BI had significant influences on UB. Experience had moderating effects among SI and BI.ConclusionsBased on the results, recommendations for physical education teachers and schools are proposed. Furthermore, research limitations and future directions are discussed. creator: Hsiu-Chin Huang creator: Ya-Tzu Kung creator: Ruey-Rong Huang creator: Wui-Chiu Mui creator: Yu-Chien Su uri: https://doi.org/10.7717/peerj.18743 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Huang et al. title: A comparative evaluation of haematological and biochemical parameters of Nemipterus randalli and Pagellus erythrinus species living in Gökova Bay, Türkiye link: https://peerj.com/articles/18784 last-modified: 2025-01-20 description: This study aims to determine and compare the reference values of the haematological and biochemical blood parameters of two fish species collected from the Gökova Bay (Muğla, South-Western of Türkiye): the non-native and invasive Randall’s threadfin bream, Nemipterus randalli and the native Common pandora, Pagellus erythrinus. Both species inhabit the same environment and compete for resources. Blood samples were collected from a total of 100 fish samples (50 N. randalli and 50 P. erythrinus) which were caught from a depth of 30 to 60 meters between February 2023 and July 2024. Therefore, sampling could be carried out in summer and winter seasons when the water temperature varies significantly. The results indicate that red blood cell (RBC), haemoglobin (Hb) and haematocrit (Hct) levels significantly increases in summer (p < 0.05). Statistical analyses revealed that all of the haematological parameters of N. randalli are higher than the P. erythrinus (p < 0.05). In terms of serum biochemical parameters, glucose (GLU), triglyceride (TRIG), cholesterol (CHOL), total protein (TP), aspartate aminotransferase (AST) and alkaline phosphatase (ALP) levels of two species had showed no significant difference in both summer and winter samples (p > 0.05). However, serum alanine aminotransferase (ALT) levels of N. randalli were statistically significant different compared to P. erythrinus in summer and winter samples (p < 0.05). Additionally, the highest lactate dehydrogenase (LDH) value was measured from N. randalli in summer sampling and this was found to be significantly different from other groups (p < 0.05). Multidimensional scaling (MDS) analysis revealed differences between the blood parameter results of N. randalli and P. erythrinus individuals. This study provides important data about the physiological adaptations of haematological and biochemical blood parameters of the two species to environmental factors. The similarity in haematological and biochemical parameters revealed the possibility that N. randalli could distribute to new habitats where P. erythrinus is distributed. This suggests a further potential distribution of the invasive N. randalli and the need for a careful monitoring. creator: Rifat Tezel creator: Ümit Acar creator: Sercan Yapıcı uri: https://doi.org/10.7717/peerj.18784 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tezel et al. title: Insights in biomarkers complexity and routine clinical practice for the diagnosis of thyroid nodules and cancer link: https://peerj.com/articles/18801 last-modified: 2025-01-20 description: BackgroundThe differential diagnosis between benign and malignant thyroid nodules continues to be a major challenge in clinical practice. The rising incidence of thyroid neoplasm and the low incidence of aggressive thyroid carcinoma, urges the exploration of strategies to improve the diagnostic accuracy in a pre-surgical phase, particularly for indeterminate nodules, and to prevent unnecessary surgeries. Only in 2022, the 5th WHO Classification of Endocrine and Neuroendocrine Tumors, and in 2023, the 3rd Bethesda System for Reporting Thyroid Cytopathology and the European Thyroid Association included biomarkers in their guidelines. In this review, we discuss the integration of biomarkers within the routine clinical practice for diagnosis of thyroid nodules and cancer.MethodologyThe literature search for this review was performed through Pub Med, Science Direct, and Google Scholar. We selected 156 publications with significant contributions to this topic, with the majority (86, or 55.1%) published between January 2019 and March 2024, including some publications from our group during those periods. The inclusion criteria were based on articles published in recognized scientific journals with high contributions to the proposed topic. We excluded articles not emphasizing molecular biomarkers in refine the pre-surgical diagnosis of thyroid nodules.ResultsWe explored genetic biomarkers, considering the division of thyroid neoplasm into BRAF-like tumor and RAS-like tumor. The specificity of BRAF mutation in the diagnosis of papillary thyroid carcinoma (PTC) is nearly 100% but its sensitivity is below 35%. RAS mutations are found in a broad spectrum of thyroid neoplasm, from benign to malignant follicular-patterned tumors, but do not increase the ability to distinguish benign from malignant lesions. The overexpression of miRNAs is correlated with tumor aggressiveness, high tumor node metastasis (TMN) stage, and recurrence, representing a real signature of thyroid cancer, particularly PTC. In addition, associations between the expression levels of selected miRNAs and the presence of specific genetic mutations have been related with aggressiveness and worse prognosis.ConclusionsThe knowledge of genetic and molecular biomarkers has achieved a high level of complexity, and the difficulties related to its applicability determine that their implementation in clinical practice is not yet a reality. More studies with larger series are needed to optimize their use in routine practice. Additionally, the improvement of new techniques, such as liquid biopsy and/or artificial intelligence, may be the future for a better understanding of molecular biomarkers in thyroid nodular disease. creator: Maria de Lurdes Godinho de Matos creator: Mafalda Pinto creator: Ana Gonçalves creator: Sule Canberk creator: Maria João Martins Bugalho creator: Paula Soares uri: https://doi.org/10.7717/peerj.18801 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 de Matos et al. title: Transcription factor specificity protein (SP) family in renal physiology and diseases link: https://peerj.com/articles/18820 last-modified: 2025-01-20 description: Dysregulated specificity proteins (SPs), members of the C2H2 zinc-finger family, are crucial transcription factors (TFs) with implications for renal physiology and diseases. This comprehensive review focuses on the role of SP family members, particularly SP1 and SP3, in renal physiology and pathology. A detailed analysis of their expression and cellular localization in the healthy human kidney is presented, highlighting their involvement in fatty acid metabolism, electrolyte regulation, and the synthesis of important molecules. The review also delves into the diverse roles of SPs in various renal diseases, including renal ischemia/reperfusion injury, diabetic nephropathy, renal interstitial fibrosis, and lupus nephritis, elucidating their molecular mechanisms and potential as therapeutic targets. The review further discusses pharmacological modulation of SPs and its implications for treatment. Our findings provide a comprehensive understanding of SPs in renal health and disease, offering new avenues for targeted therapeutic interventions and precision medicine in nephrology. creator: Wei Zhou creator: Jiaxi Fang creator: Qingqing Jia creator: Hanyan Meng creator: Fei Liu creator: Jianhua Mao uri: https://doi.org/10.7717/peerj.18820 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhou et al. title: Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms link: https://peerj.com/articles/18835 last-modified: 2025-01-20 description: BackgroundPeriodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.Materials and MethodsIn this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.ResultsCultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.ConclusionOverall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis. creator: Qian Zhang creator: Min Zhen creator: Xiaochen Wang creator: FengXiang Zhao creator: Yang Dong creator: Xiaoya Wang creator: Shengtao Gao creator: Jinfeng Wang creator: Wenyu Shi creator: Yifei Zhang uri: https://doi.org/10.7717/peerj.18835 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Evaluation of urinary density as a biomarker for the diagnosis of acute heart failure link: https://peerj.com/articles/18836 last-modified: 2025-01-20 description: BackgroundHeart failure (HF) has become a public healthcare concern with significant costs to countries because of the aging world population. Acute heart failure (AHF) is a common condition faced frequently in emergency departments, and patients often present to hospitals with complaints of breathlessness. The patient must be evaluated with anamnesis, physical examination, blood, and imaging results to diagnose AHF. Brain natriuretic peptide (BNP) is a widely accepted biomarker for the diagnosis of HF.MethodsThe files of the patients who applied to the emergency department with complaints of breathlessness were scanned, and BNP and urinary density (UD) levels were evaluated for the diagnosis of HF in patients.ResultsThe results support that BNP is an effective biomarker in AHF, as is widely accepted. When the correlation between BNP and UD measurements was examined in the present study, a negative correlation was detected between the parameters. The results also suggested that low UD values may help diagnose AHF.ConclusionIf similar results are obtained in prospective multicenter studies with the participation of more patients, UD value can be used as a biomarker for the diagnosis of AHF. creator: Mustafa Ahmet Akçalı creator: Semih Çınar creator: Kemal Abid Tekin creator: Recep Murat Mert creator: Sena Erduhan creator: Ertuğ Dinçer creator: Yusuf Altunöz creator: Arif Aksu creator: Esra Akçalı uri: https://doi.org/10.7717/peerj.18836 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Akçalı et al. title: Examining ozone effects on the tropical C4 crop Sorghum bicolor link: https://peerj.com/articles/18844 last-modified: 2025-01-20 description: Ozone (O3), a major air pollutant, can negatively impact plant growth and yield. While O3 impacts have been widely documented in crops such as wheat and soybean, few studies have looked at the effects of O3 on sorghum, a C4 plant and the fifth most important cereal crop worldwide. We exposed grain sorghum (Sorghum bicolor cv. HAT150843) to a range of O3 concentrations (daytime mean O3 concentrations ranged between 20 and 97 ppb) in open-top chambers, and examined how whole plant and leaf morphological traits varied in response to O3 exposure. Results showed no significant impact of realistic O3 exposure on whole plant biomass and its partitioning in sorghum. These findings suggest that sorghum is generally resistant to O3 and should be considered as a favourable crop in O3 polluted regions, while acknowledging further research is needed to understand the mechanistic basis of O3 tolerance in sorghum. creator: Mst Nahid Farha creator: Flossie Brown creator: Lucas A. Cernusak creator: Stephen Sitch creator: Alexander W. Cheesman uri: https://doi.org/10.7717/peerj.18844 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Farha et al. title: Prevalence of nasopharyngeal bacteria during naturally occurring bovine respiratory disease in commercial stocker cattle link: https://peerj.com/articles/18858 last-modified: 2025-01-20 description: Bovine respiratory disease (BRD) is one of the most common economic and health challenges to the beef cattle industry. Prophylactic use of antimicrobial drugs can alter the microbial communities in the respiratory tract. Considering that the bovine upper respiratory tract microbiome has been associated with generalized health, understanding the microenvironment that influences this microbiome may provide insights into the pathogenesis of BRD. This study aimed to determine temporal variation in nasopharyngeal (NP) microbiome in naturally occurring BRD in newly received stocker calves. Mixed breed steers (n = 40) were purchased from an auction market and housed in a commercial stocker farm. Clinical signs were used to identify BRD affected animals, and calves were categorized based on the number of treatments (NumTrt) received (0, 1, 2). On days 0, 7, 14, and 21, NP samples were collected, and subsequent DNA were isolated and sequenced. After sequencing, 16S rRNA V4 gene was amplified and utilized for NP bacterial determination. The difference in relative abundance based on day and NumTrt was measured using repeated measures ANOVA (PROC GLIMMIX; SAS 9.4). Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Verrucomicrobiota were the top phyla and Mycoplasma, Histophilus, Geobacillus, Saccharococcus, Lactobacillus, and Pasteurella were the top genera. In healthy calves, the relative abundance of Mycoplasma differed by day (P = 0.01), whereas on day 7, calves had five times greater abundance compared to day 0 (d 0: 0.06 ± 0.05; d 7: 0.30 ± 0.05). No differences were observed in the alpha diversity matrices based on day or NumTrt (P > 0.05). Results of this study suggest compositional variations in NP microbial populations occur during disease conditions. creator: Afroza Akter creator: Hannah Teddleton creator: Marc Caldwell creator: Gina Pighetti creator: Phillip R. Myer creator: Madison T. Henniger creator: Liesel Schneider creator: Elizabeth Shepherd uri: https://doi.org/10.7717/peerj.18858 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Akter et al. title: Deep cryptic diversity in the Craugastor podiciferus Species Group (Anura: Craugastoridae) of Isthmian Central America revealed by mitochondrial and nuclear data link: https://peerj.com/articles/18212 last-modified: 2025-01-17 description: The Craugastor podiciferus Species Group contains eleven species of terraranan frogs distributed from eastern Honduras to eastern Panama. All species have remarkable color pattern polymorphisms, which may contribute to potential taxonomic problems. We performed exhaustive sampling throughout the geographic distribution of the group to evaluate the phylogenetic relationships and biogeographic history of all named species based on two mitochondrial markers and nuclear ddRAD loci. We also implemented various species delimitation methods to test for the presence of unconfirmed candidate species within the group. Molecular phylogenetic analyses showed that the group contains four major clades. All currently named species are supported by molecular data, yet species richness within the group is clearly underestimated. Species delimitation was discordant between the mitochondrial and nuclear datasets and among analytical methods. Adopting a conservative approach, we propose that the C. podiciferus species group contains at least 12 unconfirmed candidate species. Ancestral area reconstruction showed that the group originated and diversified in the highlands of the Talamancan montane forest ecoregion of Costa Rica and western Panama. creator: Erick Arias creator: Andrew J. Crawford creator: Andreas Hertz creator: Gabriela Parra Olea uri: https://doi.org/10.7717/peerj.18212 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Arias et al. title: What ‘unexplored’ means: mapping regions with digitized natural history records to look for ‘biodiversity blindspots’ link: https://peerj.com/articles/18511 last-modified: 2025-01-17 description: We examined global records of accessible natural history voucher collections (with publicly available data and reliable locality data) for terrestrial and freshwater vascular plants, fungi, freshwater fishes, birds, mammals, and herpetofauna (amphibians and reptiles) and highlight areas of the world that would be considered undersampled and sometimes called ‘unexplored’ (i.e., have relatively low, or no evidence of, past sampling efforts) under typical Western-scientific descriptions. We also question what ‘unexplored’ may mean in these contexts and explain how replacing the term in favor of more nuanced phrasing (e.g., ‘biodiversity blindspots,’ which emphasizes the lack of publicly available data about specimens) can mitigate future misunderstandings of natural history science. We also highlight geographic regions where there are relatively few or no publicly available natural history records to raise awareness about habitats that might be worthy of future natural history research and conservation. A major finding is that many of the areas that appear ‘unexplored’ may be in countries whose collections are not digitized (i.e., they don’t have metadata such as GPS coordinates about their voucher specimens publicly available). We call for museums to prioritize digitizing those collections from these ‘biodiversity blindspots’ and for increased funding for museums to aid in these efforts. We also argue for increased scientific infrastructure so that more reference collections with vouchers can be kept in the countries of origin (particularly those countries lacking such infrastructure currently). creator: Laymon Ball creator: Sheila Rodríguez-Machado creator: Diego Paredes-Burneo creator: Samantha Rutledge creator: David A. Boyd creator: David Vander Pluym creator: Spenser Babb-Biernacki creator: Austin S. Chipps creator: Rafet Ç. Öztürk creator: Yahya Terzi creator: Prosanta Chakrabarty uri: https://doi.org/10.7717/peerj.18511 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ball et al. title: The pattern and burden of non-communicable diseases in armed conflict-exposed populations in Northeastern Nigeria link: https://peerj.com/articles/18520 last-modified: 2025-01-17 description: BackgroundThe risk of non-communicable diseases (NCDs) in conflict and post-conflict settings in Northeastern Nigeria has not been evaluated to date. As this region undergoes recovery, understanding the prevalence of NCDs, such as hypertension, diabetes, depression, and obesity, and the associated behavioral coping mechanisms, is crucial for developing tailored healthcare solutions. Therefore, this study aimed to assess the impact of conflict on the prevalence of NCDs in conflict-exposed areas in Northeastern Nigeria compared with non-conflict regions.MethodsThis study was an unmatched cross-sectional study. The participants were selected from inpatients and outpatients at general hospitals in Mubi (conflict-exposed) and Jada (non-conflict), which are local government areas in Adamawa, a state in Northeastern Nigeria. The study was conducted over four months, and data on various health indicators were collected. Multivariable binary logistic regression and complementary log regression were performed to investigate the effects of individual risk factors and regional settings on the prevalence of NCDs.FindingsA sample of 973 individuals from both locations was analyzed. The prevalence of hypertension, diabetes, abdominal obesity, and depression in the entire cohort was 22.92%, 5.04%, 44.19%, and 17.94%, respectively. The rates of hypertension and abdominal obesity in the conflict-exposed Mubi were lower, and the rate of depression was higher than those recorded in Jada. Females showed higher rates of hypertension, obesity, and depression than males. The residents of Mubi had lower odds of having abdominal obesity (adjusted odds ratio (aOR) = 0.18; 95% confidence interval (CI) [0.11–0.28]) but a higher risk of depression (incidence risk ratio (IRR) = 4.78; 95% CI [2.51–9.22]) than those in Jada. However, the participants affected by insurgency showed higher odds of having both abdominal obesity (aOR = 1.95; 95% CI [1.23–3.08]) and depression (IRR = 1.76; 95% CI [1.08–2.88]) than those who were not affected by the conflict.ConclusionsThe findings of this study underscore the urgent need for mental health support in conflict-affected regions and comprehensive healthcare strategies for the aging population. As adjustment of lifestyle factors is crucial for addressing NCDs, effective case management and food security are essential for reducing the risk of NCDs in conflict-exposed populations. creator: Roland I. Stephen creator: Jennifer A. Tyndall creator: Jamiu S. Olumoh creator: Malachy I. Okeke creator: Jacob A. Dunga creator: Tonde G. Elijah creator: Dillys M. Bello creator: Oyelola A. Adegboye creator: Jimmy A. Reyes uri: https://doi.org/10.7717/peerj.18520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Stephen et al. title: The relationship between steroid treatment and mortality in patients with COVID-19 followed up in an intensive care unit link: https://peerj.com/articles/18606 last-modified: 2025-01-17 description: AimOptimal treatment of the coronavirus disease (COVID-19) is still unclear. It has been reported that the use of different doses of corticosteroid treatments may reduce mortality. In our study, we aimed to find the effect of corticosteroid treatment dose on mortality of patients followed up in intensive care due to COVID-19.MethodsOur retrospective, descriptive and single-centre study included 102 patients diagnosed with COVID-19 who were followed up in intensive care unit, 28 of whom received pulse steroids and 74 of whom received high dose steroids. Laboratory values, duration of intensive care unit and mortality rates of the patients were evaluated.ResultsMortality was found to be statistically significantly lower in the group receiving pulse steroid compared to the group receiving high dose steroid. In multivariate logistic regression analysis, age and pulse steroid were found to be independent predictors of mortality. According to this analysis, each 10-year increase in age increased mortality by 4.8%, whereas pulse steroid decreased mortality by 79.4%.ConclusionIn our study, we found that mortality was statistically significantly lower in the group of patients receiving pulse steroids than in the group receiving high dose steroids. We found that the number of patients using pulse steroids was statistically significantly lower in the group with mortality. We found that age and pulse steroid independently determined the patients with mortality. creator: Huseyin Ali Ozturk creator: Fatih Necip Arici uri: https://doi.org/10.7717/peerj.18606 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ozturk and Arici title: Body size prediction in scorpions: a phylogenetic comparative examination of linear measurements of individual body parts link: https://peerj.com/articles/18621 last-modified: 2025-01-17 description: Body size has always been the focus of several ecological studies due to its undeniable influence on other life-history traits. The conventional representation of body size in arthropods typically relies on linear measures, such as total body length, or the length of specific body parts that can be used to represent body size. While these measures offer simplicity over more complicated alternatives (e.g., dry mass), technical problems persist for arthropods with complex body structures, as is the case for scorpions. In these animals, accurate measurements often require extensive handling, including the stretching of body parts. In light of the difficulties associated with directly measuring total length and carapace length in scorpions (two prevalent proxies for body size in the group), this study evaluates the ability of seven simple linear measurements in predicting length measures of boy size in scorpions under a phylogenetic framework. Predictive equations derived from phylogenetic mixed linear models fitted under Bayesian framework were implemented in custom R functions that can be applied for size prediction in a wide range of scorpions. Overall, accurate predictions of total length and carapace length could be achieved using any of the studied traits as single predictors. However, the most accurate predictions for total length were obtained using the length of metasomal segment V, while the best predictions for carapace length were achieved using telson length. The addition of a secondary predictor had low impact on the quality of the size predictions, indicating that increasing model complexity by incorporating additional predictors is not necessary to achieve accurate size estimates. Technical advantages and limitations associated with each linear measurement are