title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2024-10 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The behavior patterns of giraffes (Giraffa camelopardalis) housed across 18 US zoos link: https://peerj.com/articles/18164 last-modified: 2024-10-31 description: Interpreting animal behavior in the context of welfare can be inherently challenging given the limited behavior data available for many species housed in zoos. Describing common behavior patterns may help animal managers by providing additional background when assessing the individuals in their care. Although valuable, these efforts require a large, collaborative approach and have, consequently, been rare. Here, we share the behavior patterns of zoo-housed giraffes, an iconic and commonly housed megafauna in zoos. Behavior data were evaluated for 66 giraffes living across 18 AZA-accredited zoos using the ZooMonitor Community platform. Data were recorded during 10-minute observation sessions. Observations were conducted during daytime hours over the course of approximately one year at each zoo (mean total observed time per individual = 23.2 hr). The most common behaviors observed were feeding/ foraging behaviors, which accounted for 38.6% of the mean visible time budget across giraffes. Time spent in these behaviors varied by individual and ranged from 14.3% to 69.3% of visible time. Stereotypic behaviors occurred in all study individuals, with oral stereotypic behaviors being most common. Although prevalent, stereotypic behaviors varied considerably across giraffes, with some individuals exhibiting these behaviors only on a few occasions to an individual that exhibited these behaviors once every few minutes. This study provides a robust evaluation of giraffe behavior across zoos to present a picture of their common behavior patterns in managed care. We hope these multi-institutional behavior patterns can provide perspective to aid animal managers in evaluating giraffes in their care. creator: Jason D. Wark creator: Katherine A. Cronin uri: https://doi.org/10.7717/peerj.18164 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wark and Cronin title: Phylogenetic and taxonomic revisions of Jurassic sea stars support a delayed evolutionary origin of the Asteriidae link: https://peerj.com/articles/18169 last-modified: 2024-10-31 description: BackgroundThe superorder Forcipulatacea is a major clade of sea stars with approximately 400 extant species across three orders (Forcipulatida, Brisingida, Zorocallida). Over the past century, the systematics of Forcipulatacea have undergone multiple revisions by various authors, with some considering numerous families such as Asteriidae, Zoroasteridae, Pedicellasteridae, Stichasteridae, Heliasteridae, Labidiasteridae, and Neomorphasteridae, while others recognized only two families (i.e., Asteriidae and Zoroasteridae). Recent molecular analyses have shown the artificial nature of some of these groupings. Notably, four well-supported clades (Zorocallida, Brisingida, Stichasteridae, and Asteriidae) emerged from a synthesis of morphological and molecular evidence. The majority of extinct forcipulatacean species have been placed in modern families. However, many of these fossil species are in need of revision, especially those species placed within the Asteriidae, the largest of all forcipulatacean families.MethodsIn light of recent advancements in forcipulatacean systematics, we comprehensively reassess six well-preserved Jurassic forcipulatacean taxa, including the earliest crown-group members from the Hettangian (∼201.4 Ma), and also describe two new Jurassic genera, Forbesasterias gen. nov. and Marbleaster gen. nov. We assembled the largest and most comprehensive phylogenetic matrix for this group, sampling 42 fossil and extant forcipulatacean species for 120 morphological characters. To infer phylogenetic relationships and construct an evolutionary timeline for the diversification of major clades, we conducted a Bayesian tip-dating analysis incorporating the fossilized birth-death process. A total of 13 fossil species were sampled in our analysis, including six taxonomically revaluated herein, two recently reappraised species from the Jurassic, and five additional species from the Cretaceous and Miocene.ResultsContrary to prior assumptions, our results indicate that none of the Jurassic taxa investigated belong to Asteriidae or any other modern families, and instead represent stem-forcipulatids. Furthermore, our phylogenetic results suggest that Asteriidae likely originated during the late Cretaceous. Our findings highlight a greater early diversity within the Forcipulatacea than previously presumed, challenging existing perceptions of the evolutionary history of this significant clade of marine invertebrates. creator: Marine Fau creator: David F. Wright creator: Timothy A.M. Ewin creator: Andrew S. Gale creator: Loïc Villier uri: https://doi.org/10.7717/peerj.18169 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fau et al. title: Effect of bioceramic-based and resin-based sealers on postoperative discomfort following root canal therapy: a systematic review and meta-analysis link: https://peerj.com/articles/18198 last-modified: 2024-10-31 description: BackgroundThe aim of this systematic review and meta-analysis was to furnish evidence-based recommendations for the utilization of bioceramic-based and resin-based sealers in clinical endodontics, with a focus on reducing postoperative discomfort.MethodsThe investigation’s methodology was registered on the International Prospective Database of Systematic Reviews (PROSPERO: CRD42022355506) and executed using the 2020 PRISMA protocol. Articles were selected utilizing the PICO technique and applying specific inclusion and exclusion criteria. Articles published between January 2000 and August 2022, PubMed, MEDLINE, and DOAJ were utilized as primary data sources. After the identification of studies, two autonomous reviewers evaluated the titles and abstracts, and data from qualifying studies were extracted.ResultsNine published studies were included in this analysis. The findings indicate that there were no significant differences in the Visual Analog Scale (VAS) scores between resin-based and bioceramic root canal sealers at intervals of 6 hours, 12 hours, 24 hours, and 48 hours after treatment.ConclusionThe findings of this systematic review and meta-analysis suggest that after the utilization of bioceramic sealers during root canal therapy, the pain and discomfort levels were not significantly different from those experienced pain after the use of resin-based sealers. creator: Mansi Supare creator: Ajinkya M. Pawar creator: Kashmira Sawant creator: Dian Agustin Wahjuningrum creator: Suraj Arora creator: Firas Elmsmari creator: Mohmed Isaqali Karobari creator: Bhagyashree Thakur uri: https://doi.org/10.7717/peerj.18198 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Supare et al. title: Assessing population structure and morpho-molecular characterization of sunflower (Helianthus annuus L.) for elite germplasm identification link: https://peerj.com/articles/18205 last-modified: 2024-10-31 description: Sunflower (Helianthus annuus L.), known for its adaptability and high yield potential, is vital in global edible oil production. Estimating genetic diversity is a key pre-breeding activity in crop breeding. The current study comprised of 48 genotypes which were assessed for their biometrical traits at department of Oilseeds, Tamil Nadu Agricultural University, during the rainy season of 2022. The lines were subsequently characterised using 103 simple sequence repeat (SSR) markers for molecular diversity analysis. The results indicated that the net nucleotide distances indicated varying genetic divergence, with subpopulations II and V showing the highest (0.056) and I and IV the lowest (0.014). Subpopulation IV exhibited the highest heterozygosity (0.352), while subpopulation III had the lowest heterozygosity and a low Fst (0.173). Principal components analysis (PCA) and hierarchical cluster analysis were employed for assessing the morphological diversity, facilitating genotype grouping and parent selection for breeding programs. The first four components cumulatively accounted for 86.72% of the total variation. Cluster Analysis grouped 48 sunflower genotypes into three clusters based on genetic diversity. COSF 13B stands out for its high head diameter, oil content, seed yield, and oil yield based on mean performance of morphological data. Principal coordinate analysis (PCoA) mirrored the groupings from the Neighbor Joining method, with the first three components explaining 27.24% of the total variation. Molecular data analysis identified five distinct clusters among the germplasm. By integrating morphological and molecular marker data with genetic distance analysis, substantial diversity was revealed with the genotypes RHA 273 and GMU 325 consistently demonstrated high oil yield per plant. The genotypes GMU 477, GMU 450, COSF 13B, RHA 102, CMS 1103B, and RHA GPR 58 have been identified as suitable parents for enhancing oil content in sunflower breeding programs. These findings also aid in selecting SSR markers for genotype characterization and in choosing diverse parents for breeding programs. creator: Sampath Lavudya creator: Kalaimagal Thiyagarajan creator: Sasikala Ramasamy creator: Harish Sankarasubramanian creator: Senthivelu Muniyandi creator: Anita Bellie creator: Sushil Kumar creator: Susmitha Dhanapal uri: https://doi.org/10.7717/peerj.18205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lavudya et al. title: Study on the effect of chlorogenic acid on the antimicrobial effect, physical properties and model accuracy of alginate impression materials link: https://peerj.com/articles/18228 last-modified: 2024-10-31 description: BackgroundDental impressions are essential for accurately capturing the detailed anatomy of teeth and surrounding oral structures. However, these impressions often become contaminated with saliva and blood, making proper disinfection necessary. The application of chemical disinfectants has been associated with negative side effects, leading to suboptimal disinfection practices in clinical settings.ObjectiveThe purpose of this study was to evaluate the effectiveness of chlorogenic acid (CA) as a disinfectant for alginate impression materials, the impact of CA disinfection on the physical properties and dimensional accuracy of alginate impressions was also investigated.MethodsThe physical properties of alginate impression materials, such as elastic recovery, strain-in-compression, initial setting time, and fluidity, were assessed after mixing the alginate impression materials with three different concentrations of CA solution (10 mg/mL, 15 mg/mL, 20 mg/mL). To evaluate the antimicrobial effect of CA, alginate impressions mixed with a 10 mg/mL CA solution and impressions mixed with distilled water (control group) were contaminated with four types of microorganism: Escherichia coli, Staphylococcus aureus, Candida albicans, and Streptococcus pneumoniae. Following a five-minute incubation period, a CA solution at a concentration of either 50 mg/mL, 55 mg/mL, or 60 mg/mL was sprayed on the samples for disinfection. Samples were collected at different time intervals (10 min, 20 min, 30 min) and cultured to determine the number of colony-forming units (CFU/mL), providing insight into the antimicrobial efficacy of these CA solutions. The dimensional accuracy of alginate impressions was assessed in three groups: one with alginate impressions mixed with distilled water, another with alginate impressions sterilized with available chlorine (2,000 mg/L) mixed with distilled water, and the last group consisting of alginate impressions mixed with 10 mg/mL CA solution and sprayed with 60 mg/mL CA solution. Both the standard model and the plaster model underwent 3D scanning, and the data were processed and compared by software. The root mean square (RMS) was used as a parameter to evaluate the deviation between models.ResultsAll alginate impression materials mixed with either 10 mg/mL, 15 mg/mL, or 20 mg/mL concentrations of CA solution met the ISO 21563 standard for elastic recovery, strain-in-compression, and fluidity. However, only the material mixed with a concentration of 10 mg/mL CA had an initial setting time within the range specified by the T-6505 Japanese industrial standard. The application of CA solution by mixing or spraying showed significant antimicrobial effects on Staphylococcus aureus, Escherichia coli, Candida albicans, and Streptococcus pneumoniae. There was no significant difference in the dimensional accuracy of the alginate impressions between the group of the CA solution applied, the blank group, or the chlorine intervention group. creator: Shuling Jiang creator: Fu-Qing Chen creator: Qiao-qiao Hu creator: Fen Yang creator: Niya Hu creator: Xi Nan Luo creator: Yewen Zhang creator: Nuodan Wu creator: Na Li uri: https://doi.org/10.7717/peerj.18228 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Jiang et al. title: Identification and validation of a prognostic model based on immune-related genes in ovarian carcinoma link: https://peerj.com/articles/18235 last-modified: 2024-10-31 description: BackgroundA novel valuable prognostic model has been developed on the basis of immune-related genes (IRGs), which could be used to estimate overall survival (OS) in ovarian cancer (OC) patients in The Cancer Genome Atlas (TCGA) dataset and the International Cancer Genome Consortium (ICGC) dataset.MethodsThis prognostic model was engineered by employing LASSO regression in training cohort (TCGA dataset). The corresponding growth predictive values of this model for individualized survival was evaluated using survival analysis, receiver operating characteristic curve (ROC curve), and risk curve analysis. Combined with clinical characteristics, a model risk score nomogram for OS was well built. Thereafter, depended on the model risk score, patients were divided into high and low risk subgroups. The survival difference between these subgroups was measured using Kaplan-Meier survival method. In addition, correlations containing pathway enrichment, treatment, immune cell infiltration and the prognostic model were also analyzed. We established the ovarian cancer cell line W038 for this study and identified the performances of GBP1P1 knockdown on a series of activities including cellular proliferation, apoptosis, migration, and invasion of W038 cells in vitro.ResultsWe constructed a 25-genes prognostic model (TNFAIP8L3, PI3, TMEM181, GBP1P1 (LOC400759), STX18, KIF26B, MRPS11, CACNA1C, PACSIN3, GMPR, MANF, PYGB, SNRPA1, ST7L, ZBP1, BMPR1B-DT, STAC2, LINC02585, LYPD6, NSG1, ACOT13, FAM120B, LEFTY1, SULT1A2, FZD3). The areas under the curves (AUC) of 1, 2 and 3 years were 0.806, 0.773 and 0.762, in the TCGA cohort, respectively. Besides, the effectiveness of the model was verified using ICGC testing data. Univariate and multivariate Cox regression analysis exposes the risk score as an independent prognosis predictor for OS both in the TCGA and ICGC cohort. In summary, we utilized comprehensive bioinformatics analysis to build an effective prognostic gene model for OC patients. These bioinformatic results suggested that GBP1P1 could act as a novel biomarker for OC. GBP1P1 knockdown substantially inhibited the proliferation, migration, and invasion of W038 cells in vitro, and increased the percentage of apoptotic W038 cells.ConclusionsThe analyses of genetic status of patients with 25-genes model might improve the ability to predict the prognosis of patients with OC and help to select patients suit able to therapies. Immune-related gene GBP1P1 might serve as prognostic biomarker for OC. creator: Min Yu creator: Dan Li creator: Li Zhang creator: Ke Wang uri: https://doi.org/10.7717/peerj.18235 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yu et al. title: The significance of biowaste drying analysis as a key pre-treatment for transforming it into a sustainable biomass feedstock link: https://peerj.com/articles/18248 last-modified: 2024-10-31 description: The objective of this study is to investigate the drying kinetics of fruit and vegetable peel biowaste using a sustainable technique as a key-pretreatment for its conversion into useful feedstock. Biowaste represents a missed potential source of bioenergy and bioproducts, but moisture removal is required, and conventional drying methods are expensive since they require great quantity of energy supplied, almost always, by a non-renewable energy. In this study six batches with the same quantity of biowaste, and heterogeneous physical composition were dried under open-sun conditions. We evaluated the influence of the interaction between drying area and the initial moisture content on drying rate. Eight semi-theoretical models were fitted using Levenberg–Marquardt algorithm to predict drying rate, and their accuracy was assessed through goodness-of-fit tests. Maximum moisture content to preserve biomass (10%) was reached on 5th day and the equilibrium on 16th day of drying. According to goodness-of-fit test (R2 = 0.999, χ2 = 4.666 × 10−5, RMSE = 0.00683) the best model to predict drying rate was Two-term model. The mathematical model obtained from Fick’s second law is reliable to predict drying kinetics, R2 (0.9648 ± 0.0106); despite the variation between drying area and initial moisture content. Kruskal-Wallis test showed that drying rates between batches are not significantly different (p = 0.639; 0.05); nor effective diffusion coefficient (Deff = 4.97 × 10−11  ±  0.3491 × 10−11), (p = 0.723; 0.05). The study of drying kinetics is crucial for selecting the optimal biowaste treatment based on its generation context. This could enable its use as feedstock for bioproduct or bioenergy production, thereby reducing waste accumulation in landfills and environmental impact. creator: Fernando Damián Barajas Godoy creator: Marco A. Martínez-Cinco creator: José G. Rutiaga-Quiñones creator: Otoniel Buenrostro-Delgado creator: Jose Mendoza uri: https://doi.org/10.7717/peerj.18248 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Barajas Godoy et al. title: A comparative study on the lipid layer thickness analysis of medical staff before and after work link: https://peerj.com/articles/18258 last-modified: 2024-10-31 description: Background & AimsTo study the change of the lipid layer thickness analysis in medical staff (MS) before and after work, and to explore the significance of measuring lipid layer thickness (LLT) respectively in four quadrants.MethodsOcular Surface Disease Index (OSDI) questionnaire and video display terminal using time for 55 MS were collected (the informed consent was obtained from all patients). Noninvasive tear break-up time, LLT, tear meniscus height (TMH), meibomian glands (MG) dropout, and blink pattern before and after work (worked for more than 4 h) of 110 eyes were measured by Gaush iDea Ocular surface analyzer. Lid margin abnormalities were evaluated by the slit-lamp microscopy.ResultsThe average OSDI score of 55 MS was 25.68 ± 14.91. The average LLT of 110 eyes after work (65.12 ± 3.63 nm) was significantly reduced compared to before work (66.54 ± 4.16 nm), p < 0.05. The LLT in the superior quadrant was significantly thinner than that in the other three quadrants, p < 0.01. The average LLT was positively correlated with the LLT in the inferior (r = 0.822, p < 0.001), nasal (r = 0.261, p < 0.001), and temporal quadrant (r = 0.372, p < 0.001), while was negatively correlated with the MG dropout in lower lid (r = −0.209, p = 0.002). There was a significant correlation between the LLT in the inferior quadrant and the VDTt (r = −0.173, p = 0.01). The LLT of inferior quadrant were positively related to the TMH (r = 0.149, p = 0.027) and negatively related to MG dropout in lower lid (r = −0.162, p = 0.017).ConclusionThe LLT significantly decreases after work in MS. The distribution of the lipid layer on the ocular surface is uneven. It is unreasonable for current detection instruments to measure the inferior quadrant LLT alone to represent average LLT. creator: Qian Li creator: Xiufen Liu creator: Yu Ren creator: Tianlong He creator: Fei Shao creator: Nuerailimu Yimingtuohuti creator: Dan Li creator: Chengwei Lu uri: https://doi.org/10.7717/peerj.18258 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: The influence of inactivated entomopathogenic bacterium Bacillus thuringiensis on the immune responses of the Colorado potato beetle link: https://peerj.com/articles/18259 last-modified: 2024-10-31 description: BackgroundInvasion of microorganisms into the gut of insects triggers a cascade of immune reactions accompanied by increased synthesis of effectors (such as antimicrobial peptides, cytokines, and amino acids), leading to changes in the physiological state of the host. We hypothesized that even an inactivated bacterium can induce an immune response in an insect. The aim of this study was to compare the roles of reactive oxygen species (ROS) formation and of the response of detoxification and antioxidant systems in a Colorado potato beetle (CPB) larval model in the first hours after invasion by either an inactivated or live bacterium.MethodsThe influence of per os inoculation with inactivated entomopathogenic bacterium Bacillus thuringiensis var. tenebrionis (Bt) on the survival and physiological and biochemical parameters of CPB larvae was assessed as changes in the total hemocyte count (THC), activity of phenoloxidases (POs), glutathione-S-transferases (GSTs), nonspecific esterases (ESTs), catalase, peroxidases, superoxide dismutases (SODs) and formation of reactive oxygen species (ROS).ResultsA series of changes occurred within the hemolymph and the midgut of CPBs inoculated with inactivated Bt at 12 h after inoculation. These physiological and biochemical alterations serve to mediate generalized resistance to pathogens. The changes were associated with an increase in the THC and a 1.4–2.2-fold enhancement of detoxification enzymatic activities (such as GST and EST) as well as increased levels of antioxidants (especially peroxidases) in hemolymph in comparison to the control group. Suppressed EST activity and reduced ROS formation were simultaneously detectable in the larval midgut. Inoculation of beetle larvae with active Bt cells yielded similar results (elevated THC and suppressed PO activity). A fundamental difference in the immune activation processes between larvae that ingested the inactivated bacterium and larvae that had consumed the active bacterium was that the inactivated bacterium did not influence ROS formation in the hemolymph but did reduce their formation in the midgut. At 24 h postinfection with active Bt, ROS levels went up in both the hemolymph and the midgut. This was accompanied by a significant 5.7-fold enhancement of SOD activity and a 5.3-fold suppression of peroxidase activity. The observed alterations may be due to within-gut toxicity caused by early-stage bacteriosis. The imbalance in the antioxidant system and the accumulation of products toxic to the “putative” pathogen can activate detoxification mechanisms, including those of an enzymatic nature (EST and GST). The activation of detoxification processes and of innate immune responses is probably due to the recognition of the “putative” pathogen by gut epithelial cells and is similar in many respects to the immune response at early stages of bacteriosis. creator: Olga V. Polenogova creator: Natalia A. Kryukova creator: Tatyana Klementeva creator: Anna S. Artemchenko creator: Alexander D. Lukin creator: Viktor P. Khodyrev creator: Irina Slepneva creator: Yana Vorontsova creator: Viktor V. Glupov uri: https://doi.org/10.7717/peerj.18259 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Polenogova et al. title: Compositions of the major ions, variations in their sources, and a risk assessment of the Qingshuijiang River Basin in Southwest China: a 10-year comparison of hydrochemical measurements link: https://peerj.com/articles/18284 last-modified: 2024-10-31 description: Rivers in karst areas face increased risks from persistent growth in human activity that leads to changes in water chemistry and threatens the water environment. In this study, principal component analysis (PCA), ion ratio measurements, and other methods were used to study the water chemistry of the Qingshuijiang River Basin over the past 10 years. The results showed that the main ions in the river were Ca2+ and HCO3–, with a cation order of Ca2+ (mean: 0.93 mmol/L) > Mg2+ (mean: 0.51 mmol/L) > Na+ (mean: 0.30 mmol/L) > K+ (mean: 0.06 mmol/L) and HCO3– (mean: 2.00 mmol/L) > SO42– (mean: 0.49 mmol/L) > Cl– (mean: 0.15 mmol/L) > NO3– (mean: 0.096 mmol/L) > F– (mean : 0.012 mmol/L). In the past 10 years, the concentration of major ions in the river water in the basin has increased significantly. The weathering input of rock (mainly upstream carbonate) was the main source of Mg2+, Ca2+, and HCO3−, though sulfuric acid was also involved in this process. While K+ and Na+ were affected by the combination of human activity and the weathering input of silicate rock in the middle and lower reaches of the river, human activity was the main source of SO42−, NO3−, and F− ions. Irrigation water quality and health risks were evaluated by calculating the sodium adsorption ratio (SAR), soluble sodium percentage (Na%), residual sodium carbonate (RSC), and hazard quotient (HQ). The findings indicated that the river water was generally safe for irrigation and drinking, and the health risks were gradually reduced over time. However, long-term monitoring of the river basin is still essential, especially for the risk of excessive F− in a few tributaries in the basin. creator: Jiemei Lv creator: Tianhao Yang creator: Yanling An uri: https://doi.org/10.7717/peerj.18284 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lv et al. title: Deep-ocean macrofaunal assemblages on ferromanganese and phosphorite-rich substrates in the Southern California Borderland link: https://peerj.com/articles/18290 last-modified: 2024-10-31 description: Mineral-rich hardgrounds, such as ferromanganese (FeMn) crusts and phosphorites, occur on seamounts and continental margins, gaining attention for their resource potential due to their enrichment in valuable metals in some regions. This study focuses on the Southern California Borderland (SCB), an area characterized by uneven and heterogeneous topography featuring FeMn crusts, phosphorites, basalt, and sedimentary rocks that occur at varying depths and are exposed to a range of oxygen concentrations. Due to its heterogeneity, this region serves as an optimal setting for investigating the relationship between mineral-rich hardgrounds and benthic fauna. This study characterizes the density, diversity, and community composition of macrofauna (>300 μm) on hardgrounds as a function of substrate type and environment (depth and oxygen ranges). Rocks and their macrofauna were sampled quantitatively using remotely operated vehicles (ROVs) during expeditions in 2020 and 2021 at depths above, within, and below the oxygen minimum zone (OMZ). A total of 3,555 macrofauna individuals were counted and 416 different morphospecies (excluding encrusting bryozoans and hydrozoans) were identified from 82 rocks at depths between 231 and 2,688 m. Average density for SCB macrofauna was 11.08 ± 0.87 ind. 200 cm−2 and mean Shannon-Wiener diversity per rock (H′[loge]) was 2.22 ± 0.07. A relationship was found between substrate type and macrofaunal communities. Phosphorite rocks had the highest H′ of the four substrates compared on a per-rock basis. However, when samples were pooled by substrate, FeMn crusts had the highest H′ and rarefaction diversity. Of all the environmental variables examined, water depth explained the largest variance in macrofaunal community composition. Macrofaunal density and diversity values were similar at sites within and outside the OMZ. This study is the first to analyze the macrofaunal communities of mineral-rich hardgrounds in the SCB, which support deep-ocean biodiversity by acting as specialized substrates for macrofaunal communities. Understanding the intricate relationships between macrofaunal assemblages and mineral-rich substrates may inform effects from environmental disruptions associated with deep-seabed mining or climate change. The findings contribute baseline information useful for effective conservation and management of the SCB and will support scientists in monitoring changes in these communities due to environmental disturbance or human impact in the future. creator: Michelle Guraieb creator: Guillermo Mendoza creator: Kira Mizell creator: Greg Rouse creator: Ryan A. McCarthy creator: Olívia S. Pereira creator: Lisa A. Levin uri: https://doi.org/10.7717/peerj.18290 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Guraieb et al. title: Prioritising non-native fish species for management actions in three Polish rivers using the newly developed tool—dispersal-origin-status-impact scheme link: https://peerj.com/articles/18300 last-modified: 2024-10-31 description: BackgroundBiological invasions are a major threat to global biodiversity, with freshwater ecosystems being among the most susceptible to the successful establishment of non-native species and their respective potential impacts. In Poland, the introduction and spreading of non-native fish has led to biodiversity loss and ecosystem homogenisation.MethodsOur study applies the Dispersal-Origin-Status-Impact (DOSI) assessment scheme, which is a population-level specific assessment that integrates multiple factors, including dispersal mechanisms, origin, status, and impacts, providing a nuanced framework for assessing invasion risks at local and regional levels. We used this tool to evaluate the risks associated with non-native fish species across three major Polish rivers (Pilica, Bzura, and Skrwa Prawa) and to prioritise them for management actions.ResultsUsing DOSI, we assessed eight non-native species identified in the three studied rivers: seven in both Pilica and Bzura and four in Skrwa Prawa. The DOSI assessment scheme identified high variability in the ecological impacts and management priorities among the identified non-native species. Notably, species such as the Ponto-Caspian gobies exhibited higher risk levels due to their rapid spread and considerable ecological effects, contrasting with other species that demonstrated lower impact levels and, hence, received a lower priority for intervention.ConclusionThe adoption of the DOSI scheme in three major rivers in Poland has provided valuable insights into the complexities of managing biological invasions, suggesting that localised, detailed assessments are crucial for effective conservation strategies and highlighting the importance of managing non-native populations locally. creator: Dagmara Błońska creator: Joanna Grabowska creator: Ali S. Tarkan creator: Ismael Soto creator: Phillip J. Haubrock uri: https://doi.org/10.7717/peerj.18300 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Błońska et al. title: FastProtein—an automated software for in silico proteomic analysis link: https://peerj.com/articles/18309 last-modified: 2024-10-31 description: Although various tools provide proteomic information, each tool has limitations related to execution platforms, libraries, versions, and data output format. Integrating data generated from different software is a laborious process that can prolong analysis time. Here, we present FastProtein, a protein analysis pipeline that is user-friendly, easily installable, and outputs important information about subcellular location, transmembrane domains, signal peptide, molecular weight, isoelectric point, hydropathy, aromaticity, gene ontology, endoplasmic reticulum retention domains, and N-glycosylation domains. It also helps determine the presence of glycosylphosphatidylinositol and obtain functional information from InterProScan, PANTHER, Pfam, and alignment-based annotation searches. FastProtein provides the scientific community with an easy-to-use computational tool for proteomic data analysis. It is applicable to both small datasets and proteome-wide studies. It can be used through the command line interface mode or a web interface installed on a local server. FastProtein significantly enhances proteomics analysis workflows by producing multiple results in a single-step process, thereby streamlining and accelerating the overall analysis. The software is open-source and freely available. Installation and execution instructions, as well as the source code and test files generated for tool validation, are available at https://github.com/bioinformatics-ufsc/FastProtein. creator: Renato Simões Moreira creator: Vilmar Benetti Filho creator: Guilherme Augusto Maia creator: Tatiany Aparecida Teixeira Soratto creator: Eric Kazuo Kawagoe creator: Bruna Caroline Russi creator: Luiz Cláudio Miletti creator: Glauber Wagner uri: https://doi.org/10.7717/peerj.18309 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Moreira et al. title: Factors influencing health-promoting behavior among single mothers in Northeastern Malaysia: a cross-sectional study link: https://peerj.com/articles/18359 last-modified: 2024-10-31 description: IntroductionHealth-promoting behaviors (HPB) play a vital role in maintaining and enhancing overall well-being. Single mothers are at higher risk of cardiovascular disease (CVD) and less involvement in HPB due to psychosocial disadvantages.ObjectiveThis study aimed to determine the HPB scores and factors influencing HPB among single mothers in Kelantan (Northeastern, Malaysia).MethodsThis study employed a cross-sectional design, selecting 242 single mothers from Kelantan through proportional stratified sampling. Data were gathered through questionnaires covering sociodemographic details, the Health-Promoting Lifestyle Profile-II (HPLP-II), the Malay Version of Health Beliefs Related to Cardiovascular Disease (HBCVD-M), and Multidimensional Perceived Social Support (MPSS). The relationships between the dependent variable (HPB) and independent variables were analyzed using multivariable linear regression models.ResultsThe respondents achieved an average HPB score of 118.03 (SD = 19.2), with the highest mean scores in spiritual growth (22.46 [SD = 3.70]) and interpersonal relationships (22.05 [SD = 3.67]). Physical activity had the lowest mean score at 15.09 (SD = 4.62). Significant positive associations were found between HPB and perceived severity of CVD (adjusted β = 1.60; 95% CI [0.68–2.53]; p < 0.001) as well as perceived social support (adjusted β = 0.63; 95% CI [0.37–0.90]; p < 0.001). Conversely, educational level (adjusted β = −10.36; 95% CI [−16.06 to −4.67]; p < 0.001) and perceived benefits of reducing CVD risk (adjusted β = −1.43; 95% CI [−2.37 to −0.48]; p < 0.001) were negatively associated with HPB.ConclusionsThe findings highlight the importance of health beliefs, social support, and education in shaping HPB among single mothers. Community health initiatives targeting this population should develop strategies to strengthen individuals’ health beliefs and promote a supportive environment. creator: Saidah Adilah Mohamed Yusof creator: Tengku Alina Tengku Ismail creator: Kamarul Imran Musa creator: Hasmaryanti Kamaruzzaman uri: https://doi.org/10.7717/peerj.18359 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mohamed Yusof et al. title: Prognostic and therapeutic potential of gene profiles related to tertiary lymphoid structures in colorectal cancer link: https://peerj.com/articles/18401 last-modified: 2024-10-31 description: The role of tertiary lymphoid structures (TLS) in oncology is gaining interest, particularly in colorectal carcinoma, yet a thorough analysis remains elusive. This study pioneered a novel TLS quantification system for prognostic and therapeutic response prediction in colorectal carcinoma, alongside a comprehensive depiction of the TLS landscape. Utilizing single-cell sequencing, we established a TLS score within the Tumor Immune Microenvironment (TIME). Analysis of tertiary lymphoid structure-related genes (TLSRGs) in 1,184 patients with colon adenocarcinoma/rectum adenocarcinoma (COADREAD) from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases led to the identification of two distinct molecular subtypes. Differentially expressed genes (DEGs) further segregated these patients into gene subtypes. A TLS score was formulated using gene set variation analysis (GSVA) and its efficacy in predicting immunotherapy outcomes was validated in two independent cohorts. High-scoring patients exhibited a ‘hot’ immune phenotype, correlating with enhanced immunotherapy efficacy. Key genes in our model, including C5AR1, APOE, CYR1P1, and SPP1, were implicated in COADREAD cell proliferation, invasion, and PD-L1 expression. These insights offer a novel approach to colorectal carcinoma treatment, emphasizing TLS targeting as a potential anti-tumor strategy. creator: Jinglu Yu creator: Yabin Gong creator: Xiaowei Huang creator: Yufang Bao uri: https://doi.org/10.7717/peerj.18401 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yu et al. title: The role and underlying mechanisms of irisin in exercise-mediated cardiovascular protection link: https://peerj.com/articles/18413 last-modified: 2024-10-31 description: Irisin, a product of the post-translational processing of fibronectin type III domain-containing protein 5 (FNDC5), is a novel myokine which is upregulated during exercise. This hormone not only promotes the transformation of white adipose tissue into a brown-fat-like phenotype but also enhances energy expenditure and mitigates fat accumulation. Its role is crucial in the management of certain metabolic disorders such as diabetes and heart disease. Of note, the type of exercise performed significantly affects blood irisin levels, indicating the critical role of physical activity in regulating this hormone. This article aims to summarize the current scientific understanding of the role of irisin and the mechanisms through which it mediates cardiovascular protection through exercise. Moreover, this article aims to establish irisin as a potential target for preventing and treating cardiovascular diseases. creator: Wenhuang Guo creator: Jianwei Peng creator: Jiarui Su creator: Jingbo Xia creator: Weiji Deng creator: Peilun Li creator: Yilin Chen creator: Guoqing Liu creator: Shen Wang creator: Junhao Huang uri: https://doi.org/10.7717/peerj.18413 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Guo et al. title: Rotating cell culture system-induced injectable self-assembled microtissues with epidermal stem cells for full-thickness skin repair link: https://peerj.com/articles/18418 last-modified: 2024-10-31 description: Epidermal stem cells (EpSCs) are crucial for wound healing and tissue regeneration, and traditional culture methods often lead to their inactivation. It is urgent to increase the yield of high quality EpSCs. In this study, primary EpSCs were isolated and cultured in a serum-free, feeder-free culture system. EpSCs are then expanded in a dynamic 3D environment using a rotating cell culture system (RCCS) with biodegradable porous microcarriers (MC). Over a period of 14 days, the cells self-assembled into microtissues with superior cell proliferation compared to 3D static culture. Immunofluorescence and qPCR analyses consistently showed that the stemness of the 3D microtissues was preserved, especially the COL17A1 associated with anti-aging was highly expressed in RCCS induced microtissues. In vivo experiments demonstrated that the group treated with 3D microtissues loaded with EpSCs showed enhanced early wound healing, and the injectable 3D microtissues were more conducive to maintaining cell viability and differentiation potential. Our study provides valuable insights into the dynamic 3D culture of EpSCs and introduces an injectable therapy using 3D microtissues loaded with EpSCs, which provides a new and effective approach for cell delivery and offering a promising strategy for guiding the regeneration of full-thickness skin defects. creator: Min Zhang creator: Meng Huang creator: Xixi Dong creator: Yibo Wang creator: Luyue Zhang creator: Zhaoxiang Wang creator: Junkai Cao uri: https://doi.org/10.7717/peerj.18418 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Use of intravenous immunoglobulin in antiphospholipid antibody positive patients with high risk of miscarriage: a systematic review and meta-analysis link: https://peerj.com/articles/18419 last-modified: 2024-10-31 description: ObjectiveThe purpose of the present study was to evaluate whether intravenous immunoglobulin (IVIG) increases live birth rates and improves neonatal results in patients with antiphospholipid antibodies (aPL) at high-risk for miscarriage.BackgroundPositivity of aPL in pregnant women is a high-risk factor for miscarriage, and IVIG treatment has emerged as a potential intervention.MethodsThe Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was employed to search multiple electronic databases for articles published until August 20, 2023, including PubMed, Web of Science, Embase, Scopus and Medline. The inclusion criteria encompassed studies assessing the efficacy of IVIG in aPL-positive patients with a high risk of miscarriage. Relevant articles were assessed for the quality and data were extracted for analysis. Two independent reviewers performed study selection, data extraction, and quality assessments. The risk of bias was evaluated according to the Cochrane risk of bias tool. All analyses were conducted using Review Manager 5.3.ResultsThis systematic review included nine randomized controlled trials, with 366 aPL-positive women at high risk of miscarriage. These studies included in this review were randomized controlled trials. The primary outcome measures were successful pregnancy outcomes and live birth rates. The secondary outcomes included obstetric complications, and neonatal outcomes (such as birth weight and live-birth rate). The comparison between the intervention and control groups revealed no significant differences in terms of obstetric complications and neonatal outcomes. The group receiving IVIG treatment had a higher prevalence of preterm deliveries than controls (OR = 2.05, I2 = 46%, 95% CI [0.58–5.24]), but also exhibited a partial improvement in live birth rates (OR = 2.86, I2 = 52%, 95% CI [1.04–7.90]), because it reduced the number of miscarriages (OR = 0.35, I2 = 52%, 95% CI [0.13–0.96]).ConclusionBased on the available evidence, IVIG intervention appears to be a potentially effective approach for managing of aPL-positive pregnant women with high risk of miscarriage. While IVIG shows significant potential in tripling the chances of having a live-born child, further large-scale randomized controlled trials are necessary, preferably comparing IVIG with hydroxychloroquine or lifestyle and dietary interventions, to refine treatment protocols and ensure the most effective application. creator: Xin Yuan creator: Wei Zhang creator: Tong Wang creator: Peng Jiang creator: Zong-kui Wang creator: Chang-qing Li uri: https://doi.org/10.7717/peerj.18419 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yuan et al. title: Prevalence of anxiety, depression, stress and insomnia among healthcare professionals during COVID-19 in Africa: umbrella review of existing meta-analyses link: https://peerj.com/articles/18108 last-modified: 2024-10-30 description: IntroductionIn Africa, healthcare professionals experienced various mental health problems during COVID-19. However, very little was done on the extensive evidence regarding mental disorders. The purpose of this umbrella review is to provide comprehensive data on the prevalence of anxiety, depression, stress, and insomnia among healthcare professionals during the COVID-19 pandemic in Africa.Materials and MethodsSystematic searches of databases African Journals Online, MedRxiv, PubMed, and Google Scholar were used to identify studies from the occurrence of COVID-19 from December 2019 to March 2023 were included. To pool the gathered data for results with a 95% confidence interval (CI), DerSimonian-Laird random effects meta-analysis was used. For heterogeneity examination, I2 was used. The quality assessment was evaluated by using the Joanna Briggs Institute (JBI) critical appraisal checklist.ResultsA total of five studies reported the prevalence of depression, the pooled prevalence was 53.75% (95% CI [40.80–66.70], I2 = 63.6%, p = 0.027). In a total of four studies, the pooled prevalence of anxiety was 49.97% (95% CI [34.71–65.23], I2 = 71.26%, p = 0.014). From a total of two studies, the pooled prevalence of stress was 57.27% (95% CI [42.28–72.25], I2 = 58.9%, p = 0.119). From a total of four studies, the pooled prevalence of insomnia was 45.16% (95% CI [32.94–57.39], I2 = 50.8%, p = 0.107).ConclusionsThe COVID-19 pandemic highly affects the mental health of healthcare professionals in Africa. Stress, depression, anxiety, and insomnia symptoms were representing the most common based on evidences from existing meta-analyses. This evidence can help experts when executing specific interventions that address mental health problems among healthcare professionals during future public health crises. creator: Aragaw Asfaw Hasen creator: Ahmed Adem Mohammed creator: Abubeker Alebachew Seid uri: https://doi.org/10.7717/peerj.18108 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hasen et al. title: The Argyreia collinsiae species complex (Convolvulaceae): phenetic analysis and geographic distribution reveal subspecies new to science link: https://peerj.com/articles/18294 last-modified: 2024-10-30 description: Argyreia Lour. is a speciose genus in the Convolvulaceae. However, the genus contains several problematic species complexes due to their morphological similarity. In this study, we aimed to resolve the Argyreia collinsiae complex, which consists of four similar operational taxonomic units (OTUs), i.e., A. collinsiae (Craib) Na Songkhla & Traiperm, A. dokmaihom Traiperm & Staples, A. versicolor (Kerr) Staples & Traiperm, and a peculiar OTU typically known as the large-bract morphotype of A. collinsiae. Following morphological comparison and phenetic analysis, all four OTUs were found to be distinct. However, the large-bract morphotype of A. collinsiae was confirmed to be more closely related to the original morphotype of A. collinsiae than to the other two species. Species distribution modeling (SDM) was then conducted for both morphotypes of A. collinsiae, revealing different geographical ranges of suitable habitat for each. In conclusion, the large-bract morphotype of A. collinsiae was described in this study as a new subspecies, A. collinsiae subsp. megabracteata Traiperm & Srisombat, subsp. nov., based on morphological differences and separate geographic range. We also provide here an identification key, description, detailed illustrations, distribution data, and ecological notes of the new subspecies. An updated description of A. versicolor and an assessment of its conservation status were also prepared since the original description was based solely on dried herbarium specimens and lacks key details. creator: Poompat Srisombat creator: Natthaphong Chitchak creator: Pantamith Rattanakrajang creator: Alyssa B. Stewart creator: Paweena Traiperm uri: https://doi.org/10.7717/peerj.18294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Srisombat et al. title: Impact of three weeks of integrative neuromuscular training on the athletic performance of elite female boxers link: https://peerj.com/articles/18311 last-modified: 2024-10-30 description: ObjectivesTo investigate the effects of integrative neuromuscular training (INT) on the athletic performance of elite female boxers.MethodsA before-and-after controlled experiment was conducted on 37 elite Chinese female boxers (Age: 26.00 ± 3.11 years). All included athletes have competed at the international level. The INT intervention was administered 11 times per week for 3 weeks. This training includes strength training, explosive training, core stability, agility exercises, high intensity intervals and sprint intervals. Basic physical fitness tests, including the deep squat and bench press one-repetition maximum (1RM), vertical long jump, 30 m sprint run, 400 m run, 3,000 m run, 1-minute hexagonal jump, and 3-minute double shake; as well as specialized striking ability tests, including single-punch striking and 10-second, 30-second, and 3-minute continuous punching, were conducted before and after the intervention.ResultsCompared with pre-intervention baseline data, significant differences were found in the athletes’ post-intervention baseline physical fitness, including squat and beach press (1RM), vertical jump, 30 m sprint run, 400 m run, 3,000 m run, 1-minute hexagonal jump, and 3-minute double shake (p < 0.05). Additionally, 10-second, 30-second, and 3-minute continuous punching were significantly different compared with pre-intervention (p < 0.05). However, no significant differences were found in single punch power (p > 0.05).ConclusionThe 3-week INT can significantly improve the maximum strength, vertical explosive power, linear acceleration, agility, and continuous punching abilities of Chinese elite female boxers. The use of INT in physical training may enhance their athletic performance. creator: Zhen Niu creator: Zijing Huang creator: Gan Zhao creator: Chao Chen uri: https://doi.org/10.7717/peerj.18311 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Niu et al. title: Research progress on V delta 1+ T cells and their effect on pathogen infection link: https://peerj.com/articles/18313 last-modified: 2024-10-30 description: The ongoing high occurrence of harmful infectious diseases significantly threatens human health. Existing methods used to control such diseases primarily involve targeting the pathogens, usually neglecting the vital role of host factors in disease advancement. Gamma delta (γδ) T cells act as a bridge between innate and adaptive immunity, playing a crucial role in combating pathogen invasion. Among these γδT cell subsets, which are categorized based on T cell receptor delta variable expression patterns, V delta (δ) 1+ T cells possess unique recognition abilities and regulatory characteristics and actively engage in various immune responses. The differentiation, development, and immune reactivity of Vδ1+ T cells are closely associated with the initial and progressive stages of infectious diseases. This article provides an overview of the classification, distribution, differentiation, and development of Vδ1+ T cells and their mechanisms in combating pathogenic infections, offering new insights for disease diagnosis and treatment. creator: Yuxia Li creator: Yanfei Liu creator: Xiaoxiao Bu creator: Yuanyuan Qin creator: Yanyan Zhang uri: https://doi.org/10.7717/peerj.18313 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Li et al. title: Meta-analysis of the efficacy of the erector spinae plane block after spinal fusion surgery link: https://peerj.com/articles/18332 last-modified: 2024-10-30 description: ObjectiveTo investigate the efficacy of erector spinal plane block (ESPB) after spinal fusion surgery in this study.MethodsThe PubMed, Embase, Cochrane library, and Web of Science databases were searched with a search deadline of March 30, 2024, and Stata 15.0 was used to analyze the data from the included studies.ResultNine randomized controlled trials involving 663 patients were included. Meta-analysis showed that EPSB could reduce pain scores at 2h (standard mean difference (SMD) = −0.78, 95% CI [−1.38 to −0.19], GRADE: Moderate), 6 h (SMD = −0.81, 95% CI [−1.23 to −0.38], GRADE: Moderate), 12 h (SMD = −0.59, 95% CI [−1.05 to −0.13], GRADE: Moderate), 24 h (SMD = −0.54, 95% CI [−0.86 to −0.21], GRADE: Moderate), 48 h (SMD = −0.40, 95% CI [−0.75 to −0.05], GRADE: Moderate) after spinal fusion surgery, as well as the PCA (analgesia medication use) (SMD = −1.67, 95% CI [−2.67 to −0.67], GRADE: Moderate). However, EPSB had no effect on intraoperative blood loss (SMD = −0.28, 95% CI [−1.03 to 0.47], GRADE: Low) and length of hospital stay (SMD = −0.27, 95% CI [−0.60–0.06], GRADE: Low).ConclusionCombined with the current findings, EPSB may reduce pain scores in spinal fusion surgery, possibly reducing the use of postoperative analgesics. However, due to the limitations of the study, we need more high-quality, multi-center, large sample randomized controlled trials to merge. creator: Yi He creator: Heng Liu creator: Peng Ma creator: Jing Zhang creator: Qiulian He uri: https://doi.org/10.7717/peerj.18332 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 He et al. title: The critical need for child and youth perceptions of active living in India: capturing context complexity in rural and urban regions link: https://peerj.com/articles/18350 last-modified: 2024-10-30 description: BackgroundThe physical inactivity pandemic not only has a negative impact on the physical and mental health of children and youth, but it is also a key contributor to the non-communicable disease (NCD) burden, particularly among low- and middle-income countries. The widespread effects of climate change, ranging from extreme weather events to worsening air quality, are exacerbating the physical inactivity pandemic, highlighting the need to undertake holistic interventions to address environmental barriers while promoting physical activity. Despite the potential benefits of active school transportation (AST) on physical activity and the environment, no study has examined the intersection between perceptions of AST, environmental perceptions, and moderate-to-vigorous physical activity (MVPA) among children and youth in India from a child and youth perspective.MethodsAs a part of this cross-sectional, observational study, digital survey links were administered to 1,042 children and youth aged 5 to 17 (50.3% boys; 49.7% girls). Participants were recruited from 41 schools across 28 rural and urban regions in India. Children and youth provided information on various sociodemographic factors, perceptions of crime and air pollution, and peer support factors. MVPA data were collected using an adapted version of the IPAQ short-form questionnaire. The overall sample was stratified by age, gender, and location, resulting in a total of seven multiple linear regression models to assess the association between AST and MVPA.ResultsChildren and youth who engaged in AST were associated with higher MVPA than those who did not engage in AST (β = 18.020, 95% CI [5.890 to 30.149], p = 0.004), after adjusting for age, gender, and location. In contrast, perceptions of high crime in the neighbourhood (β =  − 21.921, CI [−36.195 to −7.647], p = 0.003) and perceptions of air pollution (β =  − 12.472, CI [−23.797 to −1.147], p = 0.031) were associated with lower MVPA. Moreover, having active friends was associated with higher MVPA (β = 32.391, CI [9.264 to 55.518], p = 0.006) than not having active friends. AST was significantly associated with higher MVPA in the boys, rural, and aged 13 to 17 models; however, this association was not statistically significant in the girls, urban, and aged 5 to 12 models.ConclusionsThese findings highlight that promoting AST can potentially promote MVPA and contribute to mitigating the NCD burden among children and youth in India. Future policies and interventions should prioritize initiatives that promote AST, considering diverse sociodemographic factors, and addressing environmental challenges such as perceptions of crime and air pollution. creator: Tarun Reddy Katapally creator: Jamin Patel creator: Anuradha Khadilkar creator: Jasmin Bhawra uri: https://doi.org/10.7717/peerj.18350 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Katapally et al. title: Differences in cardiovascular disease mortality between northern and southern China under exposure to different temperatures: a systematic review link: https://peerj.com/articles/18355 last-modified: 2024-10-30 description: BackgroundDue to differences in climate and other environmental factors, exposure to different temperatures in China has different effects on the relative risk (RR) of cardiovascular disease (CVD) mortality. It is therefore important to compare the effects of exposure to different temperatures on CVD mortality in different regions of China.MethodsTo compare these effects, we performed a meta-analysis of 21 studies identified by a search of the Web of Science and China National Knowledge Infrastructure databases from January 1, 2014 to January 1, 2024. We performed the Cochran Q test and I2 statistics test to evaluate heterogeneity and Egger’s test to evaluate publication bias.ResultsThe pooled estimated size of the relationship between exposure to different temperatures and CVD mortality was 1.60 (95% confidence interval [CI]: [1.42–1.80]) for the extreme cold, 1.17 (95% CI [1.10–1.25]) for the extreme heat, and 1.16 (95% CI [1.10–1.24]) for extremely high diurnal temperature range (DTR). The Egger’s test showed potential publication bias in studies analyzing both the extreme cold and the extreme heat.DiscussionExtreme cold, extreme heat, and extremely high DTR are associated with an increase in CVD mortality in China, with extreme cold having the most significant effect. Residents of northern regions are more susceptible to high temperatures, while residents of southern regions are more sensitive to low temperatures. creator: Guangyu Zhai creator: Ziqing Jiang creator: Wenjuan Zhou uri: https://doi.org/10.7717/peerj.18355 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhai et al. title: Identification and validation of autophagy-related genes in Hirschsprung’s disease link: https://peerj.com/articles/18376 last-modified: 2024-10-30 description: BackgroundHirschsprung’s disease (HSCR) is a congenital disorder characterized by aganglionosis in the intermuscular and submucosal nerve plexuses of the gut, leading to impaired gastrointestinal function. Although the precise cause and pathophysiology of HSCR remain elusive, increasing evidence points to a significant role of autophagy in its development, warranting further investigation into its underlying mechanisms.MethodsThis study utilized publicly available microarray expression profiling datasets, GSE96854 and GSE98502, from the Gene Expression Omnibus (GEO). The R software (version 4.2.0) was employed to identify autophagy-related genes potentially showing differential expression in HSCR. Subsequent analyses included correlation analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analysis using the STRING database (version 11.0) and Cytoscape software (version 3.8.2). Ultimately, HSCR samples were used to verify the mRNA levels of important genes by quantitative real-time polymerase chain reaction (qRT-PCR) in a laboratory setting.ResultsWe have discovered 20 genes that are involved in autophagy and show variable expression. Among these genes, 15 are up-regulated and five are down-regulated. The enrichment analysis using the GO and KEGG pathways revealed a notable enrichment in pathways related to the control of autophagy. Nine hub genes were found via the investigation of the PPI network constructed from STRING database and module analysis using Cytoscape. Moreover, the concordance between SIRT1 expression in the HSCR model and the bioinformatics analysis of mRNA chip findings was validated using qRT-PCR.ConclusionUtilizing bioinformatics analysis, we identified 20 potential genes associated with Hirschsprung’s disease that play a role in autophagy. Notably, the upregulation of SIRT1 may profoundly influence the progression of HSCR by regulating autophagy-related pathways, offering a novel perspective on the disease’s pathogenesis. creator: Ting Yao creator: Zenghui Hao creator: Wei Fan creator: Jinbao Han creator: Shuyu Wang creator: Zaiqun Jiang creator: Yunting Wang creator: Xiao Qian Yang creator: Zhilin Xu uri: https://doi.org/10.7717/peerj.18376 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yao et al. title: Optimization of fermentation conditions for physcion production of Aspergillus chevalieri BYST01 by response surface