title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2024-12 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effect of salt stress on different tiller positions in rice and the regulatory effect of prohexadione calcium link: https://peerj.com/articles/18357 last-modified: 2024-12-27 description: Soil salinization has resulted in a significant decrease in crop yields, particularly affecting the production of crops like rice (Oryza sativa L.). Prohexadione calcium (Pro-Ca) can enhance crop resilience against failure by managing plant height. However, its impact on various tiller positions during the tillering phase of rice under salt stress remains unknown. This study explores the distinct effects of salt stress on the physiological traits of the main stem and different tiller segments of rice plants, along with the role of Pro-Ca in mitigating salt stress. The findings revealed that under salt stress conditions, the number of tillers and leaves on the main stem decreased significantly in rice. Moreover, the levels of malondialdehyde (MDA) and H2O2 in the leaves and stems of each tiller position notably increased. The percentage of tillers experiencing reduction or elevation was higher than that of the main stem compared to the respective control. Application of Pro-Ca through foliar spraying under NaCl stress effectively alleviated the impact of salt stress on the tiller growth of rice during the tillering phase. It also boosted the activities of antioxidant enzymes like superoxide dismutase (SOD) and peroxidase (POD) in the leaves and stems of the tillers. Furthermore, it successfully mitigated the damage inflicted by salt stress on the cell membrane of rice tillers during the tillering phase. The regulatory effect of calcium on cyclic acid was particularly pronounced in alleviating the impact on the tillers under salt stress conditions. creator: Rongjun Zhang creator: Dianfeng Zheng creator: Naijie Feng creator: Linfeng Linfeng creator: Jinning Ma creator: Xiayi Yuan creator: Junyu Huang creator: Lisha Huang uri: https://doi.org/10.7717/peerj.18357 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Traumatic dental injuries in permanent teeth among Arab children: prevalence, and associated risk factors—a systematic review and meta-analysis link: https://peerj.com/articles/18366 last-modified: 2024-12-24 description: IntroductionThere is no clear literature present till date assessing the prevalence of traumatic dental injuries and associated factors in children living in Arab countries. The purpose of this study was to systematically assess the prevalence, trends, and potential risk factors of traumatic dental injury (TDI) in permanent teeth among children and adolescents in Arab countries.MethodsThis study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The researchers conducted a comprehensive literature search in various databases, including PubMed, Cochrane library of systematic reviews, Directory of Open Access Journals (DOAJ), Google Scholar, and gray literature sources such as MDS dissertations and manuscripts. To analyze the collected data, the researchers used a random effects model for conducting meta-analyses. Pooled estimates of prevalence and odds ratios were derived, along with 95% confidence intervals (CI), to provide a measure of statistical precision and variability in the findings. For the studies that were considered, trend analysis was done. The risk of bias assessment of included studies was done using Newcastle–Ottawa tool for cross-sectional studies.ResultsA total of 545 articles were identified, of which 23 articles fulfilled the inclusion criteria. Quality assessment of included studies showed that twenty studies were of high quality and three studies showed low quality. The frequency of dental trauma in Arab children was 26% (95% CI [10–43]). Children with overjet of more than 3.5 mm were shown to be 1.78 times more likely to have dental injury than children with normal overjet (pooled odds ratio 1.78; 95% CI [1.17–2.70]). Males had a 2.06 times odds of TDI compared to females. Children with insufficient lip coverage had an odds ratio of 2.57, indicating a higher likelihood of oral injuries compared to those with appropriate lip coverage.ConclusionSignificant correlations were obtained between the prevalence of dental trauma and other variables such as male gender, increased overjet, inadequate lip coverage, etc. Future population-based analytical research should concentrate on documenting the incidence and/or prevalence of TDI among marginalized communities in order to better understand the primary causes of TDI. creator: Raghad Hashim creator: Alexander Maniangat Luke creator: Afraa Salah creator: Simy Mathew uri: https://doi.org/10.7717/peerj.18366 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hashim et al. title: The effect of aging on the ciliary muscle and its potential relationship with presbyopia: a literature review link: https://peerj.com/articles/18437 last-modified: 2024-12-24 description: BackgroundThe ciliary muscle is known to play a part in presbyopia, but the mechanism has not received a comprehensive review, which this study aims to achieve. We examined relevant articles published from 1975 through 2022 that explored various properties of the muscle and related tissues in humans and rhesus monkeys. These properties include geometry, elasticity, rigidity, and composition, and were studied using a range of imaging technologies, computer models, and surgical methods. We identified a notable age-related displacement of the ciliary muscle apex that is characterized by anterior and medial shifts, and hypothesized to be primarily attributed to the accrual of connective tissue and tension exerted by the thickening lens. Other factors could also contribute to the movement, particularly the “inward bowing” of the sclera. Another noteworthy observation is that while the ciliary muscle experiences increasing constraint with advancing age due to adjacent anatomical structures, its contractile capacity remains unaltered, alongside the sustained constancy in both the concentration of muscarinic receptors and their binding affinity. Overall, more studies on human ciliary muscle are needed, as it ages differently from that of monkeys’ ciliary muscle. These studies should explore other perspectives, including those regarding changes in the physical properties of the tissue and its relationship with other connected tissues.MethodologyThis literature review utilized a systematic methodology to identify and analyze pertinent studies of the presbyopia and ciliary muscles. The approach encompassed a thorough examination of available literature across different academic databases, such as PubMed, Embase, and Cochrane Library.ResultsMany studies have identified age-related thickening in the ciliary muscle and its potential causes, including the heightened deposition of connective tissues and traction exerted by the thickening lens. Notably, these inquiries culminated in the formulation of a geometric theory positing that the morphology of the ciliary muscle and its spatial relationship with adjacent structures exert pivotal influence over the tension exerted on zonular fibers.ConclusionThe decline in the accommodative response of the muscle is prevalent in advanced age, with reduced mobility likely attributable to the increased stiffness of the Bruch’s Membrane-Choroid Complex (BMCC), where the tendons of the ciliary muscle insert, as well as the thickening and stiffening of the lens. Importantly, the ciliary muscle forces do not change with age. creator: Hangjia Zuo creator: Hong Cheng creator: Meiting Lin creator: Xiang Gao creator: Yongguo Xiang creator: Tong Zhang creator: Ning Gao creator: Miaomiao Du creator: Yonglin Chen creator: Shijie Zheng creator: Rongxi Huang creator: Wenjuan Wan creator: Ke Hu uri: https://doi.org/10.7717/peerj.18437 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zuo et al. title: Regulation of lymphoma in vitro by CLP36 through the PI3K/AKT/CREB signaling pathway link: https://peerj.com/articles/18693 last-modified: 2024-12-24 description: BackgroundCLP36 is also known as PDZ and LIM Domain 1 (PDLIM1) that is a ubiquitously-expressed α-actinin-binding cytoskeletal protein involved in carcinogenesis, and our current study aims to explore its involvement in lymphoma.MethodsAccordingly, the CLP36 expression pattern in lymphoma and its association with the overall survival was predicted. Then, qPCR was applied to gauge CLP36 expression in lymphoma cells and determine the knockdown efficiency. The survival, proliferation and apoptosis of CLP36-silencing lymphoma cells were tested. Cell viability, proliferation and apoptosis were assessed based on cell counting kit-8 (CCK-8) assay, colony formation assay, EdU staining, and flow cytometry, respectively. Additionally, qPCR was used to calculate the expressions of proteins associated with metastasis and apoptosis, while immunoblotting was employed to determine the phosphorylation status of phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/cAMP-response element binding protein (CREB).ResultsCLP36 expression was relatively higher in lymphoma, which was associated with a poor prognosis. Also, CLP36 was highly-expressed in lymphoma cells and the silencing of CLP36 contributed to the suppressed survival and proliferation as well as the enhanced apoptosis of lymphoma cells. Further, CLP36 silencing repressed the expressions of Cadherin 2 (CDH2) and Vimentin (VIM) yet promoted those of Bax and Caspase 3 in lymphoma cells, concurrent with the reduction on the phosphorylation of PI3K, AKT and CREB, all of which were confirmed to be positively correlated with CLP36.ConclusionThis study, so far as we are concerned, provided evidence on the involvement of CLP36/PI3K/AKT/CREB axis in lymphoma, which may be contributive for the identification on the relevant molecular targets of lymphoma. creator: Chao Lv creator: Guannan Chen creator: Shuang Lv uri: https://doi.org/10.7717/peerj.18693 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lv et al. title: Antimicrobial activity and synergistic effect of phage-encoded antimicrobial peptides with colistin and outer membrane permeabilizing agents against Acinetobacter baumannii link: https://peerj.com/articles/18722 last-modified: 2024-12-24 description: BackgroundAcinetobacter baumannii poses a significant public health threat. Phage-encoded antimicrobial peptides (AMPs) have emerged as promising candidates in the battle against antibiotic-resistant A. baumannii.MethodsAntimicrobial peptides from the endolysin of A. baumannii bacteriophage were designed from bacteriophage vB_AbaM_PhT2 and vB_AbaAut_ChT04. The peptides’ minimum inhibitory concentration (MIC) and the synergistic effect of peptides with outer membrane-permeabilizing agents and colistin were determined. Cytotoxicity effects using HepG2 cell lines were evaluated for 24 h with various concentrations of peptides. Biofilm eradication assay was determined using the MIC concentration of each peptide. Galleria mellonella infection assay of phage-encoded antimicrobial peptides was investigated and recorded daily for 10 days.ResultsThe current research indicates that three peptides, specifically PE04-1, PE04-1(NH2), and PE04-2, encoded from the endolysin of vB_AbaAut_ChT04 demonstrated significant antimicrobial activity, with minimum inhibitory concentrations (MIC) ranging from 156.25 to 312.5 µg/ml. The peptides showed antimicrobial activity against multidrug-resistant (MDR) and extensively drug-resistant (XDR) A. baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis. We found a strong synergistic effect of three peptides with colistin and citric acid, which showed high inhibition percentages (>90%) and low fractional inhibitory concentration (FIC) indexes. The peptides exhibited a high ability to inhibit biofilm formation against twenty A. baumannii strains, with PE04-2 showing the most potent inhibition (91.92%). The cytotoxicity effects of the peptides on human hepatoma cell lines showed that the concentrations at the MIC level did not affect the cell viability. The peptides improved survival rates in the G. mellonella model, exceeding 80% by day 10.Conclusions/significant findingPeptides PE04-1, PE04-1(NH2), and PE04-2 showed sequence similarity to mammalian cathelicidin antimicrobial peptides. They are cationic peptides with a positive charge, exhibiting high hydrophobic ratios and high hydropathy values. The modified PE04-2 was designed by enhancing cationic through amino acid substitutions and shows powerful antibiofilm effects due to its cationic, amphipathic, and hydrophobic properties to destroy biofilm. The peptides improved survival rates in G. mellonella infection models and showed no cytotoxicity effect on human cell lines, ensuring their safety for potential therapeutic applications. In conclusion, this study highlights the antimicrobial ability of phage-encoded peptides against multidrug-resistant A. baumannii. It can be an innovative tool, paving the way for future research to optimize their clinical application. creator: Punnaphat Rothong creator: Udomluk Leungtongkam creator: Supat Khongfak creator: Chanatinat Homkaew creator: Sirorat Samathi creator: Sarunporn Tandhavanant creator: Jatuporn Ngoenkam creator: Apichat Vitta creator: Aunchalee Thanwisai creator: Sutthirat Sitthisak uri: https://doi.org/10.7717/peerj.18722 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rothong et al. title: Description of two new Apseudopsis species (A. larnacensis sp. nov and A. salinus sp. nov.) (Tanaidacea: Crustacea) from the Mediterranean and a biogeographic overview of the genus link: https://peerj.com/articles/18740 last-modified: 2024-12-24 description: The Mediterranean Sea is recognized as one of the most threatened marine environments due to pollution, the unintentional spread of invasive species, and habitat destruction. Understanding the biodiversity patterns within this sea is crucial for effective resource management and conservation planning. During a research cruise aimed at assessing biodiversity near desalination plants in the vicinity of Larnaca, Cyprus, conducted as part of the WATER-MINING project (Horizon 2020), specimens of the tanaidacean genus Apseudopsis were collected. These were classified into two species, identified as new to science, and are described herein as Apseudopsis larnacensis sp. nov and Apseudopsis salinus sp. nov. Apseudopsis larnacensis sp. nov is distinguished from its congeners by the presence of a lateral apophysis on pleonite 5, which is longer than those on pleonites 1–4, hyposphenia on pereonites 2–6, and six ventral spines on the propodus of pereopod 1. Apseudopsis salinus sp. nov. is characterized by a rounded posterolateral margin on pereonite 6, hyposphenia on pereonites 1–6, and four ventral spines on the propodus of pereopod 1. An updated key to the Atlantic and Mediterranean Apseudopsis species is provided. This study provides an overview of the distribution, bathymetric, and habitat preference of all known Apseudopsis species. Data extracted from the literature and two popular online databases were analyzed to identify diversity patterns across seas and ecoregions. Our analysis reveals that the Mediterranean is the most diverse region for Apseudopsis, with the Levantine Sea hosting ten species and the South European Atlantic Shelf seven species. Shallow waters and muddy and sandy habitats are conducive for Apseudopsis occurrence. creator: Anna Stępień creator: Piotr Jóźwiak creator: Sergio C. Garcia Gómez creator: Eleni Avramidi creator: Kleopatra Grammatiki creator: Myrsini Lymperaki creator: Frithjof C. Küpper creator: Patricia Esquete uri: https://doi.org/10.7717/peerj.18740 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Stępień et al. title: The influence of rhizosphere microbial diversity on the accumulation of active compounds in farmed Scutellaria baicalensis link: https://peerj.com/articles/18749 last-modified: 2024-12-24 description: Rhizosphere microorganisms are important factors affecting herb quality and secondary metabolite accumulation. In this study, we investigated the diversity of rhizosphere microbial communities (bacteria and fungi) and their correlations with soil physicochemical properties and active compounds of Scutellaria baicalensis (baicalin, oroxindin, baicalein, wogonin, and oroxylin A) from cultivated Scutellaria baicalensis with three different origins via high-throughput sequencing and correlation analysis to further clarify the role of soil factors in the accumulation of the active compounds of Scutellaria baicalensis. The results are summarized as follows. A total of 28 dominant bacterial genera, such as Arthrobacter, Rubrobacter, Microvirga, and Sphingomonas, and 42 dominant fungal genera, such as Alternaria, Spegazzinia, and Minimedusa, were detected. The soil microbial communities associated with cultivated Scutellaria baicalensis were very diverse, but there were some differences in the relative abundances of microbial taxa. Correlation analysis revealed that the bacterial genera Rubrobacter, Ellin6055, Gaiella, norank__f__norank__o___norank__c__bacteriap25, unclassified__f__Micromonosporaceae, norank__f__ Gemmatimonadaceae, Arthrobacter, and Sphingomonas and the fungal genera Tausonia, Minimedusa, Cercospora, Botrytis, Alternaria, Boeremia, Titaea, Solicoccozyma, and Mortierella were positively or negatively correlated with each active component of Scutellaria baicalensis and were important genera affecting the accumulation of the active compounds of Scutellaria baicalensis and correlated with soil physiochemistry to different degrees. These results suggest that rhizosphere microorganisms may play a role in the accumulation of active compounds in medicinal plants and provide a scientific basis for guiding the cultivation of Scutellaria baicalensis, developing biofertilizers, and improving the quality of Scutellaria baicalensis medicinal materials. creator: Ping Dong creator: Yang Lu creator: Jia Bai creator: Chunying Zhao creator: Zhongsi Li creator: Yu Cao creator: Yingzhe Li uri: https://doi.org/10.7717/peerj.18749 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dong et al. title: New findings of Dunyu (Eugaleaspiformes, Galeaspida) from the Xiaoxi Formation in South China and their biostratigraphic significance link: https://peerj.com/articles/18760 last-modified: 2024-12-24 description: New discoveries of the late Silurian fossil fish Dunyu (Eugaleaspidae, Eugaleaspiformes, Galeaspida), Dunyu tianlu sp. nov. and Dunyu sp., are described from the Xiaoxi Formation in Xiushan of Chongqing and Xiushui of Jiangxi, China respectively. D. tianlu sp. nov. can be distinguished from D. longiforus and D. xiushanensis in its nearly equal preorbital and postorbital regions of the headshield. As the currently only known genus of Eugaleaspiformes during the late Silurian, Dunyu not only displays a large morphological difference with galeaspids from both the early Silurian and Early Devonian but also occupies a phylogenetic position that is far from the root of Eugaleaspiformes, which indicates that the lineages nested between Yongdongaspidae and Eugaleaspidae should have diversified before the early Ludlow, even during the Telychian. Discovery of new specimens of Dunyu provides direct evidence on the genus level for the correlation of the late Ludlow strata between the margin and interior of the Yangtze Platform, further supporting that the central part of the Yangtze Platform suffered from widespread transgression in the late Silurian. creator: Qiang Li creator: Xianren Shan creator: Zhikun Gai creator: Yang Chen creator: Lijian Peng creator: Jiaqi Zheng creator: Xianghong Lin creator: Wenjin Zhao creator: Min Zhu uri: https://doi.org/10.7717/peerj.18760 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: An efficient propagation system through stem cuttings of a multipurpose plant—Ficus tikoua Bur link: https://peerj.com/articles/18768 last-modified: 2024-12-24 description: Ficus tikoua Bur., a versatile plant with medicinal, edible, landscaping, and ecological applications, holds significant economic value and boasts a long-standing history of utilization in China. Despite its robust adaptability, rapid growth, and extensive distribution, the current research gap concerning the physiological mechanisms underlying stem cutting propagation hampers the development of efficient strategies for commercial-scale propagation of F. tikoua, particularly for large-scale cultivation. To address this, we investigated the effects of habitat heterogeneity, physiological indicators, and environmental factors on the cutting propagation of F. tikoua. Stem segments were collected from grassland, sandy, rocky and understory habitats in the field and subjected to comprehensive analyses using a two-factor mixed experimental design and progressive group experiments. Our findings indicate that stem segments of F. tikoua with a length of 10 cm and a diameter of 0.5∼0.7 cm exhibited the highest shoot induction rate and total multiplication coefficient. Optimal results were achieved with a vertical burial depth of 5∼7 cm. Stem segments aged 2∼3 years produced the highest number of seedlings, and the most suitable propagation period for cuttings was from March to April. The best substrate-habitat combinations for overall seeding yield were grassland-T4 (loam: light substrate: humus = 2:1:1), sandy-T6 (loam: light substrate: humus = 2:3:1), rocky-T5 (loam: light substrate: humus = 2:2:1), understory-T3 (loam: light substrate: humus = 1:1:1), respectively. Mantel test analyses revealed that the ability of F. tikoua cuttings from different habitats to form adventitious roots (ARs) largely determined the functional traits associated with cutting propagation. Overall, our results suggest that stem segment from grassland habitat are the most suitable for F. tikoua cutting propagation, with a loam: light substrate: humus ratio of 2:1:1 being the most favorable substrate. In contrast, F. tikoua from rocky habitat is not suitable for cutting propagation, particularly for large-scale seedling production. creator: Tinghong Tan creator: Yu Peng creator: Biling An creator: Fan Gao creator: Yanni Sun creator: Chuandong Yang creator: Hong Yang creator: Zhihong Lu uri: https://doi.org/10.7717/peerj.18768 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tan et al. title: Effects of nitrogen doses on stomatal characteristics, chlorophyll content, and agronomic traits in wheat (Triticum aestivum L.) link: https://peerj.com/articles/18792 last-modified: 2024-12-24 description: It is very important to determine the chlorophyll content (SPAD) and nitrogen (N) requirement in order to increase the seed yield and nutritional quality of wheat. This research was carried out with three N doses (0, 50, 100 kg ha−1) and nine wheat cultivars (Alpu-2001, Soyer-02, Kate-A1, Bezostaja-1, Altay-2000, Müfitbey, Nacibey, Harmankaya-99 and Sönmez-2001) during 2-years field condition according to factorial randomized complete block design and three replications. In this study, with the increase of N dose (N50), seed yield increased by 13%, plant height by 10.8%, 1,000 seed weight by 10.5% compared to control plants (N0). The increase of N dose from 50 kg ha−1 to 100 kg gave lower increase rates in the same criteria (11.7%, 11.4%, 10.3%, respectively). However, the spike number per plant, spikelet number in spike, seed number in spike, spike length showed statistically significant differences between N doses and varieties. Boost of N doses caused a significant increase compared to plants without N application. The chlorophyll content and flag leaf area index were determined at three growth times (1st growth time; early, 2nd growth time; the middle and end of flowering, 3rd growth time; with a 10-day interval). Chlorophyll content was significantly (p < 0.01) affected by the N dose, variety and growth time. As N doses increased, chlorophyll content increased, and it was higher at both N doses compared with N0. The chlorophyll content had the highest rates (30.22%) at 1st growth time and it decreased as the growth period progressed. N doses, varieties and their interactions had significant effects on the flag leaf area index. The highest flag leaf area index (41.9 cm2) was determined from variety Bezostaja-1 and 100 kg ha−1 N dose treatment. The effect of N dose was found significantly on abaxial and adaxial stomata width-length and epidermal cells. The adaxial and abaxial stomata width were higher than N0 at both N levels. The highest adaxial and abaxial stomata width- length was obtained from 100 kg ha−1 N dose. As nitrogen concentration increased, both stomatal density and stomatal index increased. The stomatal index varied between 19% and 36%. The lowest stomata density had appeared in the 100 kg ha−1 N dose and Bezostaja-1 variety. As a result, stomatal characteristics, chlorophyll content, and agronomic traits of wheat were significantly affected by increasing N doses. creator: Fatih Oner uri: https://doi.org/10.7717/peerj.18792 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Oner title: Evaluating techniques for determining elasmobranch body size: a review of current methodologies link: https://peerj.com/articles/18646 last-modified: 2024-12-23 description: There is global awareness that many species of elasmobranchs (sharks and rays) have life history characteristics that make them susceptible to overexploitation. The study of these animals is critical, as it contributes to increasing knowledge of these specimens and aids in their conservation. In particular, growth rate, age, fecundity, and size at maturity are key parameters for defining management and conservation strategies in elasmobranchs. Biometric data collection allows these parameters to be determined and considered in the evaluation of population demography. Over the last decades, several methodologies for measuring elasmobranch size have evolved, progressing from traditional capture-based methods to sophisticated, non-intrusive photographic techniques. The present review aims to understand and analyse all the existing non-invasive techniques that currently allow the collection of zoometric data in elasmobranchs and, later, to highlight the advantages and limitations of each technique, with comments on their application to fieldwork. To this end, 49 articles were selected, encompassing seven measurement techniques: photogrammetry using distance to the individual, bar photogrammetry, laser photogrammetry, stereo-DOV, stereo-BRUV, stereo-ROV, and aerial photogrammetry. Globally, the last four techniques are excellent alternatives to methods that involve animal capture or death, as they are practical, simple to use, minimally invasive, and potentially highly accurate. Each technique’s requirements related to equipment and cost, limitations, and distinctive features are presented here and summarized to guide researchers on what’s available and how to select the most appropriate for their studies. creator: Ana S. Ferreira creator: Márcia A. Naré creator: Joana I. Robalo creator: Núria D. Baylina uri: https://doi.org/10.7717/peerj.18646 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ferreira et al. title: DNA metabarcoding reveals diet diversity and niche partitioning by two sympatric herbivores in summer link: https://peerj.com/articles/18665 last-modified: 2024-12-23 description: BackgroundFood provides essential nutrients and energy necessary for animals to sustain life activities. Accordingly, dietary niche analysis facilitates the exploration of foraging strategies and interspecific relationships among wildlife. The vegetation succession has reduced understory forage resources (i.e., shrubs and herbs) available to sika deer (Cervus nippon kopschi). Little is known about the summer foraging strategies or the interspecific relationship between sika deer and Reeves’ muntjac (Muntiacus reevesi).MethodsThe present study used high-throughput sequencing and DNA metabarcoding techniques to investigate the feeding habits and interspecific relationships between sika deer and Reeves’ muntjac in our study.ResultsA total of 458 amplicon sequence variants (ASVs) were identified from fecal samples, with 88 ASVs (~19.21%) unique to sika deer and 52 ASVs (~11.35%) unique to Reeves’ muntjac, suggesting the consumption and utilization of specific food items for the two species. The family Rosaceae was the most abundant for both species, especially Rubus spp. and Smilax china. Alpha diversity (local species richness) indicated that the dietary species richness of sika deer was higher than that of Reeves’ muntjac, but the difference was not statistically significant. Sika deer also exhibited a higher evenness index (J′ = 0.514) than Reeves’ muntjac (J′ = 0.442). Linear discriminant effect size analysis revealed significant differences in forage plants between the two herbivores. The niche breadths of sika deer and Reeves’ muntjac were 11.36 and 14.06, respectively, and the dietary niche overlap index was 0.44. Our findings indicate the diet partitioning primarily manifested in the differentiation of food items and the proportion, which ultimately reduces the overlap of nutritional niches and helps avoid conflicts resulting from resource utilization. This study provides a deeper insight into the diversity of foraging strategies and the interspecific relationship of herbivores from the food dimension. creator: Ruofei Li creator: Dandan Wang creator: Zhiming Cao creator: Yuqin Liu creator: Wenguo Wu creator: Wuhua Liu creator: Jianwen Zhan creator: Yongtao Xu uri: https://doi.org/10.7717/peerj.18665 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Identification of the whole genome of alternative splicing and RNA-binding proteins involved in nintedanib-induced apoptosis in gastric cancer cells link: https://peerj.com/articles/18697 last-modified: 2024-12-23 description: BackgroundIt has been demonstrated that nintedanib can inhibit the proliferation of gastric cancer cells, but the specific mechanism of action is unclear.ObjectiveInvestigating the changes of key factors involved in gene transcription and post-transcriptional regulation during the process of treating gastric cancer with nintedanib.MethodsIn this study, we performed transcriptome sequencing on gastric cancer cell groups treated with nintedanib and control groups. The SUVA (Splice sites Usage Variation Analysis) software was used to identify differential alternative splicing (AS) events between the nintedanib-treated group and the control group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to assess the functional differences and pathways associated with these events. Finally, a co-expression regulatory network of differentially expressed RNA-binding proteins (RBPs) and differentially spliced genes was established. Results: A total of 915 differential AS events were identified between the two groups, and these differential genes were closely related to the apoptosis pathway. Further analysis revealed that differential RBPs (TAGLN2, TAGLN, SRSF6, PKM, SRSF2, NOC2L, IPO4, C1QBP, DHX9) may affect the anti-proliferative effect of nintedanib on gastric cancer cells by regulating downstream genes involved in cell proliferation and angiogenesis (NR4A1, BBC3, IFI27) through alternative splicing.ConclusionThis study systematically identified important changes in alternative splicing and RNA-binding proteins during the process of nintedanib-induced apoptosis in gastric cancer cells. It innovatively revealed the mechanisms of action of nintedanib in gastric cancer cells and expanded the selection of new targets for gastric cancer treatment. creator: Xiaohua Dong creator: Zhilong Liu creator: Miao Yu creator: Xiaojun Yang creator: Hui Cai uri: https://doi.org/10.7717/peerj.18697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dong et al. title: Quality of life and subjective well-being comparison between traumatic, nontraumatic chronic spinal cord injury, and healthy individuals in China link: https://peerj.com/articles/18709 last-modified: 2024-12-23 description: BackgroundDifferentiating between traumatic and non-traumatic spinal cord injuries (NT-SCI) is critical, as these classifications may significantly impact patients’ health outcomes and overall well-being, potentially resulting in differences in treatment protocols and therapeutic efficacy.ObjectiveThis study aims to compare the quality of life (QoL) and satisfaction with life (SWL) among individuals with traumatic spinal cord injuries (T-SCI), NT-SCI, and the healthy population in China.MethodA quantitative, cross-sectional survey was conducted between July and December 2020 in the Rehabilitation and Physiotherapy Department of Tongji Hospital, Hubei University of Science and Technology. The World Health Organization Quality of Life Brief Version (WHOQOL-BREF) and the Satisfaction with Life Scale (SWLS) were administered to evaluate QoL and subjective well-being (SWB). An independent t-test was performed to assess differences within the SCI population, while Pearson’s correlation coefficient was utilized to explore relationships between the WHOQOL-BREF domains and the SWLS. Multiple linear regression analysis was applied to identify key determinants influencing World Health Organization Quality of Life (WHOQOL) domain scores and overall SWLS score.ResultParticipants with NT-SCI exhibited significant differences in overall health as measured by the WHOQOL-BREF domains compared to those with T-SCI (p < 0.05). Both the NT-SCI and T-SCI groups demonstrated lower mean scores across all four WHOQOL-BREF domains compared to healthy individuals. No significant differences were observed between the NT-SCI and T-SCI groups in the SWLS, although both groups scored lower than the healthy population. Additionally, SWB was moderately positively correlated with QoL (p < 0.01). Collectively, the predictor variables explained 22.28% of the variance in physical health, 6.43% in psychological health, 28.67% in social health, and 25.68% in environmental health. Furthermore, the independent variables accounted for approximately 22.67% of the variance in the SWLS.ConclusionsIndividuals with NT-SCI experience significantly worse overall health outcomes compared to those with T-SCI, although both groups report QoL and life satisfaction than healthy individuals. No significant differences in life satisfaction were found between two groups. Additionally, SWB shows a moderate positive correlation with QoL, highlighting the close relationship between mental and physical health in SCI populations. creator: Ruba Altahla creator: Jamal Alshorman creator: Sayed Zulfiqar Ali-Shah creator: Mohammad Nasb creator: Xu Tao uri: https://doi.org/10.7717/peerj.18709 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Altahla et al. title: Spatial heterogeneity of soil properties in planted mixed forests in the rocky desertification areas of the Wuling Mountain link: https://peerj.com/articles/18724 last-modified: 2024-12-23 description: In this study, experiments were conducted on soil samples collected from depths of 0–15 cm, 15–30 cm, and 30–50 cm at the National Long-term Scientific Research Base for the Comprehensive Management of Rocky Desertification in the Wuling Mountains. The aim was to determine the physicochemical indexes and explore the nature and spatial heterogeneity of the soil of the planted mixed forests within the rocky desertification area of the Wuling Mountain. Various analytical methods were employed, including descriptive statistical analysis, correlation analysis, analysis of variance, principal component analysis, spatial interpolation analysis, and kriging interpolation, to fit the optimal model of the semi-variance function of soil physicochemical properties and analyze the model’s parameters. The results indicated that soil physical and chemical properties varied with depth and were generally correlated. The relationship between soil organic matter and total nitrogen content was the closest. Additionally, there was a certain degree of correlation between soils at different depths in the vertical profile, generally the correlation between layer B (15–30 cm) and layer C (30–50 cm) > that between layer A (0–15 cm) and layer B (15–30 cm) > that between layer A (0–15 cm) and layer C (30–50 cm). The weighting coefficients of the principal components of soil physicochemical properties indicated that soil organic matter, nitrogen, phosphorus, potassium, pH, total porosity, and capillary porosity are key factors in the soil properties of karst desertification areas. The spatial variability of soil physicochemical properties at different depths ranged from 21.91 to 87.59 m, and the abutment ratio (Co/Co+C) of these properties ranged from 12.99% to 89.53%. Using kriging interpolation in ArcGIS, the spatial distribution pattern of soil physical and chemical properties was mapped, revealing that these indicators were distributed with heterogeneous patches of various sizes and shapes. Therefore, the degree of rocky desertification significantly influences the spatial distribution pattern of soil physical and chemical properties. creator: Ziqian Pan creator: Yanyan Dong creator: Gongxiu He creator: Tongtong Guo creator: Ninghua Zhu uri: https://doi.org/10.7717/peerj.18724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Pan et al. title: Malignant behaviors and immune response in melanoma: Epstein-Barr virus induced gene 3 as a therapeutic target based on an in-vitro exploration link: https://peerj.com/articles/18730 last-modified: 2024-12-23 description: BackgroundEpstein-Barr virus induced gene 3 (EBI3), a member of the IL-12 family, is known to be involved in malignant progression in a variety of cancers, but its role in melanoma is unclear. The aim of this study was to explore the effects of EBI3 on the malignant phenotype melanoma to reveal its potential as a therapeutic target.MethodsIn this study, we used bioinformatics to analyze the expression of EBI3 in pan-cancer and verified its expression level in melanoma cells by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Subsequently, the effects of EBI3 knockdown on cell proliferation, migration and invasion were detected using the Cell Counting Kit-8 (CCK-8) and Transwell assays. Changes in immune-related cytokines were detected by ELISA, and macrophage polarization was observed using immunofluorescence. Finally, the phosphorylation levels of signaling pathways such as Smad3, STAT6 and cGAS-STING were analyzed by Western blot.ResultsEBI3 was evidently highly-expressed in melanoma, and silencing of EBI3 could visibly suppress the survival and migration/invasion of melanoma cells, concurrent with the increased levels of BAX and CDH1 and the decreased expressions of BCL2 and CDH2. Meanwhile, EBI3 knockdown diminished the phosphorylation levels of both Smad3 and STAT6 and the levels of immune response-relevant cytokines in melanoma cells, while aggravating the macrophage M1 polarization and the expression of cGAS, p-STING and p-IRE1 α in THP-1 monocyte-derived macrophages co-cultured with EBI3-silenced melanoma cells.ConclusionThis study filled the blank on the involvement of EBI3 in melanoma, hinting the possibility of controlling EBI3 as a therapeutic strategy in the management of melanoma. creator: Ying Zhang creator: Fengrui Cheng creator: Xingrui Cai creator: Jingping Wu uri: https://doi.org/10.7717/peerj.18730 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Enrichment effects on growth, health, and reproduction in a single clone of the asexual Amazon molly, Poecilia formosa link: https://peerj.com/articles/18734 last-modified: 2024-12-23 description: This study examines the impact of two types of environmental enrichment on the growth of the Amazon molly (Poecilia formosa), a clonal fish species. We investigated the effects of two welfare-related enrichment factors: physical enrichment (presence of a halfpipe PVC and gravel substrate, E) and social enrichment (presence of visible neighbor fish, N). Fish were divided into four treatment groups: (1) both physical and social enrichment (EN), (2) no physical enrichment but social enrichment (nEN), (3) physical enrichment without social enrichment (EnN,), and (4) no enrichment (nEnN). Results showed that individuals, which received both types of enrichment, exhibited faster growth rates and lower early life mortality compared to the other groups, indicating improved health and welfare. However, this initial advantage did not persist into adulthood, suggesting that the benefits of enrichment may be stage specific. These findings highlight the importance of environmental factors in promoting welfare in a particular species, especially during early developmental stages. This study may have implications for early life-stage fish research indicating that some environmental factors may play a role in enhancing growth, reproductive competence, and reduced mortality. Enrichment effects on growth, health, and reproduction in a single clone of the asexual Amazon molly, Poecilia formosa. creator: Debbie Cunningham creator: Tyler Reich creator: Theresa E. Rizzi creator: Chance Powell creator: Ingo Schlupp uri: https://doi.org/10.7717/peerj.18734 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Cunningham et al. title: Association of tyrosine kinase 2 polymorphisms with susceptibility to microscopic polyangiitis in a Guangxi population link: https://peerj.com/articles/18735 last-modified: 2024-12-23 description: BackgroundHeredity and epigenetics affect the pathogenesis of microscopic polyangiitis (MPA). Tyrosine kinase 2 (TYK2) polymorphisms (rs2304256C > A, rs280519A > G, and rs12720270G > A) may be potential protective factors against anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Current research suggests that TYK2 is associated with various autoimmune diseases; however, no study has examined the relationship between TYK2 polymorphisms and AAV. This study assessed the effect of TYK2 polymorphisms on susceptibility to MPA.MethodsOverall, 562 Chinese participants (265 patients with MPA and 297 healthy volunteers) were recruited. Polymerase chain reactions combined with high-throughput sequencing were used to analyze polymorphic loci, while logistic regression analysis was used to assess the relationship between polymorphism of the TYK2 gene and MPA susceptibility.ResultsIn males, individuals with the CA genotype (rs2304256) in the overdominant model showed a significantly reduced risk of MPA (odds ratio (OR) = 0.52; 95% confidence interval (CI) [0.29–0.93]; p = 0.025). Regarding rs280519, male carriers of the AG genotype had a significantly lower risk of developing MPA in both the codominant (OR = 0.51; 95% CI [0.28–0.93]; p = 0.039) and overdominant (OR = 0.48; 95% CI [0.27–0.86]; p = 0.013) models. The GA genotype of rs12720270 was associated with low susceptibility to MPA in males (OR = 0.52; 95% CI [0.29–0.93]; p = 0.027).ConclusionsThis study indicates that mutations in the TYK2 gene (rs2304256, rs280519, and rs12720270) may be associated with a reduced risk of MPA in the male Chinese population in Guangxi. The A allele of single nucleotide polymorphism (SNP) rs2304256 may be a protective factor against MPA, while the G alleles of SNPs rs280519 and rs12720270 are protective factors against MPA. creator: Binglan Yang creator: Liepeng Chu creator: Fei Feng creator: Shurong Lu creator: Chao Xue uri: https://doi.org/10.7717/peerj.18735 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Malignant solid tumor-related spontaneous intracerebral hemorrhage: a propensity score matching study link: https://peerj.com/articles/18737 last-modified: 2024-12-23 description: BackgroundSpontaneous intracerebral hemorrhage (sICH) is a severe event with high mortality. Recently, evidence has emerged