discussed. In conclusion, this study broadens the repertoire of methods available for accurately estimating body size in scorpions, particularly in instances where body size information can only be obtained indirectly through allometric relationships. creator: Stênio Í. A. Foerster uri: https://doi.org/10.7717/peerj.18621 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Foerster title: Optimizing soil health through activated acacia biochar under varying irrigation regimes and cultivars for sustainable wheat cultivation link: https://peerj.com/articles/18748 last-modified: 2025-01-17 description: Wheat, a staple food crop globally, faces the challenges of limited water resources and sustainable soil management practices. The pivotal elements of the current study include the integration of activated acacia biochar (AAB) in wheat cultivation under varying irrigation regimes (IR). A field trial was conducted in the Botanical Garden, University of the Punjab, Lahore during 2023–2024, designed as a split-split-plot arrangement with RCBD comprising three AAB levels (0T, 5T, and 10T, T = tons per hectare) three wheat cultivars (Dilkash-2020, Akbar-2019, and FSD-08) receiving five IR levels (100%, 80%, 70%, 60%, and 50% field capacity). Biochar amended soil showed improved BET surface area, pore size, and volume. Carbon recovery (45%) and carbon sequestration capacity (49%) of 10T-AAB amended soil were better than non-amended soil (0.43% and 0.13%, respectively). The 10T-AAB amendment significantly improved the soil’s microporosity and water retention capacity, increasing it by 1.1 and 2.2 times, respectively. Statistical analysis showed that a reduction in IR negatively affected plant growth and yield. The 10T-AAB levels significantly increased sugar contents (14%), relative water content (10–28%), membrane stability index (27–55%), and photosynthetic pigments (18–26%) of wheat leaves under deficit irrigation among all the cultivars. Maximum stress markers (catalase, proline, peroxidase, and superoxide dismutase) were observed from Akbar under 50% irrigation with 0T-AAB, and the least were observed from 50% irrigated Dilkash-2020 with 10T-AAB amended soil. Among cultivars, Dilkash-2020 was observed to be the best for maximum yield, followed by FSD-08 and Akbar-2019, respectively. When compared to other IR levels, 10T-AAB amended soil had the highest yield enhancement (12, 11, and 9.2 times for Dilkash-2020, FSD-08, and Akbar-2019, respectively). Hence, AAB enhanced wheat production by improving soil properties, drought resilience, and yield attributes. creator: Lubaba Komal creator: Summera Jahan creator: Atif Kamran creator: Abeer Hashem creator: Graciela Dolores Avila-Quezada creator: Elsayed Fathi Abd_Allah uri: https://doi.org/10.7717/peerj.18748 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Komal et al. title: The role of fMRI in the mind decoding process in adults: a systematic review link: https://peerj.com/articles/18795 last-modified: 2025-01-17 description: BackgroundFunctional magnetic resonance imaging (fMRI) has revolutionized our understanding of brain activity by non-invasively detecting changes in blood oxygen levels. This review explores how fMRI is used to study mind-reading processes in adults.MethodologyA systematic search was conducted across Web of Science, PubMed, and Google Scholar. Studies were selected based on strict inclusion and exclusion criteria: peer-reviewed; published between 2000 and 2024 (in English); focused on adults; investigated mind-reading (mental state decoding, brain-computer interfaces) or related processes; and employed various mind-reading techniques (pattern classification, multivariate analysis, decoding algorithms).ResultsThis review highlights the critical role of fMRI in uncovering the neural mechanisms of mind-reading. Key brain regions involved include the superior temporal sulcus (STS), medial prefrontal cortex (mPFC), and temporoparietal junction (TPJ), all crucial for mentalizing (understanding others’ mental states).ConclusionsThis review emphasizes the importance of fMRI in advancing our knowledge of how the brain interprets and processes mental states. It offers valuable insights into the current state of mind-reading research in adults and paves the way for future exploration in this field. creator: Sahal Alotaibi creator: Maher Mohammed Alotaibi creator: Faisal Saleh Alghamdi creator: Mishaal Abdullah Alshehri creator: Khaled Majed Bamusa creator: Ziyad Faiz Almalki creator: Sultan Alamri creator: Ahmad Joman Alghamdi creator: Mohammed Alhazmi creator: Hamid Osman creator: Mayeen U. Khandaker uri: https://doi.org/10.7717/peerj.18795 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alotaibi et al. title: The effectiveness of arbuscular mycorrhizal fungal species (Funneliformis mosseae, Rhizophagus intraradices, and Claroideoglomus etunicatum) in the biocontrol of root and crown rot pathogens, Fusarium solani and Fusarium mixture in pepper link: https://peerj.com/articles/18438 last-modified: 2025-01-16 description: This study evaluated the effectiveness of arbuscular mycorrhizal fungi (AMF) species, including Funneliformis mosseae (FM), Rhizophagus intraradices (RI), Claroideoglomus etunicatum (CE), and a Mycorrhizal mix (MM) comprising these three species, on pepper plants (Capsicum annuum L.) inoculated with two isolates of Fusarium solani (48-F. solani and 18-F. solani) and two isolates of Fusarium mix (50-F. mixture and 147-F. mixture). Analysis of variance (ANOVA)-Tukey statistics revealed that the effects of AMF inoculations on morphological parameters, disease severity, root colonization, and total spore numbers in pathogen-infected plants varied significantly depending on the AMF species and pathogen group. AMF colonization significantly reduced disease severity, with disease inhibition (DI) reaching up to 58%, depending on the specific pathogen. However, there were a few instances where the application of AMF did not lead to a reduction in disease severity. Single AMF species were more effective in enhancing the growth of pathogen-treated host plants and suppressing disease compared to the mixed AMF. The mixed AMF was only more effective in balancing pathogen-induced decreases in plant nutrients (Copper (Cu), Magnesium (Mg), Zinc (Zn), and Phosphorus (P)). Among the compared mycorrhizae, C. etunicatum (CE) was the most effective in disease suppression due to its relatively more positive effects on plant root structure, increasing root fresh weight by up to 49% in the CE+pathogen plant group compared to the control group. Root colonization rates were generally higher in plants treated with both mycorrhiza and pathogens compared to plants treated with mycorrhiza alone. Overall, the curative effects of AMFs on plants following pathogen application varied concurrently with disease severity rates caused primarily by pathogens. AMFs demonstrated greater efficacy in combating 18-F. solani, which causes less severe plant disease. However, the effectiveness of AMFs was comparatively lower against 48-F. solani and 147-F. mix., which cause more severe plant disease. This indicates that the efficacy of AMFs varies depending on the specific strain of Fusarium solani, with better results observed against strains that cause less severe plant disease. creator: Ayşin Bilgili uri: https://doi.org/10.7717/peerj.18438 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bilgili title: Assessment of complications and success rates of Percutaneous nephrolithotomy: single tract vs. multi tract approaches link: https://peerj.com/articles/18450 last-modified: 2025-01-16 description: PurposeThe objective of this study was to assess the success and complication rates of single-tract access vs. multi-tract percutaneous nephrolithotomy (PNL).Material and MethodsThe medical records of consecutive patients who underwent PNL for staghorn, partial staghorn, and complex kidney stones between 2014 and 2022 were retrospectively reviewed. The demographic data, stone volumes, fluoroscopy and operation durations, changes in hemoglobin levels, numbers of blood transfusions, stone-free rates, perioperative complications, duration of nephrostomy removal, and length of hospital stay parameters were noted. The complications and complexity of PNL were graded using the modified Clavien and Guy’s stone scores, respectively. Single and multi-tract subgroups were determined based on PNL access strategy and the subgroups were analyzed.ResultsThe study involved 208 patients, with 158 in the single-tract group and 50 in the multi-tract group. The groups were comparable in age, ASA scores, and comorbidities (p > 0.05). The characteristics of the stones, such as their location, size, and density, did not show any significant differences between the groups (p > 0.05), except for Guy’s stone score, which was higher in the multi-tract group (p = 0.028). The multi-tract group also had significantly longer fluoroscopy and operation times (p < 0.001). There was no statistically significant difference in stone-free rates between the two groups (76.0% vs. 78.0%, p = 0.766). Although the drop in hemoglobin levels was more significant in the multi-tract group (p = 0.027), transfusion rates did not differ significantly between the two groups (p = 0.334). Complication rates were higher in the multi-tract group, but this difference was not statistically significant (p = 0.896).ConclusionThis study demonstrated that multi-tract PNL can achieve high stone-free rates with a modest increase in the occurrence of acceptable complications when performed by an experienced surgeon. creator: Ömür Memik creator: Onur Karslı uri: https://doi.org/10.7717/peerj.18450 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Memik and Karslı title: Temporal drivers of abundance and community structure of scyphozoan jellyfish in tropical coastal waters link: https://peerj.com/articles/18483 last-modified: 2025-01-16 description: Population blooms of scyphozoan jellyfish in tropical shallow water regions can fuel localized fisheries but also negatively impact human welfare. However, there is a lack of baseline ecological data regarding the scyphozoans in the region, which could be used to manage a fast-growing fishery and mitigate potential impacts. Thus, this study aims to investigate the temporal factors driving the distribution of scyphozoan community along the environmental gradients under different monsoon seasons, rainfall periods, moon phases, and diel-tidal conditions in the Klang Strait located in the central region along the west coast of Peninsular Malaysia, where bloom events are increasing. Scyphozoan samples were collected using commercial bag nets during a 19-month survey. Temporal variations in species abundance and composition were evident and related to the local environmental parameters (salinity, dissolved oxygen, temperature, turbidity, and pH) that varied with the regional monsoon events, although these effects appeared to be species-specific. Phyllorhiza punctata, Acromitus flagellatus, Lychnorhiza malayensis, and Rhopilema esculentum were more abundant during the wetter northeast monsoon (NEM) while the abundance of Chrysaora chinensis and Lobonemoides robustus increased during the drier southwest monsoon (SWM). During the wet period of NEM, scyphozoan abundance was generally higher during the daytime than night-time. The regional monsoon regime and local hydrological events account for jellyfish abundance in the nearshore area with concurrent threats to coastal tourism and power plants, as well as benefits to fisheries especially during the NEM. creator: Wan Mohd Syazwan creator: Amy Yee-Hui Then creator: Ving Ching Chong creator: Mohammed Rizman-Idid uri: https://doi.org/10.7717/peerj.18483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Syazwan et al. title: Predictors of county-level diabetes-related mortality risks in Florida, USA: a retrospective ecological study link: https://peerj.com/articles/18537 last-modified: 2025-01-16 description: BackgroundDiabetes is an increasingly important public health problem due to its socioeconomic impact, high morbidity, and mortality. Although there is evidence of increasing diabetes-related deaths over the last ten years, little is known about the population level predictors of diabetes-related mortality risks (DRMR) in Florida. Identifying these predictors is important for guiding control programs geared at reducing the diabetes burden and improving population health. Therefore, the objective of this study was to identify geographic disparities and predictors of county-level DRMR in Florida.MethodsThe 2019 mortality data for the state of Florida were obtained from the Florida Department of Health. The 10th International Classification of Disease codes E10-E14 were used to identify diabetes-related deaths which were then aggregated to the county-level. County-level DRMR were computed and presented as number of deaths per 100,000 persons. Geographic distribution of DRMR were displayed in choropleth maps and ordinary least squares (OLS) regression model was used to identify county-level predictors of DRMR.ResultsThere was a total 6,078 diabetes-related deaths in Florida during the study time period. County-level DRMR ranged from 9.6 to 75.6 per 100,000 persons. High mortality risks were observed in the northern, central, and southcentral parts of the state. Relatively higher mortality risks were identified in rural counties compared to their urban counterparts. Significantly high county-level DRMR were observed in counties with high percentages of the population that were: 65 year and older (p < 0.001), current smokers (p = 0.032), and insufficiently physically active (p = 0.036). Additionally, percentage of households without vehicles (p = 0.022) and percentage of population with diabetes (p < 0.001) were significant predictors of DRMR.ConclusionGeographic disparities of DRMR exist in Florida, with high risks being observed in northern, central, and southcentral counties of the state. The study identified county-level predictors of these identified DRMR disparities in Florida. The findings are useful in guiding health professionals to better target intervention efforts. creator: Nirmalendu Deb Nath creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.18537 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Deb Nath and Odoi title: Study on the absorption characteristics of euscaphic acid and tiliroside in fruits of Rosa laxa Retz. link: https://peerj.com/articles/18638 last-modified: 2025-01-16 description: The fruits of Rosa laxa Retz. (FRL) have a long history of medicinal use, known for their rich composition of flavonoids, polyphenols, amino acids, sugars, and other bioactive compounds. FRL exhibits pharmacological effects such as antioxidant, antiviral, antibacterial, and antitumor activities, making it a valuable resource with significant development potential in both the food and pharmaceutical industries. This study employed a response surface methodology combined with ultra-high-performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-TQ-MS) to optimize FRL extraction. Reflux extraction was determined to be the most effective method with the following optimized parameters: 65% ethanol extraction solvent, material-to-liquid ratio of 1:35 (g/mL), and extraction time of 140 min, resulting in the FRL extract (FRLE). Under these optimized conditions, the extracted amount was extract was 51.00 ± 1.07%, the average content of total polyphenols was 126.55 ± 2.61 mg/g, and the average content of euscaphic acid was 2.90 ± 0.08 mg/g, demonstrating the efficiency of the extraction method. Using the Caco-2 cell model, the study investigated the absorption characteristics of euscaphic acid and tiliroside within FRLE. Results indicated that with increasing time, the absorbed amount (Qr) of euscaphic acid and tiliroside gradually increased, with an efflux ratio (RB→A/A→B) of less than 1.5, suggesting bidirectional drug transport with no significant directionality. Upon the addition of P-glycoprotein (P-gp) inhibitors Verapamil (Ver) and Ciclosporin A (CsA), as well as the chelating agent ethylenebis (oxyethylenenitrilo) tetraacetic acid (EGTA), Qr and Papp values notably increased, indicating that these two components are P-gp substrates with cellular basolateral efflux transport. Additionally, optimal absorption efficiency was observed under weakly acidic conditions (pH 6.0). In conclusion, euscaphic acid and tiliroside in FRLE demonstrated good membrane permeability, primarily relying on passive diffusion for absorption. This study offers experimental insights into the intestinal absorption of FRL in vivo. creator: Ning Wang creator: Li Tian uri: https://doi.org/10.7717/peerj.18638 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang and Tian title: Three new species of the family Idyanthidae (Copepoda, Harpacticoida) from sublittoral zones around the Korean Peninsula link: https://peerj.com/articles/18767 last-modified: 2025-01-16 description: There are few taxonomic studies of the harpacticoid family Idyanthidae Lang, 1944 in the Pacific Ocean. As a first report of the family in this region, one species of the monotypic genus Idyellopsis Lang, 1948 and two species of the genus Idyella Sars, 1905 are described from sublittoral habitats around the Korean Peninsula. Idyellopsis orientalis sp. nov. is distinguished from the type and only species of the genus, Idyellopsis typica Lang, 1948, in the length:width ratio of the body and genital double-somite, length of caudal seta I, and structure of the female P5 baseoendopod. Idyella dolichi sp. nov. and Idyella exochos sp. nov. share the armature of the female P5 exopod with four setae with Idyella exigua Sars, 1905, Idyella major Sars, 1920, and Idyella pallidula Sars, 1905. However, the two new species differ from the three European species in the armature of the terminal segment of the P1 endopod and female P5 baseoendopod, and in the shape of the genital double-somite. The male of Idyella dolichi sp. nov. also has two distinct features: the distal two segments of the P2 endopod are completely fused, and the third segment of the antennule has a prominent outer projection. The geographical distribution of Idyellopsis and Idyella is extended by the discovery of three new species in Korean waters. We also discuss a possible phylogenetic relationship among members of family Idyanthidae at genus level. creator: Jong Guk Kim creator: Kyuhee Cho creator: Jimin Lee uri: https://doi.org/10.7717/peerj.18767 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Kim et al. title: Nitrogen fertilizer application for improving the biomass, quality, and nitrogen fixation of alfalfa (Medicago sativa L.) at different growth stages in a saline‒alkali soil link: https://peerj.com/articles/18796 last-modified: 2025-01-16 description: BackgroundThe application of nitrogen (N) fertilizer to alfalfa (Medicago sativa L.) has received little attention due to the ability of this plant to fix N. However, N deficiency stress is often observed in marginal lands of China, especially in saline–alkali soils. Thus, this study aimed to assess the response of alfalfa yield, quality, N fixation, and soil N concentration to N fertilizer application at different stages in saline–alkali soil of Inner Mongolia. A 2-year (2020 and 2021) field experiment with five N fertilizer application rates, namely, 0 (N0), 20 (N20), 60 (N60), 120 (N120) and 180 (N180) kg N ha−1, was conducted in Inner Mongolia.ResultsThe results showed that N fertilizer application of 180 kg ha−1 significantly increased the total alfalfa yield by 29%–32% by improving the stem‒leaf ratio; however, it didn’t lead to a further increase in alfalfa quality. N fertilizer applications of 60 and 120 kg ha−1 significantly improved the crude protein by 10.6%–22.7% and reduced the acid or neutral detergent fiber by 10.0%–18.7% in vegetative and bud stages, respectively, by improving the leaf N concentration. Furthermore, the fraction of N derived from the atmosphere reached 68.6%, with a significant increase in the corresponding amount of N fixed in N60. Soil NO3−-N concentrations significantly increased by 24.1%–33.3%, and NH4+-N concentrations increased by 1 to 3 times when N fertilizer application exceeded 120 kg N ha−1 compared with that in N0.ConclusionsOverall, this study revealed the essential role of N fertilizer application at low rates in alfalfa production, as this practice not only increases alfalfa yield but also improves N fixation in saline‒alkali soil. However, it did not result in further improvement in alfalfa quality at the early flowering stage. The findings provides valuable guidance for N fertilizer application in alfalfa production on saline‒alkali soils. creator: Weifan Wan creator: Qian Liu creator: Ke Li creator: Kun Zhao creator: Fei Qi creator: Yuanshuo Li creator: Zhi Sun creator: Haigang Li uri: https://doi.org/10.7717/peerj.18796 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wan et al. title: Association between phase angle, body mass index and insulin resistance in patients with type 2 diabetes mellitus: a cross-sectional study link: https://peerj.com/articles/18815 last-modified: 2025-01-16 description: Background: The purpose of this analysis was to investigate the associations between phase angle (PhA), body mass index (BMI) and insulin resistance (IR) in patients with type 2 diabetes mellitus (T2DM).Methods: The retrospective cross-sectional study included 200 T2DM patients treated during 2018 to 2019 in Zhongda Hospital Southeast University. PhA and other body composition indicators were measured by bioelectrical impedance analysis (BIA). Subjects were classified into four groups based on body composition: low phase angle and low body mass index (LPLB), low phase angle and high body mass index (LPHB), high phase angle and low body mass index (HPLB) and high phase angle and high body mass index (HPHB).Results: Overall, in the unadjusted model and minor, all adjusted models (unadjusted model, models 1–4), homeostasis model assessment of insulin resistance (HOMA-IR) was higher in the LPHB group than in the LPLB group (P = 0.034). In the unadjusted model, Model 1 (adjustment for age), Model 2 (adjust for age+duration), Model 3 (adjust for age+duration+sex+UA+TG+TC) and Model 4 (adjust for age+duration+sex+UA+TG+TC+HDL+HbA1c), the adjusted ORs for participants were 4.4 (95% CI [1.72–11.24]), 4.41 (95% CI [1.73–11.27]), 4.75 (95% CI [1.83–12.32]), 2.93 (95% CI [1.04–8.23]) and 3.1 (95% CI [1.09–8.86]) respectively, compared to LPHB group.Conclusions: T2DM patients with the body composition of low phase angle and high body mass index exhibited the most severe degree and the highest risk of insulin resistance. creator: Yezi Hu creator: Hui Jin uri: https://doi.org/10.7717/peerj.18815 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hu and Jin title: Optimization and action mechanism of pollutant removal performance of unsaturated vertical flow constructed wetland (UVFCW) driven by substained-release carbon source link: https://peerj.com/articles/18819 last-modified: 2025-01-16 description: Constructed wetland (CW) technology has attracted much attention due to its economical and environmentally friendly features. The low dissolved oxygen (DO) and low carbon/nitrogen (C/N) ratio in the wetland influent water affect the treatment performance of CW, resulting in a decrease in the removal efficiency of ammonia nitrogen (NH4+-N) and nitrate nitrogen (NO3−-N). In order to address this problem, this study optimized the pollutants removal performance of unsaturated vertical flow constructed wetland (UVFCW) by adding sustained-release carbon sources (corn cobs + polybutylene adipate terephthalate (PBAT)). The results showed that the sustained-release of carbon source increased the carbon source in UVFCW, thus increasing the abundance and activity of denitrifying microorganisms and enhancing the denitrification reaction, ultimately improving the removal of NO3−-N, with its removal efficiency reaching up to 95.50%. The placement method of sustained-release carbon source mainly affected the distribution of carbon source and DO in water body, thus influencing the relative abundance of microorganisms, finally affecting the removal of pollutants. Among them, the removal efficiency of total nitrogen (TN), NO3−-N, and total phosphorus (TP), and the relative abundance of denitrifying microorganisms in the CWR-Cu (uniform placement of sustained-release carbon source) were significantly higher than those in the CWR-Ca (centralized placement above) and CWR-Cb (centralized placement below) (p < 0.05). The surface C:O (carbon:oxygen) ratio of sustained-release carbon source after water treatment showed a decreasing trend, and CWR-Cu exhibited the greatest decrease in C:O ratio. In summary, CWR-Cu achieved the highest utilization of the carbon source and produced the largest number of heterotrophic microorganisms. This study reveals that CWR-Cu is a structural process for the efficient removal of nitrogen and phosphorus pollutants, and our findings provide theoretical basis and technical support for actual projects. creator: Yuechang Wang creator: Lin-Lan Zhuang creator: Shuang Liu creator: Yuanjun Su creator: Zhen Hu creator: Jian Zhang creator: Xiaoping Wang creator: Shaoming Cui creator: Gang Peng creator: Shuting Xie uri: https://doi.org/10.7717/peerj.18819 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Composition of soil fungal communities and microbial activity along an elevational gradient in Mt. Jiri, Republic of Korea link: https://peerj.com/articles/18762 last-modified: 2025-01-15 description: Approximately 64% of the Republic of Korea comprises mountainous areas, which as cold and high-altitude regions are gravely affected by climate change. Within the mountainous and the alpine-subalpine ecosystems, microbial communities play a pivotal role in biogeochemical cycling and partly regulate climate change through such cycles. We investigated the composition and function of microbial communities, with a focus on fungal communities, in Republic of Korea’s second tallest mountain, Mt. Jiri, along a four-point-altitude gradient: 600-, 1,000-, 1,200-, and 1,400-m. Soil pH and elevation were negatively correlated, with soils becoming more acidic at higher altitude. Of the five soil enzyme activities analyzed, cellobiohydrolase, β-1,4-glucosidase, and β-1,4-xylosidase activity showed differences among the elevation levels, with lower activity at 600 m than that at 1,400 m. Soil microbial biomass correlated positively with increasing elevation and soil water content. The decrease in β-1,4-N-acetylglucosaminidase suggests a reduction in fungal biomass with increasing altitude, while factors other than elevation may influence the increase in activity of the cellobiohydrolase, β-1,4-glucosidase and β-1,4-xylosidase. Fungal alpha diversity did not exhibit an elevational trend, whereas beta diversity formed two clusters (600–1,000 m and 1,200–1,400 m). Community composition was similar among the elevations, with Basidiomycota being the most predominant phylum, followed by Ascomycota. Conversely, among the fungal communities at 1,000 m, Ascomycota was the most dominant, possibly due to increased pathotroph percentage. Elevational gradients induce changes in soil properties, vegetation, and climate factors such as temperature and precipitation, all of which impact soil microbial communities and altogether create a mutually reinforcing system. Hence, inspection of elevation-based microbial communities can aid in inferring ecosystem properties, specifically those related to nutrient cycling, and can partly help assess the oncoming direct and indirect effects of climate change. creator: Ana Mitcov creator: Daegeun Ko creator: Kwanyoung Ko creator: Jaeho Kim creator: Neung-Hwan Oh creator: Hyun Seok Kim creator: Hyeyeong Choe creator: Haegeun Chung uri: https://doi.org/10.7717/peerj.18762 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Mitcov et al. title: The impact of side and top arm techniques during the backstroke breakout phase on 15-meter swimming performance link: https://peerj.com/articles/18838 last-modified: 2025-01-15 description: BackgroundResearch on the swimming starts and turns in professional swimming has become increasingly refined. The breakout phase is a crucial transition from point between underwater and above-water movements. The side arm technique is commonly used during the backstroke breakout phase. However, some swimmers have also achieved good performance using the top arm technique. The impact of the two techniques during the backstroke breakout phase is yet to be explored.PurposeTo compare the velocity and key angles differences between the side arm and top arm techniques and analyze their effect on the first 15-m performance after push-off.MethodsThe subjects were 16 high-level swimmers: eight males (20.4 ± 1.6 yr) and eight females (20.9 ± 1.7 yr). Of these, 14 were backstrokers or had individual medley as their primary event. The best performances in the history of the sport’s level World Aquatics Points are 682.1 ± 59.0 and 729.3 ± 41.5 for males and females, respectively. A within-subject design was used to test both the side arm and top arm techniques. Four underwater cameras were used to capture two-dimensional data from two perspectives, focusing on the breakout phase. A two-way ANOVA used to compare segment velocity, angles, and 15-m performance between the two genders and breakout techniques. Pearson’s correlation analysis was used to explore the relationship between segment velocity and 15-m performance, and hierarchical regression was employed to investigate the impact of breakout velocity on the 15-m performance.ResultsBoth male and female swimmers exhibited a significantly faster top arm velocities of (1.72 ± 0.20 and 1.47 ± 0.16 m/s, respectively) compared to the side arm velocities (1.51 ± 0.23 and 1.29 ± 0.19 m/s, respectively) during the breakout phase. Additionally, significant differences were found between the two genders (F = 11.189, p = 0.002, η2 = 0.286) and breakout techniques (F = 8.014, p = 0.008, η2 = 0.223), with no interaction effect (F = 0.037, p = 0.849, η2 = 0.001). Furthermore, both male (R = −0.447, p = 0.109) and female (R = −0.555, p = 0.017) swimmers showed a moderate positive correlation between breakout velocity and 15-m performance, and the regression model indicated a significant impact on the 15-m performance.ConclusionThe top arm technique during backstroke may offer a velocity advantage over the traditional side arm technique during the breakout phase, influencing 15-m performance. However, considering the short duration of the breakout phase, this advantage and its impact may need to be considered in conjunction with the smoothness of the transition to the subsequent phases. creator: Zhenyu Jin creator: Yuhang Zhou creator: Dapeng Wang creator: Yuhong Wen uri: https://doi.org/10.7717/peerj.18838 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Jin et al. title: Demography and homing behavior in the poorly-known Philippine flat-headed frog Barbourula busuangensis (Anura: Bombinatoridae) link: https://peerj.com/articles/18694 last-modified: 2025-01-14 description: The flat-headed frog, Barbourula busuangensis, is a poorly known, riverine species, endemic to the province of Palawan in the Philippines. We applied capture-mark-recapture (CMR) methods to follow individuals at two sites (Malbato and San Rafael) in the island of Busuanga over 10 months in 2022–2023. We used passive internal transponders (PITs) to mark adult and subadults and single-colored visual internal elastomers (VIEs) for cohorts of juveniles. From a total of 196 frogs PIT-tagged in Malbato and 144 in San Rafael, we obtained overall recapture rates of 49% and 60% respectively. We used the POPAN formulation in MARK software to estimate abundance, survival, movement, and age-class demographics. Our best model estimated an average population size of 268 frogs at Malbato and 232 at San Rafael, and constant survival probabilities (mean ≥ 0.97) at both sites. When adding age classes to the model, abundance of adults was always higher than that of subadults producing an age structure dominated by adults at both sites. Growth rates decreased significantly with body size, being higher in juveniles (1.51 mm/month) and subadults (1.56 mm/month) than in adult frogs (0.60 mm/month). At these growth rates frogs may reach adulthood at 2.5 years, with the oldest individuals likely being over 11 years old. CMR data confirmed site fidelity, and translocation experiments revealed that frogs have the ability to home when displaced 10–50 m upstream and downstream from their original capture site. This is the first long-term study of B. busuangensis using robust field and analysis methods. Our data suggest that B. busuangensis is stable at present in Busuanga, with long-lived adults and dispersing subadults. We expect that these data may serve as baseline of current population abundance, age structure and growth rates which are factors that tend to be affected when species are threatened. In this way it may help researchers and conservation practitioners detect potential changes that may occur as this species confronts the challenges of the Anthropocene. creator: Marta Miñarro creator: Patricia Burrowes creator: Claudia Lansac creator: Gregorio Sánchez-Montes creator: Leticia E. Afuang creator: Ignacio De la Riva uri: https://doi.org/10.7717/peerj.18694 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Miñarro et al. title: Acaricidal and insecticidal activities of entomopathogenic nematodes combined with rosemary essential oil and bacterium-synthesized silver nanoparticles against camel tick, Hyalomma dromedarii and wax moth, Galleria mellonella link: https://peerj.com/articles/18782 last-modified: 2025-01-14 description: An innovative approach to ticks and insect pests management is necessary to mitigate the challenges posed by the indiscriminate use of chemical pesticides, which can lead to resistance development and environmental pollution. Despite their great potential, biological control agents have significant manufacturing, application, and stability limitations. Currently, using phytochemicals, biosynthesized nanoparticles, and bioagents to get rid of arthropods might be a good alternative that would make farmers less worried about residues and resistance. The present investigation was carried out to determine for the first time the in vitro acaricidal and insecticidal efficacies of endogenous two entomopathogenic nematodes (EPNs), Heterorhabditis indica and Steinernema sp. combined with either Proteus mirabilis-synthesized silver nanoparticles or Rosmarinus officinalis essential oil against the camel tick, Hyalomma dromedarii larvae and females, and greater wax moth, Galleria mellonella larvae as well. We also determined the potential effects of these treatments on the biological characteristics of H. dromedarii’s engorged females. We further investigated R. officinalis essential oil (EO) profiling and nanoparticle (AgNPs) characterization. All the evaluated combinations demonstrated synergistic effects on the larvae of G. mellonella and H. dromedarii, as well as on engorged females. When H. indica was mixed with EO or AgNPs, it worked well than when Steinernema sp. was mixed with EO or AgNPs. This was shown by the highest number of tick and insect mortalities and the lowest lethal concentration (LC50) values. One day after G. mellonella was exposed to H. indica (1,000 infective juveniles (IJs)) together with EO at 60 or 40 mg/mL, all tested individuals died. We obtained the same results when H. dromedarii females exposed to the same level of EPN with 60 mg/mL EO, and when H. dromedarii larvae treated with H. indica at 500 IJs + EO at 25 mg/mL. Treatments altered all biological parameters of engorged females, revealing extremely noticeable differences between the treated and untreated groups. Gas chromatography–mass spectrometry (GC-MS) analysis identified a total of 28 compounds in the R. officinalis EO. Visual observation showed a color change from yellow to dark brown for AgNPs biosynthesized from P. mirabilis; the transmission electron microscopy (TEM) image and ultraviolet–visible (UV-Vis) spectrum showed well-dispersed particles with a diameter of 5–45 nm; and the greatest surface plasmon peaked at 320 nm. The results demonstrated the high efficacy of combining EPN, H. indica, with EO to control tick and insect pests. This is due to its acaricidal activity on different stages of H. dromedarii, including larvae and engorged females, and its larvicidal effect on G. mellonella. creator: Bander Albogami creator: Hadeer Darwish creator: Akram Alghamdi creator: Ahmed BahaaEldin Darwish creator: Wafa Mohammed Al-Otaibi creator: Mohamed A. Osman creator: Zamzam M. Al Dhafar creator: Abeer Mousa Alkhaibari creator: Abadi M. Mashlawi creator: Fadi Baakdah creator: Ahmed Noureldeen uri: https://doi.org/10.7717/peerj.18782 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Albogami et al. title: Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes link: https://peerj.com/articles/18785 last-modified: 2025-01-14 description: The virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals. This study introduces a streamlined, scalable protocol for DNA extraction using a commercially-available kit as an alternative, assessing its performance against the phenol-chloroform method across human fecal, mouse fecal, and soil samples. No significant differences in virome diversity or community composition were seen between methods. Most viral operational taxonomic units (vOTUs) were common to both methods, with only a small percentage unique to either approach. Alpha- and beta-diversity analyses showed no significant impact of the extraction method on virome composition, confirming the kit’s efficacy and versatility on sample types beyond those officially supported by the manufacturer. While the kit approach offers benefits like reduced toxicity and increased throughput, it has limitations such as higher costs and potential issues reliably capturing low-abundance taxa. This protocol provides a viable option for large-scale virome studies, although the phenol-chloroform approach may still be preferable for specific sample types. creator: Michael Shamash creator: Saniya Kapoor creator: Corinne F. Maurice uri: https://doi.org/10.7717/peerj.18785 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shamash et al. title: Do goats recognise humans cross-modally? link: https://peerj.com/articles/18786 last-modified: 2025-01-14 description: Recognition plays a key role in the social lives of gregarious species, enabling animals to distinguish among social partners and tailor their behaviour accordingly. As domesticated animals regularly interact with humans, as well as members of their own species, we might expect mechanisms used to discriminate between conspecifics to also apply to humans. Given that goats can combine visual and vocal cues to recognise one another, we investigated whether this cross-modal recognition extends to discriminating among familiar humans. We presented 26 goats (17 males and nine females) with facial photographs of familiar people and two repeated playbacks of a voice, either congruent (from the same person) or incongruent with that photograph (from a different person). When cues were incongruent, violating their expectations, we expected goats to show changes in physiological parameters and moreover, respond faster and for longer after playbacks. Accordingly, heart rate decreased as the playback sequence progressed, but only when the face and voice presented were incongruent. Heart rate variability was also affected by congruency, but we were unable to determine precisely where differences lay. However, goats showed no changes in time taken to respond, or how long they responded for (our primary variables of interest). We also found evidence to suggest that shifts in cardiac responses may not have been robust. Although our findings could imply that goats had successfully perceived differences in congruency between the visual and vocal identity information presented, further evidence is needed to determine whether they are capable of cross-modal recognition of humans. creator: Marianne A. Mason creator: Stuart Semple creator: Harry H. Marshall creator: Alan G. McElligott uri: https://doi.org/10.7717/peerj.18786 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mason et al. title: Sleep-wake patterns of fencing athletes: a long-term wearable device study link: https://peerj.com/articles/18812 last-modified: 2025-01-14 description: ObjectiveSleep is the most efficient means of recovery for athletes, guaranteeing optimal athletic performance. However, many athletes frequently experience sleep problems. Our study aims to describe the sleep-wake patterns of fencing athletes and determine whether factors, such as sex, competitive level and training schedules, could affect the sleep-wake rhythm.MethodsSleep data from 23 fencing athletes were collected using the Huawei Band 6, monitoring key sleep parameters such as bedtime, wake time, duration of deep and light sleep, wake periods, REM sleep duration, and nap duration. During this period, athletes were required to wear the band continuously for 24 hours daily, except bathing, charging, and competition times.ResultsAthletes averaged 7.97 hours of sleep per night, with significant differences observed in wake time (p = 0.015) and midpoint of sleep (p = 0.048) between high-level and low-level athletes, as well as a higher frequency of naps among high-level (χ2 = 11.97, p = 0.001) and female (χ2 = 3.88, p = 0.049) athletes. Nap duration was negatively correlated with night sleep duration (r =  − 0.270, p < 0.001). Athletes were observed for changes in sleep-wake patterns from Monday to Sunday. On Mondays, Wednesdays, and Fridays, when there was no morning training, the athletes’ wake-up time and the midpoint of sleep were shifted significantly backward, and there were significant differences in sleep parameters between training days and rest days.ConclusionThe sleep patterns of athletes differ according to level and gender. The sleep-wake patterns of athletes are influenced by training schedules, indicating the presence of sleep rhythm disruption. creator: Jiansong Dai creator: Xiaofeng Xu creator: Gangrui Chen creator: Jiale Lv creator: Yang Xiao uri: https://doi.org/10.7717/peerj.18812 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dai et al. title: Identification and mechanistic insights of cell senescence-related genes in psoriasis link: https://peerj.com/articles/18818 last-modified: 2025-01-14 description: BackgroundPsoriasis is a chronic inflammatory skin disease affecting 2–3% of the global population, characterised by red scaly patches that significantly affect patients’ quality of life. Recent studies have suggested that cell senescence, a state in which cells cease to divide and secrete inflammatory mediators, plays a critical role in various chronic diseases, including psoriasis. However, the involvement and mechanisms of action of senescence-related genes in psoriasis remain unclear.MethodsThis study aimed to identify senescence-related genes associated with psoriasis and explore their molecular mechanisms. RNA sequencing data from psoriasis and control samples were obtained from the GEO database. Differential expression analysis was performed using DESeq2 to identify differentially expressed genes (DEGs). The intersection of DEGs with cell senescence-related genes from the CellAge database was used to identify the candidate genes. Protein-protein interaction networks, Gene Ontology, and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to explore the functions and pathways of these genes. Machine learning algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO) regression and Support vector machine-recursive feature elimination (SVE-RFE), were used to select feature genes that were validated by qRT-PCR. Additionally, an immune cell infiltration analysis was performed to understand the roles of these genes in the immune response to psoriasis.ResultsThis study identified 4,913 DEGs in psoriasis, of which 46 were related to cell senescence. Machine learning highlighted four key genes, CXCL1, ID4, CCND1, and IRF7, as significant. These genes were associated with immune cell infiltration and validated by qRT-PCR, suggesting their potential as therapeutic targets for psoriasis.ConclusionsThis study identified and validated key senescence-related genes involved in psoriasis, providing insights into their molecular mechanisms and potential therapeutic targets and offering a foundation for developing targeted therapies for psoriasis. creator: Guiyan Deng creator: Cheng Xu creator: Dunchang Mo uri: https://doi.org/10.7717/peerj.18818 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Deng et al. title: Exploring freshwater soundscapes of tropical marshland habitats in Southeast Asia: insights into auditory sensory adaptation of wild Siamese fighting fish Betta splendens link: https://peerj.com/articles/18491 last-modified: 2025-01-13 description: While soundscapes shape the structure and function of auditory systems over evolutionary timescales, there is limited information regarding the adaptation of wild fish populations to their natural acoustic environments. This is particularly relevant for freshwater ecosystems, which are extremely diverse and face escalating pressures from human activities and associated noise pollution. The Siamese fighting fish Betta splendens is one of the most important cultured species in the global ornamental fish market and is increasingly recognized as a model organism for genetics and behavioural studies. This air-breathing species (Anabantoidei), characterized by the presence of a suprabranchial labyrinth organ that enhances auditory sensitivity, is native to Southeast Asia and inhabits low flow freshwater ecosystems that are increasingly threatened due to habitat destruction and pollution. We characterized the underwater soundscape, along with various ecological parameters, across five marshland habitats of B. splendens, from lentic waterbodies to small canals near a lake in Chiang Rai province (Thailand). All habitats exhibited common traits of low dissolved oxygen and dense herbaceous vegetation. Soundscapes were relatively quiet with Sound Pressure Level (SPL) around 102–105 dB re 1 µPa and most spectral energy below 1,000 Hz. Sound recordings captured diverse biological sounds, including potential fish vocalizations, but primarily insect sounds. Hearing thresholds were determined using auditory evoked potential (AEP) recordings, revealing best hearing range within 100–400 Hz. Males exhibited lower hearing thresholds than females at 400 and 600 Hz. This low-frequency tuning highlights the potential susceptibility of B. splendens to anthropogenic noise activities. This study provides first characterization of the auditory sensitivity and natural soundscape of B. splendens, establishing an important ground for future hearing research in this species. The information provided on the auditory sensory adaptation of B. splendens emphasizes the importance of preserving quiet soundscapes from lentic freshwater ecosystems. creator: Andreia Ramos creator: David Gonçalves creator: Raquel O. Vasconcelos uri: https://doi.org/10.7717/peerj.18491 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ramos et al. title: Analysis of the anthropogenic effect on the Silencio River in Salvador Escalante, Michoacán, México link: https://peerj.com/articles/18531 last-modified: 2025-01-13 description: The average annual water availability worldwide is approximately 1,386 trillion cubic hectometers (hm3), of which 97.5% is saltwater and only 2.5% is freshwater. Nearly 70% is not available for human consumption as it is in glaciers, snow, and ice. It is estimated that only 0.77% is accessible freshwater for human use. Mexico has an availability of 451,584.7 million cubic meters (m3) of freshwater, with accessibility and distribution being unequal. The growth in urbanization, population, and industrialization has caused a decrease in water quality, and other parameters. Organic and inorganic contaminants evolved from various sources cause the degradation of water quality. The pollution of aquatic bodies, such as rivers and lakes, is one of the main problems in the world. In Salvador Escalante in México, the domestic wastewaters treatment plant (WWTP) is being exposed to effluents contaminated with metals like copper, cadmium, lead, and mercury. In this work, active sludges from the WWTP were analyzed. First, particle