methodology link: https://peerj.com/articles/18380 last-modified: 2024-10-30 description: This study aimed to optimize the culture conditions of the termite-derived fungus Aspergillus chevalieri BYST01 for the production of physcion, a characteristic component of the traditional herb rhubarb, which has been commercially approved as a botanical fungicide in China. First, potato dextrose broth was screened as the suitable basal medium for further optimization, with an initial yield of 28.0 mg/L. Then, the suitable carbon source, fermentation time, temperature, pH value, and the rotary shaker speed for physcion production were determined using the one-variable-at-a-time method. Based on the results of single factors experiments, the variables with statistically significant effects on physcion production were further confirmed using the Plackett-Burman design (PBD). Among the five variables, temperature, initial pH, and rotary shaker speed were identified as significant factors (P < 0.05) for physcion productivity in the PDB and were further analyzed by response surface methodology (RSM). Finally, we found that the maximum physcion production (82.0 mg/L) was achieved under the following optimized conditions:initial pH 6.6, rotary shaker speed of 177 rpm, temperature of 28 °C, and glucose concentration of 30 g/L in PDB medium after 11 d of fermentation. The yield of physcion under the optimized culture conditions was approximately threefold higher than that obtained using the basal culture medium. Furthermore, the optimum fermentation conditions in the 5-L bioreactor achieved a maximal physcion yield of 85.2 mg/L within 8 d of fermentation. Hence, response surface methodology proved to be a powerful tool for optimizing physcion production by A. chevalieri BYST01. This study may be helpful in promoting the application of physcion produced by A. chevalieri BYST01 to manage plant diseases. creator: Shuxiang Zhang creator: Zhou Jiang creator: Suwen An creator: Xiaolan Jiang creator: Yinglao Zhang uri: https://doi.org/10.7717/peerj.18380 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil link: https://peerj.com/articles/18383 last-modified: 2024-10-30 description: Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices. creator: Nattanan Rueangmongkolrat creator: Pichahpuk Uthaipaisanwong creator: Kanthida Kusonmano creator: Sasipa Pruksangkul creator: Prinpida Sonthiphand uri: https://doi.org/10.7717/peerj.18383 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rueangmongkolrat et al. title: Using vessels of opportunity for determining important habitats of bottlenose dolphins in Port Phillip Bay, south-eastern Australia link: https://peerj.com/articles/18400 last-modified: 2024-10-30 description: Understanding species’ critical habitat requirements is crucial for effective conservation and management. However, such information can be challenging to obtain, particularly for highly mobile, wide-ranging species such as cetaceans. In the absence of systematic surveys, alternative economically viable methods are needed, such as the use of data collected from platforms of opportunity, and modelling techniques to predict species distribution in un-surveyed areas. The present study used data collected by ecotourism and other vessels of opportunity to investigate important habitats of a small, poorly studied population of bottlenose dolphins in Port Phillip Bay, south-eastern Australia. Using 16 years of dolphin sighting location data, an ensemble habitat suitability model was built from which physical factors influencing dolphin distribution were identified. Results indicated that important habitats were those areas close to shipping channels and coastlines with these factors primarily influencing the variation in the likelihood of dolphin presence. The relatively good performance of the ensemble model suggests that simple presence-background data may be sufficient for predicting the species distribution where sighting data are limited. However, additional data from the center of Port Phillip Bay is required to further support this contention. Important habitat features identified in the study are likely to relate to favorable foraging conditions for dolphins as they are known to provide feeding, breeding, and spawning habitat for a diverse range of fish and cephalopod prey species. The results of the present study highlight the importance of affordable community-based data collection, such as ecotourism vessels, for obtaining information critical for effective management. creator: Maddison J. Ledwidge creator: Jacquomo Monk creator: Suzanne J. Mason creator: John P. Y. Arnould uri: https://doi.org/10.7717/peerj.18400 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ledwidge et al. title: Kinematic differences between female national and provincial athletes in the tennis serve link: https://peerj.com/articles/18410 last-modified: 2024-10-30 description: BackgroundTennis, the second-largest ball game in the world, has a particularly wide audience. To date, little research has been conducted on the biomechanics of female serves.PurposeThe purpose of this study was to capture the key moments by using 1,000 frames/s high-speed video analysis, to analyze the kinematics of the serving techniques of national athletes and provincial athletes, to determine the differences between the two levels of athletes, and to provide theoretical references for the improvement of scientific training level.MethodsTen female athletes were selected as participants for this study, five of whom are national athletes, and the other are provincial athletes. Three-dimensional filming techniques were employed to capture videos of the first and second serve techniques. Simi Motion was applied to obtain the 3D kinematic data. Statistical analyses were performed using IBM SPSS Statistics 27.0, and Mann–Whitney U tests were conducted to determine differences between groups.ResultsSignificant differences in kinematics were found between national and provincial athletes. At the moment of the left knee’s minimum flexion (T2), in the first serve, national athletes had a smaller shoulder-hip vertical plane angle (−18.281 ± 6.142° vs. −25.631 ± 3.497°; p = 0.047) and a larger hip vertical plane rotation angle (−9.378 ± 4.263° vs. −0.470 ± 4.724°; p = 0.047). In the second serve, national athletes had a smaller hip horizontal plane rotation angle (−1.720 ± 4.683° vs. 24.146 ± 24.014°; p = 0.047) but a larger hip vertical plane rotation angle (−11.553 ± 1.949° vs. −0.422 ± 4.958°; p = 0.009). At the moment of impact (T4), in the second serve, national athletes’ batting position (0.296 ± 0.088 m vs. 0.446 ± 0.094 m; p = 0.047) was further back. Additionally, in the second serve, national athletes consistently had their body center of gravity further back at T2 (−0.106 ± 0.052 m vs. −0.018 ± 0.048 m; p = 0.028), T3 (0.002 ± 0.038 m vs. 0.132 ± 0.039 m; p = 0.009), and T4 (0.073 ± 0.050 m vs. 0.217 ± 0.034 m; p = 0.009).ConclusionsThe results of this study indicated several significant kinematic differences between national and provincial athletes, these variations were noted in the shoulder, hip, and body center of gravity. In summary, for the overall first and second serves, it is recommended that national athletes increase the horizontal plane angle of the shoulders and hips at T2, whereas provincial athletes decrease the horizontal plane angle of the shoulder–hip. In addition, provincial athletes need to increase the vertical plane angle of the hip joint, so that the top of the hip can be increased more, and provincial athletes need to be careful not to have the center of gravity too far in front of the body at T2, T3, and T4, so that it can hit the ball at a higher position to increase the swing speed. creator: Yan Chen creator: Tianyang Wang creator: Yuyan Zhao creator: Genghao Zhan creator: Yinchao Tang creator: Zefeng Wang uri: https://doi.org/10.7717/peerj.18410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Development and internal and external validation of a nomogram model for predicting the risk of chronic kidney disease progression in IgA nephropathy patients link: https://peerj.com/articles/18416 last-modified: 2024-10-30 description: BackgroundIgA nephropathy (IgAN) is the most common primary glomerular disease in chronic kidney disease (CKD), exhibiting significant heterogeneity in both clinical and pathological presentations. We aimed to explore the risk factors influencing short-term prognosis (≥90 days) and to construct a nomogram model for evaluating the risk of CKD progression in IgAN patients.MethodsClinical and pathological data of patients diagnosed with IgAN through biopsy at two centers were retrospectively collected. Logistic regression was employed to analyze the training cohort dataset and identify the independent predictors to construct a nomogram model based on the final variables. The predictive model was validated both internally and externally, with its performance assessed using the area under the curve (AUC), calibration curves, and decision curve analysis.ResultsOut of the patients in the modeling group, 129 individuals (41.6%) did not achieve remission following 3 months of treatment, indicating a high risk of CKD progression. A multivariate logistic regression analysis demonstrated that body mass index, urinary protein excretion, and tubular atrophy/interstitial fibrosis were identified as independent predictors for risk stratification. A nomogram model was formulated utilizing the final variables. The AUCs for the training set, internal validation set, and external validation set were 0.746 (95% confidence intervals (CI) [0.691–0.8]), 0.764 (95% CI [0.68–0.85]), and 0.749 (95% CI [0.65–0.85]), respectively. The validation of the subgroup analysis also demonstrated a satisfactory AUC.ConclusionThis study developed and validated a practical nomogram that can individually predict short-term treatment outcomes (≥90 days) and the risk of CKD progression in IgAN patients. It provides reliable guidance for timely and personalized intervention and treatment strategies. creator: Ying Zhang creator: Zhixin Wang creator: Wenwu Tang creator: Xinzhu Yuan creator: Xisheng Xie uri: https://doi.org/10.7717/peerj.18416 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Identification of common and specific cold resistance pathways from cold tolerant and non-cold tolerant mango varieties link: https://peerj.com/articles/18431 last-modified: 2024-10-30 description: Mango has frequently encountered severe climate and environmental challenges such as low temperatures, seriously affecting the sustainable development of the industry. In the study, physiological measurements showed that the activities of superoxide dismutase (SOD) and peroxidase (POD) were found to be higher in Jinhuang (JH) mango plants than those of Tainong (TN) mango plants under cold stress, indicating cold tolerant (JH) and non-cold tolerant (TN) mango varieties were firstly determined. Subsequently, transcriptomics showed 8,337 and 7,996 differentially expressed genes (DEGs) were respectively identified in JH and TN mango varieties treated at 4 °C for 36 h, while more DEGs (10,683 and 10,723) were screened when treated at 4 °C for 72 h. Quantitative real-time PCR (qRT-PCR) of the selected DEGs confirmed their transcriptional levels displayed agreement to the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed two primary cold resistant regulation pathways, photosynthesis-antenna proteins pathway and photosynthesis pathway, were both significant annotated in the two mango varieties, indicating share the common regulation mechanism response to cold stress. However, five specific cold resistant pathways, such as amino acid and carbohydrate metabolisms, were identified in JH mango variety with cold stress for longer duration, indicating the specific regulation pathways in the cold tolerant mango varieties. Furthermore, 43 ethylene-responsive transcription factors (ERFs) were significantly annotated in JH mango after cold-treated for 72 h comparing with the control group, and three of them ERF109-1, ERF017-1 and ERF017-2 were highly expressed, which may play important regulatory roles in plant cold resistance. These results provided insights into the primary and specific molecular mechanisms of different mango varieties resistance to chill. creator: Jian-hua Wang creator: Xiaoyan Feng creator: Muhammad Aleem Ashraf creator: Yufeng Li creator: Yu Kong creator: Qiuliang Cai creator: Shuli Xian creator: Huixiang Yin creator: Nai-tong Yu uri: https://doi.org/10.7717/peerj.18431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Reliability and validity of My Jump 2® app to measure the vertical jump in visually impaired five-a-side soccer athletes link: https://peerj.com/articles/18170 last-modified: 2024-10-29 description: BackgroundAlthough My Jump 2® consistently presented excellent values of reliability and validity when compared to force platforms (FPs) and contact mats, to date no scientific investigation assessed the validity and reliability of My Jump 2® to measure jump height in visually impaired five-a-side soccer athletes. Thus, the study aimed at analyzing the validity and reliability of the My Jump 2® to measure the vertical jump of five-a-side soccer athletes.MethodsTwelve visually impaired five-a-side soccer athletes, volunteered for this study. Each player performed five countermovement jumps (CMJs) and squat jumps (SJs) on a contact platform (CP) while they were simultaneously recorded using MyJump 2®.ResultsThere was almost perfect agreement between the My Jump 2® and the contact platform measurements of CMJ (intraclass correlation coefficient = 0.99; p < 0.001) and SJ (intraclass correlation coefficient = 0.99; p < 0.001), heights for athletes during the first and second measurement days. Bland-Altman analysis showed a bias of 0.25 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.88 for CMJ, while that Bland-Altman analysis showed bias 0.18 ± 0.5 cm; maximum SD = 1.3; minimum SD = −0.96, for SJ.ConclusionWe can conclude that the My Jump 2® is a valid and reliable method to measure CMJ and SJ in visually impaired five-a-side soccer athletes. creator: Julio Cesar Silva creator: Kalinne Fernandes Silva creator: Vitor Bruno Torres creator: Maria Socorro Cirilo-Sousa creator: Alexandre Igor Araripe Medeiros creator: Jacques Eanes Esmeraldo Melo creator: Gilmário Ricarte Batista uri: https://doi.org/10.7717/peerj.18170 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Silva et al. title: Risk factors for recovery from oculomotor nerve palsy after aneurysm surgery: a meta-analysis link: https://peerj.com/articles/18207 last-modified: 2024-10-29 description: BackgroundRisk factors for recovery from oculomotor nerve palsy (ONP) after aneurysm surgery explored by meta-analysis.MethodsThe PubMed, Embase, web of science, Cochrane library, China Knowledge, Wan fang, and VIP databases were searched for case-control or cohort studies on risk factors of oculomotor nerve palsy recovery after aneurysm surgery, with a cut-off date of 14 February 2024, and data were analyzed using Stata 15.ResultA total of 12 articles involving 866 individuals were included, meta-analysis results suggesting that gender (OR = 0.75, 95% CI [0.51–1.10]), age (OR = 1.00, 95% CI [0.93–1.07]), aneurysm size (OR = 0.85, 95% CI [−0.71 to 1.01]), treatment time (OR = 1.01, 95% CI [0.91–1.13]) is not a risk factor for recovery of motor nerve palsy after aneurysm surgery. Preoperative complete ONP (OR = 2.27, 95% CI [1.07–4.81]), surgery (OR = 9.88, 95% CI [2.53–38.57]), subarachnoid hemorrhage (OR = 1.29, 95% CI [1.06–1.56]) is a risk factor for recovery of motor nerve palsy after aneurysm surgery.ConclusionBased on the results of the studies we included, we found that complete ONP before surgery led to poorer recovery, but patients with post-operative and subarachnoid hemorrhage had better recovery. creator: Yuan Li creator: Ming Zhao creator: Xuemei Li creator: Tiejuan Liu creator: Lin Zheng creator: Deyu Hu creator: Tongyan Liu creator: Lingyun Zhou uri: https://doi.org/10.7717/peerj.18207 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Clocks at a snail pace: biological rhythms in terrestrial gastropods link: https://peerj.com/articles/18318 last-modified: 2024-10-29 description: Biological rhythms are ubiquitous across the tree of life. Organisms must allocate their activities into moments of the day and of the season that will increase their probability of surviving and reproducing, which is done in the form of daily and annual rhythms. So far, the vast majority of studies on biological rhythms have focused on classical laboratory model species. Still, the use of non-model species is gaining traction, as part of an effort to achieve a more holistic understanding of clock/calendar mechanisms in the “real world” but this requires species that can be studied in both the lab and in nature. Terrestrial gastropods, i.e., land snails and slugs, have the potential to be exciting models for the study of biological rhythms in nature. Therefore, we provide a review of the research on biological rhythms in terrestrial gastropods, with a focus on ecology and evolution. We present the state of the art in the field while giving a historical perspective of the studies, exploring each of the main lineages of terrestrial gastropods. We also point out some interesting directions that future studies could take to fill some of the more urgent gaps in current knowledge. We hope that our contribution will renew interest in this area and spark novel projects. creator: Rodrigo Brincalepe Salvador creator: Barbara Mizumo Tomotani uri: https://doi.org/10.7717/peerj.18318 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Salvador and Tomotani title: Cordyceps cateniannulata, a new potential strain for controlling Allantus luctifer from China link: https://peerj.com/articles/18345 last-modified: 2024-10-29 description: Allantus luctifer is one of the most serious pests of buckwheat, with its larvae mainly damaging leaves during the seedling and flowering stages. Entomogenous fungi play a crucial role as biological regulators of arthropod populations in nature. In this paper, a newly isolated strain 19GZAl-1, was identified as Cordyceps. cateniannulata through the observetions of macroscopic and microscopic morphological features, and the results of rDNA- ITS sequence alignment and phylogenetic analysis. By comparing the efficacy of ten entomopathogenic fungal strains, including six strains of C. cateniannulata and four other Cordyceps species, against A. luctifer larvae, the new strain 19GZAl-1 exhibited the highest mortality rate. Mortality rates of A. luctifer larvae treated by spraying with the strain 19GZAl-1 increased as larval stage decreased, with first instar larvae showing the highest mortality rate of 85%. The appressorium from conidia invaded the larval body through areas with thin cuticle, such as larva pod base and internode folds, after which the hyphae grew rapidly, filling the haemocoel, and finally protruding from the integument upon melanization and decomposition of the intestinal wall cells. The results suggest that the strain 19GZAL-1 of C. cateniannulata has potential against A. luctifer larvae, which is significant for further study on the infection mechanism of C. cateniannulata on insects. creator: Xiaona Zhang creator: Yu Wu creator: Xue Peng creator: Can Liu creator: Guimin Yang creator: Qingfu Chen creator: Daochao Jin uri: https://doi.org/10.7717/peerj.18345 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhang et al. title: In-depth study of pyroptosis-related genes and immune infiltration in colon cancer link: https://peerj.com/articles/18374 last-modified: 2024-10-29 description: BackgroundPyroptosis is a form of regulated necrosis that occurs in many cell and tissue types and plays a critical role in tumor progression. The diagnostic value of pyroptosis-related genes (PRGs) in colon cancer has been widely investigated. In the present study, we explored the relationship between PRG expression and colon cancer.MethodsWe retrieved genomic and clinical data pertaining to The Cancer Genome Atlas-Colon Adenocarcinoma from the UCSC Xena database, along with the corresponding genome annotation information from the GENCODE data portal. Utilising these data and a list of 33 pyrogenic genes, we performed principal component analysis and unsupervised clustering analysis to assess the pyroptosis subtypes. We analysed the differential expression between these subtypes to obtain PRGs, ultimately selecting 10 PRGs. We conducted Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set variation analysis, protein–protein interaction, and immune infiltration analyses of these PRGs. We validated the expression of TNNC1 via immunohistochemistry (IHC) and real-time quantitative PCR.ResultsAfter rigorous screening, excluding patients with incomplete survival data and unmatched transcriptomes, we refined our study cohort to 431 patients. We performed differential mRNA analysis and identified 445 PRGs, 10 of which were selected as hub genes. These genes were associated with various immune cell types. Specifically, TNNC1 expression was positively associated with immature dendritic cells and NK CD56+ cells. IHC staining indicated higher TNNC1 expression levels in tumor samples. Notably, TNNC1 expression levels were high in all the colon cancer cell lines, particularly in SW480 cells.ConclusionIn this study, we explored the characteristics of PRGs in colon cancer and identified novel biological targets for early individualised treatment and accurate diagnosis of colon cancer, thus contributing to the advancement of clinical oncology. creator: Bingbing Shang creator: Haiyan Qiao creator: Liang Wang creator: Jingyu Wang uri: https://doi.org/10.7717/peerj.18374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Shang et al. title: Genomic evaluation of the probiotic and pathogenic features of Enterococcus faecalis from human breast milk and comparison with the isolates from animal milk and clinical specimens link: https://peerj.com/articles/18392 last-modified: 2024-10-29 description: Enterococcus faecalis is considered a probiotic, commensal lactic acid bacterium in human breast milk (HBM), but there are circulating antibiotic resistant and virulence determinants that could pose a risk in some strains. The study aimed to conduct genomic analysis of E. faecalis isolates recovered from HBM and animal milk and to evaluate their probiotic and pathogenic features through comparative genomics with isolates from clinical specimens (e.g., urine, wound, and blood). Genomic analysis of 61 isolates was performed, including E. faecalis isolates recovered from HBM in Saudi Arabia. Genome sequencing was conducted using the MiSeq system. The fewest antibiotic resistance genes (lsaA, tetM, ermB) were identified in isolates from HBM and animal milk compared to clinical isolates. Several known and unknown mutations in the gyrA and parC genes were observed in clinical isolates. However, 11 virulence genes were commonly found in more than 95% of isolates, and 13 virulence genes were consistently present in the HBM isolates. Phylogenetically, the HBM isolates from China clustered with the probiotic reference strain Symbioflor 1, but all isolates from HBM and animal milk clustered separately from the clinical reference strain V583. Subsystem functions 188 of 263 were common in all analyzed genome assemblies. Regardless of the source of isolation, genes associated with carbohydrate metabolism, fatty acid, and vitamin biosynthesis were commonly found in E. faecalis isolates. In conclusion, comparative genomic analysis can help distinguish the probiotic or pathogenic potential of E. faecalis based on genomic features. creator: Lobna Badr creator: Muhammad Yasir creator: Areej A. Alkhaldy creator: Samah A. Soliman creator: Magdah Ganash creator: Safaa A. Turkistani creator: Asif A. Jiman-Fatani creator: Ibrahim A. Al-Zahrani creator: Esam I. Azhar uri: https://doi.org/10.7717/peerj.18392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Badr et al. title: Forkhead box D subfamily genes in colorectal cancer: potential biomarkers and therapeutic targets link: https://peerj.com/articles/18406 last-modified: 2024-10-29 description: BackgroundThe forkhead box (FOX) family members regulate gene transcription and expression. FOX family members regulate various biological processes, such as cell proliferation and tumorigenesis. FOXD, a FOX protein subfamily, is associated with poor prognosis for various cancers. However, the potential clinical value of FOXD subfamily members in colorectal cancer (CRC) has not yet been elucidated. Therefore, in this study, we aimed to determine the role of the FOXD subfamily members in CRC development.MethodsUsing HTSeq-count data, clinical data, and single-nucleotide polymorphisms (obtained from The Cancer Genome Atlas Project), and bioinformatics analyses (using DESEQ2 software), we identified differentially expressed genes (DEGs) in CRC. Next, each DEG expression was validated in vitro using reverse transcription-quantitative polymerase chain reaction, western blotting, and immunohistochemistry (IHC).ResultsAmong the FOXD subfamily members, the area under the receiver operating characteristic curve of FOXD3 was 0.949, indicating that FOXD3 has a high overall diagnostic accuracy for CRC. Gene Set Enrichment Analysis revealed that FOXD-DEGs were mainly related to pathways such as cytokine, cytokine, and extracellular matrix receptor interactions. Kaplan–Meier curves and nomograms showed that FOXD1, FOXD3, and FOXD4 were prognostically significant. In conclusion, FOXD subfamily members (especially FOXD3) could serve as diagnostic and prognostic biomarkers for CRC and an immunotherapy target in patients with CRC. creator: Ying Chen creator: Haiyan Qiao creator: Ruiqi Zhong creator: Lei Sun creator: Bingbing Shang uri: https://doi.org/10.7717/peerj.18406 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Using a natural capital risk register to support the funding of seagrass habitat enhancement in Plymouth Sound link: https://peerj.com/articles/17969 last-modified: 2024-10-28 description: Seagrass is an important marine habitat that provides benefits to society in the form of ecosystem services. Services include the provision of food via fisheries, the regulation of water quality and the ability to sequester and store carbon. In the UK, seagrass beds are in decline, increasing the risk of ecosystem service loss. Current efforts to protect, restore and create seagrass habitat, beyond spatial management measures, rely on grant funding and donations. Emerging carbon, biodiversity and wider ecosystem service markets offering potential revenue sources could facilitate the enhancement of seagrass habitat at scale. Participation in ecosystem service markets, requires that projects deliver on the ecosystem service benefits defined. As the benefits will have been paid for, there are risks associated with not delivering on ecosystem service benefits. It is important that the risk is clearly defined. In this study we further the marine natural capital and risk register approach and apply the method to a case study area to support the development of sustainable funding options for seagrass habitat enhancement in Plymouth Sound, UK. Habitat Suitability modelling is also used to map potential areas for seagrass habitat enhancement. We find that, in the Plymouth Sound area, the risk of loss of ecosystem services for subtidal seagrass habitats is, at present, high. This is primarily linked to the declining extent and condition of subtidal seagrass assets. Under current governance, all of Plymouth Sound’s subtidal seagrass are within a Marine Protected Area, though this conservation designation does not guarantee that the seagrass bed is protected from damaging activity. Under current environmental conditions there is opportunity for widespread seagrass restoration and creation. Risk to seagrass beds and any future private funding could be reduced by governance actions that enable effective direct protection of the seagrass assets and mitigate harmful pressures (e.g., reduction of water pollution). Emerging financial ‘products’ from seagrass ecosystem services that can support restoration and creation, require a high degree of integrity. The natural capital asset and risk register framework can provide information to underpin product development. With the development of revenue streams from ecosystem services there is a need for more intentional governance and site-based monitoring of these habitats as natural capital assets. Further research is needed to define any social or economic outcomes.Synthesis and ApplicationBy assessing the risk to the status of seagrass assets through this approach, it is possible to determine the complementary governance actions needed to underpin investment in seagrass habitat enhancement. The methods are transferable to other locations where data exists to define the asset status. These specific findings are relevant nationally where similar vectors of risk (pressures) are identified. creator: Guy Hooper creator: Matthew Ashley creator: Tom Mullier creator: Martin Attrill creator: Amelia Sturgeon creator: Zoe Sydenham creator: Mark Parry creator: Katey Valentine creator: Sian Rees uri: https://doi.org/10.7717/peerj.17969 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hooper et al. title: An interpretable deep learning model for detecting BRCA pathogenic variants of breast cancer from hematoxylin and eosin-stained pathological images link: https://peerj.com/articles/18098 last-modified: 2024-10-28 description: BackgroundDetermining the status of breast cancer susceptibility genes (BRCA) is crucial for guiding breast cancer treatment. Nevertheless, the need for BRCA genetic testing among breast cancer patients remains unmet due to high costs and limited resources. This study aimed to develop a Bi-directional Self-Attention Multiple Instance Learning (BiAMIL) algorithm to detect BRCA status from hematoxylin and eosin (H&E) pathological images.MethodsA total of 319 histopathological slides from 254 breast cancer patients were included, comprising two dependent cohorts. Following image pre-processing, 633,484 tumor tiles from the training dataset were employed to train the self-developed deep-learning model. The performance of the network was evaluated in the internal and external test sets.ResultsBiAMIL achieved AUC values of 0.819 (95% CI [0.673–0.965]) in the internal test set, and 0.817 (95% CI [0.712–0.923]) in the external test set. To explore the relationship between BRCA status and interpretable morphological features in pathological images, we utilized Class Activation Mapping (CAM) technique and cluster analysis to investigate the connections between BRCA gene mutation status and tissue and cell features. Significantly, we observed that tumor-infiltrating lymphocytes and the morphological characteristics of tumor cells appeared to be potential features associated with BRCA status.ConclusionsAn interpretable deep neural network model based on the attention mechanism was developed to predict the BRCA status in breast cancer. Keywords: Breast cancer, BRCA, deep learning, self-attention, interpretability. creator: Yi Li creator: Xiaomin Xiong creator: Xiaohua Liu creator: Yihan Wu creator: Xiaoju Li creator: Bo Liu creator: Bo Lin creator: Yu Li creator: Bo Xu uri: https://doi.org/10.7717/peerj.18098 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: The impact of the filling technique with two sealers in bulk or associated with gutta-percha on the fatigue behavior and failure patterns of endodontically treated teeth link: https://peerj.com/articles/18221 last-modified: 2024-10-28 description: BackgroundThe present in vitro study aimed to evaluate the fatigue behavior of teeth filled with a calcium silicate-based sealer (Bio-C Sealer, BC) or an epoxy resin-based sealer (AH Plus, AH), in bulk or associated with gutta-percha as main core material.MethodsSeventy-two sound human maxillary anterior teeth were initially selected. Sixty of them, were randomly chosen, and had their root canals prepared using nickel-titanium reciprocating instruments, being again randomly assigned to five experimental groups (n = 12): C+ (control + prepared but not filled); BC-B (BC in bulk); BC-GP (BC+ gutta-percha); AP-B (AH in bulk); AP-GP (AH+ gutta-percha). An additional negative control group (C−) was considered (n = 12), consisting only on sound teeth, without preparation and filling. The specimens were submitted to a survival analysis after the cyclic fatigue test.ResultsSound teeth (C−) presented the best fatigue performance (P < 0.05), being similar only to the AP-GP group (P > 0.05). Despite that, all experimental groups showed similar fatigue behavior (P > 0.05) to C+ (BC-B = BC-GP = AP-B = AP-GP = C+). Based on that, it can be seen that the use of gutta-percha, as a main core material, associated with the AH Plus sealer, reestablished the mechanical fatigue performance of endodontically treated teeth comparable to sound teeth, still consisting on the most promising approach to rehabilitate such scenario. Teeth filled in bulk, had discreetly higher risk of premature failures and inferior fatigue performance. creator: Isabella Marian Lena creator: Luiza Colpo Chiaratti creator: Rafaela Oliveira Pilecco creator: Renan Vaz Machry creator: João Paulo Mendes Tribst creator: Cornelis Johannes Kleverlaan creator: Gabriel Kalil Rocha Pereira creator: Renata Dornelles Morgental uri: https://doi.org/10.7717/peerj.18221 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lena et al. title: Seed priming enhances seed germination and plant growth in four neglected cultivars of Capsicum annuum L. link: https://peerj.com/articles/18293 last-modified: 2024-10-28 description: Priming is basically a water-based technique inducing controlled seed rehydration to trigger the metabolic processes normally activated during the early phase of germination. It is regarded as an ecofriendly approach alternative to fertilizers in traditional agriculture, but also a method to synchronize off-field crops and resume stored seeds, improving vigor, and allowing for a rapid, uniform seedling emergence. In this work we tested several methods of seed priming (i.e., hydro-priming, halopriming by KNO3, and acid priming with HCl) in four ancient and neglected cultivars of Capsicum annuum L., a crop species belonging to Solanaceae family cultivated worldwide. We followed germination performance, seedling growth and selected morphological traits, antioxidant production in the leaves, and protein content of the seeds. Apart from acid priming, which inhibited root emergence, both hydropriming and halopriming decreased the mean germination time in all cultivars. The best treatments were KNO3 6% for 96 h > KNO3 4% for 48 h > hydropriming for 24 h. In particular, KNO3 6% for 96 h in all four cultivars significantly increased plant growth, simple vigor index, development germination index, leaf antioxidant concentration and protein content in the seeds, in comparison to control and other priming treatments, indicating the prompt activation of pre-germinative processes. creator: Angelo Granata creator: Fiore Capozzi creator: Anna Gaglione creator: Riccardo Riccardi creator: Patrizia Spigno creator: Simonetta Giordano creator: Maria Cristina Sorrentino creator: Valeria Spagnuolo uri: https://doi.org/10.7717/peerj.18293 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Granata et al. title: Genome-wide identification and expression analysis of the OSC gene family in Platycodon grandiflorus link: https://peerj.com/articles/18322 last-modified: 2024-10-28 description: Platycodon grandiflorus stands as one of the most extensively utilized traditional Chinese medicinal herbs, with triterpenoids and their derivatives serving as its primary medicinal components. Oxido squalene cyclase (OSC), serving as a crucial enzyme in the triterpenoid synthesis pathway, has the capability to enzymatically generate significant quantities of sterols and triterpenoid intermediates. While the OSC gene family has been identified in numerous species, bioinformatics research on this family remains scant. Presently, the specific members of this gene family in Platycodon grandiflorus have yet to be definitively determined. In this study, we successfully identified a total of 15 PgOSC genes within the genome of Platycodon grandiflorus by conducting homology comparisons. These genes were discovered to be unevenly distributed across the five chromosomes of the species, organized in the form of gene clusters. Subsequently, we conducted a thorough analysis of the OSC gene family’s evolutionary relationship by constructing a phylogenetic tree. Other characteristics of PgOSC family members, including gene structure, conserved motifs, protein three-dimensional structure, subcellular localization, and cis-acting elements were thoroughly characterized. Furthermore, We analyzed the expression of PgOSC gene in different tissues of Platycodon grandiflorus by qRT-PCR, and found that the expression of PgOSC genes in root was higher than that in stem and leaf. Upon comparing the effects of salt, heat, and drought treatments, we observed a significant induction of PgOSC gene expression in Platycodon grandiflorus specifically under salt stress conditions. In summary, this study comprehensively identified and analyzed the OSC gene family, aiming to provide basic biological information for exploring the members of PgOSC gene family. creator: Xiaoqin Wang creator: Dong Yan creator: Ling Chen uri: https://doi.org/10.7717/peerj.18322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Association of thyroid hormones with the severity of chronic kidney disease: a cross-sectional observational study at Tabuk, Saudi Arabia link: https://peerj.com/articles/18338 last-modified: 2024-10-28 description: BackgroundThe interplay between chronic kidney disease (CKD) and thyroid dysfunction is becoming more evident in the biomedical community. However, the intricacies of their relationship warrant deeper investigation to understand the clinical implications fully.ObjectiveThis study aims to systematically evaluate the correlation between thyroid hormone levels, including thyroid-stimulating hormone (TSH), triiodothyronine (T3), and thyroxine (T4), and markers of renal disease severity. These markers include serum creatinine, urea, and parathyroid hormone (PTH) levels in individuals diagnosed with CK).MethodsWe conducted a cross-sectional observational study involving a cohort of 86 participants with CKD recruited from the renal clinic at King Fahad Hospital in Tabuk. Biochemical parameters, encompassing plasma electrolytes and thyroid hormone concentrations, were quantitatively assessed. These measurements were performed with the aid of a Roche Cobas E411 analyzer. The Pearson correlation coefficient was employed to delineate the strength and direction of the associations between the thyroid function markers and renal disease indicators.ResultsThe statistical analysis highlighted a generally weak correlation between the concentrations of thyroid hormones and the indicators of renal disease severity, with Pearson correlation coefficients between −0.319 and 0.815. Critically, no significant correlation was found between creatinine and thyroid hormones (TSH, T3, T4), nor was any substantial correlation between urea and thyroid hormones. Conversely, a robust positive correlation was noted between the levels of parathyroid hormone and serum creatinine (r = 0.718, p < 0.001).ConclusionThe data suggests that thyroid hormone levels have a minimal correlation with the severity of renal disease markers. In contrast, the pronounced correlation between PTH and creatinine underscores the importance of considering PTH as a significant factor in managing and therapeutic intervention of CKD complications. These initial findings catalyze further research to thoroughly investigate the pathophysiological relationships and potential therapeutic targets concerning thyroid dysfunction in patients with renal impairment. creator: Basmah Awwaadh creator: Amal Hussain Mohammed creator: Basmah F. Alharbi creator: Abdulmohsen Alruwetei creator: Tarique Sarwar creator: Hajed Obaid Alharbi creator: Fahad Alhumaydhi uri: https://doi.org/10.7717/peerj.18338 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Awwaadh et al. title: COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression link: https://peerj.com/articles/18347 last-modified: 2024-10-28 description: BackgroundColorectal cancer is a common condition with an uncommon burden of disease, heterogeneity in manifestation, and no definitive treatment in the advanced stages. Renewed efforts to unravel the genetic drivers of colorectal cancer progression are paramount. Early-stage detection contributes to the success of cancer therapy and increases the likelihood of a favorable prognosis. Here, we have executed a comprehensive computational workflow aimed at uncovering the discrete stagewise genomic drivers of colorectal cancer progression.MethodsUsing the TCGA COADREAD expression data and clinical metadata, we constructed stage-specific linear models as well as contrast models to identify stage-salient differentially expressed genes. Stage-salient differentially expressed genes with a significant monotone trend of expression across the stages were identified as progression-significant biomarkers. The stage-salient genes were benchmarked using normals-augmented dataset, and cross-referenced with existing knowledge. The candidate biomarkers were used to construct the feature space for learning an optimal model for the digital screening of early-stage colorectal cancers. The candidate biomarkers were also examined for constructing a prognostic model based on survival analysis.ResultsAmong the biomarkers identified are: CRLF1, CALB2, STAC2, UCHL1, KCNG1 (stage-I salient), KLHL34, LPHN3, GREM2, ADCY5, PLAC2, DMRT3 (stage-II salient), PIGR, HABP2, SLC26A9 (stage-III salient), GABRD, DKK1, DLX3, CST6, HOTAIR (stage-IV salient), and CDH3, KRT80, AADACL2, OTOP2, FAM135B, HSP90AB1 (top linear model genes). In particular the study yielded 31 genes that are progression-significant such as ESM1, DKK1, SPDYC, IGFBP1, BIRC7, NKD1, CXCL13, VGLL1, PLAC1, SPERT, UPK2, and interestingly three members of the LY6G6 family. Significant monotonic linear model genes included HIGD1A, ACADS, PEX26, and SPIB. A feature space of just seven biomarkers, namely ESM1, DHRS7C, OTOP3, AADACL2, LPHN3, GABRD, and LPAR1, was sufficient to optimize a RandomForest model that achieved > 98% balanced accuracy (and performant recall) of cancer vs. normal on external validation. Design of an optimal multivariate model based on survival analysis yielded a prognostic panel of three stage-IV salient genes, namely HOTAIR, GABRD, and DKK1. Based on the above sparse signatures, we have developed COADREADx, a web-server for potentially assisting colorectal cancer screening and patient risk stratification. COADREADx provides uncertainty measures for its predictions and needs clinical validation. It has been deployed for experimental non-commercial use at: https://apalanialab.shinyapps.io/coadreadx/. creator: Ashok Palaniappan creator: Sangeetha Muthamilselvan creator: Arjun Sarathi uri: https://doi.org/10.7717/peerj.18347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Palaniappan et al. title: The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures link: https://peerj.com/articles/18361 last-modified: 2024-10-28 description: BackgroundStrain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate (${\mathrm{NO}}_{3}^{-}$NO3−) reduction. Strain JAM1T can reduce ${\mathrm{NO}}_{3}^{-}$NO3− to nitrite (${\mathrm{NO}}_{2}^{-}$NO2−) but not ${\mathrm{NO}}_{2}^{-}$NO2− to nitric oxide (NO) as it lacks a NO-forming ${\mathrm{NO}}_{2}^{-}$NO2− reductase. Strain GP59 on the other hand can carry the complete reduction of ${\mathrm{NO}}_{3}^{-}$NO3− to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before ${\mathrm{NO}}_{3}^{-}$NO3− reduction occurs. In strain JAM1T cultures, ${\mathrm{NO}}_{3}^{-}$NO3− reduction begins immediately with accumulation of ${\mathrm{NO}}_{2}^{-}$NO2−. Furthermore, ${\mathrm{NO}}_{3}^{-}$NO3− is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth.MethodsBoth strains were cultured under oxic conditions either with or without ${\mathrm{NO}}_{3}^{-}$NO3−, or under anoxic conditions with ${\mathrm{NO}}_{3}^{-}$NO3−. Transcript levels of selected denitrification genes (nar1 and nar2 encoding ${\mathrm{NO}}_{3}^{-}$NO3− reductases, nirK encoding ${\mathrm{NO}}_{2}^{-}$NO2− reductase, narK12f encoding ${\mathrm{NO}}_{3}^{-}$NO3−/${\mathrm{NO}}_{2}^{-}$NO2−transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles.ResultsThe transcript levels of nar1 were very low in strain GP59 cultured under oxic conditions without ${\mathrm{NO}}_{3}^{-}$NO3−. These levels were 37 times higher in strain JAM1T cultured under the same conditions, suggesting that Nar1 was expressed at sufficient levels in strain JAM1T before the inoculation of the oxic and anoxic cultures to carry ${\mathrm{NO}}_{3}^{-}$NO3− reduction with no lag phase. Transcriptomic analysis revealed that each strain had distinct relative gene expression profiles, and oxygen had high impact on these profiles. Among denitrification genes and regulatory genes, the nnrS3 gene encoding factor involved in NO-response function had its relative gene transcript levels 5 to 10 times higher in strain GP59 cultured under oxic conditions with ${\mathrm{NO}}_{3}^{-}$NO3− than those in both strains cultured under oxic conditions without ${\mathrm{NO}}_{3}^{-}$NO3−. Since NnrS senses NO, these results suggest that strain GP59 reduced ${\mathrm{NO}}_{3}^{-}$NO3− to NO under oxic conditions, but because of the oxic environment, NO is oxidized back to ${\mathrm{NO}}_{3}^{-}$NO3− by flavohemoproteins (NO dioxygenase; Hmp), explaining why ${\mathrm{NO}}_{3}^{-}$NO3− reduction is not observed in strain GP59 cultured under oxic conditions.ConclusionsUnderstanding how these two strains manage the regulation of the denitrification pathway provided some clues on how they response to environmental changes in the original biofilm community, and, by extension, how this community adapts in providing efficient denitrifying activities. creator: Livie Lestin creator: Richard Villemur uri: https://doi.org/10.7717/peerj.18361 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lestin and Villemur title: Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis link: https://peerj.com/articles/18362 last-modified: 2024-10-28 description: ObjectiveThis study aimed to explore the heterogeneity of tumor endothelial cells (TECs) in hepatocellular carcinoma (HCC) and their role in tumor progression, with the goal of identifying new therapeutic targets and strategies to improve patient prognosis.MethodsSingle-cell RNA sequencing data from nine primary liver cancer samples were analyzed, obtained from the Gene Expression Omnibus (GEO) database. Data preprocessing, normalization, dimensionality reduction, and batch effect correction were performed based on the Seurat package. HCC cell types were identified using uniform manifold approximation and projection (UMAP) and cluster analysis, and the different cell types were annotated using the CellMarker database. Pseudotime trajectory analysis was conducted with Monocle to explore the differentiation trajectory of TECs. MAPK signaling pathway activity and copy number variations (CNV) in TECs were analyzed in conjunction with data from The Cancer Genome Atlas (TCGA), the trans-well and wound healing assay was used for cell invasion and migration activity assessment.ResultsTwo subgroups of TECs (TECs 1 and TECs 2) were identified, exhibiting distinct functional activities and signaling pathways. Specifically, TECs 1 may be involved in tumor cell proliferation and inflammatory responses, whereas TECs 2 is not only involved in cell proliferation pathways, but also enriched in pathways such as metabolic synthesis. Pseudotime analysis revealed dynamic changes in TECs subgroups during HCC progression, correlating specific gene expressions (such as PDGFRB, PGF, JUN, and NR4A1). Subsequently, the JUN gene was predicted by performing binding sites and was shown to act as a transcription factor that may regulate the expression of the PGF gene. CNV analysis highlighted key genes and pathways in TECs that might influence HCC progression, and the PGF as key regulatory factor mediated cell proliferation and migration.ConclusionThe study revealed the heterogeneity of TECs in HCC and their potential roles in tumor progression, offering new perspectives and potential therapeutic targets for HCC molecular mechanisms. The findings emphasize the importance of further exploring TECs heterogeneity for understanding HCC pathogenesis and developing personalized treatment strategies. creator: Jiachun Sun creator: Shujun Zhang creator: Yafeng Liu creator: Kaijie Liu creator: Xinyu Gu uri: https://doi.org/10.7717/peerj.18362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sun et al. title: Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index link: https://peerj.com/articles/18368 last-modified: 2024-10-28 description: Changes in the ecological environment quality (EEQ) in the main inland Tarim River Basin in China substantially impact the regional development. Indeed, comprehensive ecological environment measures have been implemented in the Tarim River Basin since 2000. In this context, the main objective of the present study was to investigate the spatiotemporal evolution of the EEQ and monitor the effectiveness of ecological restoration measures in the Tarim River Basin over the 2000–2020 period using remote sensing data. First, a Remote Sensing Ecological Index (RSEI) was constructed based on the Moderate Resolution Imaging Spectroradiometer remote sensing data. Second, the spatial distributions and factors of the RSEI were analyzed by using Moran’s Index and Geodetector. The results indicated that the overall RSEI values for the Tarim River Basin increased from 0.22 in 2000 to 0.25 in 2020. Moreover, the values for areas with poor EEQ decreased from 50.7% to 44.73%, while those with moderate EEQ increased from 11.45% to 16.91%. Therefore, the results demonstrated a slight overall improvement in the EEQ of the study area over the 2000–2020 period. On the other hand, the EEQ in the Tarim River Basin exhibited a significant spatial autocorrelation in the 2000–2020 period, with a relatively stable overall spatial distribution. Areas with high–high aggregation were distributed in the high-elevation mountainous areas in the western, northern, and southern parts of the study area. In contrast, areas with low–low aggregation were observed in the central and eastern low-elevation desert areas. The EEQ in the Tarim River Basin was driven by the interactions of several factors, including the normalized difference vegetation index, land surface moisture, land surface temperature, normalized differential build-up and bare soil index, and elevation. In particular, heat was the main driving factor that severely impacted the EEQ in the study area. Indeed, increase in the heat values could directly enhance meltwater runoff from glaciers in the basin, thereby resulting in short-term improvement in the basin EEQ. Furthermore, rapid urbanization from 2015 to 2020 resulted in a decrease in the average RSEI value of the Tarim River Basin by 0.1 over this period, consequently, the EEQ level decreased slightly. Briefly, the EEQ in the Tarim River Basin showed an overall increasing trend from 2000 to 2020, further demonstrating the effectiveness of a series of implemented ecological restoration measures in the Tarim River Basin over this period. creator: Congcang Tang creator: Qiao Li creator: Hongfei Tao creator: Mahemujiang Aihemaiti creator: Zhenxia Mu creator: Youwei Jiang uri: https://doi.org/10.7717/peerj.18368 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Tang et al. title: Development of a welfare assessment tool for tourist camp elephants in Asia link: https://peerj.com/articles/18370 last-modified: 2024-10-28 description: BackgroundApproximately one-third of Asian elephants are managed under human care, participating in educational, cultural, religious, and tourist activities. Management conditions vary considerably among venues, raising questions about whether welfare needs are consistently being met, particularly for Asian tourist camp elephants. To evaluate the well-being of elephants engaged in tourist activities, an evidence-based tool is needed for routine assessments to identify potential welfare risks, aid in the development of better camp standards, and enable caretakers to address specific concerns. While many animal welfare tools exist, none have been designed to consider specific environments and management practices faced by elephants living and working in tourist camps.MethodsUsing direct observations and interviews, the Elephant Welfare Assessment Tool (EWAT) was developed for tourist camp elephants using the Five Domains Model as a framework. Measures were selected based on peer-reviewed literature, existing standards and guidelines, and opinions from animal welfare experts working with zoo and tourist camp elephants. The EWAT differs from existing tools by including criteria on work activities and restraint methods (e.g., chaining and ankus use), factors common in Asia but not often encountered by western zoo elephants. Measures were scored using a 0–2 Likert Scale. The tool was tested in Thailand and determined by calculating a content validity index (CVI) and conducting inter-rater and test-retest reliability tests.ResultsThe initial tool included 18 animal-based and 21 resource-based measures across four domains: Nutrition (n = 5), Environment (n = 14), Health (n = 10), and Behavior and Mental State (n = 10). Index scores of content validity (CVI) (Item CVI (0.83), Scale CVI/Average (0.98), and Scale CVI/Universal (0.89)) were high. Measures scoring less than 0.83 were removed: the opportunity to mate, the mahout-elephant relationship, and mahout job satisfaction. The final tool consisted of 42 questions related to 36 measures, including 18 animal-based and 18 resource-based measures within the Nutrition (n = 5), Environment (n = 11), Health (n = 10), and Behavior and Mental State (n = 10) domains. Intraclass correlation coefficients (ICC) for inter-rater reliability (0.78–0.90, p < 0.05) and test-retest (0.77–0.91, p < 0.05) analyses conducted at two camps showed good agreement.ConclusionsThis new assessment tool (EWAT) is a context-specific, holistic method designed to offer a practical means of conducting individual and institutional-level assessments of elephant welfare in tourist camps. It is based on the Five Domains Model using reliable and validated animal- and resource-based measures, data collection through direct observation and interviews, and a numerical scoring system. The tool includes several criteria applicable to tourist rather than zoo venues to make it more relevant to the challenges faced by working elephants in Asia. creator: Raman Ghimire creator: Janine L. Brown creator: Chatchote Thitaram creator: Sharon S. Glaeser creator: Kannika Na-Lampang creator: Pawinee Kulnanan creator: Pakkanut Bansiddhi uri: https://doi.org/10.7717/peerj.18370 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ghimire et al. title: Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part link: https://peerj.com/articles/18389 last-modified: 2024-10-28 description: BackgroundOccupational health, grounded in occupational medicine, aims to enhance the well-being and labor productivity of the working population. Within this realm, there has been growing concern over the increasing instances of labor loss due to diminished physical capacity and the rise in musculoskeletal disorders. Chronic pain is also associated with musculoskeletal disorders. Another pressing issue related to chronic musculoskeletal pain was needed assistance services are underutilized, is referred to as a “service gap”. Understanding trends based on age and affected regions of the body is indispensable for developing strategies to address chronic musculoskeletal pain in workers. This study aimed to elucidate age-specific trends in the prevalence and number of pain sites in chronic musculoskeletal pain as well as the patterns of treatment during chronic musculoskeletal pain, categorized by age and affected site.MethodsThis study was conducted in December 2022 in contract to Cross Marketing Inc. The survey began on December 12, 2022 and ended on December 15, 2022. An online survey was administered to 1,946 participants (973 women and 973 men), and responses were collected, ensuring a roughly equal distribution of samples among men and women across six age groups ranging from their 20 to 70 s. The survey inquired about the presence of chronic pain in each of the eight body parts and the adoption of five different treatments when experiencing pain. Statistical analysis was performed using the chi-square test, with the measurement data categorized by age group and body part.ResultsThe results indicated a significantly higher prevalence of chronic pain at three or more sites among individuals in their 30 s: the prevalence of pain at each of the eight body sites varied with age. Approximately half of the participants did not engage in specific treatments during episodes of chronic pain. The presence or absence of treatment showed no significant differences according to affected site or age group. This study revealed age- and body part-related relationships with chronic musculoskeletal pain in middle-aged patients and highlighted healthcare service gaps in its management in Japan. creator: Yasumasa Oka creator: Takumi Jiroumaru creator: Michio Wachi creator: Noriyuki Kida uri: https://doi.org/10.7717/peerj.18389 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Oka et al. title: The impact of maternal serum biomarkers on maternal and neonatal outcomes in twin pregnancies: a retrospective cohort study conducted at a tertiary hospital link: https://peerj.com/articles/18415 last-modified: 2024-10-28 description: BackgroundPrior prediction models used for screening preeclampsia (PE) in twin pregnancies were found to be inadequate. In singleton pregnancies, various maternal biomarkers have been shown to be correlated with negative pregnancy outcomes. However, the impact of these biomarkers in twin pregnancies remained uncertain.MethodsA retrospective cohort study was carried out on 736 twin pregnancies at a tertiary hospital in Hangzhou, China. Multivariable logistic models were employed to examine the association between levels of serological markers and the likelihood of adverse pregnancy outcomes. The final logistic model was formulated as a user-friendly nomogram. The primary outcome assessed was the occurrence of PE. Results were presented as odds ratios (ORs) with corresponding 95% confidence intervals (CIs).ResultsThe prevalence of PE in the study was 10.3%. When comparing women diagnosed with PE to those without, it was evident that the former group experienced a significantly higher risk of unfavorable maternal and neonatal outcomes. A multivariable logistic regression analysis revealed notable associations between various factors including maternal age, parity, gestational weight gain, a family history of hypertension, as well as levels of cholesterol, albumin, and creatinine and the risk of developing PE, with a significance level of P < 0.05. The concordance index for the constructed nomogram was determined to be 0.792 (95% CI: [0.739–0.844]). Furthermore, an increment of 1 * 1012/L in red blood cell (RBC) count was associated with more than a two-fold increase in the odds of experiencing adverse maternal outcomes (OR 2.247, 95% CI: [1.229–4.107]). However, no significant correlations were identified between any of the examined variables and neonatal outcomes.ConclusionsIn this study, we developed a user-friendly predictive model that achieves notable detection