suggesting that malignant solid tumors may increase the risk of sICH through unique cancer-related factors. However, the specific risk factors and clinical characteristics of sICH in patients with malignant solid tumor remain poorly understood.ObjectiveThis study aimed to investigate the clinical characteristics of and identify the risk factors associated with sICH in individuals with malignant solid tumors.MethodsThis retrospective study was carried out in patients with active malignant solid tumors and sICH at the First Affiliated Hospital of Guangxi Medical University between January 2010 and December 2020. Patients were separated into control and malignant solid tumor-related spontaneous intracerebral hemorrhage (MST-sICH) groups. The control group consisted of patients presenting with malignant solid tumors alone who were matched to the MST-sICH group using a 1:1 propensity score matching (PSM) approach. Patient clinical data, laboratory findings, and imaging results were collected. Univariate analysis was carried out to determine the risk factors associated with MST-sICH. In addition, a receiver operator characteristic analysis was performed to identify potential predictors for poor prognosis.ResultsDecreased hemoglobin (HGB) levels, together with increased lymphocyte counts (LYCs), and an increased neutrophil-to-lymphocyte ratio (NLR) were found in the MST-sICH group compared to the control group. The results of the multivariate logistic regression analysis indicated a HGB levels (OR: 0.959, 95% CI [0.928–0.992]), an increased in LYCs (OR: 0.095, 95% CI [0.023–0.392]). Furthermore, there was an increased in NLR levels (OR: 2.137, 95% CI [1.427–3.200]). In the receiver operating characteristic (ROC) curve analysis, the area under the curve (AUC) with HGB, LYCs, and NLR as joint predictors was 0.955 (95% CI [0.901–1.000]), with a sensitivity of 100%, a specificity of 82.6%, and a Youden Index of 0.826.ConclusionDecreased HGB levels, elevated LYCs, and a higher NLR were identified as independent risk factors for sICH in patients with active solid malignancies. These markers could assist clinicians in stratifying high-risk patients, facilitating closer monitoring and informing targeted preventive strategies to mitigate the incidence of sICH in this at-risk population. creator: Shuolin Liang creator: Liuyu Liu creator: Bin Qin creator: Shengri Chen creator: Zhijian Liang uri: https://doi.org/10.7717/peerj.18737 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liang et al. title: Impact of storage and extraction methods on peat soil microbiomes link: https://peerj.com/articles/18745 last-modified: 2024-12-23 description: Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modified PowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations. creator: Dylan Cronin creator: Yueh-Fen Li creator: Paul Evans creator: Gene W. Tyson creator: Ben J. Woodcroft creator: Virginia I. Rich uri: https://doi.org/10.7717/peerj.18745 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Cronin et al. title: Implications of the SNHG10/miR-665/RASSF5/NF-κB pathway in dihydromyricetin-mediated ischemic stroke protection link: https://peerj.com/articles/18754 last-modified: 2024-12-23 description: Ischemic stroke (IS) remains a leading cause of disability and mortality worldwide, and inflammation and oxidative stress play significant roles in its pathogenesis. This study investigates the effects of dihydromyricetin (DHM) on IS using RT-qPCR and western blot with SH-SY5Y cells, focusing on its effects on the small nucleolar RNA host gene 10 (SNHG10)/microRNA (miR)-665/Ras association domain family member 5 (RASSF5) axis and nuclear factor-kappa B (NF-κB) signaling. In addition, the effects of the SNHG10/miR-665/RASSF5 axis on SH-SY5Y cell activity, apoptosis, oxidative stress, and inflammatory markers were analyzed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, flow cytometry, and enzyme-linked immunosorbent assays. Our results showed that, in response to oxygen-glucose deprivation/reperfusion (OGD/R), DHM treatment improved cell viability, reduced apoptosis, and attenuated neuroinflammation and oxidative stress in a dose-dependent manner (p < 0.05). Interestingly, lncRNA SNHG10 was overexpressed during OGD/R and suppressed by DHM. Through bioinformatics analysis and experimental validation, we identified miR-665 as a direct target of SNHG10 and RASSF5 as a direct target of miR-665. The protective effect of DHM against OGD/R injury was partially reversed by SNHG10 overexpression and further enhanced by co-transfection with the miR-665 mimic and si-RASSF5 (p < 0.05). This study identifies a novel mechanism of DHM against IS, which may act via modulation of the SNHG10/miR-665/RASSF5 axis and inactivation of NF-κB signaling, and offers a promising therapeutic target for IS. creator: Qi Zeng creator: Yan Xiao creator: Xueliang Zeng creator: Hai Xiao uri: https://doi.org/10.7717/peerj.18754 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zeng et al. title: Unique dental arrangement in a new species, Groenlandaspis howittensis (Placodermi, Arthrodira) from the Middle Devonian of Mount Howitt, Victoria, Australia. link: https://peerj.com/articles/18759 last-modified: 2024-12-23 description: Well-preserved specimens of a new species of arthrodiran placoderm, Groenlandaspis howittensis sp. nov. (Middle Devonian of Victoria, Australia), reveals previously unknown information on the dermal skeleton, body-shape and dentition of the wide-spread genus Groenlandaspis. The new material includes dual pineal plates, extrascapular plates, and cheek bones showing the presence of cutaneous sensory organs. The anterior supragnathal, usually a paired element in arthrodires, is a fused median bone in G. howittensis sp. nov. It is positioned anterior to the occlusion of the mouth between the lower jaw (infragnathals) and upper jaw (posterior supragnathals) bones, indicating a specialised feeding mechanism and broadening the known diversity of placoderm dental morphologies. G. howittensis sp. nov. differs from all other groenlandaspidids by a less pronounced posterior expansion of the nuchal plate; the shape of the posterior dorsolateral plate and the presence of a short accessory canal on the anterior dorsolateral plate. A new phylogenetic analysis positions Groenlandaspididae in a monophyly with the phlyctaeniid families Arctolepidae and Arctaspididae, however, the specific intrarelationships of groenlandaspidids remain poorly resolved. creator: Austin N. Fitzpatrick creator: Alice M. Clement creator: John A. Long uri: https://doi.org/10.7717/peerj.18759 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Fitzpatrick et al. title: Spatial variations of soil seed banks in Shanghai’s urban wasteland: a gradient analysis of urbanization effects link: https://peerj.com/articles/18764 last-modified: 2024-12-23 description: Urbanization greatly impacts both the diversity of soil seed banks and the spatial dynamics of species. These seed banks serve as a window into the ecological history and potential for recovery in urban wastelands, which are continually evolving due to urbanization. In this study, we selected 24 plots along urban-rural gradients in Shanghai, China. Soil samples were collected from each plot for seed bank germination experiment in both spring and autumn. We tested whether the seed density, species diversity, and composition of soil seed banks in wasteland varied along an urban-rural gradient. The results showed that seed density was higher in autumn than in spring and no significant difference was found along urban-rural gradients. A total of 74 species, belonging to 26 families and 69 genera, was recorded in soil seed banks, in which annuals were the dominant life form and autochory was the dominant dispersal model. The proportion of exotic species was nearly 40%. There is no significant difference along urban-rural gradients for functional composition, species diversity, and species composition, excepting that marginal significant for autumn Shannon-Wiener index and species composition among urban-rural gradients. The relative homogeneity in the seed bank across urban-rural gradients may primarily be due to the young age of the wastelands. creator: Siyi Xia creator: Shumeng Zhang creator: Yichong Cui creator: Zhiwen Gao creator: Kun Song creator: Liangjun Da uri: https://doi.org/10.7717/peerj.18764 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xia et al. title: A chromosome-scale genome assembly of mungbean (Vigna radiata) link: https://peerj.com/articles/18771 last-modified: 2024-12-23 description: BackgroundMungbean (Vigna radiata) is one of the most socio-economically important leguminous food crops of Asia and a rich source of dietary protein and micronutrients. Understanding its genetic makeup is crucial for genetic improvement and cultivar development.MethodsIn this study, we combined single-tube long-fragment reads (stLFR) sequencing technology with high-throughput chromosome conformation capture (Hi-C) technique to obtain a chromosome-level assembly of V. radiata cultivar ‘KUML4’.ResultsThe final assembly of the V. radiata genome was 468.08 Mb in size, with a scaffold N50 of 40.75 Mb. This assembly comprised 11 pseudomolecules, covering 96.94% of the estimated genome size. The genome contained 253.85 Mb (54.76%) of repetitive sequences and 27,667 protein-coding genes. Our gene prediction recovered 98.3% of the highly conserved orthologs based on Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Comparative analyses using sequence data from single-copy orthologous genes indicated that V. radiata diverged from V. mungo approximately 4.17 million years ago. Moreover, gene family analysis revealed that major gene families associated with defense responses were significantly expanded in V. radiata.ConclusionOur chromosome-scale genome assembly of V. radiata cultivar KUML4 will provide a valuable genomic resource, supporting genetic improvement and molecular breeding. This data will also be valuable for future comparative genomics studies among legume species. creator: Supaporn Khanbo creator: Poompat Phadphon creator: Chaiwat Naktang creator: Duangjai Sangsrakru creator: Pitchaporn Waiyamitra creator: Nattapol Narong creator: Chutintorn Yundaeng creator: Sithichoke Tangphatsornruang creator: Kularb Laosatit creator: Prakit Somta creator: Wirulda Pootakham uri: https://doi.org/10.7717/peerj.18771 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Khanbo et al. title: Dosimetric comparison and evaluation of different convergence modes in nasopharyngeal carcinoma using VMAT treatment deliveries link: https://peerj.com/articles/18773 last-modified: 2024-12-23 description: BackgroundThis study investigates the impact of convergence mode (CM) in Eclipse (Varian Medical Systems) on the quality and complexity of volumetric modulated arc therapy (VMAT) plans for nasopharyngeal carcinoma (NPC) patients.MethodsWe retrospectively analyzed data from 21 NPC patients. For each patient, three VMAT plans with different CM settings (Off, On, and Extended) were created using identical optimization objectives. Plan quality was assessed using indices such as the conformity index (CI) and homogeneity index (HI), as well as evaluating target coverage and sparing of organs at risk (OARs). Complexity was measured by metrics including average leaf pair opening (ALPO), modulation complexity scores for VMAT (MCSv), monitor units (MUs), and optimization time. Dosimetric verification was performed based on the gamma pass rate.ResultsDifferent CM settings can generate treatment plans that meet clinical dose objectives for planning target volumes (PTVs) and OARs. The ‘On’ or ‘Extended’ CM settings improved CI and HI for the NPC target volume and reduced OAR doses, especially the mean dose, without compromising target coverage. The ‘Extended’ CM setting produced the most favorable outcomes. ALPO values for CM settings ‘Off’, ‘On’, and ‘Extended’ were 29.1 ± 4.3 mm, 28.6 ± 4.2 mm, and 28.4 ± 4. 2 mm, respectively. MCSv values for these settings were 0.1730 ± 0.0215, 0.1691 ± 0.0204, and 0.1693 ± 0.0208, respectively. MUs were 796.2 ± 110.8 for CM ‘Off’, 798.6 ± 106.1 for CM ‘On’, and 799.7 ± 103.6 for CM ‘Extended’, with no significant differences (p > 0.05). Gamma pass rates for all plans were above 99% (3%/3 and 2%/2 mm), with no significant differences among groups (p > 0.05). The average optimization times for CM settings ‘Off’, ‘On’, and ‘Extended’ were 14.4 ± 3.2, 35.9 ± 8.9, and 145.6 ± 50.3 min, respectively (p < 0.001).ConclusionCM usage can improve the CI and HI of the target volume and decrease the dose to OARs in VMAT plans for NPC patients. This study suggests that CM can be a valuable tool in VMAT planning for nasopharyngeal carcinoma, given adequate planning time. creator: Maoying Lan creator: Rui Wu creator: Guanhua Deng creator: Bo Yang creator: Yongdong Zhuang creator: Wei Yi creator: Wenwei Xu creator: Jiancong Sun uri: https://doi.org/10.7717/peerj.18773 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lan et al. title: Effects of vegetation restoration in karst areas on soil nitrogen mineralisation link: https://peerj.com/articles/18582 last-modified: 2024-12-20 description: BackgroundNitrogen mineralization plays a critical role in the ecosystem cycle, significantly influencing both the ecosystem function and the nitrogen biogeochemical cycle. Therefore, it is essential to investigate the evolutionary characteristics of soil nitrogen mineralization during the karst vegetation restoration to better understand its importance in the terrestrial nitrogen cycle.MethodsThis study analyzed from various stages of vegetation growth, including a 40-year-old woodland, 20-year-old shrubland, 15-year-old shrubland, 5-year-old grassland, and nearby cropland. The aerobic incubation technique was used for 35 days to evaluate soil N mineralization characteristics and their correlation with soil environmental factors. The study focused on examining the variations in soil N mineralization rate (NMR), N nitrification rate (NR), net nitrification rate (AR), and NH4+-N and NO3--N levels.ResultsNitrate nitrogen, the primary form of inorganic nitrogen, increased by 19.38% in the 0–40 cm soil layer of the 20-year-old shrubland compared to the cultivated land. Soil NH4+-N levels varied during the incubation period, decreasing by the 14th day and rising again by the 21st day. Soil NO3−-N and total inorganic nitrogen levels initially increased, then declined, and eventually stabilized, reaching their highest levels on the 14th day. During vegetation restoration, the soil NR and NMR decreased gradually with increasing incubation time. The 15-year shrub, 20-year shrub, and 40-year woodland showed the potential to increase soil NR and NMR. Furthermore, the 15-year shrub and 20-year shrub also increased soil AR. The Mantel test analysis indicated positive correlations among total nitrogen (TN), total phosphorus (TP), total potassium (TK), silicon (Si), AR, NR, and NMR. While available phosphorus (AP) and NMR demonstrated positive correlations with NR and NMR. Furthermore, TN, TP, TK, and Si were found to be positively correlated with AR, NR, and NMR, whereas AP and NO3--N showed negative correlations with AR, NR, and NMR. It is worth noting that NH4+-N had the greatest effect on AR, while the bulk density (BD) significantly affected the NR. Furthermore, ammonium nitrogen (AN) and soil organic carbon (SOC) were identified as the primary contributors to NMR. This study provides a theoretical basis for comprehending the influence of vegetation restoration on soil nitrogen mineralization and its role in ecosystem restoration. creator: Jianghong Wu creator: Xianghuan Gong creator: Yingge Shu uri: https://doi.org/10.7717/peerj.18582 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wu et al. title: A new approach for increasing graduate students’ science communication capacity and confidence link: https://peerj.com/articles/18594 last-modified: 2024-12-20 description: There is an increasing demand for emerging scientists to improve their ability to communicate with public audiences, yet little research investigates the effectiveness of science communication training for graduate students. We responded to this need by developing SciWrite@URI—an interdisciplinary model for science graduate students designed around three learning outcomes based on tenets from the field of writing and rhetoric—habitual writing, multiple genres, and frequent review. SciWrite students completed courses and a science communication internship, attended writing workshops, and became tutors at a newly established Graduate Writing Center. After 2 years of training, students more frequently wrote multiple drafts and engaged in peer review, increased their confidence as writers, and decreased their apprehension about writing. We conclude the tenets of the SciWrite program helped students improve as science communicators, and we make suggestions for effective ways graduate departments and training programs might implement and build on our model. creator: Erin R. Harrington creator: Scott R. McWilliams creator: Nancy E. Karraker creator: Caroline Gottschalk Druschke creator: Jenna Morton-Aiken creator: Elaine Finan creator: Ingrid E. Lofgren uri: https://doi.org/10.7717/peerj.18594 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Harrington et al. title: Modeling the effects of water temperature on the population dynamics of Galba viatrix and infection by Fasciola hepatica: a two-year survey in Andean Patagonia, Argentina link: https://peerj.com/articles/18648 last-modified: 2024-12-20 description: BackgroundThe trematode parasite Fasciola hepatica (liver fluke) can infect livestock, wild mammals, and humans, generating serious economic losses worldwide. Aquatic or amphibious snails of the Lymnaeidae family are the intermediate host of this parasite. Both snail population dynamics and parasite development are closely associated with temperature, although most field studies have recorded air temperature rather than water temperature. Our aim was to statistically model the population dynamics of lymnaeid snails and their infection by F. hepatica under natural environmental conditions in Northwest Andean Patagonia.MethodsFor two years, we sampled snails monthly in four bodies of water, while registering water and air temperature hourly, and assessing F. hepatica infection in snails. Hierarchical Bayesian modeling allowed us to estimate the functional relationship between water temperature and population growth, the probability of detecting snails, and infection by F. hepatica.ResultsA total of 1,411 Galba viatrix snails were collected, identified, and analyzed for F. hepatica infection. All sites showed seasonal variation in the number of snails collected and in water temperature as well as sharp variations in snail counts between surveys adjacent in time. The hierarchical model revealed that water temperature acts, at least, at two different time scales: water temperature at the time of sampling determines snail detection probability, whereas the average water temperature between sampling dates affects lymnaeid population growth. We found maximum F. hepatica prevalences in snails of 40% (2/5 and 4/10), followed by 33% (65/197). These are the highest prevalences recorded in G. viatrix populations in Argentina to date. Our modeling evidenced that the positive effects of water temperature on infection probability increases with snail size and prevalence on the previous survey, while previous prevalence strongly enhances the effects of snail size.ConclusionsOur results underscore the high temporal and spatial variability in the population of snails and the prevalence of F. hepatica, as well as the major impact temperature has on detecting snails. Our models provide quantifications of the effects of water temperature on the population growth of G. viatrix, its detection, and infection under natural field conditions. These are crucial steps towards generating mechanistic models of F. hepatica transmission that would facilitate the design and simulation of potential interventions based on treatments and on environmental and livestock management, taking into account the specific characteristics of each region. creator: Paula Soler creator: Juan Manuel Gurevitz creator: Juan Manuel Morales creator: Marcela Larroza uri: https://doi.org/10.7717/peerj.18648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Soler et al. title: Quorum sensing signals of the grapevine crown gall bacterium, Novosphingobium sp. Rr2-17: use of inducible expression and polymeric resin to sequester acyl-homoserine lactones link: https://peerj.com/articles/18657 last-modified: 2024-12-20 description: BackgroundA grapevine crown gall tumor strain, Novosphingobium sp. strain Rr2-17 was previously reported to accumulate copious amounts of diverse quorum sensing signals during growth. Genome sequencing identified a single luxI homolog in strain Rr2-17, suggesting that it may encode for a AHL synthase with broad substrate range, pending functional validation. The exact identity of the complete suite of AHLs formed by novIspR1 is largely unknown.MethodsThis study validates the function of novIspR1 through inducible expression in Escherichia coli and in the wild-type parental strain Rr2-17. We further enhanced the capture of acyl homoserine lactone (AHL) signals produced by novIspR1 using polymeric resin XAD-16 and separated the AHLs by one- and two-dimensional thin layer chromatography followed by detection using AHL-dependent whole cell biosensor strains. Lastly, the complete number of AHLs produced by novIspR1 in our system was identified by LC-MS/MS analyses.ResultsThe single LuxI homolog of N. sp. Rr2-17, NovIspR1, is able to produce up to eleven different AHL signals, including AHLs: C8-, C10-, C12-, C14-homoserine lactone (HSL) as well as AHLs with OH substitutions at the third carbon and includes 3-OH-C6-, 3-OH-C8-, 3-OH-C10-, 3-OH-C12- and 3-OH-C14-HSL. The most abundant AHL produced was identified as 3-OH-C8-HSL and isopropyl-D-1-thiogalactopyranoside (IPTG) induction of novIspR1 expression in wild type parental Rr2-17 strain increased its concentration by 6.8-fold when compared to the same strain with the vector only control plasmid. Similar increases were identified with the next two most abundant AHLs, 3-OH-C10- and unsubstituted C8-HSL. The presence of 2% w/v of XAD-16 resin in the growth culture bound 99.3 percent of the major AHL (3-OH-C8-HSL) produced by IPTG-induced overexpression of novIspR1 in Rr2-17 strain. This study significantly adds to our understanding of the AHL class of quorum sensing system in a grapevine crown gall tumor associated Novosphingobium sp. Rr2-17 strain. The identity of nine AHL signals produced by this bacterium will provide a framework to identify the specific function(s) of the AHL-mediated quorum-sensing associated genes in this bacterium. creator: Han Ming Gan creator: Lucas Dailey creator: Peter Wengert creator: Nigel Halliday creator: Paul Williams creator: André O. Hudson creator: Michael A. Savka uri: https://doi.org/10.7717/peerj.18657 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gan et al. title: Exploring the potential role of ENPP2 in polycystic ovary syndrome and endometrial cancer through bioinformatic analysis link: https://peerj.com/articles/18666 last-modified: 2024-12-20 description: BackgroundGrowing evidence indicates a significant correlation between polycystic ovary syndrome (PCOS) and endometrial carcinoma (EC); nevertheless, the fundamental molecular mechanisms involved continue to be unclear.MethodsInitially, differential analysis, the least absolute shrinkage and selection operator (LASSO) regression, and support vector machine-recursive feature elimination (SVM-RFE) algorithms were employed to identify candidate genes associated with ferroptosis in PCOS. Subsequently, the TCGA-UCEC data were utilized to pinpoint the core gene. Then, the expression of ENPP2 in granulosa cells and endometrium of PCOS was validated using real-time PCR (RT-qPCR). Additionally, we investigated the role of ENPP2 in the progression from PCOS to EC through western blotting (WB), colony formation assay, cell scratch assay, transwell assay, and immunofluorescence (IF). Subsequently, ENPP2 gene set enrichment analysis (GSEA) analyses were conducted to identify common pathways involved in PCOS and EC, which were then verified by RT-qPCR. Finally, immune infiltration and the tumor microenvironment (TME) were explored to examine the involvement of ENPP2 in EC progression.ResultsThe datasets TCGA-UCEC (pertaining to EC), GSE34526, GSE137684, and GSE6798 (related to PCOS) were procured and subjected to analysis. The gene ENPP2 has been recognized as the shared element connecting PCOS and EC. Next, we observed a significant downregulation of ENPP2 expression in the granulosa cells in PCOS compared to the normal patients, while an upregulation of ENPP2 expression was observed in the endometrium of hyperandrogenic PCOS patients relative to the normal. In vitro, the WB revealed that 5-dihydrotestosterone (DHT) upregulated ENPP2 expression in Ishikawa and HEC-1-A cells. Additionally, we found that ENPP2 promoted the proliferation, migration, and invasion of Ishikawa and HEC-1-A cells. Subsequently, we discovered that overexpressed ENPP2 may lead to an increase in CYP19A1 (aromatase) and AR mRNA level. IF demonstrated that ENPP2 increased the expression of AR, suggesting a regulatory role for ENPP2 in hormonal response within PCOS and EC. Our findings indicated a significant correlation between ENPP2 expression and the modulation of immune responses. creator: Xumin Zhang creator: Jianrong Liu creator: Chunmei Bai creator: Yang Li creator: Yanxin Fan uri: https://doi.org/10.7717/peerj.18666 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Antimicrobial resistance pattern of Escherichia coli isolated from imported frozen shrimp in Saudi Arabia link: https://peerj.com/articles/18689 last-modified: 2024-12-20 description: Contamination of seafood products with multi-drug-resistant (MDR) bacteria is considered to be a potential source for the spread of MDR bacteria in communities. However, little is known about the extent of the contamination of seafood, in particular shrimp, with MDR bacteria in Saudi Arabia. In this study, imported frozen shrimp in retail markets were examined for the antimicrobial susceptibility patterns of Escherichia coli. Escherichia coli was isolated from 40 frozen shrimp samples; a total of 25 and 15 shrimp samples were imported from China and Vietnam, respectively. Of the 40 examined frozen shrimp samples, 30 tested positive for E. coli, resulting in an overall isolation rate of 75%, with a total of 180 isolates being identified. The largest number of positive samples for E. coli isolates (n = 140) were found in 22 out of 25 samples from frozen shrimp imported from China. Additionally, eight out of 15 samples from frozen shrimp imported from Vietnam were positive for E. coli, leading to the recovery of 40 isolates. Overall, the susceptibilities among E. coli isolates were observed against 99.4% for amikacin, augmentin and kanamycin, 95% for cefoxitin and 92.7% for ceftazidime and nitrofurantoin. High percentage of the isolates exhibited resistance to cephalothin (174/180, 96.6%), ampicillin (167/180, 92.7%), Cephalexin (163/180. 90.5%), piperacillin (156/180, 86.6%), ceftriaxone (123/180, 68.3%), nalidixic acid (95/180, 52.7%), trimethoprim sulphamethoxazole (90/180, 50%), and tetracycline (88/180, 48.8%). Additionally, the MDR (resistant to ≥3 different class of antimicrobials) rate among E. coli isolates was 94.4% (170/180). A relatively high intermediate resistance of 60% (108/180) was exhibited for aztreonam. Notably, E. coli showed 71 different antibiotic resistance patterns with the multiple antibiotic resistant (MAR) index ranging from 0.04 to 0.66 and 89.4% of E. coli isolates recorded very significant MAR indexes above the range of 0.2. In this study, we recorded highest antimicrobial co-resistance patterns of 162 (90%) isolates between cephalothin and ampicillin, followed by 158 (87.7%) isolates between cephalothin and cephalexin. Furthermore, and interestingly, the segregation of antimicrobial resistance patterns based on the source of country origin of frozen shrimp revealed few inter-country resistant patterns found interconnecting and this influenced 44 (24.4%) isolates overlapping between isolates origin from frozen shrimp imported from China and Vietnam. This study documents the antimicrobial resistance in E. coli isolated from imported frozen shrimp and the presence of MDR E. coli in shrimp consuming communities, which may pose a risk to public health and the transfer of resistant bacteria to the food chain and environment. creator: Ibrahim Alhabib creator: Nasreldin Elhadi uri: https://doi.org/10.7717/peerj.18689 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Alhabib and Elhadi title: Construction and clinical application of a risk model based on N6-methyladenosine regulators for colorectal cancer link: https://peerj.com/articles/18719 last-modified: 2024-12-20 description: BackgroundColorectal cancer (CRC) shows a high incidence in developed countries. This study established a prognosis signature based on N6-methyladenosine (m6A) regulators involved in CRC progression.MethodThe bulk RNA-seq data from the Atlas and Compass of Immune-Colon cancer-Microbiome interactions (AC-ICAM) and GSE33113 CRC datasets were obtained from the cBioportal and GEO databases, and a total of 21 m6A regulators genes were collected from a previous study. The scRNA-seq analysis of the GSE146771 cohort was conducted applying the Seurat and harmony R packages. Consensus clustering based on the expressions of m6A regulators was performed with the ConsensusClusterPlus package. The ggGSEA package was used for the Gene Set Enrichment Analysis (GSEA). The un/multivariate and LASSO Cox analysis were performed applying the “survival” and “glmnet” packages for developing a risk model. The pRRophetic and GSVA packages were utilized to analyze potential drugs for CRC and immune infiltration in different risk groups, followed by the Kaplan–Meier (KM) survival and ROC analysis with the “survival” and “timeROC” packages. In vitro assays included the quantitative polymerase chain reaction (qPCR), wound healing and transwell were performed.ResultsCRC patients in the AC-ICAM cohort were assigned into three molecular subtypes (S1, 2 and 3) based on nine m6A regulator genes. Specifically, the prognostic outcome of the S3 was the most favorable, while that of the S1 was the worst and this subtype was associated with the activation of NF-kB, TNF-α and hypoxia pathways. Three key genes, namely, methyltransferase-like 3 (METTL3), insulinolike Growth Factor2 mRNA-Binding Protein 3 (IGF2BP3) and YTH domain-containing protein 2 (YTHDC2), selected from the 9 m6A regulator genes were combined into a RiskScore, which showed a high classification effectiveness in dividing the patients into high- and low-risk groups. Inhibition of the expression of METTL3A or that of IGF2BP3 suppressed the invasion and migration of CRC cells. Notably, the high-risk patients had higher immune cell infiltration to support the activation of multiple immune responses and exhibited significantly poor prognosis. Meanwhile, a nomogram with practical clinical value was developed based on the RiskScore and other clinical features. Finally, eight potential drugs associated with the RiskScore were identified, and CD4+ cells and Tregs were found to be closely associated with CRC progression.ConclusionThe RiskScore model developed based on m6A regulators played a critical role in CRC development and can be considered as a prognosis predictor for patients with the cancer. The present discoveries will facilitate the diagnosis and clinical management of CRC patients. creator: Hanhan Zhu creator: Yu Yang creator: Zhenfeng Zhou uri: https://doi.org/10.7717/peerj.18719 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhu et al. title: Vegetation–soil–microbiota dynamics across a 50-year reconstructed grassland chronosequence on the Loess Plateau of China link: https://peerj.com/articles/18723 last-modified: 2024-12-20 description: Alfalfa (Medicago sativa L.) establishment is an effective strategy for grassland reconstruction in degraded ecosystems. However, the mechanisms underlying vegetation succession in reconstructed grasslands following alfalfa establishment remain elusive. In this study, we investigated vegetation community, soil quality and rhizosphere microbiota dynamics across a reconstructed grassland chronosequence in the loess region of Northwest China. A space-for-time substitution method was used to evaluate grassland vegetation coverage and alfalfa production performance in nine stands of different ages (1–50 years old). High-throughput sequencing was conducted to characterise rhizosphere microbial communities associated with alfalfa. The plant heights, yields and stem-to-leaf ratios of alfalfa all peaked in the 7-year-old stand and then decreased in older stands, with Stipa bungeana replacing alfalfa as the dominant species in the 50-year-old stand. Soil bulk density and major nutrient contents were highest in the artificial grassland (1–10 years). Soil enzyme activities (e.g., urease and sucrase) were enhanced in the transitional grassland (10–30 years), accompanied by enrichment of potentially beneficial microbial taxa (e.g., Actinobacteria and Mortierella) and functional fungi (e.g., saprotrophs and symbiotrophs) in the rhizosphere. Soil water content, total porosity and rhizosphere microbial diversity reached their maximum levels in the natural grassland (>30 years). The results indicate that alfalfa establishment alters soil structure and nutrient status in the short term, creating an optimal rhizosphere micro-environment. The improved soil conditions and rhizosphere microbiota are favourable for subsequent establishment of native grass species, leading to the formation of a stable semi-natural grasslands. creator: Yuanyuan Ma creator: Yan Shen creator: Ling Jin creator: Yu Tian creator: Hongbin Ma creator: Jian Lan creator: Bingzhe Fu uri: https://doi.org/10.7717/peerj.18723 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ma et al. title: Effect of seedling size on post-planting growth and survival of five Mexican Pinus species and their hybrids link: https://peerj.com/articles/18725 last-modified: 2024-12-20 description: BackgroundSeedling growth and survival depend on seedling quality. However, there is no experimental evidence showing that the seedling dimensions of the abundant, economically important and widely distributed tree species Pinus arizonica, P. durangensis, P. engelmannii, P. leiophylla, and P. teocote and their hybrids effectively improve survival and growth in reforestations and plantations in Mexico. Therefore, the aim was to evaluate the influence of initial morphological parameters of 2,007 nursery seedlings of these species and their hybrids on their growth and survival 44 months after planting in the Sierra Madre Occidental, Mexico.MethodsSpearman’s coefficient (rs) and the unbiased conditional pseudo coefficient of determination (R2c) between each specific predictor and each response variable and their 95% confidence interval (CI95%) were determined using Random Forest, generalized linear model, and bootstrapping. By bootstrapping, the potential environmental heterogeneity inside the trial fields and its impact on the results were also quantified.ResultsAmong the studied species and their hybrids moderate correlations were observed between the nursery seedling dimensions and the plant dimensions 44 months after planting. However, only weak significant correlations were found between survival rate (SR) and height (H) (rs = 0.10) and between SR and robustness index (HRCD) both before planting (rs = 0.06). Also, weak significant R2c values of the seedlings RCD, H and HRCD were detected with respect to the corresponding RCD, H and SR 44 months after planting, respectively. Furthermore, the predictor variable “seed provenance” (with 23 provenances) significantly explained the variation in the post-planting RCD, H and SR of the seedlings, with R2c values ranging from 0.10 to 0.15. The low width of the CI95% shows that the environmental conditions in the trial fields were quite homogeneous.DiscussionThe results also show that the inclusion of “confounding” variables in the statistical analysis of the study was crucial. Important factors to explain this low association could be the strong damage observed caused by pocket gopher, the typically low winter-spring precipitation in both field trials and adaptation factors. The study findings provide preliminary insights and information aimed at helping to design more appropriate standards for nurseries. creator: José Alberto Ponce-Figueroa creator: Pablo Antúnez creator: José Ciro Hernández-Díaz creator: José Ángel Prieto-Ruíz creator: Artemio Carrillo-Parra creator: Pablito Marcelo López-Serrano creator: Christian Wehenkel uri: https://doi.org/10.7717/peerj.18725 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ponce-Figueroa et al. title: The movement and distribution of pregnant spotted ragged-tooth sharks, Carcharias taurus, in the iSimangaliso Wetland Park, South Africa link: https://peerj.com/articles/18736 last-modified: 2024-12-20 description: The spotted ragged-tooth shark, Carcharias taurus, is widely distributed in subtropical continental coastal seas. In South Africa, it is commonly found along the entire south and east coasts, including the iSimangaliso Wetland Park (IWP) in the far north, which is the largest Marine Protected Area on the South African coast. Pregnant females occur there for much of the year, with the largest aggregations in summer. It is here we used remote underwater photography (RUP), supplemented with in-situ surveys to photo-identify individuals, using unique spot patterns. Three known aggregation sites (Raggie Reef, Quarter-Mile Reef and Mushroom Rocks) were monitored over a 5-year period between 2018 and 2023. We photo-identified 574 individuals (569 females and five males) and registered 1,200 sightings, using images of the right flank. The identification of new individuals persisted throughout the study, with the discovery curve showing no signs of reaching an asymptote. A total of 97% (n = 550) of females observed were noticeably pregnant. Individuals were consistently identified across all sample years and at all three reefs, exhibiting movements among the three monitored sites. The reproductive cycle is generally regarded as 2 years, but some females appeared to have a 2-year rest between pregnancies. Raggie Reef, which lies in the sanctuary zone, emerged as the reef with the highest index of popularity, as individuals were present almost constantly (90% of the sampling days). The findings of this study confirm the crucial role that the IWP plays in the conservation of a species that is globally Critically Endangered. creator: Sara C. Cerqueira creator: Jennifer Margaret Olbers creator: Grant Smith creator: Michelle Carpenter creator: Mário J. Pereira creator: Geremy Cliff uri: https://doi.org/10.7717/peerj.18736 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cerqueira et al. title: Visual codon: a user-friendly Python program for viewing and optimizing gene GC content link: https://peerj.com/articles/18755 last-modified: 2024-12-20 description: Due to the codon bias of different species, codon optimization is usually carried out in the process of heterologous protein expression. At present, there are a variety of codon optimization tools. However, the optimized sequences may still have high or low points of local guanine and cytosine (GC) content, which is not conducive to the primer design of gene subcloning, and also makes it difficult to perform the experiment of synthesizing the whole gene with DNA fragments by polymerase chain reaction (PCR) reaction. In this study, we present a stand-alone software written in Python, with which users can manually check and adjust the GC content of sequence-optimized genes. The software takes the codon frequency of Escherichia coli as default and can work with other species as well. It provides a Graphical User Interface (GUI) interface, which allows users to change codons and intuitively see the effect of codon changes on local GC content. Our program brings convenience for the optimization of gene GC content and the subsequent gene cloning experiments. creator: Shiming Lin creator: Fei Xu creator: Bifang Huang creator: Li-li Zhao creator: Danni Pan creator: Shiqiang Lin uri: https://doi.org/10.7717/peerj.18755 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lin et al. title: Correlation and mediation analysis between plasmapheresis donation behavior and bone mineral density and bone metabolism biomarkers: a cross-sectional study based on plasmapheresis donors at high risk of osteoporosis in China link: https://peerj.com/articles/18589 last-modified: 2024-12-19 description: BackgroundAs a group of more than 3.67 million people, the bone health of Chinese plasmapheresis donors, which the main population is also a risk group of osteoporosis (OP), has raised concerns. Therefore, this article investigates the relationship between bone mineral density (BMD), bone metabolism indicators, and plasmapheresis donation behavior among some high-risk plasmapheresis donors for OP in China, and further explores the mediating factors through reasonable statistical methods.MethodsRecruiting long-term and highly active plasmapheresis donors and new donors to measure the total calcium, albumin (ALB), 25-hydroxy vitamin D (25OHD), parathyroid hormone (PTH), type I procollagen amino-terminal peptide (P1NP), and type I collagen carboxy-terminal peptide (β-CTX) and serum ferritin (SF). Then, multiple linear regression was used to adjust confounding factors. Using restrictive cubic splines to explore the nonlinear relationship. Using the Bootstrap method, investigate whether SF has a mediating effect between plasmapheresis donation behavior and bone metabolism biomakers. Finally, analyze the differences in BMD between the two.ResultsCompared to new donors, repeat donors have a lower 25OHD, β-CTX and SF levels, while P1NP and PTH levels are high, with statistical differences. The Bootstrap analysis results show that SF level is a partial mediating factor between plasmapheresis donation behavior and bone metabolism biomakers, with a mediating effect ratio of 21.8%. There was no significant difference in the BMD between the two.ConclusionLong-term and frequently plasmapheresis donation does not affect the bone mass of even elderly donors at high risk for osteoporosis under the existing collection standards and anticoagulant use in China. However, as a self-regulation way, it does increase the osteogenic activity of the body. creator: Wan Li creator: Jia Liu creator: Changqing Li creator: Hui Yang creator: Yating Yang creator: Zhiwei Li creator: Shouqiang Yang creator: Yuan He creator: Guanglin Xiao creator: Ya Wang creator: Yongjun Chen uri: https://doi.org/10.7717/peerj.18589 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Updated range distribution of the non-native Asian green mussel Perna viridis (Linnaeus, 1758) at Guanabara Bay, Rio de Janeiro, Brazil link: https://peerj.com/articles/18649 last-modified: 2024-12-19 description: Guanabara Bay, located at Rio de Janeiro, Brazil, is a highly urbanized and polluted estuary that houses different port areas, shipyards, and marinas of intense maritime traffic. This infrastructure is widely associated with the introduction and spread of non-native sessile species. A rapid assessment of non-native benthic sessile species