size distribution of flocs was measured by a sedimentation process. Secondly, analysis of the tolerance that microorganisms exhibit to metals (i.e., factors) was performed, based on a 2$\hat {}$ ˆ(4-1) factorial design of experiments at laboratory-scale, measuring pH, chemical oxygen demand (COD) and electrical conductivity (responses). This aims to evaluate the capacity of the WWTP for improve the water quality. Microbiologic cultures were used for a qualitative study of the microorganisms contained in the active sludges; it was found that Enterobacterium does not grow in presence of heavy metals. Cadmium is the most harmful metal for microorganisms according to Pareto diagrams presented in this study. creator: Mario Alberto Pérez-Méndez creator: Guadalupe Selene Fraga-Cruz creator: Gustavo Álvarez-Gómez creator: Fabricio Nápoles-Rivera creator: Gladys Jiménez-García creator: Rafael Maya-Yescas uri: https://doi.org/10.7717/peerj.18531 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pérez-Méndez et al. title: Insecticides may facilitate the escape of weeds from biological control link: https://peerj.com/articles/18597 last-modified: 2025-01-13 description: BackgroundPreventative pesticide seed treatments (hereafter preventative pest management or PPM) are common corn and soybean treatments, and often include both fungicides and neonicotinoid insecticides. While PPM is intended to protect crops from soil-borne pathogens and early season insect pests, these seed treatments may have detrimental effects on biological control of weed seeds by insects.MethodsHere, in two 3-year corn-soy rotations in Pennsylvania USA, we investigated a PPM approach to insect management compared to an integrated pest management approach (IPM) and a “no (insect) pest management” (NPM) control. This was crossed with a grass cover crop to see if this conservation practice can help recover the ecosystem services affected by chemical pest management practices. We hypothesized that PPM and IPM approaches would release weed seeds from biological control by insects but cover crops would increase biological control. We measured the effect of these treatments on the weed-seed bank, mid-season weed biomass, granivorous insect activity-density, and weed-seed predation.ResultsWe found that, contrary to our hypothesis, planting a cover crop decreased carabid activity-density without consistent differences in weed-seed predation. Pest management and cover crop treatments also had inconsistent effects on the weed-seed bank and mid-season weed biomass, but insecticide use without a cover crop increased the biomass of likely glyphosate-resistant marestail (Erigeron canadensis L.) at the end of the trial. Our results suggest that reducing insecticide use may be important when combating herbicide-resistant weeds. We found planting cover crops and/or avoiding the use of insecticides may combat these problematic weeds. creator: Elizabeth K. Rowen creator: Kirsten Ann Pearsons creator: Richard G. Smith creator: Kyle Wickings creator: John F. Tooker uri: https://doi.org/10.7717/peerj.18597 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Rowen et al. title: Thermal ecology of the Mexican Garter Snake (Thamnophis eques): temporal and spatial variations link: https://peerj.com/articles/18641 last-modified: 2025-01-13 description: Heterogeneous environments provide different daily and seasonal thermal conditions for snakes, resulting in temporal and spatial variations in body temperature (Tb). This study analyzes the Tb of Thamnophis eques in the forest and grassland of a Mexican locality through daily and seasonal profiling. The patterns were obtained from seminatural enclosures in the field with a point sampling strategy to analyze temporal and spatial variations in Tb. The variation of Tb throughout the day was correlated with air and substrate temperatures, both in the grassland and in the forest. The average Tb in the grassland was 0.88 °C greater than in the forest. Our results indicate that T. eques showed differences in Tb between grassland and forest, principally in late spring and early summer during the early rise and late plateau phases, coinciding with the presence of foliage on the willow trees present in the study area, while in late summer and early autumn, the Tb was similar when willow trees canopy cover was absent (May–September). Our results support the hypothesis that the Tb of snakes differ between forests when the willows have leaves and is similar when canopy cover is equivalent, in this case, when tree canopy cover was absent. Our results also shown that T. eques presented daily and seasonal warming patterns similar to other Arizona populations and like those of other northern Gartersnakes. However, this result may not be valid for the entire wide distribution and consequent diversity of habitats of T. eques. The information of Tb in T. eques through daily and seasonal profiles in different habitats could aid in understanding the effects of environmental conditions on the ecological strategies deployed by snakes on habitat selection. creator: Crystian S. Venegas-Barrera creator: Armando Sunny creator: Javier Manjarrez uri: https://doi.org/10.7717/peerj.18641 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Venegas-Barrera et al. title: Common insect pests in homes and cultural heritage sites link: https://peerj.com/articles/18700 last-modified: 2025-01-13 description: Insect pests represent a threat to the integrity of historic buildings and homes, causing serious losses and irreversible damage. These pests can cause extensive damage to organic materials, including wood, textiles, and paper. Beetles, termites, booklice, moths, and cockroaches are just some of the main insect pests that are frequently found in historic buildings and homes. Beetle species such as the furniture beetle and the powderpost beetle are well recognised for their capacity to infest and feed on wood. Termite infestations can remain undetected and cause considerable damage that may even lead to the complete destruction of a building’s structural integrity. Cloth moth larvae are known to damage textiles, including carpets, furniture, clothes, and tapestries. Some wood-destroying species of cockroaches have the potential to harm historic buildings. Booklice have the ability to eat cellulose fibres found in archived articles and artefacts stored in heritage buildings, causing deterioration and damage to documents over time. This article reviews the literature and presents an overview of the major insect pests belonging to five known orders Coleoptera, Blattodea, Lepidoptera, Zygentoma (long-tailed silverfish) and Psocoptera, which pose a threat to households, museums, depositories, libraries, and cultural heritage buildings. We also discuss their biology, their impact on human health, and the various potential approaches to identifying them. creator: Bouthaina Hasnaoui creator: Fabien Fohrer creator: Philippe Parola creator: Jean-Michel Berenger uri: https://doi.org/10.7717/peerj.18700 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Hasnaoui et al. title: Single-cell transcriptome analysis reveals cellular reprogramming and changes of immune cell subsets following tetramethylpyrazine treatment in LPS-induced acute lung injury link: https://peerj.com/articles/18772 last-modified: 2025-01-13 description: BackgroundAcute lung injury (ALI) is a disordered pulmonary disease characterized by acute respiratory insufficiency with tachypnea, cyanosis refractory to oxygen and diffuse alveolar infiltrates. Despite increased research into ALI, current clinical treatments lack effectiveness. Tetramethylpyrazine (TMP) has shown potential in ALI treatment, and understanding its effects on the pulmonary microenvironment and its underlying mechanisms is imperative.MethodsWe established a mouse model of lipopolysaccharide (LPS)-induced ALI and performed single cell RNA sequencing (scRNA-seq). Bioinformatic analyses of the immune, epithelial and endothelial cells were then performed to explore the dynamic changes of the lung tissue microenvironment. We also analyzed the effects of TMP on the cell subtypes, differential gene expression and potential regulation of transcriptional factors involved. Immunohistochemistry and enzyme-linked immunosorbent assay were performed to identify the effects of TMP on immune inflammatory response.ResultsWe found that TMP efficiently protected against LPS-induced acute lung injury. Results of scRNA-seq showed that the cells were divided into seven major cell clusters, including immune cells, fibroblasts, endothelial cells and epithelial cells. Neither dexamethasone (Dex) nor TMP treatment showed any significant protective effects in these clusters. However, TMP treatment in the LPS-induced ALI model significantly increased follicular helper T cells and reduced CD8+ naive T cells, Vcan-positive monocytes and Siva-positive NK cells. In addition, TMP treatment increased the number of basal epithelial cells and lymphatic endothelial cells (LECs), indicating its protective effects on these cell types. Scenic analysis suggested that TMP likely mitigates LPS-induced injury in epithelial and endothelial cells by promoting FOSL1 in basal epithelial cells and JunB in LECs.ConclusionsOur findings suggest that TMP appears to alleviate LPS-induced lung injury by regulating the immune response, promoting epithelial cell survival and boosting the antioxidant potential of endothelial cells. This study highlights the potential therapeutic use of TMP in the management of ALI. creator: Mingyan Wu creator: Shanmei Wang creator: Xiaolan Chen creator: Li Shen creator: Jurong Ding creator: Hongbin Jiang uri: https://doi.org/10.7717/peerj.18772 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wu et al. title: Unveiling the complex double-edged sword role of exosomes in nasopharyngeal carcinoma link: https://peerj.com/articles/18783 last-modified: 2025-01-13 description: Nasopharyngeal carcinoma (NPC) is a malignancy arising from the epithelium of the nasopharynx. Given its late diagnosis, NPC raises serious considerations in Southeast Asia. In addition to resistance to conventional treatment that combines chemotherapy and radiation, NPC has high rates of metastasis and frequent recurrence. Exosomes are small membrane vesicles at the nanoscale that transport physiologically active compounds from their source cell and have a crucial function in signal transmission and intercellular message exchange. The exosomes detected in the tissues of NPC patients have recently emerged as a potential non-invasive liquid biopsy biomarker that plays a role in controlling the tumor pathophysiology. Here, we take a look back at what we know so far about the complex double-edged sword role of exosomes in NPC. Exosomes could serve as biomarkers and therapeutic agents, as well as the molecular mechanisms by which they promote cell growth, angiogenesis, metastasis, immunosuppression, radiation resistance, and chemotherapy resistance in NPC. Furthermore, we go over some of the difficulties and restrictions associated with exosome use. It is anticipated that this article would provide the reference for the apply of exosomes in clinical practice. creator: Xueyan Huang creator: Yuedi Tang uri: https://doi.org/10.7717/peerj.18783 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Huang and Tang title: To stay or to go: resource diversity alters the dispersal behavior of sympatric cryptic marine nematodes link: https://peerj.com/articles/18790 last-modified: 2025-01-13 description: Animals can use specific environmental cues to make informed decisions about whether and where to disperse. Patch conditions are known to affect the dispersal behavior of animals, but empirical studies investigating the impact of resource diversity on the dispersal of closely related species are largely lacking. In this study, we investigated how food diversity affects the dispersal behavior of three co-occurring cryptic species of the marine bacterivorous nematode complex Litoditis marina (Pm I, Pm III and Pm IV). Using microcosms composed of a local patch (inoculation plate), a connection tube, and a distant patch (dispersal plate), we examined nematode dispersal patterns with bacteria serving as the food source. Food treatments included low-, medium-, and high-diversity bacterial mixtures of 5, 10, and 15 bacterial strains, respectively. Additionally, a single-strain food resource Escherichia coli was used as a control treatment. Both local and distant patches had either identical food treatments (‘homogeneous patches’) or E. coli in the local patches and more diverse food (low-, medium-, or high-diversity food) in distant patches (‘heterogeneous patches’). Our results show that the dispersal behavior of the cryptic species varies depending on food diversity, indicating that L. marina acquire information about their environment when making dispersal decisions. All three cryptic species tend to disperse faster toward food patches that increase fitness. Pm I and Pm IV exhibited faster dispersal toward patches with a more diverse food source, while Pm III showed similar dispersal rates toward E. coli, medium-diversity, and high-diversity food. This indicates that resource diversity can alter the dispersal behavior of cryptic species and may be an important mechanism to achieve species coexistence in the field. creator: Rodgee Mae Guden creator: Sofie Derycke creator: Tom Moens uri: https://doi.org/10.7717/peerj.18790 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guden et al. title: Social presence effect in language comprehension: evidence from event-related potential (ERP) research link: https://peerj.com/articles/18798 last-modified: 2025-01-13 description: ObjectiveThis study aimed to examine the impact of social presence on Chinese reading comprehension and associated neural responses.MethodsParticipants tasked with reading Chinese sentences either alone or in the presence of others and subsequently assessing the accuracy of the sentences’ meanings. Concurrently, we recorded the participants’ electrical brain responses to critical word processing.ResultsBehavioral results indicated no significant effect of social presence on the judgment of sentence accuracy. Electroencephalogram (EEG) results, however, revealed that reading in the presence of others elicited more pronounced left anterior negativity (LAN) components in the left front of the scalp compared to reading alone. Additionally, incorrect meanings triggered larger N400 and P600 amplitudes in the mid-parietal region than correct meanings.ConclusionSocial presence intensifies early neural responses during the reading of Chinese sentences, although it does not influence semantic integration or conflict resolution. These findings support the notion that social context affects language processing. creator: Teng Yu creator: Xue Sui creator: Yu tong Li uri: https://doi.org/10.7717/peerj.18798 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yu et al. title: Effects of tropical fruit blends on fermentative and pigmentation aspects of probiotic native cultured goat milk link: https://peerj.com/articles/18813 last-modified: 2025-01-13 description: BackgroundFruits are sources of bioactive compounds such as phenolics that bring health benefits to consumers. The addition of fruit products and microorganisms with probiotic potential in fermented goat milk can facilitate the acquisition of these benefits through diet. In this sense, the objective of this study was to evaluate the effect of incorporating a mixture of ingredients from jaboticaba (Myrciaria cauliflora), jambolana (Syzygium cumini), and mandacaru (Cereus jamacaru) fruits on fermentation parameters (pH, titratable acidity, viability of the native culture Lactiplantibacillus plantarum CNPC003 and the starter culture), associated with pigmentation (phenolic compound content and color) through experimental mixture design.MethodsA simplex-centroid experimental design was conducted, comprised of seven trials totaling the addition of 30% of the fruit preparations in the final formulation of fermented milk and one control trial (without addition of preparations), with the response being the total phenolic content and the instrumental color parameter a*. Fermentations were carried out with the addition of the native culture Lactiplantibacillus plantarum CNPC003 and the starter culture Streptococcus thermophilus. Subsequently, analyses of pH, titratable acidity, viability of the native and starter cultures, total phenolic compound content, and the instrumental color parameter a* were performed.ResultsThe final pH among trials ranged from 4.55 to 4.69, titratable acidity ranged from 0.59 to 0.64, the population of L. plantarum CNPC003 reached levels exceeding 8 log CFU/g, as did the population of Streptococcus thermophilus. The content of phenolic compounds was higher in trials T1, T5, and T7, as well as the color parameter (a*). The use of experimental mixture design contributed to the development of products with high viability of L. plantarum, high content of phenolic compounds, and a characteristic color of the added fruits, bringing benefits to consumer health. creator: Isadora Kaline Camelo Pires de Oliveira Galdino creator: Gabriel Monteiro da Silva creator: Miqueas Oliveira Morais da Silva creator: Giordanni Cabral Dantas creator: Elainy Virgínia dos Santos Pereira creator: Tiago Almeida de Oliveira creator: Karina Maria Olbrich dos Santos creator: Antonio Silvio do Egito creator: Flávia Carolina Alonso Buriti creator: Haíssa Roberta Cardarelli uri: https://doi.org/10.7717/peerj.18813 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kaline Camelo Pires de Oliveira Galdino et al. title: Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence link: https://peerj.com/articles/18817 last-modified: 2025-01-13 description: Acer palmatum is a deciduous shrub or small tree. It is a popular ornamental plant because of its beautiful leaves, which change colour in autumn. This study revealed 116 ApNAC genes within the genome of A. palmatum. These genes are unevenly distributed on the 13 chromosomes of A. palmatum. An analysis of the phylogenetic tree of Arabidopsis thaliana NAC family members revealed that ApNAC proteins could be divided into 16 subgroups. A comparison of ApNAC proteins with NAC genes from other species suggested their potential involvement in evolutionary processes. Studies suggest that tandem and segmental duplications may be key drivers of the expansion of the ApNAC gene family. Analysis of the transcriptomic data and qRT‒PCR results revealed significant upregulation of most ApNAC genes during autumn leaf senescence compared with their expression levels in summer leaves. Coexpression network analysis revealed that the expression profiles of 10 ApNAC genes were significantly correlated with those of 200 other genes, most of which are involved in plant senescence processes. In conclusion, this study contributes to elucidating the theoretical foundation of the ApNAC gene family and provides a valuable basis for future investigations into the role of NAC genes in regulating leaf senescence in woody ornamental plants. creator: Xin Meng creator: Chun Feng creator: Zhu Chen creator: Faheem Afzal Shah creator: Yue Zhao creator: Yuzhi Fei creator: Hongfei Zhao creator: Jie Ren uri: https://doi.org/10.7717/peerj.18817 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Meng et al. title: The impact of induced stress on reactive and proactive control in depression link: https://peerj.com/articles/18821 last-modified: 2025-01-13 description: BackgroundDepression, a widespread mental health issue, is often marked by impaired cognitive control, particularly in managing proactive and reactive processes. The Dual Mechanisms of Control (DMC) framework differentiates between these two modes of cognitive control: proactive control involves sustained goal maintenance, while reactive control is more stimulus-driven and transient. Stress, known to exacerbate cognitive dysfunction in depression, may influence the balance between these control processes, though the specific effects remain poorly understood. This study aimed to investigate how acute stress influences proactive and reactive control in individuals with depressive symptoms.MethodsA total of 142 participants were divided into high-stress and control conditions and further categorized based on their depression levels, measured using the Beck Depression Inventory-II (BDI-II). Cognitive control was assessed using the AX-Continuous Performance Task (AX-CPT), both before and after exposure to a stress-inducing anagram task, which was designed to differentiate between high-stress and low-stress conditions.ResultsParticipants exposed to the high-stress condition reported significantly greater stress and fatigue levels compared to the control group, validating the stress manipulation. Although the balance between reactive and proactive control, as measured by the Proactive Behavioral Index (PBI), did not show significant changes, depressive individuals in the high-stress condition exhibited a significant decline in their ability to retain contextual information, as indicated by a reduction in the d’-context index. This suggests that depressive individuals may be more prone to stress-induced difficulties in proactive control.DiscussionThese findings highlight the selective impact of stress on proactive cognitive control in individuals with depressive symptoms, shedding light on a potential cognitive vulnerability in depression. While the balance between reactive and proactive control remained stable, the impaired retention of contextual information post-stress points to a specific deficit in proactive control. This could have implications for targeted cognitive interventions, such as cognitive control training, aimed at enhancing resilience against stress in depressive populations. Future research should explore the long-term effects of stress on cognitive control, particularly in clinically diagnosed individuals. creator: Akihiro Masuyama uri: https://doi.org/10.7717/peerj.18821 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Masuyama title: Genome-wide association study on color-image-based convolutional neural networks link: https://peerj.com/articles/18822 last-modified: 2025-01-13 description: BackgroundConvolutional neural networks have excellent modeling abilities to complex large-scale datasets and have been applied to genomics. It requires converting genotype data to image format when employing convolutional neural networks to genome-wide association studies. Existing studies converting the data into grayscale images have shown promising. However, the grayscale image may cause the loss of information of the genotype data.MethodsIn order to make full use of the information, we proposed a new method, color-image-based convolutional neural networks, by converting the data into color images.ResultsThe experiments on simulation and real data show that our method outperforms the existing methods proposed by Yue and Chen for converting data into grayscale images, in which the model accuracy is improved by an average of 7.61%, and the ratio of disease risk genes is increased by an average of 18.91%. The new method has better robustness and generalized performance. creator: Han-Ming Liu creator: Zhao-Fa Liu creator: Zi Li creator: Cong Yu creator: Peng-Cheng Hu creator: Qi-Feng Liu creator: Tai-Gui Shi uri: https://doi.org/10.7717/peerj.18822 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Cloning and functional verification of Geraniol-10-Hydroxylase gene in Lonicera japonica link: https://peerj.com/articles/18832 last-modified: 2025-01-13 description: BackgroundGeraniol 10-hydroxylase (G10H) is a cytochrome P450 monooxygenase involved in regulation, which is involved in the biosynthesis of monoterpene. However, G10H is not characterized at the enzymatic mechanism and regulatory function in Lonicera japonica.Methods and ResultsA gene related to the biosynthesis of monoterpenoid, geraniol 10-hydroxylase, has been cloned from the medicinal plant Lonicera japonica. The gene, LjG10H, encodes a peptide of 498 amino acids with a predicted molecular weight of 54.45 kDa. LjG10H shares a homology of 72.93–83.90% with G10H from other plants. Phylogenetic analysis suggests that the protein encoded by this gene belongs to