rates by incorporating maternal serum biomarker levels alongside maternal characteristics and medical history. Our findings indicate that the probability of adverse maternal outcomes increases with elevated levels of RBCs. Obstetricians should consider intensifying surveillance for these women in clinical practice. creator: Hanglin Wu creator: Liming Yu creator: Zhen Xie creator: Hongxia Cai creator: Caihe Wen uri: https://doi.org/10.7717/peerj.18415 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Wu et al. title: Fluconazole worsened lung inflammation, partly through lung microbiome dysbiosis in mice with ovalbumin-induced asthma link: https://peerj.com/articles/18421 last-modified: 2024-10-28 description: Innate immunity in asthma may be influenced by alterations in lung microbiota, potentially affecting disease severity. This study investigates the differences in lung inflammation and microbiome between asthma-ovalbumin (OVA) administered with and without fluconazole treatment in C57BL/6 mice. Additionally, the role of inflammation was examined in an in vitro study using a pulmonary cell line. At 30 days post-OVA administration, allergic asthma mice exhibited increased levels of IgE and IL-4 in serum and lung tissue, higher pathological scores, and elevated eosinophils in bronchoalveolar lavage fluid (BALF) compared to control mice. Asthma inflammation was characterized by elevated serum IL-6, increased lung cytokines (TNF-α, IL-6, IL-10), and higher fungal abundance confirmed by polymerase chain reaction (PCR). Fluconazole-treated asthma mice displayed higher levels of cytokines in serum and lung tissue (TNF-α and IL-6), increased pathological scores, and a higher number of mononuclear cells in BALF, with undetectable fungal levels compared to untreated mice. Lung microbiome analysis revealed similarities between control and asthma mice; however, fluconazole-treated asthma mice exhibited higher Bacteroidota levels, lower Firmicutes, and reduced bacterial abundance. Pro-inflammatory cytokine production was increased in supernatants of the pulmonary cell line (NCI-H292) after co-stimulation with LPS and beta-glucan (BG) compared to LPS alone. Fluconazole treatment in OVA-induced asthma mice exacerbated inflammation, partially due to fungi and Gram-negative bacteria, as demonstrated by LPS+BG-activated pulmonary cells. Therefore, fluconazole should be reserved for treating fungal asthma rather than asthma caused by other etiologies. creator: Jesadakorn Worasilchai creator: Piyapat Thongchaichayakon creator: Kittipat Chansri creator: Supichaya Leelahavanichkul creator: Vathin Chiewvit creator: Peerapat Visitchanakun creator: Poorichaya Somparn creator: Pratsanee Hiengrach uri: https://doi.org/10.7717/peerj.18421 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Worasilchai et al. title: Deciphering the influence of evolutionary legacy and functional constraints on the patella: an example in modern rhinoceroses amongst perissodactyls link: https://peerj.com/articles/18067 last-modified: 2024-10-25 description: In mammals, the patella is the biggest sesamoid bone of the skeleton and is of crucial importance in posture and locomotion, ensuring the role of a pulley for leg extensors while protecting and stabilizing the knee joint. Despite its central biomechanical role, the relation between the shape of the patella and functional factors, such as body mass or locomotor habit, in the light of evolutionary legacy are poorly known. Here, we propose a morphofunctional investigation of the shape variation of the patella among modern rhinoceroses and more generally among perissodactyls, this order of ungulates displaying a broad range of body plan, body mass and locomotor habits, to understand how the shape of this sesamoid bone varies between species and relatively to these functional factors. Our investigation, relying on three dimensional geometric morphometrics and comparative analyses, reveals that, within Rhinocerotidae and between the three perissodactyl families, the shape of the patella strongly follows the phylogenetic affinities rather than variations in body mass. The patellar shape is more conservative than initially expected both within and between rhinoceroses, equids and tapirs. The development of a medial angle, engendering a strong mediolateral asymmetry of the patella, appears convergent in rhinoceroses and equids, while tapirs retain a symmetric bone close to the plesiomorphic condition of the order. This asymmetric patella is likely associated with the presence of a “knee locking” mechanism in both equids and rhinos. The emergence of this condition may be related to a shared locomotor habit (transverse gallop) in both groups. Our investigation underlines unexcepted evolutionary constraints on the shape of a sesamoid bone usually considered as mostly driven by functional factors. creator: Christophe Mallet creator: Alexandra Houssaye uri: https://doi.org/10.7717/peerj.18067 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mallet and Houssaye title: Co-applied biochar and drought tolerant PGPRs induced more improvement in soil quality and wheat production than their individual applications under drought conditions link: https://peerj.com/articles/18171 last-modified: 2024-10-25 description: BackgroundPlant growth and development can be greatly impacted by drought stress. Suitable plant growth promoting rhizobacteria (PGPR) or biochar (BC) application has been shown to alleviate drought stress for plants. However, their co-application has not been extensively explored in this regard.MethodsWe isolated bacterial strains from rhizospheric soils of plants from arid soils and characterized them for plant growth promoting characteristics like IAA production and phosphate solubilization as well as for drought tolerance. Three bacterial strains or so called PGPRs, identified as Bacillus thuringiensis, Bacillus tropicus, and Bacillus paramycoides based on their 16S rRNA, were screened for further experiments. Wheat was grown on normal, where soil moisture was maintained at 75% of water holding capacity (WHC), and induced-drought (25% WHC) stressed soil in pots. PGPRs were applied alone or in combination with a biochar derived from pyrolysis of tree wood.ResultsDrought stress substantially inhibited wheat growth. However, biochar addition under stressed conditions significantly improved the wheat growth and productivity. Briefly, it increased straw yield by 25%, 100-grain weight by 15% and grain yield by 10% compared to the control. Moreover, co-application of biochar with PGPRs B. thuringiensis, B. tropicus and B. paramycoides further enhanced straw yield by 37–41%, 100-grain weight by 30–36%, and grain yield by 22–22.57%, respectively. The co-application also enhanced soil quality by increasing plant-available phosphorus by 4–31%, microbial biomass by 33–45%, and soil K+/Na+ ratio by 41–44%.ConclusionCo-application of PGPRs and biochar alleviated plant drought stress by improving nutrient availability and absorption. Acting as a nutrient reservoir, biochar worked alongside PGPRs, who solubilized nutrients from the former and promoted wheat growth. We recommend that the co-application of suitable PGPRs and biochar is a better technology to produce wheat under drought conditions than using these enhancers separately. creator: Laraib Malik creator: Sabir Hussain creator: Muhammad Shahid creator: Faisal Mahmood creator: Hayssam M. Ali creator: Mehreen Malik creator: Muhammad Sanaullah creator: Zubda Zahid creator: Tanvir Shahzad uri: https://doi.org/10.7717/peerj.18171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Malik et al. title: Myrmozercon mites are highly host specific: two new species of Myrmozercon Berlese associated with sympatric Camponotus ants in southern Quintana Roo, Mexico link: https://peerj.com/articles/18197 last-modified: 2024-10-25 description: Two new species of Myrmozercon, M. serratus sp. nov. and M. spatulatus sp. nov., are described based on adults and deutonymphs collected in association with ants in Mexico. They represent the first records of this genus from the Neotropic s.s. faunal region. Both new species are associated with hosts in the genus Camponotus from the same small area of a coastal lagoon, which share the same nesting habit preferences, providing strong evidence for host specificity. All but one colony of C. atriceps hosted mites, whereas they occurred in only half of the colonies of C. rectangularis. There was a significant positive correlation between the abundance of C. atriceps sexual ants and the abundance of mites. We summarize the known host associations for the genus Myrmozercon and discuss host specificity. Larvae of both mite species were collected on the wings of males and gynes suggesting that egg laying occurs on the hosts reproductive caste. Two hypotheses explaining this observation are discussed, larvae may be phoretic on winged sexuals, favoring mite co-dispersal with hosts, or larvae reside on the alates as a refuge from predation. creator: Gabriela Pérez-Lachaud creator: Hans Klompen creator: Shahrooz Kazemi creator: Jean-Paul Lachaud uri: https://doi.org/10.7717/peerj.18197 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pérez-Lachaud et al. title: Among the world’s smallest vertebrates: a new miniaturized flea-toad (Brachycephalidae) from the Atlantic rainforest link: https://peerj.com/articles/18265 last-modified: 2024-10-25 description: The genus Brachycephalus includes miniaturized toadlets with two distinct morphotypes: brightly colored species with a bufoniform phenotype and smaller, cryptic species with a leptodactyliform phenotype. The diversity of leptodactyliform species is still underappreciated, and we generally lack fundamental information about their biology. Recent sampling efforts, including DNA analyses and recordings of advertisement calls, have improved our understanding of this group. In the present study, we describe a new species of Brachycephalus, one of the smallest vertebrates known. This new species is distinguished from its congeners by a combination of morphological, bioacoustic, and genetic data. Despite being among the smallest frogs globally (the second smallest amphibian species), it exhibits skeletal traits typical of larger frogs, such as the presence of cranial bones that are lost or fused in other miniature frogs, including other Brachycephalus. Our description underscores how new discoveries within the megadiverse fauna of the Atlantic Forest—a rich biodiversity hotspot—can provide insights into phenotypic variation, including vertebrate body size. By describing this new species, we also aim to revisit the hypothesis that the type series of B. hermogenesi includes two species, potentially including individuals of the species described here. creator: Luís Felipe Toledo creator: Lucas Machado Botelho creator: Andres Santiago Carrasco-Medina creator: Jaimi A. Gray creator: Julia R. Ernetti creator: Joana Moura Gama creator: Mariana Lucio Lyra creator: David C. Blackburn creator: Ivan Nunes creator: Edelcio Muscat uri: https://doi.org/10.7717/peerj.18265 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Toledo et al. title: Comparative transcriptome analysis of cucumber fruit tissues reveals novel regulatory genes in ascorbic acid biosynthesis link: https://peerj.com/articles/18327 last-modified: 2024-10-25 description: Ascorbic acid (AsA) is one of the most abundant natural antioxidants, and it is an important indicator of the nutritional value of cucumber fruit. The aim of this study was to elucidate the regulatory mechanism affecting AsA metabolism in cucumber fruit. In this study, the AsA content in the fruit of two cucumber cultivars (H28 and H105) was significantly higher in the exocarp and endocarp than in the mesocarp. To clarify the regulation of AsA in cucumber fruit, the transcriptomes of three fruit tissues (i.e., the exocarp, mesocarp, and endocarp) of two cucumber cultivars (H28 and H105) were sequenced. Transcriptomic profiling combined with transcription factors (TFs) and correlation analysis were performed to reveal that three genes, including CsaV3_5G014110 (phosphomannomutase, PMM), CsaV3_2G004170 (GDP-mannose-3′, 5′-epimerase, GME) and CsaV3_5G006680 (dehydroascorbate reductase, DHAR), were expressed at higher level in the exocarp and endocarp than in the mesocarp. In both two cultivars, CsaV3_4G028360 (ethylene-responsive transcription factor, ERF) was negatively correlated with PMM and GME, and positively correlated with DHAR. CsaV3_6G042110 (ethylene-responsive transcription factor, ERF) was positively correlated with PMM and GME, and negatively correlated with DHAR. CsaV3_6G032360 (mitogen-activated protein kinase, MAPK) as positively correlated with PMM, GME and DHAR. These six genes are considered the key candidate genes for further research. This study provides insight for further study on the regulation of AsA biosynthesis in cucumber fruit and provide potential candidate genes for future genetic improvement of cucumber germplasm with enhanced AsA accumulation. creator: Jun Ren creator: Shenzao Fu creator: Hongyao Wang creator: Wenying Wang creator: Xin Wang creator: Haowen Zhang creator: Zizheng Wang creator: Min Huang creator: Zemiao Liu creator: Chaobiao Wu creator: Kun Yang uri: https://doi.org/10.7717/peerj.18327 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Ren et al. title: Antimicrobial and anti-endotoxin activity of N-acetylcysteine, calcium hydroxide and their combination against Enterococcus faecalis, Escherichia coli and lipopolysaccharides link: https://peerj.com/articles/18331 last-modified: 2024-10-25 description: BackgroundThe management of endodontic infections is a complex challenge, mainly due to the involvement of diverse microorganisms and their by-products. This study aimed to evaluate the efficacy of N-acetylcysteine (NAC), calcium hydroxide (Ca(OH)2), and their combined application as intracanal medications in combating Enterococcus faecalis, Escherichia coli, and lipopolysaccharides (LPS) from E. coli.MethodsA total of 60 single-rooted human teeth were carefully selected and divided into six groups. These tooth canals were deliberately exposed to E. faecalis (ATCC 29212) and E. coli (ATCC 25922) to induce biofilm formation. Subsequently, the specimens were treated with NAC, Ca(OH)2, or a combination of both substances. Three samples of the root canals were collected at three moments: the first sample (S1) was to confirm the initial contamination, the second sample (S2) was immediately post-instrumentation, and the third sample (S3) was collected after the use of the intracanal medication. The antimicrobial efficacy of these intracanal medications was assessed by enumerating colony-forming units per milliliter (CFU/mL). In addition to this, the kinetic chromogenic Limulus Amebocyte Lysate (LAL) assay by Lonza was used to quantify LPS from E. coli. Data tested for normality; then, Kruskal-Wallis and Friedman tests were used, and Dunn’s for multiple comparisons.ResultsThe findings of this study showed significant reductions in the microbial load of E. faecalis and E. coli by S3. Notably, there were no statistically significant differences among the treatment groups concerning these microorganisms. However, it was observed that only the combination of NAC and Ca(OH)2 led to a noteworthy decrease in the quantity of E. coli’s LPS after 7-days, demonstrating a statistically significant difference from the other treatment groups. NAC + Ca(OH)2 combination, applied for a duration of 7-days, proved to be more suitable in reducing the presence of E. faecalis, E. coli, and LPS from E. coli within the context of endodontic infections. creator: Rayana Duarte Khoury creator: Amjad Abu Hasna creator: Carolina Fedel Gagliardi creator: Renata Marques de Melo Marinho creator: Cláudio Antonio Talge Carvalho creator: Eduardo Bresciani creator: Marcia Carneiro Valera uri: https://doi.org/10.7717/peerj.18331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Khoury et al. title: House sparrows do not show a diel rhythm in double-strand DNA damage in erythrocytes link: https://peerj.com/articles/18375 last-modified: 2024-10-25 description: DNA damage can be caused by a number of intrinsic and extrinsic factors. A recent study showed that free-living house sparrows (Passer domesticus) have higher DNA damage in the summer than the winter across five different tissues. This result was consistent when house sparrows were brought into captivity and exposed to comparable light cycles, with all other variables held constant. These results generated two hypotheses: (1) seasonal variation in DNA damage is related to circadian regulation and (2) seasonal variation in DNA damage is related to the total number of active hours. To investigate these hypotheses, we first quantified erythrocyte DNA damage in wild-caught house sparrows held in captivity on a 12L:12D light cycle at six points during the day to assess a diel or circadian rhythm but did not find one. We then performed a resonance experiment, in which birds experienced unnatural light cycles, and compared DNA damage in birds held on 6L:6D and 4.5L:7.5D resonance light cycles with their natural counterparts, 12L:12D and 9L:15D, respectively. We assessed corticosterone levels and DNA damage in blood before and after the resonance light cycles and DNA damage in abdominal fat, hippocampus, hypothalamus, and liver after the resonance light cycles. While our second experiment was not able to effectively test our hypotheses, we were able to demonstrate some interesting patterns. Throughout the resonance experiment, baseline corticosterone and testes size increased, consistent with the birds being photostimulated and preparing to breed. Surprisingly, the direction of change of DNA damage throughout the resonance photoperiod differed with tissue, which is not consistent with patterns during the breeding season in the wild. Our data indicate a potential uncoupling of the breeding physiology with the effect on DNA damage due to exposure to a resonance light cycle, which the birds may have interpreted as a skeleton photoperiod. Finally, though we were unable to fully disentangle the dynamics underlying seasonal DNA damage, we show that the previously documented patterns are not simply due to diel changes or the total amount of light exposure within a 24-hour period. creator: Emma Rosen creator: Lily Mikolajczak creator: Ursula K. Beattie creator: L. Michael Romero uri: https://doi.org/10.7717/peerj.18375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rosen et al. title: The regulation role of calcium channels in mammalian sperm function: a narrative review with a focus on humans and mice link: https://peerj.com/articles/18429 last-modified: 2024-10-25 description: Mammalian sperm are characterized as specialized cells, as their transcriptional and translational processes are largely inactive. Emerging researches indicate that Ca2+ serves as a crucial second messenger in the modulation of various sperm physiological processes, such as capacitation, hyperactivation, and the acrosome reaction. Specifically, sperm-specific calcium channels, including CatSper, voltage-gated calcium channels (VGCCs), store-operated calcium channels (SOCCs), and cyclic nucleotide-gated (CNG) channels, are implicated in the regulation of calcium signaling in mammalian sperm. Calcium stores located in the sperm acrosomes, along with the IP3 receptors in the neck of the redundant nuclear envelope and the mitochondria in the tail, play significant roles in modulating intracellular Ca2+ levels in sperm. However, the functions and mechanisms of these calcium channels in modulating mammalian sperm physiological functions have not yet been well elucidated. Therefore, by focusing on humans and mice, this study aims to provide a comprehensive review of the current advancements in research regarding the roles of calcium signaling and associated calcium channels in regulating sperm function. This endeavor seeks to enhance the understanding of calcium signaling in sperm regulation and to facilitate the development of drugs for the treatment of infertility or as non-hormonal male contraceptives. creator: Yebin Yang creator: Liu Yang creator: Xiaoqun Han creator: Kuaiying Wu creator: Guangquan Mei creator: Baojian Wu creator: Yimin Cheng uri: https://doi.org/10.7717/peerj.18429 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Bacterial production of polyhydroxyalkanoates (PHAs) using various waste carbon sources link: https://peerj.com/articles/17936 last-modified: 2024-10-24 description: Synthetic plastics are in great demand in society due to their diversified properties, but they cause environmental pollution due to their non-biodegradable nature. Therefore, synthetic plastics are in need to be replaced with biodegradable plastics. Polyhydroxyalkanoates (PHAs), bacterial biopolymers are natural alternative to synthetic plastics. These are present inside the bacterial cytoplasm in granular form. Presently, the production cost of PHA is high due to expensive carbon substrates used in its biosynthesis. Therefore, this study focuses on the cost-effective production of PHA using waste carbon sources. Rice bran and sugarcane molasses were used as the carbon source for PHA production from Bacillus subtilis, Bacillus cereus, Alcaligenes sp. and Pseudomonas aeruginosa. PHA production from these bacterial strains was confirmed through Sudan Black-B screening. With rice bran, as carbon source, the highest PHA yield obtained was for P. aeruginosa, which yielded 93.7% and lowest was 35.5% for B. cereus. Surprisingly, B. cereus produced the highest cell dry mass (0.045 g/L) but its extracted PHA contents were lowest being only 0.02 g/L. Alcaligenes sp. with 0.031 g/L CDM yielded 87.1% PHA. B. subtilis had a CDM 0.029 g/L, 0.02 g/L PHA content and a yield of 69.10%. In the case of sugarcane molasses, P. aeruginosa produced 95% PHA yield, 0.02 g/L CDM, and 0.019 g/L PHA content. Alcaligenes sp. yielded 90.9% PHA, 0.011 g/L CDM, and 0.01 g/L PHA content. B. subtilis produced 91.6% PHA yield, 0.012 g/L CDM, 0.011 g/L PHA content; B. cereus produced 80% PHA yield, 0.015 g/L CDM, 0.012 g/L PHA content at 37 °C, pH 7. Higher concentrations of carbon sources increased the CDM and decreased the PHA yield. The maximum yield of PHA was obtained from sugarcane molasses. 24–48 h of incubation was optimal for B. subtilis and B. cereus, while for Alcaligenes and P. aeruginosa incubation time of 48–96 h was desirable for higher PHA yield. The extracted biopolymers were analyzed by Fourier transform infrared spectroscopy (FTIR), which identified the extracted biopolymers as poly-3-hydroxybutyrate P(3HB). The thermal properties of the extracted biopolymers, such as melting temperatures, were analyzed by differential scanning calorimetry (DSC), which confirmed the thermal stability. creator: Aansa Naseem creator: Ijaz Rasul creator: Zulfiqar Ali Raza creator: Faizan Muneer creator: Asad ur Rehman creator: Habibullah Nadeem uri: https://doi.org/10.7717/peerj.17936 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Naseem et al. title: Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream link: https://peerj.com/articles/18016 last-modified: 2024-10-24 description: Environmental DNA (eDNA) metabarcoding has emerged as a promising approach to assess biodiversity and derive ecological status classes from water samples. However, a limitation of eDNA surveys is that detected DNA molecules may originate from other places or even dead organisms, distorting local biodiversity assessments. Environmental RNA (eRNA) metabarcoding has recently been proposed as a complementary tool for more localized assessments of the biological community. In this study, we evaluated the effectiveness of eDNA and eRNA metabarcoding for inferring the richness and species distribution patterns of vertebrates and invertebrates in a Central European lowland river. We collected water samples and analyzed them using a 12S marker for vertebrates and a COI marker for invertebrates. We detected 31 fish, 16 mammal, 10 bird and one lamprey species in the vertebrate dataset. While results were largely consistent, we detected a higher number of species when analysing eRNA (mean = 30.89) than eDNA (mean = 26.16). Also, eRNA detections had a stronger local signature than eDNA detections when compared against species distribution patterns from traditional fish monitoring data. For invertebrates, we detected 109 arthropod, 22 annelid, 12 rotiferan, eight molluscan and four cnidarian species. In contrast to the pattern of vertebrate richness, we detected a higher richness using eDNA (mean = 41.37) compared to eRNA (mean = 22.42). Our findings primarily show that eDNA and eRNA-based detections are comparable for vertebrate and invertebrate taxa. Biological replication was important for both template molecules studied. Signal detections for vertebrates were more localized for eRNA compared to eDNA. Overall, the advantages of the extra steps needed for eRNA analyses depend on the study question but both methods provide important data for biodiversity monitoring and research. creator: Till-Hendrik Macher creator: Jens Arle creator: Arne J. Beermann creator: Lina Frank creator: Kamil Hupało creator: Jan Koschorreck creator: Robin Schütz creator: Florian Leese uri: https://doi.org/10.7717/peerj.18016 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Macher et al. title: Effect of acute anaerobic performance on zinc alpha 2 glycoprotein, apelin and lipasin levels link: https://peerj.com/articles/18093 last-modified: 2024-10-24 description: The aim of this study was to investigate the effects of acute anaerobic exercise on serum levels of adipokines Zinc-α2-glycoprotein (ZAG), apelin, and lipasin. Eighteen male athletes who actively played soccer and trained at least four days a week, with a mean age of 19.11 ± 2.59 years, body weight of 70.61 ± 8.17 kg, height of 176.0 ± 7.71 cm, sport age of 7.22 ± 2.60 years and BMI of 22.76 ± 1.68 kg/m2 participated in the study. Athletes were subjected to the Running-Based Anaerobic Sprint Test (RAST) for anaerobic performance. Blood samples were collected from the athletes 4 times (at rest, 10 minutes, 60 minutes, and 24 hours after exercise). The results of the study showed that acute anaerobic exercise significantly increased ZAG levels (p < 0.05). However, no statistically significant difference was detected in apelin and lipasin levels (p > 0.05). In conclusion, the findings of this study indicate that acute anaerobic exercise is associated with an increase in ZAG levels, but not apelin or lipasin levels. The observations suggest that ZAG may have a specific response to anaerobic exercise, which provides valuable insight into its potential impact on energy metabolism. creator: Şaban Ünver creator: İlknur Bıyık creator: Tülin Akman creator: Emre Şimşek creator: Hamza Küçük creator: Abdurrahim Kaplan creator: Deniz Günay Derebaşı creator: Selma İşler creator: Canberk Çınar creator: Tuba Kızılet creator: Yeliz Tanrıverdi Çaycı uri: https://doi.org/10.7717/peerj.18093 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ünver et al. title: Comparing efficacy in reducing pulling and welfare impacts of four types of leash walking equipment link: https://peerj.com/articles/18131 last-modified: 2024-10-24 description: BackgroundLeash pulling is a commonly reported problem behavior for dog owners, as a result, a variety of leash equipment types are offered to mitigate pulling force. We were particularly interested in prong collars as their inherently aversive design has made their use a subject of debate. Though banned in certain countries and widely available in others, to date, there is no research comparing them to other leash walking equipment.MethodsWe compared four types of leash walking equipment: a martingale (flat collar as baseline measure), a front-connection harness, a polymer prong-style collar (Starmark), and a standard metal prong collar. Twenty-three dogs were walked on all four types of equipment for 5-min each. Equipment was attached to a leash which was connected to a battery-powered strain gauge to measure the dog’s pulling force. All walks were video recorded for behavior analysis.ResultsThere were statistically significant differences among the leash equipment types in pulling impulse (Newtons × seconds), (χ2(2) = 30.6, p < 0.001). Post-hoc analysis revealed significant differences in impulse between the martingale and the other equipment: harness (Z = −3.69, p < 0.001), Starmark collar (Z = −3.62, p < 0.001) and prong collar (Z = −3.92, p < 0.001). No other differences among equipment types were significant. Fifteen behaviors were examined as welfare indicators but only three: looking at the handler, lip licking, and sniffing occurred across all dogs and all walks. There was a statistically significant difference in frequency of lip licking behavior across the four types of leash-equipment (χ2(2) = 8.17, p = 0.04) and post-hoc analysis showed a difference between the martingale and the harness (Z = −2.65, p = 0.008). While our research did not provide any clear evidence of poorer welfare due to equipment type, we caution the generalizability of these findings and recommend further assessment of these items of leash-walking equipment in real-life scenarios. creator: Anamarie C. Johnson creator: Clive D. L. Wynne uri: https://doi.org/10.7717/peerj.18131 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Johnson and Wynne title: Evidence for sweep signatures in antibiotic-resistant strains in three species of bacteria link: https://peerj.com/articles/18178 last-modified: 2024-10-24 description: Over the last decades antibiotic resistance has evolved and spread in many different bacterial species. From an evolutionary perspective, drug resistance is an adaptation to a new environment. Population genetic theory predicts that recent adaptations are associated with reduced diversity in the part of the population that carries the adaptive trait, due to a process known as selective sweeps. It is not known if this prediction holds for antibiotic resistance in bacterial species that infect humans. Here, we use a convenience sample of eight datasets covering three species of bacteria (Escherichia coli, Staphylococcus aureus and Enterococcus faecium). The eight datasets include multi locus sequence type information and antibiotic resistance phenotypes for between 53 to 1,094 patient samples and between three and 19 different antibiotics. Consistent with selective sweep theory, we find that, in most cases, sequence-type diversity amongst antibiotic-resistant bacterial strains is lower than amongst antibiotic-susceptible strains. Specifically, in 45 out of 59 comparisons (76%), resistant strains were significantly less diverse than susceptible strains. We also observe that while diversity is lower amongst resistant strains, in all cases there were at least several different sequence types amongst the resistant strains, which suggests that we are dealing here with soft sweeps rather than hard sweeps. Finally, we show that sequence-type diversity of antibiotic-resistant strains is lower if resistance is rare, compared to when resistance is common, which is consistent with rare resistance being due to fewer evolutionary origins. To summarize, our results show that for several different bacterial species, diversity of resistant strains is generally reduced, which is consistent with the evolution of resistance driven by selective sweeps stemming from a limited number of evolutionary origins. In future studies, more detailed analysis of such sweep signatures is warranted. creator: Anjani Pradhananga creator: Lorena Benitez-Rivera creator: Candace Clark creator: Kaho H. Tisthammer creator: Pleuni S. Pennings uri: https://doi.org/10.7717/peerj.18178 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pradhananga et al. title: Acute responses and recovery in the femoral cartilage morphology following running and cool-down protocols link: https://peerj.com/articles/18302 last-modified: 2024-10-24 description: This study compared the immediate effects of two common post-exercise cool-down methods to a control condition on subsequent morphologic change in femoral cartilage and vascular response in the posterior tibial artery after running. Sixteen healthy young males (23.6 ± 2.2 years, 172.8 ± 4.9 cm, 72.2 ± 7.1 kg) visited the laboratory during three separate sessions and performed 30-min of treadmill running (7.5 km/h for the initial 5-min, followed 8.5 km/h for 25-min). After running, participants experienced one of three 30-min cool-down protocols: active cool-down, cold application, or control (seated rest with their knee fully extended), in a counterbalanced order. Ultrasonographic assessments of femoral cartilage thickness (intercondylar, lateral, and medial) and posterior tibial artery blood flow were compared. To test condition effects over time, two-way analysis of variances and Tukey tests were used (p < 0.05) with Cohen’s d effect sizes (ES). There was no condition by time interaction in femoral cartilage thickness (intercondylar: F30,705 = 0.91, p = 0.61; lateral: F30,705 = 1.24, p = 0.18; medial: F30,705 = 0.49, p = 0.99). Regardless of time (condition effect: F2,705 > 3.24, p < 0.04 for all tests), femoral cartilage in the cold application condition was thicker than the control condition (intercondylar: p = 0.01, ES = 0.16; lateral: p < 0.0001, ES = 0.24; medial: p = 0.04. ES = 0.16). Regardless of condition (time effect: F15,705 > 10.31, p < 0.0001 for all tests), femoral cartilage thickness was decreased after running (intercondylar: p < 0.0001, ES = 1.37; lateral: p < 0.0001, ES = 1.58; medial: p < 0.0001, ES = 0.81) and returned to baseline levels within 40-min (intercondylar: p = 0.09; lateral: p = 0.64; medial: p = 0.26). Blood flow volume was different (condition × time: F30,705 = 2.36, p < 0.0001) that running-induced blood flow volume was maintained for 30-min for the active cool-down condition (p < 0.0001, ES = 1.64), whereas it returned to baseline levels within 10-min for other conditions (cold application: p = 0.67; control: p = 0.62). Neither blood flow nor temperature had a significant impact on the recovery in femoral cartilage after running. creator: Sanghyup Park creator: Junhyeong Lim creator: Jinwoo Lee creator: Seonggyu Jeon creator: Jaewon Kim creator: Jihong Park uri: https://doi.org/10.7717/peerj.18302 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Park et al. title: Molecular detection of Batrachochytrium dendrobatidis (Chytridiomycota) and culturable skin bacteria associated with three critically endangered species of Atelopus (Anura: Bufonidae) in Ecuador link: https://peerj.com/articles/18317 last-modified: 2024-10-24 description: Chytridiomycosis is a fungal disease responsible for massive amphibian die-offs worldwide, caused by the fungus Batrachochytrium dendrobatidis (Bd). Potential symbiotic relationships between frogs and the bacteria residing on their skin—referred to as skin-bacteria—may inhibit Bd growth, aiding in resistance to this lethal disease. This research had three main objectives: (1) to detect the presence of Bd in native populations of Atelopus balios, A. bomolochos, and A. nanay in the central Andes and coastal southern regions of Ecuador; (2) to identify the culturable skin-bacteria; and (3) to analyze differences among the bacterial communities in the three Atelopus species studied. Skin swabs were collected from two populations of A. balios (107–203 m a.s.l.) and one population each of A. bomolochos and A. nanay (3,064–3,800 m a.s.l.). These swabs served two purposes: first, to detect Bd using conventional PCR; and second, to isolate culturable bacteria, which were characterized through DNA sequencing, molecular phylogeny, and community composition similarity analysis (Jaccard index). Results showed that Bd was present in all species, with positive Bd PCR amplification found in 11 of the 12 sampled amphibians. The culturable skin-bacteria were classified into 10 genera: Pseudomonas (31.4%), Stenotrophomonas (14.3%), Acinetobacter (11.4%), Serratia (11.4%), Aeromonas (5.7%), Brucella (5.7%), Klebsiella (5.7%), Microbacterium (5.7%), Rhodococcus (5.7%), and Lelliottia (2.9%). The Jaccard index revealed that bacterial genera were least similar in A. bomolochos and A. balios (J = 0.10), while the highest similarity at the genus level was between A. bomolochos and A. nanay (J = 0.33). At the clade-species level, only A. bomolochos and A. nanay show common bacteria (J = 0.13). Culturable bacterial communities of specimens diagnosed as Bd positive (n = 10) or Bd negative (n = 1) share a J value of 0.1 at genus and 0.04 at species-clade level. The prevalence of Bd and the composition of cutaneous bacteria could be influenced by Bd reservoirs, Atelopus biology, and intrinsic environmental conditions. This research contributes to understanding the relationship between endangered Andean species and Bd, and explores the potential use of native skin-bacteria as biocontrol agents against Bd. creator: Jomira K. Yánez Galarza creator: Lenin Riascos-Flores creator: Leopoldo Naranjo-Briceño creator: Andrea Carrera-Gonzalez creator: H. Mauricio Ortega-Andrade uri: https://doi.org/10.7717/peerj.18317 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yánez Galarza et al. title: Cross-cultural adaptation and psychometric validation of a Chinese self-intermittent catheterization quality of life scale among patients with neurogenic bladder link: https://peerj.com/articles/18319 last-modified: 2024-10-24 description: BackgroundIntermittent self-catheterization (ISC) is widely considered the gold standard for treating patients with neurogenic bladder (NB). Healthcare professionals and catheter users must optimize ISC care to improve patients’ quality of life. To achieve this, the Intermittent Self-Catheterization Questionnaire (ISC-Q) is a valuable tool with clear and easy-to-understand items. However, this scale has yet to be adapted for use in China, and its reliability and validity need to be tested through cross-cultural adaptation.ObjectivesThe objective of this study was to culturally adapt the ISC-Q and develop the Chinese version of the ISC-Q (C-ISC-Q), and assess its reliability and validity among patients with NB.MethodsWith the authorization of the ISC-Q author, the Beaton mode was used to adapt the scale cross-culturally. The study was conducted from June 2020 to June 2021 in three phases: committee-based translation from English to Chinese, Delphi expert consultations (n = 5) for cultural adaptation, and a cross-sectional study (n = 149) for validation.ResultsThe C-ISC-Q has 24 items and four dimensions. The critical ratio of each item is over 3.0, and the correlation coefficient between each item and the scale’s total score is above 0.4. The Cronbach’s α value for the scale is 0.930, and for each dimension, it is between 0.870–0.92. The retest reliability for the scale is 0.894, and for each dimension is between 0.751–0.889. The content validity at the item level ranges from 0.8~1.0, and at the scale level is 0.9. The criterion-related validity of the scale was −0.708, and the correlation for each dimension was 0.329–0.624. The principal component analysis identified four common factors, with a cumulative contribution rate of 67.846%.ConclusionsThe C-ISC-Q is culturally sensitive, reliable, and valid to measure the quality of life for patients with NB. It can assist nurses and researchers in tailoring strategies to enhance the quality of life for patients with NB. creator: Rong Tang creator: Liqiong Zhou uri: https://doi.org/10.7717/peerj.18319 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tang and Zhou title: Association analysis of MTHFR (rs1801133 and rs1801131) gene polymorphism towards the development of type 2 diabetes mellitus in Dali area population from Yunnan Province, China link: https://peerj.com/articles/18334 last-modified: 2024-10-24 description: BackgroundType 2 diabetes mellitus (T2DM) is a common complex metabolic disorder that exhibits a strong genetic predisposition. 5,10-methylenetetrahydrofolate reductase (MTHFR) regulates folate metabolism, which has been proposed to be associated with T2DM, although the relationship is inconsistent among different geographical areas. This study aimed to investigate the effects of MTHFR C677T (rs1801133) and A1298C (rs1801131) loci polymorphisms on T2DM susceptibility in the population of the Dali area in Yunnan Province, China.MethodsThis case-control study included 445 patients with T2DM and 272 healthy control individuals from the Dali area of Yunnan Province. Genotyping of the MTHFR gene polymorphisms was performed using the competitive allele-specific PCR (KASP) method. The effects of genetic variations of the MTHFR gene on T2DM risk were evaluated using odds ratios (OR) and 95% confidence intervals.ResultsThe results of the present study revealed that the TT genotype (OR = 1.750, P = 0.030) and the T allele (OR = 1.252, P = 0.047) at the MTHFR C677T locus were considerably associated with the increased odds of developing T2DM. In addition, the CC genotype (OR = 3.132, P = 0.032) at the MTHFR A1298C locus also substantially increased the odds of developing T2DM. The T-A haplotype (OR = 1.305, P = 0.030) of MTHFR C677T and A1298C exhibited the increased odds of developing T2DM. Biochemical index analyses showed that patients with T2DM who carried the CT or TT genotype of MTHFR C677T expressed substantially higher levels of fasting blood glucose (FBG), homocysteine (Hcy), and tumor necrosis factor-alpha (TNF-α) than those of the CC genotype. Moreover, the FBG and Hcy levels were considerably higher in patients with T2DM who carried the CC or AC genotype of MTHFR A1298C than those of the AA genotype. No obvious association was observed between these MTHFR polymorphisms and cardiovascular risk in T2DM.ConclusionOur study suggests that the genetic variations of MTHFR C677T and A1298C are significantly associated with T2DM susceptibility in the population of the Dali area of Yunnan Province, China. creator: Yongxin Liu creator: Genyuan Pu creator: Caiting Yang creator: Yuqing Wang creator: Kaitai Jin creator: Shengrong Wang creator: Xiao Liang creator: Shenghe Hu creator: Shuguang Sun creator: Mingming Lai uri: https://doi.org/10.7717/peerj.18334 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Remote care instruction via the WeChat platform for female patients receiving subcutaneous anticoagulation during the COVID-19 pandemic: a retrospective analysis link: https://peerj.com/articles/18337 last-modified: 2024-10-24 description: BackgroundThe purpose of this study was to estimate the effect of remote nursing guidance based on WeChat platform for female patients receiving subcutaneous anticoagulation during the COVID-19 epidemic.MethodsRetrospective analysis of clinical data, including demographic data and anticoagulation complications, of 126 female patients who received subcutaneous anticoagulation therapy and received remote nursing guidance using WeChat platform in our hospital from January 2022 to December 2022. The Anti-Clot Treatment Scale (ACTS) and the World Health Organization Quality of Life-BREF (WHOQOL-BREF) scale were used to evaluate patients’ satisfaction with anticoagulation and quality of life at the beginning of anticoagulation, half a month after anticoagulation, and after three months of anticoagulation.ResultsIn total, 126 patients were involved in this study, all of them were female, 115 cases were natural pregnancy, 11 cases were assisted reproduction. This study included seven cases of lower extremity deep vein thrombosis, 100 cases of hypercoagulable state, 10 cases of antiphospholipid syndrome, and eight cases of protein S deficiency, one case of hyperhomocysteinemia. During the follow-up period, four patients (3.17%) had subcutaneous injection complications, including three cases of subcutaneous hemorrhage and one case of liquid leakage. A total of 123 patients had completed the planned anticoagulation therapy or were receiving anticoagulation therapy as planned, and three patients did not receive anticoagulation therapy as planned (zero cases lost contact, two cases changed treatment units, and one case refused treatment). ACTS score (55.03 ± 1.73) and WHOQOL-BREF score (62.18 ± 3.17) after three months of anticoagulation, ACTS score (54.18 ± 1.20) and WHOQOL-BREF score (60.37 ± 2.25) after half a month of anticoagulation was significantly higher than the ACTS score (47.81 ± 1.69) and WHOQOL-BREF score (55.25 ± 1.85) at the beginning of anticoagulation, and the difference was statistically significant (P value < 0.01).ConclusionsDuring the COVID-19 pandemic, remote nursing instruction via the WeChat platform for female patients receiving subcutaneous anticoagulation can increase anticoagulation compliance, satisfaction, and quality of life. creator: Chao Yun Jiang creator: Ci Juan Li creator: Rong Zhang creator: Tian Hong Cai creator: Teng Hui Zhan uri: https://doi.org/10.7717/peerj.18337 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jiang et al. title: A retrospective analysis of a newly proposed imaging-etiologic classification for acute ischemic stroke with large vascular occlusion based on MRI and pathogenesis link: https://peerj.com/articles/18342 last-modified: 2024-10-24 description: BackgroundEndovascular treatment (EVT) has emerged as the preferred initial therapeutic option for acute ischemic stroke (AIS) with large vascular occlusion (LVO). To facilitate more targeted EVT interventions, we propose a novel imaging-etiologic classification system derived from a comprehensive analysis of preoperative MRI and pathogenesis in AIS patients.MethodsFrom June 2020 to December 2021, a retrospective analysis was conducted on 184 consecutive AIS patients who underwent preoperative MRI and subsequent EVT at the Henan Provincial Cerebrovascular Hospital Stroke Center. Patients’ medical histories were comprehensively reviewed. According to MRI, anterior circulation infarction (ACI) and posterior circulation infarction (PCI) were divided into four groups respectively (A-D & a-d). Three types (1–3) of etiology were identified based on pathogenesis. The types were respectively evaluated by screening test with intra-operative finding of EVT.ResultsOur imaging-etiologic classification achieved an overall positive rate of 90.2% (166/184) when compared to the gold standard. The screening test for each type demonstrated excellent validity (Youden’s index ≥ 0.75) and reliability (Kappa ≥ 0.80).ConclusionThe imaging-etiologic classification represents a simple yet comprehensive approach that can be readily applied in the management of AIS with LVO. It can rapidly and effectively locate the vascular occlusion, and reveal the pathogenesis. creator: Hao Li creator: Zhaoshuo Li creator: Jinchao Xia creator: Lijun Shen creator: Guangming Duan creator: Ziliang Wang uri: https://doi.org/10.7717/peerj.18342 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Emerging roles of tRNA-derived small RNAs in injuries link: https://peerj.com/articles/18348 last-modified: 2024-10-24 description: tRNA-derived small RNAs (tsRNAs) are a novel class of small noncoding RNAs, precisely cleaved from tRNA, functioning as regulatory molecules. The topic of tsRNAs in injuries has not been extensively discussed, and studies on tsRNAs are entering a new era. Here, we provide a fresh perspective on this topic. We systematically reviewed the classification, generation, and biological functions of tsRNAs in response to stress, as well as their potential as biomarkers and therapeutic targets in various injuries, including lung injury, liver injury, renal injury, cardiac injury, neuronal injury, vascular injury, skeletal muscle injury, and skin injury. We also provided a fresh perspective on the association between stress-induced tsRNAs and organ injury from a clinical perspective. creator: Mengjun Wang creator: Junfeng Guo creator: Wei Chen creator: Hong Wang creator: Xiaotong Hou uri: https://doi.org/10.7717/peerj.18348 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Wang et al. title: A study on elite athletes: Orthorexia nervosa tendency is a risk factor for sleep quality link: https://peerj.com/articles/18349 last-modified: 2024-10-24 description: BackgroundElite athletes adhere to strict daily routines, particularly concerning their nutritional habits. However, these practices can occasionally lead to a pathological fixation on healthy eating known as orthorexia nervosa which may adversely affect sleep quality. The aim of this study was to examine the relationship between orthorexia nervosa tendencies and sleep quality in elite athletes, as well as to investigate potential differences in orthorexia nervosa tendencies and sleep patterns between athletes engaged in individual versus team sports.MethodsThe present study explores how orthorexia nervosa tendency affects sleep quality in 249 elite athletes (115 women: aged 19.92 ± 2.48 years, sporting tenure: 8.16 ± 3.96 years, and 134 men: aged 20.69 ± 2.72 years, sporting tenure: 7.85 ± 3.59 years). The orthorexia nervosa tendency was evaluated using the ORTO-11 scale, while their sleep quality using the Pittsburgh Sleep Quality Index.ResultsThe results of the present study indicate that orthorexia nervosa negatively affected sleep quality (rho = −0.173, p = 0.006). Additionally, no differences in the orthorexia nervosa tendency was observed between individual and group athletes (p = 0.287); however, individual athletes presented poorer sleep quality (p = 0.287).ConclusionThese results indicate that the elite athletes who present higher orthorexia nervosa tendency had a higher risk of having poorer sleep quality. creator: Musab Çağın creator: Sezen Çimen Polat creator: Halil Sarol creator: Çisem Ünlü creator: Danica Janicijevic uri: https://doi.org/10.7717/peerj.18349 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Çağin et al. title: Ceciamaralia, a new genus of Dorvilleidae (Annelida) from deep waters of the Southwest Atlantic Ocean and an insight into its relationship within the family link: https://peerj.com/articles/18358 last-modified: 2024-10-24 description: Dorvilleidae Chamberlin, 1919 is a family of Annelida containing some of the smallest ‘polychaetes’ species, being poorly studied worldwide, and with little knowledge regarding its diversity and occurrence. Samples obtained in oceanographic campaigns performed in the Southwest Atlantic Ocean (Brazilian coast) revealed a high number of specimens of dorvilleids, adding to our knowledge of the family’s biodiversity. A detailed morphological analysis of these organisms has revealed a new genus, Ceciamaraliagen. nov., with two new species. The new genus differs from other Dorvilleidae genera in (i) the robust and enlarged pharynx which are frequently everted, (ii) unique composition of maxillae, with an elongated pair of serrated basal plates and one pair of anterior free maxillary plates with a long and thin anterior spine and (iii) ventral cirri present only in few first chaetigers. Ceciamaralia lanaigen. et sp. nov. is characterized by the presence of a broad and large dorsal cirrus on a few anterior parapodia and by furcate chaeta in supra-acicular fascicles. While Ceciamaralia nonatoigen. et sp. nov. presents one geniculate chaeta instead of one furcate, the absence of dorsal cirri and, in some specimens, the absence of palps. A cladistic analysis supported the monophyly of Ceciamaraliagen. nov. by four synapomorphies related to the unique morphology of its maxillae, pharynx and appendages. This study is part of several recent taxonomic studies aiming to elucidate and increase the knowledge of Dorvilleidae, since it is part of a Ph.D project focused on the family. creator: Rafael de Oliveira Bonaldo creator: Tatiana Menchini Steiner creator: André Rinaldo Senna Garraffoni uri: https://doi.org/10.7717/peerj.18358 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bonaldo et al. title: Current status of the remaining Mexican cloud forests: landscape findings and conservation initiatives link: https://peerj.com/articles/18386 last-modified: 2024-10-24 description: Tropical montane cloud forests are known for their unique biodiversity and their critical role in sustaining ecosystem services; however, approximately 50% of their original cover in Mexico was estimated to have been lost by 1998. The Mexican ecoregion that supports these ecosystems experienced one of the highest rates of deforestation between 2001 and 2021. Thus, a more recent evaluation of Mexico’s cloud forests is required. There is limited data on the landscape structure of cloud forests in Mexico, despite the possible application of landscape factors in conservation planning. Here, we estimated the average total area, number of patches, effective mesh size, total edge, and the shape of mixed forests that was present in 2020 within polygons of cloud forests defined in 1999 by Mexico’s National Commission for the Use and Knowledge of Biodiversity (CONABIO for its acronym in Spanish). We estimated land cover using data from the North American Land Change Monitoring System, which classifies cloud forests as mixed forests. We found that eight out of the 109 polygons have no mixed forests and that an average of 49% of the 1,768,914 ha of cloud forests polygons are now covered by mixed forests distributed across 13 states. Additionally, within the remaining 101 polygons that do contain this type of vegetation, mixed forest is distributed on average across 140 patches (range = 1–1,473); 80% of these forests have very low effective mesh size values; 90% of them have low total edge values (<2,000 km); and their shapes tend to be uniformly distributed. Furthermore, most of cloud forest polygons are located outside of federal protected areas. Overall, our results suggest that the remaining Mexican cloud forests are extremely vulnerable and fragmented and that their extent has steadily declined since 1999. To ensure the survival of Mexican cloud forests, it will be crucial to prioritize high-diversity areas, strengthen protection in critical zones, establish ecological corridors, encourage sustainable practices, and actively engage local communities. This study highlights the complex issues and inherent heterogeneity that characterize cloud forest ecosystems in Mexico and provides crucial insights for conservation. creator: Wesley Dáttilo creator: Sergio A. Cabrera-Cruz creator: César A. Gallo-Gómez creator: Juan Carlos Serio-Silva creator: Rafael Villegas-Patraca uri: https://doi.org/10.7717/peerj.18386 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dáttilo et al. title: Silver nanoparticles can be sampled by ultrafiltration probe but elution into & recovery from plasma and Dulbecco’s Phosphate Buffered Saline differs in vitro link: https://peerj.com/articles/18388 last-modified: 2024-10-24 description: Locally sustained release antimicrobials such as silver nanoparticles (AgNPs) might prove useful in combating local infections. Their elution has been investigated in Phosphate Buffered Saline (PBS) including from poloxamer 407 (P407). No information exists on possible interactions with proteins, nor have ultrafiltration (UF) probes been evaluated to measure Ag. These investigations would provide helpful data prior to investigating the sustained release after subcutaneous implantation in vivo over time. We compared (1) the influence of elution fluid on AgNP elution, and (2) UF probe and direct sampling in vitro. Six AgNP-P407 specimens in a dialysis tube were placed in Dulbecco’s PPBS (DPBS) (n = 3) or canine plasma (n = 3) for 96 h on a stirred hot plate (37 °C and 600 rpm) and sampled 20 times. A 0.001 mg/mL AgNP solution was prepared in DPBS or plasma. Six pipette and UF probe samples were taken of each. Inductively coupled plasma mass spectrometry was used to analyze Ag. Stock plasma contained Ag. At 96 h, 5/6 dialysis tubes had not fully released AgNP. One peak in hourly Ag increase was present in DPBS (10–13 h), and two peaks in plasma (6–8 and 10–13 h). The hourly Ag increase in plasma decreased earlier than in DPBS. Ultrafiltration probe sampling was possible in both DPBS and plasma and resulted in higher Ag concentrations but with more variation. While in vitro use of DPBS might be more cost effective, plasma should be considered due to difference in elution and recovery. Ultrafiltration probes can be used to sample Ag, but results will have a greater degree of variation, and multiple samples and increased time points should be considered. creator: Marije Risselada creator: Robyn R. McCain creator: Miriam G. Bates creator: Makensie L. Anderson uri: https://doi.org/10.7717/peerj.18388 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Risselada et al. title: Effects of progessive vs. constant protocol whole-body vibration on muscle activation, pain, disability and functional performance in non-specific chronic low back pain patients: a randomized clinical trial link: https://peerj.com/articles/18390 last-modified: 2024-10-24 description: Background and ObjectiveNon-specific chronic low back pain (NSCLBP) is a prevalent condition causing significant disability and functional impairment. Whole-body vibration exercise (WBVE) has emerged as a new treatment method, but additional research is necessary to determine the optimal parameters of WBVE that would be beneficial for patients experiencing chronic low back pain (CLBP). This study aims to investigate the effects of two type of WBVE (constant vs progressive) on pain, disability, functional performance, and muscle activity in patients with NSCLBP.MethodsThirty-two individuals diagnosed with chronic low back pain (CLBP) without any specific causes were enrolled and randomly assigned to one of two intervention groups: a constant/fixed protocol WBVE group or a progressive protocol WBVE group. Participants underwent WBVE sessions for around 30 min, thrice weekly over a period of 8 weeks. Primary outcomes assessed included pain intensity, functional disability, functional performance, and electromyographic activity of core musculature, measured at baseline and upon completion of the intervention period. Temporal changes of each outcome variable across different periods and between groups were measured with repeated measures 2×2 mixed ANOVA. Further, the paired t-test was performed to compare pre- and post-treatment values within each group.ResultsSignificant improvements were observed in both the constant and progressive WBVE protocol groups. Pain intensity decreased by 64.2% (p < 0.001) in the constant group and by 61.1% (p < 0.001) in the progressive group. Functional disability decreased by 48.1% (p < 0.001) in the constant group and by 53.3% (p < 0.001) in the progressive group. Functional performance improved by 16.5% (p < 0.001) in the constant group and by 16.9% (p < 0.001) in the progressive group. Electromyography (EMG) demonstrated significant improvements across all measured variables except % maximum voluntary isometric contraction (%MVIC) of external obliques (EO) in both intervention groups with time (p < 0.001). There was no statistically significant difference in the magnitude of improvement between the constant and progressive WBVE protocols (p > 0.05), indicating both modalities’ effectiveness in ameliorating CLBP symptoms and associated functional impairments.ConclusionThe study demonstrates that both progressive and constant WBVE protocols are equally effective in reducing pain and disability in NSCLBP patients. These findings support the inclusion of progressive WBVE in clinical practice, offering a flexible treatment option that can be tailored to individual patient needs, ensuring both tolerability and effectiveness. This contributes valuable evidence towards optimizing WBVE protocols for managing NSCLBP. creator: Tasneem Zafar creator: Saima Zaki creator: Md Farhan Alam creator: Saurabh Sharma creator: Reem Abdullah Babkair creator: Shibili Nuhmani uri: https://doi.org/10.7717/peerj.18390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©Zafar 2024 et al. title: Combining citizen science, phylogenetics, and bioacoustics to