conducted in the bay in late 2022 across 19 sites identified a total of 83 taxa, both native and non-native, classified into the following main groups: one Cyanophyta, 13 Macroalgae, 14 Porifera, 11 Cnidaria, six Bryozoa, five Annelida, 10 Mollusca, six Crustacea, 10 Echinodermata, and seven Ascidiacea. Our findings revealed the proliferation of the Asian green mussel (Perna viridis Linnaeus, 1758), a species noted for its exceptional ability to achieve extremely high biomass levels globally. In Brazil, the bivalve was first reported less than 6 years ago in 2018 at Guanabara Bay, on a mariculture farm at Arraial do Cabo (200 km away) in 2023 and more recently in the south (Paranaguá Bay), besides two coastal islands outside Guanabara Bay on natural rocky shores. The present survey recorded P. viridis at 17 sites, including natural substrata, co-occurring with native species. No Tubastraea spp. were observed in Guanabara Bay. Controlling and mitigating the consequences of bioinvasion events can be challenging, but biosafety protocols should be adopted in the near feature to minimize the risks and impacts caused by species dispersal. creator: Luciana V. R. de Messano creator: José E. A. Gonçalves creator: Alexandre D. Kassuga creator: Alexandre R. da Silva creator: Bruno P. Masi creator: Héctor F. Messano creator: Denny Fardin creator: Ricardo Coutinho uri: https://doi.org/10.7717/peerj.18649 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 de Messano et al. title: Developing the developmental origins of health and disease (DOHaD) awareness scale to assess an education module for improving dietary behavior among college students link: https://peerj.com/articles/18669 last-modified: 2024-12-19 description: ObjectiveThis study aimed to develop and validate the Developmental Origins of Health and Disease (DOHaD) awareness scale and examine whether having a DOHaD education module may affect dietary behavior in college students.BackgroundSome studies conducted within the scope of the DOHaD hypothesis show associations between early-life environmental factors, especially maternal health and nutritional status, with the next generation’s health and disease status. Despite the increase in elucidating of the underpinning mechanisms of early life determinants and chronic disease risk, there is limited knowledge on how public perceive and understand DOHaD concepts.MethodsThe study consisted of three phases: identification of DOHaD awareness scale components, development and validation, interrater reliability of the scale, and a confirmatory study. Two-hundred college students to confirm face validity of the scale, one-hundred for reproducibility and one-hundred for the confirmatory study. Confirmatory study included a pre-intervention period in which baseline parameters (such as anthropometric measurements, HEI-2015 (Healthy Eating Index-2015), physical activity levels, and DOHaD awareness scale scores) were measured at two different time points, and an educational module on DOHaD concepts was provided to the participants. The study was reported in accordance with the Guidelines for Reporting Reliability and Agreement Studies (GRRAS).ResultsContent validity ratio, exploratory factor analysis, and Cronbach’s alpha values indicated that a reliable and valid instrument to assess the awareness of DOHaD concepts in college students was developed. Despite the lack of a control group, DOHaD concept education was associated with improved anthropometric measurements, healthier eating parameters, increased physical activity levels, and a better understanding of DOHaD concepts.ConclusionsTranslating DOHaD concepts into healthier behaviors can support improvements in lifestyle, and the use of the DOHaD awareness scale may serve as a valuable tool to encourage healthy behaviors among college students. creator: Kadriye Elif İmre creator: Aslı Akyol uri: https://doi.org/10.7717/peerj.18669 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 İmre and Akyol title: Ultrasonographic modeling of lung and diaphragm mechanics: clinical trial of a novel non-invasive method to evaluate pre-operative pulmonary function link: https://peerj.com/articles/18677 last-modified: 2024-12-19 description: BackgroundPre-operative pulmonary function testing (PFT) plays a key role in predicting postoperative complications or functional impairment. However, PFT requires the subject and examiner to cooperate and the results are influenced by both technical and personal factors. In contrast, the use of ultrasound (US) for structural and functional assessments of the lungs and diaphragm is on the rise, as it requires minimal patient cooperation. Dyspnea is mainly caused by lung or pleural lesions but may also be caused by weak respiratory muscles. As the diaphragm is a primary respiratory muscle, combining lung ultrasonography (LUS) with diaphragm ultrasound (DUS) may enable a more comprehensive assessement of pulmonary function. This study aims to introduce a novel approach for assessing pulmonary function using a mathematical model based on LUS and DUS.MethodsThis prospective study was performed at the First Affiliated Hospital of Nanchang University between June 2021 and December 2021, 208 patients were recruited and underwent PFT, LUS, and DUS examinations. An experienced physician, blinded to the clinical history and PFT results, performed LUS and DUS and explored the correlations between a mathematical model (ultrasonographic modeling score (U-score)) using LUS combined with DUS and pulmonary function parameters. Univariate, multivariate, and logistic regression analyses were also performed.ResultsAccording to the univariate and multivariable analysis, diaphragm thickness fraction in deep breathing (D-DTF) (odds ratio (OR), 0.88; 95% confidence interval (CI) [0.83–0.94]; P < 0.001), and LUS score (OR, 1.44; 95% CI [1.16–1.80]; P < 0.001) were each independently associated with pulmonary function. According to the logistics equation, a U-score of −0.126 × D-DTF + 0.368 × LUS score was produced. The U-score showed a more significant negative correlation with forced expiratory volume in the first second/forced vital capacity (FEV1/FVC) (r = −0.605, P < 0.001) than the LUS or DUS indices alone. The U-score (area under the curve (AUC) = 0.971) was greater than the other indices for assessing pulmonary function.ConclusionsWith validation, the U-score through both lung and diaphragm ultrasound measurements may assist in estimating pulmonary function. This approach facilitates the assessment of pulmonary function in patients who may be unable to reliably participate in PFT. creator: Tianyuan Li creator: Xiong-zhi Wu creator: Dingde Long creator: Huan Fu creator: Suping Guo creator: Fen Liu uri: https://doi.org/10.7717/peerj.18677 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Ferroptosis and its impact on common diseases link: https://peerj.com/articles/18708 last-modified: 2024-12-19 description: Ferroptosis is a novel form of programmed cell death characterized by iron accumulation, lipid peroxidation, and a decline in antioxidant capacity, all of which are regulated by gene expression. The onset of numerous diseases is closely associated with ferroptosis. Common diseases affect a large population, reduce the quality of life, and impose an increased burden on the healthcare system. The role of ferroptosis in common diseases, its therapeutic potential, and even its translation into clinical drug treatments are currently significant research topics worldwide. This study preliminarily explores the theoretical basis of ferroptosis, its mechanism and treatment prospect in common diseases including ischaemia-reperfusion injury, inflammatory bowel diseases, liver fibrosis, acute kidney injury, diabetic kidney disease, stroke, Alzheimer’s disease, cardiovascular disease, immune and cancer. This review provides a theoretical foundation for the further study and development of ferroptosis, as well as for the prevention and treatment of common diseases. creator: Pengjian Zou creator: Qiuming He creator: Huimin Xia creator: Wei Zhong uri: https://doi.org/10.7717/peerj.18708 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zou et al. title: Diversity analysis of microorganisms on the surface of four summer fruit varieties in Baotou, Inner Mongolia, China link: https://peerj.com/articles/18752 last-modified: 2024-12-19 description: Improper storage of post-harvest fruits leads to significant losses, especially due to microbial-induced decay. Understanding the naturally occurring microbial communities on fruit surfaces and their functions is the first step in the development of new strategies for controlling post-harvest fruit decay. These new strategies could generate significant economic value by improving fruit preservation and extending the shelf-life of fruit. In the present study, 16S rRNA and ITS high-throughput sequencing technologies were used to analyze the diversity and composition of microorganisms on the surfaces of four different fruit varieties: three plum varieties and one apple variety, all from the same orchard in Donghe District, Baotou City, China. The results displayed no notable difference in bacterial diversity on the surfaces of the four varieties of fruits (P > 0.05), but there were significant differences in fungal diversity (P < 0.05). The most abundant bacterial phyla detected on the fruit surfaces were Proteobacteria, Bacteroidota, and Firmicutes; the most abundant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. Though microbial compositions on the fruit surfaces differed between the fruits, the surface microbial community structure of the three plum varieties exhibited higher similarity, indicating that fruit type is a key factor influencing the composition of surface microorganisms. There were also differences in the epidermal microbial community composition between the fruits involved in this study and fruits of the same species reported from other regions, suggesting that geographical factors also play a critical role in microbial composition. The correlation analysis revealed significant associations between the microorganisms with the highest abundance on the surface of the fruits, suggesting the existence of symbiotic and mutualistic relationships between these microorganisms, but the specific mechanisms behind these relationships need to be further explored. This study provides a basis for the establishment of post-harvest fruit preservation strategies. creator: Shan He creator: Li Gao creator: Zhuomin Zhang creator: Zhihui Ming creator: Fang Gao creator: Shuyi Ma creator: Mingxin Zou uri: https://doi.org/10.7717/peerj.18752 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 He et al. title: A novel model based on clinical and computed tomography (CT) indices to predict the risk factors of postoperative major complications in patients undergoing pancreaticoduodenectomy link: https://peerj.com/articles/18753 last-modified: 2024-12-19 description: BackgroundPostoperative complications are prone to occur in patients after radical pancreaticoduodenectomy (PD). This study aimed to construct and validate a model for predicting postoperative major complications in patients after PD.MethodsThe clinical data of 360 patients who underwent PD were retrospectively collected from two centers between January 2019 and December 2023. Visceral adipose volume (VAV) and subcutaneous adipose volume (SAV) were measured using three-dimensional (3D) computed tomography (CT) reconstruction. According to the Clavien-Dindo classification system, the postoperative complications were graded. Subsequently, a predictive model was constructed based on the results of least absolute shrinkage and selection operator (LASSO) multivariate logistic regression analysis and stepwise (stepAIC) selection. The nomogram was internally validated by the training and test cohort. The discriminatory ability and clinical utility of the nomogram were evaluated by area under the receiver operating characteristic (ROC) curve (AUC), calibration curve, and decision curve analysis (DCA).ResultsThe major complications occurred in 13.3% (n = 48) of patients after PD. The nomogram revealed that high VAV/SAV, high system inflammation response index (SIRI), high triglyceride glucose-body mass index (TyG-BMI), low prognostic nutritional index (PNI) and CA199 ≥ 37 were independent risk factors for major complications. The C-index of this model was 0.854 (95%CI [0.800–0.907]), showing excellent discrimination. The calibration curve demonstrated satisfactory concordance between nomogram predictions and actual observations. The DCA curve indicated the substantial clinical utility of the nomogram.ConclusionThe model based on clinical and CT indices demonstrates good predictive performance and clinical benefit for major complications in patients undergoing PD. creator: Jiaqi Wang creator: Kangjing Xu creator: Changsheng Zhou creator: Xinbo Wang creator: Junbo Zuo creator: Chenghao Zeng creator: Pinwen Zhou creator: Xuejin Gao creator: Li Zhang creator: Xinying Wang uri: https://doi.org/10.7717/peerj.18753 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Comparative meta-analysis of cold snare polypectomy and endoscopic mucosal resection for colorectal polyps: assessing efficacy and safety link: https://peerj.com/articles/18757 last-modified: 2024-12-19 description: Colorectal polyps are commonly treated with surgical procedures, with cold snare polypectomy (CSP) and endoscopic mucosal resection (EMR) being the two most prevalent techniques. This meta-analysis (PROSPERO ID: CRD42022336152) aimed to compare the efficacy and safety of CSP and EMR in the management of colorectal polyps. Comprehensive searches were conducted in PubMed, Embase, CINAHL, Web of Science, and Cochrane Library databases, covering publications up until June 2024. The primary outcome was complete resection rate, and secondary outcomes included en bloc resection rate, immediate and delayed bleeding, perforation, and procedure time. The Mantel–Haenszel method was employed for the analysis of binary endpoints, while the inverse variance method was used for continuous outcomes. Subgroup analysis was performed to explore potential sources of heterogeneity. Six studies involving 15,296 patients and 17,971 polyps were included in the meta-analysis. CSP had a significantly lower complete resection rate compared to EMR (OR: 0.44, 95% CI [0.21–0.94], p = 0.0334). However, there was no significant difference between CSP and EMR in en bloc resection rate, perforation, or procedure time. Interestingly, CSP had a significantly lower delayed bleeding rate compared to EMR (OR: 0.45, 95% CI [0.27–0.77], p = 0.0034), but there was no significant difference in immediate bleeding rate. In conclusion, CSP is a safe, efficient, and effective technique comparable to EMR. The choice of technique should be based on the individual patient and polyp characteristics. creator: Shouqi Wang creator: Qi Zhang creator: Li Rong Meng creator: Ying Wu creator: Pedro Fong creator: Weixia Zhou uri: https://doi.org/10.7717/peerj.18757 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Bone histology and growth curve of the earliest ceratopsian Yinlong downsi from the Upper Jurassic of Junggar Basin, Northwest China link: https://peerj.com/articles/18761 last-modified: 2024-12-19 description: Yinlong downsi, the earliest known ceratopsian, is represented by dozens of specimens of different sizes collected from the Upper Jurassic of the Junggar Basin, northwestern China. Here, we present the first comprehensive study on the bone histology of Yinlong downsi based on ten specimens varying in size. Four ontogenetic stages are recognized: early juvenile, late juvenile, subadult, and adult. The reconstructed growth curve suggests that Yinlong may reach sexual maturity at 6 years old, which is earlier than that of the well-studied early-diverging ceratopsian Psittacosaurus (9 years old) but later than ceratopsids (about 3 to 5 years old). This may indicate that sexual maturity begins earlier during the evolution of ceratopsians, and that the giant size of ceratopsids is acquired by accelerating growth rates. The cortex of the tibia mainly consists of fibrolamellar bone tissues, but parallel-fibered bone and lines of arrested growth (LAGs) are very common throughout ontogeny, suggesting a moderate growth rate. Quantitative analysis indicates that Yinlong has a maximum growth rate similar to those of other small-sized dinosaurs such as Psittacosaurus, Dysalotosaurus, and Troodon, and their maximum growth rates are higher than those of extant squamates and crocodiles but lower than those of extant mammals and large dinosaurs. This suggests that body size plays a more important role in growth rate than other factors such as phylogenetic position and/or diet among non-avian dinosaurs. creator: Fenglu Han creator: Qi Zhao creator: Jinfeng Hu creator: Xing Xu uri: https://doi.org/10.7717/peerj.18761 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Han et al. title: Flipped classroom-based application of Peyton’s four-step approach in standardized training of ultrasound residents for thyroid and cervical lymph node zoning link: https://peerj.com/articles/18633 last-modified: 2024-12-18 description: BackgroundTo investigate whether combining the flipped classroom approach with Peyton’s four-step method can enhance teaching effectiveness in ultrasound (US) zoning of the thyroid and cervical lymph nodes for standardized residency training.MethodsA total of 66 resident training students were randomly divided into a control group and an observation group. The control group received traditional teaching methods, including “see one, do one” learning, lecture-based learning (LBL), and case-based learning (CBL). The observation group was taught using Peyton’s four-step teaching method, the flipped classroom approach, and CBL. Assessments were conducted through skill operation and clinical case analysis. A questionnaire survey was used to evaluate student satisfaction. Assessment scores and questionnaire ratings between the two teaching methods were compared.Results1) Assessment results demonstrated higher scores in skill operation and clinical case analysis for the observation group compared to the control group [(87.64 ± 3.72) vs. (80.48 ± 5.92) points, (87.94 ± 4.46) vs. (82.85 ± 4.24) points]. 2) The questionnaire survey indicated that resident trainees taught using Peyton’s four-step method showed greater improvement in learning interest [(4.61 ± 0.57) vs. (3.70 ± 0.85) points] and experienced reduced exam pressure compared to the control group [(4.52 ± 0.62) vs. (3.21 ± 0.70) points]. These differences were statistically significant (P < 0.05).ConclusionPeyton’s four-step approach combined with the flipped classroom method improved resident training students’ scores in skill operation and clinical case analysis for ultrasound zoning of the thyroid and cervical lymph nodes. It also stimulated learning interest and alleviated exam pressure, making it an effective teaching method for enhancing standardized US training outcomes in resident education. creator: Jiajia Wang creator: Yunyun Zhan creator: Biyun Sun creator: Yu Bi creator: Rubing Li creator: Fan Jiang creator: Mei Peng uri: https://doi.org/10.7717/peerj.18633 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Different prevalence and spectrum of malignancy between Chinese patients and American patients with rheumatoid arthritis: a comparative study link: https://peerj.com/articles/18650 last-modified: 2024-12-18 description: ObjectiveTo characterize the epidemiological characteristics of malignancy in Chinese patients with rheumatoid arthritis (RA) versus American patients and investigate their associated factors.MethodsData were collected from a real-world Chinese RA population and American patients with RA from the National Health and Nutritional Examination Survey. The prevalence and subtypes of malignancy and their potential associated factors were investigated in both populations.ResultsA total of 2,073 Chinese and 2,928 American patients with RA were included. There was a lower prevalence of malignancy in Chinese than in their American counterparts before (5.7% vs. 17.1%) and after matching (6.2% vs. 12.6%, both P < 0.001). Gender discrepancies in malignancy prevalence were observed, with a male predilection for RA with malignancy in China (8.2% vs. 5.5%), while it was the opposite in American patients (10.1% vs. 13.5%, both P < 0.05). The top type of malignancy among male patients with RA was lung cancer in Chinese (2.29%), but non-melanoma skin cancer (3.43%) in American; while among female patients was breast cancer both in Chinese (1.72%) and American (3.43%). Multivariate logistic regression analyses showed that older age (odds ratio (OR) = 1.050) and positive anti-cyclic citrullinated peptide antibody (OR = 2.752) were independently associated with malignancy in Chinese patients with RA, while female (OR = 1.395), older age (OR = 1.033), active smoking (OR = 1.580) and cardiovascular diseases (OR = 1.523) in American patients.ConclusionThe prevalence, subtypes and risk factors of malignancy were substantially different in Chinese patients with RA and their American counterparts, which implied the importance of individualized malignancy screening strategies for patients with RA. creator: Zhi-Ming Ouyang creator: Yao-Wei Zou creator: Jie Pan creator: Ye Lu creator: Ying Yang creator: Qian-Hua Li creator: Jian-Da Ma creator: Pei-Wen Jia creator: Tao Wu creator: Yu-Ting Fan creator: Jian-Zi Lin creator: Xiu-Ning Wei creator: Kui-Min Yang creator: Yun Su creator: Lie Dai uri: https://doi.org/10.7717/peerj.18650 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ouyang et al. title: Comparative analysis of Hymenasplenium (Aspleniaceae) chloroplast genomes from China link: https://peerj.com/articles/18667 last-modified: 2024-12-18 description: Hymenasplenium is one of the two genera in the large fern family Aspleniaceae. A previous study explored the molecular phylogeny of this genus using several chloroplast DNA fragments and identified three major clades, one of which is the monophyletic Old World clade with southwestern China as its diversity center. To date, there were only a few studies conducted on chloroplast genomes in Hymenasplenium or Aspleniaceae, limiting the understanding of the plastome features and its role in evolution of this group. Here, we studied the complete chloroplast genomes of 12 Hymenasplenium species covering all four subclades of the Old World clade distributed in China. The length of the Hymenasplenium plastomes ranged from 151,617 to 151,930 bp, and contained 129 genes in total, comprising 87 protein-coding, 34 tRNA, and eight rRNA genes. The GC content ranged from 41.8% to 42.1%. Comparative analyses of the Hymenasplenium chloroplast genomes displayed conserved genomic structure and identical gene arrangement. A total of 1,375 simple sequence repeats and 1,639 large repeats were detected. In addition, we detailed hypervariable regions that can be helpful for further phylogenetic research and species delimitation in Hymenasplenium. Furthermore, we supported phylogenetic relationships among major groups as well as possible cryptic speciation found in previous research in the genus. Our study provides new insights into evolutionary history and basic resources for phylogenetic and taxonomic studies of the genus Hymenasplenium. creator: Yanfen Chang creator: Zhixin Wang creator: Guocheng Zhang creator: Na Wang creator: Limin Cao uri: https://doi.org/10.7717/peerj.18667 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chang et al. title: The effect of varying thicknesses of mineral trioxide aggregate (MTA) and Biodentine as apical plugs on the fracture resistance of teeth with simulated open apices: a comparative in vitro study link: https://peerj.com/articles/18691 last-modified: 2024-12-18 description: BackgroundThis study evaluates the fracture resistance of apical plugs created from Biodentine and mineral trioxide aggregate (MTA) in thicknesses of 3 and 5 mm within simulated open apex tooth models.MethodsFifty human maxillary central incisors were obtained from a pool of freshly extracted teeth. In order to replicate open apices without cavity preparation, ten teeth in the control group received apical-to-coronal preparation with Peeso reamers. The remaining 40 teeth were randomly assigned to four experimental groups and received either 3 or 5 mm Biodentine or MTA apical plugs.ResultsThe mean fracture loads observed in this study were as follows: control group, 431.48 N (±34.55); 3 mm MTA, 774.88 N (±62.74); 5 mm MTA, 752.65 N (±73.79); 3 mm Biodentine, 918.25 N (±59.09); and 5 mm Biodentine, 903.42 N (±24.48). Specifically, teeth in the Biodentine group demonstrated considerably stronger fracture resistance compared to those in the MTA group (p < 0.001). However, no significant differences were observed between the 3 and 5 mm thicknesses (MTA: p = 0.98, Biodentine: p = 0.99), suggesting that plug thickness did not affect fracture resistance within both groups.ConclusionBiodentine apical plugs provided the highest fracture resistance among the materials, regardless of thickness. creator: Pankaj Panjwani creator: Kulvinder Banga creator: Jatin Atram creator: Dian Agustin Wahjuningrum creator: Alexander Maniangat Luke creator: Krishna Prasad Shetty creator: Ajinkya M. Pawar uri: https://doi.org/10.7717/peerj.18691 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Panjwani et al. title: A comparative perception and impact of pictorial warnings on cigarette packaging among Malaysian smokers and non-smokers link: https://peerj.com/articles/18713 last-modified: 2024-12-18 description: IntroductionIn 2003, the World Health Organization (WHO) recommended that pictorial warnings on tobacco products be used to educate consumers on the negative health impacts associated with tobacco use. This study aimed to assess the effectiveness of pictorial warnings on cigarette packaging among smokers and non-smokers.MethodsA cross-sectional study using a self-administered questionnaire was conducted in Kuala Lumpur. Four components assessed the respondents’ socio-demographics, smoking status, perceptions, and impact of pictorial warnings. Six standard cigarette pictorial warning images were included in the questionnaire. Data collected were analysed using SPSS version 29.0. Frequencies and percentages were used for categorical data, while means and standard deviations were used for continuous data. Statistically significant results were set at p-value < 0.05. Non-parametric tests, the Chi-square test and the One-Way ANOVA test were used to calculate the differences between the variables, as the data was not normally distributed.ResultsThree hundred seventy-eight respondents participated in this study, with smokers and non-smokers divided equally, 189. Most respondents were 20–29 years old (n = 223, 59.0%) and had tertiary education (n = 207, 54.8%). Most smokers were male (n = 172, 91.0%), and most non-smokers were female (n = 119, 63.0%). Most respondents (n = 364, 96.3%, p = 0.276) noticed the pictorial warnings on cigarette packs. Nevertheless, significantly (p < 0.001) more smokers (n = 73, 38.6%) seldomly read the content compared to non-smokers (n = 57, 30.2%). Most smokers (n = 48, 12.7%) sometimes consider quitting smoking upon exposure to pictorial warnings on cigarette packs. However, most non-smokers (n = 161, 42.6%) never had the urge to smoke upon looking at the pictorial warnings. The most impactful image on cigarette packs among smokers was ‘Lung cancer’ (n = 74, 39.2%), while for non-smokers was ‘Mouth cancer’ (n = 59, 31.2%) with p < 0.001.ConclusionWhile non-smokers demonstrated greater engagement with and emotional responses to the warnings, smokers showed less frequent interaction and a tendency toward desensitisation. Although pictorial warnings play a vital role in raising awareness of the health risks of smoking, particularly lung and mouth cancer, their effectiveness in encouraging smoking cessation among smokers remains limited. creator: Nurul Asyikin Yahya creator: Nur Aqilah Mohamed Kutty creator: Nurul Afira Saleh uri: https://doi.org/10.7717/peerj.18713 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yahya et al. title: Wound healing potential of mouth gel containing isopimarane diterpene from Kaempferia galanga rhizomes for treatment of oral stomatitis link: https://peerj.com/articles/18716 last-modified: 2024-12-18 description: BackgroundOral ulcers have an impact on 25% of the global population including patients who are suffering from chemotherapy and radiotherapy treatments. Kaempferia galanga L. has been traditionally used for treatment of mouth sores and tongue blisters. However, the wound healing study of isopimarane diterpenes isolated from K. galanga is still limited.ObjectiveThis study aims to evaluate the wound healing potential of 6β-acetoxysandaracopimaradiene-1α,9α-diol (KG6), a compound isolated from Kaempferia galanga, by examining its biological activities. Additionally, we investigate the physicochemical and biological properties of (KG6) in formulated mouth gels.MethodsThe KG6 mouth gels at 0.10%, 0.25% and 0.50% w/w were formulated using sodium carboxymethylcellulose as a gelling agent, and their physicochemical and biological stabilities were assessed through a heating-cooling acceleration test. The quantification of KG6 contents in KG6 mouth gels was determined using gas chromatography. Both KG6 and KG6 mouth gels were evaluated for their wound healing properties including cell proliferation, cell migration, and antioxidant activity (H2O2-induced oxidative stress) in human gingival fibroblast (HGF-1-ATCC CRL-2014) (HGF-1). In addition, the anti-inflammatory activity against nitric oxide (NO) production was investigated in macrophage cells (RAW 264.7).ResultsAfter KG6 mouth gels were incubated under heating-cooling acceleration condition, the physicochemical properties of the KG6 mouth gels remain stable across various parameters, including appearance, color, smell, texture, pH, viscosity, separation, and KG6 content. The biological studies indicated that the KG6 compound possessed good wound healing potential. The 0.50% KG6 mouth gel exhibited marked anti-inflammatory effect by inhibiting NO production with an IC50 of 557.7 µg/ml, comparable to that of Khaolaor mouth gel, a positive control. The 0.25% KG6 mouth gel increased HGF-1 cell proliferation to 101.7–103.5%, whereas all formulations of KG6 mouth gel enhanced HGF-1 cell migration to 94.7–98.9%, higher than Khaolaor mouth gel (73.5%). Moreover, 0.50% KG6 mouth gel also showed a good antioxidant effect under H2O2-induced oxidative stress.ConclusionThis study substantiates the significant biological activities related to the wound healing property of 0.50% KG6 mouth gel for treatment of aphthous ulcers and oral stomatitis from chemotherapy and radiotherapy treatments. creator: Anupon Iadnut creator: Tanawan Sae-lee creator: Supinya Tewtrakul uri: https://doi.org/10.7717/peerj.18716 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Iadnut et al. title: First discovery of actinopterygian cutting-edged teeth from the middle Norian (Late Triassic) at the Tulong section, southern Tibet, China link: https://peerj.com/articles/18728 last-modified: 2024-12-18 description: Actinopterygians (ray-finned fishes) successfully passed through the Permian-Triassic Mass Extinction (PTME) and flourished in the Triassic with diverse feeding specializations and occupation of various trophic levels. Birgeria, one of the largest actinopterygian fish of the Triassic, was characterized by a strong, blunt rostrum and three rows of sharp cutting-edged teeth, making them the top predators in the Early Mesozoic oceanic ecosystem. These fishes rapidly radiated and diversified globally during the Early and Middle Triassic, but the fossil record is rare for the Neo-Tethys in the Late Triassic. Here, we report new actinopterygian teeth with cutting edges from Norian-age strata in the Tulong section, which was located on the northern margin of the Indian Plate at that time. The tooth features, such as the polished acrodin cap, the ratio of the acrodin cap in length, and the tiny vertical striae at the tooth base, suggest an affinity with Birgeria, which is reported in this region for the first time. Furthermore, we infer that the carnivorous Birgeria, which co-occurred with the enigmatic ichthyosaur Himalayasaurus tibetensis, played the role of predator in this part of the Neo-Tethys marine realm during the Late Triassic. These new findings increase the known diversity of actinopterygians during the Late Triassic and provide further insight into the marine fauna of this epoch. creator: Zichen Fang creator: Long Cheng creator: Haishui Jiang creator: Xianlang Wu creator: Xulong Lai creator: James G. Ogg uri: https://doi.org/10.7717/peerj.18728 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Fang et al. title: Retention of indoxyl sulfate in different genotypes of ABCC2 may explain variation in tacrolimus pharmacokinetics link: https://peerj.com/articles/18729 last-modified: 2024-12-18 description: BackgroundMicrobiota-derived toxins indoxyl sulfate and hippuric acid were previously reported to be associated with altered pharmacokinetics of the immunosuppressant tacrolimus in liver transplant recipients, and ABC transporter proteins are likely to be involved in the transport of such substances, but the in vivo role has not been elucidated. The aim of this study was to assess the retention of indoxyl sulfate and hippuric acid in the plasma of liver transplantation subjects carrying different genotypes of ABCB1 and ABCC2 (changes in transporter activity due to genetic variation), and to explore whether genetic variation is involved in altering the relationship between microbe-derived toxins and tacrolimus pharmacokinetics.MethodsLiver transplantation subjects treated with the immunosuppressive regimen tacrolimus, corticosteroids, and mycophyolate mofetil were included and divided into normal renal function group and chronic kidney disease group. The plasma concentrations of indoxyl sulfate and hippuric acid in two groups of liver transplantation subjects carrying different genotypes of ABCB1 and ABCC2 were compared. For genotype carriers with significant differences, the Pearson Correlation Coefficient method was further used to investigate the correlation between plasma indoxyl sulfate level and tacrolimus dose-corrected trough concentration in patients with different renal function status.ResultsCarriers of the rs717620-24T variant exhibited high plasma indoxyl sulfate retention in patients with normal renal function, and furthermore, chronic kidney disease patients and patients with normal renal function exhibited indoxyl sulfate and tacrolimus in the ABCC2 normal function (β = −0.740, p = 0.020) and reduced function groups (β = −0.526, p = 0.005), respectively, showing a strong correlation with tacrolimus.ConclusionABCC2 may be one of the pathways by which tacrolimus pharmacokinetics is altered by indoxyl sulfate. creator: Jing Wang creator: Siqi Huang creator: Yuanchen Li creator: Qiu Fang creator: Min Wang creator: Huaijun Zhu uri: https://doi.org/10.7717/peerj.18729 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Validation study on the assay method for anti-factor IIa potency of enoxaparin sodium link: https://peerj.com/articles/18732 last-modified: 2024-12-18 description: Enoxaparin sodium is a low molecular mass heparin essential for effective anticoagulation therapy. However, significant variations in testing methods across different manufacturers have led to poor reproducibility of results, increasing the risks associated with drug quality evaluation by manufacturers and regulatory oversight. This study integrates the strengths of various testing methods to establish a reproducible assay that has been thoroughly validated. The validation results demonstrate that the method exhibits excellent specificity, linearity, robustness, precision, and accuracy, with recovery rates ranging from 98.0% to 102.0%. The new method demonstrated high consistency and reproducibility, with an RSD value of less than 2.0%, and showed the potential to replace the European Pharmacopoeia method by reducing reagent usage, experimental costs, and equipment requirements. The reliable results of this method facilitate its adoption across different laboratories, enhance the quality control of enoxaparin sodium, and provide a reference for new manufacturers and drug regulatory authorities, thereby ensuring medication safety. creator: Xiaorong Yang creator: Hanyan Zou creator: Yixue Dong creator: Bing Liu creator: Ying Wang creator: Mengying Wang uri: https://doi.org/10.7717/peerj.18732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: The role of circRNA in breast cancer drug resistance link: https://peerj.com/articles/18733 last-modified: 2024-12-18 description: Among women with cancer, breast cancer has surpassed lung cancer to become the most prevalent type of cancer globally. High-throughput sequencing of breast cancer tissues from many patients has revealed significant variations in circRNA expression across different types of breast cancer. Chemotherapy is currently a very important method for treating breast cancer; however, as the number of chemotherapy sessions increases and considering factors such as the patient’s immune response, drug resistance has become a challenging issue in treating breast cancer. It is well known that drug resistance is associated with multiple factors, and different resistance mechanisms involve different roles of circRNA. This review consolidates literature from the past 5 years and addresses the shortcomings in the broad description of circRNA’s role in breast cancer drug resistance. It categorizes and describes the drug resistance and its mechanisms in different types of breast cancer, as well as the roles of circRNA and signaling pathways in drug resistance. creator: Shaofeng Yang creator: Donghai Li uri: https://doi.org/10.7717/peerj.18733 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang and Li title: Validation and modification of existing bleeding complications prediction models for percutaneous renal biopsy: a prospective study link: https://peerj.com/articles/18741 last-modified: 2024-12-18 description: BackgroundBleeding complications following percutaneous renal biopsy (PRB) are a significant clinical concern. This study aimed to validate and refine existing prediction models for post-biopsy bleeding to support more accurate clinical decision-making.MethodsClinical data from 471 PRB patients were examined in this prospective analysis. Ultrasounds were performed immediately and 6 h post-biopsy to identify perinephric hematomas. Patients exhibiting severe pain, a hemoglobin drop of >10 g/L, symptomatic hypotension, hematuria within 7 days post-procedure underwent repeat ultrasound to assess for bleeding complications. Univariate and multivariable logistic regression analyses were conducted to identify factors associated with bleeding risk. The predictive performance of three kidney biopsy risk calculators (KBRC) was evaluated using the area under the receiver operating characteristic (AUROC) curve, net reclassification improvement (NRI), integrated discrimination improvement (IDI), and decision curve analysis (DCA) to determine clinical utility. Nomograms were developed for each model to facilitate clinical application.ResultsUnivariate analysis identified body mass index (BMI), hemoglobin, and ultrasound findings as significant predictors of bleeding complications. In multivariable analysis, BMI, immediate ultrasound, and 6-h ultrasound data remained significant (p < 0.05). The three models compared included: KBRC-5 (age, body mass index (BMI), platelet count, hemoglobin, kidney size), KBRC-5 with immediate ultrasound data (IKBRC), and KBRC-5 with 6-h hematoma size (SKBRC). The AUROC values for these models were 0.683, 0.786, and 0.867, respectively (p < 0.001). NRI and IDI analyses demonstrated that adding immediate or 6-h ultrasound data significantly improved the risk reclassification ability of the KBRC-5 model (p < 0.05). DCA indicated that IKBRC provided the highest net benefit for risk thresholds between 25% and 77%, while SKBRC was superior for thresholds between 10% and 95%. Nomograms were constructed for each model, allowing clinicians to estimate the probability of bleeding complications by summing scores for each predictor. Calibration curves showed good agreement between predicted and observed probabilities.ConclusionIncorporating real-time ultrasound data post-PRB significantly enhances the predictive accuracy and risk reclassification capability of bleeding risk models. These findings provide critical insights for guiding clinical management decisions in patients undergoing renal biopsy. creator: Xing Li creator: Min Liu creator: Di-fei Duan creator: Yu Yan creator: Dengyan Ma uri: https://doi.org/10.7717/peerj.18741 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Effects of aqueous and ethanolic extracts of Chinese propolis on dental pulp stem cell viability, migration and cytokine expression link: https://peerj.com/articles/18742 last-modified: 2024-12-18 description: BackgroundPropolis is a natural substance produced by honeybees that has various biological properties including, anti-inflammatory, antioxidant and antimicrobial properties. Although previous studies have evaluated the antimicrobial effects of propolis in dentistry, its effects on dental pulp stem cell (DPSC) viability, migration, and differentiation are yet not well understood. The objective of this study was to investigate the effects of Chinese propolis on viability/proliferation, migration, differentiation and cytokine expression in DPSCs.MethodsCommercially available DPSCs (Lonza) were treated with aqueous extract of propolis (AEP) or ethanolic extract of propolis (EEP), and viability/proliferation was evaluated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assays and quantification of nuclear staining. DPSC differentiation into mineralizing cells was evaluated with Alizarin red staining and cell migration was assessed using Boyden Chamber Transwell inserts. Cytokine expression was measured by RT-qPCR. AEP and EEP at 0.03 and 0.1 mg/mL did not affect DPSC viability/proliferation for up to 7-days treatment.ResultsHigher doses (0.33–33 mg/mL) induced a dose dependent decrease in DPSC viability/proliferation with a more prominent effect with EEP at 7 days. Neither AEP nor EEP induced DPSC differentiation into mineralizing cells, but both AEP and EEP (0.03–0.1 mg/ml) induced a dose dependent increase in DPSC migration. In addition, EEP prevents the upregulation of IL1b and IL6 but not IL8 and CCL2 in response to lipopolysaccharide stimulation. AEP has less potent anti-inflammatory effects and prevents only IL1b upregulation.ConclusionThis study provides new information about the biologic properties of ethanolic and aqueous extracts of propolis and shows that propolis, at doses that do not affect cell viability, induces DPSC migration and has anti-inflammatory properties. These data highlight the potential use of propolis as an alternative intra-canal medicament for regenerative endodontic procedures. creator: Ha Bin Park creator: Yen Dinh creator: Pilar Yesares Rubi creator: Jennifer L. Gibbs creator: Benoit Michot uri: https://doi.org/10.7717/peerj.18742 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Park et al. title: Time series (ARIMA) as a tool to predict the temperature-humidity index in the dairy region of the northern desert of Mexico link: https://peerj.com/articles/18744 last-modified: 2024-12-18 description: The environment in which an animal is situated