the cytochrome P450 monooxygenase family. Tissue-specific expression analysis revealed that LjG10H is most highly expressed in flowers. Through heterologous expression in E. coli, the LjG10H protein was purified and its catalytic activity was studied. The results show that the enzyme can catalyze the hydroxylation of geraniol to 10-hydroxygeraniol. Additionally, analysis of Lonicera japonica seedlings with silenced LjG10H revealed a reduction in monoterpenoid content.ConclusionsThis study demonstrates that LjG10H plays an important role in the biosynthetic pathway of iridoids. This is the first article that ascribes G10H to be associated with the biosynthetic pathway of iridoid. This study provides a theoretical basis for the functional mechanism of LjG10H in regulating iridoid synthesis and provides a valuable resource for molecular breeding studies. creator: Shuping Zhang creator: Zhenhua Liu creator: Jia Li creator: Qian Liu creator: Yongqing Zhang creator: Gaobin Pu uri: https://doi.org/10.7717/peerj.18832 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Association between maternal rectovaginal group B streptococcus and the risk of stillbirth: a meta-analysis link: https://peerj.com/articles/18834 last-modified: 2025-01-13 description: BackgroundGroup B streptococcus (GBS) colonization in pregnant women is associated with adverse perinatal outcomes, including stillbirth. This meta-analysis investigated the relationship between maternal rectovaginal GBS colonization and the risk of stillbirth.MethodsWe conducted a comprehensive literature search across several databases, including PubMed, Embase, Web of Science, Wanfang, and China National Knowledge Infrastructure, covering studies published from the inception of the database until September 9, 2024. The search focused on observational studies comparing the risk of stillbirth in pregnant women with and without rectovaginal GBS colonization. Results were summarized using odds ratios (ORs) and 95% confidence intervals (CIs), and a random-effects model was used to account for potential heterogeneity.ResultsA total of ten studies comprising 121,195 pregnant women were included in the analysis. The pooled results indicated no significant overall association between maternal rectovaginal GBS colonization and the risk of stillbirth (OR: 1.66, 95% CI [0.95–2.91], p = 0.08; I2 = 84%). However, sensitivity analyses revealed a significant association in studies that included intrapartum antibiotic prophylaxis (IAP) (OR: 1.36, 95% CI [1.02–1.80], p = 0.03). Subgroup analyses demonstrated a significant association between maternal rectovaginal GBS colonization and stillbirth risk in retrospective studies (OR: 2.62, p = 0.04) and in studies employing multivariate analysis (OR: 2.11, p = 0.04).ConclusionsWhile the meta-analysis did not find a significant overall association between maternal rectovaginal GBS colonization and stillbirth, significant associations were noted under specific conditions, such as studies using IAP, retrospective designs, and multivariate analyses. Further research is needed to clarify these associations. creator: Yujue Wang creator: Jingjing Liu creator: Jinlian Song creator: Teng Zhang uri: https://doi.org/10.7717/peerj.18834 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Wang et al. title: Treatment options for Achilles tendinopathy: a scoping review of preclinical studies link: https://peerj.com/articles/18143 last-modified: 2025-01-10 description: BackgroundAchilles tendinopathy (AT) management can be difficult, given the paucity of effective treatment options and the degenerative nature of the condition. Innovative therapies for Achilles tendinopathy are therefore direly needed. New therapeutic developments predominantly begin with preclinical animal and in vitro studies to understand the effects at the molecular level and to evaluate toxicity. Despite the publication of many preclinical studies, a comprehensive, quality-assessed review of the basic molecular mechanisms in Achilles tendinopathy is lacking.ObjectivesThis scoping review aims to summarize the literature regarding in vitro and in vivo animal studies examining AT treatments and evaluate their effect on tendon properties. Also, a quality assessment of the included animal studies is done. We provide a comprehensive insight into the current state of preclinical AT treatment research which may guide preclinical researchers in future research.Eligibility criteriaTreatment options of Achilles tendinopathy in chemically or mechanically induced in vivo or in vitro Achilles tendinopathy models, reporting biomechanical, histological, and/or biochemical outcomes were included.Sources of evidenceA systematically conducted scoping review was performed in PubMed, Embase.com, Clarivate Analytics/Web of Science, and the Wiley/Cochrane Library. Studies up to May 4, 2023 were included.Charting MethodsData from the included articles were extracted and categorized inductively in tables by one reviewer. The risk-of-bias quality assessment of the included animal studies is done with Systematic Review Centre for Laboratory Animal Experimentation risk-of-bias tool.ResultsA total of 98 studies is included, which investigated 65 different treatment options. 80% of studies reported significant improvement in the Achilles tendon characteristics after treatment. The main results were; maximum load and stiffness improvement; fibre structure recovered and less inflammation was observed; collagen I fibrils increased, collagen III fibrils decreased, and fewer inflammatory cells were observed after treatment. However, 65.4% to 92.5% of the studies had an uncertain to high risk of bias according to the risk-of-bias tool of the Systematic Review Centre for Laboratory Animal Experimentation.ConclusionsDespite promising preclinical treatment outcomes, translation to clinical practice lags behind. This may be due to the poor face validity of animal models, heterogeneity in Achilles tendinopathy induction, and low quality of the included studies. Preclinical treatments that improved the biomechanical, histological, and biochemical tendon properties may be interesting for clinical trial investigation. Future efforts should focus on developing standardized preclinical Achilles tendinopathy models, improving reporting standards to minimize risk of bias, and facilitating translation to clinical practice. creator: Nathanael Opoku Agyeman-Prempeh creator: Huub Maas creator: George L. Burchell creator: Neal L. Millar creator: Maarten H. Moen creator: Theodoor Henri Smit uri: https://doi.org/10.7717/peerj.18143 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Agyeman-Prempeh et al. title: Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation link: https://peerj.com/articles/18515 last-modified: 2025-01-10 description: Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality. Virseqimprover first examines whether there is any chimeric sequence based on read coverage, breaks the sequence into segments if there is, then extends the longest segment with uniform depth of coverage, and repeats these procedures until the sequence cannot be extended. Finally, Virseqimprover annotates the gene content of the resulting sequence. Results show that Virseqimprover has good performances on correcting and extending viral contigs to their full lengths, hence can be a useful tool to improve the completeness and minimize the assembly errors of viral contigs. Both a web server and a conda package for Virseqimprover are provided to the research community free of charge. creator: Haoqiu Song creator: Saima Sultana Tithi creator: Connor Brown creator: Frank O. Aylward creator: Roderick Jensen creator: Liqing Zhang uri: https://doi.org/10.7717/peerj.18515 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Song et al. title: Soil polluted system shapes endophytic fungi communities associated with Arundo donax: a field experiment link: https://peerj.com/articles/18789 last-modified: 2025-01-10 description: With the expansion of the mining industry, environmental pollution from microelements (MP) and red mud (RM) has become a pressing issue. While bioremediation offers a cost-effective and sustainable solution, plant growth in these polluted environments remains difficult. Arundo donax is one of the few plants capable of surviving in RM-affected soils. To identify endophytic fungi that support A. donax in different contaminated environments and to inform future research combining mycorrhizal techniques with hyperaccumulator plants, we conducted a field experiment. The study compared endophytic fungal communities in A. donax grown in uncontaminated, MP soils contaminated with cadmium (Cd), arsenic (As), and lead (Pb), and RM-contaminated soils. Our findings showed that soil nutrient profiles differed by contamination type, with Cd concentrations in MP soils exceeding national pollution standards (GB 15168-2018) and RM soils characterized by high aluminum (Al), iron (Fe), and alkalinity. There were significant differences in the endophytic fungal community structures across the three soil types (p < 0.001). Co-occurrence network analysis revealed that endophytic fungi in MP soils exhibited competitive niche dynamics, whereas fungi in RM soils tended to share niches. Notably, Pleosporales sp., which accounted for 18% of the relative abundance in RM soils, was identified as a dominant and beneficial endophyte, making it a promising candidate for future bioremediation efforts. This study provides valuable insights into the role of endophytic fungi in phytoremediation and highlights their potential as resources for improving plant-microbe interactions in contaminated environments. creator: Xiaohui Wang creator: Yao Wang creator: Yingqiang Sun creator: Keyi Wang creator: Junbo Yang creator: Danjuan Zeng creator: Ling Mo creator: Jianxiong Liao creator: Qianshu Peng creator: Yu Yao creator: Gaozhong Pu uri: https://doi.org/10.7717/peerj.18789 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al. title: Application of indole-3-butyric acid (IBA) enhances agronomic, physiological and antioxidant traits of Salvia fruticosa under saline conditions: a practical approach link: https://peerj.com/articles/18846 last-modified: 2025-01-10 description: BackgroundSalinity stress is a significant challenge in agriculture, particularly in regions where soil salinity is increasing due to factors such as irrigation practices and climate change. This stress adversely affects plant growth, development, and yield, posing a threat to the cultivation of economically important plants like Salvia fruticosa. This study aims to evaluate the effectiveness by proactively applying indole-3-butyric acid (IBA) to Salvia fruticosa cuttings as a practical and efficient method for mitigating the adverse effects of salinity stress.MethodsThe factors were arranged as three different IBA doses (0, 1, and 2 g/L) and four different salinity concentrations (0, 6, 12, and 18 dS/m) in controlled greenhouse conditions. Plant height (PH), flower spike length (FSL), fresh shoot length (FRL), root length (RL), fresh root weight (FRW), fresh shoot weight (FSW), dried root weight (DRW), dried shoot weight (DSW), root/shoot index, drog (g/plant), relative water content (RWC), relative membrane permeability (RMP), chlorophyll content (SPAD), extraction yield (%), DPPH (2,2-Diphenyl-1-picrylhydrazyl), phenol content, flavonoid content, and ABTS (2,2′-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)) values were measured.ResultsThe results show that as salinity doses increased, all parameters showed a decline. However, with a one-time IBA application to the plant cuttings before the rooting stage, particularly at a concentration of 2 g/L, was effective for mitigating the negative effects of salinity stress. Across all measured parameters, IBA significantly reduced the adverse impacts of salinity on Salvia fruticosa. creator: Uğur Tan uri: https://doi.org/10.7717/peerj.18846 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tan title: Habitat sharing and interspecies interactions in caves used by bats in the Republic of Congo link: https://peerj.com/articles/18145 last-modified: 2025-01-09 description: Bats play key roles in ecosystem functions and provide services to human populations. There is a need to protect bat populations and to mitigate the risks associated with pathogen spillover. Caves are key habitats for many bat species, which use them as roosting and breeding sites. Caves, bats and their guano also attract many other animals along trophic chains which might favor direct or indirect interspecies interactions. Two caves hosting colonies of insectivorous bats have been investigated in the Republic of Congo to characterize habitat sharing and interactions between bats, humans and animals. We set up a camera-trap monitoring protocol during 19 months at the entrance of and inside each cave. Our results demonstrated the richness and complexity of the species interactions around and within these caves. We identified and/or quantified mainly rodents, but also numerous categories of animals such as insects, birds, reptiles and carnivores using the caves. We investigated the temporal variation in the use of caves and the potential interactions between humans, wild animals and bat colonies. Our study contributes to the understanding of the interface and interactions, for the first time quantified, between cave-dwelling animal species, including humans. This knowledge is important to promote the conservation of cave ecosystems and better understand the ecology of infectious diseases. creator: Morgane Labadie creator: Serge Morand creator: Mathieu Bourgarel creator: Fabien Roch Niama creator: Guytrich Franel Nguilili creator: N’Kaya Tobi creator: Alexandre Caron creator: Helene De Nys uri: https://doi.org/10.7717/peerj.18145 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Labadie et al. title: Role of polyethylene glycol to alleviate lead stress in Raphanus sativus link: https://peerj.com/articles/18147 last-modified: 2025-01-09 description: The continuous contamination of heavy metals (HMs) in our ecosystem due to industrialization, urbanization and other anthropogenic activities has become a serious environmental constraint to successful crop production. Lead (Pb) toxicity causes ionic, oxidative and osmotic injuries which induce various morphological, physiological, metabolic and molecular abnormalities in plants. Polyethylene glycol (PEG) is widely used to elucidate drought stress induction and alleviation mechanisms in treated plants. Some recent studies have unveiled the potential of PEG in regulating plant growth and developmental procedures including seed germination, root and shoot growth and alleviating the detrimental impacts of abiotic stresses in plants. Therefore, the current study aimed to assess the effects of seed priming with various concentrations (10%, 20%, 30% and 40%) of PEG on the growth and development of radish plants growing under Pb stress (75 mg/kg soil). Lead toxicity reduced root growth (32.89%), shoot growth (32.81%), total chlorophyll (56.25%) and protein content (58.66%) in treated plants. Similarly, plants showed reduced biomass production of root (35.48%) and shoot (31.25%) under Pb stress, while 30% PEG seed priming enhanced biomass production of root (28.57%) and shoot (35.29%) under Pb contaminated regimes. On the other hand, seedlings obtained from 30% PEG priming demonstrated a notable augmentation in the concentrations of photosynthetic pigments, antioxidative activity and biomass accumulation of the plants. PEG-treated plants showed modulations in the enzymatic activities of peroxidase (PO), catalase (CAT) and superoxide dismutase (SOD). These changes collectively played a role in mitigating the adverse effects of Pb on plant physiology. Our data revealed that PEG interceded stress extenuation encompasses numerous regulatory mechanisms including scavenging of ROS through antioxidant and non-antioxidants, improved photosynthetic activity and appropriate nutrition. Hence, it becomes necessary to elucidate the beneficial role of PEG in developing approaches for improving plant growth and stress tolerance. creator: Muhammad Sajid creator: Shakil Ahmed creator: Rehana Sardar creator: Aamir Ali creator: Nasim Ahmad Yasin uri: https://doi.org/10.7717/peerj.18147 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sajid et al. title: A morpho-histological analysis of the exoskeleton of Clathrozoella medeae (Cnidaria, Hydrozoa) reveals insights into the taxonomy of Clathrozoellidae and Hydroidolina link: https://peerj.com/articles/18407 last-modified: 2025-01-09 description: The taxonomic complexity of the families Clathrozoidae and Clathrozoellidae, rooted in early 20th-century hydroid descriptions, highlights the need for comprehensive and detailed morphological analyses. This study aimed to elucidate the histology of the polypoid stage of Clathrozoella medeae Peña Cantero, Vervoort & Watson, 2003, with a particular emphasis on its exoskeletal structure. Specimens from the National Museum of Natural History were examined histologically using different staining techniques. The results revealed a three-layered mesoglea, diverse gland cells, and an exoskeleton comprising chitin and structural proteins, with notable differences from other anthoathecate hydroids. These results have significant implications for the taxonomy and evolutionary relationships of Clathrozoellidae and Hydroidolina, as they highlight the importance of detailed histological data in understanding the unique exoskeletal architecture of C. medeae, termed “exoskeleton tube”, which distinguishes it from other hydroids, and provide critical insights into the homology and phylogenetic position of Clathrozoellidae. creator: María A. Mendoza-Becerril creator: Antonio C. Marques uri: https://doi.org/10.7717/peerj.18407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mendoza-Becerril and Marques title: The feasibility of virtual reality therapy for upper extremity mobilization during and after intensive care unit admission link: https://peerj.com/articles/18461 last-modified: 2025-01-09 description: IntroductionEarly mobilization reduces long-term muscle weakness after intensive care unit (ICU) admission, but barriers (e.g., anxiety, lack of motivation) may complicate patients’ adherence to exercise. Virtual reality (VR) presents immersive stimuli, which may increase motivation and adherence. This study aimed to examine the feasibility of VR-therapy using a VR-headset during ICU- and subsequent general ward admission. Furthermore, physical parameters before and after training were explored.Materials & MethodsTen adult ICU-patients with a median age of 71 [63–79], 70% of male registered birth sex, mechanically ventilated for ≥48 h, and willing to participate, were included. VR-therapy was offered three times a week for 20 minutes in addition to standard care. To train upper extremity functionality, patients were instructed to complete puzzles with increasing level of difficulty. Feasibility was based on patient satisfaction, session efficiency, and adherence levels during the training. Fatigue was measured after each session using the Borg Rating of Perceived Exertion Scale. Patients’ hand-grip strength and Morton Mobility Index (MMI) were evaluated at the start of VR-therapy and after four weeks of training or at hospital discharge.ResultsOn average, patients followed three VR-therapy sessions of 20 min per week with 13 min of actual training time, over the course of 1 to 3 weeks depending on their length of stay. Session efficiency ranged from 25% to 93%. In total, patients adhered to 60% of the VR-therapy sessions. MMI scores increased significantly from the start (26 [24–44]) to the end of the VR-therapy training period (57 [41–85], p = 0.005), indicating improved balance and mobility.ConclusionVR-therapy for upper extremity rehabilitation in ICU-patients is feasible during stay in the ICU and general ward. creator: Mirthe de Vries creator: Lise F.E. Beumeler creator: Johan van der Meulen creator: Carina Bethlehem creator: Rob den Otter creator: E. Christiaan Boerma uri: https://doi.org/10.7717/peerj.18461 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 de Vries et al. title: Identification of crucial extracellular genes as potential biomarkers in newly diagnosed Type 1 diabetes via integrated bioinformatics analysis link: https://peerj.com/articles/18660 last-modified: 2025-01-09 description: PurposeIn this study, we aimed to study the role of extracellular proteins as biomarkers associated with newly diagnosed Type 1 diabetes (NT1D) diagnosis and prognosis.Patients and MethodsWe retrieved and analyzed the GSE55098 microarray dataset from the Gene Expression Omnibus (GEO) database. Using R software, we screened out the extracellular protein-differentially expressed genes (EP-DEGs) through several protein-related databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied to describe the role and function of these EP-DEGs. We used the STRING database to construct the interaction of proteins, Cytoscape software to visualize the protein-protein interaction (PPI) networks, and its plugin CytoHubba to identify the crucial genes between PPI networks. Finally, we used the comparative toxicogenomics database (CTD) to evaluate the connection between NT1D with the potential crucial genes and we validated our conclusions with another dataset (GSE33440) and some clinical samples.ResultsWe identified 422 DEGs and 122 EP-DEGs from a dataset that includes (12) NT1D patients compared with (10) healthy people. Protein digestion and absorption, toll-like receptor signaling, and T cell receptor signaling were the most meaningful pathways defined by KEGG enrichment analyses. We recognized nine important extracellular genes: GZMB, CCL4, TNF, MMP9, CCL5, IFNG, CXCL1, GNLY, and LCN2. CTD analyses showed that LCN2, IFNG, and TNF had higher levels in NT1D and hypoglycemia; while TNF, IFNG and MMP9 increased in hyperglycemia. Further verification showed that LCN2, MMP9, TNF and IFNG were elevated in NT1D patients.ConclusionThe nine identified key extracellular genes, particularly LCN2, IFNG, TNF, and MMP9, may be potential diagnostic biomarkers for NT1D. Our findings provide new insights into the molecular mechanisms and novel therapeutic targets of NT1D. creator: Ming Gao creator: Qing Liu creator: Lingyu Zhang creator: Fatema Tabak creator: Yifei Hua creator: Wei Shao creator: Yangyang Li creator: Li Qian creator: Yu Liu uri: https://doi.org/10.7717/peerj.18660 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Gao et al. title: Efficacy of root canal treatment for autotransplanted third molars: a 6-Year cohort study of 167 teeth in southern China link: https://peerj.com/articles/18824 last-modified: 2025-01-09 description: BackgroundAutogenous tooth transplantation offers significant advantages and promising success rates for replacing non-retainable teeth. This study aimed to investigate the prognostic factors, especially the impact of root canal treatment (RCT), of autotransplanted teeth in an up-to-6-year follow-up cohort of 167 teeth in Southern China.MethodsWe enrolled adult patients from the Southern Medical University-Shenzhen Stomatology Hospital between 2017 and 2023. Patients underwent autogenous tooth transplantation to replace non-retainable molars with upper or lower third molars with Moorrees tooth development stage ≥5. All surgical procedures were performed by an experienced surgeon. The included patients were followed up for 6~72 (median 28.5) months. Success, failure, and survival rate and prognostic factors were evaluated using univariable Kaplan-Meier, multivariable generalized linear regression, and multivariable COX regression analyses.ResultsThe overall success rate is 97.6% with four unsuccessful cases. Herein, two of them were removed, leading to an overall survival rate of 98.8%. A total of 159 cases (95%) received RCT in 3 months. Univariable log-rank analysis showed that RCT (RR 0.109, 95%CI 0.010 to 1.202, P = 0.028) and site relationship between donor and receipt sites (RR 3.359, 95% CI [1.210–9.329], P = 0.020) were two significant prognostic factors of autotransplanted teeth. Multivariable generalized linear regression revealed that RCT is the only significant factor protecting the success rate of autotransplanted teeth (HR 0.003, 