inform taxonomy and conservation of the Near Threatened Proceratophrys paviotii (Anura, Odontophrynidae) link: https://peerj.com/articles/17990 last-modified: 2024-10-23 description: Herein, basel on novel data gathered by citizens scientists and specialists, we contribute to the improvement of scientific knowledge and conservation of the Near Threatened Proceratophrys paviotii in order to: 1) test for the first time the phylogenetic position and a species delimitation of P. paviotii through a molecular approach; 2) describe a larger sample of its advertisement call to properly encompass the species intraspecific variation; 3) describe for the first time the P. paviotii release call; and 4) provide novel insights on the species conservation status. Our 16S tree confidently grouped P. paviotii with P. cururu, P. renalis, and P. laticeps. The average sequence divergence between P. paviotii and its congeners ranged from 2.2% (P. laticeps) to 9.1% (P. redacta). Advertisement calls consisted of a single note with duration of 0.26–0.58 s, 17–41 pulses emitted at rate of 54.19–77.49 pulses/s and peak frequency of 775.19–947.46 Hz. Release calls consisted of a single note with duration of 0.04–0.43 s, 2–13 pulses emitted at rate of 21.17–81.58 pulses/s and peak frequency of 689.1–1,722.6 Hz. Additionally, our study strongly supports the notion that Citizen Science approaches can yield invaluable information concerning species’ geographic distribution and conservation. creator: João Victor Andrade Lacerda creator: Diego J. Santana creator: Carla Guimarães creator: Alice Zanoni dos Santos creator: Alan P. Araujo creator: Natalia Pirani Ghilardi-Lopes creator: Sarah Mângia uri: https://doi.org/10.7717/peerj.17990 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lacerda et al. title: Surface-functionalized PAN fiber membranes for the sensitive detection of airborne specific markers link: https://peerj.com/articles/18077 last-modified: 2024-10-23 description: PAN fibers are characterized by having a large surface-to-volume ratio and small pores, which are beneficial for applications in filtration and specific molecular detection systems. Naturally, larger items are filtered, and a lower ratio between specific and nonspecific binding is expected since small pores do not allow larger elements to penetrate through membranes; thus, nonspecific binding is enhanced. We prepared and tested fiber membranes (diameter cca 700 nm) functionalized with a specific antibody to prove that even microscopic systems such as bacteria could be specifically identified. In addition, we established a methodology that enabled the effective binding of bacteria in not only an aqueous environment but also air. Our data clearly prove that even large systems such as bacteria could be specifically identified by fiber membranes surface-functionalized with a specific antibody. This research opens the door to the construction of biosensors for the fast, inexpensive, and sensitive identification of airborne bacterial contaminants and other airborne pollutants. creator: Leontyna Varvarovska creator: Bruno Sopko creator: Dana Gaskova creator: Tomas Bartl creator: Evzen Amler creator: Tatana Jarosikova uri: https://doi.org/10.7717/peerj.18077 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Varvarovska et al. title: Spontaneous space closure after extraction of young first permanent molar. Retrospective cohort study link: https://peerj.com/articles/18276 last-modified: 2024-10-23 description: BackgroundEarly compromised first-permanent-molar (FPM) extraction can adversely affect occlusion. However, the current literature does not provide sufficient support for definitive early extraction outcome. This cohort study aimed to evaluate the pattern of post-FPM extraction spontaneous space closure and its pre-extraction indicators.MethodsPatients of 7–13 years, with compromised FPM at three-tertiary-centers between 2015 and 2019 were retrospectively screened. Pre-extraction indicators were evaluated (extraction location, direction of the second permanent molar (SPM) long-axis, and SPM Demirjian development stage). Spontaneous space closure pattern was evaluated clinically and radiographically using the American Board of Orthodontics (ABO) grading system.ResultsIn total, 112 FPMs (73-patients) were identified and five (4.5%) of the extraction sites showed favorable combined-ABO-scores. Distal direction of the SPM long-axis in the maxillary arch significantly decreased the relative risk (RR) of having a SPM rotation/alignment ABO score-1 (P = 0.002; RR = 0.64). For the mandibular arch, Demirjian stage D and E significantly decreased the RR of having ABO score-1 for spacing between the SPMs and second premolars (P = 0.029; RR:0.57, P = 0.004; RR:0.53, respectively) and vertical dimension (P = 0.02; RR = 0.53).ConclusionsThe direction of the SPM long-axis and its developmental stage are key indicators of the favorable outcome pattern of spontaneous space closure after FPM early extraction. creator: Heba Jafar Sabbagh creator: Ahmad Adnan Samara creator: Shoroog Hassan Agou creator: Jihan Turkistani creator: Manal Ibrahim Al Malik creator: Hadeel Abdulatief Alotaibi creator: Abrar Shimi Dhaifallah Alsolami creator: Nada Othman Bamashmous uri: https://doi.org/10.7717/peerj.18276 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sabbagh et al. title: Effect of donor GSTM3 rs7483 genetic variant on tacrolimus elimination in the early period after liver transplantation link: https://peerj.com/articles/18360 last-modified: 2024-10-23 description: PurposeGlutathione S-transferase mu (GSTM) belongs to the group of phase II drug-metabolizing enzymes, and the GSTM1 genetic variant has been reported to have a potential association with the metabolism of immunosuppressive drug after renal transplantation. The effect of donor and recipient GSTMs genetic variants on tacrolimus (Tac) metabolism was the focus of our investigation in this study.MethodsA total of 203 liver transplant patients were recruited for the study. In the training set (n = 110), twenty-one SNPs in five genes (GSTM1-5) were genotyped by the drug-metabolizing enzymes and transporter (DMET) microarray. CYP3A5 rs776746 and GSTM3 rs7483 were genotyped using a Mass ARRAY platform in the validating set (n = 93).ResultsTac C/D ratios of donor GSTM3 rs7483 AA carriers were significantly lower than those with the G allele at weeks 1, 2, 3 and 4 after liver transplantation (LT). Multivariate analysis was conducted on the training set and validating set, donor and recipient CYP3A5 rs776746, donor GSTM3 rs7483 and total bilirubin were identified as independent predictors of Tac C/D ratios in the early period after LT. Combining CYP3A5 rs776746 and donor GSTM3 rs7483 genotypes, Tac C/D ratios were observed to be increasingly lower with increasing numbers of alleles associated with fast metabolism. Moreover, the risk of a supratherapeutic C0 (Tac > 15 ug/L) was significantly higher for poor metabolizers than the other groups at week 1 after LT.ConclusionsThere was a significant association between the donor GSTM3 rs7483 genetic variant and Tac metabolism in the early period after LT. Genotype classification might have a better predictive ability of the initial Tac doses. creator: Tao Zhang creator: Xiaorong Chen creator: Yuan Liu creator: Lei Zhang uri: https://doi.org/10.7717/peerj.18360 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Association between plain ropivacaine dose and spinal hypotension for cesarean delivery: a retrospective study link: https://peerj.com/articles/18398 last-modified: 2024-10-23 description: BackgroundData on the association between the plain ropivacaine dose and maternal hypotension during cesarean delivery are limited. Thus, this study aimed to explore this association.MethodsThis retrospective study included patients undergoing cesarean sections under spinal or combined spinal-epidural anesthesia with plain ropivacaine at The First Hospital of Fuyang, Hangzhou, China, between 2018 and 2022. Data were obtained from the anesthesia information management system. Liner trend tests were used to distinguish the linear relationship between spinal hypotension and the plain ropivacaine dose, and receiver operating characteristic curves were used to calculate the dose threshold. Logistic regression was used to adjust for confounders. Sensitivity analyses were performed to evaluate the stability of the results. The secondary outcome was vasopressor use (metaraminol and ephedrine).ResultsIn total, 1,219 women were included. The incidence of hypotension linearly correlated with the plain ropivacaine dose (adjusted P-value for trend, P < 0.001). Thus, we used a dose threshold of 17.5 mg to compare the dose as a binary variable (≥17.5 mg vs. < 17.5 mg). Plain ropivacaine doses of ≥17.5 mg were associated with a higher incidence of spinal hypotension (adjusted odds ratio: 2.71; 95% confidence interval [1.85–3.95]; P < 0.001). The sensitivity analyses yielded similar results. The plain ropivacaine dose also correlated with metaraminol use but not ephedrine use.ConclusionsThe incidence of spinal-induced hypotension in women undergoing cesarean section linearly correlated with the plain ropivacaine dose. The dose threshold for hypotension risk was 17.5 mg. creator: Min Li creator: Guohao Xie creator: Lihua Chu creator: Xiangming Fang uri: https://doi.org/10.7717/peerj.18398 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil link: https://peerj.com/articles/18433 last-modified: 2024-10-23 description: Livestock grazing has been proposed as a cost-effective way to reclaim post-mining lands. It can enhance soil fertility and biodiversity, but its impacts on soil quality and microbial communities vary across soil types. Moreover, waste from grazing raises concerns about pathogens that could pose risks to animal and human health. This study investigated the effects of grazing on post-mining perlite-rich soil in central Thailand. A comparative analysis of soil physicochemical properties and bacterial diversity was conducted between grazed and ungrazed sites. Bacterial diversity was assessed using 16S amplicon sequencing. The perlite-rich soil was found to be sandy, acidic, and to have low nutritional content. Grazing significantly improved the soil texture and nutrient content, suggesting its potential as a cost-effective reclamation strategy. The 16S metagenomic sequencing analysis revealed that microbial communities were impacted by livestock grazing. Specifically, shifts in the dominant bacterial phyla were identified, with increases in Firmicutes and Chloroflexi and a decrease in Actinobacteria. Concerns about increased levels of pathogenic Enterobacteriaceae due to grazing were not substantiated in perlite-rich soil. These bacteria were consistently found at low levels in all soil samples, regardless of livestock grazing. This study also identified a diverse population of Streptomycetaceae, including previously uncharacterized strains/species. This finding could be valuable given that this bacterial family is known for producing antibiotics and other secondary metabolites. However, grazing adversely impacted the abundance and diversity of Streptomycetaceae in this specific soil type. In line with previous research, this study demonstrated that the response of soil microbial communities to grazing varies significantly depending on the soil type, with unique responses appearing to be associated with perlite-rich soil. This emphasizes the importance of soil-specific research in understanding how grazing affects microbial communities. Future research should focus on optimizing grazing practices for perlite-rich soil and characterizing the Streptomycetaceae community for potential antibiotic and secondary metabolite discovery. The obtained findings should ultimately contribute to sustainable post-mining reclamation through livestock grazing and the preservation of valuable microbial resources. creator: Jiraphan Premsuriya creator: Nontaphat Leerach creator: Phatcharin Laosena creator: Woranich Hinthong uri: https://doi.org/10.7717/peerj.18433 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Premsuriya et al. title: A classification system for identifying persons with an unknown cardiovascular disease (CVD) status for a multiracial/ ethnic Caribbean population link: https://peerj.com/articles/17948 last-modified: 2024-10-22 description: BackgroundThe need for classification systems for cardiovascular disease (CVD) that is population-specific is important towards understanding the clinical disease and diagnostics associated with the disease. This paper presents the form and validation results of this classification system.MethodThe survey data used was captured from 778 participants, 526 persons with no prior CVD, and 252 who reported prior CVD. Binomial logistic regression and Discriminant analysis were utilised to develop classification models. This classification system provided a general measure of severity of disease by utilising scores estimated from two algorithms developed from 13 routine physiologic measurements, along with demographic information of age and ethnicity, inter alia, and previous health status.ResultsFor each model, specific score ranges were identified, which gave the best classification for those with a prior CVD incident (higher scores) and for others labelled as non-CVD (lower scores). The two classification models (Logistic Regression Model and Discriminant Analysis Model) developed had high area under the receiver-operating characteristic (AUROC) values (98% & 99%) and sensitivity (86 and 90%), which improved discrimination between Non-CVD and CVD participants and, more importantly, correctly classified a greater proportion of CVD participants. New to this type of research was the estimation and detailed evaluation of a range of scores, labelled non-differentiating, which fell in the middle of the spectrum and which contained the higher-end scores for the non-CVD individuals and the lower-end scores for CVD patients, all of whom were incorrectly classified, based on their prior history.ConclusionThe classification system of scores is able to differentiate the CVD status of individuals, with good predictability, and could assist physicians with recommending different treatment plans. The two models in this classification system each individually outperformed the three established models in terms of the strength of their correct classifications of individuals with or without prior reported CVD incidents. More importantly, they have smaller non-differentiating ranges than the three known models and, in that range, the two new models have lower CVD/non-CVD ratios suggesting they are more likely to misclassify non-CVD individuals compared to CVD patients, which is a more benign misclassification. Further, when used in combination, the two models increased the sensitivity, in classifying individuals of different ethnicities, beyond that of either one used independently or of any of the three standard European/North American models. These efforts will be instrumental in advancing personalised CVD management strategies and improving health outcomes across diverse populations. creator: Amalia Hosein creator: Valerie Stoute creator: Natasha Singh uri: https://doi.org/10.7717/peerj.17948 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hosein et al. title: Muscle synergies during the walk-run and run-walk transitions link: https://peerj.com/articles/18162 last-modified: 2024-10-22 description: BackgroundMuscular synergies could represent the patterns of muscular activation used by the central nervous system (CNS) to simplify the production of movement. Studies in walking-running transitions described up to nine synergy modules, and an earlier activation of flexor and extension ankle muscular groups compared to running or walking. Our project aims to study the behaviour of muscle synergies in different stance and swing variations of walking-running (WRT) and running-walking (RWT) transitions.MethodsTwenty-four trained men participated in this study. A variable speed protocol on a treadmill was developed to record the activity of 14 muscle during walking, running and relative transitions. The protocol was based on five ramps of 50 seconds each around ± 10 and 20% of the WRT speed. WRT and RWT were identified according to an abrupt change of the duty factor. Analysing surface electromyography using non-negative matrix factorization (NMF) we obtained synergy modules and temporal activation profiles. Alpha threshold for statistical tests set at 0.05.ResultsWe described four different transition strides, two for increasing speed transitions, and two for decreasing speed transitions. Four to six synergy modules were found in each condition. According to the maximum cosine similarity results, the two identified WRT conditions shared five modules, while the two RWT conditions shared four modules. WRT and RWT overall shared 4.33 ± 0.58 modules. The activation profiles and centres of activation revealed differences among conditions.DiscussionTransition occurred at step level, and transition strides were composed by walk-like and run-like steps. Compared with previous studies in running and walking, both transitions needed earlier activation of a comparable number of synergy modules. Synergies were affected by acceleration: during RWT the need to dissipate energy, to decrease the speed, was achieved by increasing the number of co-activating muscles. This was reflected in fewer synergy modules and different activation profiles compared to WRT. We believe that our results could be enforced in different applied fields, like clinical gait analysis, physiotherapy and rehabilitation, where plans including co-activation of specific muscular groups could be useful. Gait transitions are common in different sports, and therefore also application in training and sport science would be possible. creator: Leonardo Lagos-Hausheer creator: Samuel Vergara creator: Victor Munoz-Martel creator: Germán Pequera creator: Renata L. Bona creator: Carlo M. Biancardi uri: https://doi.org/10.7717/peerj.18162 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lagos-Hausheer et al. title: Ecological features and insecticide resistance of Aedes albopictus in Xi’an, a high-risk dengue transmission area in China link: https://peerj.com/articles/18246 last-modified: 2024-10-22 description: BackgroundDengue, a mosquito-borne viral disease, has occurred in many cities in China, and it tends to spread to higher latitudes (Huang et al., 2023). Xi’an, situated in central-west China, has witnessed an increase imported cases in the past few years, raising concerns of local dengue transmission. It is crucial to investigate the population density of Aedes albopictus and its insecticides resistance to enhance early warning of dengue fever.MethodsEight sampling sites in eight counties (YT, BL, WY, CH, YL, LN, LT, ZZ) of Xi’an city were surveyed by larval dipping and human-baited double net trap biweekly from June 2021 to September 2022. The Breteau Index (BI, number of positive containers per 100 houses) and Container Index (CI, the percentage of containers containing larvae or pupae) were used to assess larval density, and the human-baited double net trap (HDN, the number of Ae. albopictus females collected per person per hour) to indicate human bating rate (HBR). Meanwhile, the association between the meteorological factors and mosquito density was analyzed. The Ae. albopictus adult insecticides resistance was evaluated by the World Health Organization (WHO) standard resistance bioassay. Adult females were exposed to insecticide-impregnated paper for 1 h, then transferred to the recovery tube, and mortality rate was calculated after 24 h. According to the Implementation Plan for National Vector Surveillance (2016), resistance status was classified into three levels based on mortality: <80% mortality as resistant, between 80% and 98% mortality as possibly resistant, and >98% mortality as sensitive.ResultsFrom June 2021 to September 2022, a total of 1,065 houses were surveyed for water holding containers, and 99 of 430 water holding containers were checked to be positive for Ae. albopictus larvae and pupae. A total of 1,048 Ae. albopictus females were collected. The average BI, CI and HBR were 10.39, 21.41, and 11.20 female/man/hour in 2021 and 8.86, 20.86, and 11.63 f/m/h in 2022, respectively. The findings showed that the BI exceeded 5 in most months and reached above 20 in specific months. The CI varied in different months and monitoring sites, with the highest CI in August 2021 and July 2022. The discarded tires had the highest positivity rate, with up to 40.32% testing positive for Ae. albopictus larvae. The monthly average temperature showed a positive correlation with CI (r = 0.77), and the monthly BI was positively associated with CI (r = 0.93). The BI, CI, and HBR were significantly higher in the rainy season than other seasons. The bioassay results showed that the mortality rate of Ae. albopictus at the YT monitoring site was 76.92%, indicating resistance to deltamethrin. The mortality rate of Ae. Albopictus at BL, WY, CH, YL, LN, LT, and ZZ sampling sites were varying from 81.25%∼100%, suggesting possibly resistant or still sensitive to beta-cypermethrin, alpha-cypermethrin, malathion, chlorpyrifos, and propoxur. creator: Xiaogang Lei creator: Songtao Pang creator: Qipeng Zhang creator: Kun Xu creator: Wei Xue creator: Mingxu Wu creator: Xiangdong Li creator: Liangdong Jin creator: Guangshuai Li creator: Baozhong Chen uri: https://doi.org/10.7717/peerj.18246 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lei et al. title: Identifying a cis-element in PtoCP1 promoter for efficiently controlling constitutive gene expression in Populus tomentosa link: https://peerj.com/articles/18292 last-modified: 2024-10-22 description: Gene expression is regulated by transcription factors binding to cis-elements in promoters. However, efficient cis-elements for genetic engineering are rarely reported. In this study, we identified an 11 bp cis-element in the PtoCP1 promoter that drives strong constitutive gene expression in Populus tomentosa. A 2,270 bp promoter region upstream of the PtoCP1 gene’s translation start site was cloned and named ProPtoCP1. This promoter controls GUS reporter gene expression in the roots, leaves, and stems of Arabidopsis seedlings. Based on the location and density of cis-elements, the PtoCP1 promoter was divided into four fragments by 5′-end deletions. GUS staining and RT-qPCR revealed a key cis-element at −466 to −441 bp essential for gene expression. Further analysis showed that the MYB-TGACG cis-element is a positive regulator, whereas neither MYB nor TGACG alone drove gene expression. This study enhances our understanding of gene expression regulation by cis-elements and provides a valuable tool for genetic engineering. creator: Yu Peng creator: Xueqin Guo creator: Yawei Fan creator: Han Liu creator: Leiqian Sun creator: Di Liu creator: Hui Li creator: Xin Wang creator: Hongli Guo creator: Hai Lu uri: https://doi.org/10.7717/peerj.18292 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Peng et al. title: Ecological and taxonomic dissimilarity in species and higher taxa of reptiles in western Mexico link: https://peerj.com/articles/18343 last-modified: 2024-10-22 description: Reptiles are one of the most diverse groups of vertebrates in the world that are distributed in almost all ecosystems. Many of these studies have focused on exploring their diversity patterns across different environments; and recent studies on reptile alpha and beta diversity have incorporated a multifaceted approach into their analysis to have more comprehensive evaluations. This study presents an assessment of the taxonomic diversity of reptile patterns using methods that incorporate the assessment of higher taxa. Likewise, the taxonomic dissimilarities between reptile communities in the physiographic regions of the state of Jalisco were analyzed. Evaluations for the groups of snakes and lizards independently are presented. We use the taxonomic distinctiveness index that assesses the complexity of the taxonomic structure of communities through hierarchical classification above the species level to measure the relationships between taxa. The dissimilarity of the taxonomic structure in each community was also analyzed. Beta diversity partitions were performed to identify the contribution of turnover and the differences in richness. We determined that alpha diversity of species and higher taxa maintain different patterns, indicating that Jalisco presents regions with overrepresentation of reptile families and genera, as well as regions with an opposite trend. The representation of higher taxa is higher in the lizard group, although in terms of species richness snakes are the most prominent group. The turnover is the most important component at species and higher taxa, with similar values for lizards and snakes. The findings presented show that incorporating phylogenetic information about species through taxonomic relationships provides complementary information that species diversity per se, especially at the level of alpha diversity. creator: Jaime Manuel Calderón-Patrón creator: Jorge Téllez-López creator: Eréndira Canales-Gómez creator: Karen Elizabeth Peña-Joya uri: https://doi.org/10.7717/peerj.18343 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Calderón-Patrón et al. title: Spatiotemporal gait characteristics post-total hip arthroplasty and its impact on locomotive syndrome: a before-after comparative study in hip osteoarthritis patients link: https://peerj.com/articles/18351 last-modified: 2024-10-22 description: BackgroundUnderstanding the gait pattern of patients eligible for total hip arthroplasty (THA) due to hip osteoarthritis (OA) offers valuable information for improving locomotive syndrome (LS). This study aims to measure the gait patterns of THA-eligible patients using an optical motion capture system and to analyze these patterns using principal component analysis (PCA). Additionally, this study examines the relationship between THA-induced gait patterns and LS.MethodsThis before-after study included 237 patients who underwent unilateral primary THA due to hip OA. The primary outcome measures were spatiotemporal gait parameters. Secondary outcome measures included three LS risk tests: a stand-up test, a two-step test, a 25-question Geriatric Locomotive Function Scale (GLFS-25), and total clinical decision limits stages. PCA was performed using 16 spatiotemporal gait parameters collected before and three months after THA. Principal components (PC) were selected to achieve a cumulative contribution rate of 90% (0.9) or higher. Each summarized PC was compared using a paired t-test before and three months after THA. Furthermore, multiple regression analysis was conducted to determine how changes in each PC between before and three months after THA related to changes in the four LS evaluation items.ResultsPCA identified three principal components (PC1, PC2, PC3) that accounted for a cumulative contribution rate of 0.910 using 16 spatiotemporal gait parameters. When comparing before and three months after THA for all three PCs, significant differences were observed in each PC (p < 0.001), with overall walking ability and stance phase being higher three months after THA than before THA, while the asymmetry of support time was lower three months after THA. The results of multiple regression analysis revealed that PC1, PC2, and PC3 were the most influential factors in total clinical decision limits stage. For each LS risk test, the factors related to the stand-up test were identified as PC1, PC2, and PC3, while the factors related to the two-step test were identified as PC1 and PC2. The factors related to the GLFS-25 were also identified as PC1 and PC2.ConclusionsThe most important findings of this study indicate that the three PCs represent over 90% of the 16 spatiotemporal gait parameters, which are associated with total clinical decision limits stage and LS risk tests. The present results suggest that PC1 represents overall walking ability, PC2 represents the stance phase, and PC3 represents asymmetry of support time. Gait pattern characteristics, such as overall walking ability, stance phase, and asymmetry of support time, were clearly defined by these PCs. Regarding the relationship between PC and LS, all three PCs are related to total clinical decision limits stage. In addition, PC1 and PC2 related to all three LS risk tests, and PC3 related only to the stand-up test. creator: Shigeaki Miyazaki creator: Yoshinori Fujii creator: Kurumi Tsuruta creator: Saori Yoshinaga creator: Amy Hombu creator: Taro Funamoto creator: Takero Sakamoto creator: Takuya Tajima creator: Hideki Arakawa creator: Tsubasa Kawaguchi creator: Jun Nakatake creator: Etsuo Chosa uri: https://doi.org/10.7717/peerj.18351 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Miyazaki et al. title: The mitochondrial genome sequences of eleven leafhopper species of Batracomorphus (Hemiptera: Cicadellidae: Iassinae) reveal new gene rearrangements and phylogenetic implications link: https://peerj.com/articles/18352 last-modified: 2024-10-22 description: Batracomorphus is the most diverse and widely distributed genus of Iassinae. Nevertheless, there has been no systematic analysis of the genome structure and phylogenetic relationships of the genus. To determine the characteristics of the mitogenomes of Batracomorphus species as well as the phylogenetic relationships between them, we sequenced and compared the mitogenomes of 11 representative Batracomorphus species. The results revealed that the mitogenomes of the 11 Batracomorphus species exhibited highly similar gene and nucleotide composition, and codon usage compared with other reported mitogenomes of Iassinae. Of these 11 species, we found that the mitogenomes of four species were rearranged in the region from trnI-trnQ-trnM to trnQ-trnI-trnM, whereas the remaining species presented a typical gene order. The topologies of six phylogenetic trees were in agreement. Eurymelinae consistently formed paraphyletic groups. Ledrinae and Evacanthinae formed sister taxa within the same clade. Similarly, Typhlocybinae and Mileewinae consistently clustered together. All phylogenetic trees supported the monophyly of Iassinae, indicating its evolutionary distinctiveness while also revealing its sister relationship with Coelidiinae. Notably, the nodes for all species of the genus Batracomorphus were well supported and these taxa clustered into a large branch that indicated monophyly. Within this large branch, four Batracomorphus species with a gene rearrangement (trnQ-trnI-trnM) exhibited distinctive clustering, which divided the large branch into three minor branches. These findings expand our understanding of the taxonomy, evolution, genetics, and systematics of the genus Batracomorphus and broader Iassinae groups. creator: Jikai Lu creator: Jiajia Wang creator: Renhuai Dai creator: Xianyi Wang uri: https://doi.org/10.7717/peerj.18352 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lu et al. title: A Python program to merge Sanger sequences: an update link: https://peerj.com/articles/18363 last-modified: 2024-10-22 description: Gene cloning is an important step in investigating gene structure and function. To verify gene sequence, Sanger sequencing is used, which may produce several overlapping sequencing files that need to be merged before alignment to the target gene sequence is performed. Previously, we reported the Python program to Merge Sanger sequences (https://peerj.com/articles/11354/), which ran in command line and relied heavily on EMBOSS suite. In this updated version of the program, we have made several remarkable improvements. It provides a graphical user interface (GUI) written with tkinter, which is convenient and stable. It does not require users to rename the input sequences before performing merging. With regard to the implementation, the updated version utilizes Python function (Align.PairwiseAligner) to align adjacent sequences, which is more flexible (can adjust program parameter i.e., the number of first-time consecutive matching bases). The new version of the program makes merging Sanger sequences much more convenient and facilitates gene study. creator: Shiming Lin creator: Bifang Huang creator: Li-li Zhao creator: Fei Xu creator: Danni Pan creator: Xuanyang Chen creator: Shiqiang Lin uri: https://doi.org/10.7717/peerj.18363 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Exploring reported population differences in Norway lobster (Nephrops norvegicus) in the Pomo Pits region of the Adriatic Sea using genome-wide markers link: https://peerj.com/articles/17852 last-modified: 2024-10-21 description: The Norway lobster (Nephrops norvegicus) is one of the most important decapod crustacean seafood species in the Adriatic Sea. Previous research has identified significant differences in growth rates and maturation timing of Nephrops in the Pomo/Jabuka Pits area compared to other subpopulations in Adriatic fishing grounds. Here, we use 1,623 genome-wide single nucleotide polymorphisms (SNPs) to investigate whether the Pomo Pits subpopulation is genetically different from other sites in the Adriatic and neighbouring seas. We found no genetic differentiation among all sampled Adriatic sites, suggesting high gene flow between Pomo Pits Nephrops and those of surrounding areas. We also found genetic homogeneity between the Adriatic sites and single-site samples from the Aegean and Tyrrhenian Seas. However, we detected distinct genetic differentiation between all Mediterranean sites and an Atlantic site in western Scotland, which provides evidence for a phylogenetic break between the Atlantic and the Mediterranean. Our results indicate that Pomo Pits Nephrops are not genetically different from others sampled in the Adriatic and that key biological parameters in Pomo Pits Nephrops could be driven by spatial variation in fishing pressure and/or environmental factors rather than geographic isolation. creator: Tom L. Jenkins creator: Michela Martinelli creator: Charlie D. Ellis creator: Jamie R. Stevens uri: https://doi.org/10.7717/peerj.17852 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jenkins et al. title: Foot darkening with age in Spheniscus penguins: applications and functions link: https://peerj.com/articles/17937 last-modified: 2024-10-21 description: The proportions of individuals in various age classes in a population of wild animals affect population trends, behaviors, learning, and social structures. Knowledge of age structure is needed for effective conservation and management of populations. However, it is not always possible to determine the age or age class of individual animals, and hence the age structure of the population. Penguins, like most birds, cannot be aged once they molt into adult plumage. Spheniscus penguins attain adult plumage at 6 to 24 months of age, and individuals can live more than 30 years. We studied foot darkening in the four species of Spheniscus penguins to determine if age class can be determined from foot color. We compared how foot color changes with age among the four species to investigate potential functions of the darkening. We found that Spheniscus penguins have pale feet at hatching and the feet become darker with age throughout the lives of individuals. We showed that we can accurately predict the age structure of a colony of Magellanic penguins Spheniscus magellanicus, but not the ages of individual penguins, based on a sample of foot colors. The timing of foot darkening within species was consistent with foot color functioning in protection from UV radiation, and not with foot color functioning in thermoregulation. The species that breeds at the lowest latitudes and experiences the highest UV radiation (Galápagos penguins Spheniscus mendiculus) had feet that darkened at the earliest ages, and the species that breed at higher latitudes and experience less intense insolation (African S. demersus and Magellanic penguins) had feet that darkened latest. Humboldt penguins S. humboldti breed mostly at low latitudes and foot darkening was intermediate between Galápagos and Magellanic penguins. We also found that males’ feet darken somewhat earlier than females’ feet, likely because females spend more time in their nests (burrows or under vegetation) than males and have less sun exposure. We found that feet darkened in an individual over years, but not within a breeding season. The color change is a life-long process, likely an evolutionary adaptation within species, not a seasonal, temporary response to UV radiation. We propose foot darkening as a way to assess age structure in Spheniscus penguins. Foot color in a colony of Magellanic penguins can provide a rapid, noninvasive method to estimate the age structure of the colony. creator: Ginger A. Rebstock creator: K. Pearl Wellington creator: P. Dee Boersma uri: https://doi.org/10.7717/peerj.17937 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rebstock et al. title: Unraveling the dynamics of Xanthomonas’ flagella: insights into host-pathogen interactions link: https://peerj.com/articles/18204 last-modified: 2024-10-21 description: Understanding the intricate interplay between plants and bacteria is paramount for elucidating mechanisms of immunity and disease. This review synthesizes current knowledge on the role of flagella in bacterial motility and host recognition, shedding light on the molecular mechanisms underlying plant immunity and bacterial pathogenicity. We delve into the sophisticated signaling network of plants, highlighting the pivotal role of pattern recognition receptors (PRRs) in detecting conserved molecular patterns known as microbe-associated molecular patterns (MAMPs), with a particular focus on flagellin as a key MAMP. Additionally, we explore recent discoveries of solanaceous-specific receptors, such as FLAGELLIN SENSING 3 (FLS3), and their implications for plant defense responses. Furthermore, we examine the role of bacterial motility in host colonization and infection, emphasizing the multifaceted relationship between flagella-mediated chemotaxis and bacterial virulence. Through a comprehensive analysis of flagellin polymorphisms within the genus Xanthomonas, we elucidate their potential impact on host recognition and bacterial pathogenicity, offering insights into strategies for developing disease-resistant crops. This review is intended for professionals within the fields of crops sciences and microbiology. creator: Maria L. Malvino uri: https://doi.org/10.7717/peerj.18204 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Malvino title: Identification of candidate genes associating with soybean cyst nematode in soybean (Glycine max L.) using BSA-seq link: https://peerj.com/articles/18252 last-modified: 2024-10-21 description: Soybean cyst nematode disease represents the major soil-borne disease of soybean. Identifying disease-resistant genes in soybean has a substantial impact on breeding of disease-resistant crops and genetic improvement. The present work created the F2 population with the disease-resistant line H-10 and disease-susceptible line Chidou4. 30 respective F2disease-resistant and disease-susceptible individuals for forming two DNA pools for whole-genome re-sequencing were selected. As a result, a total of 11,522,230 single nucleotide polymorphism (SNPs) markers from these two parental lines and two mixed pools were obtained. Accordng to SNP-index based association analysis, there were altogether 741 genes out of 99% confidence interval, which were mainly enriched into regions of 38,524,128∼39,849,988 bp with a total length of 1.33 Mb contain 111 genes on chromosome 2, 27,821,012∼29,612,574 bp with a total length of 1.79 Mb contain 92 genes on chromosome 3, 308∼348,214 bp with a total of length 0.35 Mb contain 34 genes on chromosome 10, and 53,867,581∼58,017, 852 bp with a total length of 4.15 Mb contain 504 genes on chromosome 18. Bulk segregant analysis in F2 generations (BSA-seq) was correlated with a disease resistance interval containing 15 genes. Then, using bioinformatics analysis and differential expression analysis, five candidate genes were identified: Glyma.02G211400, Glyma.18G252800, Glyma.18G285800, Glyma.18G287400 and Glyma.18G298200. Our results provides a key basis for analyzing the soybean resistance mechanism against soybean cyst nematode and cloning soybean resistance genes. creator: Haibo Hu creator: Liuxi Yi creator: Depeng Wu creator: Litong Zhang creator: Xuechao Zhou creator: Yang Wu creator: Huimin Shi creator: Yunshan Wei creator: Jianhua Hou uri: https://doi.org/10.7717/peerj.18252 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hu et al. title: Distinct role of Klotho in long bone and craniofacial bone: skeletal development, repair and regeneration link: https://peerj.com/articles/18269 last-modified: 2024-10-21 description: Bone defects are highly prevalent diseases caused by trauma, tumors, inflammation, congenital malformations and endocrine abnormalities. Ideally effective and side effect free approach to dealing with bone defects remains a clinical conundrum. Klotho is an important protein, which plays an essential role in regulating aging and mineral ion homeostasis. More recently, research revealed the function of Klotho in regulating skeleton development and regeneration. Klotho has been identified in mesenchymal stem cells, osteoblasts, osteocytes and osteoclasts in different skeleton regions. The specific function and regulatory mechanisms of Klotho in long bone and craniofacial bone vary due to their different embryonic development, ossification and cell types, which remain unclear and without conclusion. Moreover, studies have confirmed that Klotho is a multifunctional protein that can inhibit inflammation, resist cancer and regulate the endocrine system, which may further accentuate the potential of Klotho to be the ideal molecule in inducing bone restoration clinically. Besides, as an endogenous protein, Klotho has a promising potential for clinical therapy without side effects. In the current review, we summarized the specific function of Klotho in long bone and craniofacial skeleton from phenotype to cellular alternation and signaling pathway. Moreover, we illustrated the possible future clinical application for Klotho. Further research on Klotho might help to solve the existing clinical difficulties in bone healing and increase the life quality of patients with bone injury and the elderly. creator: Xinyu Chen creator: Yali Wei creator: Zucen Li creator: Chenchen Zhou creator: Yi Fan uri: https://doi.org/10.7717/peerj.18269 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Single-cell RNA-seq analysis revealed the stemness of a specific cluster of B cells in acute lymphoblastic leukemia progression link: https://peerj.com/articles/18296 last-modified: 2024-10-21 description: BackgroundChildhood acute lymphoblastic leukemia (ALL) is a common pediatric cancer. The heterogeneous characterization of B cells in ALL progression poses new challenges to researchers. We used single-cell sequencing to explore the critical role of B cells in regulating the ALL immune microenvironment.MethodWe collected the single cell (sc) RNA-seq data of ALL and health sample from the gene expression omnibus (GEO) database, the “Seurat” and “harmony” R package was used for quality control and scRNA-seq analysis, in which the CellMarker2.0 database was used for cell type annotation. Subsequently, the FindAllMarkers function was used to identify the differentially expressed genes (DEGs) among various cell types and the DAVID database was applied for the biological process of DEGs. Then, the “inferCNV” package was used for copy number variation, regulons and cell communication were performed by SCENIC tool and CellChat package. The role of the target gene in regulating ALL progression was assessed using RT-qPCR, Transwell and scratch healing assays.ResultsWe identified nine mainly cell clusters after scRNA-seq analysis, in which the B cells had higher infiltration proportion in the ALL samples and were sub-clustered into five cell sub-groups. The B cells 1 is closely associated with cell proliferation and stemness (TNFAIP3 and KDM5B), and the significant CNV of amplification occurred on chr6 and chr21 that supported stemness of B cells1. RXRB is a key transcription factor mediated the proliferation of B cells 1, which in turn suppressed hematopoietic stem cells (HSCs) proliferation and promoted cytotoxic NK/T cells activation through diverse cell communication ways. One of the key regulators of B cells is MYC, which promotes the migration and invasive ability of cell line leukemia cell lines.ConclusionThis study reveals the stemness characteristics of B cells and their critical role in ALL progression, a finding that provides new potential directions for the development of targeted therapies against ALL. creator: Guifang Wang creator: Ensheng Zhang creator: An Chen creator: Dachuan Meng uri: https://doi.org/10.7717/peerj.18296 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Assessing acute effects of two motor-cognitive training modalities on cognitive functions, postural control, and gait stability in older adults: a randomized crossover study link: https://peerj.com/articles/18306 last-modified: 2024-10-21 description: BackgroundThe process of aging often accompanies a decline in cognitive function, postural control, and gait stability, consequently increasing the susceptibility to falls among older individuals. In response to these challenges, motor-cognitive training has emerged as a potential intervention to mitigate age-related declines.ObjectiveThis study aims to assess the acute effects of two distinct motor-cognitive training modalities, treadmill dual-task training (TMDT) and interactive motor-cognitive training (IMCT), on cognitive function, postural control, walking ability, and dual-task performance in the elderly population.MethodIn this randomized crossover study, 35 healthy elderly individuals (aged 60–75) participated in three acute training sessions involving TMDT, IMCT, and a control reading condition. Assessments of executive function, postural control, gait performance, and cognitive accuracy were conducted both before and after each session.ResultsBoth TMDT and IMCT improved executive functions. Notably, IMCT resulted in a significant enhancement in correct response rates and a reduction in reaction times in the Stroop task (p < 0.05) compared to TMDT and the control condition. IMCT also led to an increase in dual-task gait speed (p < 0.001) and showed a trend towards improved cognitive accuracy (p = 0.07). Conversely, TMDT increased postural sway with eyes open (p = 0.013), indicating a potential detriment to postural control.ConclusionThe findings suggest that IMCT holds greater immediate efficacy in enhancing cognitive function and gait stability among older adults compared to TMDT, with a lesser adverse impact on postural control. This underscores the potential of IMCT as a preferred approach for mitigating fall risk and enhancing both cognitive and physical functions in the elderly population. creator: Ran Li creator: Ping Qu creator: Xue Hu creator: Xiaojing Li creator: Haiqing Zeng creator: Binghong Gao creator: Zhiyuan Sun uri: https://doi.org/10.7717/peerj.18306 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Indigo alleviates psoriasis through the AhR/NF-κB signaling pathway: an in vitro and in vivo study link: https://peerj.com/articles/18326 last-modified: 2024-10-21 description: BackgroundPsoriasis is a chronic inflammatory skin disease. A strong association between the AhR/ NFκB axis and the inflammatory response in psoriasis. Indigo (IDG) has demonstrated significant anti-inflammatory properties. This study aimed to assess the anti-psoriatic efficacy of IDG while investigating the underlying mechanisms involved.MethodsIn the in vitro experiments, cell viability was assessed using the CCK-8. qRT-PCR was employed to measure the mRNA levels of NF-κB, TNF-α, IL-1β, AhR, and CYP1A1. Western blotting was conducted to examine alterations in cytoplasmic and nuclear AhR protein levels. Additionally, an IDG nanoemulsion (NE) cream was prepared for the in vivo experiments. A psoriasis-like skin lesion mice model was induced using IMQ (62.5 mg/day for 7 days). The severity of psoriasis was evaluated using PASI, and skin lesions were scored while epidermal thickness was assessed via HE staining. The expression of inflammatory markers, including IL-6, IL-13, IL-17A, MCP-1, and TNF-α, was detected in skin lesions using Luminex. The levels of CYP1A1, p65, and p-p65 proteins were determined by Western blotting.ResultsLPS stimulation significantly elevated TNF-α, IL-6, and NF-κB mRNA levels, which were notably reduced by IDG treatment. Additionally, IDG significantly enhanced the expression of AhR and CYP1A1 mRNA. Further investigation revealed that IDG facilitated AhR translocation from the cytoplasm to the nucleus. In the IMQ-induced psoriasis-like mouse model, IDG NE substantially ameliorated the severity of skin lesions. Moreover, IDG NE treatment reduced the upregulation of inflammatory cytokines such as IL-6, IL-17A, MCP-1, and TNF-α in IMQ-induced skin lesions. It was also observed that IDG NE treatment increased CYP1A1 protein expression while inhibiting p65 and p-p65 protein expression.ConclusionIDG emerges as a promising treatment for psoriasis, demonstrating effective therapeutic outcomes. Its mechanism of action is likely linked to the modulation of the AhR/NFκB signaling pathway. creator: Yu Lin creator: Lihong Yang creator: Dongxiang Wang creator: Haiqing Lei creator: Yuelin Zhang creator: Wen Sun creator: Jing Liu uri: https://doi.org/10.7717/peerj.18326 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lin et al. title: Sequence characteristics, expression and subcellular localization of PtCYP721A57 gene from cytochrome P450 family in Polygala tenuifolia willd link: https://peerj.com/articles/18089 last-modified: 2024-10-18 description: The Cytochrome P450 (CYP450) family is the largest enzyme protein family in plants, distributed across various organs and involved in significant catalytic activities in primary and secondary metabolic processes. In this study, we cloned the PtCYP721A57 gene, characterized its open reading frame (ORF), and conducted comprehensive analyses including physicochemical properties, evolutionary relationships, subcellular localization, prokaryotic expression, and correlation between the relative expression of different parts and the content of tenuifolin, hormones, and abiotic stress response associated with the encoded protein. The ORF of PtCYP721A57 was 1,521 bp, with a secondary structure predominantly composed of α-helices and random coils. Subcellular localization experiments confirmed the presence of PtCYP721A57 in the endoplasmic reticulum. For prokaryotic expression, we constructed the recombinant plasmid pET28a-PtCYP721A57 using pET28a as the vector, which was then transformed into BL21(DE3). Induction with Isopropyl β-D-1-thiogalactopyranoside (IPTG) at temperatures of 16 and 25 °C and varying concentrations (0.1, 0.2, 0.5, 1, 2 mM) resulted in the formation of inclusion bodies, with higher expression observed at 25 °C. Our qPCR analyses revealed that PtCYP721A57 exhibited the highest expression in the cortex of Polygala tenuifolia, followed by roots and xylem, correlating with the observed tenuifolin content distribution. Induction with abscisic acid (ABA) and chitosan (CHT) initially decreased PtCYP721A57 expression followed by a subsequent increase, peaking at 48 h. Similarly, drought stress induced a gradual increase in PtCYP721A57 expression, also peaking at 48 h. NaCl treatment for 6 h significantly upregulated PtCYP721A57 expression. In conclusion, our study provides foundational insights into the PtCYP721A57 gene in Polygala tenuifolia, laying the groundwork for further exploration of its role in the biosynthesis pathway of triterpenoid saponins. creator: Yao Luo creator: Benxiang Hu creator: Haiyue Ji creator: Yiyao Jing creator: Gang Zhang creator: Yonggang Yan creator: Bingyue Yang creator: Liang Peng uri: https://doi.org/10.7717/peerj.18089 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Luo et al. title: Biodiversity assessment and environmental risk analysis of the single line transgenic pod borer resistant cowpea link: https://peerj.com/articles/18094 last-modified: 2024-10-18 description: BackgroundThe discussion surrounding biological diversity has reached a critical point with the introduction of Nigeria’s first transgenic food crop, the pod borer-resistant (PBR) cowpea. Questions have been raised about the potential risks of the transgenic Maruca vitrata-resistant cowpea to human health and beneficial insects. Public apprehension, coupled with social activists’ calling for the removal of this crop from the nation’s food market, persists. However, there is a lack of data to counter the assertion that cultivating PBR cowpea may have adverse effects on biodiversity and the overall ecological system. This research, with its multifaceted objective of examining the environmental safety of PBR cowpea and assessing its impact on biodiversity compared to its non-transgenic counterpart, IT97KN, is of utmost importance in providing the necessary data to address these concerns.MethodsSeeds for both the transgenic PBR cowpea and its isoline were obtained from the Institute for Agricultural Research (IAR) Zaria before planting at various farm sites (Addae et al., 2020). Throughout the experiment, local cultural practices were strictly followed to cultivate both transgenic and non-transgenic cowpeas. Elaborate taxonomic keys were used to identify arthropods and other non-targeted organisms. Principal component analysis (PCA) was used to evaluate potential modifications in all ecological niches of the crops. The lmer function of the R package lme4 was used to analyze diversity indices, including Shannon, Pielou, and Simpson. The Bray–Curtis index was used to analyzed potential modifications in the dissimilarities of non-targeted organisms’ communities.ResultsExamination of ecological species abundance per counting week (CW) revealed no disruption in the biological properties of non-targeted species due to the cultivation of transgenic PBR cowpea. Analysis of species evenness and diversity indices indicated no significant difference between the fields of transgenic PBR cowpea and its isoline. Principal component analysis results demonstrated that planting PBR cowpea did not create an imbalance in the distribution of ecological species. All species and families observed during this study were more abundant in transgenic PBR cowpea fields than in non-transgenic cowpea fields, suggesting that the transformation of cowpea does not negatively impact non-targeted organisms and their communities. Evolution dynamics of the species community between transgenic and non-transgenic cowpea fields showed a similar trend throughout the study period, with no significant divergence induced in the community structure because of PBR cowpea planting. This study concludes that planting transgenic PBR cowpea positively influences biodiversity and the environment. creator: Abraham Isah creator: Rebeccah Wusa Ndana creator: Yoila David Malann creator: Onyekachi Francis Nwankwo creator: Abdulrazak Baba Ibrahim creator: Rose Suniso Gidado uri: https://doi.org/10.7717/peerj.18094 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Isah et al. title: The impact of combined application of biochar and fertilizer on the biochemical properties of soil in soybean fields link: https://peerj.com/articles/18172 last-modified: 2024-10-18 description: BackgroundHeilongjiang Province is a major soybean production area in China. To improve soil structure and increase soybean yield, this study examined the effects of combined biochar and chemical fertilizer application on the biochemical properties of soil in a maize-soybean rotation system.MethodsThe research were conducted from 2021 to 2022 at Heshan Farm Science Park in Heilongjiang Province, this field plot experiment utilized two soybean varieties, Heihe 43 (a high-protein variety) and Keshan 1 (a high-oil variety). In 2021, two plots with similar fertility levels were selected for planting soybeans and maize. In 2022, a maize-soybean rotation was implemented with five treatments: conventional fertilization (CK), increased biochar+reduced fertilizer 1 (F1+B), reduced fertilizer 1 (F1), increased biochar+reduced fertilizer 2 (F2+B), and reduced fertilizer 2 (F2). The study systematically analyzed the effects of combined biochar and chemical fertilizer application on soil chemical properties and microbial characteristics.ResultsOver 2 years, results showed that combined application effectively improved soil chemical traits. Compared to conventional fertilization (CK) and reduced fertilization (F1, F2), t he combined application of biochar and chemical fertilizer (F1+B, F2+B) increased soil pH, EC and the absolute value of zeta potential of soil surface, the CEC of soil significantly increased by 15.6–44.3%, the soil surface charge density and the soil surface charge quantity significantly increased by 16.4–73.5%. The combined application of biochar and chemical fertilizer also effectively enhanced the abundance and diversity of soil microbes. Dominant bacterial groups in soybean field soils under different treatments included Actinobacteria, Acidobacteria, Chloroflexi, and Proteobacteria; while dominant fungal groups were Ascomycota, Basidiomycota, and Mortierellomycota. Alpha and Beta diversity analyses revealed that the F1+B treatment significantly enhanced the species richness and diversity of bacteria and fungi in the soil, increasing the proportion and evenness of dominant and beneficial genera. creator: Mingcong Zhang creator: Wei Xie creator: Xingjie Zhong creator: Yuqing Wang creator: Siyan Li creator: Yanhong Zhou creator: Chen Wang uri: https://doi.org/10.7717/peerj.18172 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Bioconversion of mango peels into itaconic acid through submerged fermentation and statistical optimization of parameters through response surface methodology link: https://peerj.com/articles/18188 last-modified: 2024-10-18 description: Itaconic acid is an industrially crucial organic acid due to its broad range of applications. The main hurdle in itaconic acid production is the high cost of the substrate, i.e., pure glucose, required for the fermentation process. Pakistan annually produces about 1.7 to 1.8 million metric tonnes of mango fruit. Keeping this in view, the potential of a sugar-rich fruit by-product, i.e., mango peels, was analyzed to be used as a substrate for the biosynthesis of itaconic acid using Aspergillus niger by submerged fermentation. Different physicochemical parameters (incubation period, temperature, agitation rate, inoculum size, and pH) were optimized using the central composite design (CCD) design of response surface methodology (RSM). The maximum production of itaconic acid, i.e., 4.6 g/L, was analyzed using 10% mango peels w/v (water hydrolysate), 3 mL inoculum volume after 5 days of fermentation period at pH 3, and a temperature of 32 °C when the media was kept at a 200-rpm agitation speed. The itaconic acid extraction from mango peels was done using the solvent extraction method using n-butanol. The identification and quantification of itaconic acid produced in the study were done using the Fourier Transform Infrared Spectroscopy (FTIR) spectrum and the High-Performance Liquid Chromatography (HPLC) method. According to HPLC analysis, 98.74% purity of itaconic acid was obtained in the research. Hence, it is concluded from the results that sugar-rich mango peels can act as a promising substrate for the biosynthesis of itaconic acid. Further conditions can be optimized at the bioreactor level to meet industrial requirements. creator: Shagufta Saeed creator: Sibtain Ahmed creator: Fatima Qureshi creator: Muhammad Sheraz Yasin creator: Rida Waseem creator: Tahir