can have a profound impact on its health, welfare, and productivity. This phenomenon is particularly evident in the case of dairy cattle, then, in order to quantify the impact of ambient temperature (°C) and the relative humidity (%) on dairy cattle, the temperature-humidity index (THI) is employed as a metric. This indicator enables the practical estimation of the stress imposed on cattle by ambient temperature and humidity. A seasonal autoregressive integrated moving average (SARIMA) (4,1,0)(0,1,0)365 model was estimated using daily data from the maximum daily THI of 4 years (2016–2019) of the Comarca Lagunera, an arid region of central-northern Mexico. The resulting model indicated that the THI of any given day in the area can be estimated based on the THI values of the previous four days. Furthermore, the data demonstrate an annual increase in the number of days the THI indicates a risk of heat stress. It is essential to continue building predictive models to develop effective strategies to mitigate the adverse effects of heat stress in dairy cattle (and other species) in the region. creator: José Luis Herrera-González creator: Rafael Rodríguez-Venegas creator: Martín Alfredo Legarreta-González creator: Pedro Antonio Robles-Trillo creator: Ángeles De-Santiago-Miramontes creator: Darithsa Loya-González creator: Rafael Rodríguez-Martínez uri: https://doi.org/10.7717/peerj.18744 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Herrera-González et al. title: Genome-wide association study reveals the advantaged genes regulating japonica rice grain shape traits in northern China link: https://peerj.com/articles/18746 last-modified: 2024-12-18 description: BackgroundRice, a staple food for over half of the global population, exhibits significant diversity in grain shape characteristics, which impact not only appearance and milling quality but also grain weight and yield. Identifying genes and loci underlying these traits is crucial for improving rice breeding programs. Previous studies have identified multiple quantitative trait loci (QTLs) and genes regulating grain length, width, and length-width ratio; however, further investigation is necessary to elucidate their regulatory pathways and their practical application in crop improvement.MethodsThis study employed a genome-wide association study (GWAS) on 280 japonica rice varieties from northern China to decipher the genetic basis of grain shape traits. Phenotyping included measurements of 11 grain-related traits, such as grain length, width, and area, along with their brown and white rice counterparts. High-density single nucleotide polymorphism (SNP) markers (33,579) were utilized for genotyping, and GWAS was performed using a mixed linear model (MLM) incorporating principal component analysis (PCA) and kinship (K) matrix to account for population structure and relatedness.ResultsOur analysis detected 15 QTLs associated with the 11 grain shape traits, of which five major QTL clusters emerged as crucial. Candidate genes, including LOC_Os01g50720 (qGL1), OsMKK4 (LOC_Os02g54600, influencing qBA2, qWL2, and qWA2), GW5 (LOC_Os05g09520, controlling qGW5, qBW5, qBR5, qWW5, and qWR5), GW6a (LOC_Os06g44100, associated with qGW6, qBW6, qBR6, qWW6, and qWR6), and FZP (LOC_Os07g47330, linked to qWL7), were identified based on functional annotations and haplotype analysis. These findings offer valuable insights into the genetic mechanisms underlying rice grain shape and suggest promising targets for marker-assisted selection to enhance rice quality and yield. creator: Hongwei Chen creator: Xue Zhang creator: Shujun Tian creator: Hong Gao creator: Jian Sun creator: Xiu Pang creator: Xiaowan Li creator: Quanying Li creator: Wenxiao Xie creator: Lili Wang creator: Chengwei Liang creator: Guomin Sui creator: Wenjing Zheng creator: Zuobin Ma uri: https://doi.org/10.7717/peerj.18746 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Incidence and risk factors of hepatitis E virus infection in women with gynecological tumors in Eastern China link: https://peerj.com/articles/18747 last-modified: 2024-12-18 description: BackgroundRecently, there has been increasing interest in the exploration of the association between the hepatitis E virus (HEV) infection and malignancies; however, epidemiological data for HEV infection among women with a gynecological tumors (GT) are limited. Herein, we investigated the correlation between HEV and GT in Chinese women.MethodsWe recruited 452 women diagnosed with a primary GT and 452 healthy volunteers to investigate the possible routes and risk factors for HEV infection. The serum antibody levels of anti-HEV IgG and IgM were measured by enzyme-linked immunoassays once a year.ResultsAfter a median follow-up time of 5.4 years (range 4 to 7 years), the overall detection rate of anti-HEV antibodies in patients with GT and in controls were 69/452 (15.27%) and 23/452 (5.09%) (P = 0.001), respectively. The seroprevalence of anti-HEV IgG antibodies was significant higher in patients with GT (15.27%) than in healthy controls (5.09%) (P = 0.001). Moreover, 13 (2.88%) patients with GT were positive for IgM antibodies, while only 4 (0.88%) healthy controls tested positive for anti-HEV IgM antibodies (P = 0.028). The highest prevalence of HEV antibodies were detected in patients with ovarian borderline tumors (40%), followed by patients with ovarian cancer (20.54%) and endometrial cancer (18.46%). Multivariable analysis revealed that contact with dogs (OR, 1.88; 95% CI [1.10–3.22]; P = 0.015) and a history of anti-tumor chemotherapy (OR, 1.85; 95% CI [1.07–3.20]; P = 0.028) were independent risk factors for HEV infection.ConclusionOverall, the present study showed that patients with GT are more susceptible to HEV infection in Eastern China, particularly in patients with ovarian borderline tumors. Thus, effective strategies are needed to reduce HEV infection in patients with GT. creator: Wenye Bai creator: Xiao Wu creator: Shuchao Zhao creator: Yang Yu creator: Zhongjun Wang creator: Xiu Li creator: Na Zhou uri: https://doi.org/10.7717/peerj.18747 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bai et al. title: Antimicrobial activity of Ruta angustifolia L. Pers against periodontal pathogen: Porphyromonas gingivalis link: https://peerj.com/articles/18751 last-modified: 2024-12-18 description: BackgroundPorphyromonas gingivalis is widely recognised as a periodontal pathogen. In recent years, there has been growing interest in the use of medicinal plant extracts as alternative treatments for periodontitis to combat the emergence of antibiotic-resistant bacteria. Ruta angustifolia L. Pers has been traditionally used to treat various ailments, including oral bacterial infections. However, the antimicrobial potential of R. angustifolia extracts against the periodontal pathogen P. gingivalis remains unexplored. Hence, the aim of this study was to investigate the antimicrobial activity of R. angustifolia extracts against P. gingivalis.MethodsThe antimicrobial activity of R. angustifolia extracts (crude methanol, hexane and chloroform fractionated extracts) against P. gingivalis was evaluated using the well diffusion method. Additionally, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined. Biofilm biomass assessment and live/dead cell viability assays were performed to analyse the effect of R. angustifolia extracts. Ultrastructural morphological changes in P. gingivalis cells were determined using field emission scanning electron microscopy (FE-SEM).ResultsIt was found that P. gingivalis was susceptible to R. angustifolia extracts, with the chloroform fractionated extract exhibiting the highest inhibition zones. The MIC and MBC of chloroform fractionated extract were determined to be 6.25 mg/mL which substantially reduced P. gingivalis biofilm biomass. Live/dead cell viability assays showed the highest percentage of dead P. gingivalis cells after 48 h of incubation. FE-SEM confirmed that the chloroform fractionated extract effectively damaged the bacterial cell wall and altered the ultrastructural morphology of P. gingivalis.ConclusionThe results indicated that extracts of R. angustifolia has the potential to be used as an alternative treatment in addition to conventional periodontal therapies. creator: Husna Hazirah Bakri creator: Syarifah Nur Syed Abdul Rahman creator: Zarith Safinaz Dol Bakri creator: Elly Munadziroh creator: Wan Himratul Aznita Wan Harun uri: https://doi.org/10.7717/peerj.18751 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bakri et al. title: Non-obese non-alcoholic fatty liver disease and the risk of chronic kidney disease: a systematic review and meta-analysis link: https://peerj.com/articles/18459 last-modified: 2024-12-17 description: BackgroundData on risk of developing chronic kidney disease (CKD) between non-obese and obese non-alcoholic fatty liver disease (NAFLD) patients are limited. We aimed to reveal the risk difference of incident CKD between non-obese and obese NAFLD patients.MethodsWe searched PubMed, Embase, and Web of Science databases for studies which reported the incidence of CKD in non-obese and obese NAFLD from inception to 10 March 2024. The primary and secondary outcomes were pooled. Subgroup analysis was used to examine the heterogeneity.ResultsA total of 15 studies were incorporated. The incidence of CKD in non-obese and obese NAFLD were 1,450/38,720 (3.74%) and 3,067/84,154 (3.64%), respectively. Non-obese NAFLD patients had a comparable risk of CKD as obese NAFLD (odds ratio [OR] 0.92, 95% confidence interval [95% CI] [0.72–1.19], I2 = 88%). No differences in estimated glomerular filtration rate and serum creatinine between non-obese and obese NAFLD were found. The mean differences (MD) and 95% CI were 0.01 [−0.02 to 0.04] and 0.50 [−0.90 to 1.90], respectively. In subgroup analyses, non-obese NAFLD had higher eGFR when diagnosed with ultrasound (MD 1.45, 95% CI [0.11–2.79], I2 = 21%). Non-obese NAFLD had higher creatinine in non-Asian (MD 0.06, 95% CI [0.01–0.11], I2 = 55%) and when taking BMI > 30 as the criterion for obesity (MD 0.06, 95% CI [0.00–0.12], I2 = 76%). The occurrence of CKD did not differ when non-obese NAFLD were categorized into overweight and normal-weight types.ConclusionsNon-obese NAFLD patients experienced the same risk of CKD compared to obese NAFLD. creator: Yixian You creator: Xiong Pei creator: Wei Jiang creator: Qingmin Zeng creator: Lang Bai creator: Taoyou Zhou creator: Xiaoju Lv creator: Hong Tang creator: Dongbo Wu uri: https://doi.org/10.7717/peerj.18459 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 You et al. title: Coral reef rehabilitation following Hurricane Irma using nano-engineered artificial reefs in Sint Maarten link: https://peerj.com/articles/18487 last-modified: 2024-12-17 description: Artificial reefs are being increasingly deployed as a coral reef restoration strategy. Additional reef habitats made from conventional substrates (e.g., metal, concrete, etc.) have had limited success in addressing conservation objectives on degraded coral reefs due to structure size and lack of standardized monitoring, and inability to enhance select ecological, and species variables. Technological advances and new restoration methods must be quickly tested and applied on a large scale to curb further deterioration of coral reefs. Here, we present the results of the first deployment of Oceanite artificial reefs (ARs). We compare the composition of the benthic community and associated fish assemblages on Oceanite ARs 14 months after deployment in a marine protected area (MPA) and two unprotected sites in Philipsburg, Sint Maarten. We also examined fish abundance and behaviour on the ARs. The initial results from this pilot study suggest that Oceanite mineral matrices can enhance local biodiversity, attract coral recruits, provide food and protection for large fish communities, and develop an early stage, healthy coral reef community in 14 months. We suggest that further research and testing of Oceanite capabilities will allow us to develop site-, species-, and function-specific nanotechnology-enabled substrates to optimize AR conservation goals. Oceanite mix designs can be tuned to precise parameters to promote reef restoration and stressor mitigation (e.g., pH, leachate emissions, surface texture, porosity, void structure, and hydrophobic, heat-absorbing, and disease-fighting properties). Using both bottom-up and top-down restoration processes, we suggest that deploying bio-enhancing habitats with targeted microclimate stressor treatments on the world’s critical reefs will allow to build global refuges resilient to climate change and provide much needed ecosystem services. creator: Emily Higgins creator: Kyralai Duppel creator: Megan Connell creator: Guyon Brenna creator: Konstantin Sobolev uri: https://doi.org/10.7717/peerj.18487 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Higgins et al. title: Prognostic value of inflammatory and nutritional indexes among patients with unresectable advanced gastric cancer receiving immune checkpoint inhibitors combined with chemotherapy—a retrospective study link: https://peerj.com/articles/18659 last-modified: 2024-12-17 description: BackgroundRecent studies have revealed that inflammatory factors and nutritional status of patients with advanced gastric cancer (AGC) are related to the efficacy of drug therapy and patient prognosis. This study seeks to evaluate the correlation between inflammatory markers, nutritional status, and clinical outcomes of immune checkpoint inhibitor (ICI)-based therapies among inoperable AGC patients.MethodThis retrospective study included 88 AGC patients who received ICIs combined with chemotherapy. Inflammatory and nutritional indicators from patients before and after two cycles of treatment were collected. Finally, the correlations between these indicators and the clinical response and survival of AGC patients with ICI treatment were examined.ResultsThe results revealed that an Eastern Cooperative Oncology Group performance status (ECOG PS) score of 0, neutrophil count to lymphocyte count ratio (NLR) < 2.84, platelet count to lymphocyte count ratio (PLR) < 82.23, lymphocyte count to monocyte count ratio ≥ 2.35, the hemoglobin, albumin, lymphocyte and platelet score (HALP) ≥ 31.17, prognostic nutritional index (PNI) ≥ 46.53, albumin ≥ 41.65, the decreased HALP group and the decreased PNI group were significantly correlated with improved objective response rate. Additionally, an ECOG PS score of 0, NLR < 2.84 and the decreased HALP group was associated with a superior disease control rate. Meanwhile, an ECOG PS score of 0 (progression-free survival (PFS): P = 0.003; overall survival (OS): P = 0.001) and decreased PLR following treatment (PFS: P = 0.011; OS: P = 0.008) were significant independent predictors of PFS and OS. Lastly, a systemic immune inflammation index ≥ 814.8 was also a positive independent predictor of OS among AGC patients.ConclusionOur study supports the potential of inflammatory and nutritional factors to serve as predictors of the efficacy and prognosis in patients undergoing ICI-based therapies for AGC. However, further investigations are necessary to validate these findings. creator: Meiqin Zhu creator: Lin-Ting Zhang creator: Wenjuan Lai creator: Fang Yang creator: Danyang Zhou creator: Ruilian Xu creator: Gangling Tong uri: https://doi.org/10.7717/peerj.18659 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhu et al. title: The relationship between mitochondrial DNA haplotype and its copy number on body weight and morphological traits of Wuliangshan black-bone chickens link: https://peerj.com/articles/17989 last-modified: 2024-12-16 description: Mitochondria play a pivotal role as carriers of genetic information through their circular DNA molecules. The rapid evolution of the D-loop region in mitochondria makes it an ideal molecular marker for exploring genetic differentiation among individuals within species and populations with close kinship. However, the influence of mtDNA D-loop region haplotypes and mtDNA copy numbers on phenotypic traits, particularly production traits in chickens, remains poorly understood. In this comprehensive study, we conducted D-loop region amplification and sequencing in the blood mitochondria of 232 female Wuliangshan black-bone chickens. Our investigation identified a total of 38 haplotypes, with a focus on 10 haplotypes that included more than five individuals. We meticulously analyzed the correlations between these haplotypes and a range of traits, encompassing body weight, tibial length, tibial circumference, body oblique length, chest width, and chest depth. The results unveiled significant disparities in specific tested traits across different haplotypes, indicating a tangible association between mtDNA haplotypes and traits in chickens. These findings underscore the potential impact of mitochondrial DNA variations on energy metabolism, ultimately leading to divergent chicken phenotypes. Furthermore, our examination revealed positive correlations between mtDNA copy numbers and tested traits for select haplotypes, while other haplotypes exhibited non-uniform relationships between traits and mtDNA copy numbers. In addition, phylogenetic analysis disclosed the involvement of two subspecies of red jungle chicken in the origin of Wuliangshan black-bone chickens. Consequently, our research contributes novel insights into mitochondrial genomic selection, augments comprehension of the roles played by haplotypes and mtDNA copy numbers in chicken population genetics and phylogenetic analysis, and furnishes fundamental data crucial for the preservation and provenance determination of black-bone chickens. creator: Wenpeng Li creator: Zhen Yang creator: Chao Yan creator: Siyu Chen creator: Xingbo Zhao uri: https://doi.org/10.7717/peerj.17989 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Hydrogen gas inhalation prior to high-intensity training reduces attenuation of nitric oxide bioavailability in male rugby players link: https://peerj.com/articles/18503 last-modified: 2024-12-16 description: BackgroundInhalation of hydrogen gas (H2) as an antioxidant supplement may alleviate exercise-induced oxidative damage and protect post-exercise hydrogen peroxide signaling, which may help mediate beneficial exercise adaptation. The aims of this study were to determine the effects of H2 inhalation on plasma nitric oxide (NO) level and its synthesis precursor in professional athletes.MethodsA randomized, placebo-controlled, double-blind, crossover trial was conducted with professional male rugby players for 3 weeks. Participants underwent 1 week of H2 supplementation and 1 week of placebo treatment prior to daily sessions of high-intensity exercise training, separated by 1 week of low-intensity training as a washout.ResultsTwo-way (supplementation and time) repeated-measures analyses of variance showed that NO, L-arginine, and tetrahydrobiopterin levels in the H2 inhalation group were significantly higher than those in the placebo group after exercise (D6) and remained higher after 24 h of rest (D7). Levels of hydroxydeoxyguanosine and interleukin 6 were lower in the H2 inhalation week than in the placebo week on D6 and D7. In addition, total antioxidant levels were significantly higher with H2 inhalation than with placebo.SignificanceThese results suggest that H2 inhalation helps to maintain NO signaling after exercise and to alleviate inflammation and oxidative stress induced by high-intensity exercise training in professional athletes. creator: Yuqi Zhao creator: Chaoqun Li creator: Shi Zhou creator: Zhiguang Xu creator: Xin Huang creator: Li Wen uri: https://doi.org/10.7717/peerj.18503 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhao et al. title: Characteristics, source apportionment and health risks of indoor and outdoor fine particle-bound polycyclic aromatic hydrocarbons in Jinan, North China link: https://peerj.com/articles/18553 last-modified: 2024-12-16 description: To investigate the pollution characteristics of polycyclic aromatic hydrocarbons (PAHs) indoors and outdoors and their influencing factors, PM2.5 samples were systematically collected from both environments in Jinan during the summer and autumn seasons. During the observation period, the concentration of ∑ 19PAHs was 18.57 ± 10.50 ng/m3 indoors and 23.79 ± 16.13 ng/m3 outdoors. Most PAHs exhibited indoor-to-outdoor (I/O) ratios less than 1, indicating that indoor PAHs were primarily derived from the infiltration of outdoor sources. Correlation analysis underscored the significant influence of temperature on both outdoor concentrations and I/O ratios of PAHs. By utilizing diagnostic ratios and principal component analysis (PCA), vehicle emissions were identified as the predominant source of outdoor PAHs. Our study found that the toxic equivalents of benzo[a]pyrene (TEQBaP) values exceeded the European Commission’s standard of 1 ng/m3, with indoor values at 2.78 ng/m3 and outdoor values at 3.57 ng/m3. Moreover, the total incremental lifetime cancer risk (ILCRTotal) associated with exposure to PM2.5-bound PAHs surpassed the acceptable level of 10E-6, indicating potential adverse health effects. These results underscore the urgent necessity for more stringent regulatory measures to reduce PAH emissions. Additionally, our findings provide valuable insights into how environmental factors shape the relationship between indoor and outdoor PAHs. creator: Xiaomei Gao creator: Ziyi Wang creator: Xiaoyan Sun creator: Weidong Gao creator: Wei Jiang creator: Xi Wang creator: Fenfen Zhang creator: Xinfeng Wang creator: Lingxiao Yang creator: Yang Zhou uri: https://doi.org/10.7717/peerj.18553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gao et al. title: Length-mass relationships of pond macroinvertebrates do not hold between Southern and Northern Europe link: https://peerj.com/articles/18576 last-modified: 2024-12-16 description: The lack of reliable data on length-mass relationships, essential to obtain accurate biomass estimates, limits our ability to easily assess secondary production by aquatic invertebrates. In the absence of published equations from similar habitat conditions, authors often borrow equations developed in geographic regions with different climate conditions, which may bias biomass estimates. A literature overview of published size-mass relationships for Portugal and Sweden highlights the need for further data within these biogeographic regions. We increased the number of equations available to Southern and Northern Europe, developing 18 new length-mass relationships for two families and 10 genera in Portugal and Sweden. All equations were published for the first time for these countries, except the genus Asellus. Our length-mass relationships were obtained from specimens collected on a one-time sampling of eight ponds in Portugal and five ponds in Sweden during late spring in 2023. Dry mass (DM) was modelled as a function of body length (BL), using the natural log-linear function with a power model (ln DM = ln a + b × ln BL). The equations obtained were compared with linear mixed models testing the fixed effects of “body length” and “country”, as well as their interaction. A comparison of the equations developed in this study showed country-specific differences for all taxa, expect the genus Caenis, indicating a low potential transferability of the equations between Southern and Northern Europe. In contrast, the comparison of the equation obtained for A. aquaticus in this study with an equation published for this taxon in Sweden showed great similarities, suggesting a high transferability. Recommending caution in the borrowing of published length-mass equations, that can differ drastically between different geographic and climatic regions, especially at larger sizes, we provide a series of guidelines and good practices in this field. creator: Vladimíra Dekanová creator: Marek Svitok creator: Sara Bento creator: João Caramelo creator: Pedro Peixe e Sousa creator: Bruno M. Carreira uri: https://doi.org/10.7717/peerj.18576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dekanová et al. title: Charting the global footprint of borderline oxacillin-resistant Staphylococcus aureus (BORSA): the first systematic review and meta-analysis link: https://peerj.com/articles/18604 last-modified: 2024-12-16 description: Borderline oxacillin-resistant Staphylococcus aureus (BORSA) has been a persistent yet under-researched concern in the realm of antibiotic resistance, characterized by unique resistance mechanisms and potential for severe infections. This systematic review and meta-analysis consolidates data from 29 studies encompassing 18,781 samples, revealing a global BORSA prevalence of 6.6% (95% CI [4.0–10.7]). The highest prevalence was found in animals (46.3%), followed by food (8.9%), and humans (5.1%). Notably, significant regional disparities were observed, with Brazil exhibiting the highest prevalence at 70.0%, while The Netherlands reported just 0.5%. These findings underscore the multifaceted nature of BORSA epidemiology, influenced by local antibiotic usage practices and healthcare infrastructures. The analysis also reveals substantial heterogeneity (I2 = 96.802%), highlighting the need for improved reporting practices and tailored surveillance protocols that account for the specific contexts of each study. As antibiotic resistance continues to escalate, understanding BORSA’s global footprint is crucial for informing targeted interventions and optimizing antibiotic stewardship programs. This study fills critical gaps in current knowledge of BORSA and highlights the need for coordinated efforts among researchers, healthcare providers, and policymakers to develop effective strategies for addressing the rising threat of antibiotic-resistant pathogens like BORSA, including further exploration of its genetic and phenotypic characteristics. creator: Engku Nur Syafirah Engku Abd Rahman creator: Ahmad Adebayo Irekeola creator: Dina Yamin creator: Abdirahman Hussein Elmi creator: Yean Yean Chan uri: https://doi.org/10.7717/peerj.18604 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Engku Abd Rahman et al. title: Comparative effectiveness and safety of Angio-Seal and StarClose vascular closure devices: a systematic review and meta-analysis link: https://peerj.com/articles/18652 last-modified: 2024-12-16 description: ObjectiveThis systematic review and meta-analysis aims to evaluate the effectiveness and safety of Angio-Seal and StarClose vascular closure devices (VCDs) in achieving hemostasis after interventional surgery.MethodsRandomized controlled trials (RCTs) and observational studies comparing Angio-Seal and StarClose were identified through systematic searches. Data on vascular closure success rate, complication rates, hematoma formation, pseudoaneurysm, arterial occlusion, and surgical intervention were extracted and pooled using a random effects model.ResultsNine studies met the inclusion criteria, total 5,466 patients. The meta-analysis revealed a slight, statistically significant difference in the success rate of vascular closure in favor of Angio-Seal (risk ratio (RR) 1.05, 95% confidence interval (CI) [1.00–1.09], p = 0.03). No significant difference was found in the overall complication rate, hematoma formation, pseudoaneurysm, arterial occlusion, or surgical intervention.ConclusionsAngio-Seal demonstrated a slightly higher success rate in vessel closure compared to StarClose. Both devices had a comparable safety profile with no significant differences in major complications. creator: Kun Lai creator: Jingquan Chen creator: Qiang Tan creator: Lan Luo uri: https://doi.org/10.7717/peerj.18652 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lai et al. title: Identification of chromosome ploidy and karyotype analysis of cherries (Prunus pseudocerasus Lindl.) in Guizhou link: https://peerj.com/articles/18668 last-modified: 2024-12-16 description: The present study aimed to characterize the chromosome features of cherry (Prunus pseudocerasus Lindl.) germplasm in Guizhou Province, China, in order to facilitate the selection and breeding programs of this economically and ornamentally valuable species. The stem tip chromosome preparation technique was employed for ploidy identification and karyotype analysis, and the results were further validated by flow cytometry. The findings revealed that the 28 cherry accessions from Guizhou province exhibited a chromosomal base of x = 8, comprising 19 tetraploid and nine hexaploid individuals. Karyotype analysis showed two chromosome types, “m” and “sm,” with the longest chromosome/shortest chromosome (Lc/Sc) ranging from 1.6 to 2.65, the mean arm ratio (MAR) varying from 1.15 to 1.56, and index of the karyotypic asymmetry (As.K) ranging from 53.74 to 61.6. Three karyotype types, “1A,” “1B,” and “2B,” were identified among the studied accessions. The most evolutionarily advanced accession was HZ152, while DCZC27 represented the most primitive karyotype. This study expands the ploidy database of Chinese cherry and provides valuable information for the conservation and utilization of cherry germplasm resources in Guizhou province. creator: Nian Chen creator: Yali Wang creator: Mei He creator: Fei An creator: Jiyue Wang creator: Changmei Song uri: https://doi.org/10.7717/peerj.18668 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Association between hand grip strength and quality of life in children with cerebral palsy: a cross-sectional study link: https://peerj.com/articles/18679 last-modified: 2024-12-16 description: BackgroundCerebral palsy (CP) covers a wide range of causes and symptoms. It is characterized by persistent motor and postural dysfunction caused by a non-progressing pathological lesion of the immature brain. Development of fine motor skills, such as the ability to manipulate objects with smaller muscles, is crucial for a child’s development. It is evident that there is a lack of hand grip strength (HGS) and quality of life (QoL) data in children with CP compared to typically developed (TD) children. Understanding the relationship between these factors might help facilitate healthcare provision and provide insight into rehabilitation programs. The aim of this study is to investigate the relationship between HGS and health-related quality of life (HRQoL) in children with CP compared to TD children.MethodsAn experimental cross-sectional study was conducted and 60 children (30 CP and 30 TD) were chosen; age, gender, height, weight, body mass index, preferred hand, number of siblings, school attendance, and housing type data were collected. HGS was measured using a standard hand dynamometer, and HRQoL was measured using the KIDSCREEN-10 item questionnaire.ResultsThere was a statistically significant main effect of gender on the average HGS, F (1, 56) = 24.09, p < 0.001, and the KIDSCREEN-10 sum score, F (1, 56) = 8.66, p < 0.001, and the main effect of group on the KIDSCREEN-10 sum score, F (1, 56) = 17.64, p < 0.001. A significant correlation between HGS and the KIDSCREEN-10 sum score in the CP group (r = 0.35, p = 0.03), and the TD group (r = 0.56, p = 0.001).ConclusionHGS was lower in children with CP, and girls had significantly lower HGS compared to boys in both groups, CP and TD children. HRQoL was significantly lower in children with CP, with boys reporting higher HRQoL on the KIDSCREEN-10 questionnaire compared to girls. Our data showed that the higher the KIDSCREEN-10 sum score is, the stronger the HGS of children in both groups. The results of this study indicate that hand grip strength may significantly impact the QoL of children with CP. A correlation between HGS and HRQoL points to the importance of improving strength in children with CP through interventions and directed rehabilitation programs. creator: Mshari Alghadier creator: Nada Almasoud creator: Dalia Alharthi creator: Omar Alrashdi creator: Reem Albesher uri: https://doi.org/10.7717/peerj.18679 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Alghadier et al. title: Ontogenetic feeding shifts in two thresher shark species in the Galapagos Marine Reserve link: https://peerj.com/articles/18681 last-modified: 2024-12-16 description: BackgroundThe morphology and hunting behavior of thresher sharks make them easily distinguishable. These species are distributed across the Tropical Pacific Ocean feeding on squid and small fish. However, ontogenetic changes in their feeding strategies and habitat use are still unknown in this region.MethodsWe examined the δ13C and δ15N signatures in vertebral collagen from populations of Alopias pelagicus and Alopias superciliosus inhabiting the Galapagos Marine Reserve, focusing on three maturity stages: neonate, juvenile and adult. The vertebrae samples were taken from the seizure of illegal fishing activities carried out by a foreign fleet within the Galapagos archipelago. A total of thirty-three vertebrae from A. pelagicus and twenty-one from A. superciliosus were analyzed.ResultsBoth species displayed significant differences in their δ15N values (p < 0.001), but not in δ13C (p = 0.230), suggesting a similar habitat use, but different prey consumption. Throughout their ontogeny, A. pelagicus displayed isotopic differences (p < 0.001), where neonates showed lower δ13C values and higher δ15N values compared to juveniles, probably because they still reflect the isotopic signatures of their mothers even after the first year of life. This study highlights trophic differences between both species, accompanied by an ontogenetic variation in A. pelagicus, aspects that allow us to understand the role of these species within the dynamics of the Eastern Tropical Pacific ecosystem. creator: Camila Arnés-Urgellés creator: Felipe Galván-Magaña creator: Fernando R. Elorriaga-Verplancken creator: Antonio Delgado-Huertas creator: Diego Páez-Rosas uri: https://doi.org/10.7717/peerj.18681 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Arnés-Urgellés et al. title: Analysis of the current status of knowledge, attitudes, and practices among stroke-related healthcare professionals in the treatment of shoulder pain in hemiplegic patients link: https://peerj.com/articles/18684 last-modified: 2024-12-16 description: ObjectiveTo investigate the current status of knowledge, attitude, and practice (KAP) of healthcare professionals in stroke-related departments of primary-level tertiary hospitals regarding the prevention and treatment of hemiplegic shoulder pain, and to analyze influencing factors. This aims to provide a reference for further training, guidance, and management of hemiplegic shoulder pain.MethodsA total of 123 healthcare professionals from stroke-related departments of two tertiary hospitals in a county-level city in Zhejiang province were selected as the research subjects from March 6, 2023, to March 14, 2023. Written informed consent was obtained from all study participants prior to their inclusion in the study. A questionnaire survey was conducted to assess their KAP status on the prevention and treatment of hemiplegic shoulder pain, and statistical analysis was performed using SPSS 23.ResultsThe scores for knowledge (29.97 ± 9.94), attitude (27.7 ± 2.81), and behavior (29.86 ± 7.86) among the 123 healthcare professionals indicated that department and position were influencing factors for KAP (P < 0.05).ConclusionThe overall KAP of healthcare professionals in stroke-related departments of primary hospitals regarding the prevention and treatment of hemiplegic shoulder pain needs improvement. Strengthening relevant knowledge and skills training is necessary to reduce the incidence of hemiplegic shoulder pain and improve patients’ quality of life. creator: Bin Huang creator: Feng Gao uri: https://doi.org/10.7717/peerj.18684 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Huang and Gao title: Prevalence of Theileria ovis in sheep and goats in northwestern Saudi Arabia with notes on potential vectors link: https://peerj.com/articles/18687 last-modified: 2024-12-16 description: The prevalence of Theileria spp. infecting sheep and goats were investigated in two cities and surroundings in northwest Saudi Arabia. Blood samples from 403 sheep and goats from Madina (n = 201) and Tabuk (n = 202) cities (177 from sheep and 226 from goats) were investigated. Blood samples were examined microscopically for the presence of intraerythrocytic bodies suggestive of Theileria as well as they were investigated using molecular techniques. DNA was extracted from blood and ticks and subjected to polymerase chain reaction amplification using specific primers. The primers used amplified a fragment of the 18S rRNA region (450 bp) targeting the hypervariable region IV. A total of 63 ticks belonging to five species were collected from sheep and goats for determination of their involvement of lifecycle of Theileria. Ticks were identified morphologically and confirmed molecularly utilizing cytochrome oxidase C subunit 1 gene (COXI) amplification. The results indicated that: microscopic examination revealed 24 (6%) of the samples investigated showed intraerythrocytic bodies suggestive of Theileria. Positive samples were only obtained from sheep whereas goats yielded negative results. A total of 33 (18.6%) sheep samples were positive for Theileria infection using polymerase chain reaction targeting the partial 18S rDNA and DNA sequencing. Theileria infection was more prevalent in animals that were less than 2 years of age compared with older animals. There was no difference in the prevalence of the infection between male and female sheep in both cities. All positive sheep were detected during the summer and none of the samples collected during the winter were positive. Phylogenetic analysis revealed that the sequences obtained from Theileria species reported in the present study grouped with sequences from Theileria ovis from different countries. Ticks were identified as Hyalomma dromedarii, Hyalomma, marginatum, Hyalomma impeltatum and Hyalomma anatolicum anatolicum. T. ovis DNA was detected from Hyalomma dromedarii and Hyalomma impeltatum suggesting that they are potential vectors of this piroplasm in sheep from Madina and Tabuk cities. This report is considered the first report of T. ovis infecting sheep from Madina and Tabuk, furthermore, it is the first report determining the vectors responsible for transmission of the infection in sheep in northwest Saudi Arabia. The data generated from this study will undoubtedly pave the way for the detection and control of ovine and caprine theileriosis in Madina and Tabuk regions. creator: Ruoa S. Almahallawi creator: Sawsan A. Omer creator: Esam M. Al-Shaebi creator: Nawal Al-Hoshani creator: Esam S. Al-Malki creator: Rewaida Abdel-Gaber creator: Osama B. Mohammed uri: https://doi.org/10.7717/peerj.18687 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Almahallawi et al. title: Analysis of the characteristic patterns and risk factors impacting the severity of intraoperative hypothermia in neonates link: https://peerj.com/articles/18702 last-modified: 2024-12-16 description: BackgroundAlthough maintaining a stable body temperature during the perioperative period is crucial for the recovery of neonates, hypothermia frequently occurs during surgical procedures in this vulnerable population. A comprehensive analysis of intraoperative details, including medical history and monitoring, is therefore essential for understanding temperature variations and identifying risk factors for severe hypothermia.ObjectiveIn this study, we delineated the characteristic patterns of intraoperative temperature fluctuations in neonates and determined the risk factors impacting the severity of hypothermia.MethodsWe conducted a retrospective, single-center study, enrolling 648 subjects who underwent surgery under general anesthesia and collected demographic, perioperative, and intraoperative data.ResultsIntraoperative hypothermia occurred in 79.17% of the neonates. Significant risk factors for severe hypothermia included surgery type (OR, 1.183; 95%, CI [1.028–1.358]; p = 0.018), preoperative weight (OR, 0.556; 95% CI [0.412–0.748]; p < 0.01), infusion and transfusion volume (mL/kg) (OR, 1.011; 95% CI [1.001–1.022]; p = 0.018), and duration of hypothermia (OR, 1.011; 95% CI [1.007–1.014]; p < 0.01). Preterm neonates experienced a greater temperature drop than did full-term neonates. The nadir of intraoperative temperature occurred approximately 90 min after surgery, followed by a brief stabilization period and a slow recovery process.ConclusionThe significant incidence of intraoperative hypothermia in neonates highlights the need for efficient strategies that reduce both the frequency and severity of this condition. creator: Kun Dai creator: Yuanling Liu creator: Lijiao Qin creator: Jiaxuan Mai creator: Jingjing Xiao creator: Jing Ruan uri: https://doi.org/10.7717/peerj.18702 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dai et al. title: Insights and progress on the biosynthesis, metabolism, and physiological functions of gamma-aminobutyric acid (GABA): a review link: https://peerj.com/articles/18712 last-modified: 2024-12-16 description: GABA (γ-aminobutyric acid) is a non-protein amino acid that occurs naturally in the human brain, animals, plants and microorganisms. It is primarily produced by the irreversible action of glutamic acid decarboxylase (GAD) on the α-decarboxylation of L-glutamic acid. As a major neurotransmitter in the brain, GABA plays a crucial role in behavior, cognition, and the body’s stress response. GABA is mainly synthesized through the GABA shunt and the polyamine degradation pathways. It works through three receptors (GABAA, GABAB, and GABAC), each exhibiting different pharmacological and physiological characteristics. GABA has a variety of physiological roles and applications. In plants, it regulates growth, development and stress responses. In mammals, it influences physiological functions such as nervous system regulation, blood pressure equilibrium, liver and kidneys enhancement, hormone secretion regulation, immunity enhancement, cancer prevention, as well as anti-aging effects. As a biologically active ingredient, GABA possesses unique physiological effects and medicinal value, leading to its widespread application and substantially increased market demand in the food and pharmaceutical industries. GABA is primarily produced through chemical synthesis, plant enrichment and microbial fermentation. In this review, we first make an overview of GABA, focusing on its synthesis, metabolism, GABA receptors and physiological functions. Next, we describe the industrial production methods of GABA. Finally, we discuss the development of ligands for the GABA receptor binding site, the prospects of GABA production and application, as well as its clinical trials in potential drugs or compounds targeting GABA for the treatment of epilepsy. The purpose of this review is to attract researchers from various fields to focus on GABA research, promote multidisciplinary communications and collaborations, break down disciplinary barriers, stimulate innovative research ideas and methods, and advance the development and application of GABA in medicine, agriculture, food and other fields. creator: Qingli Zhang creator: Lei Zhu creator: Hailong Li creator: Qu Chen creator: Nan Li creator: Jiansheng Li creator: Zichu Zhao creator: Di Xiao creator: Tingting Tang creator: Chunhua Bi creator: Yan Zhang creator: Haili Zhang creator: Guizhen Zhang creator: Mingyang Li creator: Yanli Zhu creator: Jingjing Zhang creator: Jingjing Kong uri: https://doi.org/10.7717/peerj.18712 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Diversity and habitat preferences of bdelloid rotifers in mosses and liverworts from beach forest along sand dunes in Thailand link: https://peerj.com/articles/18721 last-modified: 