95% CI [0.000–0.249], P = 0.010). However, in the Cox regression model, the effects of RCT (HR 0.009, 95% CI [0.000–2.514], P = 0.101) did not reach statistical significance. Other factors did not demonstrate a significant impact in this cohort. These results supported that autogenous tooth transplantation is a viable alternative to conventional implant treatment with strict indications. Our findings underscore the importance of RCT in transplanted teeth with closed or semi-closed apices. Multi-center observational studies with larger sample size and extended follow-up duration may be needed to validate the conclusion. creator: Bangfeng Han creator: Liu Liu creator: Zhishen Jiang creator: Li Ye creator: Yubin Cao creator: Jian Pan uri: https://doi.org/10.7717/peerj.18824 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Han et al. title: Genetic analysis of Pinna rudis L 1758 (Mollusca, Bivalvia, Pinnidae) in the Northwest Cabo Verde Islands (Central-East Atlantic) link: https://peerj.com/articles/18328 last-modified: 2025-01-08 description: The rough pen shell Pinna rudis Linnaeus, 1758 (family Pinnidae) is a mollusc with an Atlantic–Mediterranean distribution, typically inhabiting coarse sandy substrates. Habitat degradation is considered the primary cause of population decline, leading to the designation ‘Vulnerable’ in certain regions. In this study, we conducted a genetic analysis of populations of P. rudis from Cabo Verde and compared them with populations from the Mediterranean and Macaronesia. We based our analysis on two mitochondrial DNA markers, cytochrome oxidase I (COI) and 16S rRNA, and one nuclear marker, 28S rRNA. The results showed a strong genetic structuring among Macaronesia populations, with each island tending to have unique or exclusive haplotypes, though some sharing occurred between islands. We found significant genetic divergence between the population from Cabo Verde and the other sampled population, suggesting that P. rudis is not monotypic, but may include several cryptic species. Bayesian and maximum-likelihood phylogenetic analysis, including all Pinnidae species, indicated that P. rudis from Gorée Island (Senegal) and Baía das Gatas (São Vicente Island) might be undergoing speciation. The high genetic structure found for P. rudis could be influenced by hydrodynamic barriers, local currents and hydrographic isolation, in association with the short larval duration (planktotrophic) reported for this species. Altogether, our findings highlight significant genetic divergence in P. rudis populations, possibly supporting speciation events in the Cabo Verde archipelago among widely distributed taxonomic groups. creator: Evandro P. Lopes creator: Sarah Santos creator: Raquel Xavier creator: Joana L. Santos creator: M. Pilar Cabezas creator: Fernando Sequeira creator: António M. Santos uri: https://doi.org/10.7717/peerj.18328 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lopes et al. title: Niche-related processes explain phylogenetic structure of acoustic bird communities in Mexico link: https://peerj.com/articles/18412 last-modified: 2025-01-08 description: Acoustic communities are acoustically active species aggregations within a habitat, where vocal interactions between species can interfere their communication. The acoustic adaptation hypothesis (AAH) explains how the habitat favors the transmission of acoustic signals. To understand how bird acoustic communities are structured, we tested the effect of habitat structure on the phylogenetic structure, and on the phylogenetic and vocal diversity of acoustic communities in a semi-arid zone of Mexico. From autonomous recordings in three types of vegetation (crop fields, tetecheras, and mesquiteras), which differ in terms of complexity and canopy openness, we evaluated sound attenuation, and estimated metrics of phylogenetic structure and diversity as well as acoustic diversity with the use of two indices. Mesquiteras showed greater vegetation density, more attenuation, more vocal diversity, as well as a phylogenetic structure that tended towards overdispersion, in contrast to crop fields that showed less vegetation density, less attenuation, less vocal diversity and more phylogenetic relatedness, while tetecheras showed intermediate patterns. Phylogenetic structure was explained by vegetation density and excess attenuation. The higher vocal diversity, phylogenetic structure tended towards overdispersion. These results suggest a role for environmental filters in the crop fields, where more closely related species with similar vocal characteristics coexist (supporting AAH), and probably competitive exclusion in the mesquiteras, where more distantly related species coexist, promoting vocal diversity. This study offers information about the influence of habitat on the acoustic community structure, which could inform our understanding of the distribution of species from acoustic perspective. creator: Christian D. Morán-Titla creator: Juan-Hector García-Chávez creator: Leonel Lopez-Toledo creator: Clementina González uri: https://doi.org/10.7717/peerj.18412 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Morán-Titla et al. title: The impact of a disaster medicine clinical training program on medical students’ disaster literacy link: https://peerj.com/articles/18800 last-modified: 2025-01-08 description: BackgroundThis study was conducted to assess how students’ disaster literacy was affected by the Disaster Medicine Clinical Training Program at the Izmir Democracy University Faculty of Medicine (IDUFM) during the academic year 2022–2023.MethodsUsing an experimental method involving experimental and control groups, measurements were made at different times. The sample consisted of 5th-year students at IDUFM for the experimental group, while the control group was composed of 3rd- and 4th-year students from different buildings with limited interaction with the experimental group. The clinical training program was organized to improve the clinical practice skills of students in the field of disaster medicine and provide theoretical information. Throughout their internship, the students were provided with a program including information on types of disasters, preparation, response, relief, emergency surgical procedures, hospital disaster plans, national and international organizations and institutions working in disasters, and other relevant topics. The Disaster Literacy Scale (DLS) was used to collect data. This scale is a self-report scale that was developed to evaluate knowledge levels about disasters. In this study, the scale was applied as a pretest and a posttest, and the obtained data were analyzed using independent samples and paired-sample t-tests.ResultThe DLS scores of the experimental group showed significant improvement after the training program compared to their pretest scores (Total Scale: p < 0.001, Damage Mitigation: p = 0.002, Preparation: p < 0.001, Response: p < 0.001, and Relief: p = 0.004). When comparing the posttest results of the experimental group with the control group, the experimental group demonstrated significantly higher scores in Total Scale (p = 0.01), Damage Mitigation (p = 0.02), Response (p = 0.03), and Relief (p < 0.001). However, no significant differences were observed between the experimental group’s pretest (T1) scores and the control group’s posttest (T3) scores (p > 0.05p > 0.05p > 0.05), indicating that the knowledge levels of the experimental and control groups were homogeneous prior to the training intervention. These findings confirm the effectiveness of the Disaster Medicine Training Program in improving disaster literacy and response skills among medical students.ConclusionThis study, which aimed to determine the effects of the Disaster Medicine Clinical Training Program on the disaster literacy of medical students, revealed that the program increased the literacy levels of the students and contributed to their responsible decision-making. It is thought that such education programs can make significant contributions to the effective management of healthcare services in disaster situations. creator: Aysel Başer creator: Zeynep Sofuoğlu uri: https://doi.org/10.7717/peerj.18800 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Başer and Sofuoğlu title: Clinical characteristics of pathogens in children with community-acquired pneumonia were analyzed via targeted next-generation sequencing detection link: https://peerj.com/articles/18810 last-modified: 2025-01-08 description: BackgroundThe primary purpose of this study was to detect the pathogen species using targeted next-generation sequencing (tNGS) to investigate the characteristics of community-acquired pneumonia (CAP)-related pathogens in children in Xiantao city, Hubei province, China.MethodsA total of 1,527 children with CAP were prospectively recruited from our hospital between May 2022 and February 2023. Information on age and sex was collected from the medical records. Pathogen detection was performed using standard detection methods and tNGS.ResultsThe positive coincidence rate of standard detection methods and tNGS were 61.95% (946/1,527) and 97.05% (1,482/1,527), respectively. Among the 1,482 children with CAP, the numbers of bacteria, virus, chlamydia, and mycoplasma infection were 1,188, 975, 321, and 1, respectively. Co-existing species showed high prevalence in CAP, and the prevalence of children infected with only one pathogen was 20.31%. The numbers of children infected with two and three pathogens were the highest, accounting for 29.22% and 25.17%, respectively. Among the 44 pathogens detected using tNGS, 17 species of bacteria, 25 species of viruses, one species of chlamydia, and one species of mycoplasma were documented. Among all infectious pathogens, the top five were Haemophilus influenzae, Acinetobacter baumannii, Streptococcus pneumoniae, human herpes virus type 5 (HHV-5), and Mycoplasma pneumoniae. The results showed that pathogenic infections in children with CAP were related to age but not to gender.ConclusionThe infection pathogens in children with CAP were complex and the incidence of co-existence was observed to be high. The pathogens involved in CAP were closely related to the age of the child. In addition, tNGS was shown to better identify pathogens than the standard detection method, which is crucial for improving the accuracy of early CAP diagnosis and initiating appropriate treatment in a timely manner, ultimately enhancing treatment outcomes. creator: Junhua Zhao creator: Mingfeng Xu creator: Zheng Tian creator: Yu Wang uri: https://doi.org/10.7717/peerj.18810 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: The potential of serum elabela levels as a marker of diabetic retinopathy: results from a pilot cross-sectional study link: https://peerj.com/articles/18841 last-modified: 2025-01-08 description: BackgroundThe aim of this study is to examine the relationship between elabela (ELA), a recently identified peptide also known as Toddler and Apela, and diabetic retinopathy (DR). ELA, produced in various tissues, acts as a natural ligand for the apelin receptor (APJ). Upon reviewing the existing literature, only one study was found investigating ELA, one of the APJ ligands, in the pathogenesis of DR.MethodsIn our study the patient group comprising individuals diagnosed with type 2 diabetes mellitus (DM), categorized into three subgroups based on detailed fundus examination: those without DR (non-DR) (n = 20), non-proliferative DR (NPDR) (n = 20), and proliferative DR (PDR) (n = 20). A control group (n = 20) consisted of individuals without DM. Blood samples were collected during outpatient clinic admission to measure serum ELA levels, which were determined using a commercial ELISA kit.ResultsThe age, sex, and body mass index of the between groups were similar (p = 0.905, 0.985 and 0.241, respectively). The HbA1c levels of the between DM subgroups were similar (p = 0.199). Serum ELA levels were 217.19 ± 97.54 pg/mL in the non-DR group, 221.76 ± 93.12 pg/mL in the NPDR group, 302.35 ± 146.17 pg/mL in the PDR group and 216.49 ± 58.85 pg/mL in the control group. While ELA levels were higher in DM patients compared to the control group, this elevation did not reach statistical significance. Further analysis dividing DM patients into subgroups (non-DR, NPDR, and PDR) revealed higher ELA levels in the PDR group compared to the other subgroups, but this increase was not statistically significant.ConclusionDespite the absence of a significant difference in our study, the identification of elevated ELA levels in the PDR group offers valuable insights for future investigations exploring the association between DR and ELA. creator: Muhammed Seyithanoğlu creator: Selma Meşen creator: Aysegul Comez creator: Ali Meşen creator: Abdullah Beyoğlu creator: Yaşarcan Baykişi creator: Filiz Alkan Baylan uri: https://doi.org/10.7717/peerj.18841 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Seyithanoğlu et al. title: Deregulation mechanisms and therapeutic opportunities of p53-responsive microRNAs in diffuse large B-cell lymphoma link: https://peerj.com/articles/18661 last-modified: 2025-01-07 description: Here, we have discussed the molecular mechanisms of p53-responsive microRNAs dysregulation in response to genotoxic stress in diffuse large B-cell lymphoma (DLBCL) patients. The role of micro ribonucleic acids (microRNAs) in p53-signaling cellular stress has been studied. MicroRNAs are the small non-coding RNAs, which regulate genes expression at post-transcriptional level. Many of them play a crucial role in carcinogenesis and may act as oncogenes or suppressor of tumor growth. The understanding of the effect of p53-responsive microRNA dysregulation on oncogenesis achieved in recent decades opens wide opportunities for the diagnosis, prediction and of microRNA-based cancer therapy. Development of new bioinformatics tools and databases for microRNA supports DLBCL research. We overview the studies on the role of miRNAs in regulating gene expression associated with tumorigenesis processes, with particular emphasis on their role as tumor growth-suppressing factors. The starting point is a brief description of the classical microRNA biogenesis pathway and the role of p53 in regulating the expression of these molecules. We analyze various molecular mechanisms leading to this dysregulation, including mutations in the TP53 gene, DNA methylation, changes in host-genes expression or microRNA gene copy number, mutations in microRNA and microRNA biogenesis genes. creator: Elena N. Voropaeva creator: Yuriy L. Orlov creator: Anastasia B. Loginova creator: Olga B. Seregina creator: Vladimir N. Maksimov creator: Tatiana I. Pospelova uri: https://doi.org/10.7717/peerj.18661 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Voropaeva et al. title: Reproductive strategies in loggerhead sea turtle Caretta caretta: polyandry and polygyny in a Southwest Atlantic rookery link: https://peerj.com/articles/18714 last-modified: 2025-01-07 description: Sea turtles are highly migratory and predominantly inhabit oceanic environments, which poses significant challenges to the study of their life cycles. Research has traditionally focused on nesting females, utilizing nest counts and mark-recapture methods, while male behavior remains understudied. To address this gap, previous studies have analyzed the genotypes of females and hatchlings to indirectly infer male genotypes and evaluate the extent of multiple paternity within populations. Our research aimed to investigate the presence of multiple paternity in loggerhead turtle (Caretta caretta) nests for the first time in Brazil. We analyzed 534 hatchlings from 43 nests associated with 42 females during the 2017/18 to 2019/20 nesting seasons, using four highly polymorphic, species-specific microsatellite markers (nDNA). Parentage tests were conducted to reconstruct paternal genotypes and determine the rates of multiple paternity within clutches. Our results revealed that 72.09% of clutches were sired by multiple males, with contributions ranging from one to six males per clutch. Additionally, seven out of 88 males (7.95%) were found to have sired clutches from multiple females, with some males contributing to more than one clutch within and across breeding seasons. The breeding sex ratio (BSR) was calculated to be 2.09 males per female. While multiple paternity is a common phenomenon among sea turtles, this study is the first to document polyandry in loggerheads in Brazil and the first to provide evidence of polygyny in this species globally. This research establishes a crucial database for future studies in Brazil, with a focus on the BSR of the Southwest Atlantic subpopulation, offering essential insights for developing effective management strategies for this vulnerable population. creator: Laís Amorim creator: Lara Chieza creator: Jake A. Lasala creator: Sarah de Souza Alves Teodoro creator: Wesley D. Colombo creator: Ana Carolina Barcelos creator: Paula Rodrigues Lopes Guimarães creator: João Luiz Guedes da Fonseca creator: Ana Claudia Jorge Marcondes creator: Alexsandro Santos creator: Sarah Vargas uri: https://doi.org/10.7717/peerj.18714 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Amorim et al. title: Recognising depression in non-human primates: a narrative review of reported signs of depression link: https://peerj.com/articles/18766 last-modified: 2025-01-07 description: Major depressive disorder (depression) is a highly heterogenous human mental disorder that may have equivalents in non-human animals. Research into non-human depression teaches us about human depression and can contribute to enhance welfare of non-human animals. Here, we narratively review how signs of depression in non-human primates (NHPs) can be observed based on symptoms of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5). Furthermore, we propose diagnostic criteria of NHP depression and we review reports on signs of depression in NHPs. We diagnose an NHP with depression when it shows a core sign (depressed mood or anhedonia) alongside at least three other DSM-5-derived signs of depression. Results show that four out of six observable signs of depression are present in NHPs, occasionally lasting for months. However, only a group of six NHPs in one study met our proposed criteria for a diagnosis of depression. We call for more research into the co-occurrence of depressive symptoms in individual NHPs to establish the prevalence of depression in NHPs. creator: Jonas C. P. van Oosten creator: Annemie Ploeger creator: Elisabeth H. M. Sterck uri: https://doi.org/10.7717/peerj.18766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 van Oosten et al. title: Trunk muscle behaviors during the full-cycle stoop and squat lifting tasks link: https://peerj.com/articles/18797 last-modified: 2025-01-07 description: BackgroundLifting is generally considered as a risk factor for low back pain. A thorough investigation of the muscle function during lifting is essential for a better assessment of the potential risk of muscle impairment and towards improvements in lifting strategy. We aimed to compare the activities of the trunk muscles between the stoop and the squat lifting tasks.MethodsA surface electromyography device was used to measure the muscle activity during the full-cycle squat and the stoop lifting tasks of a 5-kg weight. Each task was divided into four stages: stage 1 was bending forward to reach the weight, stage 2 was lifting the weight up, stage 3 was lowering the weight down, and stage 4 was returning to the upright position. The maximum electromyographic (EMG) activities among different tasks and different stages were compared. Eighteen males aged 20–35 years without low back pain were included, with a mean age of 26.55 ± 2.12 years, body height of 175.18 ± 4.29 cm, body weight of 69.27 ± 4.29 kg, and BMI of 22.56 ± 0.87 kg/m2.ResultsDuring stoop lifting, the median values of the absolute EMG of the left multifidus were 53.96, 70.32, 51.08 and 64.14 uV from stage 1 to stage 4, which were all non-significantly lower than those during squat lifting for 79.84, 103.64, 71.72 and 95.72, respectively (P > 0.05). The absolute EMG was greatest during stage 2, then during stage 4, stages 1 and 3 came next (Effect size = 0.879, P < 0.001). The median values of the normalized EMG of each muscle during stoop lifting were also non-significantly lower than those during squat lifting at each stage (P > 0.05). The normalized EMG was also greatest during stage 2, then during stage 4, and was lowest during stages 1 and 3 (Effect size = 0.932, P < 0.001).ConclusionThe trunk muscles were similarly activated during squat and stoop lifting. During lowering the weight down, the trunk muscles were less activated than during extension to the upright position without weight in hands. These results could help to develop subject-specific strategies for lifting tasks to prevent or alleviate occupational low back pain. creator: Fumin Pan creator: Wei Wang creator: Chao Kong creator: Shibao Lu uri: https://doi.org/10.7717/peerj.18797 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pan et al. title: Antimicrobial activity of Lactobacillus spp. isolated from fermented foods and their inhibitory effect against foodborne pathogens link: https://peerj.com/articles/18541 last-modified: 2025-01-06 description: Lactic acid bacteria (LAB), known for their health benefits, exhibit antimicrobial and antibiofilm properties. This study investigated the cell-free supernatant (CFS) of Lactobacillus spp., particularly L. plantarum KR3, against the common foodborne pathogens S. aureus, E. coli and Salmonella spp. Lactobacillus strains were isolated from cheese, pickles and yoghurt. They were then identified by morphological, physiological and biochemical characteristics and confirmed by 16S rRNA gene sequencing. Culture supernatants from seven lactobacilli isolates showed varying inhibitory activities. Notably, L. plantarum KR3 and L. pentosus had the highest bacteriocin gene counts. L. plantarum KR3 CFS demonstrated significant antibacterial activity, with inhibition zones of 20 ± 0.34 mm for S. aureus, 23 ± 1.64 mm for E. coli, and 17.1 ± 1.70 mm for Salmonella spp. The CFS also exhibited substantial antibiofilm activity, with 59.12 ± 0.03% against S. aureus, 83.50 ± 0.01% against E. coli, and 60. ± 0.04% against Salmonella spp., which were enhanced at the minimum inhibitory concentration (MIC). These results highlighted the potential of L. plantarum KR3 in antimicrobial applications, however, further research is needed to evaluate its viability and functional properties for probiotic use. Additionally, the CFS demonstrated exceptional thermal stability, reinforcing its promise as an antimicrobial agent. creator: Athraa Oudah Hussein creator: Khalida Khalil creator: Nurul Aqilah Mohd Zaini creator: Ahmed Khassaf Al Atya creator: Wan Syaidatul Aqma uri: https://doi.org/10.7717/peerj.18541 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hussein et al. title: Contact zone of slow worms Anguis fragilis Linnaeus, 1758 and Anguis colchica (Nordmann, 1840) in Poland link: https://peerj.com/articles/18563 last-modified: 2025-01-06 description: BackgroundLegless lizards, the slow worms of the genus Anguis, are forming secondary contact zones within their Europe-wide distribution.MethodsWe examined 35 populations of A. fragilis and A. colchica to identify the level of morphological and genetic divergence in Poland. We applied a conventional study approach using metric, meristic, and categorial (coloration) features for a phenotype analysis, and two standard molecular markers, a mitochondrial (NADH-ubiquinone oxidoreductase chain 2; ND2) and a nuclear (V(D)J recombination-activating protein 1; RAG1) one.ResultsWe found clear differences between A. fragilis and A. colchica in molecular markers and phenotype—in meristic features, e.g., ear opening, number of scales rows around the body, and higher than so far known diversity in ND2 and RAG1 haplotypes. The presence of five hybrids was detected in three populations in the Polish part of the European contact zone. In all hybrids, homozygous alleles of RAG1 were detected, which suggests a back-crossing within the genus.ConclusionsThe ability to produce fertile offspring by A. fragilis x A. colchica hybrids shows inefficient mechanisms of reproductive isolation of the two legless