Mehmood uri: https://doi.org/10.7717/peerj.18188 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Saeed et al. title: ALKBH5 modulation of ferroptosis in recurrent miscarriage: implications in cytotrophoblast dysfunction link: https://peerj.com/articles/18227 last-modified: 2024-10-18 description: BackgroundAs one of the most common and abundant internal modifications of eukaryotic mRNA, N6-methyladenosine (m6A) modifications are closely related to placental development. Ferroptosis is a newly discovered form of programmed cell death. During placental development, placental trophoblasts are susceptible to ferroptosis. However, the interactions of m6A and ferroptosis in trophoblast physiology and injury are unclear.MethodsRecurrent miscarriage (RM) was selected as the main gestational disease in this study. Published data (GSE76862) were used to analyze the gene expression profiles in patients with RM. The extent of m6A modification in total RNA of villous tissues between patients with RM and healthy controls (HC) was compared. ALKBH5 (encoding AlkB homolog 5, RNA demethylase) was selected as the candidate gene for further research. Quantitative real-time reverse transcription PCR, western blotting, and immunohistochemistry (IHC) confirmed the elevated expression of ALKBH5 in the cytotrophoblasts of patients with RM. Then, cell counting kit-8 assays, glutathione disulfide/glutathione quantification, 2′,7′-dichlorfluorescein-diacetate staining, and malonaldehyde assays were used to explore the alterations of ferroptosis-related characteristics following RAS-selective lethal (RSL3) stimulation after overexpression of ALKBH5. Thereafter, we re-analyzed the published RNA sequencing data upon knockdown of ALKBH5, combined with published tissue RNA-seq data, and FTL (encoding ferritin light chain) was identified as the ferroptosis-related gene in cytotrophoblasts of patients with RM that is regulated by ALKBH5. Finally, western blotting and IHC confirmed the increased expression of FTL in the cytotrophoblasts from patients with RM.ResultsTotal m6A levels were decreased in patients with RM. The most significant differentially m6A-related gene was ALKBH5, which was increased in patients with RM. In vitro cell experiments showed that treatment with RSL3 resulted in increased cell death and upregulated ALKBH5 expression. Overexpression of ALKBH5 alleviated RSL3-induced HTR8 cell death and caused decreased levels of intracellular oxidation products. Published transcriptome sequencing revealed that FTL was the major ferroptosis-related gene regulated by ALKBH5 in the villous tissues of patients with RM. Consistent with the expression of ALKBH5, FTL was increased by RSL3-induction and increased in patients with RM.ConclusionElevated ALKBH5 alleviated RSL3-induced cytotrophoblast cell death by promoting the expression of FTL in patients with RM. Our results supported the view that ALKBH5 is an important regulator of the ferroptosis-related etiology of RM and suggested that ALKBH5 could be responsible for epigenetic aberrations in RM pathogenesis. creator: Chuanmei Qin creator: Jiayi Wu creator: Xiaowei Wei creator: Xueqing Liu creator: Yi Lin uri: https://doi.org/10.7717/peerj.18227 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Qin et al. title: Predicting the influence of extreme temperatures on grain production in the Middle-Lower Yangtze Plains using a spatially-aware deep learning model link: https://peerj.com/articles/18234 last-modified: 2024-10-18 description: Grain crops are vulnerable to anthropogenic climate change and extreme temperature events. Despite this, previous studies have often neglected the impact of the spatio-temporal distribution of extreme temperature events on regional grain outputs. This research focuses on the Middle-Lower Yangtze Plains and aims to address this gap as well as to provide a renewed projection of climate-induced grain production variability for the rest of the century. The proposed model performs significantly superior to the benchmark multilinear grain production model. By 2100, grain production in the MLYP is projected to decrease by over 100 tons for the low-radiative-forcing/sustainable development scenario (SSP126) and the medium-radiative-forcing scenario (SSP245), and about 270 tons for the high-radiative-forcing/fossil-fueled development scenario (SSP585). Grain production may experience less decline than previously projected by studies using Representative Concentration Pathways. This difference is likely due to a decrease in coldwave frequency, which can offset the effects of more frequent heatwaves on grain production, combined with alterations in supply-side policies. Notably, the frequency of encoded heatwaves and coldwaves has a stronger impact on grain production compared to precipitation and labor indicators; higher levels of projected heatwaves frequency correspond with increased output variability over time. This study emphasizes the need for developing crop-specific mitigation/adaptation strategies against heat and cold stress amidst global warming. creator: Zijun Mu creator: Junfei Xia uri: https://doi.org/10.7717/peerj.18234 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mu and Xia title: Exploring the scale effect of nonpoint source pollution risk on water quality in Lake Basins of Central Yunnan Plateau using the Minimum Cumulative Resistance model link: https://peerj.com/articles/18247 last-modified: 2024-10-18 description: Nonpoint source (NPS) pollution has emerged as the predominant water environment issue confronting plateau lakes in central Yunnan. Quantitative analysis of the impact of NPS pollution on water quality constitutes the key to preventing and controlling water pollution. However, currently, there is a dearth of research on identifying NPS pollution risks and exploring their relationship with water quality based on the Minimum Cumulative Resistance (MCR) model in the plateau lake basins of central Yunnan. Particularly, studies on the spatial heterogeneity of the impact of NPS pollution on water quality from a multi-scale perspective are scarce. Therefore, this study focuses on three typical lake basins in the Central Yunnan Plateau–Fuxian Lake, Xingyun Lake, and Qilu Lake (the Three Lakes). Utilizing the MCR model to identify NPS pollution risks, the study analyzes seven different scales, including sub-basins, riparian buffer zones (100 m, 300 m, 500 m, 700 m, and 1,000 m) and lakeshore zones, to reveal the multi-scale effects of NPS pollution on water quality through correlation analysis. The results indicate that: (1) Over 60% of the areas in the Three Lakes Basin are at high or extremely high risk, mainly concentrated in flat terrain and around inflow rivers; (2) The area of NPS pollution from paddy field source landscape (PFSL) is greater than that from construction land source landscape (CLSL), and the high-risk areas of NPS pollution are also larger for PFSL compared to CLSL; (3) The mean resistance values of PFSL and CLSL show a significant negative correlation with monthly mean values of water quality indexes (NH3-N, TP, CODCr), with the 1,000 m riparian buffer zone scale showing the greatest correlation with most water quality indexes, especially NH3-N; (4) The correlation between the mean resistance value of CLSL and the monthly mean values of water quality indexes is significantly higher than that of PFSL, indicating a greater impact of CLSL on water quality compared to PFSL. In summary, PFSL and CLSL are the primary sources of NPS pollution in the Three Lakes Basins. The 1,000 m riparian buffer zone scale is the most sensitive to the impact of NPS pollution on water quality. This study provides scientific references for landscape pattern optimization and precise control of NPS pollution risks in the Central Yunnan Plateau lake basins and offers a new research perspective for exploring multi-scale effects of NPS pollution on water quality. creator: Li Fu creator: Xiaoliang Ma creator: Shuangyun Peng creator: Luping Gong creator: Rui Zhang creator: Bangmei Huang uri: https://doi.org/10.7717/peerj.18247 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fu et al. title: The effect of multi-directional sprint training on change-of-direction speed and reactive agility of collegiate tennis players link: https://peerj.com/articles/18263 last-modified: 2024-10-18 description: ObjectiveThe aim of this study was to evaluate the effect of random route multi-directional sprint training (MDST) compared to fixed route MDST on change-of-direction speed (CODS) and reactive agility (RA), and to investigate the correlation between CODS, RA and short-distance straight sprint speed (SDSS).MethodA total of 19 collegiate tennis players from Beijing Sport University were randomly assigned to either the random route MDST group (RR group, N = 9, age: 22.22 ± 2.22 years) or the fixed route MDST group (FR group, N = 10, age: 21.90 ± 1.66 years). Both groups completed a progressive load intervention training for 3 weeks, three times a week. The RR group’s random route, mirroring the distance and number of change-of-direction (COD) in the FR group’s fixed route, was specifically designed. The spider run, T-drill, RA test and 5-m straight line sprint test were performed before and after the intervention.ResultsBoth groups showed improved performance in the spider run (p < 0.05), T-drill (p < 0.01) and 5-m straight (p < 0.001) line sprint test after the intervention. Additionally, there was no significant difference in the improvement of CODS and SDSS between the two groups (p > 0.05). The RA of the RR and FR groups after the intervention was significantly higher than before intervention (p < 0.001), and RR group showed greater improvement in RA compared to the FR group. There was a moderate correlation between spider run and T-drill (r = 0.523), RA (r = 0.388), and no significant correlation between spider run and 5-m straight sprint (p > 0.05). T-drill was moderately correlated with RA (r = 0.347) and 5-m straight sprint (r = 0.321). RA was moderately correlated with 5-m straight sprint (r = 0.551).ConclusionThree-week multi-directional sprint training can effectively improve the change-of-direction speed, reactive agility and short-distance straight sprint speed of collegiate tennis players. And random route multi-directional sprint training has better effect on improving reactive agility. creator: Zhihui Zhou creator: Chenxi Xin creator: Yue Zhao creator: Haijun Wu uri: https://doi.org/10.7717/peerj.18263 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: A systematic review on machine learning approaches in cerebral palsy research link: https://peerj.com/articles/18270 last-modified: 2024-10-18 description: BackgroundThis review aims to explore advances in the field of cerebral palsy (CP) focusing on machine learning (ML) models. The objectives of this study is to analyze the advances in the application of ML models in the field of CP and to compare the performance of different ML algorithms in terms of their effectiveness in CP identification, classifying CP into its subtypes, prediction of abnormalities in CP, and its management. These objectives guide the review in examining how ML techniques are applied to CP and their potential impact on improving outcomes in CP research and treatment.MethodologyA total of 20 studies were identified on ML for CP from 2013 to 2023. Search Engines used during the review included electronic databases like PubMed for accessing biomedical and life sciences, IEEE Xplore for technical literature in computer, Google Scholar for a broad range of academic publications, Scopus and Web of Science for multidisciplinary high impact journals. Inclusion criteria included articles containing keywords such as cerebral palsy, machine learning approaches, outcome response, identification, classification, diagnosis, and treatment prediction. Studies were included if they reported the application of ML techniques for CP patients. Peer reviewed articles from 2013 to 2023 were only included for the review. We selected full-text articles, clinical trials, randomized control trial, systematic reviews, narrative reviews, and meta-analyses published in English. Exclusion criteria for the review included studies not directly related to CP. Editorials, opinion pieces, and non-peer-reviewed articles were also excluded. To ensure the validity and reliability of the findings in this review, we thoroughly examined the study designs, focusing on the appropriateness of their methodologies and sample sizes. To synthesize and present the results, data were extracted and organized into tables for easy comparison. The results were presented through a combination of text, tables, and figures, with key findings emphasized in summary tables and relevant graphs.ResultsRandom forest (RF) is mainly used for classifying movements and deformities due to CP. Support vector machine (SVM), decision tree (DT), RF, and K-nearest neighbors (KNN) show 100% accuracy in exercise evaluation. RF and DT show 94% accuracy in the classification of gait patterns, multilayer perceptron (MLP) shows 84% accuracy in the classification of CP children, Bayesian causal forests (BCF) have 74% accuracy in predicting the average treatment effect on various orthopedic and neurological conditions. Neural networks are 94.17% accurate in diagnosing CP using eye images. However, the studies varied significantly in their design, sample size, and quality of data, which limits the generalizability of the findings.ConclusionClinical data are primarily used in ML models in the CP field, accounting for almost 47%. With the rise in popularity of machine learning techniques, there has been a rise in interest in developing automated and data-driven approaches to explore the use of ML in CP. creator: Anjuman Nahar creator: Sudip Paul creator: Manob Jyoti Saikia uri: https://doi.org/10.7717/peerj.18270 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Nahar et al. title: Insights into water insecurity in Indigenous communities in Canada: assessing microbial risks and innovative solutions, a multifaceted review link: https://peerj.com/articles/18277 last-modified: 2024-10-18 description: Canada is considered a freshwater-rich country, despite this, several Indigenous reserves struggle with household water insecurity. In fact, some of these communities have lacked access to safe water for almost 30 years. Water quality in Canadian Indigenous reserves is influenced by several factors including source water quality, drinking water treatments applied, water distribution systems, and water storage tanks when piped water is unavailable. The objective of this multifaceted review is to spot the challenges and consequences of inadequate drinking water systems (DWS) and the available technical and microbiological alternatives to address water sanitation coverage in Indigenous reserves of Canada, North America (also known as Turtle Island). A comprehensive literature review was conducted using national web portals from both federal and provincial governments, as well as academic databases to identify the following topics: The status of water insecurity in Indigenous communities across Canada; Microbiological, chemical, and natural causes contributing to water insecurity; Limitations of applying urban-style drinking water systems in Indigenous reserves in Canada and the management of DWS for Indigenous communities in other high-income countries; and the importance of determining the microbiome inhabiting drinking water systems along with the cutting-edge technology available for its analysis. A total of 169 scientific articles matched the inclusion criteria. The major themes discussed include: The status of water insecurity and water advisories in Canada; the risks of pathogenic microorganisms (i.e., Escherichia coli and total coliforms) and other chemicals (i.e., disinfection by-products) found in water storage tanks; the most common technologies available for water treatment including coagulation, high- and low-pressure membrane filtration procedures, ozone, ion exchange, and biological ion exchange and their limitations when applying them in remote Indigenous communities. Furthermore, we reviewed the benefits and drawbacks that high throughput tools such as metagenomics (the study of genomes of microbial communities), culturomics (a high-efficiency culture approach), and microfluidics devices (microminiaturized instruments) and what they could represent for water monitoring in Indigenous reserves. This multifaceted review demonstrates that water insecurity in Canada is a reflection of the institutional structures of marginalization that persist in the country and other parts of Turtle Island. DWS on Indigenous reserves are in urgent need of upgrades. Source water protection, and drinking water monitoring plus a comprehensive design of culturally adapted, and sustainable water services are required. Collaborative efforts between First Nations authorities and federal, provincial, and territorial governments are imperative to ensure equitable access to safe drinking water in Indigenous reserves. creator: Jocelyn I. Zambrano-Alvarado creator: Miguel I. Uyaguari-Diaz uri: https://doi.org/10.7717/peerj.18277 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zambrano-Alvarado and Uyaguari-Diaz title: Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region link: https://peerj.com/articles/18282 last-modified: 2024-10-18 description: Mangrove vegetation, a threatened and unique inter-tidal ecosystem, harbours a complex and largely unexplored bacterial community crucial for nutrient cycling and the degradation of toxic pollutants in coastal areas. Despite its importance, the bacterial community composition of the gray mangrove (Avicennia marina) in the Red Sea coastal regions remains under-studied. This study aims to elucidate the structural and functional diversity of the microbiome in the bulk and rhizospheric soils associated with A. marina in the coastal areas of Ras Alshabaan-Umluj (Umluj) and Almunibrah-Al-Wajh (Al-Wajh) within the Tabuk region of Saudi Arabia. Amplicon sequencing targeting the 16S rRNA was performed using the metagenomic DNAs from the bulk and rhizospheric soil samples from Umluj and Al-Wajh. A total of 6,876 OTUs were recovered from all samples, of which 1,857 OTUs were common to all locations while the total number of OTUs unique to Al-wajh was higher (3,011 OTUs) than the total number of OTUs observed (1,324 OTUs) at Umluj site. Based on diversity indices, overall bacterial diversity was comparatively higher in rhizospheric soil samples of both sites. Comparing the diversity indices for the rhizosphere samples from the two sites revealed that the diversity was much higher in the rhizosphere samples from Al-Wajh as compared to those from Umluj. The most dominant genera in rhizosphere sample of Al-Wajh were Geminicoccus and Thermodesulfovibrio while the same habitat of the Umluj site was dominated by Propionibacterium, Corynebacterium and Staphylococcus. Bacterial functional potential prediction analyses showed that bacteria from two locations have almost similar patterns of functional genes including amino acids and carbohydrates metabolisms, sulfate reduction and C-1 compound metabolism and xenobiotics biodegradation. However, the rhizosphere samples of both sites harbour more genes involved in the utilization and assimilation of C-1 compounds. Our results reveal that bacterial communities inhabiting the rhizosphere of A. marina differed significantly from those in the bulk soil, suggesting a possible role of A. marina roots in shaping these bacterial communities. Additionally, not only vegetation but also geographical location appears to influence the overall bacterial composition at the two sites. creator: Hanaa Ghabban creator: Doha A. Albalawi creator: Amenah S. Al-otaibi creator: Dikhnah Alshehri creator: Asma Massad Alenzi creator: Marfat Alatawy creator: Hanan Ali Alatawi creator: Dalia Kamal Alnagar creator: Ahmad Bahieldin uri: https://doi.org/10.7717/peerj.18282 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ghabban et al. title: The relationship between allergic rhinitis and attention deficit hyperactivity disorder: a systematic review and meta-analysis link: https://peerj.com/articles/18287 last-modified: 2024-10-18 description: BackgroundNumerous investigations have examined the potential link between allergic rhinitis (AR) and attention deficit hyperactivity disorder (ADHD). However, some studies show no association between the two diseases. The connection between these two conditions remains inconclusive. This study aimed to conduct a meta-analysis exploring the correlation between AR and ADHD.MethodsWe conducted systematic searches of the MEDLINE, EMBASE, Cochrane Library, ERIC, PubMed, Web of Science, and CINAHL databases, up to the year 2023. Subsequently, we conducted a meta-analysis using R 4.2.2, where we computed the pooled odds ratio with a 95% confidence interval to assess the relationship between AR and ADHD within studies exhibiting similar characteristics. Statistical heterogeneity was evaluated by computing the value using the Cochrane Intervention Manual’s guidelines. Additionally, subgroup analyses were conducted by stratifying the study population according to gender, age, etc. Sensitivity analysis was performed by systematically removing individual studies.ResultsIn this systematic review, we incorporated 12 eligible studies, collectively encompassing a sample size of 530,360 participants. Within the included studies, heterogeneity was observed, and the utilization of a random-effects model demonstrated a noteworthy correlation between children with ADHD and the presence of AR. Similarly, children with AR exhibited a significant correlation with the occurrence of ADHD. We also found some relationships in subgroup analyses.ConclusionA substantial correlation is evident between AR and ADHD in children and adolescents. AR may potentially contribute as a risk factor for the onset of ADHD, and conversely, ADHD may heighten the likelihood of developing AR. creator: Qian Wang creator: Ruikun Wang creator: Mengyao Li creator: Jieqiong Liang creator: Xiaojun Zhan creator: Yingxia Lu creator: Guimin Huang creator: Qinglong Gu uri: https://doi.org/10.7717/peerj.18287 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Kinematic characterization of backhand stroke accuracy in squash based on kinematic variables between two different skill levels—a preliminary cross-sectional study link: https://peerj.com/articles/18333 last-modified: 2024-10-18 description: BackgroundThe aim of this study was to compare differences in shot placement and accuracy between national and international level squash players. Squash is a technically demanding sport and understanding the biomechanical characteristics of athletes at different levels is important for developing effective training strategies.MethodsThe study used a three-dimensional motion analysis system, a high-speed video camera, and a professional tee for biomechanical testing. Participants included national and international level squash players. The kinematic characteristics of the shoulder, elbow, and wrist joints of the upper extremity for backhand strokes, as well as the accuracy of the strokes, were analyzed to compare the differences between the two groups of athletes in terms of stroke posture and accuracy.ResultsThe kinematic analysis of the backward backhand stroke revealed that national squash players showed significant differences compared to international players in several key parameters. Specifically, national players had significantly greater trunk flexion (P = 0.018) and less shoulder medial rotation (P = 0.027). They also had lower racket velocity in the X-direction (P = 0.043). However, there were no significant differences in trunk lateral flexion (P = 0.487), trunk rotation (P = 0.293), shoulder extension/flexion (P = 0.396), elbow flexion/extension (P = 0.818), wrist flexion/extension (P = 0.177), wrist rotation (P = 0.476), racket pitch (P = 0.112), racket velocity in the Y-direction (P = 0.587), or racket velocity in the Z-direction (P = 0.327). Additionally, data for racket yaw, racket roll, and racket Vx were not provided with significant values, indicating that these parameters do not show significant differences.ConclusionInternational level players outperformed national level players in squash stroke accuracy and control. Key kinematic factors influencing accuracy include trunk forward flexion, shoulder abduction, shoulder internal rotation, and racket angles. The study recommends that coaches design training to enhance technical details and positional control to improve squash performance. creator: Rui Huang creator: Haojie Li creator: Jian Jiang creator: Zhitao Zhou creator: Chen Xiu uri: https://doi.org/10.7717/peerj.18333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Huang et al. title: Effect of alpha-linolenic acid on aminoglycoside nephrotoxicity and RhoA/Rho-kinase pathway in kidney link: https://peerj.com/articles/18335 last-modified: 2024-10-18 description: Aminoglycoside nephrotoxicity stands as a primary contributor to the development of acute intrinsic renal failure. Distinctive characteristic associated with this nephrotoxicity is the occurrence of tubular necrosis, which is why it is commonly referred to as acute tubular necrosis. Studies have demonstrated that inhibiting rhoA/rho-kinase pathway is beneficial for kidney damage induced by diabetes and renal ischemia. Comparable pathological conditions can be observed in aminoglycoside nephrotoxicity, like those found in diabetes and renal ischemia. Gentamicin, an aminoglycoside, is known to activate Rho/Rho-kinase pathway. The primary goal of this study is to explore influence of oxidative stress on this pathway by concurrently administering gentamicin and alpha-linolenic acid (ALA) possessing known antioxidant properties. To achieve this, gentamicin (100 mg kg−1) and ALA (70 mg kg−1) were administered to mice for a period of 9 days, and Rho/Rho-kinase pathway was examined by using ELISA. Administration of gentamicin to mice led to an elevation in RhoA and rho-kinase II levels, along with the activity of rho-kinase in kidneys. However, ALA effectively reversed this heightened response. ALA, known for its antioxidant properties, inhibited activation of Rho/Rho-kinase pathway induced by gentamicin. This finding suggests that gentamicin induces nephrotoxicity through oxidative stress. creator: Percin Pazarci creator: Serkan Özler creator: Halil Mahir Kaplan uri: https://doi.org/10.7717/peerj.18335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pazarci et al. title: Research progress and mitigation strategies for pod shattering resistance in rapeseed link: https://peerj.com/articles/18105 last-modified: 2024-10-17 description: BackgroundMature rapeseed pods typically shatter when harvested, resulting in approximately 8–12% yield loss. Adverse weather conditions and mechanized harvesting can diminish pod yield by up to 50%, primarily owing to delays in harvesting and mechanical collisions. The pod shatter resistance index (PSRI) assesses pod damage. Recent research focused on comparing pod shatter resistance among varieties, evaluating methods, and studying gene knockout mechanisms. However, there remains a pressing need to broaden the scope of research. In particular, it is essential to recognize that pod shatter, a complex trait, influenced by genetics, environment, agronomic practices, and harvest techniques. Future studies should integrate these factors to develop comprehensive strategies to mitigate pod shatter, enhancing rapeseed yields and agricultural mechanization. This review explores factors affecting pod shatter resistance and strategies to improve it.MethodologyScoping literature review that adhered to the methodological framework for systematic reviews was performed using search engines such as Google Scholar, Web of Science, and the Chinese National Knowledge Infrastructure. This review aimed to identify pertinent articles, which were subsequently subjected to thorough screening and evaluation. The protocol for this literature review involved the following key steps: definition of research questions, development of a search strategy, development of data extraction strategy, synthesis of the extracted data, and organization and analysis of the extracted data.ResultsThe review presents strategies for enhancing rapeseed yield during mechanized harvesting, focusing on four key areas: (i) selecting and breeding shatter-resistant varieties using DNA markers to establish a robust germplasm resource; (ii) optimizing cultivation technologies and agronomic measures to elicit favorable interactions between compact plant-type genotypes and the environment, thereby facilitating nutrient-related regulatory mechanisms of rapeseed pods to improve pod dry weight and resistance; (iii) innovating combine header design and structure to better suit rapeseed harvesting; and (iv) providing training for operators to enhance their harvesting skills. These comprehensive measures aim to minimize yield loss, increase production efficiency.ConclusionTo effectively reduce yield loss during mechanized harvesting of rapeseed, it is crucial to enhance resistance to pod shattering by addressing both internal physiological factors and external environmental conditions. This requires a holistic approach that includes genetic improvements, optimization of ecological conditions, careful cultivation management, and precise harvesting timing, along with ongoing research into traits related to machine harvesting to boost production efficiency and sustainability. creator: Li Liu creator: Hafiz Hassan Javed creator: Yue Hu creator: Yu-Qin Luo creator: Xiao Peng creator: Yong-Cheng Wu uri: https://doi.org/10.7717/peerj.18105 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Electronic cigarettes and their association with stress, depression, and anxiety among dental students in the UAE—a pilot cross sectional study link: https://peerj.com/articles/18167 last-modified: 2024-10-17 description: BackgroundDuring dental school, students may encounter stressful events that contribute to stress, anxiety, and depression; in response to these factors, some students use vaping or electronic cigarettes.ObjectiveTo evaluate the relationship between electronic cigarettes use and stress, anxiety, and depression among dental students.MethodsA cross-sectional study included 142 dental students in their preclinical, clinical, or internship year was conducted. The 142 participants were split evenly between two groups: smokers and nonsmokers. The average age of the study’s male and female participants was 21.6 years. Using the DASS 21 scale, participants were instructed to complete an electronic questionnaire assessing the association between electronic cigarettes use and stress, anxiety, and depression in smokers and nonsmokers.ResultsAccording to the findings of this study, stress, anxiety, and depression were significantly associated with electronic cigarette use. Compared to non-smokers, electronic cigarette smokers reported higher levels of severe/extremely severe depression (OR: 10.34, 95% CI: [4.23–24.1]), anxiety (OR: 13.8, 95% CI: [5.4–30.1]) and stress (OR: 27.6, 95% CI: [8.9–85.8]). Compared to males, females were 2.5 times (95% CI: [1.02–6.1]) more likely to report severe/extremely severe anxiety (P < 0.05).ConclusionThis study demonstrates a significant correlation between the use of electronic cigarettes and elevated levels of stress, anxiety, and depression among dental students in the UAE. creator: Waseem Tawba creator: Mohamed El Qadiri creator: Mustafa Al-Adhami creator: Nour Almehmeed creator: Natheer H. Al-Rawi creator: Manal Awad uri: https://doi.org/10.7717/peerj.18167 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tawba et al. title: Development of multiplex real-time PCR for simultaneous detection of common fungal pathogens in invasive mycoses link: https://peerj.com/articles/18238 last-modified: 2024-10-17 description: BackgroundFungi are common opportunistic pathogens that pose a significant threat to immunocompromised patients, particularly when late detection occurs.MethodsIn this study a multiplex real-time PCR has been developed for simultaneous detection of common fungal pathogens associated with invasive mycoses in a diagnostic setting.ResultsThe specificity of the assay was rigorously tested on 40 types of organisms (n = 65), demonstrating 100% specificity. The limit of detection was determined to be 100 pg/μl (106 copies/μl), achievable within a rapid 3-h timeframe. The PCR assay efficiency exhibited a range between 89.77% and 104.30% for each target organism, with linearity falling between 0.9780 and 0.9983.ConclusionThis multiplex real-time PCR assay holds promise for enhancing the timely and accurate diagnosis of invasive mycoses, particularly in immunocompromised patient populations. creator: Yasmin Khairani Muhammad Ismadi creator: Suharni Mohamad creator: Azian Harun uri: https://doi.org/10.7717/peerj.18238 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ismadi et al. title: Diabetes self-care and its associated factors among type 2 diabetes mellitus with chronic kidney disease patients in the East Coast of Peninsular Malaysia link: https://peerj.com/articles/18303 last-modified: 2024-10-17 description: IntroductionDiabetes self-care among diabetic patients is crucial as it determines how patients care for their illness in their daily routine for better diabetes control. This study aims to calculate the average score for diabetes self-care among patients with type 2 diabetes mellitus and chronic kidney disease and to identify factors that are associated with this score.Materials and MethodsThis cross-sectional study enrols patients over 18 years old with type 2 diabetes mellitus and chronic renal disease with an eGFR of less than 60 mL/min/1.73 m2 in a tertiary hospital in Malaysia. The Malay version of the Summary of Diabetic Self-Care Activities (SDSCA) was used to assess diabetes self-care, the Malay version of the diabetes-related distress questionnaire (DDS-17) was used to assess diabetes distress, and the Malay version of the Patient Health Questionnaire-9 (PHQ-9) was used to assess depression. Data analysis was performed using both simple and multiple linear regression models to determine the associations between variables.ResultOne hundred and seventy-six eligible patients were recruited for this study. The mean score for diabetes self-care is 3.62. The eGFR (p = 0.002) and diabetes distress (p = 0.004) are the significant associated factors for diabetes self-care among type 2 diabetes mellitus patients with chronic kidney disease.ConclusionThe mean score for diabetes self-care indicated a moderate level of self-care. The eGFR level and diabetes distress were important factors influencing diabetes self-care practices. creator: Siti Aisyah Ramli creator: Nani Draman creator: Juliawati Muhammad creator: Siti Suhaila Mohd Yusoff uri: https://doi.org/10.7717/peerj.18303 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ramli et al. title: Oral reading promotes predictive processing in Chinese sentence reading: eye movement evidence link: https://peerj.com/articles/18307 last-modified: 2024-10-17 description: BackgroundFluent sentence reading is widely acknowledged to depend on top-down contextual prediction, wherein sentential and contextual cues guide the pre-activation of linguistic representations before encountering stimuli, facilitating subsequent comprehension. The Prediction-by-Production hypothesis posits an explanation for predictive processes in language comprehension, suggesting that prediction during comprehension involves processes associated with language production. However, there is a lack of eye movement evidence supporting this hypothesis within sentence reading contexts. Thus, we manipulated reading mode and word predictability to examine the influence of language production on predictive processing.MethodsParticipants engaged in silent or oral reading of sentences containing either high or low-predictable target words. Eye movements were recorded using the Eyelink1000 eye tracker.ResultsThe findings revealed a higher skipping rate and shorter fixation times for high-predictable words compared to low-predictable ones, and for silent compared to oral reading. Notably, interactive effects were observed in the time measures (FFD, SFD, GD) during first-pass reading, indicating that word predictability effects were more pronounced during oral reading than silent reading.DiscussionThe observed pattern of results suggests that the activation of the production system enhances predictive processing during the early lexical access, providing empirical support for the Prediction-by-Production hypothesis in eye movement sentence reading situations, extending the current understanding of the timing and nature of predictions in reading comprehension. creator: Min Chang creator: Zhenying Pu creator: Jingxin Wang uri: https://doi.org/10.7717/peerj.18307 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chang et al. title: Comparative transcriptome analysis to identify the important mRNA and lncRNA associated with salinity tolerance in alfalfa link: https://peerj.com/articles/18236 last-modified: 2024-10-16 description: Salinity represents a fatal factor affecting the productivity of alfalfa. But the regulation of salinity tolerance via lncRNAs and mRNAs remains largely unclear within alfalfa. For evaluating salinity stress resistance-related lncRNAs and mRNAs within alfalfa, we analyzed root transcriptomics in two alfalfa varieties, GN5 (salinity-tolerant) and GN3 (salinity-sensitive), after treatments with NaCl at 0 and 150 mM. There were altogether 117,677 lncRNAs and 172,986 mRNAs detected, including 1,466 lncRNAs and 2,288 mRNAs with significant differential expression in GN5150/GN50, GN3150/GN30, GN50/GN30, and GN5150/GN3150. As revealed by GO as well as KEGG enrichment, some ionic and osmotic stress-associated genes, such as HPCA1-LRR, PP2C60, PP2C71, CRK1, APX3, HXK2, BAG6, and ARF1, had up-regulated levels in GN5 compared with in GN3. In addition, NaCl treatment markedly decreased CNGC1 expression in GN5. According to co-expressed network analyses, six lncRNAs (TCONS_00113549, TCONS_00399794, TCONS_00297228, TCONS_00004647, TCONS_00033214 and TCONS_00285177) modulated 66 genes including ARF1, BAG6, PP2C71, and CNGC1 in alfalfa roots, suggesting that these nine genes and six lncRNAs probably facilitated the different salinity resistance in GN5 vs. GN3. These results shed more lights on molecular mechanisms underlying genotype difference in salinity tolerance among alfalfas. creator: Gaimei Yang creator: Zhengyan Li creator: Mengru Rong creator: Rugang Yu creator: Qiting Zhang creator: Guoliang Wang creator: Zhiming Xu creator: Xueling Du creator: Xian Xu uri: https://doi.org/10.7717/peerj.18236 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Proteomic analysis of giant panda testicular tissue of different age groups link: https://peerj.com/articles/18249 last-modified: 2024-10-16 description: BackgroundThe reproductive ability of male giant pandas has been a major complicating factor in the ex-situ conservation of the species. While it is well known that the testis produces sperm and secretes androgens, a process that requires precise regulation of various proteins, at present, there has been no systematic study on the composition of proteins in the testis of the giant pandas. Therefore, this study aims to apply proteomics to explore the regulation of proteins in the testes of giant pandas.MethodsSamples from the testes of three giant pandas (22 years, 18 years, 8 days) were studied to assess the protein’s function. A label-free quantitative method was used to isolate testicular proteins from each male, 139,039 peptides and 11,435 proteins were obtained.ResultsGene Ontology (GO) annotates most of the proteins involved in the processes of protein phosphorylation, oxidation-reduction, proteolysis, and signal transduction. KEGG pathway indicated that most of the proteins were involved in the pathway of signal transduction, transport, and catabolism. The protein kinase and WD40 repeats were involved in protein-protein interaction, which in turn regulates gene expression in the testicular tissue of giant pandas.ConclusionsThis study is the first to conduct an in-depth proteomic analysis of testicular tissue in giant pandas. The results revealed the important role of proteins in testicular tissue on spermatogenesis, testosterone production, and testicular microenvironment, providing clues for further research on male giant panda reproduction. creator: Jing Peng creator: Tao Wang creator: Feiping Li creator: Shenfei Wang creator: Mengshi Zhang creator: James Ayala creator: Yuliang Liu creator: Rong Hou creator: Kailai Cai uri: https://doi.org/10.7717/peerj.18249 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Peng et al. title: Factors associated with quality of life among newly diagnosed acute ischemic stroke patients: a community-based case-control study link: https://peerj.com/articles/18266 last-modified: 2024-10-16 description: BackgroundStroke burden is expected to increase and surviving a bout of stroke may leave one with a chronic or disabling outcome decreasing significantly the quality of life of the sufferer. The study aimed to explore the association between quality of life (QoL) in stroke and non-stroke individuals in a predominantly agricultural community.MethodA community-based case-control study was conducted among 154 cases aged 18 and 75 diagnosed with incident stroke. Controls were 554 non-stroke individuals (n = 554) recruited from a community where cases resided. Cases and controls were matched for age, gender and residential area. Using a self-reported questionnaire of the World Health Organization Quality of Life (WHOQOL-BREF), socio-demographic characteristics and lifestyle habits were measured in association with QoL. Statistical analyses included multivariable logistic regression models, adjusted odds ratio (aOR) and 95% confidence interval (CI).ResultsSignificant predictors associated with low-medium QoL were having a larger waist circumference (aOR = 1.619, 95%CI [1.003–2.612]) and being a farmer (aOR = 2.976, 95%CI [1.143–7.750]) but having a current smoking habit and being male were at lesser odds with low-medium QoL (aOR = 0.381, 95%CI [0.191–0.757]) and (aOR = 0.564, 95%CI [0.323–0.985]) respectively. In all domains, women were at a higher risk of low-medium QoL while in physical health and environment domains, it was having a larger waist circumference. In both physical health and psychological domains, being married was protective to low-medium QoL so also being age 39 or younger and having a higher education in social relationship domain.ConclusionWaist circumference, occupation, smoking habit and gender are associated with low-medium QoL. Addressing the influence of such factors could create an additional therapeutic line in the primary prevention of stroke in at-risk populations. creator: Fatima Ibrahim Abdulsalam creator: Prapatsorn Somsri creator: Piyapong Papitak creator: Kittipod Tussanabunyong creator: Wisit Chaveepojnkamjorn creator: Nitikorn Phoosuwan uri: https://doi.org/10.7717/peerj.18266 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Abdulsalam et al. title: Estimation methods for the variance of Birnbaum-Saunders distribution containing zero values with application to wind speed data in Thailand link: https://peerj.com/articles/18272 last-modified: 2024-10-16 description: Thailand is currently grappling with a severe problem of air pollution, especially from small particulate matter (PM), which poses considerable threats to public health. The speed of the wind is pivotal in spreading these harmful particles across the atmosphere. Given the inherently unpredictable wind speed behavior, our focus lies in establishing the confidence interval (CI) for the variance of wind speed data. To achieve this, we will employ the delta-Birnbaum-Saunders (delta-BirSau) distribution. This statistical model allows for analyzing wind speed data and offers valuable insights into its variability and potential implications for air quality. The intervals are derived from ten different methods: generalized confidence interval (GCI), bootstrap confidence interval (BCI), generalized fiducial confidence interval (GFCI), and normal approximation (NA). Specifically, we apply GCI, BCI, and GFCI while considering the estimation of the proportion of zeros using the variance stabilized transformation (VST), Wilson, and Hannig methods. To evaluate the performance of these methods, we conduct a simulation study using Monte Carlo simulations in the R statistical software. The study assesses the coverage probabilities and average widths of the proposed confidence intervals. The simulation results reveal that GFCI based on the Wilson method is optimal for small sample sizes, GFCI based on the Hannig method excels for medium sample sizes, and GFCI based on the VST method stands out for large sample sizes. To further validate the practical application of these methods, we employ daily wind speed data from an industrial area in Prachin Buri and Rayong provinces, Thailand. creator: Natchaya Ratasukharom creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.18272 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ratasukharom et al. title: Larval growth rate is not a major determinant of adult wing shape and eyespot size in the seasonally polyphenic butterfly Melanitis leda link: https://peerj.com/articles/18295 last-modified: 2024-10-16 description: BackgroundInsects often show adaptive phenotypic plasticity where environmental cues during early stages are used to produce a phenotype that matches the environment experienced by adults. Many tropical satyrine butterflies (Nymphalidae: Satyrinae) are seasonally polyphenic and produce distinct wet- and dry-season form adults, providing tight environment-phenotype matching in seasonal environments. In studied Mycalesina butterflies, dry-season forms can be induced in the laboratory by growing larvae at low temperatures or on poor food quality. Since both these factors also tend to reduce larval growth rate, larval growth rate may be an internal cue that translates the environmental cues into the expression of phenotypes. If this is the case, we predict that slower-growing larvae would be more likely to develop a dry-season phenotype.MethodsWe performed the first experimental study on seasonal polyphenism of a butterfly in the tribe Melanitini. We measured both larval growth rate and adult phenotype (eyespot size and wing shape) of common evening brown butterflies (Melanitis leda), reared at various temperatures and on various host-plant species. We constructed provisional reaction norms, and tested the hypothesis that growth rate mediates between external cues and adult phenotype.ResultsReaction norms were similar to those found in Mycalesina butterflies. We found that both among and within treatments, larvae with lower growth rates (low temperature, particular host plants) were more likely to develop dry-season phenotypes (small eyespots, falcate wing tips). However, among temperature treatments, similar growth rates could lead to very different wing phenotypes, and within treatments the relationships were weak. Moreover, males and females responded differently, and eyespot size and wing shape were not strongly correlated with each other. Overall, larval growth rate seems to be weakly related to eyespot size and wing shape, indicating that seasonal plasticity in M. leda is primarily mediated by other mechanisms. creator: Freerk Molleman creator: M. Elizabeth Moore creator: Sridhar Halali creator: Ullasa Kodandaramaiah creator: Dheeraj Halali creator: Erik van Bergen creator: Paul M. Brakefield creator: Vicencio Oostra uri: https://doi.org/10.7717/peerj.18295 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: A pooled analysis of the incidence and mortality risk of atrial fibrillation in patients with COVID-19 link: https://peerj.com/articles/18330 last-modified: 2024-10-16 description: BackgroundThere exist serious cardiovascular complications subsequent to SARS-Cov2 infection (COVID-19); however, the association between COVID-19 and atrial fibrillation (AF) remains to be elucidated. We aimed to assess the prevalence of AF among COVID-19 patients and its associated risk of death.MethodsThe present systematic review was performed in accordance with the PRISMA guidelines. The protocol was registered with CRD42022306523. A comprehensive literature search was performed across PubMed, Embase, and Cochrane databases to identify studies reporting on the prevalence of pre-existing or new-onset fibrillation (AF), and/or the associated clinical outcomes in patients with COVID-19 from January 2020 to December 2023. The random-effect model was used to estimate the prevalence of AF and its related mortality.ResultsA total of 80 studies, including 39,062,868 COVID-19 patients, were identified in the present investigation. The prevalence rates of pre-existing AF or new-onset AF were 10.5% (95% CI [9.3–11.7%]) or 10.3% (95% CI [6.2–14.5%]), respectively. Subgroup analysis revealed a two fold higher incidence of AF in older patients (≥65 years) compared to younger patients (<65 years) (14.4% vs. 6.4%). The highest rate of AF was observed in Europeans (10.7%, 95% CI [10.2–11.2%]), followed by Northern Americans (10.0%, 95% CI [8.2–11.7%]), while Asians demonstrated a lower prevalence (2.7%, 95% CI [2.2–3.3%]). Notably, severe COVID-19 patients displayed a significantly elevated prevalence of AF at 14.l% (95% CI [13.3–14.9%]), which was approximately 2.5-fold higher than that in non-severe patients (5.2%, 95% CI [4.8–5.5%]). Both pre-existing (HR: 1.83, 95% CI [1.49–2.17]) and new-onset AF (HR: 3.47, 95% CI [2.26–5.33]) were associated with an increased mortality risk among COVID-19 patients. Furthermore, the effect on mortality risk was more significant in Asians (HR: 5.33, 95% CI [1.62–9.04]), compared to Europeans (HR: 1.68, 95% CI [1.24–2.13]) and North Americans (HR: 2.01, 95% CI [1.18–2.83]).ConclusionThis study comprehensively investigated the association between AF and COVID-19 in a real-world setting. Notably, a high prevalence of AF was observed among older individuals, severe COVID-19 patients, and in Europe and Northern America. Moreover, co-existing AF was found to be associated with an increased risk for mortality. Further investigations are warranted to improve the management and outcomes of COVID-19 patients with AF. creator: Nan-Nan Shen creator: Jia-Liang Wang creator: Xin-Wen Liu creator: Yong-Ping Fu creator: Xue-Fang Chen uri: https://doi.org/10.7717/peerj.18330 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shen et al. title: Determination of natural populations to be included in breeding program in St. John’s wort species (Hypericum perforatum L.) link: https://peerj.com/articles/18336 last-modified: 2024-10-16 description: St. John’s wort (Hypericum perforatum L.) is a medicinal and aromatic plant of rapidly increasing importance. The cultural production of this species, which is of economic importance due to its medicinal properties, is limited. One of the main ways to increase production is to develop cultivars. Thus, the homogeneous raw material required for a standard product will be provided. This study aimed to determine the characteristics of natural populations to obtain productive cultivars with high hypericin and hyperforin that can meet market demands. In addition to yield and quality values, other characteristic features of the plant such as flower diameter, petal length and petal width, which directly affect productivity, were revealed in the study. The study was conducted under field conditions for two years with three replications. Fresh flower weight among the populations varied between 30.15 and 240.28 g/plant, while the hypericin ratio varied between 51.32 and 105.31 (mg/100 g). The study determined a wide variation among the populations, and the populations with superior characteristics were included in the breeding program. creator: Fatma Uysal Bayar uri: https://doi.org/10.7717/peerj.18336 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Uysal Bayar title: Age trends of genetic parameters and genotype-by-environment interactions for growth traits of Eucalyptus urophylla clones in South-China link: https://peerj.com/articles/18218 last-modified: 2024-10-15 description: Eucalyptus urophylla S.T. Blake, an important economic tree species, is widely cultivated as a raw material source for pulpwood, veneer plywood, and sawlog timber in southern China. As a tree in multiple environments, tree-breeding programs can assess genotype by environment (G × E) interactions and identify the suitable genotype for a specific environment. G × E interactions related to growth traits and soil factors have not been adequately studied for clones of Eucalyptus urophylla and its hybrids. To examine this important question, trials containing 20 clones of E. urophylla and its hybrids were established at three sites in southern China: Shankou (SK), Tiantang (TT), and Xiniujiao (XNJ). These sites each have different soil conditions but similar geographical and climatic conditions. With the data across nearly eight years, average phenotypic trends and broad sense repeatability (H2) were modeled, G×E interactions between clones and diverse soil environments were estimated, genetic gains of clones were calculated, and the adaptabilities of E. urophylla clones in different soil environments were compared. Average survival trends for clones tended to show a moderate decrease while growth traits tended to show sharp increases with age. At the same age, sites were ordered for average survival and growth traits as TT>SK>XNJ while H2 values for growth traits by site followed the basic order TT>SK>XNJ. The H2 values for growth traits at SK tended to increase at first, platform, and then smooth with age. The H2 values for growth traits at TT were high and stable across ages, and those at XNJ tended to undulate largely at a relatively low level across ages. Genetic correlations for growth traits between any pair of sites tended to increase at first and then decrease. A genetic correlation was strong between SK and TT, intermediate between SK and XNJ, and weak between TT and XNJ. It was concluded that: (1) clones tended to be adapted better to an environment with acidic and loamy soil with a clay content of about 45.6%, the soil depth from the surface to parent material about 1.5 m, and the previous vegetation of Eucalypts. (2) The G×E interactions between clones and sites are weaker if the environmental conditions between the sites are similar, and which are stronger if the environmental conditions between the sites are different. (3) The optimum selection age for clones ranged from 1.5 to 3.5 years old, while the optimum selection growth trait is individual tree volume. creator: Guangyou Li creator: Zhaohua Lu creator: Deming Yang creator: Yang Hu creator: Jianmin Xu uri: https://doi.org/10.7717/peerj.18218 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: The effects of subjective family status and subjective school status on depression and suicidal ideation among adolescents: the role of anxiety and psychological resilience link: https://peerj.com/articles/18225 last-modified: 2024-10-15 description: BackgroundDepression and suicidal tendencies are notably prevalent among adolescents, yet few studies have revealed the impact of social status on them. This study aimed to explore the mediating and moderating effects of anxiety and psychological resilience on family status, school status, depression, and suicidal ideation.MethodsA total of 1,190 secondary school students aged 13 to 17 years (mean age: 13.57 ± 2.02 years) were evaluated depression, anxiety, and suicidal ideation using the PHQ-8 and GAD-7 questionnaires. Subjective family and school status were also assessed. Data analysis was conducted using Mplus, SPSS’s Process, and the RSA 3.0 plugin.ResultsSubjective family/school status, anxiety, psychological resilience, depression, and suicidal ideation were significantly correlated. Anxiety played a partial mediating role in the influence of subjective family status and subjective school on depression and suicidal ideation, and psychological resilience moderated the impact of anxiety on adolescent depression and suicidal ideation (βdepression = −0.05, p < 0.01; βsuicidal ideation = −0.06, p < 0.05).ConclusionsSubjective family status and school status played important roles in depression and suicidal ideation in adolescents, and anxiety and psychological resilience played mediating and moderating roles. creator: Zhan Shu creator: Shurui Chen creator: Hui Chen creator: Xianliang Chen creator: Huajia Tang creator: Jiawei Zhou creator: Yusheng Tian creator: Xiaoping Wang creator: Jiansong Zhou uri: https://doi.org/10.7717/peerj.18225 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shu et al. title: Risk factors associated with air embolism following computed tomography-guided percutaneous lung biopsy: a retrospective case-control study link: https://peerj.com/articles/18232 last-modified: 2024-10-15 description: BackgroundRetrospective analysis to identify the risk factors for air embolism following computed tomography (CT)-guided percutaneous transthoracic needle biopsy (TNB).MethodsA retrospective analysis of patients who underwent CT-TNB at The First Affiliated Hospital of Zhengzhou University and Xuzhou Cancer Hospital from January 2017 to December 2021 was performed. A total of 21 factors relevant to air embolisms were collected. Risk factors associated with air embolisms were determined by the least absolute shrinkage and selection operator (LASSO). The receiver-operator characteristic (ROC) was used to assess the ability of these factors to identify air embolisms.ResultsOf these 32,748 patients, 28 experienced air embolisms (19 at The First Affiliated Hospital of Zhengzhou University (incidence, 1.46%) and nine at Xuzhou Cancer Hospital (incidence, 0.69%); total incidence, 2.16%). Only seven patients exhibited symptoms (symptom rate, 25.00%). A total of 21 patients were asymptomatic at the time of swept-source CT. No deaths occurred. We found through univariate and multivariate analysis that eight out of these 21 factors are associated with the occurrence of air embolism. The area under the ROC curve was 0.721, indicating good predictive power (P < 0.05).ConclusionCough during the procedure, hemoptysis during the procedure, the distance between the mass and the pulmonary vein, the presence of a cavity in the lesion, lesion location, number of samples, abnormalities in the patient’s coagulation mechanism, and the puncture position may be the risk factors for air embolism in CT-TNB. creator: Tingting Wu creator: Shuai Li creator: Mengyu Gao creator: Bin Yang creator: Yufeng Wang creator: Tao Xie uri: https://doi.org/10.7717/peerj.18232 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Wu et al. title: Heme oxygenase-1: potential therapeutic targets for periodontitis link: https://peerj.com/articles/18237 last-modified: 2024-10-15 description: Periodontitis is one of the most prevalent inflammatory disease worldwide, which affects 11% of the global population and is a major cause of tooth loss. Recently, oxidative stress (OS) has been found to be the pivital pathophysiological mechanism of periodontitis, and overactivated OS will lead to inflammation, apoptosis, pyroptosis and alveolar bone resorption. Interestingly, heme oxygenase-1 (HO-1), a rate-limiting enzyme in heme degradation, can exert antioxidant activites through its products—carbon monoxide (CO), Fe2+, biliverdin and bilirubin in the inflammatory microenvironment, thus exhibiting anti-inflammatory, anti-apoptotic, anti-pyroptosis and bone homeostasis-regulating properties. In this review, particular focus is given to the role of HO-1 in periodontitis, including the spatial-temporal expression in periodental tissues and pathophysiological