2024-12-16 description: Microscopic animals are often thought to be widely distributed due to their small size and specific adaptations. However, evidences show that bdelloid rotifers in bryophytes exhibit habitat specialization, with species composition varying by microhabitat. This indicates that their distribution is influenced by complex ecological processes, warranting further research, particularly at the microscale. In this study, we tested whether species richness and composition of bdelloid rotifers differ across bryophyte species, forms, characteristics, and seasons to understand their ecological distribution and habitat preferences in limnoterrestrial environments. Bdelloid rotifers were identified and counted from bryophyte samples collected in April (low rainfall), August (moderate rainfall), and December 2022 (high rainfall) at Bang Burd Beach Forest, Chumphon Province, Thailand. The results revealed high bdelloid diversity, with 22 species identified, 14 of which are new records for Thailand, raising the known number to 30. However, species richness did not vary across bryophyte variables or seasons, with substantial overlap in species composition across these variables. Additionally, there was no strong habitat preference between bdelloid rotifers and bryophyte species. These results confirm a low degree of habitat specialization of bdelloid rotifers in tropical limnoterrestrial environments. creator: Sittikron Jattupan creator: Rapeepan Jaturapruek creator: Phannee Sa-ardrit creator: Janejaree Inuthai creator: Chatchai Ngernsaengsaruay creator: Supiyanit Maiphae uri: https://doi.org/10.7717/peerj.18721 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jattupan et al. title: Beeswax waste improves the mycelial growth, fruiting body yield, and quality of oyster mushrooms (Pleurotus ostreatus) link: https://peerj.com/articles/18726 last-modified: 2024-12-16 description: Heilongjiang Province has the third largest bee population in China, producing over 2,000 tons of beeswax waste (BW) each year. Most of this BW is discarded or burned. Therefore, we urgently need to find sustainable applications of BW. Pleurotus ostreatus mushrooms, commonly referred to as oyster mushrooms, are cultivated for both food and medicine. The substrate used to grow P. ostreatus mushrooms often contains wheat bran as a nitrogen source. The goal of this study was to explore the feasibility of substituting this wheat bran with BW to cultivate P. ostreatus mushrooms. Five treatments were established, with BW making up 0%, 3%, 5%, 7%, and 9% of the total substrate, and the effects on the mycelial growth and development, biological efficiency (BE), and yield were evaluated along with changes in the chemical biomass composition of the fruiting bodies. Adding BW increased the number of days needed for primordia initiation and the number of days between flushes of P. ostreatus mushrooms. With increasing BW, the total fresh weight of P. ostreatus mushrooms first increased and then decreased. The 5% BW treatment resulted in the highest yield and biological efficiency (BE) of 1,478.96 ± 9.61 g bag−1 and 92.43 ± 0.60%, respectively, which exceeded the values of the control by 4.14% (control: 1,420.15 ± 9.53 g bag−1 and 88.76 ± 0.60%, respectively). The 5% BW treatment also resulted in the highest mushroom crude protein content (23.47 ± 0.18 g 100 g−1), which was 28.18% higher compared with the control (18.31 ± 0.05 g 100 g−1). The 9% BW treatment resulted in the highest crude polysaccharide content (10.33 ± 0.76 g 100 g−1), which was 2.42-fold that of the control (4.26 ± 0.30 g 100 g−1). This study suggests that BW could serve as an effective source of nitrogen to cultivate P. ostreatus. BW is a promising, cost-effective, and efficient additive to mushroom substrate, improving the yield and quality of P. ostreatus mushrooms while providing a sustainable use for an otherwise difficult to dispose of waste product. creator: Chunlei Pan creator: Chunge Sheng creator: Kang Wang creator: Yi Zhang creator: Chunguang Liu creator: Zhihao Zhang creator: Liang Tao creator: Yang Lv creator: Fuchao Gao uri: https://doi.org/10.7717/peerj.18726 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Pan et al. title: Correlation between hematological indicators in acclimatized high-altitude individuals and acute mountain sickness link: https://peerj.com/articles/18738 last-modified: 2024-12-16 description: BackgroundThe impact of acute mountain sickness (AMS) on individuals ascending to plateaus, soon after exposure to high altitudes, is well-documented. However, the specific relationship between AMS and alterations in blood parameters remains unclear.MethodsA total of 40 healthy volunteers were recruited. Following their arrival at an altitude of 3,300 m, an AMS questionnaire survey was administered 48 h later. Based on the AMS scores obtained, participants were categorized into three groups: non-AMS, mild AMS, and moderate/severe AMS (encompassing both moderate and severe cases). Blood routine tests were performed on all groups at 3-, 7-, and 30-days post-arrival at the plateau, with blood oxygen saturation tests conducted at 3 and 30 days after rapidly entering the plateau.ResultsIn the current investigation, a total of 40 participants were stratified into non-AMS (n = 24), mild-AMS (n = 8), and moderate/severe-AMS (n = 8) cohorts subsequent to rapid ascension to an altitude of 3,300 m. The incidence of AMS in this study was 40%. Noteworthy elevations in red blood cells (RBC), hemoglobin (Hb), and hematocrit (HCT) levels were noted at the 3-day mark post-ascent across all delineated groups. By the 7th day, the moderate/severe-AMS cohort displayed sustained increments in Hb and HCT levels, whereas solely HCT levels rose in the mild-AMS and non-AMS cohorts. Upon reaching the 30-day milestone, the moderate/severe-AMS group demonstrated a reduction in RBC, Hb, and HCT levels, while only HCT levels decreased in the mild-AMS and non-AMS groups. Furthermore, it was observed that all groups exhibited notable reductions in oxygen saturation (SpO2) at 3 days post-ascent, followed by a partial recovery at 30 days, albeit remaining below baseline levels. The correlation analysis results indicated that RBC, Hb, and HCT exhibited a positive correlation with the severity of AMS after a 7-day acclimatization period at high altitude. Conversely, SpO2 demonstrated a negative correlation with the severity of AMS following the same duration at high altitude. The findings of the study suggest a strong association between alterations in RBC, Hb, and HCT levels and AMS, particularly among individuals in the moderate/severe-AMS category who displayed more significant fluctuations in these parameters.ConclusionIndividuals suffering from moderate to severe AMS demonstrated increased levels of RBC, Hb, and HCT, as well as reduced SpO2, indicating a greater need for oxygen adaptation to high-altitude hypoxia. These findings emphasize the physiological adjustments to high altitudes and their potential implications for the treatment of AMS. creator: Zhicai Li creator: Jun Xiao creator: Cuiying Li creator: Xiaowei Li creator: Daoju Ren uri: https://doi.org/10.7717/peerj.18738 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: The association between fibroblast growth factor 21 with diabetes retinopathy among type 2 diabetes mellitus patients: a systematic review, meta-analysis, and meta-regression link: https://peerj.com/articles/18308 last-modified: 2024-12-13 description: BackgroundDiabetic retinopathy (DR), a leading cause of vision loss worldwide, is a common complication of type 2 diabetes mellitus (T2DM) driven by chronic hyperglycemia and microvascular damage. Fibroblast growth factor 21 (FGF21) is crucial in blood sugar regulation and has been linked to DR incidence and severity. While some studies suggest that FGF21 levels may contribute to the DR incidence, others propose a protective role. This discrepancy necessitates further analysis, prompting this study to evaluate the association between FGF21 levels and DR incidence and severity in T2DM patients.MethodsA systematic search was conducted through MEDLINE, Web of Science, Scopus, and Embase up to May 2024 for studies evaluating the association between FGF21 and DR incidence and severity. A random-effect model meta-analysis was performed to calculate the pooled standardized mean difference (SMD) and 95% confidence intervals (CI). A univariate meta-regression was performed to analyze factors influencing pooled size estimates. All statistical analyses were performed using STATA 17 software.ResultThis systematic review and meta-analysis of 5,852 participants revealed that FGF21 was positively correlated with DR (SMD 3.11; 95% CI [0.92–5.30], p = 0.005) and sight-threatening DR (STDR) incidence (SMD 3.61; 95% CI [0.82–6.41], p = 0.01). There was no significant difference in FGF21 levels in DR vs STDR (p = 0.79). Subgroup analysis revealed a significant difference in DR incidence between LDL groups, with higher DR incidence in the group with low-density lipoprotein (LDL) levels >100 (P < 0.00001). Meta-regression revealed no variables significantly influenced the pooled size estimates.ConclusionA higher level of FGF21 was associated with higher DR and STDR incidence among T2DM patients, highlighting its potential utilization as a biomarker for DR detection and enabling the exploration of FGF21-based treatment strategies. However, variables independently predicting DR among patients with elevated FGF21 levels shall be explored further.PROSPERO IDCRD42024559142. creator: Herni Basir creator: Annisa Salsabilla Dwi Nugrahani creator: Andi Makbul Aman creator: Syakib Bakri creator: Haerani Rasyid creator: Husaini Umar creator: Faridin H. P. creator: Andi Muhammad Ichsan creator: Andi Alfian Zainuddin uri: https://doi.org/10.7717/peerj.18308 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Basir et al. title: A machine learning approach for identifying anatomical biomarkers of early mild cognitive impairment link: https://peerj.com/articles/18490 last-modified: 2024-12-13 description: BackgroundAlzheimer’s Disease (AD) poses a major challenge as a neurodegenerative disorder, and early detection is critical for effective intervention. Magnetic resonance imaging (MRI) is a critical tool in AD research due to its availability and cost-effectiveness in clinical settings.ObjectiveThis study aims to conduct a comprehensive analysis of machine learning (ML) methods for MRI-based biomarker selection and classification to investigate early cognitive decline in AD. The focus to discriminate between classifying healthy control (HC) participants who remained stable and those who developed mild cognitive impairment (MCI) within five years (unstable HC or uHC).Methods3-Tesla (3T) MRI data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and Open Access Series of Imaging Studies 3 (OASIS-3) were used, focusing on HC and uHC groups. Freesurfer’s recon-all and other tools were used to extract anatomical biomarkers from subcortical and cortical brain regions. ML techniques were applied for feature selection and classification, using the MATLAB Classification Learner (MCL) app for initial analysis, followed by advanced methods such as nested cross-validation and Bayesian optimization, which were evaluated within a Monte Carlo replication analysis as implemented in our customized pipeline. Additionally, polynomial regression-based data harmonization techniques were used to enhance ML and statistical analysis. In our study, ML classifiers were evaluated using performance metrics such as Accuracy (Acc), area under the receiver operating characteristic curve (AROC), F1-score, and a normalized Matthew’s correlation coefficient (MCC′).ResultsFeature selection consistently identified biomarkers across ADNI and OASIS-3, with the entorhinal, hippocampus, lateral ventricle, and lateral orbitofrontal regions being the most affected. Classification results varied between balanced and imbalanced datasets and between ADNI and OASIS-3. For ADNI balanced datasets, the naíve Bayes model using z-score harmonization and ReliefF feature selection performed best (Acc = 69.17%, AROC = 77.73%, F1 = 69.21%, MCC’ = 69.28%). For OASIS-3 balanced datasets, SVM with zscore-corrected data outperformed others (Acc = 66.58%, AROC = 72.01%, MCC’ = 66.78%), while logistic regression had the best F1-score (66.68%). In imbalanced data, RUSBoost showed the strongest overall performance on ADNI (F1 = 50.60%, AROC = 81.54%) and OASIS-3 (MCC’ = 63.31%). Support vector machine (SVM) excelled on ADNI in terms of Acc (82.93%) and MCC’ (70.21%), while naïve Bayes performed best on OASIS-3 by F1 (42.54%) and AROC (70.33%).ConclusionData harmonization significantly improved the consistency and performance of feature selection and ML classification, with z-score harmonization yielding the best results. This study also highlights the importance of nested cross-validation (CV) to control overfitting and the potential of a semi-automatic pipeline for early AD detection using MRI, with future applications integrating other neuroimaging data to enhance prediction. creator: Alwani Liyana Ahmad creator: Jose M. Sanchez-Bornot creator: Roberto C. Sotero creator: Damien Coyle creator: Zamzuri Idris creator: Ibrahima Faye uri: https://doi.org/10.7717/peerj.18490 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ahmad et al. title: The bile acid metabolome in umbilical cord blood and meconium of healthy newborns: distinct characteristics and implications link: https://peerj.com/articles/18506 last-modified: 2024-12-13 description: ObjectiveTo characterize the bile acid metabolomic profiles of umbilical cord blood and meconium in healthy newborns.MethodsFifteen healthy newborns, which born in the Obstetrics Department of the Affiliated Hospital of Southwest Medical University between July 1 and August 31, 2023, were selected as study subjects. Umbilical cord blood and meconium samples were collected, and bile acid metabolomics were analyzed using ultra-high performance liquid chromatography-tandem mass spectrometry.ResultsThe ratio of primary to secondary bile acids in cord blood was significantly higher than in meconium [2.64 (2.49, 5.70) vs. 0.99 (0.37, 1.58), Z = −3.80, P < 0.05]. The ratio of unconjugated to conjugated bile acids was notably higher in cord blood than in meconium [0.14 (0.07, 0.18) vs. 0.01 (0.01, 0.04), Z = −3.88, P < 0.05]. The ratio of cholic acid to chenodeoxycholic acid in conjugated primary bile acids was significantly lower in cord blood than in meconium [0.59 (0.19, 0.75) vs. 2.21 (1.34, 3.04), Z = −4.21, P < 0.05], but the ratio of cholic acid to chenodeoxycholic acid in secondary bile acids was significantly higher in cord blood than in meconium [0.42 (0.21, 0.63) vs. 0.03 (0.01, 0.05), Z = −4.54, P < 0.05]. Only three primary bile acids (taurochenodeoxycholic acid, glycochenodeoxycholic acid, and glycochenodeoxycholic acid 3-glucoside in umbilical cord blood) were correlated with their downstream metabolites in meconium (with hyodesoxycholic acid (r = −0.66, P = 0.01), tauro-ω-muricholic acid (r = 0.52, P = 0.048) and ursodeoxycholic acid-7S (r = −0.53, P = 0.04), respectively). In meconium, most of primary bile acids were correlated with their downstream metabolites (P all < 0.05): cholic acid was positively correlated with 3-dehydrocholic acid, taurocholic acid was positively correlated with taurodeoxycholic acid and 3-dehydrocholic acid, glycocholic acid was positively correlated with 3-dehydrocholic acid, chenodeoxycholic acid was positively correlated with glycoursodeoxycholic acid, taurolithocholic acid, and 7-keto lithocholic acid and negatively correlated with isolithocholic acid. Taurochenodeoxycholic acid was positively correlated with taurohyodeoxycholic acid, tauroursodeoxycholic acid, glycoursodeoxycholic acid, taurolithocholic acid, tauro-ω-muricholic acid, and glycohyodeoxycholic acid, while glycochenodeoxycholic acid was positively correlated with tauroursodeoxycholic acid, glycoursodeoxycholic acid, taurolithocholic acid, and glycohyodeoxycholic acid, and negatively correlated with isolithocholic acid.ConclusionThe bile acid metabolites in umbilical cord blood and meconium differ significantly, and the downstream bile acid metabolites in meconium are predominantly correlated with their upstream bile acids in meconium, but not those bile acids in umbilical cord blood. These findings contribute to a better understanding of bile acid metabolism in utero and lay the foundation for future research in this topic. creator: Chunxia Lu creator: Zhiyong Gao creator: Siqi Zhang creator: Ke Du creator: Die Xu creator: Wenbin Dong creator: Yujiao Zhang creator: Xiaoping Lei uri: https://doi.org/10.7717/peerj.18506 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lu et al. title: Stirring up the muck: the systematics of soft-sediment Fionidae (Nudibranchia: Aeolidina) from the tropical Indo-Pacific link: https://peerj.com/articles/18517 last-modified: 2024-12-13 description: The tropical Indo-Pacific aeolid nudibranchs of the Fionidae are poorly known and have not been studied in a concerted manner. Many undescribed species are found throughout the Indian and Pacific Oceans and are concentrated in the Coral Triangle. With the recent publication of a revised systematic arrangement of the Fionidae, documentation and description of new taxa of Fionidae is especially warranted. Here we describe Tenellia bughaw Kim & Gosliner sp. nov., Tenellia puti Kim & Gosliner sp. nov., Tenellia nakapila Kim & Gosliner sp. nov., Abronica payaso Kim & Gosliner, sp. nov. and Abronica turon Gosliner & Kim sp. nov. from the waters of the Coral Triangle. Their phylogenetic placement in Fionidae is reviewed using three genes: cytochrome oxidase I (COI), 16s rRNA, and histone 3 (H3) in a Bayesian and maximum likelihood framework. A redescription of Tenellia yamasui (Hamatani, 1993) is also provided to clarify its distinctiveness from T. bughaw and T. puti. This study confirms that all four known species of Abronica are characterized by having an acutely pointed curved penial stylet, thus confirming a unique morphological synapomorphy for members of this genus. A discussion on conflicts in the classification of fionid aeolid nudibranchs addresses concerns with extreme splitting based on novel innovations that emphasize evolutionary novelty over phyletic kinship. Instead, a more conservative approach is suggested, especially within the context of taxa that still have much undocumented primary diversity. creator: Ashley Y. Kim creator: Samantha A. Donohoo creator: Terrence M. Gosliner uri: https://doi.org/10.7717/peerj.18517 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Kim et al. title: Geographic variation and core microbiota composition of Anastrepha ludens (Diptera: Tephritidae) infesting a single host across latitudinal and altitudinal gradients link: https://peerj.com/articles/18555 last-modified: 2024-12-13 description: Anastrepha ludens is a pestiferous tephritid fly species exhibiting extreme polyphagy. It develops optimally in hosts rich in sugar but low nitrogen content. We studied the geographical influence on the composition of A. ludens’s larval and newly emerged adult gut microbiota in altitudinal (0–2,000 masl) and latitudinal (ca. 800 km from 17° to 22°N latitude) transects along the coastline of the state of Veracruz, Mexico. In the 16 collection sites, we only collected Citrus x aurantium fruit (238 samples of A. ludens larvae and adults, plus 73 samples of pulp) to control for host effect, hypothesizing that there exists a conserved core microbiota that would be dominated by nitrogen-fixing bacteria. We found that latitude triggered more significant changes in the gut microbiota than altitude. Northern and southernmost samples differed the most in microbiota composition, with a trade-off between Acetobacteraceae and Rhizobiaceae driving these differences. As hypothesized, the core microbiota in each sampling site, contained the functional group of nitrogen-fixing bacteria. We conclude that A. ludens larvae can acquire multiple diazotrophic symbionts along its wide distribution range where it infests fruit with a high C:N ratio in the pulp. creator: Martín Aluja creator: Daniel Cerqueda-García creator: Alma Altúzar-Molina creator: Larissa Guillén creator: Emilio Acosta-Velasco creator: Juan Conde-Alarcón creator: Andrés Moya uri: https://doi.org/10.7717/peerj.18555 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Aluja et al. title: Temporal disruption in tuberculosis incidence patterns during COVID-19: a time series analysis in China link: https://peerj.com/articles/18573 last-modified: 2024-12-13 description: BackgroundDespite extensive knowledge of tuberculosis (TB) and its control, there remains a significant gap in understanding the comprehensive impact of the COVID-19 pandemic on TB incidence patterns. This study aims to explore the impact of COVID-19 on the pattern of pulmonary tuberculosis in China and examine the application of time series models in the analysis of these patterns, providing valuable insights for TB prevention and control.MethodsWe used pre-COVID-19 pulmonary tuberculosis (PTB) data (2007–2018) to fit SARIMA, Prophet, and LSTM models, assessing their ability to predict PTB incidence trends. These models were then applied to compare the predicted PTB incidence patterns with actual reported cases during the COVID-19 pandemic (2020–2023), using deviations between predicted and actual values to reflect the impact of COVID-19 countermeasures on PTB incidence.ResultsPrior to the COVID-19 outbreak, PTB incidence in China exhibited a steady decline with strong seasonal fluctuations, characterized by two annual peaks—one in March and another in December. These seasonal trends persisted until 2019. During the COVID-19 pandemic, there was a significant reduction in PTB cases, with actual reported cases falling below the predicted values. The disruption in PTB incidence appears to be temporary, as 2023 data indicate a gradual return to pre-pandemic trends, though the incidence rate remains slightly lower than pre-COVID levels. Additionally, we compared the fitting and forecasting performance of the SARIMA, Prophet, and LSTM models using RMSE (root mean squared error), MAE (mean absolute error), and MAPE (mean absolute percentage error) indexes prior to the COVID-19 outbreak. We found that the Prophet model had the lowest values for all three indexes, demonstrating the best fitting and prediction performance.ConclusionsThe COVID-19 pandemic has had a temporary but significant impact on PTB incidence in China, leading to a reduction in reported cases during the pandemic. However, as pandemic control measures relax and the healthcare system stabilizes, PTB incidence patterns are expected to return to pre-COVID-19 levels. The Prophet model demonstrated the best predictive performance and proves to be a valuable tool for analyzing PTB trends and guiding public health planning in the post-pandemic era. creator: Jiarui Zhang creator: Zhong Sun creator: Qi Deng creator: Yidan Yu creator: Xingyue Dian creator: Juan Luo creator: Thilakavathy Karuppiah creator: Narcisse Joseph creator: Guozhong He uri: https://doi.org/10.7717/peerj.18573 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhang et al. title: Computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago link: https://peerj.com/articles/18584 last-modified: 2024-12-13 description: BackgroundModern workplace requirements in the banking sector require bankers to work on screens for more than 6 h a day, putting much stress and strain on their eyes, which leads to computer vision syndrome. Therefore, this study aimed to assess the prevalence of computer vision syndrome and associated factors among urban and rural bankers in Trinidad and Tobago.Methods and materialsA cross-sectional design was applied to collect data from 399 bankers between April and June 2023. The collected data was entered into Excel worksheets and later uploaded to SPSS for further analysis. A variable with a P-value of 0.25 in binary logistic regression is a candidate for multi-variable logistic regression analysis. Finally, a variable with a P-value of 0.05 was used to declare statistical significance.ResultsA total of 371 participants were enrolled in this study, leading to a response rate of 92.9%. Of the total participants, 277 (74.7%) had computer vision syndrome. Working in rural areas (AOR = 2.69; 95% CI [1.41–5.13]) and using eyesight glasses (AOR = 0.57; 95% CI [0.33–0.97]) was associated with computer vision syndrome.ConclusionDespite being easily preventable, computer vision syndrome is substantially prevalent among bankers in Trinidad. The use of eye-sight glasses and the working area are significantly associated with computer vision syndrome. Therefore, it is necessary to improve workplace practices by encouraging the use of anti-glare screens and glasses for employees who work long hours on the computer. creator: Kingsley Ekemiri creator: Devonte McKnight creator: Chioma Ekemiri creator: Ngozika Ezinne creator: Henrietta Ashang creator: Virginia Victor creator: Osaze Okonedo creator: Ayishetu Oshoke Shuaibu creator: Robin Seemongal-Dass uri: https://doi.org/10.7717/peerj.18584 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ekemiri et al. title: Companion animal foster caregiving: a scoping review exploring animal and caregiver welfare, barriers to caregiver recruitment and retention, and best practices for foster care programs in animal shelters link: https://peerj.com/articles/18623 last-modified: 2024-12-13 description: Each year, millions of animals enter animal shelters across the United States and are met with a variety of potential stressors that can negatively impact their experience, including noise, confinement, and social isolation. Foster care, a unique form of human–animal interaction, is increasingly understood to be an effective tool for improving welfare by allowing animals to escape the stressors of the shelter, providing an environment that allows for greater social interaction, and offering opportunities for improved health and behavior. This review includes 42 published articles, reports, master’s theses, and doctoral dissertations that have previously evaluated companion animal foster care programs. While scientific literature in this area has increased over the last decade, no review of the research exploring companion animal fostering has been published. Here, we examine foster care programs and their effects on human and animal welfare, evaluate the successes and challenges of supporting shelter foster care programs, recommend best practices for programmatic success, illuminate discrepancies in equity and diversity of caregiver engagement, and offer directions for future research in animal foster caregiving. The examinations in this review conclude that fostering provides both proximate (i.e., physiological and behavioral) and distal (i.e., length of stay and adoption outcomes) welfare benefits for shelter animals as well as their caregivers. Companion animal foster care programs may be further improved by providing greater caregiver support and increasing the diversity and extent of community engagement. Meanwhile, scientific investigations should explore lesser-researched components of foster care programs that are not yet well understood. creator: Grace E. Phillips creator: Lisa M. Gunter uri: https://doi.org/10.7717/peerj.18623 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Phillips and Gunter title: A comparative study on leaf anatomy and photosynthetic characteristics of different growth stages of Horsfieldia hainanensis link: https://peerj.com/articles/18640 last-modified: 2024-12-13 description: The rare and endangered wild plant, Horsfieldia hainanensis, has been listed as a second-level key protected plant in China. Currently, its habitat is severely damaged, and the population has dramatically declined, necessitating urgent intervention for protection. In this study, the aim was to explore the correlations and differences from the perspectives of photosynthetic characteristics and leaf structure, providing scientific references for in-situ conservation and ex-situ cultivation. The results revealed the following: (1) The maximum net photosynthetic rate (Pmax) and light saturation point (LSP) of mature trees were significantly higher than those of seedlings, while the light compensation point (LCP), CO2 compensation point (CCP), and CO2 saturation point (CSP) were significantly lower in seedlings. (2) The average daily net photosynthetic rate of mature trees was significantly higher than that of seedlings. When both mature trees and seedlings exhibited a “midday depression” phenomenon, accompanied by an increase in intercellular CO2 concentration (Ci), it indicated that the “midday depression” was caused by non-stomatal limiting factors. (4) Both mature trees and seedlings showed peak values of water use efficiency (WUE) under low light conditions. Mature trees had smaller upper and lower epidermis thickness but larger leaf thickness, and their leaf structure, characterized by well-developed palisade and spongy tissues, conformed to the cellular structure adaptations for low light. Therefore, both were more adapted to low light conditions. (5) The stomatal density (SD) and individual stomatal area (SA) of seedlings were significantly higher than those of mature trees. (6) The total chlorophyll content of mature trees was significantly higher than that of seedlings, while the chlorophyll a/chlorophyll b ratio was significantly lower in mature trees and remained below three in both cases. In summary, the photosynthetic capacity and light adaptability of mature trees are stronger than those of seedlings, but both mature trees and seedlings exhibit shade-tolerant characteristics. For in-situ conservation, it is possible to promote the growth and development of seedlings by appropriately employing artificial “windowing” or shading methods based on the actual growth environment of the seedlings. In the case of ex-situ cultivation, seedlings should be provided with appropriate shading initially, while ensuring sufficient moisture and CO2 concentration. As the plants grow, the shading intensity can be gradually reduced. Once the plants reach maturity, they have a broader range of light adaptability and can be transplanted to environments with less shading. creator: Jianwang Xu creator: Jianmin Tang creator: Haolong Jiang creator: Rong Zou creator: Xiao Wei uri: https://doi.org/10.7717/peerj.18640 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Xu et al. title: N6-methyladenosine (m6A) modification in inflammation: a bibliometric analysis and literature review link: https://peerj.com/articles/18645 last-modified: 2024-12-13 description: N6-methyladenosine (m6A) is the most abundant internal messenger RNA modification in eukaryotes, influencing various physiological and pathological processes by regulating RNA metabolism. Numerous studies have investigated the role of m6A in inflammatory responses and inflammatory diseases. In this study, VOSviewer and Citespace were used to perform bibliometric analysis to systematically evaluating the current landscape of research on the association between m6A and inflammation. The literature was sourced from the Web of Science Core Collection, with characteristics including year, country/region, institution, author, journal, citation, and keywords. According to the bibliometric analysis results of keywords, we present a narrative summary of the potential mechanisms by which m6A regulates inflammation. The results showed that the key mechanisms by which m6A modulates inflammation include apoptosis, autophagy, oxidative stress, immune cell dysfunction, and dysregulation of signaling pathways. creator: Zewen Li creator: Yongfeng Lao creator: Rui Yan creator: Xin Guan creator: Yanan Bai creator: Fuhan Li creator: Zhilong Dong uri: https://doi.org/10.7717/peerj.18645 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Isolation and identification of serotonin compound from banana hump: a reproductive stimulant for tiger shrimp Penaeus monodon broodstock enhancement link: https://peerj.com/articles/18670 last-modified: 2024-12-13 description: BackgroundThe banana plant is claimed to contain a serotonin compound that has the potential to stimulate and improve the reproductive performance of crustacean species. This study aimed to isolate and characterize the serotonin compound from the banana hump and its application to enhance the reproductive performance of tiger shrimp broodstock.MethodsBanana hump as a part of the plant was extracted by using the maceration technique. The chemical structure of the serotonin compound was identified and characterized based on spectroscopic data, including high-performance liquid chromatography (HPLC), ultraviolet-visible (UV-Vis) spectroscopy, and infrared (IR) spectroscopy, and a comparison was made with the standard compound and the literature. The extract herb in a dose of 50 µg/g body weight was injected into the tiger shrimp broodstock in four-time administrations. During 2 months of broodstock gonadal maturation, the parameters of molting, reproduction, and gene expression related to reproduction were observed.ResultsBased on the chemical structure analysis, the stimulant component of the banana hump was identified as a serotonin compound (5-hydroxytryptamine) at a concentration of 0.7% of dry weight. The number of spawned broodstock was higher in the serotonin extract treatment (60%) than in the control treatment (40%), and the broodstock injected serotonin spawned up to the second re-maturation. In contrast, no re-maturation was obtained in the control treatment. The egg number was significantly higher using the serotonin extract (286,550 ± 46,402 eggs) than the control shrimp (148,585 ± 23,647 eggs), in which the serotonin extract treatment showed a comparatively larger egg diameter number. The higher expression of the genes related to female and male reproduction was observed in the tiger shrimp injected with serotonin extract than in the control treatment. creator: Andi Parenrengi creator: Emma Suryati creator: Rachman Syah creator: Andi Tenriulo creator: Samuel Lante creator: Elmi Nurhaidah Zainuddin creator: Ratu Siti Aliah creator: Nuril Farizah creator: Agus Nawang creator: Sulaeman Sulaeman creator: Makmur Makmur creator: Rosmiati Rosmiati creator: Gunarto Gunarto creator: Herlinah Herlinah uri: https://doi.org/10.7717/peerj.18670 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Parenrengi et al. title: Development of machine learning models for the prediction of the skin sensitization potential of cosmetic compounds link: https://peerj.com/articles/18672 last-modified: 2024-12-13 description: BackgroundTo enhance the accuracy of allergen detection in cosmetic compounds, we developed a co-culture system that combines HaCaT keratinocytes (transfected with a luciferase plasmid driven by the AKR1C2 promoter) and THP-1 cells for machine learning applications.MethodsFollowing chemical exposure, cell cytotoxicity was assessed using CCK-8 to determine appropriate stimulation concentrations. RNA-Seq was subsequently employed to analyze THP-1 cells, followed by differential expression gene (DEG) analysis and weighted gene co-expression net-work analysis (WGCNA). Using two data preprocessing methods and three feature extraction techniques, we constructed and validated models with eight machine learning algorithms.ResultsOur results demonstrated the effectiveness of this integrated approach. The best performing models were random forest (RF) and voom-based diagonal quadratic discriminant analysis (voomDQDA), both achieving 100% accuracy. Support vector machine (SVM) and voom based nearest shrunken centroids (voomNSC) showed excellent performance with 96.7% test accuracy, followed by voom-based diagonal linear discriminant analysis (voomDLDA) at 95.2%. Nearest shrunken centroids (NSC), Poisson linear discriminant analysis (PLDA) and negative binomial linear discriminant analysis (NBLDA) achieved 90.5% and 90.2% accuracy, respectively. K-nearest neighbors (KNN) showed the lowest accuracy at 85.7%.ConclusionThis study highlights the potential of integrating co-culture systems, RNA-Seq, and machine learning to develop more accurate and comprehensive in vitro methods for skin sensitization testing. Our findings contribute to the advancement of cosmetic safety assessments, potentially reducing the reliance on animal testing. creator: Wu Qiao creator: Tong Xie creator: Jing Lu creator: Tinghan Jia uri: https://doi.org/10.7717/peerj.18672 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Qiao et al. title: Effects of prophylactic nebulized antibiotics on the prevention of ICU-acquired pneumonia: a systematic review and meta-analysis link: https://peerj.com/articles/18686 last-modified: 2024-12-13 description: ObjectiveTo evaluate the efficacy and safety of prophylactic nebulized antibiotics in preventing intensive care unit (ICU)-acquired pneumonia through a meta-analysis.MethodsRandomized controlled trials (RCTs) investigating the potential reduction in the incidence of ICU-acquired pneumonia through prophylactic nebulized antibiotics were collected by searching the PubMed, Embase, and Cochrane Library databases from their inception to January 23, 2024. The primary endpoint was the incidence of ICU-acquired pneumonia, while the secondary endpoints included mortality, length of ICU stay, mechanical ventilation days, and nebulization-related side effects. Statistical analyses were performed using RevMan 5.3 and STATA 14.0 software.ResultsA total of six RCTs were included in the analysis, involving 1,287 patients (636 patients in the study group received prophylactic antibiotic therapy, including Polymyxin B, Tobramycin, Ceftazidime, Colistimethate sodium, and amikacin; 651 patients in the control group primarily received saline). The results indicated that prophylactic nebulized antibiotic therapy significantly reduced the incidence of ICU-acquired pneumonia compared to that in the control group (odds ratio (OR) = 0.57, 95% confidence interval (CI) [0.43–0.74], P < 0.0001). No significant difference was observed in the mortality rate between the treatment and control groups (OR = 0.86, 95% CI [0.68–1.10], P = 0.24). Prophylactic nebulized antibiotic therapy also did not significantly reduce the length of ICU stay (MD = 0.2 days; 95% CI [−0.81 to 1.20], P = 0.70) or the number of mechanical ventilation days (MD = 0.43 days; 95% CI [−0.47 to 1.33], P = 0.35). Additionally, there was no evidence that prophylactic nebulized antibiotic therapy contributed to the development of multiple drug-resistant (MDR) bacterial pneumonia or increased the incidence of associated side effects, such as airway spasms.ConclusionsThis meta-analysis suggests that ICU-acquired pneumonia can be prevented by prophylactic nebulized antibiotic therapy in critically ill patients without increasing the risk of MDR bacterial infections or airway spasms. However, the reduction in the incidence of ICU-acquired pneumonia did not result in significant improvements in mortality or length of ICU stay. creator: Ming Gao creator: Xiaoxu Yu creator: Xiaoxuan Liu creator: Yuan Xu creator: Hua Zhou creator: Yan Zhu uri: https://doi.org/10.7717/peerj.18686 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gao et al. title: Identification of immunogenic cell death gene-related subtypes and risk model predicts prognosis and response to immunotherapy in ovarian cancer link: https://peerj.com/articles/18690 last-modified: 2024-12-13 description: BackgroundImmunogenic cell death (ICD) has been associated with enhanced anti-tumor immunotherapy by stimulating adaptive immune responses and remodeling the immune microenvironment in tumors. Nevertheless, the role of ICD-related genes in ovarian cancer (OC) and tumor microenvironment remains unexplored.MethodsIn this study, high-throughput transcriptomic data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases as training and validation sets separately were obtained and proceeded to explore ICD-related clusters, and an ICD-related risk signature was conducted based on the least absolute shrinkage and selection operator (LASSO) Cox regression model by iteration. Multiple tools including CIBERSORT, ESTIMATE, GSEA, TIDE, and immunohistochemistry were further applied to illustrate the biological roles of ICD-related genes as well as the prognostic capacity of ICD risk signature in OC.ResultsTwo ICD-related subtypes were identified, with the ICD-high subtype showing more intense immune cell infiltration and higher activities of immune response signaling, along with a favorable prognosis. Additionally, four candidate ICD genes (IFNG, NLRP3, FOXP3, and IL1B) were determined to potentially impact OC prognosis, with an upregulated expression of NLRP3 in OC and metastatic omental tissues. A prognostic model based on these genes was established, which could predict overall survival (OS) and response to immunotherapy for OC patients, with lower-risk patients benefiting more from immunotherapy.ConclusionOur research conducted a prognostic and prediction of immunotherapy response model based on ICD genes, which could be instrumental in assessing prognosis and assigning immunotherapeutic strategies for OC patients. NLRP3 is a promising target for prognosis in OC. creator: Wenjing Pan creator: Zhaoyang Jia creator: Xibo Zhao creator: Kexin Chang creator: Wei Liu creator: Wenhua Tan uri: https://doi.org/10.7717/peerj.18690 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Pan et al. title: Efficacy of different dietary therapy strategies in active pediatric Crohn’s disease: a systematic review and network meta-analysis link: https://peerj.com/articles/18692 last-modified: 2024-12-13 description: BackgroundDietary therapy strategies play an important role in the treatment of pediatric patients with Crohn’s disease (CD), but the relative efficacy of different dietary therapy strategies for Crohn’s remission is unknown. This study aims to compare the effectiveness and tolerance of these dietary therapy strategies for active pediatric CD.MethodsWe searched the medical literature up to August 30, 2024 to identify randomized controlled trials (RCTs) of dietary therapy strategies for pediatric CD. The primary outcomes were clinical remission rate and tolerance, secondary outcomes included differences between pre- and post-treatment levels of albumin, C-reactive protein (CRP), and fecal calprotectin levels. A network meta-analysis (NMA) was performed by using the frequentist model. For binary outcome variables and continuous outcome variables, odds ratios (OR) and mean differences (MD) with corresponding 95% confidence intervals (CI) were utilized, respectively. The ranking of dietary therapy strategies was determined based on the surface under the cumulative ranking area (SUCRA) for each comparison analyzed.ResultsOverall, 14 studies involving 564 participants were included. In terms of clinical remission rate, the partial enteral nutrition (PEN) plus Crohn’s disease exclusion diet (PEN+CDED) (OR = 7.86, 95% CI [1.85–33.40]) and exclusive enteral nutrition (EEN) (OR = 3.74, 95% CI [1.30–10.76]) exhibited significant superiority over PEN alone. The tolerance of PEN+CDED was significantly higher than that of EEN (OR = 0.07, 95% CI [0.01–0.61]). According to the surface under the cumulative ranking area (SUCRA) values, the PEN+CDED intervention (90.5%) achieved the highest ranking in clinical remission rate. In terms of tolerance, PEN+CDED ranked first (88.0%), while EEN ranked last (16.3%).ConclusionsIn conclusion, PEN+CDED was associated with the highest clinical remission rate and tolerance among the various