lizards. The hybrids were indistinguishable from parental species in head proportions (principal components and discriminant analyses) but more resembling A. colchica in meristic traits. creator: Grzegorz Skórzewski creator: Bartosz Borczyk creator: Stanisław Bury creator: Daniel Kulik creator: Jan Kotusz uri: https://doi.org/10.7717/peerj.18563 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Skórzewski et al. title: Research progress on the impact of climate change on wheat production in China link: https://peerj.com/articles/18569 last-modified: 2025-01-06 description: It is crucial to elucidate the impact of climate change on wheat production in China. This article provides a review of the current climate change scenario and its effects on wheat cultivation in China, along with an examination of potential future impacts and possible response strategies. Against the backdrop of climate change, several key trends emerge: increasing temperature during the wheat growing season, raising precipitation, elevated CO2 concentration, and diminished radiation. Agricultural disasters primarily stem from oscillations in temperature and precipitation, with the northern wheat region being mostly affected. The impact on wheat production is manifested in a reduction in the area under cultivation, with the most rapid reduction in spring wheat, and a shift in the center of cultivation to the west. Furthermore, climate change accelerates the nutritional stage and shortens phenology. Climate change has also led to an increase in yields in the Northeast spring wheat region, the Northern spring wheat region, the Northwest spring wheat region, and the North China winter wheat region, and a decrease in yields in the middle and lower reaches of the Yangtze River winter wheat region, the Southwest winter wheat region, and the South China winter wheat region. To cope with climate change, Chinese wheat can adopt adaptation strategies and measures such as breeding different wheat varieties for different wheat-growing regions, implementing differentiated farmland management measures, promoting regional ecological farmland construction, and establishing scientific monitoring and early warning systems. While future climate change may stimulate wheat yield potential, it could cause climate-induced issues such as weeds, diseases, and pests worsen, thereby posing challenges to the sustainability of farmland. Moreover, it is essential to conduct comprehensive research on pivotal areas such as the microscopic mechanism of climate change and wheat growth, the comprehensive influence of multiple climate factors, and the application of new monitoring and simulation technologies. This will facilitate the advancement of related research and provide invaluable insights. creator: Yu-chen Fan creator: Ya-qi Yuan creator: Ya-chao Yuan creator: Wen-jing Duan creator: Zhi-qiang Gao uri: https://doi.org/10.7717/peerj.18569 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Fan et al. title: Reproductive management: conditioning, spawning and development of Peruvian grunt Anisotremus scapularis in southern Peru link: https://peerj.com/articles/18655 last-modified: 2025-01-06 description: The Peruvian grunt, Anisotremus scapularis, is beginning its domestication as a candidate species for marine aquaculture. The optimal management of fingerling production requires precise knowledge on early development. Herein, we report the methodology for capturing and conditioning wild specimens to find a viable broodstock. The speed of capture and transportation (about 30 min), the post capture preventive treatment (60 min with tetracycline), and the 6-days preventive antiparasitic treatment (29 ppm formalin) maximized survival and a rapid feeding adaptation. Progressive diets based on the copepod Emerita analoga, fish meal, pellets and processed feedstuff prompted the spontaneous broodstock spawning 7 months post-capture. The interannual spawning of this broodstock since September 2016 indicated the optimal control of its reproduction in captivity. The morphogenetic process of the embryo lasted 42 h at 18 °C compared to (31–41) h at 19 °C in northern Peruvian latitudes. The knowledge generated allowed us to work out broodstock and egg management protocols in southern Pacific latitudes (southern Peru and northern Chile). Such protocols would help to escalate larval and juvenile production and to alleviate fishing pressure on the overexploited Peruvian grunt population. creator: Renzo Pepe-Victoriano creator: Jordan I. Huanacuni creator: Pablo Presa creator: Luis Antonio Espinoza-Ramos uri: https://doi.org/10.7717/peerj.18655 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Pepe-Victoriano et al. title: A novel nomogram based on the patient’s clinical data and CT signs to predict poor outcomes in AIS patients link: https://peerj.com/articles/18662 last-modified: 2025-01-06 description: BackgroundThe 2019 American Heart Association/American Stroke Association (AHA/ASA) guidelines strongly advise using non-contrast CT (NCCT) of the head as a mandatory test for all patients with suspected acute ischemic stroke (AIS) due to CT’s advantages of affordability and speed of imaging. Therefore, our objective was to combine patient clinical data with head CT signs to create a nomogram to predict poor outcomes in AIS patients.MethodsA retrospective analysis was conducted on 161 patients with acute ischemic stroke who underwent mechanical thrombectomy at the Guangzhou Hospital of Integrated Traditional and Western Medicine from January 2019 to June 2023. All patients were randomly assigned to either the training cohort (n = 113) or the validation cohort (n = 48) at a 7:3 ratio. According to the National Institute of Health Stroke Scale (NIHSS) score 7 days after mechanical thrombectomy, the patients were divided into the good outcome group (<15) and the poor outcome group (≥15). Predictive factors were selected through univariate analyses, LASSO regression analysis, and multivariate logistic regression analysis, followed by the construction of a nomogram predictive model. The receiver operating characteristic (ROC) curve was used to evaluate the predictive performance of the model, and bootstrapped ROC area under the curve (AUC) estimates were calculated to provide a more stable evaluation of the model’s accuracy. The model’s calibration performance was evaluated through the Hosmer-Lemeshow goodness-of-fit test and calibration plot, and the clinical effectiveness of the model was analyzed through decision curve analysis (DCA).ResultsMultivariate logistic regression analysis showed that hyperdense middle cerebral artery sign (HMCAS) (OR 9.113; 95% CI [1.945–42.708]; P = 0.005), the Alberta Stroke Program Early Computed Tomography Score (ASPECTS) > 6 (OR 7.707; 95% CI [2.201–26.991]; P = 0.001), NIHSS score (OR 1.085; 95% CI [1.009–1.166]; P = 0.027), age (OR 1.077; 95% CI [1.020–1.138]; P = 0.008) and white blood cell count (WBC) (OR 1.200; 95% CI [1.008–1.428]; P = 0.040) were independent risk factors for early poor outcomes after mechanical thrombectomy. The nomogram model was constructed based on the above factors. The training set achieved an AUC of 0.894, while the validation set had an AUC of 0.848. The bootstrapped ROC AUC estimates were 0.905 (95% CI [0.842–0.960]) for the training set and 0.848 (95% CI [0.689–0.972]) for the validation set. Results from the Hosmer-Lemeshow goodness-of-fit test and calibration plot indicated consistent performance of the prediction model across both training and validation cohorts. Furthermore, the DCA curve demonstrated the model’s favorable clinical practicality.ConclusionThis study introduces a novel practical nomogram based on HMCAS, ASPECTS > 6, NIHSS score, age, and WBC that can well predict the probability of poor outcomes after MT in patients with AIS. creator: Jingyao Yang creator: Fangfang Deng creator: Qian Zhang creator: Zhuyin Zhang creator: Qinghua Luo creator: Yeyu Xiao uri: https://doi.org/10.7717/peerj.18662 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yang et al. title: Comparative analysis of volume growth processes of Masson pine and Chinese fir forests in different regions of southern China link: https://peerj.com/articles/18706 last-modified: 2025-01-06 description: Masson pine (Pinus massoniana Lamb.) and Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) are important coniferous species commonly found in southern China and play crucial ecological and economic roles. Understanding how regionally variable conditions influence their growth patterns can support effective forest management strategies and conservation efforts. Here, we used the Richards growth equation to comprehensively analyze their volumetric growth processes through multiple diverse regions in southern China, representing a pioneering large-scale application of unified modeling techniques. This work provides theoretical and technical knowledge to support the sustainable stewardship of these vital forest ecosystems. We found that: (1) The highest per-hectare volume accumulation occurs in southwestern China, at 97.455 m3 hm−2 for P. massoniana and 85.288 m3 hm−2 for C. lanceolata. These values are higher than in the southeastern (71.424 m3 hm−2 and 79.520 m3 hm−2, respectively) or south-central regions (70.697 m3 hm−2 and 65.647 m3 hm−2), predominantly due to varying stand maturity across these regions. (2) Both species exhibit age-dependent growth patterns in the first 100 years of forest development, characterized by rapid early growth and transitioning into slower, stable phases. The highest total volume growth for P. massoniana occurred in the southwest, followed by the southeast and south-central regions. Conversely, C. lanceolata growth is highest in the southeast, followed by south-central and the southwest. (3) Quantitative maturity for P. massoniana ranges from 27 to 29 years (average: 30 years) whereas C. lanceolata matures earlier, between 16 to 19 years (average: 20 years). Climate and soil factors significantly influence their growth dynamics, with precipitation, temperature variation, and soil characteristics driving differences in suitability and growth potential across distinct regions in southern China. Tailored management practices that align with local climatic and environmental conditions are recommended to optimize growth and ensure sustainable management and development of P. massoniana and C. lanceolata forests. creator: YuHui Chen creator: Zongzheng Chai uri: https://doi.org/10.7717/peerj.18706 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Chen and Chai title: Responses of fungal communities at different soil depths to grazing intensity in a desert steppe link: https://peerj.com/articles/18791 last-modified: 2025-01-06 description: Grazing can alter the physicochemical properties of soil and quickly influence the composition of microbial communities. However, the effects of grazing intensity on fungal community composition in different soil depth remain unclear. On the Inner Mongolia Plateau, we studied the effects of grazing intensity treatments including no grazing (NG), light grazing (LG), moderate grazing (MG), heavy grazing (HG), and over grazing (OG) on the physicochemical properties and fungal community composition of surface (0–20 cm) and subsurface (20–40 cm) soil layers. The α-diversity of fungi in subsurface soil decreased under the influence of grazing. The relative abundance of Ascomycota in the subsoil was higher than that in the topsoil, while the situation of Basidiomycota was the opposite. This was caused by the differences in the soil carbon (C) environment for the growth of oligotrophic and copiotrophic fungi. In the subsoil, grazing affected nutrient contents such as soil organic matter (SOM) and total nitrogen (TN), resulting in significantly lower relative abundance of Ortierellomycota under LG, HG, and OG than in the NG. HG showed much higher relative abundance of Glomeromycota. Results of a multiple regression tree (MRT) analysis revealed that TN and nitrate nitrogen affected the fungal α-diversity in top- and subsoils, respectively; the main driving factor regulating fungal community changes was soil water content (SWC) in the topsoil, while it was ammonium nitrogen and nitrate nitrogen in the subsoil. The results of our study indicate that grazing changes the soil environment by changing TN, SWC, nitrate nitrogen, ammonium nitrogen, and affects the diversity and community structure of soil fungi. This provides empirical support for coping with the impact of grazing on soil microbiomes in desert steppes. creator: Xiangjian Tu creator: Paul C. Struik creator: Shixian Sun creator: Zhang Wenbo creator: Yong Zhang creator: Ke Jin creator: Zhen Wang uri: https://doi.org/10.7717/peerj.18791 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tu et al. title: Exploring the phenotypic and molecular diversity of Calendula officinalis L. cultivars featuring varying flower types link: https://peerj.com/articles/18814 last-modified: 2025-01-06 description: Pot marigold is an ornamental plant of great importance in pharmacy and cosmetology. However, there is limited published information on the diversity of the species at both the morphological and genetic levels. This paper aimed to determine the morphological and genetic diversity of selected marigold varieties. The research focused on varieties with different flower colours, and the most important morphological features of flowers and plant height were analysed. Genetic diversity analyses were performed using start codon target (SCoT) markers. The correlation coefficients between the analysed morphological features of the studied marigold varieties showed a significant positive relationship between plant height, the number of inflorescences per plant and inflorescence diameter. Genetic analyses grouped the studied varieties according to the colour of their flowers. The results obtained in our work indicate that, despite the variability observed in morphological features, the gene pool of the analysed marigold varieties is limited. This information can be valuable for marigold breeders, particularly for selecting varieties suitable for crossbreeding in breeding programs. Additionally, it offers insights into the genetic resources of the species and highlights the importance of their bioconservation. creator: Aleksandra Nucia creator: Tomasz Ociepa creator: Beata Król creator: Sylwia Okoń uri: https://doi.org/10.7717/peerj.18814 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nucia et al. title: Construction and validation of prognosis and treatment outcome models based on plasma membrane tension characteristics in bladder cancer link: https://peerj.com/articles/18816 last-modified: 2025-01-06 description: BackgroundPlasma membrane tension-related genes (MTRGs) are known to play a crucial role in tumor progression by influencing cell migration and adhesion. However, their specific mechanisms in bladder cancer (BLCA) remain unclear.MethodsTranscriptomic, clinical and mutation data from BLCA patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Clusters associated with MTRGs were identified by consensus unsupervised cluster analysis. The genes of different clusters were analyzed by GO and KEGG gene enrichment analysis. Differentially expressed genes (DEGs) were screened from different clusters. Consensus cluster analysis of prognostic DEGs was performed to identify gene subtypes. Patients were then randomly divided into training and validation groups, and MTRG scores were constructed by logistic minimum absolute contraction and selection operator (LASSO) and Cox regression analysis. We assessed changes in clinical outcomes and immune-related factors between different patient groups. The single-cell RNA sequencing (scRNA-seq) dataset for BLCA was collected and analyzed from the Tumor Immune Single-cell Hub (TISCH) database. Biological functions were investigated using a series of experiments including quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), wound healing, transwell, etc.ResultsOur MTRG score is based on eight genes (HTRA1, GOLT1A, DCBLD2, UGT1A1, FOSL1, DSC2, IGFBP3 and TAC3). Higher scores were characterized by lower cancer stem cell (CSC) indices, as well as higher tumor microenvironment (TME) stromal and immune scores, suggesting that high scores were associated with poorer prognosis. In addition, some drugs such as cisplatin, paclitaxel, doxorubicin, and docetaxel exhibited lower IC50 values in the high MTRG score group. Functional experiments have demonstrated that downregulation of DCBLD2 affects tumor cell migration, but not proliferation.ConclusionsOur study sheds light on the prognostic significance of MTRGs within the TME and their correlation with immune infiltration patterns, ultimately impacting patient survival in BLCA. Notably, our findings highlight DCBLD2 as a promising candidate for targeted therapeutic interventions in the clinical management of BLCA. creator: Zhipeng Wang creator: Sheng Li creator: Fuchun Zheng creator: Situ Xiong creator: Lei Zhang creator: Liangwei Wan creator: Chen Wang creator: Xiaoqiang Liu creator: Jun Deng uri: https://doi.org/10.7717/peerj.18816 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wang et al. title: Coral histology reveals consistent declines in tissue integrity during a marine heatwave despite differences in bleaching severity link: https://peerj.com/articles/18654 last-modified: 2025-01-03 description: Marine heatwaves are starting to occur several times a decade, yet we do not understand the effect this has on corals across biological scales. This study combines tissue-, organism-, and community-level analyses to investigate the effects of a marine heatwave on reef-building corals. Adjacent conspecific pairs of coral colonies of Montipora capitata and Porites compressa that showed contrasting phenotypic responses (i.e., bleached vs. not bleached) were first identified during a marine heatwave that occurred in 2015 in Kāne’ohe Bay, Hawai‘ i. These conspecific pairs of bleaching-resistant and bleaching-susceptible colonies were sampled for histology and photographed before, during, and after a subsequent marine heatwave that occurred in 2019. Histology samples were quantified for: (i) abundance of mesenterial filaments, (ii) tissue structural integrity, (iii) clarity of epidermis, and (iv) cellular integrity (lack of necrosis/granulation) on a 1–5 scale and averaged for an overall tissue integrity score. Tissue integrity scores revealed a significant decline in overall tissue health during the 2019 heatwave relative to the months prior to the heatwave for individuals of both species, regardless of past bleaching history in 2015 or bleaching severity during the 2019 heatwave. Coral tissue integrity scores were then compared to concurrent colony bleaching severity, which revealed that tissue integrity was significantly correlated with colony bleaching severity and suggests that the stability of the symbiosis is related to host tissue health. Colony partial mortality was also quantified as the cumulative proportion of each colony that appeared dead 2.5 years following the 2019 bleaching event, and tissue integrity during the heatwave was found to be strongly predictive of the extent of partial mortality following the heatwave for M. capitata but not P. compressa, the latter of which suffered little to no mortality. Surprisingly, bleaching severity and partial mortality were not significantly correlated for either species, suggesting that tissue integrity was a better predictor of mortality than bleaching severity in M. capitata. Despite negative effects of heat stress at the tissue- and colony-level, no significant changes in coral cover were detected, indicating resilience at the community level. However, declines in tissue integrity in response to heat stress that are not accompanied by a visible bleaching response may still have long-term consequences for fitness, and this is an important area of future investigation as heat stress is commonly associated with long-term decreases in coral fecundity and growth. Our results suggest that histology is a valuable tool for revealing the harmful effects of marine heatwaves on corals before they are visually evident as bleaching, and may thus improve the predictability of ecosystem changes following climate change-driven heat stress by providing a more comprehensive assessment of coral health. creator: Elisa Kruse creator: Kristen T. Brown creator: Katie L. Barott uri: https://doi.org/10.7717/peerj.18654 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kruse et al. title: The non-indigenous dung beetle (Onthophagus nuchicornis) can effectively reproduce using the dung of indigenous eastern North American mammals link: https://peerj.com/articles/18674 last-modified: 2025-01-03 description: Non-indigenous dung beetle (Coleoptera: Scarabaeoidea) species in North America are important contributors to ecosystem functions, particularly in pasture-based livestock systems. Despite the significant body of research surrounding non-indigenous (and often invasive) dung beetles in agricultural contexts, there has been minimal study concerning the impact that these species may have on indigenous dung beetle populations in natural environments. Here we examine the possible impact of the introduced dung beetle Onthophagus nuchicornis on indigenous dung beetle populations via use of indigenous mammal dung. Using a controlled laboratory experiment, we quantified how readily beetles could use dung from bobcat (Lynx rufus), red fox (Vulpes vulpes), moose (Alces alces), raccoon (Procyon lotor), and domestic sheep (Ovis aries). To determine the suitability of each dung type for reproduction, we measured offspring abundance and fitness. While the number of developed offspring was significantly different among treatments, offspring fitness did not vary significantly across dung types. Our results demonstrate the generalist feeding habits of the non-indigenous dung beetle O. nuchicornis can allow this species to use the dung of various wild animals indigenous to eastern North America. creator: Alexe Indigo creator: Katelyn Stokes creator: Olivia Burchell creator: Paul Manning uri: https://doi.org/10.7717/peerj.18674 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Indigo et al. title: The effect of the Wnt pathway on the osteogenic differentiation of periodontal ligament stem cells in different environments link: https://peerj.com/articles/18770 last-modified: 2025-01-03 description: Alveolar bone defects have always been an urgent problem in the oral cavity. For some patients with periodontal disease or undergoing orthodontic treatment or implant restoration, alveolar bone defects can greatly inconvenience clinical diagnosis and treatment. Periodontal ligament stem cells (PDLSCs) are considered a promising source for stem cell therapy due to their high osteogenic differentiation capability. The osteogenic differentiation of PDLSCs is influenced by various cytokines mediating signaling pathways, as well as a range of biochemical, physical, and chemical factors. Different environments typically impact the Wnt signaling pathway and consequently affect the osteogenic differentiation of PDLSCs. Understanding the effects of the Wnt signaling pathway on the osteogenic differentiation of periodontal ligament stem cells in various environments contributes to addressing the diverse clinical scenarios encountered in the oral environment. This knowledge aids in influencing the pathway through bioengineering or the development of novel materials, thereby enhancing the osteogenic potential of stem cells and providing new diagnostic and therapeutic strategies for clinical practice. creator: Qi Su creator: Fengqiong Huang creator: XiuLei Fang creator: Qiang Lin uri: https://doi.org/10.7717/peerj.18770 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Su et al. title: The status quo and influencing factors of breastfeeding social support in China based on LASSO regression model link: https://peerj.com/articles/18779 last-modified: 2025-01-03 description: BackgroundIn China, the rate of exclusive breastfeeding at 6 months is only 29.2%, well below the global breastfeeding collective target of at least 50% by 2025. This study explores the status quo of breastfeeding social support among puerpera and analyses its influencing