mechanisms of HO-1 in periodontitis, as well as the current therapeutic applications of HO-1 targeted drugs for periodontitis. This review aims to elucidate the potential applications of various HO-1 targeted drug therapy in the management of periodontitis, investigate the influence of diverse functional groups on HO-1 and periodontitis, and pave the way for the development of a new generation of therapeutics that will benefit patients suffering from periodontitis. creator: Weiwei Lv creator: Shichen Hu creator: Fei Yang creator: Dong Lin creator: Haodong Zou creator: Wanyan Zhang creator: Qin Yang creator: Lihua Li creator: Xiaowen Chen creator: Yan Wu uri: https://doi.org/10.7717/peerj.18237 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lv et al. title: Interaction of CTCF and CTCFL in genome regulation through chromatin architecture during the spermatogenesis and carcinogenesis link: https://peerj.com/articles/18240 last-modified: 2024-10-15 description: The zinc finger protein CTCF is ubiquitously expressed and is integral to the regulation of chromatin architecture through its interaction with cohesin. Conversely, CTCFL expression is predominantly restricted to the adult male testis but is aberrantly expressed in certain cancers. Despite their distinct expression patterns, the cooperative and competitive mechanisms by which CTCF and CTCFL regulate target gene expression in spermatocytes and cancer cells remain inadequately understood. In this review, we comprehensively examine the literature on the divergent amino acid sequences, target sites, expression profiles and functions of CTCF and CTCFL in normal tissues and cancers. We further elucidate the mechanisms by which CTCFL competitively or cooperatively binds to CTCF target sites during spermatogenesis and carcinogenesis to modulate chromatin architecture. We mainly focus on the role of CTCFL in testicular and cancer development, highlighting its interaction with CTCF at CTCF binding sites to regulate target genes. In the testis, CTCF and CTCFL cooperate to regulate the expression of testis-specific genes, essential for proper germ cell progression. In cancers, CTCFL overexpression competes with CTCF for DNA binding, leading to aberrant gene expression, a more relaxed chromatin state, and altered chromatin loops. By uncovering the roles of CTCF and CTCFL in spermatogenesis and carcinogenesis, we can better understand the implications of aberrant CTCFL expression in altering chromatin loops and its contribution to disease pathogenesis. creator: Xin Tong creator: Yang Gao creator: Zhongjing Su uri: https://doi.org/10.7717/peerj.18240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tong et al. title: Expression of neutrophil extracellular trap-related proteins and its correlation with IL-17 and TNF-α in patients with oral lichen planus link: https://peerj.com/articles/18260 last-modified: 2024-10-15 description: BackgroundNeutrophil extracellular traps (NETs) are produced by polymorphonuclear neutrophils (PMNs) stimulated by interleukin-17 (IL-17) and tumor necrosis factor α (TNF-α). However, the level and role of NETs in oral lichen planus (OLP) remain poorly understood.ObjectiveThis study aimed to investigate the expression of NETs in OLP and explore the correlation between NETs and the levels of IL-17 and TNF-α.MethodsThe expression and distribution of NET-related proteins in tissue samples from each group were assessed using hematoxylin-eosin (HE) staining and immunofluorescence (IF). Additionally, the expression of NET-related proteins in peripheral blood samples from each group was evaluated using cell IF technique and fluorescence spectrophotometry. The relative formation level of NETs in each group was determined by fluorescence spectrophotometry via plasma co-culture. Furthermore, the levels of inflammatory cytokines IL-17 and TNF-α in plasma and culture supernatant were measured using enzyme-linked immunosorbent assay (ELISA).ResultsNET-related proteins were located in the subepithelial and lamina propria layers of OLP lesions. OLP had significantly higher expression of NET-related proteins in lesion tissues and peripheral blood compared to the healthy control (HC) group (p < 0.05). The rate of NETs formation in the erosive-stage OLP (EOLP) group was significantly higher than that in the HC group (p < 0.05), in contrast, no significant increase was observed in the non-erosive OLP (NEOLP) group (p > 0.05). Furthermore, the levels of IL-17 and TNF-α in the EOLP group were significantly elevated compared to those in the NEOLP group and HC group (p < 0.05), while the levels in the NEOLP group did not significantly differ from those in the HC group (p > 0.05). The rate of NETs formation showed a positive correlation with the levels of IL-17 and TNF-α in plasma.ConclusionThe expression of NET-related proteins was upregulated in OLP lesion tissues and peripheral blood. Elevated levels of IL-17 and TNF-α in peripheral blood plasma positively correlated with the rate of NETs formation, suggesting that IL-17 and TNF-α mediate the formation of NETs in OLP patients, and may thereby contribute to the development of OLP. creator: Juehua Cheng creator: Chenyu Zhou creator: Jia Liu creator: Yanlin Geng creator: Lin Liu creator: Yuan Fan uri: https://doi.org/10.7717/peerj.18260 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cheng et al. title: Nervous system guides behavioral immunity in Caenorhabditis elegans link: https://peerj.com/articles/18289 last-modified: 2024-10-15 description: Caenorhabditis elegans is a versatile model organism for exploring complex biological systems. Microbes and the external environment can affect the nervous system and drive behavioral changes in C. elegans. For better survival, C. elegans may develop behavioral immunity to avoid potential environmental pathogens. However, the molecular and cellular mechanisms underlying this avoidance behavior are not fully understood. The dissection of sensorimotor circuits in behavioral immunity may promote advancements in research on the neuronal connectome in uncovering neuronal regulators of behavioral immunity. In this review, we discuss how the nervous system coordinates behavioral immunity by translating various pathogen-derived cues and physiological damage to motor output in response to pathogenic threats in C. elegans. This understanding may provide insights into the fundamental principles of immune strategies that can be applied across species and potentially contribute to the development of novel therapies for immune-related diseases. creator: Yu Wang creator: Xuehong Sun creator: Lixiang Feng creator: Kui Zhang creator: Wenxing Yang uri: https://doi.org/10.7717/peerj.18289 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: New insights into the Devonian sea spiders of the Hunsrück Slate (Arthropoda: Pycnogonida) link: https://peerj.com/articles/17766 last-modified: 2024-10-14 description: BackgroundThe sea spiders (Pycnogonida Latreille, 1810) of the Hunsrück Slate (Lower Devonian, ~400 million years ago) are iconic in their abundance, exquisite pyritic preservation, and in their distinctive body plan compared to extant sea spiders (Pantopoda Gerstäcker, 1863). Consequently, the Hunsrück sea spiders are important in understanding the deep evolutionary history of Pycnogonida, yet they remain poorly characterised, impacting upon attempts to establish a time-calibrated phylogeny of sea spiders.MethodsHere, we investigated previously described and new material representing four of the five Hunsrück pycnogonids: Flagellopantopus blocki Poschmann & Dunlop, 2006; Palaeoisopus problematicus Broili, 1928; Palaeopantopus maucheri Broili, 1929; and Pentapantopus vogteli Kühl, Poschmann & Rust, 2013; as well as a few unidentified specimens. Using X-ray microtomography and Reflectance Transformation Imaging, we describe new fossils, provide evidence for newly revealed anatomical features, and interpret these data in comparison to extant species. We also reinterpret the previously published illustration of the (probably lost) holotype of Palaeothea devonica Bergström, Stürmer & Winter, 1980.ResultsWe provide the first detailed description of the cephalic appendages of Palaeoisopus problematicus and revise the interpretation of the organisation of its ocular tubercle. Furthermore, we provide new insights into the structure of the legs and the proboscis of Palaeopantopus maucheri, the first description of the body of Flagellopantopus blocki and describe a new specimen of Pentapantopus vogteli, demonstrating that it had eight legs, in contrast to previous interpretations. We argue that, contrary to previous suggestions, Palaeothea devonica probably had a different body plan from extant pantopods. We discuss the ecological traits of the Hunsrück pycnogonids based on their morphological adaptations, and conclude that there is no compelling evidence of Pantopoda in the Devonian. Through comparative interpretation of the legs as well as general morphology, we can divide the Hunsrück pycnogonids into two morphological groups, while Pantopoda constitutes a third morphological group. creator: Romain Sabroux creator: Russell J. Garwood creator: Davide Pisani creator: Philip C. J. Donoghue creator: Gregory D. Edgecombe uri: https://doi.org/10.7717/peerj.17766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sabroux et al. title: Predicting maintenance lithium response for bipolar disorder from electronic health records—a retrospective study link: https://peerj.com/articles/17841 last-modified: 2024-10-14 description: BackgroundOptimising maintenance drug treatment selection for people with bipolar disorder is challenging. There is some evidence that clinical and demographic features may predict response to lithium. However, attempts to personalise treatment choice have been limited.MethodWe aimed to determine if machine learning methods applied to electronic health records could predict differential response to lithium or olanzapine. From electronic United Kingdom primary care records, we extracted a cohort of individuals prescribed either lithium (19,106 individuals) or olanzapine (12,412) monotherapy. Machine learning models were used to predict successful monotherapy maintenance treatment, using 113 clinical and demographic variables, 8,017 (41.96%) lithium responders and 3,831 (30.87%) olanzapine responders.ResultsWe found a quantitative structural difference in that lithium maintenance responders were weakly predictable in our holdout sample, consisting of the 5% of patients with the most recent exposure. Age at first diagnosis, age at first treatment and the time between these were the most important variables in all models.DiscussionEven if we failed to predict successful monotherapy olanzapine treatment, and so to definitively separate lithium vs. olanzapine responders, the characterization of the two groups may be used for classification by proxy. This can, in turn, be useful for establishing maintenance therapy. The further exploration of machine learning methods on EHR data for drug treatment selection could in the future play a role for clinical decision support. Signals in the data encourage further experiments with larger datasets to definitively separate lithium vs. olanzapine responders. creator: Joseph F. Hayes creator: Fehmi Ben Abdesslem creator: Sandra Eloranta creator: David P. J. Osborn creator: Magnus Boman uri: https://doi.org/10.7717/peerj.17841 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hayes et al. title: Optimization of ultrasonic-assisted debittering of Ganoderma lucidum using response surface methodology, characterization, and evaluation of antioxidant activity link: https://peerj.com/articles/17943 last-modified: 2024-10-14 description: BackgroundGanoderma lucidum (G. lucidum) has gained increasing attention as a potential health care product and food source. However, the bitter taste of G. lucidum has limited its development and utilization for the food industry.MethondsThe response surface methodology was employed to optimize the inclusion conditions for the debittering of G. lucidum. The effects of 2-hydroxypropyl-β-cyclodextrin concentration (12–14 g/mL), ultrasound temperature (20–40 °C and host—guest ratio (1:1–2:1) on response variables were studied. The physical characteristics of inclusion complexes prepared through spray drying and freeze drying were analyzed. The antioxidant activity of the different treated samples was subsequently investigated.ResultsStudy results showed that, in comparison to the control group, the inclusion solution displayed a significantly enhanced taste profile under optimal processing conditions, exhibiting an 80.74% reduction in bitterness value. Fourier transform infrared spectroscopy (FTIR) and proton nuclear magnetic resonance (NMR) studies indicated the successful formation of inclusion compounds. The moisture content and bulk density of spray-dried powder were found to be significantly superior to those of freeze-dried powder (p < 0.05). In comparison to the diluted solution, the inclusion liquid demonstrated a 20.27%, 30.01% and 36.55% increase in ferric ion reducing antioxidant power (FRAP), hydroxyl radical scavenging and 2,2-diphenyl-1-picrylhydrazyl radical (DPPH) scavenging respectively. Further, the DPPH clearance of microencapsulated powder was not significantly different from that of tocopherol at a concentration of 25 mg/mL.ConclusionsIn summary, the study provides theoretical basis and methodological guidance to eliminate the bitterness of G. lucidum, and therefore provide potential options to the use of G. lucidum as a food source. creator: Shuting Chen creator: Shiying Song creator: Yumei Tan creator: Shengling He creator: Xiyi Ren creator: Zhu Li creator: Yongxiang Liu uri: https://doi.org/10.7717/peerj.17943 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Effect of environmental DNA sampling resolution in detecting nearshore fish biodiversity compared to capture surveys link: https://peerj.com/articles/17967 last-modified: 2024-10-14 description: Sampling and sequencing marine environmental DNA (eDNA) provides a tool that can increase our ability to monitor biodiversity, but movement and mixing of eDNA after release from organisms before collection could affect our inference of species distributions. To assess how conditions at differing spatial scales influence the inferred species richness and compositional turnover, we conducted a paired eDNA metabarcoding and capture (beach seining) survey of fishes on the coast of British Columbia. We found more taxa were typically detected using eDNA compared to beach seining. eDNA identified more taxa with alternative habitat preferences, and this richness difference was greater in areas of high seawater movement, suggesting eDNA has a larger spatial grain influenced by water motion. By contrast, we found that eDNA consistently missed low biomass species present in seining surveys. Spatial turnover of communities surveyed using beach seining differed from that of the eDNA and was better explained by factors that vary at small (10–1000s meters) spatial scales. Specifically, vegetation cover and shoreline exposure explained most species turnover from seining, while eDNA turnover was not explained by those factors and showed a distance decay pattern (a change from 10% to 25% similarity from 2 km to 10 km of distance), suggesting unmeasured environmental variation at larger scales drives its turnover. Our findings indicate that the eDNA sample grain is larger than that of capture surveys. Whereas seining can detect differences in fish distributions at scales of 10s–100s of meters, eDNA can best summarize fish biodiversity at larger scales possibly more relevant to regional biodiversity assessments. creator: Ben Millard-Martin creator: Kate Sheridan creator: Evan Morien creator: Matthew A. Lemay creator: Margot Hessing-Lewis creator: Rute B.G. Clemente-Carvalho creator: Jennifer M. Sunday uri: https://doi.org/10.7717/peerj.17967 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Millard-Martin et al. title: Saliva as a diagnostic tool in soccer: a scoping review link: https://peerj.com/articles/18032 last-modified: 2024-10-14 description: BackgroundA high-performance sport like soccer requires training strategies that aim to reach peak performance at the right time for the desired competitions. Thus, the investigation of biochemical markers in saliva is a tool that is beginning to be used in athletes within the physical training process. There is still no evidence on universal saliva collection and analysis protocols in soccer. This review aims to map the use of saliva as a tool for analyzing athletic performance in soccer, from the biomarkers used to the validated protocols for these analyses.MethodsA broad systematic literature search was carried out in the electronic databases Web of Science, Livivo, Scopus, PubMed, LILACS and gray literature (Google Scholar and ProQuest). Two reviewers selected the studies and extracted data on the type of salivary collection used, the salivary biomarker evaluated and monitored.ResultsNinety-three articles were included. The most frequently analyzed salivary biomarkers were cortisol (n = 53), testosterone (n = 35), secretory immunoglobulin A (SIgA) (n = 33), salivary alpha amylase (n = 7), genetic polymorphisms (n = 4) and miRNAs (n = 2). The results of the studies indicated beneficial effects in monitoring salivary biomarkers in the assessment of sports performance, although most studies did not include a control group capable of comparison. Salivary collection and analysis protocols were varied and commonly not reported.ConclusionsThis scoping review provides a comprehensive overview of the current landscape of salivary biomarker research in soccer. The findings underscore the importance of these biomarkers in assessing athletes’ physiological responses and overall well-being. Future research should focus on refining methodologies, exploring additional biomarkers, and investigating the practical implications of salivary biomarker monitoring in soccer and other sports. creator: Joyce Ferreira creator: Manuel Jimenez creator: Agatha Cerqueira creator: Joana Rodrigues da Silva creator: Bruno Souza creator: Lucas Berard creator: Andre L.L. Bachi creator: Naile Dame-Teixeira creator: Neide Coto creator: Debora Heller uri: https://doi.org/10.7717/peerj.18032 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ferreira et al. title: Evaluation of shaping ability, apical transportation and centering ratio of T-Endo Must, WaveOne Gold, and Trunatomy in resin blocks link: https://peerj.com/articles/18088 last-modified: 2024-10-14 description: PurposeThis study aimed to compare the shaping abilities of different nickel-titanium file systems.Materials and MethodsSixty-six j-shaped resin blocks were randomly divided into three groups (n = 22): Group T-Endo MUST (TE), Group WaveOne (W), Group TruNatomy (TR). After canal preparation, the amount of material removed from the canal, the centering ratio of the file systems, the direction and amount of canal transportation, and shaping errors were evaluated. Shaping time was calculated. Data of shaping time were analyzed with ANOVA and Tamhane test. Data on the shaping ability were analyzed with two- and three-way ROBUST ANOVA. The significance level was set at p = 0.05.ResultsThere was a statistically significant difference between all groups for shaping time (p < 0.001). There was a statistically significant difference between groups for the total amount of material removed (p < 0.001). The directions of canal transportation were the inner surface of the curvature for W and TR and the outer for TE. There was no statistically significant difference between the groups for the amount of transportation (p > 0.05). The centering ratio of TE and W was statistically higher than TruNatomy (p < 0.001).ConclusionsTruNatomy removed the least material that supported the minimally invasive endodontic approach. All file systems caused similar transportation and did not change the original canal shape. creator: Aybüke Karaca Sakallı creator: Mügem Aslı Ekici uri: https://doi.org/10.7717/peerj.18088 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Karaca Sakallı and Ekici title: Wind energy and insects: reviewing the state of knowledge and identifying potential interactions link: https://peerj.com/articles/18153 last-modified: 2024-10-14 description: In 2023 the wind industry hit a milestone of one terawatt of installed capacity globally. That amount is expected to double within the next decade as billions of dollars are invested in new wind projects annually. Wildlife mortality is a primary concern regarding the proliferation of wind power, and many studies have investigated bird and bat interactions. Little is known about the interactions between wind turbines and insects, despite these animals composing far more biomass than vertebrates. Turbine placement, coloration, shape, heat output, and lighting may attract insects to turbines. Insects attract insectivorous animals, which may be killed by the turbines. Compiling current knowledge about these interactions and identifying gaps in knowledge is critical as wind power grows rapidly. We reviewed the state of the literature investigating insects and wind energy facilities, and evaluated hypotheses regarding insect attraction to turbines. We found evidence of insect attraction due to turbine location, paint color, shape, and temperature output. We provide empirical data on insect abundance and richness near turbines and introduce a risk assessment tool for comparing wind development with suitable climate for insects of concern. This understudied topic merits further investigation as insects decline globally. Compiling information will provide a resource for mitigation and management strategies, and will inform conservation agencies on what insects may be most vulnerable to the expansion of wind technologies. creator: Michelle Weschler creator: Lusha Tronstad uri: https://doi.org/10.7717/peerj.18153 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Weschler and Tronstad title: The effects of resistance training to near volitional failure on motor unit recruitment during neuromuscular fatigue link: https://peerj.com/articles/18163 last-modified: 2024-10-14 description: BackgroundIt is unclear whether chronically training close to volitional failure influences motor unit recruitment strategies during fatigue.PurposeWe compared resistance training to near volitional failure vs. non-failure on individual motor unit action potential amplitude (MUAP) and surface electromyographic excitation (sEMG) during fatiguing contractions.MethodsNineteen resistance-trained adults (11 males, 8 females) underwent 5 weeks (3×/week) of either low repetitions-in-reserve (RIR; 0–1 RIR) or high RIR training (4–6 RIR). Before and after the intervention, participants performed isometric contractions of the knee extensors at 30% of maximal peak torque until exhaustion while vastus lateralis sEMG signals were recorded and later decomposed. MUAP and sEMG excitation for the vastus lateralis were quantified at the beginning, middle, and end of the fatigue assessment.ResultsBoth training groups improved time-to-task failure (mean change = 43.3 s, 24.0%), with no significant differences between low and high RIR training groups (low RIR = 28.7%, high RIR = 19.4%). Our fatigue assessment revealed reduced isometric torque steadiness and increased MUAP amplitude and sEMG excitation during the fatiguing task, but these changes were consistent between groups.ConclusionBoth low and high RIR training improved time-to-task failure, but resulted in comparable motor unit recruitment during fatiguing contractions. Our findings indicate that both low and high RIR training can be used to enhance fatiguability among previously resistance-trained adults. creator: Jonathan P. Beausejour creator: Kevan S. Knowles creator: Jason I. Pagan creator: Juan P. Rodriguez creator: Daniel Sheldon creator: Bradley A. Ruple creator: Daniel L. Plotkin creator: Morgan A. Smith creator: Joshua S. Godwin creator: Casey L. Sexton creator: Mason C. McIntosh creator: Nicholas J. Kontos creator: Cleiton A. Libardi creator: Kaelin Young creator: Michael D. Roberts creator: Matt S. Stock uri: https://doi.org/10.7717/peerj.18163 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Beausejour et al. title: Characterization of the complete mitochondrial genome of the Sunda stink-badger (Mydaus javanensis) from the island of Borneo link: https://peerj.com/articles/18190 last-modified: 2024-10-14 description: BackgroundThe Mephitidae is a family of skunks and stink-badgers that includes 12 extant species in four genera, namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only genus within Mephitidae found outside the American continent, with its distribution limited to the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e., javanensis and marchei. Currently, complete mitogenomes are unavailable for either species. Here, we present the characterization of the first complete mitogenome for the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.MethodsMuscle tissue was obtained and the DNA was sequenced using a combination of Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome was annotated with MITOS and manually checked for accuracy. A circular map of the mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were aligned with reference sequences from GenBank and used for the construction of phylogenetic trees (maximum liklihood (ML) and Bayesian inference (BI)). Additionally, due to the lack of available complete genomes in public databases, we constructed another tree with the cyt b gene.ResultsThe complete circular mitogenome was 16,391 base pairs in length. It comprises the typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR) and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly clustered the species with other members of the Mephitidae family but were unique enough to set it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the species. creator: Vijay Kumar Subbiah creator: Chrishen Robert Gomez creator: Dexter Miller Robben creator: Ranjita Subramaniam creator: Andrew James Hearn uri: https://doi.org/10.7717/peerj.18190 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Subbiah et al. title: UV-B irradiation promotes anthocyanin biosynthesis in the leaves of Lycium ruthenicum Murray link: https://peerj.com/articles/18199 last-modified: 2024-10-14 description: Anthocyanins are the most valuable pigments in Lycium ruthenicum Murray (L. ruthenicum). Although ultraviolet-B (UV-B) irradiation is a key environmental factor influencing anthocyanin biosynthesis in L. ruthenicum, the deep molecular mechanism remains unclear. Herein, we examined the changes in the total anthocyanin content and transcriptomic characteristics of L. ruthenicum leaves following UV-B irradiation treatment. The results showed a twofold increase in anthocyanin content in the leaves of L. ruthenicum after the treatment. The transcriptome analysis showed that the expression of 24 structural genes identified in the anthocyanin synthesis pathway was up-regulated. In particular, F3’H (Unigene0009145) and C4H (Unigene0046607) exhibit notable up-regulation, suggesting their potential roles in anthocyanin synthesis. Protein interaction network results revealed that MYB1 (Unigene0047706) had the highest connectivity, followed by bHLH (Unigene0014085). Additionally, UVR8 (Unigene0067978) and COP1 (Unigene0008780) were found to be highly involved in UV-B signal transduction. These findings provide new insights into the genetic and biochemical mechanisms that regulate anthocyanin production, and could guide agricultural practices to reduce environmental impacts and improve crop yield and quality. creator: Shengrong Chen creator: Yunzhang Xu creator: Weimin Zhao creator: Guomin Shi creator: Shuai Wang creator: Tao He uri: https://doi.org/10.7717/peerj.18199 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Exploring the density and morphology of coconut structures at two locations: a time-based analysis using computer tomography link: https://peerj.com/articles/18206 last-modified: 2024-10-14 description: BackgroundThe study aimed to observe the internal structure of coconuts from two locations (coastal and non-coastal) using computed tomography (CT).MethodsSeventy-six mature coconuts were collected from Wenchang and Ding’an cities in Hainan Province. These coconuts were scanned four times using CT, with a two-week interval between each scan. CT data were post-processed to reconstruct two-dimensional slices and three-dimensional models. The density and morphological parameters of coconut structures were measured, and the differences in these characteristics between the two groups and the changes over time were analyzed.ResultsTime and location had interactive effects on CT values of embryos, solid endosperms and mesocarps, morphological information such as major axis of coconut, thickness of mesocarp, volume of coconut water and height of bud (p < 0.05).ConclusionsPlanting location and observation time can affect the density and morphology of some coconut structures. creator: Shenghuang Lin creator: Chengxu Sun creator: Li’an Luo creator: Mengxing Huang creator: JeromeJeyakumar John Martin creator: Hongxing Cao creator: Jinyue Hu creator: Zhiming Bai creator: Zhanping He creator: Yu Zhang creator: Jing Chen uri: https://doi.org/10.7717/peerj.18206 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Effects of different ratios of nitrogen base fertilizer to topdressing on soil nitrogen form and enzyme activity in sugar beet under shallow drip irrigation link: https://peerj.com/articles/18219 last-modified: 2024-10-14 description: Sugar beets account for 30% of global sugar production each year, and their byproducts are an important source of bioethanol and animal feed. Sugar beet is an important cash crop in Inner Mongolia, China. To achieve high yields and sugar content, it is essential to supply nitrogen fertilizer in accordance with the growth characteristics of sugar beet, thereby enhancing the efficiency of nitrogen fertilizer utilization. A two-year experiment was carried out in the experimental field of the Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences. The impact of varying ratios of nitrogen-based fertilizer to topdressing on nitrate nitrogen and ammonium nitrogen levels in the 20–60 cm soil layer, as well as the activities of protease, urease, catalase, and sucrose in the 20–40 cm soil layer were investigated during the rapid leaf growth period and root and sugar growth period. Results indicated that different ratios of nitrogen-based fertilizer to topdressing significantly influenced the levels of nitrate nitrogen and ammonium nitrogen, and the activities of protease and urease in the 0–20 cm soil layer, with these effects diminishing as soil depth increased. The activities of catalase and sucrose were minimally impacted. Nitrogen was applied at 150 kg/ha during the growth period of sugar beet, according to the growth characteristics of sugar beet to maximize nitrogen utilization efficiency. Topdressing was completed with irrigation at the rapid growth stage. The nitrogen-based fertilizer to topdressing ratio of 6:4 resulted in optimal crop yield and sugar yield of sugar beet under shallow drip irrigation. Additionally, the activities of protease and urease in different soil treatments were significantly different, and the activities of protease and urease in the 0–40 cm soil layer were identified as useful soil physiological indicators for nitrogen utilization in sugar beet. creator: Zhi Li creator: Caiyuan Jian creator: Xiaoxia Guo creator: Lu Tian creator: Kang Han creator: Yinghao Li creator: Peng Zhang creator: Dejuan Kong creator: Huimin Ren creator: Alehesi Jiaerdemulati creator: Zhenzhen Wang creator: Huiyu Liu creator: Chunyan Huang creator: Wenbin Su uri: https://doi.org/10.7717/peerj.18219 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens link: https://peerj.com/articles/18229 last-modified: 2024-10-14 description: Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity. creator: Mihaela C. Ion creator: Caitlin C. Bloomer creator: Tudor I. Bărăscu creator: Francisco J. Oficialdegui creator: Nathaniel F. Shoobs creator: Bronwyn W. Williams creator: Kevin Scheers creator: Miguel Clavero creator: Frédéric Grandjean creator: Marc Collas creator: Thomas Baudry creator: Zachary Loughman creator: Jeremy J. Wright creator: Timo J. Ruokonen creator: Christoph Chucholl creator: Simone Guareschi creator: Bram Koese creator: Zsombor M. Banyai creator: James Hodson creator: Margo Hurt creator: Katrin Kaldre creator: Boris Lipták creator: James W. Fetzner creator: Tommaso Cancellario creator: András Weiperth creator: Jạnis Birzaks creator: Teodora Trichkova creator: Milcho Todorov creator: Maksims Balalaikins creator: Bogna Griffin creator: Olga N. Petko creator: Ada Acevedo-Alonso creator: Guillermo D’Elía creator: Karolina Śliwińska creator: Anatoly Alekhnovich creator: Henry Choong creator: Josie South creator: Nick Whiterod creator: Katarina Zorić creator: Peter Haase creator: Ismael Soto creator: Daniel J. Brady creator: Phillip J. Haubrock creator: Pedro J. Torres creator: Denis Şadrin creator: Pavel Vlach creator: Cüneyt Kaya creator: Sang Woo Jung creator: Jin-Young Kim creator: Xavier H.C. Vermeersch creator: Maciej Bonk creator: Radu Guiaşu creator: Muzaffer M. Harlioğlu creator: Jane Devlin creator: Irmak Kurtul creator: Dagmara Błońska creator: Pieter Boets creator: Hossein Masigol creator: Paul R. Cabe creator: Japo Jussila creator: Trude Vrålstad creator: David V. Beresford creator: Scott M. Reid creator: Jiří Patoka creator: David A. Strand creator: Ali S. Tarkan creator: Frédérique Steen creator: Thomas Abeel creator: Matthew Harwood creator: Samuel Auer creator: Sandor Kelly creator: Ioannis A. Giantsis creator: Rafał Maciaszek creator: Maria V. Alvanou creator: Önder Aksu creator: David M. Hayes creator: Tadashi Kawai creator: Elena Tricarico creator: Adroit Chakandinakira creator: Zanethia C. Barnett creator: Ştefan G. Kudor creator: Andreea E. Beda creator: Lucian Vîlcea creator: Alexandru E. Mizeranschi creator: Marian Neagul creator: Anton Licz creator: Andra D. Cotoarbă creator: Adam Petrusek creator: Antonín Kouba creator: Christopher A. Taylor creator: Lucian Pârvulescu uri: https://doi.org/10.7717/peerj.18229 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ion et al. title: The impact of scabies in tent cities in Kahramanmaraş after the Turkish earthquakes: oral pharmacologic treatment efficacy link: https://peerj.com/articles/18242 last-modified: 2024-10-14 description: BackgroundOur study was conducted to determine the impact of scabies in people living in collective living areas such as tent cities and container cities after the February 6 Kahramanmaraş earthquakes and to show the effectiveness of oral ivermectin treatment on scabies cases because topical treatments could not be used in this period when access to water was limited.MethodsAmong 233 patients diagnosed and treated with scabies in tent and container cities, 192 patients who met the criteria were included in the study. Descriptive statistics were given as number (n), percentage (%), mean, median, standard deviation (SD). In the comparison of categorical data, the chi-square test was applied; in the comparison of numerical data ANOVA analyses was applied.ResultsA total of 192 scabies patients (82.4%), 47.9% (N:92) of whom were women, were included in the study. The frequency of scabies in the total population in tent cities and container cities was found to be at least 0.54%. The most common symptoms were pruritis (99.0%) and rash (97.9%). The most common sites of lesion involvement were the umbilicus (87.0.%), forearm (75.0%), and back (70.3%). After the first dose of ivermectin, 159 (82.8%) patients showed complete recovery, while 30 (15.6%) patients showed partial recovery. 3 (1.6%) patients showed no improvement. After the second dose of ivermectin, 173 (90.1%) patients showed complete recovery. There were two (1.0%) patients who did not show improvement after two doses. Due to the deterioration of urban infrastructure after devastating earthquakes, the irregularity of mass living areas, the lack of hygiene conditions, and the difficulty of accessing clean, usable water, oral ivermectin may be the first choice for treatment in terms of ease of use and effectiveness. creator: Muhammed Mustafa Beyoğlu creator: Mehmet Enes Gokler uri: https://doi.org/10.7717/peerj.18242 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Beyoğlu and Gokler title: Comparative transcriptome and hormone analyses of roots in apple among three rootstocks with different rooting abilities link: https://peerj.com/articles/18244 last-modified: 2024-10-14 description: BackgroundRoot plays an important role in the growth and development of fruit trees; however, the molecular mechanisms behind the differences among rootstock varie-ties remain unclear.MethodsThis study examined the effects of different rootstocks on root structure and the endogenous hormone content of 1-year old apple seedlings in combinations of Tianhong 2 (T2)/Malus robusta (HT), T2/G935, and T2/Jizhen 2 (J2).ResultsThe results showed that the T2/HT treatment had greater root length, surface area, volume, average diameter, tips and forks, followed by G935 and J2. In T2/HT leaves and roots, the indole-3-acetic acid (IAA) and gibberellins (GA3) levels were highest, and the abscisic acid (ABA) levels were the lowest. A root transcriptome analysis detected 10,064, 10,511, and 8,719 differentially expressed genes in T2/HT vs. T2/G935, T2/HT vs. T2/J2, and T2/J2 vs. T2/G935, respectively. The analysis of Gene Ontology (GO) terms indicated a significant enrichment in biological processes, cellular components, and molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that plant hormone signaling, MAPK signaling pathway–plant, and plant–pathogen interaction played important roles in differences in the rooting ability of different rootstocks. In addition, some key differential genes were associated with root growth and development and were involved in these metabolic pathways. This study is important for enriching theoretical studies of fruit tree roots. creator: Zhongyong Li creator: Yang Cao creator: Jie Zhu creator: Jin Liu creator: Feng Li creator: Shasha Zhou creator: Xueying Zhang creator: Jizhong Xu creator: Bowen Liang uri: https://doi.org/10.7717/peerj.18244 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Association of serum Metrnl levels and high-density lipoprotein cholesterol in patients with type 2 diabetes mellitus: a cross-sectional study link: https://peerj.com/articles/18264 last-modified: 2024-10-14 description: PurposeMeteorin-like (Metrnl) is a novel adipokine which is highly expressed in adipose tissue and has a beneficial effect on glucose and lipid metabolism. High density lipoprotein cholesterol (HDL-C) is well recognized to be inversely associated with cardiovascular events. However, the relationship between serum Metrnl levels and HDL-C in the type 2 diabetes mellitus (T2DM) remains unclear. Therefore, the present study aimed to evaluate the association of serum Metrnl with HDL-C levels in T2DM.Materials and MethodsEighty participants with T2DM were included in this cross-sectional study. They were divided into two groups according to HDL-C levels: Group1 (lower HDL-C group): HDL-C < 1.04 mmol/L; Group2 (higher HDL-C group): HDL-C ≥ 1.04 mmol/L. Serum Metrnl levels were measured by enzyme-linked immunosorbent assay (ELISA).ResultsAs compared with lower HDL-C levels groups, serum Metrnl levels were significantly higher in the group with higher HDL-C. Binary logistic regression analysis showed serum Metrnl levels were positively associated with HDL-C group after adjustment with sex, age, body mass index (BMI), mean arterial pressure (MAP), fasting blood glucose (FPG), triglyceride (TG). Furthermore, serum Metrnl levels were inversely correlated with insulin resistance index (HOMA-IR). HDL-C levels were lowest in the group with the lowest Metrnl levels group and remained positively associated with Metrnl after adjustment for sex, age, BMI, TG, and HOMA-IR by using multivariate logistic regression analysis.ConclusionSerum Metrnl levels were positively associated with HDL-C levels in patients with T2DM.This suggests that increasing serum Metrnl levels maybe a candidate for improving lipid metabolism and preventing cardiovascular events in T2DM.Registry and the Registration No. of the Study/TrialThe study was registered in the Chinese clinical trial registry (ChiCTR- 2100047148). creator: Chenxia Zhou creator: Juli Zeng creator: Xiangyu Gao creator: Da Chen creator: Qiugen Zhu creator: Bo Feng creator: Jun Song uri: https://doi.org/10.7717/peerj.18264 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Ultra-rapid detection of nuclear protein of severe fever with thrombocytopenia syndrome virus by colloidal gold immunochromatography assay link: https://peerj.com/articles/18275 last-modified: 2024-10-14 description: In 2009, severe fever with thrombocytopenia syndrome virus (SFTSV), also known as the Dabie bandavirus (DBV), was first discovered in Henan, China. It is a tick-borne zoonotic virus with a fatality rate ranging from 6% to 30%. Currently, we lack safe and effective vaccines or antiviral drugs to treat SFTSV infection. Therefore, the development of a specific, sensitive, and cost-effective detection method is crucial. Using inactivated SFTSV and recombinant SFTSV nucleocapsid protein (SFTSV-NP), we repeatedly immunized mice with different adjuvants and obtained two monoclonal antibodies against SFTSV-NP, which were used to develop a colloidal gold immunochromatographic assay (ICA) rapid test kit for SFTSV. Compared with nucleic acid testing (gold standard), the ICA test strips are 97.67% accurate in testing clinical serum samples (36 cases of clinical serum samples and seven cases of whole blood samples). The test kit was 100% accurate in detecting different SFTSV strains. No false-positive results were generated when detecting other arboviruses. Therefore, our developed SFTSV test kit conveniently, rapidly, and effectively detects SFTSV. creator: Zhiwei Huang creator: Jianhua Li creator: Wentao Wei creator: Hongyu Li creator: Hao Yan creator: Ruyi Chen creator: Jiaxuan Li creator: Xiaotian Tie creator: Di Wang creator: Guangshang Wu creator: Ling Zhang creator: Yanjun Zhang creator: Keda Chen creator: Yongliang Lou uri: https://doi.org/10.7717/peerj.18275 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Huang et al. title: A small venomous reptile from the Late Triassic (Norian) of the southwestern United States link: https://peerj.com/articles/18279 last-modified: 2024-10-14 description: Reptile feeding strategies encompass a wide variety of diets and accompanying diversity in methods for subduing prey. One such strategy, the use of venom for prey capture, is found in living reptile clades like helodermatid (beaded) lizards and some groups of snakes, and venom secreting glands are also present in some monitor lizards and iguanians. The fossil record of some of these groups shows strong evidence for venom use, and this feeding strategy also has been hypothesized for a variety of extinct reptiles (e.g., archosauromorphs, anguimorphs, and a sphenodontian). However, evidence of systems for venom delivery in extinct groups and its evolutionary origins has been scarce, especially when based on more than isolated teeth. Here, we describe a potentially venomous new reptile, Microzemiotes sonselaensis gen. et sp. nov., from a partial left dentary recovered from the Sonsela Member of the Chinle Formation (middle Norian, Upper Triassic) of northeastern Arizona, U.S.A. The three dentary teeth have apices that are distally reclined relative to their bases and the tip of the posteriormost tooth curves mesially. The teeth show subthecodont implantation and are interspaced by empty sockets that terminate above the Meckelian canal, which is dorsoventrally expanded posteriorly. Replacement tooth sockets are positioned distolingually to the active teeth as in varanid-like replacement. We identify this new specimen as a diapsid reptile based on its monocuspid teeth that lack carinae and serrations. A more exclusive phylogenetic position within Diapsida is not well supported and remains uncertain. Several features of this new taxon, such as the presence of an intramandibular septum, are shared with some anguimorph squamates; however, these likely evolved independently. The teeth of the new taxon are distinctively marked by external grooves that occur on the entire length of the crown on the labial and lingual sides, as seen in the teeth of living beaded lizards. If these grooves are functionally similar to those of beaded lizards, which use the grooves to deliver venom, this new taxon represents the oldest known reptile where venom-conducting teeth are preserved within a jaw. The teeth of the new species are anatomically distinct from and ~10x smaller than those of the only other known Late Triassic hypothesized venomous reptile, Uatchitodon, supporting venom use across multiple groups of different body size classes. This new species represents the third Late Triassic reptile species to possibly have used envenomation as a feeding (and/or defensive) strategy, adding to the small number of venomous reptiles known from the Mesozoic Era. creator: Helen E. Burch creator: Hannah-Marie S. Eddins creator: Michelle R. Stocker creator: Ben T. Kligman creator: Adam D. Marsh creator: William G. Parker creator: Sterling J. Nesbitt uri: https://doi.org/10.7717/peerj.18279 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Mangrove afforestation as an ecological control of invasive Spartina alterniflora affects rhizosphere soil physicochemical properties and bacterial community in a subtropical tidal estuarine wetland link: https://peerj.com/articles/18291 last-modified: 2024-10-14 description: BackgroundThe planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem.MethodsHigh-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora, mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray–Curtis metrics) was used to identify key soil factors driving bacterial community structure.ResultsS. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO3−-N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata, were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors.ConclusionsEcological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community. creator: Jinwang Wang creator: Xi Lin creator: Xia An creator: Shuangshuang Liu creator: Xin Wei creator: Tianpei Zhou creator: Qianchen Li creator: Qiuxia Chen creator: Xing Liu uri: https://doi.org/10.7717/peerj.18291 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Identification of an additive interaction using parameter regularization and model selection in epidemiology link: https://peerj.com/articles/18304 last-modified: 2024-10-14 description: BackgroundIn epidemiology, indicators such as the relative excess risk due to interaction (RERI), attributable proportion (AP), and synergy index (S) are commonly used to assess additive interactions between two variables. However, the results of these indicators are sometimes inconsistent in real world applications and it may be difficult to draw conclusions from them.MethodBased on the relationship between the RERI, AP, and S, we propose a method with consistent results, which are achieved by constraining $e^{\theta_3}-e^{\theta_1}-e^{\theta_2}+1=0$eθ3−eθ1−eθ2+1=0, and the interpretation of the results is simple and clear. We present two pathways to achieve this end: one is to complete the constraint by adding a regular penalty term to the model likelihood function; the other is to use model selection.ResultUsing simulated and real data, our proposed methods effectively identified additive interactions and proved to be applicable to real-world data. Simulations were used to evaluate the performance of the methods in scenarios with and without additive interactions. The penalty term converged to 0 with increasing λ, and the final models matched the expected interaction status, demonstrating that regularized estimation could effectively identify additive interactions. Model selection was compared with classical methods (delta and bootstrap) across various scenarios with different interaction strengths, and the additive interactions were closely observed and the results aligned closely with bootstrap results. The coefficients in the model without interaction adhered to a simplifying equation, reinforcing that there was no significant interaction between smoking and alcohol use on oral cancer risk.ConclusionIn summary, the model selection method based on the Hannan-Quinn criterion (HQ) appears to be a competitive alternative to the bootstrap method for identifying additive interactions. Furthermore, when using RERI, AP, and S to assess the additive interaction, the results are more consistent and the results are simple and easy to understand. creator: Chanchan Hu creator: Zhifeng Lin creator: Zhijian Hu creator: Shaowei Lin uri: https://doi.org/10.7717/peerj.18304 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hu et al. title: The relationship between functional movement patterns, dynamic balance and ice speed and agility in young elite male ice hockey players link: https://peerj.com/articles/18092 last-modified: 2024-10-11 description: BackgroundUnderstanding the relationship between the functional state of the musculoskeletal system and skating performance in ice hockey players is essential, as it can provide valuable insights for the development of training programs tailored to the specific needs of athletes. This study investigated the relationship between functional movement patterns, dynamic balance, and ice speed and agility in young elite male ice hockey players.MethodsThe study involved sixty elite male ice hockey players aged 14 to 18 years, with an average age of 15.9 ± 0.85 years and training experience ranging from 7 to 9 years. Functional movement patterns were evaluated using the Functional Movement Screen™ (FMSTM). Dynamic balance was assessed using the lower quarter Y-Balance test (YBT-LQ). Fitness tests on ice were conducted using a professional Smart Speed measurement system.ResultsNegative correlations were found between the in-line lunge and the results of the 5-m forward (rho = −0.31, p = 0.018) and 5-m backward (rho = −0.27, p = 0.040), as well as between the hurdle step and the 30-m forward skating test result (rho = −0.26, p = 0.043). Positive correlations were observed between shoulder mobility and both forward (5-m: rho = 0.27, p = 0.035) and backward skating results (5-m: rho = 0.35, p = 0.006; 30-m: rho = 0.26, p = 0.047), and between active straight leg rise and both the 5-m forward skating (rho = 0.38, p = 0.002) and agility tests (rho = 0.39, p = 0.002). The study also revealed positive correlations between the magnitude of asymmetries in the anterior reach distance of the right and left legs and the results of 5-m forward (rho = 0.34, p = 0.009) and backward skating (rho = 0.32, p = 0.013). Additionally, a positive correlation was found between the agility test and the magnitude of asymmetries in the posteromedial reach distance (r = 0.32, p = 0.012) as well as the composite YBT score (r = 0.28, p = 0.031). Negative correlations were found between normalized reach distances in the YBT-LQ and performance outcomes in both forward and backward skating, as well as in the agility test, indicating that greater reach distance corresponds to faster skating.ConclusionsThese findings suggest the potential impact of balance and hip mobility on skating speed and agility and emphasize the importance of symmetry for optimal performance among ice hockey players. creator: Małgorzata Grabara creator: Anna Bieniec uri: https://doi.org/10.7717/peerj.18092 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Grabara and Bieniec title: Applications of dry chain technology to maintain high seed viability in tropical climates link: https://peerj.com/articles/18146 last-modified: 2024-10-11 description: Seed storage life in tropical areas is shortened by high humidity and temperature and the general inaccessibility to dehumidifying and refrigeration systems, resulting in rapid decreases in seed viability in storage as well as a high incidence of fungal and insect infestations. The dry chain, based on rapid and deep drying of seeds after harvest followed by packaging in moisture-proof containers, has been proposed as an effective method to maintain seed quality during medium-term storage in humid climates, even without refrigeration. In addition, seed drying with zeolite drying beads can be more effective and economical than sun or heated-air drying under these warm, humid conditions. In this paper, we review recent published literature regarding the dry chain, considering different crop species, storage environments and seed traits. In addition, we provide new original data on the application of dry chain methods and their implementation at larger scales in South Asia, Latin America and Pacific Island Countries. The clear conclusion is that the combination of reusable drying beads and waterproof storage containers enables the implementation of the dry chain in tropical climates, enhancing seed viability and quality in storage of many crop species. The dry chain approach can therefore significantly enhance seed security for farmers in many tropical countries. Finally, we propose actions and strategies that could guide further scaling-up implementation of this technology. creator: Filippo Guzzon creator: Denise E. Costich creator: Irfan Afzal creator: Luis Barboza Barquero creator: Andrés Antonio Monge Vargas creator: Ester Vargas Ramírez creator: Pedro Bello creator: Peetambar Dahal creator: César Sánchez Cano creator: Cristian Zavala Espinosa creator: Shakeel Imran creator: Soane Patolo creator: Tevita Ngaloafe Tukia creator: Johan Van Asbrouck creator: Elina Nabubuniyaka-Young creator: Maraeva Gianella creator: Kent J. Bradford uri: https://doi.org/10.7717/peerj.18146 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Guzzon et al. title: Transcription factor EB, a promising therapeutic target in cardiovascular disease link: https://peerj.com/articles/18209 last-modified: 2024-10-11 description: Cardiovascular disease (CVD) remains the major cause of morbidity and mortality around the world. Transcription factor EB (TFEB) is a master regulator of lysosome biogenesis and autophagy. Emerging studies revealed that TFEB also mediates cellular adaptation responses to various stimuli, such as mitochondrial dysfunction, pathogen infection and metabolic toxin. Based on its significant capability to modulate the autophagy-lysosome process (ALP), TFEB plays a critical role in the development of CVD. In this review, we briefly summarize that TFEB regulates cardiac dysfunction mainly through ameliorating lysosomal and mitochondrial dysfunction and reducing inflammation. creator: Xin Yan creator: Li Yang creator: Xiaolei Fu creator: Xin Luo creator: Chengming Wang creator: Qiu Ping Xie creator: Fan OuYang uri: https://doi.org/10.7717/peerj.18209 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Yan et al. title: Three new species of Talaromyces sect. Talaromyces discovered in China link: https://peerj.com/articles/18253 last-modified: 2024-10-11 description: BackgroundTalaromyces species play an important role in the nutrient cycle in natural ecosystems, degradation of vegetal biomass in industries and the implications in medicine. However, the species diversity of this genus is still far from fully understood.MethodsThe polyphasic taxonomic approach integrating morphological comparisons and molecular phylogenetic analyses based on BenA, CaM, Rpb2 and ITS sequences was used to propose three new Talaromyces species.ResultsThree new species of sect. Talaromyces isolated from soil are proposed, namely, T. disparis (ex-type AS3.26221), T. funiformis (ex-type AS3.26220) and T. jianfengicus (ex-type AS3.26253). T. disparis is unique in low growth rate, velvety texture, limited to moderate sporulation, biverticillate, monoverticillate and irregular penicilli bearing a portion of abnormally large globose conidia, it has no close relatives in phylogeny. Being a member of T. pinophilus complex, T. funiformis produces mycelial funicles on Czapek yeast autolysate agar (CYA), 5% malt extract agar (MEA) and yeast extract (YES), sparse sporulation on Czapek agar (Cz), CYA, MEA and YES while abundant on oatmeal agar (OA), bearing appressed biverticillate penicilli and globose to pyriform conida with smooth to finely rough walls. T. jianfengicus belongs to T. verruculosus complex, is characterized by velvety colony texture with moderate to abundant elm-green conidia en masse, producing biverticillate penicilli, globose conidia with verrucose walls.ConclusionIt is now a common practice in establishing new species of Aspergillus, Penicillium and Talaromyces based on morphological characters and phylogenetic analyses of BenA, CaM, Rpb2 and ITS sequences. The proposal of the three novelties of Talaromyces in this article is not only supported by their morphological distinctiveness, but also confirmed by the phylogenetic analyses of the concatenated BenA-CaM-Rpb2 and BenA-CaM-ITS, as well as the individual BenA, CaM, Rpb2 and ITS sequence matrices. creator: Xin-Tong Ren creator: Saifei Li creator: Yongming Ruan creator: Long Wang uri: https://doi.org/10.7717/peerj.18253 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ren et al. title: The characteristics and associations between trait and state time perspective in adolescents with depression: a questionnaire and sandplay study link: https://peerj.com/articles/18257 last-modified: 2024-10-11 description: BackgroundTime perspective is strongly associated with depression. However, the characteristics and associations between trait and state time perspective in adolescents with depression remain unknown.MethodsA total of 211 adolescents with depression (mean age: 14.60 ± 1.69 years) and 215 healthy controls (mean age: 14.66 ± 1.73 years) were selected and assessed using the Chinese version of the Zimbardo Time Perspective Inventory to quantify their trait time perspective. Thirty adolescents were randomly selected from each group to create nine-grid sandplay productions to assess their state time perspective.Results(1) Regarding the trait time perspective, depressed adolescents scored significantly higher on past negative, present fatalistic, present impulsive, and deviation-balanced time perspective (p < 0.001) and significantly lower on past positive and future (p < 0.05) compared to the control group. (2) In terms of state time perspective, depressed adolescents showed a significantly higher number of squares related to past negative, present negative, and future negative in their nine-grid sandplay productions compared to the control group (p < 0.01).Conversely, they had significantly fewer squares associated with past positive, present positive, future positive than the control group (p < 0.05). (3) Past negative, present fatalistic, and deviation from balanced time perspective traits were negatively correlated with positive state time perspective and positively correlated with negative state time perspective. Past positive and future traits were positively correlated with positive state time perspective and negatively correlated with negative state time perspective.ConclusionAdolescents with depression are characterized by dwelling on the past, having a severely negative attitude toward the past, being pessimistic about the future, and having a tendency to blame fate or external forces for their problems. In the future, standardized methods for measuring state time perspective should be further explored, as well as the effectiveness of the nine-grid sandplay, for improving time perspective in patients with depression. creator: Hanlin Ren creator: Qing Zhang creator: Donghuan Rong creator: Yating Zhang creator: Yanzhen