dietary therapy strategies evaluated. Despite limitations in the studies, this systematic review provides evidence that PEN+CDED can be used as an alternative treatment to exclusive enteral nutrition and is more suitable for long-term management in children. creator: Jiaze Ma creator: Jinchen Chong creator: Zhengxi Qiu creator: Yuji Wang creator: Tuo Chen creator: Yugen Chen uri: https://doi.org/10.7717/peerj.18692 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ma et al. title: Adiposity and body fat distribution based on skinfold thicknesses and body circumferences in Czech preschool children, secular changes link: https://peerj.com/articles/18695 last-modified: 2024-12-13 description: BackgroundThe long-standing widespread prevalence of obesity includes issues of its evaluation. Nutritional status may be assessed using various tools and methods; among others simple anthropometric measurements are well established. Widely used body mass index (BMI), presents an obstacle of needing to calculate a standard deviation score (SD) for correct use in the child population. As BMI overlooks body composition, it is necessary to evaluate fat and muscle mass with different methods. Established skinfolds and circumferences are used in many variations and equations to accomplish that goal; however, the parameters used in these methods also undergo secular changes. Furthermore, secular changes have been documented in fat mass distribution. The aim of the study is to assess secular changes of skinfolds thickness and body circumferences and evaluate their validity for use in clinical practice and population research.Methods and sampleOur database consisted of a recent (2016–2022) sample with 594 participants (298 males) and a reference sample (from 1990) with 2,910 participants (1,207 males). Both cohorts comprised Czech preschool children, aged 4.00 to 6.99 years. With standard methodology, anthropometric parameters were obtained for 13 skinfolds and eight circumferences, by trained staff. The equations of Slaughter, Durnin and Deurenberg were correspondingly calculated. Statistical evaluation was conducted in the R programming language, using Welch’s test, Cohen’s d and the Bland–Altman method.ResultsOur study found significant increases in skinfold thickness on the abdomen, chest I. and forearm, with high clinical relevance (p ≥ 0.01; d = range from 0.20 to 0.70). Contrastingly, apart from the abdominal area, a decrease of circumferences was observed. The body fat percentage estimation equations were tested for bias in the recent sample in the context of bioimpedance analysis with the Bland–Altman method. All equations are suitable for application in clinical use.DiscussionDocumented secular changes in fat mass distribution are only part of a contemporary accelerating trend of obesity prevalence. Our findings support the trend of a decline of circumferences and rise of skinfold thickness in corresponding areas, especially on the limbs, that is evidenced by the trend of latent obesity. The results of the study show the need to complement established diagnostic procedures in childhood obesitology with abdominal and midthigh circumferences and optionally even the maximal circumference of the forearm. These circumferences should always be measured alongside the skinfold thickness of the region. Only in this way can the overall adiposity of an individual with regard to secular changes, including the detection of latent obesity, be objectively evaluated. creator: Anna Vážná creator: Jan M. Novák creator: Robert Daniš creator: Petr Sedlak uri: https://doi.org/10.7717/peerj.18695 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Vážná et al. title: Virtual reality therapy in managing cancer pain in middle-aged and elderly: a systematic review and meta-analysis link: https://peerj.com/articles/18701 last-modified: 2024-12-13 description: BackgroundVirtual reality technology has been proposed to rehabilitate cancer patients. This study aimed to summarize the effectiveness of virtual reality (VR)--based therapies for pain management in middle-aged and elderly cancer patients.MethodsThis meta-analysis was registered in PROSPERO (CRD42023400432). We searched the randomized controlled trials (RCTs) in PubMed, Scopus, the Cochrane Library, Web of Science, and Embase, conducted from construction until November 1, 2024. The study examined the effects of VR treatment on pain levels in middle-aged and elderly cancer patients using RCTs as primary or secondary outcome measures. Articles were evaluated for eligibility according to predetermined criteria, and each of the three researchers independently collected the data. The researchers used the heterogeneous selection effects model to calculate the mean effect sizes.ResultsThis meta-analysis included seven RCTs involving 476 patients. The meta-analysis confirmed the significant effect of VR therapy on the management of pain, anxiety, and depression in the middle-aged and elderly cancer population.ConclusionsOur research shows that VR could be a significant device for cancer pain management in the middle-aged and elderly and that VR scene therapy may be more effective. Nevertheless, it is essential to use caution when interpreting the findings since the number of research included is small. creator: Yang Chen creator: Hui Meng creator: Qian Chen creator: Wendong Wu creator: HaiBin Liu creator: Shi Lv creator: Liang Huai uri: https://doi.org/10.7717/peerj.18701 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Pepper power: short-term impact of pepper consumption on the gut bacteriome composition in healthy volunteers link: https://peerj.com/articles/18707 last-modified: 2024-12-13 description: BackgroundPepper from Capsicum species is a well-established spice with a rich history of culinary use. Some observations have linked its consumption to gastrointestinal discomfort and alterations in stool patterns while it is considered beneficial in some cultures. However, there is lack of information on the direct effect of pepper consumption on human gut microbiota, we conducted dietary intervention studies to assess the impact of pepper on gut bacteriome composition in humans.MethodsTen healthy volunteers were recruited, and each person received 200 ml of 0.14 g/ml fresh Habanero Pepper (Capsicum chinense) daily over a 4-day period after which they abstained from pepper consumption for the subsequent 4 days before resumption of their normal diet. Stool samples were collected at baseline, after pepper consumption, after 4 days without pepper and after 4- and 6-days resumption of normal diet. We sequenced the V3-V4 region of the 16S rRNA gene and analyzed microbial diversity and composition using the QIIME2 pipeline and relevant R packages.ResultsConsumption of pepper over a 4-day period led to a higher abundance of Verrucomicrobia, a phylum rarely found in significant proportions at other time points. There was a gradual depletion of Shigella and Staphylococcus spp. from baseline untill the end of the study. Other taxa showed timepoint specific associations, emphasizing the potential impact of short-term dietary interventions on the relative abundance of these genera.ConclusionsOur study adds nuance to the understanding of diet-microbiota interactions, highlighting the intricate relationship between pepper consumption and gut bacteriome composition. Further exploration of these dynamics holds promise for personalized dietary recommendations and targeted interventions to support gut microbial health. creator: Oluwafayoke Owolo creator: Haruna J. Audu creator: Ayorinde O. Afolayan creator: Funmilola A. Ayeni uri: https://doi.org/10.7717/peerj.18707 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Owolo et al. title: Prognostic value of serum Mrp 8/14 in sepsis-induced acute respiratory distress syndrome patients: a retrospective cohort study link: https://peerj.com/articles/18718 last-modified: 2024-12-13 description: BackgroundMrp 8/14 is abundantly secreted by activated neutrophils during infection and inflammation. However, its prognostic value in acute respiratory distress dyndrome (ARDS) induced by sepsis is poorly understood. Our aim was to investigate the relationship between serum Mrp 8/14 and the prognosis in sepsis-induced ARDS patients admitted to the intensive care unit (ICU).MethodsSerum Mrp 8/14 concentrations were analyzed in 118 ARDS patients induced by sepsis included in the analytical study. Patients were enrolled upon admission to the ICU of Nanjing Hospital affiliated to Nanjing Medical University. The baseline information and clinical outcomes were obtained. Patients were divided into survivor group and non-survivor group according to whether they died during ICU hospitalization.ResultsThe serum Mrp 8/14 levels were significantly increased in the non-survivor group compared to the survivor group (P < 0.05). Logistic regression analysis showed that serum Mrp 8/14, albumin and APACHE II were the independent factors for predicting the prognosis of sepsis-induced ARDS during ICU hospitalization after adjustment. Additionally, the area under the receiver operating characteristic curve for Mrp 8/14 combined with albumin was associated with ICU mortality and was higher than that of Mrp 8/14, albumin, APACHE II and Mrp 8/14 combined with APACHE II (all P < 0.05). A nomogram was constructed to predict ICU mortality and the c-indexes of predictive accuracy was 0.830 in the cohort (P < 0.05).ConclusionsThe serum Mrp 8/14 upon ICU admission in septic patients may be useful for predicting mortality in sepsis-induced ARDS patients during ICU hospitalization. creator: Caizhi Sun creator: Yongpeng Xie creator: Chenchen Zhu creator: Lei Guo creator: Bowen Xu creator: Haidong Qin creator: Xiaomin Li uri: https://doi.org/10.7717/peerj.18718 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sun et al. title: Phylogeography of the Mesa Silverside fish Chirostoma jordani (Woolman, 1894) throughout the Mexican Plateau link: https://peerj.com/articles/18256 last-modified: 2024-12-12 description: BackgroundUnderstanding the processes that influence distribution of organisms is a major goal in evolutionary biology. Speciation in freshwater fishes is mainly associated with the “island-like” model of evolution, in which the formation of land barriers between different hydrographic basins interrupts gene flow and promotes isolation. Freshwater fish therefore provide an excellent model system for macro- and micro-evolutionary studies. The Mesa Silverside, Chirostoma jordani, is one of the most widespread freshwater fish species in the Mexican Plateau, a geologically complex physiographic region with a long history of genesis, destruction and compartmentalization of hydrographic basins that has promoted the dispersal and isolation of freshwater fishes.MethodsWe used mitochondrial (Cytb and D-loop) and nuclear (first intron of the ribosomal protein S7) data and used phylogeographic and coalescent based methods to elucidate the evolutionary history of C. jordani throughout its distributional range on the Mexican Plateau.ResultsThe results obtained in the present study revealed that C. jordani consists of two main genetic groups with geographical correspondence. Clade I occur exclusively in north-western basin and shows population structure. Clade II is widely distributed across the west, central and eastern basins without population structure. The split between these two main clades was estimated at 1.4 Mya. This cladogenetic event may be associated with the allopatric process promoted by the fragmentation and compartmentalization of hydrographic basins induced by the geological and climatic history of the Mexican Plateau. creator: Isai Betancourt-Resendes creator: Rodolfo Pérez-Rodríguez creator: Kyle R. Piller creator: Omar Domínguez-Domínguez uri: https://doi.org/10.7717/peerj.18256 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Betancourt-Resendes et al. title: A polyphasic approach in the identification and biochemical characterization of Dunaliella tertiolecta with biodiesel potential from a saltern in Mauritius link: https://peerj.com/articles/18325 last-modified: 2024-12-12 description: Bioprospecting robust and oleaginous strain is crucial for the commercialization of microalgae-based biodiesel. In this study, a microalgal strain SCH18 was isolated from a solar saltern located in Mauritius. This isolate was identified as Dunaliella tertiolecta based on a polyphasic approach that combined molecular, physiological, and morphological analyses. Furthermore, the effect of different salinities on the biochemical composition and fatty acid profile of this microalga was investigated to explore its potential in producing biodiesel. Results from the growth studies showed that salinity of 1.0 M NaCl was optimal for achieving a high growth rate. Under this salt concentration, the growth rate and the doubling time were calculated as 0.39 ± 0.003 day−1 and 1.79 ± 0.01 days, respectively. In terms of biochemical composition, a substantial amount of carbohydrate (42.02 ± 5.20%), moderate amount of protein (30.35 ± 0.18%) and a low lipid content (17.81 ± 2.4%) were obtained under optimal NaCl concentration. The fatty acid analysis indicated the presence of palmitic acid, stearic acid, palmitoleic acid, oleic acid, linoleic acid, gamma, and alpha-linolenic acids, which are suitable for biodiesel synthesis. The predicted biodiesel properties were in accordance with the standard of ASTM 6751, indicating that the microalgal isolate D. tertiolecta SCH18 is a potential candidate for use in biodiesel production. creator: Kamlesh Ramdhony creator: Daneshwar Puchooa creator: Turki Kh. Faraj creator: Abdulwahed Fahad Alrefaei creator: JunFu Li creator: Rajesh Jeewon uri: https://doi.org/10.7717/peerj.18325 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ramdhony et al. title: Study of TRAF3IP3 for prognosis and immune infiltration in hepatocellular carcinoma link: https://peerj.com/articles/18538 last-modified: 2024-12-12 description: BackgroundTumor necrosis factor receptor-associated factor 3 (TRAF3)-interacting protein 3 (TRAF3IP3) expressed in various tumor cell. However, its role in hepatocellular carcinoma (HCC) was unclear. We aimed to demonstrate the relationship between TRAF3IP3 and HCC and explore the potential role of TRAF3IP3 in HCC.MethodsThe Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Genotype-Tissue Expression (GTEx), KM-Plotter, University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), and Xiantao Academic Online Website were utilized for the systematic analysis of TRAF3IP3. This analysis included mRNA expression, protein expression, prognostic value, enrichment analysis, and immune cell infiltration in HCC. Subsequently, immunohistochemistry was performed to assess the expression levels of TRAF3IP3 in both cancer and non-cancer tissues of patients with HCC.ResultsAnalysis of public databases and immunohistochemical staining on 20 pairs of samples confirmed a decrease in TRAF3IP3 expression in HCC. Both the TCGA database and GSE14520 indicated that patients with high TRAF3IP3 expression had a more favorable prognosis in terms of overall survival (OS) and progression-free interval (PFI), as shown by KM curve results. Multivariate Cox regression analysis further demonstrated that high TRAF3IP3 expression was an independent protective factor for HCC prognosis (hazard ratio (HR): 0.619, 95% confidence interval (CI) [0.399–0.959]; p < 0.05). In the high TRAF3IP3 expression group, various immune response-related molecular pathways, particularly B lymphocyte-mediated pathways, were activated. The level of TRAF3IP3 expression showed a significant correlation with the presence of tumor-infiltrating CD8+ T cells. Additionally, a positive correlation was observed between immunophenoscore (IPS) and TRAF3IP3 expression. Notably, the half-maximal inhibitory concentration (IC50) of commonly used chemotherapeutic drugs, such as lapatinib and mitomycin, was inversely associated with TRAF3IP3 expression in HCC patients.ConclusionTRAF3IP3 may be as a novel and promising biomarker for prognosis prediction and immunological evaluation of HCC. creator: Xing Wang creator: Xin Gao creator: Airu Liu creator: Yan Qin creator: Zhi-Yu Ni creator: Xiao Lan Zhang uri: https://doi.org/10.7717/peerj.18538 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Variation in behaviour of native prey mediates the impact of an invasive species on plankton communities link: https://peerj.com/articles/18608 last-modified: 2024-12-12 description: Trait variation in predator populations can influence the outcome of predator-prey dynamics, with consequences for trophic dynamics and ecosystem functioning. However, the influence of prey trait variation on the impacts of predators is not well understood, especially for introduced predators where variation in prey can shape invasion outcomes. In this study, we investigated if intra-specific differences in vertical position of Daphnia influenced the impacts of the invasive zooplankton predator, Bythotrephes cederströmii, on plankton communities. Our results show that vertical position of Daphnia influenced Bythotrephes predation on smaller cladoceran species and impacts on primary production. Larger reductions in small cladoceran density and greater algal biomass were observed in mesocosms with less spatial overlap between Daphnia and Bythotrephes. These results suggest that differences in vertical position of Daphnia can alter the type and magnitude of Bythotrephes impacts in invaded systems. creator: Sarah S. Hasnain creator: Shelley E. Arnott uri: https://doi.org/10.7717/peerj.18608 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hasnain and Arnott title: ClBRN1 from Chrysanthemum lavandulifolium enhances the stress resistance of transgenic Arabidopsis link: https://peerj.com/articles/18620 last-modified: 2024-12-12 description: BackgroundChrysanthemum (Chrysanthemum×morifolium Ramat.) is a particularly important autumn perennial flower for potted plant, flower bed and border, and cut flower with high ornamental value. However, abiotic stress can affect the ornamental quality of Chrysanthemum. NAC (NAM, ATAF1-2, and CUC2) transcription factors (TFs) play an important role in regulating plant growth and development, as well as responding to abiotic stresses.MethodsIn this study, the ClBRN1 (Chrysanthemum lavandulifolium BEARSKIN gene) was isolated from the Chrysanthemum model plant C. lavandulifolium. And analyze the function of the gene through bioinformatics, subcellular localization and overexpression.ResultsBioinformatics analysis showed that the ClBRN1 gene was a member of the NAC TFs family, with a CDS (coding sequence) length of 1,080 bp and encoding 359 amino acids. The subcellular localization results found that the gene was located in the nucleus and cell membrane. Furthermore, the transgenic results in Arabidopsis thaliana showed that the gene significantly reduces plant height while improving salt and low temperature tolerance. Observation of paraffin sections of Arabidopsis stems also revealed that the secondary cell wall of overexpressing Arabidopsis stems was significantly thicker than that of wild-type. The above results indicate that the ClBRN1 gene may play an important role in regulating plant resistance to abiotic stress. This study will provide new insights for molecular breeding of resistant chrysanthemums in the future. creator: Yanxi Li creator: Wenting He creator: Yueyue Liu creator: Chendi Mei creator: Hai Wang creator: Xuebin Song uri: https://doi.org/10.7717/peerj.18620 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: The largest sauropodomorph skull from the Lower Jurassic Lufeng Formation of China link: https://peerj.com/articles/18629 last-modified: 2024-12-12 description: The Lower Jurassic Lufeng Formation of China has long been recognized for its diverse early-diverging sauropodomorph dinosaurs, with eight genera and ten species, representing more than half the Laurasian records. In this paper, we describe a new genus and species of non-sauropodan sauropodomorph, Lishulong wangi gen. et sp. nov., from Yunnan Province in southwestern China. This new taxon is represented by a partial skeleton including the skull and nine articulated cervical vertebrae, which differs from other Lufeng forms in both cranial and cervical characteristics. It bears several autapomorphies of the nasal process, the maxillary neurovascular foramen, and the cervical neural spine. Phylogenetic analysis reveals that Lishulong is an early-diverging member of the Sauropodiformes, and the sister-taxon of Yunnanosaurus. Elucidating the novel osteology of Lishulong, it possessed the largest sauropodomorph cranial material currently identified from the Lufeng Formation, not only enriches the diversity of the Lufeng dinosaur assemblage, but also enhances our understanding of the character evolution in early-diverging sauropodiforms. Furthermore, information about paleobiogeographic distributions indicates that Early Jurassic sauropodomorphs, especially Chinese taxa, have maintained multiple dispersions and exchanges within Pangaea. creator: Qian-Nan Zhang creator: Lei Jia creator: Tao Wang creator: Yu-Guang Zhang creator: Hai-Lu You uri: https://doi.org/10.7717/peerj.18629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Preoperative 3D printing planning technology combined with orthopedic surgical robot-assisted minimally invasive screw fixation for the treatment of pelvic fractures: a retrospective study link: https://peerj.com/articles/18632 last-modified: 2024-12-12 description: ObjectiveTo explore the advantages and effectiveness of preoperative 3D printing planning technology combined with orthopedic surgical robot-assisted screw placement in the minimally invasive treatment of pelvic fractures compared to orthopedic surgical robot-assisted screw placement alone.MethodsA retrospective analysis of the clinical data of 29 patients with unstable pelvic fractures treated with orthopedic surgical robot-assisted percutaneous screw fixation from July 2021 to August 2023 was conducted. Among them, 13 patients who underwent preoperative 3D printing technology for screw planning were assigned to the experimental group, and the remaining 16 patients were assigned to the control group. All patients underwent screw fixation alone or combined with other fixation methods for fracture fixation. The application of preoperative 3D printing planning in orthopedic surgical robot operations was described. The intraoperative screw drawing time, invasive operation time, number of fluoroscopies during invasive operation, postoperative evaluation of screw accuracy, fracture healing, complications, and functional outcomes were recorded and compared between the two groups.ResultsAll patients successfully underwent surgery, with one patient in the control group experiencing numbness in the sciatic nerve innervation area. All patients were followed up for 4–15 months, with an average of 8 months, and all fractures achieved healing. The experimental group had a total of 26 screws inserted, while the control group had 30 screws. In the experimental group, the intraoperative screw drawing time was 3.0 (3.0, 3.37) min, significantly shorter than 4.0 (3.6, 4.0) min in the control group (P < 0.05). The proportion of screws not penetrating the bone postoperatively was 88.5% in the experimental group, significantly higher than 63.3% in the control group (P < 0.05). In the experimental group, the postoperative screw position, compared to the planned screw position, had an average position deviation of 3.05 ± 0.673 mm and an average spatial angle deviation of 2.22 ± 0.605°. At the last follow-up, the Majeed score was used to assess function, with the experimental group having an excellent and good rate of 84.6%, slightly higher than 75.0% in the control group, but the difference was not statistically significant (P > 0.05).ConclusionIn the treatment of pelvic fractures using screw fixation, preoperative 3D printing technology planning combined with orthopedic surgical robots, compared to orthopedic surgical robot-assisted screw placement alone, can significantly reduce intraoperative screw drawing time, decrease drawing difficulty, enhance screw placement accuracy, and does not increase invasive operation time or the number of fluoroscopies. This approach makes the surgery safer and is a method worth applying. creator: YuLong Jing creator: LiMing Chang creator: Bo Cong creator: JianHang Wang creator: MingQi Chen creator: ZhiFeng Tang creator: JingJie Luan creator: ZiYin Han creator: YangDe Liu creator: Tao Sun uri: https://doi.org/10.7717/peerj.18632 license: https://creativecommons.org/licenses/by/4.0 rights: ©2024 Jing et al. title: Exploration of key mechanisms underlying the therapeutic effects of AMD3100 on attenuating lipopolysaccharide-induced acute lung injury in mice link: https://peerj.com/articles/18698 last-modified: 2024-12-12 description: ContextAMD3100, a CXCR4 antagonist, has beneficial effects immaculate in the treatment of acute lung injury (ALI).ObjectiveALI is a severe inflammatory condition associated with poor prognosis and limited treatment options. AMD3100, has therapeutic effects that reduce ALI. Our study explored the regulatory mechanisms of AMD3100 in alleviating the injury of lipopolysaccharide (LPS)-induced ALI in mice.Materials and MethodsMale ICR mice were randomly divided into control, LPS-treated, AMD3100-treated, and LPS + AMD3100-treatment groups. The histological changes of lung tissues from different groups were evaluated using hematoxylin and eosin staining. Lung injury was measured by ELISA and lung wet/dry ratio. Moreover, lung tissues from the four groups were subjected to transcriptome sequencing followed by differential expression, functional enrichment, protein-protein interaction (PPI) networks, and transcription factor analyses. The validation of mRNAs and protein levels were conducted with qRT-PCR and ELISA.ResultsHematoxylin and eosin staining combined with the concentration of IL-1 and IL1-β and lung wet/dry ratios revealed that AMD3100 reduced the level of LPS-induced lung injury. Analysis of the transcriptome sequencing data identified 294 differentially expressed genes in the LPS-induced ALI mouse model. Based on the PPI network and module analysis, hub targets of AMD3100, such as Cxcl10 and Cxcl9, were identified in module 1, and hub targets, such as Cxcl12 and Cxcl1, were identified in module 2. Cxcl10 and Cxcl9 are involved in the Toll-like receptor signaling pathway, and Cxcl12 and Cxcl1 arae enriched in the nuclear factor-kappa B signaling pathway. Cxcl19, Cxcl10, and Cxcl1 are targeted by transcription factors like NF-κB. The validation of mRNAs and protein levels conducted by PCR and ELISA supported our transcriptome data.ConclusionsOur findings indicate that AMD3100 may exhibit a therapeutic effect on LPS-induced ALI in mice by modulating multiple chemokines to inhibit the Toll-like receptor/nuclear factor-kappa B signaling pathway. creator: Zhou Lv creator: Bohan Zhang creator: Hui Zhang creator: Yanfei Mao creator: Qihong Yu creator: Wenwen Dong uri: https://doi.org/10.7717/peerj.18698 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lv et al. title: Habitual tea consumption is associated with a lower prevalence of kidney stone disease in postmenopausal women link: https://peerj.com/articles/18639 last-modified: 2024-12-11 description: BackgroundMenopause is associated with an increased risk of kidney stone disease (KSD). However, for postmenopausal women, how to avoid KSD has rarely been studied. The aim of this study was to explore whether drinking tea is associated with a reduction in the prevalence of KSD in postmenopausal women.MethodsWe collected 11,484 postmenopausal women from the Taiwan Biobank, and used questionnaires to obtain information on tea drinking, KSD, and comorbidities. The participants were divided into two groups according to habitual tea consumption: tea-drinking and non-tea-drinking groups. The association between habitual tea consumption and KSD was examined by logistic regression analysis.ResultsThere were 2,035 postmenopausal women in the tea-drinking group and 9,449 postmenopausal women in the non-tea-drinking group. The mean age of all participants was 61 years. Compared to the non-tea-drinking group, the tea-drinking group had a significantly lower prevalence of KSD (7% vs. 5%). The odds ratio (OR) of KSD was lower in those who habitually drank tea than in those who did not (OR = 0.78; 95% confidence interval [CI] [0.63 to 0.96]) after adjusting for confounders. Moreover, postmenopausal women with a daily intake of two cups of tea or more had a 30% reduced risk of KSD compared to those who did not habitually drink tea (OR = 0.71, 95% CI [0.56 to 0.90]).ConclusionsOur results suggest that habitual tea drinking may be associated with a reduction in the prevalence of KSD in postmenopausal women. Further studies are warranted to investigate the protective effect of tea on the development of KSD. creator: Kuan-Hsien Wu creator: Jia-In Lee creator: Yung-Chin Lee creator: Jung-Tsung Shen creator: Hsun-Shuan Wang creator: Yao-Hsuan Tsao creator: Yi-Hsuan Wu creator: Shu-Pin Huang creator: Szu-Chia Chen creator: Jhen-Hao Jhan creator: Jiun-Hung Geng uri: https://doi.org/10.7717/peerj.18639 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Wu et al. title: Effects of defeat and entrapment on suicide risk in university population: the role of rumination and sex link: https://peerj.com/articles/18673 last-modified: 2024-12-11 description: BackgroundSuicide is recognized as a significant public health issue, with adolescents/young people being a risk group of concern. Taking the integrated motivational-volitional model as a reference, this study focuses on analyzing the association between defeat and entrapment, on the one hand, and suicide risk, on the other, in a university population without depressive symptoms, while also considering the role of rumination and sex.MethodThe survey study involved a community sample of 650 Spanish university students. A total of 524 students (150 men (Mage = 20.6, SD = 3.7) and 374 women (Mage = 20.4, SD = 3.6)) completed self-report measures of suicide risk, defeat, entrapment, and rumination.ResultsDefeat and entrapment were significantly associated with suicide risk, and higher rumination was both directly and indirectly associated with higher levels of entrapment through the variable of defeat. However, the effect of rumination on entrapment varied by sex.ConclusionDespite being a cross-sectional preliminary study, this work identifies important variables in the trajectory of suicidal ideation. Adolescence and young adulthood are a critical stage for intervening to reduce the risk of death by suicide, and this study provides findings that may inform preventive approaches. creator: Inmaculada Nayara Silvestre Vidal creator: Marta Nieto creator: Jorge Ricarte creator: María Dolores Vizcaíno Alcantud creator: David Hallford creator: Laura Ros uri: https://doi.org/10.7717/peerj.18673 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Silvestre Vidal et al. title: Characterization and clinical outcomes of outpatients with subacute or chronic post COVID-19 cough: a real-world study link: https://peerj.com/articles/18705 last-modified: 2024-12-11 description: BackgroundLimited research exists on the features and management of post-COVID cough. This real-world study investigates outpatients with subacute or chronic post-COVID cough, aiming to delineate characteristics and regimen responses within the population.MethodWe enrolled eligible patients from our outpatient unit between August 2023 and February 2024. Comprehensive clinical data, prescriptions, and patient-reported cough severity were collected during the primary visit and subsequent follow-ups.ResultA total of 141 patients, aged: 42 ± 14 years old, were included, with 70% being female. The median cough duration was 8 weeks (interquartile range 4–12 weeks). Sixty percent presented with a dry cough, while the rest had coughs with phlegm. Over half reported abnormal laryngeal sensations (54%). Twenty-one percent coughed during the day, while 32% coughed constantly, and 48% experienced nocturnal episodes. Compound methoxyphenamine capsules were the most prescribed, but our study found ICS/LABA to be the most effective, followed by compound methoxyphenamine capsules, montelukast, and Chinese patent drugs.ConclusionFemales exhibit a higher prevalence of post-COVID cough, and our study recommends ICS/LABA as the preferred treatment. These findings warrant validation through larger, prospectively designed studies. creator: Chun Yao creator: Dongliang Cheng creator: Wenhong Yang creator: Yun Guo creator: Tong Zhou uri: https://doi.org/10.7717/peerj.18705 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yao et al. title: Differential circulating miRNA profiles identified miR-423-5p, miR-93-5p, and miR-4532 as potential biomarkers for cholangiocarcinoma diagnosis link: https://peerj.com/articles/18367 last-modified: 2024-12-10 description: BackgroundCholangiocarcinoma (CCA) is high in morbidity and mortality rates which may be due to asymptomatic and effective diagnostic methods not available. Therefore, an effective diagnosis is urgently needed.MethodsInvestigation of plasma circulating miRNA (cir-miRNA) was divided into two phases, including the discovery phase (pooled 10 samples each from three pools in each group) and the validation phase (17, 16, and 35 subjects of healthy control (HC), O. viverrini (OV), and CCA groups, respectively). The plasma from healthy control subjects, O. viverrini infected subjects, and CCA subjects was used. In the discovery phase, plasma was pooled by adding an equal volume of plasma, and cir-miRNA was isolated and analyzed with the nCounter® SPRINT Profiler. The significantly different cir-miRNAs were selected for the validation phase. In the validation phase, cir-miRNA was isolated and analyzed using real time-quantitative polymerase chain reaction (RT-qPCR). Subsequently, statistical analysis was conducted, and diagnostic parameters were calculated.ResultsDifferential plasma cir-miRNA profile showed at least three candidates including miR-423-5p, miR-93-5p, and miR-4532 as potential biomarkers. From validation of these cir-miRNAs by RT-qPCR, the result showed that the satisfied sensitivity and specificity to differential CCA group from HC and OV group was obtained from miR-4532 (P < 0.05) while miR-423-5p and miR-93-5p can be used for differential CCA from OV and HC group (P < 0.05) with high specificity but limited the sensitivity. In conclusion, candidate cir-miRNAs have been identified as potential biomarkers including miR-423-5p, miR-93-5p and miR-4532. Screening by miR-4532 and confirmed with miR-423-5p, miR-93-5p were suggested for differential CCA patients in the endemic area of O. viverrini. creator: Kittiya Supradit creator: Sattrachai Prasopdee creator: Teva Phanaksri creator: Sithichoke Tangphatsornruang creator: Montinee Pholhelm creator: Siraphatsorn Yusuk creator: Kritiya Butthongkomvong creator: Kanokpan Wongprasert creator: Jutharat Kulsantiwong creator: Amnat Chukan creator: Smarn Tesana creator: Veerachai Thitapakorn uri: https://doi.org/10.7717/peerj.18367 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Supradit et al. title: Comparative leaf anatomy of two species of Ipomoea L. (Convolvulaceae): taxonomic importance and adaptations to xeric conditions of the cangas link: https://peerj.com/articles/18599 last-modified: 2024-12-10 description: BackgroundAccurate species identification is the first step towards establishing conservation strategies, especially regarding rare and threatened species, such as those studied here. Moreover, understanding the responses to the environment and growing conditions of endemic species is necessary for its conservation. This study compares the leaf anatomy of Ipomoea cavalcantei and I. marabaensis, which grow on the Brazilian ironstone outcrops (cangas) and exhibit morphological convergence.MethodsLeaf anatomical characters of the species were described. Additionally, the leaf adaptive potential of I. cavalcantei was evaluated, comparing individuals grown in natural canga areas (in situ) and cultivated in topsoil (ex situ). Quantitative analysis evaluated stomatal density, polar and equatorial diameter of stomata, and thickness of the epidermis and mesophyll.ResultsIpomoea cavalcantei and I. marabaensis can be distinguished by the mesophyll type. Ipomoea marabaensis is also characterized by the presence of lateral protuberances on the abaxial surface of the midrib. Individuals of I. cavalcantei under cultivation have lower stomatal density, although their functionality (polar/equatorial diameter) is more significant than those grown in a natural environment; these individuals also exhibit leaves with a thinner cuticle, abaxial epidermal cells with more sinuous walls, a lower occurrence of trichomes and secretory cells (laticifers), and more druse-containing idioblasts in the mesophyll. All these traits are adaptations to growing conditions that include lower light and the absence of water stress.ConclusionsLeaf anatomical traits showed to be useful to delimit Ipomoea cavalcantei and I. marabaensis in the non-reproductive stage. For individuals of I. cavalcantei cultivated in topsoil, some features, especially of the epidermis, respond to light and water supply. creator: Joyce C. R. Silva creator: Kleber R. Silva creator: Cecilio F. Caldeira creator: Aline Oriani creator: Mauricio T. C. Watanabe uri: https://doi.org/10.7717/peerj.18599 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Silva et al. title: Endorsement of reporting guidelines and clinical trial registration across urological medical journals: a cross-sectional study link: https://peerj.com/articles/18619 last-modified: 2024-12-10 description: IntroductionOver the years, funding for urologic diseases has witnessed a steady rise, reaching $587 million in 2020 from $541 million in 2018. In parallel, there has been a notable increase in the total number of urology journals from 2011 to 2018. This surge in research funding and journal publications calls for urologists to effectively navigate through a vast body of evidence to make the best evidence-based clinical decisions. Our primary objective was to assess the “instructions for authors” of these journals to determine the extent of endorsement of reporting guidelines for common study designs in medical research.MethodsTop urology journals were identified using the 2021 Scopus CiteScore and confirmed via Google Scholar Metrics h5-index. In a masked, duplicate manner, two investigators retrieved data from the “instructions for authors” webpages of the included journals. For each journal investigated in our study, the following data were extracted: journal title, 5-year impact factor, email responses of journal editors, mention of the EQUATOR Network in the “instructions for authors,” mention of the ICMJE in the “instruction for authors,” geographical region of publication and statements about clinical trial registration.ResultsOf the 92 urology journals examined, only one-third (32/92) mentioned the EQUATOR network in their “instructions for authors.” A total of 17 journals (17/92, 18.5%) did not mention a single reporting guideline. The most endorsed guideline was CONSORT at 67.4% (62/92). Clinical trial registration was not mentioned by 28 (30%), recommended by 27 (29%), and required by 37 journals (40%).ConclusionOur findings indicate that urology journals inconsistently endorse reporting guidelines and clinical trial registration. Based on these results, we propose that urology journals adopt a standardized approach, incorporating explicit requirements for reporting guidelines such as those listed on the EQUATOR Network and clinical trial registration for all relevant study designs. Specifically, journals should consider clearly stating mandatory or recommended guidelines for clinical trials, observational studies, and systematic reviews, among others. Future efforts should focus on evaluating the implementation of these policies and identifying barriers that hinder their adoption. creator: Alex Hagood creator: Joseph Case creator: Trevor Magee creator: Caleb Smith creator: Danya Nees creator: Griffin Hughes creator: Matt Vassar uri: https://doi.org/10.7717/peerj.18619 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hagood et al. title: Interspecies differences in the transcriptome response of corals to acute heat stress link: https://peerj.com/articles/18627 last-modified: 2024-12-10 description: Rising sea surface temperatures threaten the survival of corals worldwide, with coral bleaching events becoming more commonplace. However, different coral species are known to exhibit variable levels of susceptibility to thermal stress. To elucidate genetic mechanisms that may underlie these differences, we compared the gene repertoire of four coral species, Favites colemani, Montipora digitata, Acropora digitifera, and Seriatopora caliendrum, that were previously demonstrated to have differing responses to acute thermal stress. We found that more tolerant species, like F. colemani and M. digitata, possess a greater abundance of antioxidant protein families and chaperones. Under acute thermal stress conditions, only S. caliendrum showed a significant bleaching response, which was accompanied by activation of the DNA damage response network and drastic upregulation of stress response genes (SRGs). This suggests that differences in SRG orthologs, as well as the mechanisms that control SRG expression response, contribute to the ability of corals to maintain stability of physiological functions required to survive shifts in seawater temperature. creator: Jeric Da-Anoy creator: Niño Posadas creator: Cecilia Conaco uri: https://doi.org/10.7717/peerj.18627 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Da-Anoy et al. title: Construction and validation of a predictive model for the risk of malnutrition in hospitalized patients over 65 years of age with malignant tumours: a single-centre retrospective cross-sectional study link: https://peerj.com/articles/18685 last-modified: 2024-12-10 description: BackgroundNutritional status is a critical indicator of overall health in individuals suffering from malignant tumours, reflecting the complex interplay of various contributing factors. This research focused on identifying and analysing the factors influencing malnutrition among older patients aged ≥65 with malignant tumours and aimed to develop a comprehensive risk model for predicting malnutrition.MethodsThis study conducted a retrospective analysis of clinical data from 3,387 older inpatients aged ≥65 years with malignant tumours collected at our hospital from July 1, 2021, to December 31, 2023. The dataset was subsequently divided into training and validation sets at an 8:2 ratio. The nutritional status of these patients was evaluated using the Nutritional Risk Screening Tool 2002 (NRS-2002) and the 2018 Global Leadership Initiative on Malnutrition (GLIM) Standards for Clinical Nutrition and Metabolism. Based on these assessments, patients were categorized into either malnutrition or non-malnutrition groups. Subsequently, a risk prediction model was developed and presented through a nomogram for practical application.ResultsThe analysis encompassed 2,715 individuals in the development cohort and 672 in the validation cohort, with a malnutrition prevalence of 40.42%. A significant positive correlation between the incidence of malnutrition and age was observed. Independent risk factors identified included systemic factors, tumour staging (TNM stage), age, Karnofsky Performance Status (KPS) score, history of alcohol