factors, in order to provide a basis for improving breastfeeding rate in China.MethodsA total of 251 puerpera were selected to fill in the general information questionnaire and the Breastfeeding Social Support Scale from three community health service centers in the city of Chengde, Hebei province, China, from September to November 2023 by completed random cluster sampling method. And the LASSO regression was used to screen and order the influencing factors of breastfeeding social support.ResultsThe total score of the Breastfeeding Social Support Scale was (48.95 ± 7.93). The results of LASSO regression showed that when the lambda (λ) value was 0.7428, the error was the smallest, and the corresponding number of influencing factors was four, and the top four independent variables in importance ranking were whether or not breastfeeding at night, employment status, the feeding mode of the youngest baby, partner attended school/lecture for pregnant women.ConclusionThe level of breastfeeding social support remains to be improved; health care providers were suggested to develop targeted intervention according to the influencing factors. creator: Tian Sun creator: Chanzhi Duan creator: Yan Wang creator: Qing Li uri: https://doi.org/10.7717/peerj.18779 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Sun et al. title: Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers link: https://peerj.com/articles/18323 last-modified: 2025-01-02 description: BackgroundUnderstanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico.MethodsWe used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2.ResultsThe workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data. creator: Stephanie Hereira-Pacheco creator: Itzel Arias-Del Razo creator: Alejandra Miranda-Carrazco creator: Luc Dendooven creator: Arturo Estrada-Torres creator: Yendi E. Navarro-Noya uri: https://doi.org/10.7717/peerj.18323 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hereira-Pacheco et al. title: Knowledge, attitudes, practices, and vaccination coverage of medical students toward hepatitis B virus in North Sudan, 2023 link: https://peerj.com/articles/18339 last-modified: 2025-01-02 description: BackgroundHepatitis B virus (HBV) is a global health issue, particularly among healthcare personnel, including students because of its occupational exposure pattern. Healthcare Workers and medical students are recommended to have better knowledge, attitudes and good practices and vaccination toward infection control in general and HBV in particular. This study aimed to assess the knowledge, attitudes, and practices of medical students from North Sudan regarding HBV and its vaccination coverage.MethodsA cross-sectional study was conducted from January to June 2023 among medical students in North Sudan. Data were collected using a structured scale using online Google Forms. Descriptive and comparative analyses were performed using SPSS version 26. Statistical significance was set at p ≤ 0.05.ResultsA total of 426 medical students were included in the study. The majority had good knowledge about HBV (86%) and its transmission methods (77%). The majority showed a favorable attitude (77%). The practice score was however very low (15.5%). Older age and advanced academic level were significantly associated with good knowledge (aOR: 3.9; CI 95% [3.69–12.92]; p = 0.016, and aOR: 2.6; CI 95% [1.16–6.15]; p = 0.020, respectively). Only a third of the students were vaccinated (33.0%), with only a few of them received complete doses (18.6%).ConclusionStudents from medical colleges in North Sudan had good knowledge and favorable attitudes toward HBV. However, good practice was low. Older age and advanced academic level were significantly associated with knowledge level. Vaccination coverage was also low among the students in this study. creator: Osama M.I. Mohamed creator: Hassan S.H. Mohammedali creator: Shimaa N.A. Mohamed creator: Hussein A.S. Ahmed creator: Alaa A.M. Mohamedsalih creator: Ola M.A. Abdalgani creator: Tebian A.A. Mohammedosman creator: Alaa A.A. Ali creator: Thuiba A.H. Ali creator: Othman N.O. Amin creator: Mohamed A. Issak creator: Mohamed O. Abdelaziz uri: https://doi.org/10.7717/peerj.18339 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mohamed et al. title: Constructing age-structured matrix population models for all fishes link: https://peerj.com/articles/18387 last-modified: 2025-01-02 description: Matrix population models are essential tools in conservation biology, offering key metrics to guide species management and conservation planning. However, the development of these models is often limited by insufficient life history data, particularly for non-charismatic species. This study addresses this gap by using life history data from FishBase and the FishLife R package, complemented by size-dependent natural mortality estimates, to parameterize age-structured matrix population models applicable to most fish species. The method was applied to 30 fish species common around oil and gas platforms in the Northern Gulf of Mexico, generating seven key metrics: damping ratio, resilience, generation time, stable age distribution, reproductive value, sensitivity matrix, and elasticity matrix. The damping ratio reflects how quickly a population returns to a stable age distribution after a disturbance, while resilience indicates the speed of recovery from perturbations. Generation time captures the average age of reproduction, and the stable age distribution represents the long-term proportion of individuals in each age class. Reproductive value quantifies future reproductive potential by age class. The sensitivity matrix highlights the age-class transitions most affecting population growth, and the elasticity matrix shows the proportional influence of these factors on population growth. The results demonstrate that robust population models can be constructed with limited species-specific data and reveal notable differences in population dynamics among species. For example, species with longer generation times, like the greater barracuda (Sphyraena guachancho), have lower damping ratios, indicating prolonged transient dynamics. In contrast, species such as the round scad (Decapterus punctatus) exhibit shorter generation times and higher damping ratios, suggesting faster returns to equilibrium. These findings underscore the importance of life history variability in shaping conservation strategies. Additionally, metrics like stable age distributions and reproductive values provide insight into population structure and individual contributions to future populations, while sensitivity and elasticity matrices inform management interventions such as size limits in fisheries. By integrating extensive databases and predictive tools, this study offers a scalable approach for developing matrix population models across diverse fish species. This methodology enhances our understanding of fish population dynamics, particularly for data-deficient species, and supports more informed conservation efforts. It also promotes ecosystem-based management by enabling species comparisons through standardized metrics, contributing to the sustainability of marine ecosystems. creator: Masami Fujiwara uri: https://doi.org/10.7717/peerj.18387 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fujiwara title: Mapping species of greatest conservation need and solar energy potential in the arid Southwest for future sustainable development link: https://peerj.com/articles/18568 last-modified: 2025-01-02 description: The need for renewable energy has become increasingly evident in response to the climate change crisis, presenting a paradoxical challenge to biodiversity conservation. The Southwest United States is desirable for large-scale solar energy development (SED) due to its high global horizontal irradiance (GHI) values and vast open landscapes. However, this region is also rich in unique ecological and biological diversity. Several distinct species have garnered special attention as human population growth, habitat alteration, and climate change have accelerated in recent decades (i.e., LeConte’s Thrasher (Toxostoma lecontei), Bendire’s Thrasher (Toxostoma bendirei), Sonoran Desert Tortoise (Gopherus morafkai), Mojave Desert Tortoise (Gopherus agassizii), and the Southwestern population of the Burrowing Owl (Athene cunicularia). As the United States prepares to increase its development in renewable energies, particularly solar energy, there has been a growing concern about how this development will further impact these species. In this study, we propose a novel combined approach to find areas of high habitat suitability for endangered species within areas of high SED potential. Specifically, we employed species distribution modeling (SDM) to identify areas with suitable habitats and likely species presence, and we conducted a site suitability analysis for potential SED locations within the Southwest. As a result, we found significant overlap between potential SED locations and the high-priority habitats of all target species, thus underlining the importance of prioritizing conservation efforts as more solar projects are reviewed in these Southwestern states. Our study aims to inform conservationists and developers in making sustainable decisions for the region’s future development. creator: Kylee Fleckenstein creator: Adam Stein creator: Heather L. Bateman creator: Fabio De Albuquerque uri: https://doi.org/10.7717/peerj.18568 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Fleckenstein et al. title: A giant specimen of Rhamphorhynchus muensteri and comments on the ontogeny of rhamphorhynchines link: https://peerj.com/articles/18587 last-modified: 2025-01-02 description: Rhamphorhynchus is one of the best-known pterosaurs, with well over 100 specimens being held in public collections. Most of these represent juvenile animals, and the adults known are typically around 1 m in wingspan. Here we describe a near complete skeleton, preserved partially in 3D, of an animal with a wingspan of around 1.8 m, that is considerably larger than other known specimens, and is among the largest known non-pterodactyloid pterosaurs. This animal shows differences in the anatomy not seen in smaller specimens, revealing details of late-stage ontogeny in this genus. The specimen exhibits a disproportionate reduction in the size of the orbit and increase in the size of the lower temporal fenestra, a reduction in the proportional mandibular symphysis, and unusually laterally flattened teeth, which may point to a changing diet as these animals grew. These features show a transition from smaller to larger specimens of Rhamphorhynchus and also appear in other large specimens of rhamphorhyhchines and point to a consistent pattern in their development. creator: David W.E. Hone creator: Skye N. McDavid uri: https://doi.org/10.7717/peerj.18587 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hone and McDavid title: The application of deep learning in early enamel demineralization detection link: https://peerj.com/articles/18593 last-modified: 2025-01-02 description: ObjectiveThe study aims to develop a diagnostic model using intraoral photographs to accurately detect and classify early detection of enamel demineralization on tooth surfaces.MethodsA retrospective analysis was conducted with 208 patients aged 14 to 44. A total of 624 high-quality digital images captured under standardized conditions were used to construct a deep learning model based on the Mask region-based convolutional neural network (Mask R-CNN). The model was trained to automate the detection of enamel demineralization. Its performance was compared to two junior dentists’ diagnostic abilities.ResultsThe model achieved an F1-score of 0.856 for detecting demineralized teeth on the validation set, a metric that reflects comprehensive diagnostic performance, demonstrating performance close to that of senior dentists. With the the model’s assistance, the junior dentists’ average F1-scores improved significantly—from 0.713 and 0.689 to 0.897 and 0.949, respectively (p < 0.05). The model accurately segmented tooth surfaces and detected demineralized areas, allowing for precise detection of demineralized areas and monitoring of lesion progression.ConclusionDeep learning can accurately segment tooth surfaces and lesion contours, enhancing the precision, accuracy, and efficiency of enamel demineralization diagnosis and area delineation. creator: Ketai He creator: Rongxiu Zhang creator: Muchun Liang creator: Keyue Tian creator: Kaihui Luo creator: Ruoshi Chen creator: Jianpeng Ren creator: Jiajun Wang creator: Juan Li uri: https://doi.org/10.7717/peerj.18593 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 He et al. title: The inter-trial and inter-session reliability of Theia3D-derived markerless gait analysis in tight versus loose clothing link: https://peerj.com/articles/18613 last-modified: 2025-01-02 description: BackgroundGait analysis is traditionally conducted using marker-based methods yet markerless motion capture is emerging as an alternative. Initial studies have begun to evaluate the reliability of markerless motion capture yet the evaluation of different clothing conditions across sessions and complete evaluation of the lower limb and pelvis reliability have yet to be considered. The aim of this study was to evaluate the inter-trial, inter-session and inter-session-clothing variation and root mean square differences between tight- or loose-fitting clothing during walking.MethodTwenty-two healthy adult participants walked along an indoor walkway whilst eight video cameras recorded their gait in either tight- or loose-fitting clothing. A commercial markerless motion capture system (Theia3D) provided gait kinematics for evaluation.ResultsReliability results showed average inter-trial variation of <2°, inter-session variation of <3° and inter-session-clothing variation <3.5°. Root mean square differences (RMSD) between clothing conditions were <2°.DiscussionPelvis variations were smaller than those at the hip, knee and ankle. Our results showed smaller variation than in previous studies which may be due to updates to software. The demonstration of the reliability of markerless motion capture for gait analysis in healthy adults should prompt further evaluation in clinical conditions and reconsideration of multi-assessor marker-based gait analysis protocols, where variation is highest. creator: Sylvia Augustine creator: Richard Foster creator: Gabor Barton creator: Mark J. Lake creator: Raihana Sharir creator: Mark A. Robinson uri: https://doi.org/10.7717/peerj.18613 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Augustine et al. title: How many reptile and amphibian species are in Uganda, and why it matters for global biodiversity conservation link: https://peerj.com/articles/18704 last-modified: 2025-01-02 description: Biodiversity is unevenly distributed across the globe. Regional differences in biodiversity impact conservation through the allocation of financial resources, development of infrastructure, and public attention. Such resources are often prioritized to areas that are in more need than others. However, reasons for deciding which locations are more deserving are derived from an accurate knowledge of the number and composition of species that occur in each region. Regional differences in biodiversity, however, can reflect differences in the source of information consulted, rather than bona fide differences between areas. As a result, conservation resources may not be directed to regions in proportion to their actual need, especially if there is no consensus among sources of information. Here, we compared major sources of information on species of reptiles and amphibians that occur in Uganda, Africa. We found that none of the sources agreed on the total number, nor composition, of species in the country, with estimates for amphibians ranging more widely than those for reptiles. Notably, sources with similar species richness differed in species composition, which had an impact on the number of threatened species in the country. These results for a conspicuous group of vertebrates suggest that lesser-known groups are also likely misrepresented in sources, especially in other underexplored regions of tropical Africa. We discuss the implications for biodiversity conservation that are derived from inaccurate species lists that are commonly used by agencies, scientists, and practitioners. We argue that more critical evaluations of biodiversity resources, in addition to greater capacity building for field programs, taxonomy, and museum collections, will be essential to ensure that resources are allocated to regions that need them the most. creator: Daniel F. Hughes creator: Mathias Behangana uri: https://doi.org/10.7717/peerj.18704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hughes and Behangana title: Basis of single-seed formation in chestnut: cytomorphological observations reveal ovule developmental patterns of Castanea henryi link: https://peerj.com/articles/18711 last-modified: 2025-01-02 description: BackgroundMany plants, including those commonly found in the Fagaceae family, produce more flowers and ovules than mature fruits and seeds. In Castanea henryi, an ovary contains 16–24 ovules, but only one develops into a seed. The other ovules abort or otherwise fail to fully develop, but the reason for this is unknown. Such a strict reproductive screening mechanism is rare in plants.MethodsIn this study, controlled pollination scheme were adopted, and conventional paraffin embedding and semi-thin sectioning techniques, followed by microscopy, were used for cytological studies of ovule development in C. henryi.ResultsPollination affected not only the process of ovule development, but also the proportion of ovules that formed mature embryo sacs. Approximately 53.53% of the ovules in the pollinated treatment developed normally, while only 16.55% of the ovules in the unpollinated treatment developed into mature embryo sacs with a seven-cell, eight-nucleated structure. Failure to form mature embryo sacs and the abnormal divisions of the zygote, respectively, were the reasons for the pre- and post-fertilization ovule failures. Our findings not only provide basic information on the reproductive biology and also information on seed production of C. henryi. creator: Qi Qiu creator: Xiaoming Tian creator: Guolong Wu creator: Juntao Wu creator: Deyi Yuan creator: Xiaoming Fan uri: https://doi.org/10.7717/peerj.18711 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Qiu et al. title: Effect of low-dose radiation pre-irradiation on postoperative local chest wall recurrence of breast cancer—A retrospective study link: https://peerj.com/articles/18717 last-modified: 2025-01-02 description: PurposeThe purpose of this study was to determine the efficacy and safety of low-dose radiotherapy (LDR) for postoperative local chest wall recurrence of breast cancer.MethodsThe records of 52 patients with postoperative local chest wall recurrent breast cancer treated at our cancer center from January 2019 to December 2022. The t-test was used to compare the means of the LDR group and non LDR group. Categorical data were compared using the chi-square test. The Kaplan-Meier method were used to determine the factors associated the survival.ResultsCompared to patients who did not undergo LDR, patients in the LDR group showed a higher incidence of grade I side effects in their skin and soft tissue systems (p = 0.002), a significant reduction in grade II side effects (p < 0.05), and no grade III side effects. Compared with the non LDR group, the complete response rates were 42.3% vs. 38.5%, p = 0.777, the partial response rates were 53.8% vs. 50.0%, p = 0.781, and the objective relief rates were 96.2% vs. 88.5%, p = 0.833, respectively. The 3-year overall survival rate, local recurrence free survival rate, distant metastasis-free survival rate and disease-specific survival rate comparison between LDR group and non LDR group was 54.8% vs. 55.8%, p = 0.845 and 54.2% vs. 52.9%, p = 0.751, 67.9% vs. 51.9%, p = 0.097 and 39.2% vs. 49.6%, p = 0.993, respectively.ConclusionCompared with traditional radiotherapy, LDR pre-irradiation has better tolerance and efficacy in patients with local chest wall recurrence of breast cancer after operation. creator: Ruifang Zeng creator: Hanyu Wang creator: Xiaojun Cai creator: Junhao Lin creator: Pengfei Li creator: Shan Zeng creator: Aimin Li uri: https://doi.org/10.7717/peerj.18717 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zeng et al. title: Visualizing and quantifying biomineral preservation in fossil vertebrate dental remains link: https://peerj.com/articles/18763 last-modified: 2025-01-02 description: In this study, we attempt to illustrate fossil vertebrate dental tissue geochemistry and, by inference, its extent of diagenetic alteration, using quantitative, semi-quantitative and optical tools to evaluate bioapatite preservation. We present visual comparisons of elemental compositions in fish and plesiosaur dental remains ranging in age from Silurian to Cretaceous, based on a combination of micro-scale optical cathodoluminescence (CL) observations (optical images and scanning electron microscope) with in-situ minor, trace and rare earth element (REE) compositions (EDS, maps and REE profiles), as a tool for assessing diagenetic processes and biomineral preservation during fossilization of vertebrate dental apatite. Tissue-selective REE values have been obtained using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), indicating areas of potential REE enrichment, combined with cathodoluminescence (CL) analysis. Energy dispersive X-ray spectroscopy (EDS) mapping was also used to identify major elemental components and identify areas of contamination or diagenetic replacement. We conclude that the relative abilities of different dental tissues to resist alteration and proximity to the exposure surface largely determine the REE composition and, accordingly, the inferred quality of preserved bioapatite. creator: Matthew B. Cowen creator: Marc de Rafélis creator: Loïc Ségalen creator: Benjamin P. Kear creator: Maïtena Dumont creator: Živilė Žigaitė uri: https://doi.org/10.7717/peerj.18763 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Cowen et al. title: Analysis of the correlation between the serum triglyceride glucose index and the risk of death in patients on maintenance hemodialysis: a retrospective cohort study link: https://peerj.com/articles/18781 last-modified: 2025-01-02 description: BackgroundPatients with end-stage renal disease (ESRD) have increased insulin resistance (IR). The triglyceride glucose (TyG) index is a marker of IR and is associated with the prognosis of patients on maintenance hemodialysis (MHD). The aim of this study was to examine the relationship between the TyG index and the risk of death in patients on MHD.MethodsIn a retrospective cohort analysis of 368 patients with MHD over an 11-year period from July 1, 2012, to June 30, 2023, the TyG index and other baseline characteristics were measured at the beginning of MHD treatment. A regression model was used to evaluate the correlation between the TyG index and all-cause mortality or cardiovascular mortality in patients on MHD.ResultsThe TyG index was associated with all-cause mortality and cardiovascular mortality in MHD patients (P = 0.002 & P = 0.015). After adjusting for various confounding factors, the TyG index remained an independent predictor of all-cause mortality and cardiovascular mortality in MHD patients (P < 0.001 & P = 0.044). Compared with MHD patients with low TyG index levels, the risk of all-cause mortality and cardiovascular mortality in MHD patients with high TyG index levels increased by 1.790 and 1.735 times, respectively (P = 0.006 & P = 0.022). The predictive time-AUC values of the TyG index for all-cause and cardiovascular death in MHD patients were between 0.698 to 0.819.ConclusionThe baseline TyG index may be an independent predictor of all-cause mortality and cardiovascular mortality in MHD patients. creator: Xiaokeng Chi creator: Shuxin Chen creator: Zhe Huang creator: Rong Zhou creator: Zhicheng Su creator: Qiujun Mai creator: Yilin Xu creator: Jianxin Wan uri: https://doi.org/10.7717/peerj.18781 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Chi et al.