Ren creator: Xiaobao Li uri: https://doi.org/10.7717/peerj.18257 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ren et al. title: Spatial patterns and driving factors of plant diversity along the urban–rural gradient in the context of urbanization in Zhengzhou, China link: https://peerj.com/articles/18261 last-modified: 2024-10-11 description: Plant diversity is the basis for human survival and development, directly affecting the function and stability of urban ecosystems. Its distribution pattern and causes have been a central issue in ecological and landscape gardening research. Rapid urbanization in Zhengzhou City has led to the fragmentation of urban green spaces and damage to ecosystems, seriously affecting urban biodiversity conservation. Understanding the distribution pattern of plant diversity in the region and its relationship with environmental factors is crucial for maintaining and enhancing urban plant diversity. Plant data from 178 sample plots in the built-up area of Zhengzhou City were collected and combined with environmental factors, and the characteristics of plant diversity, richness patterns, and their main environmental explanations in Zhengzhou City were explored. Results showed that there were 596 plant species belonging to 357 genera and 110 families in the study area. There were five dominant families and four dominant genera. Four distinct spatial patterns of plant diversity were identified along the urban–rural gradient. Urbanization factors such as GDP per capita, house prices, and imperviousness within 500 m from the patch significantly influenced plant diversity. There was an imbalance between the spatial pattern of plant diversity and application of urban landscape greening in Zhengzhou City. Future studies should focus on the application of native plants, curb plant homogenization, and reduce anthropogenic interference, which are conducive to protecting and enhancing urban plant diversity. These results can provide a basis for understanding the distribution pattern and influence mechanism of urbanization factors on plant diversity and serve as a reference for policymakers and planners of plant diversity conservation in Zhengzhou City. creator: Lingling Zhang creator: Chong Du creator: Wenhan Li creator: Yongjiang Liu creator: Ge Zhang creator: Shanshan Xie creator: Yiping Liu creator: Dezheng Kong uri: https://doi.org/10.7717/peerj.18261 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Association between risk factors and bone mineral density and the development of a self-assessment tool for early osteoporosis screening in postmenopausal women with type 2 diabetes link: https://peerj.com/articles/18283 last-modified: 2024-10-11 description: BackgroundBoth diabetes and osteoporosis have developed into major global public health problems due to the increasing aging population. It is crucial to screen populations at higher risk of developing osteoporosis for disease prevention and management in postmenopausal women with type 2 diabetes (T2D). This study aims to quantitatively investigate the association between risk factors and bone mineral density (BMD) and develop a self-assessment tool for early osteoporosis screening in postmenopausal women with T2D.MethodsWe retrospectively enrolled 1,309 postmenopausal women with T2D. Linear regression methods were used to assess the association between risk factors and BMD. Additionally, a multivariate logistic regression analysis was performed to identify independent risk factors associated with osteoporosis. Utilizing the logistic regression machine learning algorithm, we developed an osteoporosis screening tool that categorizes the population into three risk regions based on age and body mass index (BMI), indicating low, moderate, and high prevalence of osteoporosis in the age-BMI plane.ResultsOlder age and lower BMI were independently associated with decreased BMD. The BMD at the total hip, femur neck, and lumbar spine differed by 12.9, 10.9, and 15.5 mg/cm2 for each 1 unit increase in BMI, respectively. Both age and BMI were identified as independent predictors of osteoporosis. The osteoporosis screening tool was developed by using two straight lines with equations of BMI = 0.56 * age−4.12 and BMI = 0.56 * age−10.88; there were no significant differences in the prevalence of osteoporosis among the training, internal test, and external test datasets in the low-, moderate-, and high-risk regions.ConclusionWe have successfully developed and validated a self-assessment tool for early osteoporosis screening in postmenopausal women with T2D for the first time. BMI was identified as a significant modifiable risk factor. Our study may improve awareness of osteoporosis and is valuable for disease prevention and management for postmenopausal women with T2D. creator: Xiaoyu Chen creator: Xiufen Jia creator: Junping Lan creator: Wenjun Wu creator: Xianwu Ni creator: Yuguo Wei creator: Xiangwu Zheng creator: Jinjin Liu uri: https://doi.org/10.7717/peerj.18283 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Demography and predatory potential of Orius strigicollis on eggs of Plutella xylostella at two temperatures link: https://peerj.com/articles/18044 last-modified: 2024-10-10 description: BackgroundThe polyphagous predatory bug Orius strigicollis Poppius (Heteroptera: Anthocoridae) is an active predator used to control many insect pests of agricultural crops. Orius species are significantly affected by the type of food and temperature.MethodA study of O. strigicollis feeding on Plutella xylostella L. (Lepidoptera: Plutellidae) eggs in climate chambers at 28 and 32 °C, 70 ± 5% relative humidity, 16:8 photoperiod, was conducted to determine the effects of different temperatures on the predation activity, biological characteristics and demographic parameters of O. strigicollis. Twosex-MS Charts were used to determine the age-stages and characteristics of this species.ResultsThe results showed that the daily consumption of pre-adults on eggs of P. xylostella was highest at 28 °C, and at this temperature, there was a greater probability that O. strigicollis would survive to adulthood (42.5%) than at 32 °C (25.0%). It has also been found that at 28 °C there was a long oviposition period (9.38 days) and the greatest female fecundity (44.2 eggs/female) In addition to the highest life expectancy of O. strigicollis (16.96 days) at 28 °C, the intrinsic rate of increase (0.087 d−1) was also highest. According to our results, O. strigicollis has the potential to grow and develop on the eggs of P. xylostella at 28 °C and, therefore, could potentially be used as a biological control agent in integrated pest management (IPM) programs. creator: Shakeel Ur Rehman creator: Xingfu Jiang creator: Mahnoor Saleem creator: Xingmiao Zhou creator: Bangqing Chen creator: Khalid Ali Khan creator: Ibrahim Osman Ibrahim creator: Hamed A. Ghramh uri: https://doi.org/10.7717/peerj.18044 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ur Rehman et al. title: Comparative cytogenetics of three Zoraptera species as a basis for understanding chromosomal evolution in Polyneoptera insects link: https://peerj.com/articles/18051 last-modified: 2024-10-10 description: Zoraptera (also called “angel insects”) is one of the most unexplored insect orders. However, it holds promise for understanding the evolution of insect karyotypes and genome organization given its status as an early branching group of Polyneoptera and Pterygota (winged insects) during the Paleozoic. Here, we provide karyotype descriptions of three Zorapteran species: Brazilozoros huxleyi (2n♂; ♀ = 42; 42), B. kukalovae (2n♂; ♀ = 43; 44) and Latinozoros cacaoensis (2n♂; ♀ = 36; 36). These species represent two of the four recently recognized Zorapteran subfamilies. Contrary to an earlier suggestion that Zoraptera has holocentric chromosomes, we found karyotypes that were always monocentric. Interestingly, we detected both X0 (B. kukalovae) and XY (B. huxleyi, L. cacaoensis) sex chromosome systems. In addition to conventional karyotype descriptions, we applied fluorescent in situ hybridization for the first time in Zoraptera to map karyotype distributions of 18S rDNA, histone H3 genes, telomeres and (CAG)n and (GATA)n microsatellites. This study provides a foundation for cytogenetic research in Zoraptera. creator: Marek Jankásek creator: Petr Kočárek creator: František Št’áhlavský uri: https://doi.org/10.7717/peerj.18051 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jankásek et al. title: Extraction and characterization of collagen and gelatin from body wall of sea cucumbers Stichopus horrens and Holothuria arenicola link: https://peerj.com/articles/18149 last-modified: 2024-10-10 description: BackgroundMarine invertebrates, including sponges, molluscs, jellyfish, mussels, and sea cucumbers, are abundant sources of high-quality collagen and offer advantages such as availability, ease of processing, lower inflammatory response, and good metabolic compatibility. Approximately 70% of the total protein in the body wall of sea cucumbers is collagen. Gelatin is a water-soluble protein produced from heat-denatured collagen and has various industrial applications.MethodsPepsin-solubilized collagen was extracted from the body wall of two sea cucumber Stichopus horrens and Holothuria arenicola, species found in the Oman Sea and characterized with SDS-PAGE and amino acid composition. Then gelatin was extracted from pepsin-solubilized collagen of S. horrens and some rheological properties were measured.ResultsAmino acid composition and SDS-PAGE analysis showed that the collagen from both species was type I, with one α1 chain and β chains, with molecular weights of 125 and 250 kDa, respectively. Glycine was the most abundant amino acid in the collagen from both sea cucumber species. The pepsin-soluble collagens from both species had high levels of glycine, proline, alanine, glutamic acid, and hydroxyproline. The gelatin from S. horrens had a melting point of 30 °C and displayed exceptional thermal stability, surpassing that of mammalian gelatin. Its gelling point was 5 °C, like that of cold-water fish gelatin, with a viscosity of 2.065 cp-lower than mammal gelatins. These findings suggested that collagen and gelatin from sea cucumbers could be useful in nutraceutical, pharmaceutical and cosmetic industries. creator: Noora Barzkar creator: Gilan Attaran-Fariman creator: Ali Taheri creator: Balu Alagar Venmathi Maran uri: https://doi.org/10.7717/peerj.18149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Barzkar et al. title: Spring haul-out behavior of seals in the Bering and Chukchi Seas: implications for abundance estimation link: https://peerj.com/articles/18160 last-modified: 2024-10-10 description: Ice-associated seals rely on sea ice for a variety of activities, including pupping, breeding, molting, and resting. In the Arctic, many of these activities occur in spring (April through June) as sea ice begins to melt and retreat northward. Rapid acceleration of climate change in Arctic ecosystems is therefore of concern as the quantity and quality of suitable habitat is forecast to decrease. Robust estimates of seal population abundance are needed to properly monitor the impacts of these changes over time. Aerial surveys of seals on ice are an efficient method for counting seals but must be paired with estimates of the proportion of seals out of the water to derive population abundance. In this paper, we use hourly percent-dry data from satellite-linked bio-loggers deployed between 2005 and 2021 to quantify the proportion of seals hauled out on ice. This information is needed to accurately estimate abundance from aerial survey counts of ice-associated seals (i.e., to correct for the proportion of animals that are in the water, and so are not counted, while surveys are conducted). In addition to providing essential data for survey ‘availability’ calculations, our analysis also provides insights into the seasonal timing and environmental factors affecting haul-out behavior by ice-associated seals. We specifically focused on bearded (Erignathus barbatus), ribbon (Histriophoca fasciata), and spotted seals (Phoca largha) in the Bering and Chukchi seas. Because ringed seals (Phoca (pusa) hispida) can be out of the water but hidden from view in snow lairs analysis of their ‘availability’ to surveys requires special consideration; therefore, they were not included in this analysis. Using generalized linear mixed pseudo-models to properly account for temporal autocorrelation, we fit models with covariates of interest (e.g., day-of-year, solar hour, age and sex class, wind speed, barometric pressure, temperature, precipitation) to examine their ability to explain variation in haul-out probability. We found evidence for strong diel and within-season patterns in haul-out behavior, as well as strong weather effects (particularly wind and temperature). In general, seals were more likely to haul out on ice in the middle of the day and when wind speed was low and temperatures were higher. Haul-out probability increased through March and April, peaking in May and early June before declining again. The timing and frequency of haul-out events also varied based on species and age-sex class. For ribbon and spotted seals, models with year effects were highly supported, indicating that the timing and magnitude of haul-out behavior varied among years. However, we did not find broad evidence that haul-out timing was linked to annual sea-ice extent. Our analysis emphasizes the importance of accounting for seasonal and temporal variation in haul-out behavior, as well as associated environmental covariates, when interpreting the number of seals counted in aerial surveys. creator: Josh M. London creator: Paul B. Conn creator: Stacie M. Koslovsky creator: Erin L. Richmond creator: Jay M. Ver Hoef creator: Michael F. Cameron creator: Justin A. Crawford creator: Andrew L. Von Duyke creator: Lori Quakenbush creator: Peter L. Boveng uri: https://doi.org/10.7717/peerj.18160 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 London et al. title: Study on mid-term outcomes of atherectomy for patients with femoral popliteal artery lesions with different Global Limb Anatomic Staging System grades link: https://peerj.com/articles/18189 last-modified: 2024-10-10 description: ObjectiveTo investigate the mid-term efficacy and patency rate of TurboHawk peripheral plaque excision system in the treatment of femoral popliteal artery lesions with different Global Limb Anatomic Staging System (GLASS) grades.MethodsThe clinical data of 141 patients with femoral popliteal arteriosclerosis obliterans who were treated with TurboHawk from January 2018 to July 2022 in our institution were retrospectively analyzed. There were 109 male patients and 32 female patients. Recordings were made of the patient’s symptoms of limb ischemia, technical success rate, primary patency rate of target vessels, ankle brachial index (ABI), GLASS grades, postoperative complications, and a statistical analysis with the patient’s preoperative treatment was conducted.ResultsAll patients had improved limb ischemia symptoms to varying degrees after surgery, with a technical success rate of 100% (femoral artery puncture and superficial femoral artery recanalization) without bleeding, hematoma, pseudoaneurysm, arteriovenous fistula or other complications. The follow-up period was 1-24 months, during which the severity of claudication, resting pain, and toe ulcers significantly improved. The primary patency rate of the target vessel was 98.58% (139/141), and the ABI significantly increased on the second day, three months, and six months after surgery compared to before surgery. No major adverse events were found during follow-up. The patency rates at 1, 6, 12 and 24 months after intervention were 100%, 80%, 75% and 60% respectively.ConclusionThe mid-term efficacy and patency rate of TurboHawk in the treatment of femoral popliteal artery lesions with GLASS I patients have the best mid-term prognosis, the highest mid-term survival rate, and the highest vascular patency. The plaque removal system has proven to be an effective treatment for individual localized chronic total occlusion lesions. Additionally, the TurboHawk system provides a safe and minimally invasive treatment alternative for superficial femoral artery conditions, achieving significant therapeutic results within a brief period. creator: Yanyu Yue creator: Youjia Zhang creator: Liang Zhang creator: Zheng Gao creator: Xiaolong Du creator: Feng Ran uri: https://doi.org/10.7717/peerj.18189 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yue et al. title: Knowledge, attitude and purchasing behavior of Saudi mothers towards food additives and dietary pattern of preschool children link: https://peerj.com/articles/18223 last-modified: 2024-10-10 description: BackgroundThere are over 506 children’s products containing one or more types of additives. Maternal awareness of these additives is essential for the health of preschool-aged children, as this period is vital for children’s growth and development. This study aims to assess the knowledge, attitudes, and purchasing behaviors related to food additives among mothers living in the western region of Saudi Arabia, as well as the dietary patterns of preschool children.MethodA cross-sectional study was conducted using an online survey with a convenience sample of 521 mothers of preschool-aged children (3–5 years old). The survey gathered data on the child’s age, number of children, the youngest child’s weight and height, food intolerance, tooth decay, as well as the dietary patterns of preschool children. It also assessed the mother’s knowledge, attitude, and purchasing behaviors related to food additives.ResultsThe study found that 46.6% of mothers demonstrated good knowledge of food additives, while 56.0% demonstrated fair attitudes and 78.5% good purchasing behavior regarding additives. Additionally, the majority of mothers reported favorable dietary patterns for their preschool-aged children. “Biscuits and crackers” had the highest consumption frequency (4.98 ± 1.50), with 36.7% of children consuming them once daily, while “Soft beverages” had the lowest consumption frequency (2.73 ± 2.04), with 46.6% of children never consuming them. Statistically significant differences were identified between mothers’ knowledge and their age, education level, occupation status, and economic status (p < 0.05). ANOVA results also indicated a statistically significant difference between mothers’ attitudes and occupation status (p < 0.05). Furthermore, there were significant positive correlations between mothers’ knowledge of food additives and their attitudes (r = 0.293) and purchasing behaviors (r = 0.284) related to additives.ConclusionThe findings suggest that mothers possess a relatively good level of knowledge of food additives and hold fair attitudes toward them, tending to result in healthier purchasing behaviors and dietary practices for their preschool-aged children. To increase awareness, nutrition intervention programs are required across various socio-economic groups of mothers in the western region of Saudi Arabia. These programs can significantly contribute to promoting healthier dietary practices for preschool-aged children and improving overall family health and well-being. creator: Reem H. Almoabadi creator: Mahitab A. Hanbazaza uri: https://doi.org/10.7717/peerj.18223 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Almoabadi and Hanbazaza title: Parental thermal conditions affect the brain activity response to alarm cue in larval zebrafish link: https://peerj.com/articles/18241 last-modified: 2024-10-10 description: Temperature is a crucial factor affecting the physiology of ectothermic animals, but exposure to elevated temperature during specific life stages and across generations may confer fish resilience through phenotypic plasticity. In this study, we investigate the effects of developmental and parental temperature on brain activity response to an olfactory cue in the larval zebrafish, Danio rerio. We exposed parents during reproduction and their offspring during development to control (28 °C) or elevated temperature (30 °C) and observed the response of the larval telencephalon to an alarm cue using live calcium imaging. Parental exposure to elevated temperature decreased the time till maximum brain activity response regardless of the offspring’s developmental temperature, revealing that parental thermal conditions can affect the excitability of the offspring’s neural circuitry. Furthermore, brain activity duration was affected by the interaction between parental and offspring thermal conditions, where longer brain activity duration was seen when either parents or offspring were exposed to elevated temperature. Conversely, we found shorter brain activity duration when the offspring were exposed to the same temperature as their parents, in both control and elevated temperature. This could represent an anticipatory parental effect influencing the offspring’s brain response to match the parental environment, or an early developmental effect occurring within a susceptible short time window post-fertilization. Overall, our results suggest that warming can alter processes involved in brain transmission and show that parental conditions could aid in the preparation of their offspring to respond to olfactory stimuli in a warming environment. creator: Jade M. Sourisse creator: Julie L. Semmelhack creator: Celia Schunter uri: https://doi.org/10.7717/peerj.18241 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sourisse et al. title: Assessment of genetic diversity by phenological traits, field performance, and Start Codon Targeted (SCoT) polymorphism marker of seventeen soybean genotypes (Glycine max L.) link: https://peerj.com/articles/17868 last-modified: 2024-10-09 description: The Egyptian-farmed soybeans have a wide range of genetic diversity which is most important in plant improvement programs in order to develop new higher yielding soybean genotypes. The present study is designed to determine the genetic variability among seventeen genotypes of cultivated soybean (Glycine max L.) by examining the phenotypic level at the seedling stage, field performance over two years 2022/2023 and genetically using Start Codon Targeted (SCoT) markers. Results indicated that the SCoT markers, 100 seed weight, and tip angle (TA) traits were positively correlated with H2L12, DR 101, H15L5, and H117 genotypes. In addition, the number of branches per plant and plant height were associated with H113, H32, Crowford, H129, and D7512035. Furthermore, the length of the first internode (LFI), root width (RW), root length (RL), and shoot length (SL) were more associated with Giza 111, NC105, and Hutcheson. The hierarchical cluster analysis (HCA) and its associated heatmap explored the differences among the genotypes. It showed that all examined parameters were clustered into four distinct clusters. The obtained results showed that genotypes NC105, H30, D75_12035, and H2L12 have promising phenological and morphological traits besides tracking the inheritance of nearby genes surrounding the ATG translation start codon since they are in a monoclades. The obtained results will help the breeder plan appropriate selection strategies for improving seed yield in soybeans through hybridization from divergent clusters. creator: Mahmoud Abdel-Sattar creator: Ehab M. Zayed creator: Mohamed K. Abou-Shlell creator: Hail Z. Rihan creator: Ahmed A. Helal creator: Nabil E.G. Mekhaile creator: Ghada E. El-Badan uri: https://doi.org/10.7717/peerj.17868 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Abdel-Sattar et al. title: Dynamic perspectives on biodiversity quantification: beyond conventional metrics link: https://peerj.com/articles/17924 last-modified: 2024-10-09 description: Our research addresses the pressing need to assess biodiversity in the face of increasing habitat destruction and species extinctions. Several researchers have modelled conventional measures to assess biodiversity. Every measure evaluates biodiversity by considering different properties. Among them Simpson and Shannon indices are widely used, they primarily focus on species richness and abundance, overlooking the importance of rare or unique species. This limitation makes it challenging to identify which species drive changes in biodiversity and hampers conservation efforts. Moreover, these measures are sensitive to sample size and biased towards dominant species, leading to inaccurate estimations. To overcome these challenges, we propose a novel mathematical model that provides a comprehensive assessment of biodiversity. Our model accounts for species dominance, addresses sample size sensitivity, and highlights the significance of rare species within a community. By applying our measure to real-time scenarios and comparing it with traditional methods using the same dataset, proposed measure demonstrated its efficacy in capturing biodiversity dynamics over time. creator: Manjula Josephine Bollarapu creator: Swarna Kuchibhotla creator: Ramarao Kvsn creator: Harshita Patel uri: https://doi.org/10.7717/peerj.17924 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bollarapu et al. title: The relationship between virtual simulation, critical thinking, and self-directed learning abilities of nursing students in Riyadh, Saudi Arabia link: https://peerj.com/articles/18150 last-modified: 2024-10-09 description: ObjectiveThe use of virtual simulation in nursing education is an effective approach for improving nursing critical thinking and self-learning abilities, but the previous studies were limited to providing the required evidence that supports the association. This study aimed to assess the relationship between virtual simulation and critical thinking disposition and self-directed learning abilities among nursing students.MethodsThis is a descriptive correlational, non-experimental study. It was conducted among 201 third- and fourth-year nursing students at the Academic Institution, Saudi Arabia. A non-probability convenience sampling technique was used to select the participants; then, an online, adapted questionnaire was sent to the participants, the data from which was analyzed by SPSS.ResultsThe study findings showed that virtual simulation benefited nursing students. Most participants (56%) agreed that it helped them to think critically, and approximately 27% strongly agreed. It also enhanced their self-directed learning abilities, and the majority of the students agreed that they often review the way nursing practice is conducted. Furthermore, the results showed a significant, positive relationship between virtual simulation and the critical thinking disposition of nursing students (p-value = 0.03; correlation coefficient = 0.65), a strong positive relationship with self-directed learning abilities of nursing students (p-value = 0.004; correlation coefficient = 0.78), and a strong positive relationship between critical thinking disposition with self-directed learning abilities of nursing students (p-value = 0.01; correlation coefficient = 0.72).ConclusionThere are significant relationships between virtual simulation and the critical thinking disposition and self-directed learning abilities of nursing students. Furthermore, virtual simulation made the students practice critical thinking and self-learning, so, they simulate events and try to seek out and solve the problems. creator: Hanan F. Alharbi creator: Amjad Alsubaie creator: Rahaf Gharawi creator: Rawan Ba Mazroo creator: Shaikhah Alajaleen creator: Munerah Alsultan creator: Munira Alsaleem creator: Nora Alsubihi creator: Norah Alsahli creator: Nashwa Alqahtani creator: Raghad Rayzah uri: https://doi.org/10.7717/peerj.18150 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Alharbi et al. title: Health perceptions of patients with forgotten double-J stent link: https://peerj.com/articles/18156 last-modified: 2024-10-09 description: AimIn this article, we aimed to determine the health perceptions of the patients who did not apply for double-J stent (DJS) removal on time and evaluate whether health perceptions impact this behavior.Materials and MethodsHealth perceptions of 22 patients who were treated for forgotten double-J stent (FDJS) between January 2017–October 2020 and 25 patients who applied for DJS removal during the given appointment time in the urology department of Elazig Training and Research Hospital and Elazig Fethi Sekin City Hospital were compared using the “Health Perception Scale”.ResultsHealth perception scale scores in the FDJS group and control group were 62-68 (mean = 64.27 ± 1.75) and 63-68 (mean = 65.36 ± 1.55), respectively. With regard to the sub-factors of the scale, control center scores were 21.86 ± 0.77 and 22.08 ± 1.15; precision scores were 16.54 ± 0.80 and 16.56 ± 0.82; importance of health scores were 12.77 ± 0, 92 and 13.32 ± 0.74; and self-awareness points were 13.04  ± 0.72 and 13.48 ± 0.58, respectively. There was a statistically significant difference between the health perception scale in total, importance of health, and self-awareness scores between the two groups. At the same time, there was no difference in terms of the control center and precision scores (p∗ = 0.029, p∗ = 0.030, p∗ = 0.028, p = 0.460, p = 0.951).ConclusionPatients’ and their families’ educational status, income levels and lack of follow-up by healthcare professionals play an important role in forgotten DJS cases and patients’ perception of health may also have an impact on this behavior. creator: Mehmet Sezai Ogras creator: Kadir Yildirim uri: https://doi.org/10.7717/peerj.18156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ogras and Yildirim title: Effects of video game immersion and task interference on cognitive performance: a study on immediate and delayed recall and recognition accuracy link: https://peerj.com/articles/18195 last-modified: 2024-10-09 description: This study investigates the cognitive impacts of video game immersion and task interference on immediate and delayed recall as well as recognition tasks. We enrolled 160 subjects aged 18 to 29, who were regular players of “shoot-em-up” video games for at least 3 years. Participants were assigned to one of three experimental groups or a control group. The experimental conditions varied in the timing and type of tasks: the first group performed a video game session between recall tasks, the second group multitasked with video games and recall tasks simultaneously, and the third group engaged in task switching from video games to recall tasks. Using the Rey Auditory Verbal Learning Test, we measured the effects of these conditions on cognitive performance, focusing on error types and recall accuracy. Results indicated that multitasking and task switching significantly affected the subjects’ performance, with notable decrements in recall and recognition accuracy in conditions of high task interference. The study highlights the cognitive costs associated with multitasking in immersive digital games and provides insights into how task similarity and interference might increase error rates and affect memory performance. creator: Stefania Mancone creator: Beatrice Tosti creator: Stefano Corrado creator: Pierluigi Diotaiuti uri: https://doi.org/10.7717/peerj.18195 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mancone et al. title: Integrating whole genome sequencing and machine learning for predicting antimicrobial resistance in critical pathogens: a systematic review of antimicrobial susceptibility tests link: https://peerj.com/articles/18213 last-modified: 2024-10-09 description: BackgroundInfections caused by antibiotic-resistant bacteria pose a major challenge to modern healthcare. This systematic review evaluates the efficacy of machine learning (ML) approaches in predicting antimicrobial resistance (AMR) in critical pathogens (CP), considering Whole Genome Sequencing (WGS) and antimicrobial susceptibility testing (AST).MethodsThe search covered databases including PubMed/MEDLINE, EMBASE, Web of Science, SCOPUS, and SCIELO, from their inception until June 2024. The review protocol was officially registered on PROSPERO (CRD42024543099).ResultsThe review included 26 papers, analyzing data from 104,141 microbial samples. Random Forest (RF), XGBoost, and logistic regression (LR) emerged as the top-performing models, with mean Area Under the Receiver Operating Characteristic (AUC) values of 0.89, 0.87, and 0.87, respectively. RF showed superior performance with AUC values ranging from 0.66 to 0.97, while XGBoost and LR showed similar performance with AUC values ranging from 0.83 to 0.91 and 0.76 to 0.96, respectively. Most studies indicate that integrating WGS and AST data into ML models enhances predictive performance, improves antibiotic stewardship, and provides valuable clinical decision support. ML shows significant promise for predicting AMR by integrating WGS and AST data in CP. Standardized guidelines are needed to ensure consistency in future research. creator: Carlos M. Ardila creator: Pradeep K. Yadalam creator: Daniel González-Arroyave uri: https://doi.org/10.7717/peerj.18213 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ardila et al. title: Pdk3’s role in RANKL-induced osteoclast differentiation: insights from a bone marrow macrophage model link: https://peerj.com/articles/18222 last-modified: 2024-10-09 description: BackgroundOsteoporosis (OP) is a chronic disease characterized by decreased bone mass, loss of skeletal structural integrity and increased susceptibility to fracture. Available studies have shown that the pyruvate dehydrogenase kinase (PDK) family is associated with osteoclastogenesis and bone loss, but the specific role of Pdk3 in bone pathology has not been systematically investigated. MethodsA cell OP model was established in receptor activator for nuclear factor-κB Ligand (RANKL)-induced bone marrow macrophages (BMMs). Hereafter, the expression levels of Pdk3 and osteoclastogenesis feature genes including nuclear factor of activated T cells 1 (Nfatc1), Cathepsin K (Ctsk), osteoclast associated Ig-like receptor (Oscar) in BMMs-derived osteoclasts were examined based on real-time quantitative PCR and western blotting methods. Further, the phosphorylation of ERK, P65 and JAK/STAT and their correlation was Pdk3 was gauged. In particular, changes in the activity of these signaling pathways were observed by silencing experiments of the Pdk3 gene (using small interfering RNA). Finally, the effects of Pdk3 gene silencing on signaling pathway activity, osteoclastogenesis, and related inflammatory and apoptotic indicators were observed by transfection with PDK3-specific siRNA.ResultsFollowing RANKL exposure, the levels of Pdk3 and osteoclastogenesis feature genes were all elevated, and a positive correlation between Pdk3 and osteoclastogenesis feature genes was seen. Meanwhile, ERK, P65 and JAK/STAT phosphorylation was increased by RANKL, and Pdk3 was confirmed to be positively correlated with the phosphorylation of ERK, P65 and JAK/STAT. Additionally, in RANKL-exposed osteoclasts, Pdk3 knockdown diminished the phosphorylation of ERK, P65 and JAK/STAT, reduced the expressions of osteoclastogenesis feature genes. Importantly, knockdown of Pdk3 also reduced the expression of inflammatory cytokines and resulted in elevated levels of Bax and Casp3 expression, as well as downregulation of Bcl2 expression.ConclusionThis study reveals for the first time the role of Pdk3 in RANKL-induced osteoclastogenesis and OP. These findings provide a foundation for future studies on the role of Pdk3 in other bone diseases and provide new ideas for the development of OP therapeutics targeting Pdk3. creator: Nan Zhang creator: Lingting Wang creator: Xuxin Ye uri: https://doi.org/10.7717/peerj.18222 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: The impact of three thioxothiazolidin compounds on trehalase activity and development of Spodoptera frugiperda larvae link: https://peerj.com/articles/18233 last-modified: 2024-10-09 description: Trehalases (TREs), serving as crucial enzymes regulating trehalose and chitin metabolism in insects, represent prime targets for pest control strategies. We investigated the impact of three thioxothiazolidin compounds (1G, 2G, and 11G) on TRE activity and summarized their effects on the growth and development of Spodoptera frugiperda (Lepidoptera, Noctuidae). The experimental larvae of S. frugiperda were injected with the three thioxothiazolidin compounds (1G, 2G, and 11G), while the control group received an equivalent volume of 2% DMSO as a control. All three compounds had a strong effect on inhibiting TRE activity, significantly prolonging the pre-pupal development stage. However, compared with the 11G-treated group, the survival rate of larvae treated with 1G and 2G was significantly reduced by 31.11% and 27.78% respectively, while the occurrence of phenotypic abnormalities related to growth and development was higher. These results manifest that only the TRE inhibitors, 1G and 2G, modulate trehalose and chitin metabolism pathways of larvae, ultimately resulting in the failure molting and reduction of survival rates. Consequently, the thioxothiazolidin compounds, 1G and 2G, hold potential as environmentally friendly insecticides. creator: Yan Wu creator: Shangrong Hu creator: Qixuan Mao creator: Dongmei Shi creator: Xiangyu Liu creator: Busheng Liu creator: Liyuhan Hua creator: Gao Hu creator: Can Li creator: Hongxia Duan creator: Bin Tang uri: https://doi.org/10.7717/peerj.18233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wu et al. title: Enhancement of loop-mediated isothermal amplification (LAMP) with guanidine hydrochloride for the detection of Streptococcus equi subspecies equi (Strangles) link: https://peerj.com/articles/17955 last-modified: 2024-10-08 description: Streptococcus equi subspecies equi, commonly referred to as “strangles”, poses a significant biosecurity challenge across equine farms worldwide. The continuous prevalence and highly transmissibility of strangles necessitates a rapid and accurate diagnostic procedure. However, current “gold-standard” techniques, such as cultures and quantitative polymerase chain reaction (qPCR), are unreliable or inaccessible, and require lengthy periods between sample collection and results. Moreover, the lack of a standardized detection protocol can lead to variations in results. This study aimed to develop a reproducible and field-deployable diagnostic assay to detect strangles in real-time. Utilising the rapid technique loop-mediated isothermal amplification (LAMP), we developed an assay targeting a conserved region of the S. equi-specific M gene (SeM). Additionally, we optimised our assay with guanidine hydrochloride (GuHCl) to enhance the assay’s performance and detection capabilities. The Str-LAMP was able to detect S. equi within 13 minutes and 20 seconds for both synthetic DNA and clinical isolates, with a limit of detection (LOD) of  53 copies/µl. Our assay demonstrated high repeatability with the inter-coefficient of variation ranging from 0.17% to 3.93%. Furthermore, the clinical sensitivity and specificity was calculated at 91.3% and 93.3%, respectively, with a correct classification rate of 91.8%. The implementation of this newly developed strangles assay can be employed as an efficient aid for in-field surveillance programs. The assay’s reproducibility can allow for equine managers to undertake routine self-surveillance on their properties, without the requirement of specialised training. The Str-LAMP assay has the potential to be a valuable tool to help mitigate potential strangles outbreaks. creator: Alexandra Knox creator: Travis Beddoe uri: https://doi.org/10.7717/peerj.17955 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Knox and Beddoe title: Adaptation and validation of the Spanish version of the Being a Mother scale link: https://peerj.com/articles/18015 last-modified: 2024-10-08 description: BackgroundBecoming a mother is a very important process because of the impact it can have on women and their families. Currently, there is no validated questionnaire that evaluates the process of becoming a mother in the Spanish population. Moreover, no consistent results have been obtained to identify significant differences between primiparous and multiparous mothers.Aim(1) Linguistic and metric validation of the Being a Mother scale (BaM-13) in the Spanish population, (2) analysis of possible differences between primiparous and multiparous mothers’ experience of motherhood.MethodsInstrumental design. In 2016–2017, a sample of 579 mothers with children between 6 and 11 months of age completed the Spanish version of BaM-13. The instrument was translated using forward and back translation. Construct validity, internal consistency, and criterion validity were empirically analyzed.ResultsFactorial analyses showed that the scale presented two adequate factors. Internal consistency of the global scale (α = 0.818, ω = 0.861), the Postnatal bonding factor (α = 0.773, ω = 0.784), and the Adult’s experience factor (α = 0.710, ω = 0.721) was adequate. Significant associations were found with postpartum depression (r = 0.560), parental competence (r =  − 0.584) and postnatal bonding (r =  − 0.327). In terms of parity, primiparous mothers have greater difficulty in postnatal bonding, compared to multiparous mothers (p = 0.006).ConclusionsThe Spanish version of the BaM-13 scale is valid for measuring mothers’ experience of motherhood in a wide range of domains. The findings of the study show the importance of considering parity in the experience of becoming a mother, highlighting the approach to postnatal bonding in primiparous mothers. Additionally, we underline that it should not be assumed that multiparous mothers experience fewer difficulties in their motherhood process. creator: Anna Riera-Martín creator: Antonio Oliver-Roig creator: Susana Cormenzana creator: Miguel Richart-Martínez creator: Ana Martínez-Pampliega uri: https://doi.org/10.7717/peerj.18015 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Riera-Martín et al. title: Passive smoking and risk of pancreatic cancer: an updated systematic review and meta-analysis link: https://peerj.com/articles/18017 last-modified: 2024-10-08 description: BackgroundPrevious meta-analysis has demonstrated that no association was validated between passive smoking and pancreatic cancer. However, there is growing evidence on this issue recently. This study aimed to confirm this association.MethodsPubMed, Embase, Web of Science, and Cochrane Library databases were searched up to April 2024 for retrieval of full articles. Studies with the exposure of passive smoking and outcome of pancreatic cancer were eligible for the analysis. We generated pooled relative risks (RRs) and 95% confidence intervals (CIs) using DerSimonian–Laird random-effects models. Quality of evidence was assessed using the GRADE system.ResultsFourteen studies were included, with 5,560 pancreatic cancer patients. Passive smoking was associated with a moderate increased risk of pancreatic cancer (RR = 1.20, 95% CI: 1.11–1.30, p < 0.001). The results were consistent in both case-control (p=0.013) and cohort studies (p < 0.001) and in studies with high (p = 0.007) and moderate quality (p < 0.001). In subgroup analysis, the risk was significant for both current (RR=1.91, 95% CI: 1.45-2.51, p < 0.001) and non-current smokers (RR = 1.17, 95% CI: 1.01-1.36, p = 0.037), for exposure both in adulthood (RR = 1.18, 95% CI: 1.06-1.31, p = 0.002) and childhood (RR = 1.20, 95% CI: 1.08-1.34, p = 0.001). However, only regular or daily exposure (RR=1.28, 95% CI: 1.08-1.50, p = 0.003), rather than exposing occasionally, seldom or few times per week (p = 0.421), to passive smoking could increase the risk of pancreatic cancer.ConclusionPassive smoking exposure confers a significant increased risk for pancreatic cancer. The risk was valid in both case-control and cohort, high and moderate quality studies, in current and non-current smokers, and for both childhood and adulthood exposure. Regular or daily exposure rather than exposing occasionally, seldom or few times per week could exert a detrimental effect on pancreatic cancer. creator: Xudong Wang creator: Zihan Wang creator: Xujie Wang uri: https://doi.org/10.7717/peerj.18017 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Wang et al. title: Bivalve microbiomes are shaped by host species, size, parasite infection, and environment link: https://peerj.com/articles/18082 last-modified: 2024-10-08 description: Many factors affect an organism’s microbiome including its environment, proximity to other organisms, and physiological condition. As filter feeders, bivalves have highly plastic microbiomes that are especially influenced by the surrounding seawater, yet they also maintain a unique core set of microbes. Using 16S ribosomal RNA sequencing, we characterized the bacterial microbiomes of four species of bivalves native to the Mid-Atlantic East Coast of North America: Crassostrea virginica, Macoma balthica, Ameritella mitchelli, and Ischadium recurvum and assessed the impact of their external environment, internal parasites, and size on their microbial communities. We found significant differences in bacterial amplicon sequence variants (ASVs) across species, with each species harboring a core ASV present across all individuals. We further found that some C. virginica co-cultured with I. recurvum had high abundances of the I. recurvum core ASV. We identified ASVs associated with infection by the parasites Perkinsus marinus and Zaops ostreum as well others associated with bivalve size. Several of these ASV are candidates for further investigation as potential probiotics, as they were found positively correlated with bivalve size and health. This research represents the first description of the microbiomes of A. mitchelli, I. recurvum, and M. balthica. We document that all four species have highly plastic microbiomes, while maintaining certain core bacteria, with important implications for growth, health, and adaptation to new environments. creator: Sarah Gignoux-Wolfsohn creator: Monserrat Garcia Ruiz creator: Diana Portugal Barron creator: Gregory Ruiz creator: Katrina Lohan uri: https://doi.org/10.7717/peerj.18082 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gignoux-Wolfsohn et al. title: Brain tissue oxygen pressure combined with intracranial pressure monitoring may improve clinical outcomes for patients with severe traumatic brain injury: a systemic review and meta-analysis link: https://peerj.com/articles/18086 last-modified: 2024-10-08 description: BackgroundAlthough the optimization of brain oxygenation is thought to improve the prognosis, the effect of brain tissue oxygen pressure (PbtO2) for patients with severe traumatic brain injury (STBI) remains controversial. Therefore, the present study aimed to determine whether adding PbtO2 to intracranial pressure (ICP) monitoring improves clinical outcomes for patients with STBI.MethodsPubMed, Embase, Scopus and Cochrane Library were searched for eligible trials from their respective inception through April 10th, 2024. We included clinical trials contrasting the combined monitoring of PbtO2 and ICP versus isolated ICP monitoring among patients with STBI. The primary outcome was favorable neurological outcome at 6 months, and secondary outcomes including the in-hospital mortality, long-term mortality, length of stay in intensive care unit (ICU) and hospital.ResultsA total of 16 studies (four randomized studies and 12 cohort studies) were included in the meta-analysis. Compared with isolated ICP monitoring, the combined monitoring was associated with a higher favorable neurological outcome rate at 6 months (RR 1.33, 95% CI [1.17–1.51], P < 0.0001, I2 = 0%), reduced long-term mortality (RR 0.72, 95% CI [0.59–0.87], P = 0.0008, I2 = 2%). No significant difference was identified in the in-hospital mortality (RR 0.81, 95% CI 0.66 to 1.01, P = 0.06, I2 = 32%), length of stay in ICU (MD 2.10, 95% CI [−0.37–4.56], P = 0.10, I2 = 78%) and hospital (MD 1.07, 95% CI [−2.54–4.67], P = 0.56, I2 = 49%) between two groups. However, the pooled results of randomized studies did not show beneficial effect of combined monitoring in favorable neurological outcome and long-term mortality.ConclusionsCurrently, there is limited evidence to prove that the combined PbtO2 and ICP monitoring may contribute to improved neurological outcome and long-term mortality for patients with STBI. However, the benefit of combined monitoring should be further validated in more randomized studies. creator: Chengcheng Zhang creator: Lingmin Zhou creator: Kai Zhang creator: Jian Huang creator: Lanxin Cao creator: Yuhang Lou creator: Yushi Fan creator: Xinyun Zhang creator: Yesong Wang creator: Wei Cui creator: Lihua Hu creator: Gensheng Zhang uri: https://doi.org/10.7717/peerj.18086 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: A preliminary study of carbon dioxide and methane emissions from patchy tropical seagrass meadows in Thailand link: https://peerj.com/articles/18087 last-modified: 2024-10-08 description: BackgroundSeagrass meadows are a significant blue carbon sink due to their ability to store large amounts of carbon within sediment. However, the knowledge of global greenhouse gas (GHG) emissions from seagrass meadows is limited, especially from meadows in the tropical region. Therefore, in this study, CO2 and CH4 emissions and carbon metabolism were studied at a tropical seagrass meadow under various conditions.MethodsCO2 and CH4 emissions and carbon metabolism were measured using benthic chambers deployed for 18 h at Koh Mook, off the southwest coast of Thailand. The samples were collected from areas of patchy Enhalus acoroides, Thalassia hemprichii, and bare sand three times within 18 h periods of incubation: at low tide at 6 pm (t0), at low tide at 6 am (t1), and at high tide at noon (t2).ResultsSeagrass meadows at Koh Mook exhibited varying CO2 and CH4 emissions across different sampling areas. CO2 emissions were higher in patchy E. acoroides compared to patchy T. hemprichii and bare sand areas. CH4 emissions were only detected in vegetated areas (patchy E. acoroides and T. hemprichii) and were absent in bare sand. Furthermore, there were no significant differences in net community production across sampling areas, although seagrass meadows were generally considered autotrophic. Koh Mook seagrass meadows contribute only slightly to GHG emissions. The results suggested that the low GHG emissions from Koh Mook seagrass meadows do not outweigh their role as significant carbon sinks, with a value 320 t CO2−eq. This study provided baseline information for estimating GHG emissions in seagrass meadows in Thailand. creator: Muhammad Halim creator: Milica Stankovic creator: Anchana Prathep uri: https://doi.org/10.7717/peerj.18087 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Halim et al. title: The departure of sperm whales (Physeter macrocephalus) in response to the declining jumbo squid (Dosidicus gigas) population in the central portion of the Gulf of California link: https://peerj.com/articles/18117 last-modified: 2024-10-08 description: As sperm whales are important predators that control energy flux in the oceans, changes in their population can be used as a sentinel to measure of ecosystem health. The present study conducted a sperm whale survey of the eastern Midriff Islands Region in the Gulf of California over the course of nine years, recording sightings and collecting photographs of the fluke of sperm whale individuals. A photo-identification catalog was compiled, while individual recapture data were used to estimate the population size in the central portion of the Gulf of California, using a Jolly-Seber POPAN open population model. The results obtained show a yearly population of between 20 and 167 sperm whales, with a super population of 354 sperm whales observed between 2009 and 2015. However, from 2016 to 2018, no sightings of the species were recorded, which coincides with the decline observed in landings of their main prey, the jumbo squid, in the region. General additive model conducted on sperm whale sightings per unit of effort vs jumbo squid landings obtained an adjusted R2 of 0.644 and a deviance explained of 60.3%, indicating a good non-linear relationship between sightings of this odontocete and its prey availability. This evidence suggests that sperm whales departed the region between 2016 and 2018, due to a documented fishery collapse alongside changes of their main prey into its small phenotype, possibly as the result of increase warming conditions in surface and subsurface waters in the Gulf of California in the last three decades. creator: Héctor Pérez-Puig creator: Alejandro Arias Del Razo creator: Daniela Ahuatzin Gallardo creator: Jaime Bolaños uri: https://doi.org/10.7717/peerj.18117 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pérez-Puig et al. title: Assessment of combined serum sST2 and AFP levels in the diagnosis of hepatocellular carcinoma link: https://peerj.com/articles/18142 last-modified: 2024-10-08 description: BackgroundHepatocellular carcinoma (HCC) is a common malignant tumor with high morbidity and mortality. Alpha-fetoprotein (AFP) is the most widely used diagnostic serum biomarker, but it still has limited accuracy in detecting HCC, suggesting the necessity of seeking more ideal biomarkers with high sensitivity and specificity. Soluble growth stimulation gene 2 (sST2) form of growth stimulating expression gene 2 (ST2), is expressed in various organs and can bind competitively to interleukin 33 (IL-33). Whether sST2 can serve as a serum biomarker for HCC is largely unknown.ObjectiveTo investigate the value of sST2 as a serum diagnostic marker for HCC.MethodsThis study included 93 newly diagnosed HCC patients (HCC group), 90 chronic hepatitis B patients (CHB group), and 90 healthy individuals (HCs group). Spearman correlation analysis was used to explore the relationships between sST2 and the experimental indicators in HCC group. The receiver operating characteristic (ROC) curve evaluated the efficacy of sST2 alone or in combination with AFP in the diagnosis of HCC.ResultThe median level of sST2 was significantly higher in HCC group (24.00 [15.20-49.90] ng/mL) compared to CHB group (19.55 [15.23-24.95] ng/mL) and HCs group (7.65 [5.20-10.53] ng/mL). No significant correlations were found between sST2 and other clinical indicators in HCC group. The Area Under Curve (AUC) of ROC curve to distinguish HCC patients from healthy controls and CHB group was 0.861 (sensitivity 82.80%, specificity 72.10%) and 0.709 (sensitivity 80.60%, specificity 52.50%), respectively. When combined with AFP, the AUC increased to 0.963 (sensitivity 82.90%, specificity 94.20%), and 0.895 (sensitivity 72.0%, specificity 100%), respectively.ConclusionsThe serum level of sST2 increased in HCC and its diagnostic performance is comparable to that of AFP, supporting its potential as a promising biomarker for detection of HCC. The combined use of sST2 and AFP enhances diagnostic efficacy for HCC. creator: Xiuxin Tang creator: Dong Wang creator: Tangdan Ding creator: Rongqi Lin creator: Meifang He creator: Ruizhi Wang creator: Liubing Li uri: https://doi.org/10.7717/peerj.18142 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tang et al. title: Increased CD14+HLA-DR-/low myeloid-derived suppressor cells can be regarded as a biomarker on disease severity and response to therapy in acute coronary syndrome link: https://peerj.com/articles/18154 last-modified: 2024-10-08 description: PurposeThis study aimed to investigate the dynamic changes in monocytic myeloid-derived suppressor cells (M-MDSCs) and their implications in the pathogenesis of acute coronary syndrome (ACS), shedding light on potential therapeutic targets.Experimental DesignPeripheral blood samples were collected from 68 ACS patients, 35 stable angina pectoris (SAP) patients, and 30 healthy controls (HC). Multi-parameter flow cytometry was employed for analysis of M-MDSCs, explored with disease characteristics and progression.ResultsACS patients exhibited an increased frequency of circulating M-MDSCs compared to SAP patients and HC. M-MDSCs levels demonstrated associations with ACS type, coronary artery lesions, multi-vessel disease, and cardiac dysfunction severity. Higher M-MDSCs levels were found in obese patients. Notably, therapy led to a significant decrease in M-MDSCs frequency. Furthermore, ACS patients exhibited elevated levels of interleukin (IL)-6, IL-10, granulocyte-macrophage colony-stimulating factor (GM-CSF), and tumor necrosis factor-α (TNF-α) in the cytokine profile associated with M-MDSCs. Increased expression of arginase-1(Arg-1) was observed in ACS patients, with positive correlations between M-MDSCs levels and IL-6, GM-CSF, and Arg-1 expression. The diagnostic performance of triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and M-MDSCs levels varied in predicting the severity of coronary artery stenosis, with TG showing higher specificity, HDL-C displaying higher sensitivity, and M-MDSCs levels demonstrating balanced sensitivity and specificity.ConclusionsAssessment of M-MDSCs frequency holds promise as a predictive marker for disease progression and therapy response of coronary artery stenosis. The elevated presence of M-MDSCs suggests their potential role in modulating ACS-related inflammation. creator: Yinsheng Tan creator: Mingde Ren creator: Jie Hou creator: Tao Hou creator: Xianhe Lin uri: https://doi.org/10.7717/peerj.18154 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tan et al. title: The vaginal metabolomics profile with features of polycystic ovary syndrome: a pilot investigation in China link: https://peerj.com/articles/18194 last-modified: 2024-10-08 description: BackgroundPolycystic ovary syndrome (PCOS) is the most common metabolic disorder and reproductive endocrine disease, posing an elevated risk to women of reproductive age. Although metabolism differences in serum, amniotic fluid and urine have been documented in PCOS, there remains a paucity of evidence for vaginal fluid. This study aimed to identify the metabolic characteristics and potential biomarkers of PCOS in Chinese women of reproductive age.MethodsWe involved ten newly diagnosed PCOS women who attended gynecology at Zhongda Hospital and matched them with ten healthy controls who conducted health check-up programs at Gulou Maternal and Child Health Center in Nanjing, China from January 1st, 2019 to July 31st, 2020. Non-targeted metabolomics based on ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) was applied to differentially screen vaginal metabolites between PCOS group and healthy controls. Principal component analysis (PCA), orthogonal partial least-squares discriminant analysis (OPLS-DA) and enrichment analysis were used to observe differences, search for potential biomarkers and enrich related pathways.ResultsAmong the 20 participants, a total of 195 different metabolites were detected between PCOS group and healthy control group. PCOS and control groups were effectively separated by vaginal fluid. Lipids and lipid-like molecules constituted the majority of differential metabolites. Notably, dopamine exhibited an increased trend in PCOS group and emerged as the most significant differential metabolite, suggesting its potential as a biomarker for identifying PCOS. The application of UHPLC-MS/MS based vaginal metabolomics methods showed significant differences between PCOS and non-PCOS healthy control groups, especially linoleic acid metabolism disorder. Most differential metabolites were enriched in pathways associated with linoleic acid metabolism, phenylalanine metabolism, tyrosine metabolism, nicotinate and nicotinamide metabolism or arachidonic acid metabolism.ConclusionsIn this pilot investigation, significant metabolomics differences could be obtained between PCOS and healthy control groups. For PCOS women of reproductive age, vaginal metabolism is a more economical, convenient and harmless alternative to provide careful personalized health diagnosis and potential targets for therapeutic