consumption, co-infections, presence of ascites or pleural effusion, haemoglobin (HGB) levels, creatinine (Cr), and the neutrophil-to-lymphocyte ratio (NLR). The predictive model exhibited areas under the curve (AUC) of 0.793 (95% confidence interval (CI) [0.776–0.810]) for the development cohort and 0.832 (95% CI [0.801–0.863]) for the validation cohort. Calibration curves indicated Brier scores of 0.186 and 0.190, while the Hosmer–Lemeshow test yielded chi-square values of 5.633 and 2.875, respectively (P > 0.05). Decision curve analysis (DCA) demonstrated the model’s clinical applicability and superiority over the NRS-2002, highlighting its potential for valuable clinical application.ConclusionThis study successfully devised a straightforward and efficient prediction model for malnutrition among older patients aged 65 and above with malignant tumours. The model represents a significant advancement as a clinical tool for identifying individuals at high risk of malnutrition, enabling early intervention with targeted nutritional support and improving patient outcomes. creator: Xuexing Wang creator: Jie Chu creator: Chunmei Wei creator: Jinsong Xu creator: Yuan He creator: Chunmei Chen uri: https://doi.org/10.7717/peerj.18685 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Spectrum analysis of inborn errors of metabolism for expanded newborn screening in Xinjiang, China link: https://peerj.com/articles/18173 last-modified: 2024-12-09 description: To determine the disease spectrum and genetic characteristics of inborn errors of metabolism (IEM) in Xinjiang province in the northwest of China, 41,690 newborn babies were screening by tandem mass spectrometry from November 2018 to December 2021. Of these, 57 newborn babies were referred for genetic analysis by next-generation sequencing, which was validated by Sanger sequencing. A total of 36 newborn babies and one relative were diagnosed with IEM, and the overall positive predictive value was 29.03%. The overall incidence of IEM in Xinjiang was 1:1,158 (36/41,690). The incidence of amino acidemias, organic acidemias, and fatty acid oxidation disorder were 1:1,668 (25/41,690), 1:4,632 (9/41,690), and 1:20,845 (2/41,690), respectively. Phenylketonuria and methylmalonic acidemia were the two most common inborn errors of metabolism (IEM), accounting for 83% (30/36) of all confirmed cases. Some hotspot mutations were observed for several IEMs, including PAH gene c.158G > A (p.Arg53His) and c.688G > A (p.Val230Ile) for hyperphenylalaninemia. Four mutation types of the MMACHC gene (e.g., c.609G > A (p.Trp203Ter), c.567dupT (p.Ile190fs)) and six mutation types of the MMUT gene (e.g., c.729_730insT (p.Asp244fs)) were found for methylmalonic acidemia. We also found 11 mutations in six genes: PCCB, IVD, GCDH, MCCC1, SLC22A5, and ACADS in this region. This study combined tandem mass spectrometry and next-generation sequencing technology for the screening and diagnosis of IEM. The study provides effective clinical guidance, and the data provide a basis for expanding newborn screening, genetic screening, and IEM gene consultation in Xinjiang, China. creator: Jingying Zhu creator: Li Han creator: Pingjingwen Yang creator: Ziyi Feng creator: Shuyuan Xue uri: https://doi.org/10.7717/peerj.18173 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhu et al. title: Accuracy of augmented reality navigated surgery for placement of zygomatic implants: a human cadaver study link: https://peerj.com/articles/18468 last-modified: 2024-12-09 description: PurposePlacement of zygomatic implants in the most optimal prosthetic position is considered challenging due to limited bone mass of the zygoma, limited visibility, length of the drilling path and proximity to critical anatomical structures. Augmented reality (AR) navigation can eliminate some of the disadvantages of surgical guides and conventional surgical navigation, while potentially improving accuracy. In this human cadaver study, we evaluated a developed AR navigation approach for placement of zygomatic implants after total maxillectomy.MethodsThe developed AR navigation interface connects a commercial navigation system with the Microsoft HoloLens. AR navigated surgery was performed to place 20 zygomatic implants using five human cadaver skulls after total maxillectomy. To determine accuracy, postoperative scans were virtually matched with preoperative three-dimensional virtual surgical planning, and distances in mm from entry-exit points and angular deviations were calculated as outcome measures. Results were compared with a previously conducted study in which zygomatic implants were positioned with 3D printed surgical guides.ResultsThe mean entry point deviation was 2.43 ± 1.33 mm and a 3D angle deviation of 5.80 ± 4.12° (range 1.39–19.16°). The mean exit point deviation was 3.28 mm (±2.17). The abutment height deviation was on average 2.20 ± 1.35 mm. The accuracy of the abutment in the occlusal plane was 4.13 ± 2.53 mm. Surgical guides perform significantly better for the entry-point (P = 0.012) and 3D angle (P = 0.05); however, there is no significant difference in accuracy for the exit-point (P = 0.143) when using 3D printed drill guides or AR navigated surgery.ConclusionDespite the higher precision of surgical guides, AR navigation demonstrated acceptable accuracy, with potential for improvement and specialized applications. The study highlights the feasibility of AR navigation for zygomatic implant placement, offering an alternative to conventional methods. creator: Sander Tabernée Heijtmeijer creator: Haye Glas creator: Nard Janssen creator: Nathalie Vosselman creator: Sebastiaan de Visscher creator: Fred Spijkervet creator: Gerry Raghoebar creator: Remco de Bree creator: Antoine Rosenberg creator: Max Witjes creator: Joep Kraeima uri: https://doi.org/10.7717/peerj.18468 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tabernée Heijtmeijer et al. title: The role of CD47 in immune escape of colon cancer and its correlation with heterogeneity of tumor immune microenvironment link: https://peerj.com/articles/18579 last-modified: 2024-12-09 description: BackgroundCluster of differentiation 47 (CD47), a transmembrane protein, plays a critical role in regulating cellular functions and maintaining immune homeostasis. Its expression has been shown to influence cancer prognosis. In this study, we investigated the role of CD47 in tumor progression in colon adenocarcinoma (COAD) and evaluated its potential as a target for immunotherapy.Materials and MethodsWe analyzed surgical samples from 96 COAD patients. Immunohistochemical analysis was performed on 90 samples, while the remaining 6 were subjected to multiplex immunofluorescence. To explore the association between CD47 expression and clinicopathological characteristics, we integrated transcriptome data from The Cancer Genome Atlas and the Gene Expression Omnibus using R software. The Tumor Immune Estimation Resource and Kaplan-Meier plotter were utilized to assess the relationship between CD47 expression, patient prognosis, and immune infiltration. Furthermore, the single-cell Tumor Immune System Interaction Database was used to examine the correlation between CD47 expression and the tumor microenvironment (TME). All included patients gave oral and written informed consent. The study was approved by the Ethics Committee of 3201 Hospital (full name: Medical Ethics Committee of 3201 Hospital).ResultsCD47 was found to be overexpressed in various tumors, including COAD. Higher CD47 expression was significantly associated with more advanced tumor stages, including TNM staging, T staging, and N staging (P < 0.05). A robust correlation was observed between CD47 expression and immune cell infiltration in COAD. Patients with elevated CD47 expression tended to have longer disease-free intervals, although this benefit was diminished in cases with high infiltration of M1 macrophages. The immunosuppressive function of CD47 primarily acted through the CD47/SIRPα pathway. Additionally, distinct cellular compositions and distributions were identified between primary and metastatic COAD, underscoring the heterogeneity of the TME. CD47 also influenced the TME by modulating cytokine and cytokine receptor interactions.ConclusionCD47 represents a promising prognostic biomarker and a potential target for immunotherapy in COAD. These findings provide new insights into therapeutic strategies aimed at modulating the TME and improving patient outcomes. creator: Qiu-Si Tian creator: ChunMei Zhang creator: Zhi-Jun Bao creator: ZhiGang Pei uri: https://doi.org/10.7717/peerj.18579 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Tian et al. title: Observation of peri-implant bone loss rates in patients visiting dentist—A retrospective evaluation of patients of a faculty hospital for one year link: https://peerj.com/articles/18643 last-modified: 2024-12-09 description: BackgroundMany studies have been published on the relationship between different parameters with marginal bone loss around implants. The results of these studies vary, but some variables such as smoking or certain systemic conditions are more likely to predispose or exacerbate the resorption around implants. The aim of this study was to determine the rates of implants with radiographically detected marginal bone loss and to determine whether there is a relationship between the severity of destruction and certain risk factors like location of implant, restoration type, systemic condition, age, sex or smoking habits.Materials and MethodsPanoramic radiographs obtained for 1 year were examined. Patients with bone loss around the implant were classified according to the region of implant placement, type of restoration on implants, systemic diseases, and smoking habits. The rate of bone loss around the implants was recorded as the resorption score. Double and multiple comparison tests were applied to observe whether the resorption scores were related to the variables.ResultsOf 17,352 patients, 1,465 had at least one implant, and 1,116 of these had no bone loss. A total of 181 patients (863 implants) included in the study, there was a weak correlation between age (p = 0.017) and resorption rate. Implants supporting bridge restorations had higher resorption scores. Gender, age, and systemic conditions alone are not effective in increasing peri-implant bone loss (p < 0.05); therefore, placing implants in the mandible (p = 0.020) or using implants to support bridge restorations(p = 0.027) may make implants more vulnerable to resorption. creator: Ilkim Karadag creator: Halis Kurnaz creator: Mehmet Murat Akkaya creator: İrem Karadag creator: Zeynep Ilayda Konukçu Kurnaz uri: https://doi.org/10.7717/peerj.18643 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Karadag et al. title: Evaluation of the effect of a communication skills course on medical students’ attitude towards patient-centered care: a prospective study link: https://peerj.com/articles/18676 last-modified: 2024-12-09 description: BackgroundThis study aims to examine whether a communication skills course (Early Clinical Exposure–ECE) might support shaping medical students’ attitudes towards patient-centered care at Taibah University, Saudi Arabia. Attitudes were measured before and after the course using the Patient Practitioner Orientation Scale (PPOS), which assesses students’ orientation towards patient-centeredness.MethodsThis prospective observational study collected data at two points: the start of year two and the start of year four from the same cohort. The PPOS, divided into the sharing subscale (physician shares information, power, and control with the patient) and the caring subscale (physician considers the patient’s emotions, preferences, and expectations), was used to evaluate students’ attitudes. Mean scores were calculated, and independent sample t-tests were employed to assess statistical significance.ResultsOf the students targeted, 153 participated at year two (response rate = 93.5%) and 143 at year four (response rate = 89.5%). Significant progress was observed in the sharing subscale, with scores increasing from 3.23 ± 0.53 to 3.40 ± 0.60 (p = 0.015). However, the caring subscale exhibited a significant decline, with scores dropping from 4.06 ± 0.53 to 3.76 ± 0.68 (p < 0.001). As a result, there was no significant overall change in the total PPOS score (p = 0.282). Female students showed more progress in the sharing subscale than males.ConclusionsThe communication skills course might have had a positive impact on students’ attitudes towards sharing information in decision-making with patients, but notably, the medical students’ caring attitudes declined. This indicates a need for further emphasis on patient-centered communication, especially on the caring aspects, in the medical curriculum. creator: Khalid Gaffer Mohamed creator: Amer Almarabheh creator: Asim Mukhideer Almughamsi creator: Hany Atwa creator: Mohamed Hany Shehata uri: https://doi.org/10.7717/peerj.18676 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mohamed et al. title: Genetic diversity of the Khorat snail-eating turtle (Malayemys khoratensis) in Thailand link: https://peerj.com/articles/18699 last-modified: 2024-12-09 description: IntroductionMalayemys khoratensis is a freshwater turtle species endemic to northeastern Thailand and Lao PDR. While M. khoratensis is relatively common and widespread in Thailand, its population size and demographic trends remain largely unknown, as direct population estimates are lacking. This species faces significant threats from consumption, exploitation, and trade. Therefore, this study aims to investigate the genetic diversity, population structure, and demographic trends of M. khoratensis in northeastern Thailand, using two mitochondrial DNA genes, Cyt b and ND4.MethodWe grouped the turtles based on three major river basins in northeastern Thailand: Mun, Chi, and Northeast Mekong to assess population structure and test the isolation-by-basin hypothesis. The Cyt b and ND4 genes of 49 M. khoratensis individuals across 15 provinces in Thailand were sequenced, and 15 sequences from a previous study of Ihlow et al. (2016) were included into the analyses. We constructed a haplotype network from the concatenated sequences and analyzed the population structure with the analysis of molecular variance (AMOVA). Additionally, we used a Bayesian Skyline plot (BSP) analysis to estimate the effective female population size and explore the demographic history of this species.ResultsOur analysis identified 13 unique haplotypes defined by 26 polymorphic sites from 64 samples. The total haplotype diversity for M. khoratensis was 0.819, while nucleotide diversity was 0.0031. The haplotype network and AMOVA revealed no distinct population structure among the river basins, suggesting gene flow across these regions. The BSP estimated a stable effective female population size of approximately 130,000 individuals since around 100,000 years ago (late Pleistocene).ConclusionOur findings indicated no significant population structure by river basin, which may be due to natural movement between basins or potential human-mediated translocations linked to the turtle trade. The demographic trend of M. khoratensis appears to have been stable over time. However, given the ongoing exploitation of this species, we recommend regular monitoring of population trends to support its long-term survival. creator: Thotsapol Chaianunporn creator: Monthakarn Mokarat creator: Apichaya Ruangsakunporn creator: Tanapipat Walalite creator: Wibhu Kutanan creator: Khemika Lomthaisong creator: Kanokporn Chaianunporn creator: Sarun Keithmaleesatti uri: https://doi.org/10.7717/peerj.18699 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Chaianunporn et al. title: A single-center retrospective study of ectopic lymphoid tissues in idiopathic membranous nephropathy: clinical pathological characteristics and prognostic value link: https://peerj.com/articles/18703 last-modified: 2024-12-09 description: BackgroundIn recent years, ectopic lymphoid tissue (ELT) has been increasingly confirmed as a new biomarker for kidney injury or inflammation. However, there is insufficient research on the relationship between ELT grading and the progression of idiopathic membranous nephropathy (IMN).MethodsA total of 147 patients with biopsy-proven IMN in our institution from March 2020 to June 2022 were classified into five grades based on the different distribution of lymphocyte subsets in renal tissue (G0: no B cells or T cells, G1: scattered B and T cells, G2: clustered B and T cells, G3: an aggregation region of B and T cells without a central network, G4: highly organized and formed zones of B and T cells with a central network of follicular dendritic cells and scattered macrophages), and were further divided into low-grade group (G0+G1), intermediate-grade group (G2) and high-grade group (G3+G4). The clinicopathological data, induction treatment response and prognosis among the three groups were analyzed and compared retrospectively.ResultsAs the grading of ectopic lymphoid tissues increased, patients were older, with a higher prevalence of hypertension, a higher 24-h urinary protein level, lower baseline hemoglobin and estimated glomerular filtration rate (eGFR) levels, and more severe renal pathological damage. Logistic regression analysis showed that after 6 months of induction treatment, patients in the high-grade group were more likely to be in non-remission than those in the low-grade group (odds ratios [ORs] of the three adjusted models were 4.310, 4.239, and 5.088, respectively, P-values were 0.005, 0.006, and 0.001, respectively). Kaplan-Meier survival analysis indicated that patients in the intermediate- and high-grade groups had significantly lower renal cumulative survival rate than those in the low-grade group (P = 0.025). Univariate Cox analysis showed that the risk of adverse renal outcome was 3.662 times higher in the intermediate- and high-grade groups than in the low-grade group (95% confidence interval [CI] [1.078–12.435]; P = 0.037). Multivariate Cox analysis revealed that failure of remission at the first 6 months (hazard ratio [HR] = 5.769; 95% CI [1.854–17.950]; P = 0.002) remained an independent risk factor for poor renal outcome in patients with IMN.ConclusionsGrading of renal ectopic lymphoid tissues correlates with disease activity and severity in IMN patients and can be used as an indicator to assess the risk of IMN progression. creator: Jing Zhang creator: Siyu Chen creator: Haiying Zheng creator: Siyi Rao creator: Yuanyuan Lin creator: Jianxin Wan creator: Yi Chen uri: https://doi.org/10.7717/peerj.18703 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Association of vaccine intention against COVID-19 using the 5C Scale and its constructs: a Pima County, Arizona cross-sectional survey link: https://peerj.com/articles/18316 last-modified: 2024-12-06 description: BackgroundVaccine hesitancy has been ranked as one of the top 10 threats to global health by the World Health Organization. The 5C model (Confidence, Calculation of risk, Complacency, Collective Responsibility, and Constraints) and an accompanying tool to measure vaccine hesitancy, summarize several significant explanatory variables, and move beyond the most common explanatory variable, Confidence.MethodsFrom January to May 2021, we administered a cross-sectional survey among adults in Pima County, Arizona in collaboration with the local health department to assess psychological antecedents to (i.e., psychological factors that lead to) COVID-19 vaccination using the 5C Scale. Participants were recruited virtually for the survey using multiple recruitment methods. Unadjusted and adjusted hierarchical ordinal logistic regressions were conducted to determine if the 5C variables had an association with intention to vaccinate (or intent to vaccinate) against COVID-19.ResultsOf the 1,823 participants who responded to the survey, 924 (76%) were included in the final analyses. Respondents were White (71%), non-Hispanic (59%), Female (68%), Liberal (37%) and Married (46%). The average age of the participants was 43.9 (±1.3) years. Based on the 5C Scale, Confidence (adjOR:3.64, CI [3.08–4.29]), Collective Responsibility (adjOR:1.94, CI [1.57–2.39]) and Complacency (adjOR:0.64, CI [0.51–0.80]) were significantly associated with intention to vaccinate against COVID-19.ConclusionThree of the five 5C variables were associated with the intention to vaccinate, two positively and one negatively. A limitation of the study was that the sample was not weighted to be representative of Pima County. Future research should focus on determining which interventions can bolster Confidence and Collective Responsibility attitudes in communities, while dampening Complacency, to better promote vaccine uptake. creator: Maiya G. Block Ngaybe creator: Namoonga Mantina creator: Benjamin Pope creator: Veena Raghuraman creator: Jacob Marczak creator: Sonja Velickovic creator: Dominique Jordan creator: Mary Kinkade creator: Carlos Mario Perez-Velez creator: Beatrice J. Krauss creator: Shailesh M. Advani creator: Melanie Bell creator: Purnima Madhivanan uri: https://doi.org/10.7717/peerj.18316 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Block Ngaybe et al. title: Improvement of contact lens-associated dry eye disease with the use of hydrogen peroxide link: https://peerj.com/articles/18482 last-modified: 2024-12-06 description: BackgroundThe dropout rate of contact lens users has not decreased significantly over the years. Despite continuous improvements in contact lens (CL) designs, materials and surface treatments, the number of CL users who drop out remains similar to the number of new CL users. The aim of this study is to analyse the improvement in contact lens-associated dry eye disease (CLADE), quantified with the OSDI questionnaire when changing maintenance system solution from multipurpose solution to hydrogen peroxide.MethodsThis study included contact lens users for over a year as the multipurpose solution for the maintenance system, suffering from CLADE, and those who scored over 13 in the ocular surface disease index questionnaire, and did not manifest any clinical signs over 3 in the EFRON scale. The non-parametric data distribution was verified with the Kolmogorov-Smirnov test and Wilcoxon signed-rank test, which was used to compare the visual acuity (VA), OSDI score and bulbar redness (EFRON scale) of the follow-up visit against the baseline value.ResultsThirty-eight patients were included. Analysing the clinical parameters between the initial and final visit after one month of hydrogen peroxide use, a statistically significant improvement was found in the VA, bulbar hyperemia, OSDI scale and their subscales of the total sample (P < 0.04).ConclusionThis study is intended as a first step towards a standardised protocol of actions to improve CLADE in an attempt to reduce contact lens dropout using OSDI as a tool for detection. creator: Susana Castro creator: Laura Garcia-Aguilar creator: Eduardo Garcia-Brion creator: Sofia Pérez-García creator: Consuelo Rosique creator: Carmelo Baños creator: Irene Sanchez uri: https://doi.org/10.7717/peerj.18482 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Castro et al. title: The motivation to inform others: a field experiment with wild chimpanzees link: https://peerj.com/articles/18498 last-modified: 2024-12-06 description: BackgroundAccumulating evidence indicates that some ape species produce more alarm behaviors to potential dangers when in the presence of uninformed conspecifics. However, since previous studies presented naturalistic stimuli, the influence of prior experience could not be controlled for.MethodTo examine this, we investigated whether apes (wild chimpanzees of the Budongo Forest, Uganda) would communicate differently about a novel danger (an unusually large spider) depending on whether they were with an uniformed conspecific. We tested nine adult males, four of which were exposed to the danger twice alone (Non-Social group), while the remaining five were exposed to the danger first alone and then in the presence of conspecifics (Social group).ResultsWe found that both alarm calling and gaze marking (i.e., persistent gaze after stimulus detection) were more persistent in the Social than Non-Social group, although the effect of condition only reached statistical significance for gaze marking, nonetheless suggesting that chimpanzees tailored their warning behavior to the presence of others, even if they were already familiar with the potential threat. creator: Derry Taylor creator: Sam Adue creator: Monday M’Botella creator: Denis Tatone creator: Marina Davila-Ross creator: Klaus Zuberbühler creator: Guillaume Dezecache uri: https://doi.org/10.7717/peerj.18498 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Taylor et al. title: A review of fossil scorpion higher systematics link: https://peerj.com/articles/18557 last-modified: 2024-12-06 description: Scorpions (Arachnida: Scorpiones) are a diverse and widespread arachnid order with a rich and deep fossil record. Here we review the, sometimes complex, historical development of fossil scorpion higher classification. We present a chronological account of family and genus names, together with an overview of higher taxa as potential clade names. In 1884 Thorell & Lindström divided scorpions based on whether the legs were short and pointed (Apoxypoda) or ended in paired claws (Dionychopoda). Pocock in 1911 used the morphology of the ventral mesosomal sclerites, which could either be bilobed (Lobosterni) or of a modern configuration (Orthosterni). Petrunkevitch in 1949 attached importance to a putative first opisthosomal tergite being present (Protoscorpionina) or absent (Euscorpionina). Kjellesvig-Waering in 1986 recognised four major groups (Holosternina, Meristosternina, Lobosternina and Bilobosternina) based on the shape of the ventral mesosomal sclerites. The Stockwell/Jeram schemes from the 1980s and 1990s proposed a cladistic progression from early branching lineages, for which the names Protoscorpiones and Palaeoscorpiones were used, towards Scorpiones sensu stricto defined by the presence of book lungs and coxapophyses. Scorpiones was further divided into Mesoscorpionina and Neoscorpionina. Neoscorpions were characterised by a reduced number of lateral eye lenses and comprise the paleosterns, with marginal lung spiracles, and orthosterns with spiracles in the middle of the sternite. We briefly discuss the merits of these alternatives and present a summary of the current higher classification of scorpions. Forty-three extinct family groups are currently recognised, and of the 24 living families seven have fossil representatives. Including incertae sedis taxa, there are 76 extinct genera and five extant genera with fossil representatives. Both modern parvorders, Buthida and Iurida, were potentially present in the Triassic. Buthidae, Chaerilidae, Chactidae and perhaps Hormuridae have been reported from the Cretaceous. Euscorpiidae are known from the Palaeogene and Scorpionidae has potential (but unconfirmed) records from the Neogene. Given the complexity of this history and the present taxonomy of the group, we hope this contribution provides a first step towards simplifying fossil scorpion systematics. creator: Jason A. Dunlop creator: Russell J. Garwood uri: https://doi.org/10.7717/peerj.18557 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dunlop and Garwood title: Nonlinear relationship between circulating natural killer cell count and 1-year relapse rates in myasthenia gravis: a retrospective cohort study link: https://peerj.com/articles/18562 last-modified: 2024-12-06 description: BackgroundThe relapse rate in myasthenia gravis (MG) is high, and promising therapies have emerged; however, identifying potential predictive factors for relapse remains a challenge. This study aimed to explore the association between circulating natural killer (NK) cell levels and the risk of recurrence in MG.MethodsThis retrospective cohort study included 265 patients with MG whose data were included in the Neurology Department of the Affiliated Hospital of Guizhou Medical University database between March 2015 and March 2022. Data from electronic medical records were collected, which included the patients’ circulating NK cell count (exposure variable) and demographic/clinical characteristics (covariates). The primary outcome was the 1-year MG recurrence rate.ResultsThe study revealed a non-linear relationship between peripheral NK cell count and MG recurrence, with an inflection point at 5.38. Below this threshold, the risk of recurrence was low with higher NK cell counts (relative risk (RR): 0.23, 95% confidence interval (CI) [0.11–0.490]); above this threshold, no significant association was observed (RR: 1.43, 95% CI [0.62–3.34]). Furthermore, the NK cell proportion showed no significant linear or non-linear association with MG recurrence risk (RR: 0.84, 95% CI [0.57–1.2]).ConclusionThis study provides epidemiological evidence of a potential association between peripheral NK cell count and MG recurrence risk, suggesting an immunoregulatory protective effect within a specific NK cell count range. These findings may inform more personalized MG treatment strategies, warranting further validation in larger and more diverse cohorts. creator: Yifan Zhang creator: Zhiguo Wen creator: Meiqiu Chen creator: Cong Xia creator: Fang Cai creator: Lan Chu uri: https://doi.org/10.7717/peerj.18562 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Evidence of prostate cancer-linked virus zoonoses from biophysical genomic variations link: https://peerj.com/articles/18583 last-modified: 2024-12-06 description: An ongoing double-blind examination of (mathematically) smooth functional dependences of population-based genomic distributions of single nucleotide polymorphisms (SNPs) on quantified environmental parameters has flagged a SNP that has been associated with prostate cancer for dependence on zoonotic viruses. The SNP rs13091518 is an intergenic variant near the gene/pseudo-gene COX6CP6 on chromosome 3. The risk T allele, which is the major allele in all homeostatic populations considered, clearly demonstrates a negative adaptive force of about −0.1 universal genomic energy units/zoonotic virus unit. This biophysical perspective has thus provided evidence for a causative relationship between zoonotic viruses and prostate cancer. Our findings are consistent with other studies that have found an association between several zoonotic viruses and prostate cancer. This result demonstrates the significance of an intergenic variant in the adaptive response to a viral zoonotic pathogen. creator: Daniah Alsufyani creator: James Lindesay uri: https://doi.org/10.7717/peerj.18583 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Alsufyani and Lindesay title: Upregulation of HPV16E1 and E7 expression and FOXO3a mRNA downregulation in high-grade cervical neoplasia link: https://peerj.com/articles/18601 last-modified: 2024-12-06 description: BackgroundCervical cancer remains a significant global health concern, ranking as the fourth most prevalent cancer among women worldwide. Human papillomaviruses (HPV) transcribe many genes that might be responsible for cervical cancer development. This study aims to investigate the correlation between the expression of HPV16 early genes and the mRNA expression of human FOXO3a, a tumor suppressor gene, in association with various stages of cervical precancerous lesions.MethodsEighty-five positive HPV16 DNA cervical swab samples were recruited and categorized based on cytology stages, i.e., negative for intraepithelial lesion or malignancy (NILM), atypical squamous cells of undetermined significance (ASC-US), low-grade squamous intraepithelial lesion (LSIL), atypical squamous cell cannot exclude HSIL (ASC-H), high-grade squamous intraepithelial lesion (HSIL). RT-qPCR was performed to amplify HPV16E1, E4, E6, E6*I, E7, and human FOXO3a mRNA expression in all samples. The relative expression of those genes was calculated using GAPDH as a control. Detection of FOXO3a mRNA expression in the cervical cancer cell line by RT-qPCR and meta-analysis of FOXO3a expression using the RNA-Seq dataset by GEPIA2 were analyzed to support the conclusions.ResultsAmong the cervical samples, HPV16E1 and E7 were significantly increased expression correlating to disease severity. HPV16E4 mRNA expression was 100% detected in all LSIL samples, with a significant increase observed from normal to LSIL stages. Conversely, FOXO3a mRNA expression decreased with disease severity, and the lowest expression was observed in HSIL/squamous cell carcinoma (SCC) samples. In addition, similar results of FOXO3a downregulation were also found in the cervical cancer cell line and RNA-Seq dataset of cervical cancer samples.ConclusionHPV16 early mRNA levels, including E1 and E7, increase during cancer progression, and downregulation of FOXO3a mRNA is a characteristic of cervical cancer cells and HSIL/SCC. Additionally, HPV16E4 mRNA expression was consistently detected in all LSIL samples, suggesting the presence of active viral replication. These findings might lead to further investigation into the interplay between HPV gene expression and host cell factors for targeted therapeutic strategies in cervical cancer management. creator: Thanayod Sasivimolrattana creator: Aileen Gunawan creator: Warattaya Wattanathavorn creator: Chavis Pholpong creator: Arkom Chaiwongkot creator: Pattarasinee Bhattarakosol creator: Parvapan Bhattarakosol uri: https://doi.org/10.7717/peerj.18601 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sasivimolrattana et al. title: Health status and morphometrics of Galápagos magnificent frigatebirds (Fregata magnificens magnificens) determined by hematology, biochemistry, blood gas, and physical examination link: https://peerj.com/articles/18609 last-modified: 2024-12-06 description: The magnificent frigatebird (Fregata magnificens; MFB) is a widely distributed seabird. It has breeding areas in the tropical Atlantic Ocean and the Pacific Ocean (extending along Central America up to Baja California) (Schreiber & Burger, 2001). The Fregata magnificens magnificens (MFB-Gal) subspecies is native to the Galápagos Islands. This is the first-time hematology and blood chemistry parameters have been published for the F. m. magnificens (MFB-Gal) from the Galápagos Islands. Analysis was run on blood samples drawn from n = 16 adult MFB-Gal captured by hand at their nests at North Seymour and Daphne Major Islands in the Galápagos Islands (n = 10 MFB-Gal in June 2017 and n = 6 MFB-Gal in July 2022). There were ten female birds and six male birds in total. A portable blood analyzer (iSTAT) was used to obtain near immediate field results for total carbon dioxide (TCO2), hematocrit (Hct), hemoglobin (Hb), sodium (Na), potassium (K), chloride (Cl), ionized calcium (iCa), total protein (TP), anion gap and glucose. Blood lactate was measured using a portable Lactate Plus™ analyzer. Average heart rate, respiratory rate, body weight, body temperature, biochemistry and hematology parameters were comparable to healthy individuals of other Fregatidae of the same species (magnificent frigatebird subspecies from Brazil, Fregata magnificens, likely F. m. rothschildi) or similar species (great frigatebird, Fregata minor, from the Galápagos Islands). There were some statistically significant differences between the males and females F. m. magnificens (MFB-Gal) in the Galápagos, including bill depth, bill width, wing length, weight, and chloride blood value. The reported results provide baseline data that can be used for comparisons among populations and in detecting changes in health status among Galápagos magnificent frigatebirds and other populations of magnificent frigatebirds. creator: Kimberly E. Guzmán creator: Diane Deresienski creator: Juan Pablo Muñoz-Pérez creator: Ronald K. Passingham creator: Alice Skehel creator: Catalina Ulloa creator: Cristina Regalado creator: Gregory A. Lewbart creator: Carlos A. Valle uri: https://doi.org/10.7717/peerj.18609 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Guzmán et al. title: The use of phosphate rock and plant growth promoting microorganisms for the management of Urochloa decumbens (Stapf.) R.D. Webster in acidic soils link: https://peerj.com/articles/18610 last-modified: 2024-12-06 description: BackgroundForage production in tropical soils is primarily limited by nutrient deficiencies, especially nitrogen (N) and phosphorus (P). The use of phosphate rock by plants is limited by its low and slow P availability and microbial phosphate solubilization is the main mechanism for P bioavailability in the soil-root system. The objectives of this study were (i) select a nitrogen-fixing bacteria which could be used as a co-inoculant with the Penicillium rugulosum IR94MF1 phosphate-solubilizing fungus and (ii) evaluate under field conditions the effect of inoculation combined with phosphate rock (PR) application on yield and nutrient absorption of a Urochloa decumbens pasture which was previously established in a low-fertility, acidic soil.MethodsVarious laboratory and greenhouse tests allowed for the selection of Enterobacter cloacae C17 as the co-inoculant bacteria with the IR94MF1 fungus. Later, under field conditions, a factorial, completely randomized block design was used to evaluate the inoculation with the IR94MF1 fungus, the IR94MF1+C17 co-inoculation, and a non-inoculated control. Two levels of fertilization with PR treatment (0 kg/ha and 200 kg/ha P2O5) were applied to each.ResultsDuring five consecutive harvests it was observed that the addition of biofertilizers significantly increased (p < 0.05) the herbage mass and N and P assimilation compared to the non-inoculated control. However, no statistically significant differences were observed for the PR application as P source.ConclusionP. rugulosum IR94MF1 is capable of solubilizing and accumulating P from the phosphate rock, making it available for plants growing in acid soils with low N content. These inoculants represent a good option as biofertilizers for tropical grasses already established in acidic soils with low N content. creator: Alexandro Barbosa creator: Isbelia Reyes creator: Alexis Valery creator: Carlos Chacón Labrador creator: Oscar Martínez creator: Maximo F. Alonso uri: https://doi.org/10.7717/peerj.18610 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Barbosa et al. title: In vitro culture of leukemic cells in collagen scaffolds and carboxymethyl cellulose-polyethylene glycol gel link: https://peerj.com/articles/18637 last-modified: 2024-12-06 description: BackgroundChronic lymphocytic leukemia (CLL) is a common adult leukemia characterized by the accumulation of neoplastic mature B cells in blood, bone marrow, lymph nodes, and spleen. The disease biology remains unresolved in many aspects, including the processes underlying the disease progression and relapses. However, studying CLL in vitro poses a considerable challenge due to its complexity and dependency on the microenvironment. Several approaches are utilized to overcome this issue, such as co-culture of CLL cells with other cell types, supplementing culture media with growth factors, or setting up a three-dimensional (3D) culture. Previous studies have shown that 3D cultures, compared to conventional ones, can lead to enhanced cell survival and altered gene expression. 3D cultures can also give valuable information while testing treatment response in vitro since they mimic the cell spatial organization more accurately than conventional culture.MethodsIn our study, we investigated the behavior of CLL cells in two types of material: (i) solid porous collagen scaffolds and (ii) gel composed of carboxymethyl cellulose and polyethylene glycol (CMC-PEG). We studied CLL cells’ distribution, morphology, and viability in these materials by a transmitted-light and confocal microscopy. We also measured the metabolic activity of cultured cells. Additionally, the expression levels of MYC, VCAM1, MCL1, CXCR4, and CCL4 genes in CLL cells were studied by qPCR to observe whether our novel culture approaches lead to increased adhesion, lower apoptotic rates, or activation of cell signaling in relation to the enhanced contact with co-cultured cells.ResultsBoth materials were biocompatible, translucent, and permeable, as assessed by metabolic assays, cell staining, and microscopy. While collagen scaffolds featured easy manipulation, washability, transferability, and biodegradability, CMC-PEG was advantageous for its easy preparation process and low variability in the number of accommodated cells. Both materials promoted cell-to-cell and cell-to-matrix interactions due to the scaffold structure and generation of cell aggregates. The metabolic activity of CLL cells cultured in CMC-PEG gel was similar to or higher than in conventional culture. Compared to the conventional culture, there was (i) a lower expression of VCAM1 in both materials, (ii) a higher expression of CCL4 in collagen scaffolds, and (iii) a lower expression of CXCR4 and MCL1 (transcript variant 2) in collagen scaffolds, while it was higher in a CMC-PEG gel. Hence, culture in the material can suppress the expression of a pro-apoptotic gene (MCL1 in collagen scaffolds) or replicate certain gene expression patterns attributed to CLL cells in lymphoid organs (low CXCR4, high CCL4 in collagen scaffolds) or blood (high CXCR4 in CMC-PEG). creator: Hana Svozilova creator: Lucy Vojtova creator: Jana Matulova creator: Jana Bruknerova creator: Veronika Polakova creator: Lenka Radova creator: Michael Doubek creator: Karla Plevova creator: Sarka Pospisilova uri: https://doi.org/10.7717/peerj.18637 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Svozilova et al. title: The mediation role of sleep on the relationship between drinks behavior and female androgenetic alopecia link: https://peerj.com/articles/18647 last-modified: 2024-12-06 description: ObjectivesTo investigate the relationship between drinks behavior and female androgenetic alopecia (AGA) and to clarify the mediating effect of sleep behavior on such relationship.MethodsA total of 308 female AGA patients and 305 female normal controls were recruited from the hospital, and questionnaires including drinks behavior and sleep behavior were inquired among them. Blood sugar and blood lipids were detected. Then, the mediating effect of sleep behavior on the relationship between drinks behavior and AGA was analyzed.ResultsFemale AGA patients presented a higher frequency of intake of sweetened tea drinks. It was found that occasional intake (1–2 times per week; ORadj = 2.130, 95% CI [1.495–3.033]) and frequent intake (3–6 time per week; ORadj = 2.054, 95% CI [1.015–4.157]) of sweetened tea drinks were associated with AGA. The daily sugar intake from soft drinks increased the risk of AGA (ORadj = 1.025, 95% CI [1.003–1.048]), and hyperglycemia was positively associated with alopecia (ORadj = 1.897, 95% CI [1.225–2.936]). In addition, bedtime after 12 pm significantly increased the risk of developing alopecia (ORadj = 2.609, 95% CI [1.020–6.676]). Interestingly, bedtime, instead of daily sugar intake from soft drinks, could mediate the relationship between sweetened tea drinks intake and alopecia.ConclusionsSweetened tea drinks consumption increases the risk of female AGA, which is mediated by bedtime. creator: Shiqi Liu creator: Hao Gu creator: Ruxin Ji creator: Wei Shi creator: Fangfen Liu creator: Hongfu Xie creator: Ji Li creator: Yicong Liu creator: Yan Tang uri: https://doi.org/10.7717/peerj.18647 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Effects of combined immunosuppressant and hepatitis B virus antiviral use on COVID-19 vaccination in recipients of living donor liver transplantation link: https://peerj.com/articles/18651 last-modified: 2024-12-06 description: Background & AimsThe global pandemic caused by the highly contagious SARS-CoV-2 virus led to the emergency approval of COVID-19 vaccines to reduce rising morbidity and mortality. However, limited research exists on evaluating the impact of these vaccines on immunocompromised individuals, such as recipients of living donor liver transplantation, highlighting the need for further studies to better understand their effectiveness in this specific population.MethodsFrom June 2021, we followed up on the effectiveness of the vaccine for patients taking immunosuppressive drugs after living-donor liver transplantation (LDLT). A total of 105 immunocompromised individuals participated, of which 50 patients with hepatitis B were taking antiviral drugs. Patients were assessed to analyze how the combination of immunosuppressive and antiviral drugs affected the efficacy of the BNT162b2, mRNA-1273, and ChAdOx1 nCoV-19 COVID-19 vaccines.ResultsBefore and after the vaccinations, patients were monitored to establish differences between immunosuppressed patients and those additionally taking antiviral drugs. In immunocompromised patients taking antiviral drugs for hepatitis B, we confirmed that the effect of the COVID-19 vaccine was reduced when compared to immunocompromised patients. Interestingly, 23 patients (11 without and 12 additionally with hepatitis B drug administration) encountered breakthrough infections, and although there was a minor discrepancy in vaccine efficacy among the patients taking antiviral drugs for hepatitis B, it did not reach statistical significance.ConclusionsAdditional COVID-19 vaccination is recommended for patients taking immunosuppressive drugs and hepatitis B antiviral drugs after LDLT. creator: Ryunjin Lee creator: Jiwan Choi creator: Eunkyeong Lee creator: Jooyoung Lee creator: Jiye Kim creator: Seoon Kang creator: Hye-In An creator: Sung-Han Kim creator: Sung-Min Kim creator: Eun-Kyoung Jwa creator: Gil-Chun Park creator: Jung-Man Namgoong creator: Gi-Won Song creator: Young-In Yoon creator: Eunyoung Tak creator: Sung-Gyu Lee uri: https://doi.org/10.7717/peerj.18651 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lee et al. title: The epigenetic role of EZH2 in acute myeloid leukemia link: https://peerj.com/articles/18656 last-modified: 2024-12-06 description: Acute myeloid leukemia (AML), a malignant disease of the bone marrow, is characterized by the clonal expansion of myeloid progenitor cells and a block in differentiation. The high heterogeneity of AML significantly impedes the development of effective treatment strategies. Enhancer of zeste homolog 2 (EZH2), the catalytic subunit of the polycomb repressive complex 2 (PRC2), regulates the expression of downstream target genes through the trimethylation of lysine 27 on histone 3 (H3K27me3). Increasing evidence suggests that the dysregulation of EZH2 expression in various cancers is closely associated with tumorigenesis. In the review, we examine the role of EZH2 in AML, highlighting its crucial involvement in regulating stemness, proliferation, differentiation, immune response, drug resistance and recurrence. Furthermore, we summarize the application of EZH2 inhibitors in AML treatment and discuss their potential in combination with other therapeutic modalities. Therefore, targeting EZH2 may represent a novel and promising strategy for the treatment of AML. creator: Jinyong Fang creator: Jingcheng Zhang creator: Lujian Zhu creator: Xiaoru Xin creator: Huixian Hu uri: https://doi.org/10.7717/peerj.18656 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fang et al. title: The impact of nurses’ stress situation coping on somatization: a mediated moderation model link: https://peerj.com/articles/18658 last-modified: 2024-12-06 description: AimsThe purpose of this study is to investigate the impact of nurses’ stress situation coping levels on somatization symptoms, the mediating effect of depression, and the moderating effect of perceived social support.BackgroundAs a core part of the global healthcare system, nurses are crucial to patient health and rehabilitation outcomes. However, due to heavy workloads, unreasonable staffing structures, and constant exposure to occupational risks in their workplaces, these factors often place nurses in a high-intensity, high-stress environment, which directly affects their physical and mental health and professional burnout. Coping with stress situations is an important means to help individuals effectively manage stress, reduce negative impacts, and maintain mental health. However, research on the impact of nurses’ stress situation coping methods on somatization symptoms is limited.MethodsThis study conducted a cross-sectional survey from December 2022 to April 2023, and finally included 293 nurses working on the front line of tertiary hospitals. Data was collected through questionnaires and analyzed using SPSS 24.0 and the SPSS macro program’s Models 7 and 14. This study is an observational study, strictly prepared and presented according to the STROBE checklist.ResultsThe somatization symptom scores of the nurses were (27.27 ± 7.33) points, the stress situation coping scores were (59.90 ± 9.64) points, the perceived social support scores were (65.64 ± 12.90) points, and the depression scores were (4.42 ± 4.12) points. The somatization symptom scores of the nurses were positively correlated with the stress situation coping scores and depression scores, and negatively correlated with the perceived social support scores, with correlation coefficients of 0.200, 0.851, and −0.302, respectively. The stress coping level of the nurses had a direct positive impact on somatization symptoms (β = 0.081, p = 0.009), and a direct positive impact on nurse depression (β = 0.202, p = 0.001). Depression had a significant positive impact on somatization symptoms (β = 0.823, p = 0.000), and depression played a mediating role. Perceived social support had a significant negative impact on depression (β = −0.383, p = 0.000). Perceived social support had a significant moderating effect on the relationship between the stress situation coping level and depression (β = −0.121, p = 0.003).ConclusionIn this study, the stress situation coping methods of nurses had a positive impact on somatization symptoms, had a complete mediating effect on the depression level of nurses, and perceived social support had a significant moderating effect in the pathway from the stress situation coping methods of nurses to depression-mediated somatization symptoms. creator: Xiaoyan Qi creator: Hong-Ning Xu uri: https://doi.org/10.7717/peerj.18658 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Qi and Xu title: Taurine stimulation of planarian motility: a role for the dopamine receptor pathway link: https://peerj.com/articles/18671 last-modified: 2024-12-06 description: Taurine, a normal dietary component that is found in many tissues, is considered important for a number of physiological processes. It is thought to play a particular role in eye development and in the maturation of both the muscular and nervous systems, leading to its suggested use as a therapeutic for Alzheimer’s and Parkinson’s diseases. Taurine increases metabolism and has also been touted as a weight loss aid. Due to its possible benefits to health and development, taurine is added as a supplement to a wide array of products, including infant formula and energy drinks. Despite its pervasive use as a nutritional additive and implied physiological actions, there is little consensus on how taurine functions. This is likely because, mechanistically, taurine has been demonstrated to affect multiple metabolic pathways. Simple models and straightforward assay systems are required to make headway in understanding this complexity. We chose to begin this work using the planarian because these animals have basic, well-understood muscular and nervous systems and are the subjects of many well-tested assays examining how their physiology is influenced by exposure to various environmental, nutritional, and therapeutic agents. We used a simple behavioral assay, the planarian locomotor velocity test (pLmV), to gain insight into the stimulant properties of taurine. Using this assay, we observed that taurine is a mild stimulant that is not affected by sugars or subject to withdrawal. We also provide evidence that taurine makes use of the dopamine D1 receptor to mediate this stimulant effect. Given the pervasiveness of taurine in many commercial products, our findings using the planarian system provide needed insight into the stimulant properties of taurine that should be considered when adding it to the diet. creator: Elisa J. Livengood creator: Robyn A. M. V. Fong creator: Angela M. Pratt creator: Veronika O. Alinskas creator: Grace Van Gorder creator: Michael Mezzio creator: Margaret E. Mulligan creator: Evelyn B. Voura uri: https://doi.org/10.7717/peerj.18671 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Livengood et al. title: Motor competence of children in Singapore using Movement ABC-2 test link: https://peerj.com/articles/18446 last-modified: 2024-12-05 description: IntroductionThe Movement Assessment Battery for Children, 2nd Edition (MABC-2) test is a valuable tool for identifying motor delays in children globally. However, there has been a lack of data for children in Singapore.MethodsThis study compared 175 children in Singapore (SG) aged 3–6 years to MABC-2 data based on the United Kingdom (UK) population, using statistical tests to analyze age, country, and gender effects on motor competence.ResultsThe results showed a positive age effect across all tasks, with SG children excelling in balance but lagging in aiming and catching tasks compared to UK children. The interaction between age and country yielded mixed results, favoring different groups at various ages. Additionally, girls displayed better manual dexterity and static balance than boys.ConclusionEncouraging more physical activities, especially those involving object manipulation, is crucial for SG children. Establishing local norms for the MABC-2 in Singapore and considering country-specific factors in motor competence evaluations can enhance early intervention strategies. These findings emphasize the importance of tailored approaches to address motor skill development in SG children. creator: Jernice S.Y. Tan creator: Michael Chia uri: https://doi.org/10.7717/peerj.18446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tan and Chia title: Nonadjacent dependencies and sequential structure of chimpanzee action during a natural tool-use task link: https://peerj.com/articles/18484 last-modified: 2024-12-05 description: Many of the complex behaviours of humans involve the production of nonadjacent dependencies between sequence elements, which in part can be generated through the hierarchical organization of sequences. To understand how these structural properties of human behaviours evolved, we can gain valuable insight from studying the sequential behaviours of nonhuman animals. Among the behaviours of nonhuman apes, tool use has been hypothesised to be a domain of behaviour which likely involves hierarchical organization, and may therefore possess nonadjacent dependencies between sequential actions. However thus far, evidence supporting hierarchical organization of great-ape tool use comes from methodologies which have been criticised in their objectivity. Additionally, the extent to which nonadjacent dependencies appear in primate action sequences during tool use has not been formally investigated. We used estimations of mutual information (MI)—a measure of dependency strength between sequence elements—to evaluate both the extent to which wild chimpanzees produce nonadjacent dependencies during a naturalistic tool-use task (nut cracking), as well as how sequences of actions are likely organized during tool use. Half of adult chimpanzees produced nonadjacent dependencies at significantly greater sequential distances than comparable, nonhierarchical Markov models once repeated actions had been accounted for. Additionally, for the majority of chimpanzees, MI decay with increasing sequential distance included a power-law relationship, which is a key indicator that the action sequences produced by chimpanzees likely entail some degree of hierarchical organization. Our analysis offered the greatest support for a system of organization where short subroutines of actions (2–8 actions long) are hierarchically arranged into longer sequences—a finding which is consistent with previous qualitative descriptions of ape tool-use behaviours. Interindividual variability was detected within our analysis in both the maximum distance dependencies were detected, and the most likely structuring mechanism for sequential action organization. We discuss these results in light of possible interindividual variation in the systems of action organization used by chimpanzees during tool use, in addition to methodological considerations for applications of MI estimations to sequential behaviours. Moreover, we discuss our main findings alongside hypotheses for the coevolution of complex syntax in language and tool-action across hominin evolutionary history. creator: Elliot Howard-Spink creator: Misato Hayashi creator: Tetsuro Matsuzawa creator: Daniel Schofield creator: Thibaud Gruber creator: Dora Biro uri: https://doi.org/10.7717/peerj.18484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Howard-Spink et al. title: PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites link: https://peerj.com/articles/18504 last-modified: 2024-12-05 description: In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming tool, PhyIN, which deletes regions in which a large proportion of sites (characters) have conflicting phylogenetic signal. It does not require inference of a phylogenetic tree, as it finds neighbouring characters that cannot agree on any possible tree. In phylogenomic data of ultraconserved elements (UCE), PhyIN effectively finds the boundaries between chaotic (conflicted) and orderly regions of alignments with data for only a single locus. Its ability to work on individual loci allows it to preserve discord between gene trees and species trees. creator: Wayne P. Maddison uri: https://doi.org/10.7717/peerj.18504 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Maddison title: CYP3A4 and CYP3A5: the crucial roles in clinical drug metabolism and the significant implications of genetic polymorphisms link: https://peerj.com/articles/18636 last-modified: 2024-12-05 description: CYP3A, a key member of the cytochrome P450 (CYP450) superfamily, is integral to drug metabolism, processing a substantial portion of medications. Their role in drug metabolism is particularly prominent, as CYP3A4 and CYP3A5 metabolize approximately 30–50% of known drugs. The genetic polymorphism of CYP3A4/5 is significant inter-individual variability in enzymatic activity, which can result in different pharmacokinetic profiles in response to the same drug among individuals. These polymorphisms can lead to either increased drug toxicity or reduced therapeutic effects, requiring dosage adjustments based on genetic profiles. Consequently, the study of the enzymatic activity of CYP3A4/5 gene variants is of great importance for the formulation of personalized treatment regimens. This article first reviews the role of CYP3A4/5 in drug metabolism in the human body, including inhibitors and inducers of CYP3A4/5 and drug-drug interactions. In terms of genetic polymorphism, it discusses the detection methods, enzymatic kinetic characteristics, and clinical guidelines for CYP3A5. Finally, the article summarizes the importance of CYP3A4/5 in clinical applications, including personalized therapy, management of drug-drug interactions, and adjustment of drug doses. This review contributes to the understanding of the functions and genetic characteristics of CYP3A4/5, allowing for more effective clinical outcomes through optimized drug therapy. creator: Yuqing Zhang creator: Ziying Wang creator: Yuchao Wang creator: Weikai Jin creator: Zheyan Zhang creator: Lehao Jin creator: Jianchang Qian creator: Long Zheng uri: https://doi.org/10.7717/peerj.18636 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Effects of bamboo biochar on soil physicochemical properties and microbial diversity in tea gardens link: https://peerj.com/articles/18642 last-modified: 2024-12-05 description: Biochar, a carbon-rich material that has attracted considerable interest in interdisciplinary research, is produced through a process known as pyrolysis, which involves the thermal decomposition of organic material in the absence of oxygen. Bamboo biochar is a specific type of biochar, manufactured from bamboo straw through carbonisation at 800 °C and subsequent filtration through a 100-mesh sieve. There is currently a lack of research into the potential benefits of bamboo biochar in improving soil quality in tea gardens. The aim of this study was to investigate the effect of bamboo biochar on the physicochemical properties, enzymatic activity, and microbial community structure of tea garden soils. The results demonstrate that the integration of bamboo biochar into the soil significantly enhanced the soil pH, total nitrogen, available nitrogen, total phosphorus, available phosphorus, available potassium, and slowly available potassium by 15.3%, 52.0%, 91.5%, 91%, 48.4%, 94.2%, and 107.7%, respectively. In addition, soil acid phosphatase activity decreased significantly by 52.5%. In contrast, the activities of sucrase, catalase, and β-glucosidase increased substantially by 54.0%, 68.7%, and 68.4%, respectively, when organic fertilizer and bamboo biochar were applied concurrently. Additionally, the Shannon, Simpson, and Pielou diversity indices of the microbial communities were significantly enhanced. Following the incorporation of bamboo biochar in the soil samples, the relative abundance of Proteobacteria increased significantly, whereas that of Acidobacteria decreased. Various concentrations of bamboo biochar markedly influenced microbial markers in the soil. The results of this study suggest that the application of bamboo biochar to soil may modestly improve its physicochemical properties, enzyme activity, and microbial community structure. These findings provide a foundation for future investigations on soil ecological restoration. creator: Si-Hai Zhang creator: Yi Shen creator: Le-Feng Lin creator: Su-Lei Tang creator: Chun-Xiao Liu creator: Xiang-Hua Fang creator: Zhi-Ping Guo creator: Ying-Ying Wang creator: Yang-Chun Zhu uri: https://doi.org/10.7717/peerj.18642 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: A computational framework for processing time-series of earth observation data based on discrete convolution: global-scale historical Landsat cloud-free aggregates at 30 m spatial resolution link: https://peerj.com/articles/18585 last-modified: 2024-12-04 description: Processing large collections of earth observation (EO) time-series, often petabyte-sized, such as NASA’s Landsat and ESA’s Sentinel missions, can be computationally prohibitive and costly. Despite their name, even the Analysis Ready Data (ARD) versions of such collections can rarely be used as direct input for modeling because of cloud presence and/or prohibitive storage size. Existing solutions for readily using these data are not openly available, are poor in performance, or lack flexibility. Addressing this issue, we developed TSIRF (Time-Series Iteration-free Reconstruction Framework), a computational framework that can be used to apply diverse time-series processing tasks, such as temporal aggregation and time-series reconstruction by simply adjusting the convolution kernel. As the first large-scale application, TSIRF was employed to process the entire Global Land Analysis and Discovery (GLAD) ARD Landsat archive, producing a cloud-free bi-monthly aggregated product. This process, covering seven Landsat bands globally from 1997 to 2022, with more than two trillion pixels and for each one a time-series of 156 samples in the aggregated product, required approximately 28 hours of computation using 1248 Intel® Xeon® Gold 6248R CPUs. The quality of the result was assessed using a benchmark dataset derived from the aggregated product and comparing different imputation strategies. The resulting reconstructed images can be used as input for machine learning models or to map biophysical indices. To further limit the storage size the produced data was saved as 8-bit Cloud-Optimized GeoTIFFs (COG). With the hosting of about 20 TB per band/index for an entire 30 m resolution bi-monthly historical time-series distributed as open data, the product enables seamless, fast, and affordable access to the Landsat archive for environmental monitoring and analysis applications. creator: Davide Consoli creator: Leandro Parente creator: Rolf Simoes creator: Murat Şahin creator: Xuemeng Tian creator: Martijn Witjes creator: Lindsey Sloat creator: Tomislav Hengl uri: https://doi.org/10.7717/peerj.18585 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Consoli et al. title: Identification and validation of apoptosis-related genes in acute myocardial infarction based on integrated bioinformatics methods link: https://peerj.com/articles/18591 last-modified: 2024-12-04 description: BackgroundAcute myocardial infarction (AMI) is one of the most serious cardiovascular diseases. Apoptosis is a type of programmed cell death that causes DNA degradation and chromatin condensation. The role of apoptosis in AMI progression remains unclear.MethodsThree AMI-related microarray datasets (GSE48060, GSE66360 and GSE97320) were obtained from the Gene Expression Omnibus database and combined for further analysis. Differential expression analysis and enrichment analysis were performed on the combined dataset to identify differentially expressed genes (DEGs). Apoptosis-related genes (ARGs) were screened through the intersection of genes associated with apoptosis in previous studies and DEGs. The expression pattern of ARGs was studied on the basis of their raw expression data. Three machine learning algorithms, Least Absolute Shrinkage and Selection Operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and Random Forest (RF) were utilized to screen crucial genes in these ARGs. Immune infiltration was estimated by single sample gene set enrichment analysis (ssGSEA). Corresponding online databases were used to predict miRNAs, transcription factors (TFs) and therapeutic agents of crucial genes. A nomogram clinical prediction model of the crucial genes was constructed and evaluated. The Mendelian randomization analysis was employed to investigate whether there is a causal relationship between apoptosis and AMI. Finally, an AMI mouse model was established, and apoptosis in the hearts of AMI mice was assessed via TUNEL staining. qRT-PCR was employed to validate these crucial genes in the hearts of AMI mice. The external dataset GSE59867 was used for further validating the crucial genes.ResultsFifteen ARGs (GADD45A, DDIT3, FEZ1, PMAIP1, IER3, IFNGR1, CDKN1A, GNA15, IL1B, EREG, BCL10, JUN, EGR3, GADD45B, and CD14) were identified. Six crucial genes (CDKN1A, BCL10, PMAIP1, IL1B, GNA15, and CD14) were screened from ARGs by machine learning. A total of 102 miRNAs, 13 TFs and 23 therapeutic drugs were predicted targeting these crucial genes. The clinical prediction model of the crucial genes has shown good predictive capability. The Mendelian randomization analysis demonstrated that apoptosis is a risk factor for AMI. Lastly, the expression of CDKN1A, CD14 and IL1B was verified in the AMI mouse model and external dataset.ConclusionsIn this study, ARGs were screened by machine learning algorithms, and verified by qRT-PCR in the AMI mouse model. Finally, we demonstrated that CDKN1A, CD14 and IL1B were the crucial genes involved in apoptosis in AMI. These genes may provide new target for the recognition and intervention of apoptosis in AMI. creator: Haoyan Zhu creator: Mengyao Li creator: Jiahe Wu creator: Liqiu Yan creator: Wei Xiong creator: Xiaorong Hu creator: Zhibing Lu creator: Chenze Li creator: Huanhuan Cai uri: https://doi.org/10.7717/peerj.18591 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhu et al. title: Use of integrated population models for assessing density-dependence and juvenile survival in Northern Bobwhites (Colinus virginianus) link: https://peerj.com/articles/18625 last-modified: 2024-12-04 description: Management of wildlife populations is most effective with a thorough understanding of the interplay among vital rates, population growth, and density-dependent feedback; however, measuring all relevant vital rates and assessing density-dependence can prove challenging. Integrated population models have been proposed as a method to address these issues, as they allow for direct modeling of density-dependent pathways and inference on parameters without direct data. We developed integrated population models from a 25-year demography dataset of Northern Bobwhites (Colinus virginianus) from southern Georgia, USA, to assess the demographic drivers of population growth rates and to estimate the strength of multiple density-dependent processes simultaneously. Furthermore, we utilize a novel approach combining breeding productivity and post-breeding abundance and age-and-sex ratio data to infer juvenile survival. Population abundance was relatively stable for the first 14 years of the study but began growing after 2012, showing that bobwhite populations may be stable or exhibit positive population growth in areas of intensive management. Variation in breeding and non-breeding survival drove changes in population growth in a few years; however, population growth rates were most affected by productivity across the entire study duration. A similar pattern was observed for density-dependence, with relatively stronger negative effects of density on productivity than on survival. Our novel modeling approach required an informative prior but was successful at updating the prior distribution for juvenile survival. Our results show that integrated population models provide an attractive and flexible method for directly modeling all relevant density-dependent processes and for combining breeding and post-breeding data to estimate juvenile survival in the absence of direct data. creator: William B. Lewis creator: Chloé R. Nater creator: Justin A. Rectenwald creator: D. Clay Sisson creator: James A. Martin uri: https://doi.org/10.7717/peerj.18625 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lewis et al. title: DNA shuffling to improve crude-water interfacial activity in biosurfactants with OmpA protein of Escherichia coli link: https://peerj.com/articles/17239 last-modified: 2024-12-03 description: Surfactants are molecules derived primarily from petroleum that can reduce the surface tension at interfaces. Their slow degradation is a characteristic that could cause environmental issues. This and other factors contribute to the allure of biosurfactants today. Progress has been made in this area of research, which aims to satisfy the need for effective surfactants that are not harmful to the environment. In previous studies, we demonstrated the surface tension activity of the Escherichia coli transmembrane protein OmpA. Here, we carried out DNA shuffling on ompA to improve its interfacial activity. We evaluated changes in interfacial tension when exposing mutants to a water-oil interface to identify the most promising candidates. Two mutants reached an interfacial tension value lower (9.10 mN/m and 4.24 mN/m) than the original protein OmpA (14.98 mN/m). Since predicted isoelectric point values are far from neutral pH, the charge of the protein was a crucial factor in explaining the migration of proteins towards the interface. Low molecular weight mutants did not exhibit a significant difference in their migration to the interface. creator: Vanessa Lucía Nuñez Velez creator: Liseth Daniela Villamizar Gomez creator: Jhon E. Mendoza Ospina creator: Yasser Hayek-Orduz creator: Miguel Fernandez-Niño creator: Silvia Restrepo Restrepo creator: Óscar Alberto Álvarez Solano creator: Luis H. Reyes Barrios creator: Andres F. Gonzalez Barrios uri: https://doi.org/10.7717/peerj.17239 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Nuñez Velez et al. title: Studying turn performance, trunk control, and mobility in acute stroke subjects: a cross-sectional study link: https://peerj.com/articles/18501 last-modified: 2024-12-03 description: BackgroundStroke leads to various impairments like motor deficits, impaired trunk control and restricted mobility. However, rehabilitation professionals often underestimate the fundamental function of turning, which is essential for daily living activities like walking, cooking, or performing household chores. Impaired turning can be attributed to motor deficits post-stroke, resulting in restricted mobility and impaired trunk movement. Therefore, the present study aimed to determine the relationship between turn performance, trunk control, and mobility in stroke patients.Materials and MethodsA total of 63 first-time supratentorial stroke (i.e., anterior circulation stroke) patients aged 18–90 years were recruited for the study. Turn performance was assessed by asking patients to walk for 10 feet comfortably, then take a 180° turn and return to the starting position. In addition, the duration and number of steps were recorded. Following this, the Trunk Impairment Scale (TIS) and Stroke Rehabilitation Assessment of Movement (STREAM) were used to assess trunk impairment and mobility, respectively. The group turn performance was analyzed using the Kruskal–Wallis test with a post hoc Mann–Whitney U test for between-group comparisons. The turn duration and turn steps were correlated with age, trunk control, and mobility using Spearman’s rank correlation. A regression analysis was performed to determine the association of turn performance with age, trunk control, and mobility among stroke patients.ResultsThirty stroke patients had turning difficulty, and 33 did not. Hence, they were categorized into the turning difficulty (TD) and non-turning difficulty (NTD) groups. When correlated with turn duration and the number of steps taken by the stroke patients while turning, the STREAM and TIS scores revealed a significant negative correlation (p < 0.001). The subjects’ age showed a significant positive correlation with the turn duration and number of steps taken by stroke patients while turning (p < 0.001). A significant association was also found between turn performance and age and trunk control. However, there was no significant association between turn performance and mobility.ConclusionThe observed associations highlight the complexity of turning ability and trunk control necessary to complete a turn safely. Additionally, with advancing age, turn performance and turning movement are compromised in stroke patients. This indicates that turning difficulty is more pronounced in older individuals with stroke. creator: Mahima Vasyani creator: Akshatha Nayak creator: K. Vijaya Kumar creator: Zulkifli Misri creator: Pema Choezom creator: Rinita Mascarenhas creator: Jaya Shanker Tedla creator: Srikant Natarajan uri: https://doi.org/10.7717/peerj.18501 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Vasyani et al. title: Phytochemical screening and in vitro antibacterial activity of Echinops kebericho Mesfin tuber extracts: experimental studies link: https://peerj.com/articles/18554 last-modified: 2024-12-03 description: BackgroundThe application of plant extracts and their phytochemicals as potential treatments for bacterial illnesses has increased significantly in the last few decades. In Ethiopia, Echinops kebericho Mesfin is widely used to treat a range of illnesses in humans and animals. This study aimed to evaluate the antibacterial activity and phytochemical screening of Echinops kebericho Mesfin.MethodsWe carried out an in vitro experimental study after collecting the plants from their natural habitats. Then macerated in absolute methanol and petroleum ether solvents and concentrated the extracts using a rotary evaporator. In the experiment, we used Standard cultures of E. coli, K. pneumoniae, S. aureus, and P. aeruginosa. The agar-well diffusion method evaluated the antibacterial activity of the plants. The agar dilution method determined the minimum inhibitory concentration of the plant extract.ResultsThe percentage yield of the plant extracts ranged from 6.25% to 7.85%. The methanol extract of Echinops kebericho Mesfin had the highest inhibitory effect on S. aureus (ATCC 25923) (16.67 ± 0.58 mm), followed by E. coli (ATCC 25922) (11.0 ± 1.73 mm). Phytochemical screening of leaves from the methanol and petroleum ether extracts of the plant revealed the presence of phytochemicals such as alkaloids, flavonoids, tannins, and cardiac glycosides. The present study revealed that the extracts of these plants have antibacterial activity. However, researchers should conduct further studies on the safety margin and quantitative bioactive isolation of selected medicinal plants. creator: Jiregna Gari Negasa creator: Ibsa Teshome creator: Edilu Jorga Sarba creator: Bekiyad Shasho Daro uri: https://doi.org/10.7717/peerj.18554 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Negasa et al. title: Predicting epidermal growth factor receptor (EGFR) mutation status in non-small cell lung cancer (NSCLC) patients through logistic regression: a model incorporating clinical characteristics, computed tomography (CT) imaging features, and tumor marker levels link: https://peerj.com/articles/18618 last-modified: 2024-12-03 description: BackgroundApproximately 60% of Asian populations with non-small cell lung cancer (NSCLC) harbor epidermal growth factor receptor (EGFR) gene mutations, marking it as a pivotal target for genotype-directed therapies. Currently, determining EGFR mutation status relies on DNA sequencing of histological or cytological specimens. This study presents a predictive model integrating clinical parameters, computed tomography (CT) characteristics, and serum tumor markers to forecast EGFR mutation status in NSCLC patients.MethodsRetrospective data collection was conducted on NSCLC patients diagnosed between January 2018 and June 2019 at the First Affiliated Hospital of Zhengzhou University, with available molecular pathology results. Clinical information, CT imaging features, and serum tumor marker levels were compiled. Four distinct models were employed in constructing the diagnostic model. Model diagnostic efficacy was assessed through receiver operating characteristic (ROC) area under the curve (AUC) values and calibration curves. DeLong’s test was administered to validate model robustness.ResultsOur study encompassed 748 participants. Logistic regression modeling, trained with the aforementioned variables, demonstrated remarkable predictive capability, achieving an AUC of 0.805 (95% confidence interval (CI) [0.766–0.844]) in the primary cohort and 0.753 (95% CI [0.687–0.818]) in the validation cohort. Calibration plots suggested a favorable fit of the model to the data.ConclusionsThe developed logistic regression model emerges as a promising tool for forecasting EGFR mutation status. It holds potential to aid clinicians in more precisely identifying patients likely to benefit from EGFR molecular testing and facilitating targeted therapy decision-making, particularly in scenarios where molecular testing is impractical or inaccessible. creator: Jimin Hao creator: Man Liu creator: Zhigang Zhou creator: Chunling Zhao creator: Liping Dai creator: Songyun Ouyang uri: https://doi.org/10.7717/peerj.18618 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hao et al. title: Effect of mulching and organic manure on maize yield, water, and nitrogen use efficiency in the Loess Plateau of China link: https://peerj.com/articles/18644 last-modified: 2024-12-03 description: Current agricultural practices prioritize intensive food production, often at the expense of environmental sustainability. This approach results in greenhouse gas emissions and groundwater pollution due to over-fertilization. In contrast, organic agriculture promotes a more efficient use of non-renewable energy, improves soil quality, and reduces ecological damage. However, the effects of mulching and organic manure on maize yield, water use efficiency (WUE), and nitrogen use efficiency (NUE) in China’s Loess Plateau have not been sufficiently researched. In 2017 and 2018, an experiment utilizing a randomized complete block design with two factors (two mulching levels × three organic nitrogen application rates) was conducted. The water content of the upper soil layer was found to be 12.6% to 19.4% higher than that of the subsoil layer. Across all soil depths and years, the soil nitrate-N content in mulched treatments was 10% to 31.8% greater than in non-mulched treatments with varying organic nitrogen rates. Additionally, mulching resulted in an increase in grain yield of 9.4% in 2017 and 8.9% in 2018 compared to non-mulched treatments. A significant interaction was observed between mulching and organic nitrogen application rate concerning WUE, alongside a negative correlation between WUE and NUE. These findings suggest that the application of 270 kg N ha−1 of sheep manure in conjunction with mulching is a highly recommended practice for the Loess Plateau, thereby supporting sustainable agricultural strategies. creator: Yingying Xing creator: Jintao Fu creator: Xiukang Wang uri: https://doi.org/10.7717/peerj.18644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xing et al. title: Investigation of the relationships between peri-implant diseases, periodontal diseases, and conditions: a cross-sectional study link: https://peerj.com/articles/18663 last-modified: 2024-12-03 description: IntroductionPeri-implant and periodontal conditions share common underlying factors, including risk factors, microbiology, immunology, and treatment approaches.AimsThis study aims to investigate the potential co-occurrence of peri-implant and periodontal conditions.DesignOne hundred twenty-three implants were divided into three groups: peri-implantitis (41 implants), peri-implant mucositis (41 implants), and peri-implant health (41 implants). Peri-implant and periodontal statuses were assessed using the 2017 AAP/EFP World Workshop on Classification of Periodontal and Peri-implant Diseases and Conditions. All measurements were performed by a single clinician (T.Ş.). One-way analysis of variance was used to compare the study groups according to the data. An assessment was conducted regarding the coexistence of periodontal and peri-implant conditions.ResultsPatients with peri-implant mucositis predominantly had gingivitis, whereas those with peri-implant health exhibited periodontal health. In contrast, patients with peri-implantitis mostly had gingivitis, with a lower occurrence of periodontitis. A significant difference was observed between the peri-implant and periodontal groups (p = 0.003). Significant differences were observed between peri-implant and periodontal evaluations for plaque indices, gingival indices, probing depth, gingival recession, and clinical attachment level (p = 0.001), (p = 0.006).ConclusionsThe findings of this study underscore the intricate influence of implant treatment on periodontal health. This observation emphasizes the importance of elucidating the underlying factors to improve clinical management and outcomes in patients with periodontal and peri-implant diseases, highlighting the relevance and potential impact of this research in the field. creator: Tuğba Şahin uri: https://doi.org/10.7717/peerj.18663 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Şahin title: Surgery-induced neuroinflammatory transcriptional programs in medial prefrontal cortex of mice during early phase of perioperative neurocognitive disorders link: https://peerj.com/articles/18664 last-modified: 2024-12-03 description: Patients receiving anesthesia and surgery may experience cognitive dysfunction, memory deficits, and mental disturbances, which are referred to as perioperative neurocognitive disorders (PND). The function of the medial prefrontal cortex (mPFC) is disrupted during early phase of PND. To gain insight into the mechanisms of PND, we collected mouse mPFC tissues 6 h post-surgery and performed RNA sequencing analysis. In total, 178 differentially expressed genes (DEGs) were identified, including 105 upregulated and 73 downregulated genes. Bioinformatic analysis highlighted the significant enrichment of these DEGs in several immune-related biological processes and signaling pathways, suggesting that pronounced neuroinflammatory transcriptional programming in the mPFC was evoked during early phase of PND. Interleukin-6 level increased in both serum and mPFC, while the mRNA levels of Il-6, Tnf-α, and Il-1β remained unchanged. Taken together, our findings suggest that a distinct and acute neuroinflammatory response in the mPFC is evoked after peripheral surgery, which might play a key role in the development of PND. creator: Xiaodong Tang creator: Xuwu Xiang creator: Yang Yu creator: Shuyuan Huang creator: Caifei Pan creator: Shuyuan Gan creator: Yongxing Yao uri: https://doi.org/10.7717/peerj.18664 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Tang et al. title: Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke link: https://peerj.com/articles/18443 last-modified: 2024-12-02 description: BackgroundThe Myeloblastosis related (MYB) family is one of the most widely distributed transcription factor families in plants and plays a significant role in plant growth and development, hormone signal transduction, and stress response. There are many reports on MYB family species, but the research on Qingke is still limited.MethodsThis study used comparative genomics methods to analyze gene and protein structure, protein physicochemical properties, chromosome localization, and evolution. A bioinformatics approach was used to systematically analyze the HvMYB gene family. At the milk stage, soft dough stage, and mature stage, White and Blue Qingke grains were selected for RNA sequencing (RNA-seq), among which two proteins interacted (HvMYB and HvMYC). The expression of this gene family was analyzed through RNA-seq, and the expression levels of HvMYB and HvMYC in the grains of two different color varieties were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, the interaction between HvMYB and HvMYC was verified by bimolecular fluorescence complementation (BiFC) experiments.ResultsA total of 92 Qingke HvMYB genes were identified and analyzed, and 92 HvMYB proteins were classified into five categories. Cis-acting elements associated with abscisic acid response, light response, and methyl jasmonate (MeJA) response were found in the promoter regions of most MYB genes. Using qRT-PCR combined with RNA-seq analysis showed that MYB gene was highly expressed in the soft dough stage and was varietal specific. Subcellular localization indicated that HvMYB was located in the nucleus and cell membrane, HvMYC was located in the nucleus, cell membrane, and cytoplasm. Through BiFC analysis, it has been proven that HvMYB in the MYB family and HvMYC in the basic helix–loop–helix (bHLH) family can interact. This study provides a preliminary theoretical basis for understanding the function and role of the Qingke MYB gene family and provides a reference for the molecular mechanism of Qingke gene evolution. creator: Hongyan Li creator: Youhua Yao creator: Xin Li creator: Yongmei Cui creator: Likun An creator: Baojun Ding creator: Xiaohua Yao creator: Kunlun Wu uri: https://doi.org/10.7717/peerj.18443 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al.