intervention. creator: Yan Xuan creator: Xiang Hong creator: Xu Zhou creator: Tao Yan creator: Pengfei Qin creator: Danhong Peng creator: Bei Wang uri: https://doi.org/10.7717/peerj.18194 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xuan et al. title: Contribution of socio-demographic factors in prevalence of soil-transmitted helminth infections among newly arrived laborers in Jeddah, Saudi Arabia link: https://peerj.com/articles/18216 last-modified: 2024-10-08 description: BackgroundSoil-transmitted diseases are caused by intestinal worms transmitted via various routes into the human body resulting in various clinical manifestations. This study aimed to investigate the socio-demographic factors contributing mainly to the prevalence of soil-transmitted helminths (STHs) among newly arrived laborers in Jeddah, Saudi Arabia.MethodsA total of 188 stool specimens were collected and examined macroscopically and microscopically using different techniques. In addition, real-time PCR was used as a molecular tool to detect several STHs. The descriptive analysis was used to evaluate demographic data and categorical variables in association with STHs infection.ResultsOf all participants, the mean age was 26.08 ± 2.67 years, including 103 females and 85 males. A total of 86 (45.70%) were illiterate, followed by 60 (31.90%) of participants belonging to elementary level. STHs and other intestinal parasites were detected among 35 newly arrived laborers (18.61%). Nineteen cases (10.11%) were infected with STHs, including 15 cases with one STHs (four A. lumbricoides, four N. americanus, four T. trichiura, two S. stercoralis, one A. duodenale) and four cases with two STHs (two T. trichiura and N. americanus; one S. stercoralis and A. duodenale; one T. trichiura and S. stercoralis). High rates of STHs infection were detected among drivers (11.70%) followed by housemaids (11.20%), but with no significant association to occupation. Higher rates of STHs infection were detected among those used to walk on soil barefoot in their home countries before arriving in Jeddah.ConclusionThis study found that none of the newly arrived expatriate laborers in Jeddah was aware of STHs. About 10% of them had infection with one or two STHs, mainly among newly arrived laborers from Asian countries. There is a need for awareness programs and regular screening for STHs and other intestinal parasites among newly arrived expatriate laborers. creator: Majed H. Wakid creator: Mohammad F. Al-Refai uri: https://doi.org/10.7717/peerj.18216 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wakid and Al-Refai title: Cross-cultural adaptation and psychometric properties of the Arabic version of the Central Sensitization Inventory in people with chronic musculoskeletal pain link: https://peerj.com/articles/18251 last-modified: 2024-10-08 description: BackgroundThe Central Sensitization Inventory (CSI) is a patient-reported screening instrument that can be used to identify and assess central sensitization (CS)/Central Sensitization Syndrome (CSS)-related symptoms.ObjectiveThe aim was to translate the CSI into Arabic (CSI-Ar) and to subsequently validate its psychometric properties.DesignCross-sectional.MethodsThe CSI was translated and cross-culturally adapted into Arabic, and validated following international standardized guidelines. This study included patients with chronic musculoskeletal pain (n = 264) and healthy control participants (n = 56). Patients completed the CSI-Ar, Pain Catastrophizing Scale (PCS), Depression, Anxiety, and Stress scale (DASS-21), Tampa Scale of Kinesiophobia (TSK), and 5-level EuroQol-5D (EQ-5D). Patients completed the CSI-Ar twice to assess test–retest reliability. To evaluate discriminative validity, healthy controls participants completed the CSI-Ar. Statistical analyses were conducted to test the internal consistency, reliability, and structural, construct and discriminant validity of CSI-Ar.ResultsThe CSI-Ar showed acceptable internal consistency (Cronbach’s alpha = 0.919) and excellent test–retest reliability (intraclass correlation coefficient = 0.874). The CSI-Ar scale had significant correlations (P < 0.001) with all PCS subscales and total score (Spearman’s rho = 0.459–0.563, P < 0.001), all DASS-21 subscales and total score (Spearman’s rho = 0.599–0.685, P < 0.001), the TSK (Spearman’s rho = 0.395, P < 0.001), and the EQ-5D (Spearman’s rho = −0.396, P < 0.001). The Mann-Whitney U-test showed a statistically significant difference between the patient group and the healthy control group (P < 0.001), with the healthy controls displaying a lower average CSI-Ar score (12.27 ± 11.50) when compared to the patient group (27.97 ± 16.08). Factor analysis indicated that the CSI-Ar is a unidimensional tool.ConclusionThe CSI-Ar is a reliable and valid screening tool that can be used to assess CS/CSS-related symptoms in Arabic-speaking people with chronic musculoskeletal pain. creator: Sarah E. Tamboosi creator: Hosam Alzahrani creator: Fahad H. Alshehri creator: Msaad Alzhrani creator: Yasir S. Alshehri uri: https://doi.org/10.7717/peerj.18251 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tamboosi et al. title: Effectiveness of newborn infant parasympathetic evaluation (NIPE) index for guiding intraoperative fentanyl administration in children under 2 years: a randomized controlled trial link: https://peerj.com/articles/18267 last-modified: 2024-10-08 description: BackgroundAssessing pain in infants and neonates is challenging due to their inability to communicate verbally. While validated subjective tools exist, they rely on interpreting the child’s behavior, leading to potential inconsistencies and underestimation of pain. Based on heart rate variability, the newborn infant parasympathetic evaluation (NIPE) index offers a more objective approach to pain assessment in children under 2 years. Although promising, research on its effectiveness during surgery under general anesthesia remains limited and inconclusive.ObjectiveThis study compared the effectiveness of NIPE-guided fentanyl administration to traditional vital signs (heart rate and mean arterial pressure) in managing pain during surgery in children under 2 years.MethodsSeventy children undergoing head, neck, or upper extremity surgery were randomized into group N (NIPE) or group C (Control) with 35 participants in each group. Both groups received standardized anesthesia and monitoring, including NIPE. Group N received fentanyl when NIPE scores fell below 50, while group C received fentanyl upon a 20% increase in heart rate or mean arterial pressure (MAP). Postoperative pain was assessed using the Face, Legs, Activity, Cry, and Consolability (FLACC) scores, alongside fentanyl consumption, sedation levels, and potential side effects.ResultsBoth groups exhibited similar outcomes in terms of postoperative pain scores, fentanyl consumption, sedation levels, and absence of side effects (postoperative respiratory depression or nausea and vomiting). Additionally, intraoperative NIPE scores, heart rate, and MAP were comparable between the groups. There are strong correlations between both groups in terms of NIPE scores (r = 0.735, p < 0.0001), heart rate (r = 0.630, p < 0.0001), and MAP (r = 0.846, p < 0.0001). In both group C and group N, the NIPE scores reveal strong negative correlations with heart rate (r = −0.610, p < 0.0001, and r = −0.674, p < 0.0001) and MAP (r = −0.860, p < 0.0001, and r = −0.756, p < 0.0001).ConclusionNIPE-guided intraoperative fentanyl administration was not superior to heart rate/MAP-guided administration, as both achieved similar pain management outcomes in this study. However, NIPE may offer a more practical and precise approach, as it is an objective tool with a defined threshold. These findings suggest NIPE’s promise as a valuable tool for managing pain in children under 2 years undergoing surgery. However, confirmation of its widespread effectiveness requires further research with larger, multicenter studies encompassing procedures with a broader spectrum of pain severity. creator: Darunee Sripadungkul creator: Sirirat Tribuddharat creator: Thepakorn Sathitkarnmanee creator: Pimprapa Muenpirom creator: Panaratana Ratanasuwan uri: https://doi.org/10.7717/peerj.18267 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sripadungkul et al. title: Efficacy and safety of intracavitary electrocardiography-guided peripherally inserted central catheters in pediatric patients: a systematic review and meta-analysis link: https://peerj.com/articles/18274 last-modified: 2024-10-08 description: ObjectiveTo assess the efficacy and safety of intracavitary electrocardiography (IC-ECG)-guided peripherally inserted central catheter (PICC) placements in pediatric patients, emphasizing improvements over traditional placement methods.MethodsA literature search was conducted in April 2024 across PubMed, Cochrane Library, and EMBASE. Studies focusing on pediatric patients and reporting the efficacy and safety of IC-ECG-guided PICC placement via the upper extremity were included. This study was registered with the PROSPERO database (CRD42024549037) in accordance with PRISMA guidelines.ResultsEleven studies were included, comprising five randomized controlled trials (RCTs) and six quasi-experimental studies. The pooled analysis showed that IC-ECG had an applicability and feasibility of 97% and 98%, respectively. The first puncture success rate was 91%, and the overall success rate was 98%. Sensitivity and specificity were 97% and 80%, respectively. IC-ECG significantly reduced overall complications compared to traditional methods (RR: 0.31, 95% CI [0.20–0.46], p < 0.00001), particularly in phlebitis (RR: 0.25, 95% CI [0.11–0.57], p = 0.001) and arrhythmias (RR: 0.09, 95% CI [0.01–0.70], p = 0.021). Similar results were observed in neonates. Only one case of catheter-related bloodstream infection (CRBSI) was reported, and no arrhythmia events were noted.ConclusionIC-ECG-guided PICC placement is a highly effective and safe method for pediatric patients, including neonates, offering significant advantages over traditional techniques. Further high-quality studies are needed to standardize procedural techniques and explore cost-effectiveness. creator: Li Zhang creator: Min Wang creator: Mingjia Zhao creator: Siyi Pu creator: Jiao Zhao creator: Ge Zhu creator: Qin Zhang creator: Dan Li uri: https://doi.org/10.7717/peerj.18274 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Population isolation in the Plains spadefoot toad: causes and conservation implications link: https://peerj.com/articles/17968 last-modified: 2024-10-07 description: Range disjunctions appear to be common in nature, although they may be caused by various factors. They may simply be an artefact of inadequate sampling. If real, they may be the result of colonization events or habitat change. With natural habitats showing increasing fragmentation because of human activity, understanding the cause of a disjunction can have important conservation implications. We investigate the geographical range of the Plains spadefoot toad, Spea bombifrons, a widely distributed species in the midwestern and southwestern United States, with a putative disjunct population in southern Texas. We combine GIS mapping, species distribution modeling, and population genetic analysis to investigate this putative disjunction. We establish that this southern Texas population is truly geographically disjunct and genetically distinct. Further, using climate projections we show that this unique population is at high risk of local extinction. creator: Amanda J. Chunco creator: Emma Nault creator: Rebecca F. Silverman creator: Sarah Midolo creator: Hanna Harper creator: Amber M. Rice uri: https://doi.org/10.7717/peerj.17968 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chunco et al. title: Application of a reaction-based water quality model to the total dissolved solids concentration of the Pasig River link: https://peerj.com/articles/18076 last-modified: 2024-10-07 description: With the goal to support effective water resource management, water quality models have gained popularity as tools for evaluating the distributions of pollutants and sediments. This work focuses on the application of the numerical solution of an advection-dispersion-reaction (ADR) water quality model for rivers and streams to a major Philippine waterway, the Pasig River. The water quality constituent is described by a system of reaction and advection-dispersion-reaction equations. The model and method are based on a previously used strategy where Guass-Jordan decomposition is applied to the matrix system and the resulting conservative form of the model is solved numerically using the fully implicit scheme and finite element method. The methodology is demonstrated by a case study in Pasig River involving the concentrations of total dissolved solids (TDS) obtained from the Department of Environment and Natural Resources (DENR) through the Pasig River Unified Monitoring Stations (PRUMS) report. Sensitivity analysis and parameter estimation are also applied to the model to assess which parameters influence the model output the most. creator: Crisanto L. Abas creator: Arrianne Crystal Velasco creator: Carlene Arceo uri: https://doi.org/10.7717/peerj.18076 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Abas et al. title: Genotype-specific responses to in vitro drought stress in myrtle (Myrtus communis L.): integrating machine learning techniques link: https://peerj.com/articles/18081 last-modified: 2024-10-07 description: BackgroundMyrtle (Myrtus communis L.), native to the Mediterranean region of Türkiye, is a valuable plant with applications in traditional medicine, pharmaceuticals, and culinary practices. Understanding how myrtle responds to water stress is essential for sustainable cultivation as climate change exacerbates drought conditions.MethodsThis study investigated the performance of selected myrtle genotypes under in vitro drought stress by employing tissue culture techniques, rooting trials, and acclimatization processes. Genotypes were tested under varying polyethylene glycol (PEG) concentrations (1%, 2%, 4%, and 6%). Machine learning (ML) algorithms, including Gaussian process (GP), support vector machine (SVM), Random Forest (RF), and Extreme Gradient Boosting (XGBoost), were utilized to model and predict micropropagation and rooting efficiency.ResultsThe research revealed a genotype-dependent response to drought stress. Black-fruited genotypes exhibited higher micropropagation rates compared to white-fruited ones under stress conditions. The application of ML models successfully predicted micropropagation and rooting efficiency, providing insights into genotype performance.ConclusionsThe findings suggest that selecting drought-tolerant genotypes is crucial for enhancing myrtle cultivation. The results underscore the importance of genotype selection and optimization of cultivation practices to address climate change impacts. Future research should explore the molecular mechanisms of stress responses to refine breeding strategies and improve resilience in myrtle and similar economically important crops. creator: Ümit Bektaş creator: Musab A. Isak creator: Taner Bozkurt creator: Dicle Dönmez creator: Tolga İzgü creator: Mehmet Tütüncü creator: Özhan Simsek uri: https://doi.org/10.7717/peerj.18081 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bektaş et al. title: Longitudinal relations between non-suicidal self-injury and both depression and anxiety among senior high school adolescents: a cross-lagged panel network analysis link: https://peerj.com/articles/18134 last-modified: 2024-10-07 description: BackgroundComorbidity between non-suicidal self-injury (NSSI) and depression and anxiety was common. In the framework of network theory, the examination of directionality and gender differences in longitudinal relationships at the symptom level made a significant contribution to the understanding of comorbidity. Therefore, this study employed cross-lagged panel network analysis to investigate the longitudinal interrelations between NSSI and depression and anxiety in Chinese adolescents, with a focus on gender differences.MethodThe study was conducted with a sample of 884 senior high school students (F/M: 481/403; mean age: 15.19 ± 0.48 years) from Jinchang City, Gansu Province, China. All respondents completed the Adolescent Non-Suicidal Self-Injury Assessment Questionnaire and the two subscales (depression and anxiety) of the Brief Symptom Inventory at two intervals. The data were estimated in R 4.2.0 to construct the cross-lagged panel network (CLPN).ResultsThe CLPN results uncovered the gender differences. For boys, self-hitting and feeling scared emerged as central symptoms. Cutting predicted subsequent feelings of sadness (β =  − 0.57), tension (β =  − 0.52) and indifference (β =  − 0.49), potentially serving as a bridge connecting NSSI to depression and anxiety. For girls, biting themselves and feeling scared were central symptoms. Carving and skin rubbing predicted subsequent feelings of indifference (β =  − 0.31, −0.21), bridging NSSI to depression and anxiety. In addition, feeling scared emerged as the key bridge symptom connecting depression and anxiety.ConclusionThe findings showed the gender-specific developmental characteristics of the directional relations between NSSI and depression and anxiety at the symptom level. They provided new insights into the comorbidity of NSSI and depression and anxiety, carrying important implications for the screening and intervention of adolescent NSSI. creator: Haiyan Zhao creator: Aibao Zhou uri: https://doi.org/10.7717/peerj.18134 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao and Zhou title: Licorice-root extract and potassium sorbate spray improved the yield and fruit quality and decreased heat stress of the ‘osteen’ mango cultivar link: https://peerj.com/articles/18200 last-modified: 2024-10-07 description: Heat stress, low mango yields and inconsistent fruit quality are main challenges for growers. Recently, licorice-root extract (LRE) has been utilized to enhance vegetative growth, yield, and tolerance to abiotic stresses in fruit trees. Potassium sorbate (PS) also plays a significant role in various physiological and biochemical processes that are essential for mango growth, quality and abiotic stress tolerance. This work aimed to elucidate the effects of foliar sprays containing LRE and PS on the growth, yield, fruit quality, total chlorophyll content, and antioxidant enzymes of ‘Osteen’ mango trees. The mango trees were sprayed with LRE at 0, 2, 4 and 6 g/L and PS 0, 1, 2, and 3 mM. In mid-May, the mango trees were sprayed with a foliar solution, followed by monthly applications until 1 month before harvest. The results showed that trees with the highest concentration (6 g/L) of LRE exhibited the maximum leaf area, followed by those treated with the highest concentration (3 mM) of PS. Application of LRE and PS to Osteen mango trees significantly enhanced fruit weight, number of fruits per tree, yield (kg/tree), yield increasing%, and reduced number of sun-burned fruits compared to the control. LRE and PS foliar sprays to Osteen mango trees significantly enhanced fruit total soluble solids ˚Brix, TSS/acid ratio, and vitamin C content compared to the control. Meanwhile, total acidity percentage in ‘Osteen’ mango fruits significantly decreased after both LRE and PS foliar sprays. ‘Osteen’ mango trees showed a significant increase in leaf area, total chlorophyll content, total pigments, and leaf carotenoids. Our results suggest that foliar sprays containing LRE and PS significantly improved growth parameters, yield, fruit quality, antioxidant content, and total pigment concentration in ‘Osteen’ mango trees. Moreover, the most effective treatments were 3 mM PS and 6 g/L LRE. LRE and PS foliar spray caused a significant increase in yield percentage by 305.77%, and 232.44%, in the first season, and 242.55%, 232.44% in the second season, respectively. creator: Adel M. Al-Saif creator: Haitham Ahmed El-khamissi creator: Ibrahim Ahmed Elnaggar creator: Mohammed Hamdy Farouk creator: Magdy Abd El-Wahab Omar creator: Abd El-wahed Naser Abd El-wahed creator: Ashraf Ezzat Hamdy creator: Hosny Fathy Abdel-Aziz uri: https://doi.org/10.7717/peerj.18200 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Al-Saif et al. title: A novel gene silencing strategy based on tobacco rattle virus in Hibiscus mutabilis link: https://peerj.com/articles/18211 last-modified: 2024-10-07 description: BackgroundHibiscus mutabilis L. is a popular regional characteristic plant in China, cultivated for its attractive flower colors, extended bloom time, and medicinal properties. To enhance molecular breeding and gene function studies, we conducted transcriptome analysis and identified valuable genes in previous research. Nonetheless, the current inefficient and labor-intensive transformation techniques have hindered their applications. Virus-induced gene silencing (VIGS) provides a precise and effective strategy for post-transcriptional down-regulation of endogenous gene expression.MethodsWe investigated the performance of tobacco rattle virus (TRV) as a tool for targeting and silencing the gene encoding the protein involved in chloroplast development, cloroplastos alterados 1 (altered chloroplast; CLA1), of H. mutabilis through Agrobacterium tumefaciens-mediated infiltration.ResultsBy effectively suppressing the CLA1 gene associated with chloroplast development in H. mutabilis via the TRV-VIGS system, we have illustrated the inaugural implementation of VIGS in this species. Quantitative RT-PCR proved that HmCLA1 expression in agro-infiltrated plants was lower than in the mock-infiltrated (mock) and the control (CK) plants. Phenotypic observations corroborated the albino phenotype in leaves following successful HmCLA1 silencing.ConclusionsOur study showcases TRV-VIGS as a potential gene silencing tool for H. mutabilis, facilitating functional genomics studies and molecular breeding efforts in this species. creator: Shiye Sang creator: Yiqiong Liu creator: Xiu Li creator: Jiao Ma creator: Xiaoli Liu creator: Yuanzhao Yang uri: https://doi.org/10.7717/peerj.18211 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Sang et al. title: Cross-cultural adaptation and psychometric properties of the Chinese version of the Intermittent Self-Catheterization Questionnaire (ISC-Q) link: https://peerj.com/articles/18226 last-modified: 2024-10-07 description: BackgroundThe intermittent self-catheterization questionnaire (ISC-Q) is a valid and reliable tool to assess the quality of life (QOL) in patients with neurogenic lower urinary tract dysfunction (NLUTD) who engage in ISC. The aim of this research is to culturally adapt the ISC-Q and evaluate its psychometric properties within the Chinese patient population.MethodsThe cross-sectional research was meticulously conducted in two pivotal stages: initially, the focus was on cross-cultural adaptation, followed by an extensive phase of psychometric testing. This comprehensive analysis involved 405 Chinese patients with NLUTD who use ISC. Various analyses, including evaluations of the floor and ceiling effects, item analysis, content validity, exploratory and confirmatory factor analysis (EFA and CFA), assessments of convergent, discriminant, and criterion validity. Additionally, Cronbach’s alpha was utilized to determine internal consistency, and test-retest reliability was measured using the intraclass correlation coefficient (ICC).ResultsNo floor and ceiling effects were observed. The content validity index was 0.967. The EFA identified four factors, accounting for 64.953% of the total variance, and this four-factor structure was confirmed by the CFA. The fit indices in CFA were favorable, with χ2/df = 1.999, root mean square error of approximation = 0.070, comparative fit index = 0.916, Tucker–Lewis index = 0.900, goodness-of-fit index = 0.863, and incremental fit index = 0.917. The average variance extracted for the four factors ranged from 0.466 to 0.565, with composite reliability values ranging from 0.776 to 0.859. The ISC-Q showed a positive correlation with the intermittent self-catheterization acceptance questionnaire (r = 0.557, P < 0.001). The ICC overall Cronbach’s alpha coefficient for the questionnaire was 0.821, and the for test-retest reliability was 0.951 (95% CI [0.900–0.976] P < 0.001).ConclusionThe validity and reliability of the Chinese version of the ISC-Q have been verified, making it suitable for measuring the QOL in NLUTD patients who practice ISC. creator: Yingjie Hu creator: Fengming Hao creator: Ling Chen creator: Ying Wang creator: Laifu Wang creator: Dan Wu creator: Wei Ren creator: Wenzhi Cai uri: https://doi.org/10.7717/peerj.18226 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Hu et al. title: Genome-wide association study reveals genetic basis and candidate genes for chlorophyll content of leaves in maize (Zea mays L.) link: https://peerj.com/articles/18278 last-modified: 2024-10-07 description: The chlorophyll content (CC) directly affects photosynthesis, growth, and yield. However, the genetic basis of CC is still unclear in maize (Zea mays L.). Here, we conducted a genome-wide association study using mixed linear model for CC of the fifth leaves at seedling stage (CCFSS) and the ear leaves at filling stage (CCEFS) for 334 maize inbred lines. The heritability estimates for CCFSS and CCEFS, obtained via variance components analysis using the lme4 package in R, were 70.84% and 78.99%, respectively, indicating that the CC of leaves is primarily controlled by genetic factors. A total of 15 CC-related SNPs and 177 candidate genes were identified with a p-value < 4.49 × 10−5, which explained 4.98–7.59% of the phenotypic variation. Lines with more favorable gene variants showed higher CC. Meanwhile, Gene Ontology (GO) analysis implied that these candidate genes were probably related to chlorophyll biosynthesis. In addition, gene-based association analyses revealed that six variants in GRMZM2G037152, GRMZM5G816561, GRMZM2G324462, and GRMZM2G064657 genes were significantly (p-value < 0.01) correlated with CC, of which GRMZM2G064657 (encodes a phosphate transporter protein) and GRMZM5G816561 (encodes a cytochrome P450 protein) were specifically highly expressed in leaves tissues. Interestingly, these candidate genes were previously reported to involve in the regulation of the contents of chlorophyll in plants or Chlamydomonas. These results may contribute to the understanding of genetic basis and molecular mechanisms of maize CC and the selection of maize varieties with improved CC. creator: Peng Liu creator: Chenchaoyang Xiang creator: Kai Liu creator: Hong Yu creator: Zhengqiao Liao creator: Yaou Shen creator: Lei Liu creator: Langlang Ma uri: https://doi.org/10.7717/peerj.18278 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Changes in the force-time curve during a repeat power ability assessment using loaded countermovement jumps link: https://peerj.com/articles/17971 last-modified: 2024-10-04 description: BackgroundRepeat power ability (RPA) assessments traditionally use discrete variables, such as peak power output, to quantify the change in performance across a series of jumps. Rather than using a discrete variable, the analysis of the entire force-time curve may provide additional insight into RPA performance. The aims of this study were to (1) analyse changes in the force-time curve recorded during an RPA assessment using statistical parametric mapping (SPM) and (2) compare the differences in the force-time curve between participants with low and high RPA scores, as quantified by traditional analysis.Materials and MethodsEleven well-trained field hockey players performed an RPA assessment consisting of 20 loaded countermovement jumps with a 30% one repetition maximum half squat load (LCMJ20). Mean force-time series data was normalized to 100% of the movement duration and analysed using SPM. Peak power output for each jump was also derived from the force-time data and a percent decrement score calculated for jumps 2 to 19 (RPA%dec). An SPM one-way ANOVA with significance accepted at α = 0.05, was used to identify the change in the force-time curve over three distinct series of jumps across the LCMJ20 (series 1 = jumps 2–5, series 2 = jumps 9–12 and series 3 = jumps 16–19). A secondary analysis, using an independent T-test with significance accepted at p < 0.001, was also used to identify differences in the force-time curve between participants with low and high RPA%dec.ResultsPropulsive forces were significantly lower (p < 0.001) between 74–98% of the movement compared to 0–73% for changes recorded during the LCMJ20. Post hoc analysis identified the greatest differences to occur between jump series 1 and jump series 2 (p < 0.001) at 70–98% of the movement and between jump series 1 and jump series 3 (p < 0.001) at 86–99% of the movement. No significant differences were found between jump series 2 and jump series 3. Significant differences (p < 0.001) in both the braking phase at 44–48% of the jump and the propulsive phase at 74–94% of the jump were identified when participants were classified based on low or high RPA%dec scores (with low scores representing an enhanced ability to maintain peak power output than high scores).ConclusionA reduction in force during the late propulsive phase is evident as the LCMJ20 progresses. SPM analysis provides refined insight into where changes in the force-time curve occur during performance of the LCMJ20. Participants with the lower RPA%dec scores displayed both larger braking and propulsive forces across the LCMJ20 assessment. creator: Alex O. Natera creator: Steven Hughes creator: Dale W. Chapman creator: Neil D. Chapman creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.17971 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Natera et al. title: Acute psycho-physiological responses to submaximal constant-load cycling under intermittent hypoxia-hyperoxia vs. hypoxia-normoxia in young males link: https://peerj.com/articles/18027 last-modified: 2024-10-04 description: BackgroundHypoxia and hyperoxia can affect the acute psycho-physiological response to exercise. Recording various perceptual responses to exercise is of particular importance for investigating behavioral changes to physical activity, given that the perception of exercise-induced pain, discomfort or unpleasure, and a low level of exercise enjoyment are commonly associated with a low adherence to physical activity. Therefore, this study aimed to compare the acute perceptual and physiological responses to aerobic exercise under intermittent hypoxia-hyperoxia (IHHT), hypoxia-normoxia (IHT), and sustained normoxia (NOR) in young, recreational active, healthy males.MethodsUsing a randomized, single-blinded, crossover design, 15 males (age: 24.5 ± 4.2 yrs) performed 40 min of submaximal constant-load cycling (at 60% peak oxygen uptake, 80 rpm) under IHHT (5 × 4 min hypoxia and hyperoxia), IHT (5 × 4 min hypoxia and normoxia), and NOR. Inspiratory fraction of oxygen during hypoxia and hyperoxia was set to 14% and 30%, respectively. Heart rate (HR), total hemoglobin (tHb) and muscle oxygen saturation (SmO2) of the right vastus lateralis muscle were continuously recorded during cycling. Participants’ peripheral oxygen saturation (SpO2) and perceptual responses (i.e., perceived motor fatigue, effort perception, perceived physical strain, affective valence, arousal, motivation to exercise, and conflict to continue exercise) were surveyed prior, during (every 4 min), and after cycling. Prior to and after exercise, peripheral blood lactate concentration (BLC) was determined. Exercise enjoyment was ascertained after cycling. For statistical analysis, repeated measures analyses of variance were conducted.ResultsNo differences in the acute perceptual responses were found between conditions (p ≥ 0.059, ηp2 ≤ 0.18), while the physiological responses differed. Accordingly, SpO2 was higher during the hyperoxic periods during the IHHT compared to the normoxic periods during the IHT (p < 0.001, ηp2 = 0.91). Moreover, HR (p = 0.005, ηp2 = 0.33) and BLC (p = 0.033, ηp2 = 0.28) were higher during IHT compared to NOR. No differences between conditions were found for changes in tHb (p = 0.684, ηp2 = 0.03) and SmO2 (p = 0.093, ηp2 = 0.16).ConclusionIHT was associated with a higher physiological response and metabolic stress, while IHHT did not lead to an increase in HR and BLC compared to NOR. In addition, compared to IHT, IHHT seems to improve reoxygenation indicated by a higher SpO2 during the hyperoxic periods. However, there were no differences in perceptual responses and ratings of exercise enjoyment between conditions. These results suggest that replacing normoxic by hyperoxic reoxygenation-periods during submaximal constant-load cycling under intermittent hypoxia reduced the exercise-related physiological stress but had no effect on perceptual responses and perceived exercise enjoyment in young recreational active healthy males. creator: Tom Behrendt creator: Robert Bielitzki creator: Martin Behrens creator: Lina-Marie Jahns creator: Malte Boersma creator: Lutz Schega uri: https://doi.org/10.7717/peerj.18027 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Behrendt et al. title: A method for evaluating sediment-induced macroinvertebrate community composition changes in Idaho streams link: https://peerj.com/articles/18060 last-modified: 2024-10-04 description: Human activities can increase sediment delivery to streams, changing the composition, distribution, and abundance of stream aquatic life. Few U.S. states have numeric water quality standards for streambed sediment under the Clean Water Act, so managers often need to develop local application-specific benchmarks. This study developed stream surface fine sediment <2 mm (sand and fines, SF) and macroinvertebrate fine sediment biotic index (FSBI) benchmarks and an application framework to test for sediment-induced macroinvertebrate community composition changes in 1st–4th order Idaho streams. FSBI reference benchmarks were calculated as the 25th percentile FSBI value among reference sites within three ecoregion-based site classes. Two approaches were used to develop SF benchmarks. Quantile regression was used to define reach-specific SF benchmarks representing an upper bound value expected under reference conditions. In addition, logistic regression was used to predict SF values with 50% and 75% probability that FSBI is worse than reference within each stream order and site class. The strength of association between SF benchmarks and macroinvertebrate community condition was evaluated by calculating relative risk using multiple datasets and examining responses of multiple macroinvertebrate indicators to SF benchmark status. SF reference benchmarks generally had stronger associations with poor macroinvertebrate condition than SF stressor-response benchmarks. Across datasets and macroinvertebrate indicators, poor macroinvertebrate condition was 1.8–3 times more likely when SF reference benchmarks were exceeded than when achieved. We propose rating the strength of evidence for a surface fine sediment-induced macroinvertebrate community composition change at the sample event scale as ‘unlikely’ if both SF and FSBI reference benchmarks are achieved, having ‘mixed evidence’ if only one reference benchmark is achieved, and ‘likely’ if both reference benchmarks are not achieved. We recommend combining ratings with other relevant data in a weight-of-evidence approach to assess if sediment impairs aquatic life. creator: Jason Williams creator: James Efta uri: https://doi.org/10.7717/peerj.18060 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Williams and Efta title: Beyond graft function impairment after liver transplantation: the prolonged cold ischemia time impact on recurrence of hepatocellular carcinoma after liver transplantation—a single-center retrospective study link: https://peerj.com/articles/18126 last-modified: 2024-10-04 description: PurposeHepatocellular carcinoma (HCC) is one of the malignant tumors responsible for high mortality and recurrence rates. Although liver transplantation (LT) is an effective treatment option for HCC, ischemia-reperfusion injury (IRI) is a contributor to HCC recurrence after LT. Moreover, prolonged cold ischemia time (CIT) is a risk factor for IRI during LT, and there is insufficient clinical evidence regarding the impact of CIT on HCC recurrence after LT.Patients and MethodsThis retrospective study analyzed 420 patients who underwent LT for HCC between February 2015 and November 2020 at The First Affiliated Hospital, Sun Yat-sen University. The duration of CIT was defined as the time from clamping of the donor aorta until portal reperfusion.ResultsA total of 133 patients (31.7%) experienced tumor recurrence after LT, and CIT > 568 min was the independent risk factor for HCC recurrence (OR, 2.406; 95% CI [1.371–4.220]; p = 0.002). Multivariate Cox’s regression analysis revealed that the recipients’ gender, exceeding Milan criteria, poor differentiation, and alpha-fetoprotein (AFP) ≥400 ng/ml in CIT > 568 min group were independent risk factors for disease-free survival. The peak 7-day postoperative alanine aminotransferase (ALT) level (p < 0.001), the peak 7-day postoperative aspartate aminotransferase (AST) level (p < 0.001), the peak 7-day postoperative peak total bilirubin (TBIL) level (p = 0.012), and the incidence of early allograft dysfunction (EAD) (p = 0.006) were significantly higher in the CIT > 568 min group compared to the CIT ≤ 568 min group. Moreover, the amount of fresh frozen plasma (FFP) infusion during the operation increased (p = 0.02), and the time of mechanical ventilation postoperative was longer (p = 0.045).ConclusionAn effective strategy to improve the prognosis is to reduce CIT; this strategy lowers the recurrence of HCC in patients undergoing LT, especially those within the Milan criteria. creator: Jia Yu creator: Tang Yunhua creator: Yiwen Guo creator: Yuqi Dong creator: Jin long Gong creator: Tielong Wang creator: Zhitao Chen creator: Maogen Chen creator: Weiqiang Ju creator: Xiaoshun He uri: https://doi.org/10.7717/peerj.18126 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yu et al. title: Impact of foam rolling with and without vibration on muscle oxidative metabolism and microvascular reactivity link: https://peerj.com/articles/18180 last-modified: 2024-10-04 description: Background and PurposeThere is a growing interest in use vibration foam rolling as a warm up and recovery tool. However, whether vibration foam rolling offers additional benefits to traditional foam rolling is unclear. The current study aims to compare the effects of acute foam rolling, with and without vibration, on skeletal muscle metabolism and microvascular reactivity.MethodsFifteen physically active young males were tested on two different days, with gastrocnemius muscle microvascular function assessed using near-infrared spectroscopy coupled with the post-occlusive reactive hyperemia technique, before and after foam rolling, performed with or without vibration. The slope of tissue saturation index (TSI) decrease during occlusion between 120 s to 150 s (TSI occlusion slope) was assessed for muscle metabolic rate. Three commonly used microvascular function indexes, including the first10s TSI slope after occlusion (TSI10), time for TSI to reach half of peak magnitude (TSI1/2), and TSI peak reactive hyperemia, were also assessed.ResultsNone of the measured indexes showed significance for interaction or method (all p > 0.05). However, there was a main effect for time for TSI occlusion slope, TSI1/2, and TSI peak reactive hyperemia (p = 0.005, 0.034 and 0.046, respectively). No main effect for time for TSI10 was detected (p = 0.963).ConclusionsThe application of foam rolling can decrease muscle metabolism, and may improve some aspects of muscle microvascular function. However, vibration foam rolling does not seem to offer any additional benefits compared to traditional foam rolling alone. creator: Haizhen Huang creator: Bin Leng creator: Chuan Zhang uri: https://doi.org/10.7717/peerj.18180 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Huang et al. title: Association between triglyceride glycemic index and ejection fraction preserved heart failure in hypertensive patients link: https://peerj.com/articles/18220 last-modified: 2024-10-04 description: BackgroundThe triglyceride-glucose (TyG) index is regarded as an independent predictor of cardiovascular disease consequences and a reliable surrogate measure of insulin resistance (IR). However, the correlation analysis between triglyceride glucose index and heart failure with preserved ejection fraction in patients with essential hypertension remains unknown.MethodsA single-center, retrospective study was conducted with patients diagnosed with essential hypertension at the First Affiliated Hospital of Xinjiang Medical University, from December 2018 to September 2020. Participants were selected based on specific inclusion and exclusion criteria, with their clinical data and laboratory tests collected. The study employed Spearman’s correlation analysis, logistic regression models, restricted cubic spline plots, and receiver operating characteristic (ROC) curves to investigate the relationships between the TyG index and HFpEF.ResultsOut of 1,602 enrolled hypertensive patients, 992 were included in the analysis after applying exclusion criteria. Patients were categorized into tertiles based on the TyG index, which showed that patients in the highest tertile had characteristics associated with a higher risk of HFpEF, including age, body mass index (BMI), systolic blood pressure (SBP), N-terminal pro-B-type natriuretic peptide (NT-proBNP), and left ventricular mass index (LVMI). A significant, independent association between the TyG index and HFpEF was confirmed, with an odds ratio (OR) of 5.127 (95% CI [3.894–6.856]). Furthermore, an S-shaped nonlinear relationship was observed between the TyG index and the incidence of HFpEF (nonlinear p < 0.001). TyG index (AUC: 0.824, 95% CI [0.795–0.854]), NT-proBNP (AUC: 0.840, 95% CI [0.816–0.864]), and LVMI (AUC: 0.847, 95% CI [0.820–0.875]) showed good predictive ability for HFpEF. In addition, the TyG+LVMI combination demonstrated the strongest predictive ability (AUC: 0.907, 95% CI [0.887–0.927]).ConclusionThe study underscores a significant association between IR, as indicated by the TyG index, and the development of HFpEF in hypertensive patients. It highlights the critical role of metabolic dysfunction in the pathophysiology of HFpEF, advocating for a broader perspective on cardiovascular risk management. creator: Xue-Feng Shan creator: Long Yang creator: Xiao-Ming Gao uri: https://doi.org/10.7717/peerj.18220 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Shan et al. title: The non-HDL-C to APOB ratio as a predictor of inaccurate LDL-C measurement in patients with chronic intrahepatic cholestasis and jaundice: a retrospective study link: https://peerj.com/articles/18224 last-modified: 2024-10-04 description: BackgroundCholestasis is characterized by the accumulation of bile in the liver or biliary system due to obstruction or impaired flow, necessitating lipid profiling to assess lipid metabolism abnormalities. Intrahepatic cholestasis, being the most significant type of cholestasis, further complicates the assessment of lipid abnormalities. However, the accuracy of low-density lipoprotein cholesterol (LDL-C) measurement in intrahepatic cholestasis patients remains uncertain.ObjectiveThis study aimed to evaluate the consistency of the homogeneous assay and the Friedewald formula in detecting LDL-C levels and identify factors influencing LDL-C test results in intrahepatic patients with cholestasis.MethodsRetrospective analysis of laboratory data was conducted on intrahepatic cholestatic patients. Correlations between LDL-C values obtained using the homogeneous method (LDL-C(D)) and the Friedewald formula (LDL-C(F)), as well as associations between high-density lipoprotein cholesterol (HDL-C) and apolipoprotein A1 (ApoA1), LDL-C(D) and LDL-C(F), and apolipoprotein B (ApoB), were analyzed. Logistic regression analyses were employed to identify diagnostic indicators for inaccurate LDL-C measurements in intrahepatic cholestatic patients.ResultsCompared to patients with intrahepatic cholestasis without jaundice, the correlation between LDL-C(F) and LDL-C(D) was weaker in those with jaundice. Additionally, HDL-C exhibited a strong correlation with ApoA1 in both jaundice and non-jaundice cholestasis cases. Elevated non-HDL-C to APOB ratio (NH-C/B Ratio) levels (>4.5) were identified as a reliable predictor of inaccurate LDL-C measurements in patients with chronic intrahepatic cholestasis accompanied by jaundice.ConclusionsLDL-C measurement reliability is moderately weaker in patients with intrahepatic cholestasis accompanied by jaundice. Elevated levels of the NH-C/B ratio serve as a significant predictor of inaccurate LDL-C measurements in this chronic patient population, highlighting its clinical relevance for diagnostic assessments. creator: Yongjiang Cheng creator: Jingyan Ye creator: Junyuan Huang creator: Yang Wang uri: https://doi.org/10.7717/peerj.18224 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cheng et al. title: Reliability and reproducibility of an Italian questionnaire on “Knowledge of high social impact Eye Diseases” (KED-IT) link: https://peerj.com/articles/17906 last-modified: 2024-10-03 description: BackgroundHealth literacy plays an important role in public health. Although this has been demonstrated in the field of ophthalmology, there are very few specific instruments available to assess eye health literacy. This work aims to develop an Italian questionnaire on knowledge of eye diseases (Knowledge on Eye Disease, Italian version; KED-IT) and to evaluate its reliability and reproducibility. The KED-IT focuses on diseases with high social impact, specifically glaucoma, macular degeneration, diabetic retinopathy and keratoconus, which is the main cause of corneal transplant in Italy.MethodsA cross-sectional study was conducted. The KED-IT was self-administered by the study participants twice. The interval between each administration (T0 and T1) was 5 to 8 days. Reliability was assessed using the KR-20 coefficient. The test-retest Cohen’s Kappa coefficient was estimated to measure the stability and reproducibility of the results obtained between T0 and T1.ResultsA total of 60 subjects participated in the study. The response rate at T1 was 92%. The KR-20 reliability coefficient of the 14-item KED-IT questionnaire was good with a value of 0.878. The Cohen’s kappa value for all 14 items of the KED-IT questionnaire was k = 0.747, indicating good agreement.ConclusionsThe KED-IT is the first specific ophthalmic knowledge questionnaire validated in the Italian language and we hope that it may be a starting point for the study of eye health literacy in the Italian population. creator: Valeria Iannucci creator: Alice Bruscolini creator: Tiziano Melchiorre creator: Alessandro Lambiase creator: Alice Mannocci uri: https://doi.org/10.7717/peerj.17906 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Iannucci et al. title: Nanotechnology in action: silver nanoparticles for improved eco-friendly remediation link: https://peerj.com/articles/18191 last-modified: 2024-10-03 description: Nanotechnology is an exciting area with great potential for use in biotechnology due to the far-reaching effects of nanoscale materials and their size-dependent characteristics. Silver and other metal nanoparticles have attracted a lot of attention lately because of the exceptional optical, electrical, and antimicrobial characteristics they possess. Silver nanoparticles (AgNPs) stand out due to their cost-effectiveness and abundant presence in the earth’s crust, making them a compelling subject for further exploration. The vital efficacy of silver nanoparticles in addressing environmental concerns is emphasized in this thorough overview that dives into their significance in environmental remediation. Leveraging the distinctive properties of AgNPs, such as their antibacterial and catalytic characteristics, innovative solutions for efficient treatment of pollutants are being developed. The review critically examines the transformative potential of silver nanoparticles, exploring their various applications and promising achievements in enhancing environmental remediation techniques. As environmental defenders, this study advocates for intensified investigation and application of silver nanoparticles. Furthermore, this review aims to assist future investigators in developing more cost-effective and efficient innovations involving AgNPs carrying nanoprobes. These nanoprobes have the potential to detect numerous groups of contaminants simultaneously, with a low limit of detection (LOD) and reliable reproducibility. The goal is to utilize these innovations for environmental remediation purposes. creator: Suresh Babu Naidu Krishna creator: Abdul Gaffar Sheik creator: Karen Pillay creator: Manhal Ahmed Hamza creator: Mohammed Yagoub Mohammed Elamir creator: Samy Selim uri: https://doi.org/10.7717/peerj.18191 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Krishna et al. title: PotatoG-DKB: a potato gene-disease knowledge base mined from biological literature link: https://peerj.com/articles/18202 last-modified: 2024-10-03 description: BackgroundPotato is the fourth largest food crop in the world, but potato cultivation faces serious threats from various diseases and pests. Despite significant advancements in research on potato disease resistance, these findings are scattered across numerous publications. For researchers, obtaining relevant knowledge by reading and organizing a large body of literature is a time-consuming and labor-intensive process. Therefore, systematically extracting and organizing the relationships between potato genes and diseases from the literature to establish a potato gene-disease knowledge base is particularly important. Unfortunately, there is currently no such gene-disease knowledge base available.MethodsIn this study, we constructed a Potato Gene-Disease Knowledge Base (PotatoG-DKB) using natural language processing techniques and large language models. We used PubMed as the data source and obtained 2,906 article abstracts related to potato biology, extracted entities and relationships between potato genes and related disease, and stored them in a Neo4j database. Using web technology, we also constructed the Potato Gene-Disease Knowledge Portal (PotatoG-DKP), an interactive visualization platform.ResultsPotatoG-DKB encompasses 22 entity types (such as genes, diseases, species, etc.) of 5,206 nodes and 9,443 edges between entities (for example, gene-disease, pathogen-disease, etc.). PotatoG-DKP can intuitively display associative relationships extracted from literature and is a powerful assistant for potato biologists and breeders to understand potato pathogenesis and disease resistance. More details about PotatoG-DKP can be obtained at https://www.potatogd.com.cn/. creator: Congjiao Xie creator: Jing Gao creator: Junjie Chen creator: Xuyang Zhao uri: https://doi.org/10.7717/peerj.18202 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xie et al. title: Feasibility and acceptability pilot study of an online weight loss program in rural, underserved communities link: https://peerj.com/articles/18268 last-modified: 2024-10-03 description: BackgroundThe purpose of this intervention was to investigate the feasibility, acceptability, and preliminary effectiveness of an online weight loss program, EMPOWER, in rural, underserved communities.MethodsAdults with a body mass index (BMI) ≥ 25 kg/m2 living in rural counties were recruited through collaboration with University of Illinois Extension. The intervention lasted 1 year including online educations sessions, nutrition and lifestyle coaching, and diet and weight monitoring via a novel web application, MealPlot. Feasibility was measured by enrollment attainment, participant retention, online education session completion, and completion of anthropometric and dietary measures. Acceptability was measured by survey using Likert scales of satisfaction for all program components. Anthropometric measurements, 24-h dietary records, and food frequency questionnaires (FFQs) were measures of program efficacy. Additionally, two interviews were collected for program feedback.ResultsEnrollment of 16 participants was attained, however due to higher than anticipated dropout (retention 62.5%, N = 10) at 3-months, 62.5% of the education sessions were completed and 75.0% of anthropometric and dietary measures. The average satisfaction rating for the comprehensive program was 4.2/5 with lowest satisfaction being the MealPlot web application 2.7/5 (N = 11). On average a clinically significant (≥5% baseline weight) weight loss of 6.2 ± 6.0% body weight or 5.7 ± 5.3 kg and improvements to protein and fiber intake at 12 months (N = 10) were observed.ConclusionsA novel online weight loss program showed adequate to strong feasibility and acceptability and preliminary results indicating efficacy among a pilot sample of rural residents. Future studies are required to investigate means of improving retention and reducing the burden on program collaborators. creator: Ashleigh Oliveira creator: Nouf Alfouzan creator: Jin Yu creator: Asma Yahya creator: Kayla Lammy creator: Mary Liz Wright creator: Diane Reinhold creator: Lisa Peterson creator: Ashley Brewer creator: Janet Liechty creator: Manabu T. Nakamura uri: https://doi.org/10.7717/peerj.18268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Oliveira et al. title: A new species of frog of the genus Noblella Barbour, 1930 (Amphibia: Strabomantidae) from the Cordillera del Cóndor, Ecuador link: https://peerj.com/articles/17939 last-modified: 2024-10-02 description: We describe a new species of leaflitter frog of the genus Noblella from southern Ecuador, province of Zamora Chinchipe. The new species is diagnosed from all its congeners by having one or two tubercles on the upper eyelids; distal phalanges strongly T-shaped; phalangeal formula on hands 2-2-3-3; phalangeal formula on feet 2-2-3-4-3; heel with a small subconical tubercle; disc on all toes with papillae; dorsum brown or brown with gray, with V-shaped inverted or scattered irregular darker marks. We include a detailed description of its osteology and a study of its phylogenetic relationships. Finally, we evaluate its conservation status and discuss the threats that are currently impacting at the type locality. creator: David Brito-Zapata creator: Juan D. Chávez-Reyes creator: Matheo David Pallo-Robles creator: Julio C. Carrión-Olmedo creator: Diego F. Cisneros-Heredia creator: Carolina Reyes-Puig uri: https://doi.org/10.7717/peerj.17939 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Brito-Zapata et al. title: Canine companionship as a resilience factor: a quantitative inquiry into the impact of pet ownership on burnout mitigation among radiologists and radiographers link: https://peerj.com/articles/18110 last-modified: 2024-10-02 description: BackgroundThe demanding nature of diagnostic imaging, coupled with the increasing workload and exposure to high-stress scenarios, underscores the pressing concern of burnout among radiologists and radiographers in modern healthcare settings. The objective was to investigate the interplay between family characteristics, workplace characteristics, pet ownership, and the occurrence of burnout.MethodsAn online, quantitative, cross-sectional study with a non-random, purposive sampling method was carried out among Hungarian radiologists and radiographers from 1st of September to 1st of November 2022.ResultsWe examined the results of 406 responses predominantly from females (79.8%, n = 324), including 70.7% radiographers (n = 287). Cronbach’s alpha values for depersonalization (DP), emotional exhaustion (EE), and personal accomplishment (PA) were 0.74, 0.88, and 0.85, respectively. Average burnout scores were 8.35 (SD = 6.62) for DP, 26.26 (SD = 12.74) for EE, and 32.86 (SD = 9.52) for PA. DP demonstrated a balanced distribution (low: 35.7%, moderate: 27.3%, high: 36.9%). Conversely, EE and PA skewed towards high levels, with 52.5% (n = 213) and 49.5% (n = 201). Significant associations were found between gender and DP (p = 0.006), age (31–40 years) and DP/PA (p < 0.001; p = 0.004), absence of children and all burnout dimensions (p < 0.05), and pet ownership (p = 0.004) with lower EE, particularly for dog owners (p = 0.009). Occupation lacked a significant effect on burnout dimensions (p > 0.05). Employees without a second job had higher EE (p = 0.002) and lower PA (p = 0.008). Increasing healthcare experience correlated with decreased DP values (p = 0.001), while working over 40 h weekly negatively impacted all burnout dimensions (p ≤ 0.05). 15.5% (n = 63) exhibited signs of high burnout, with the age group 31–40 demonstrating the highest proportion (25.4%, n = 27) and significant associations with marital status, absence of children, pet ownership, private healthcare, 10–19 years in healthcare, and working over 40 h weekly.ConclusionsThere is a pressing need for evidence-based strategies to alleviate burnout among radiologists and radiographers. There is a growing importance of recognizing the role of pets, especially dogs, as valuable companions for emotional support and stress relief. Implementing pet-friendly policies or therapy programs can contribute to a positive and supportive workplace, potentially mitigating burnout among essential frontline healthcare professionals. creator: Dávid Sipos creator: Timea Jenei creator: Attila Pandur creator: Luca Anna Ferkai creator: Krisztina Deutsch creator: Arpad Kovács creator: Melinda Csima uri: https://doi.org/10.7717/peerj.18110 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sipos et al. title: Identification of 10 differentially expressed genes involved in the tumorigenesis of cervical cancer via next-generation sequencing link: https://peerj.com/articles/18157 last-modified: 2024-10-02 description: BackgroundThe incidence and mortality of cervical cancer remain high in female malignant tumors worldwide. There is still a lack of diagnostic and prognostic markers for cervical carcinoma. This study aimed to screen differentially expressed genes (DEGs) between normal and cervical cancer tissues to identify candidate genes for further research.MethodsUterine cervical specimens were resected from our clinical patients after radical hysterectomy. Three patients’ transcriptomic datasets were built by the next generation sequencing (NGS) results. DEGs were selected through the edgeR and DESeq2 packages in the R environment. Functional enrichment analysis, including GO/DisGeNET/KEGG/Reactome enrichment analysis, was performed. Normal and cervical cancer tissue data from the public databases TCGA and GTEx were collected to compare the expression levels of 10 selected DEGs in tumor and normal tissues. ROC curve and survival analysis were performed to compare the diagnostic and prognostic values of each gene. The expression levels of candidate genes were verified in 15 paired clinical specimens via quantitative real-time polymerase chain reaction.ResultsThere were 875 up-regulated and 1,482 down-regulated genes in cervical cancer samples compared with the paired adjacent normal cervical tissues according to the NGS analysis. The top 10 DEGs included APOD, MASP1, ACKR1, C1QTNF7, SFRP4, HSPB6, GSTM5, IGFBP6, F10 and DCN. GO, DisGeNET and Reactome analyses revealed that the DEGs were related to extracellular matrix and angiogenesis which might influence tumorigenesis. KEGG enrichment showed that PI3K-Akt signaling pathway might be involved in cervical cancer tumorigenesis and progression. The expression levels of selected genes were decreased in tumors in both the public database and our experimental clinical specimens. All the candidate genes showed excellent diagnostic value, and the AUC values exceeded 0.90. Additionally, APOD, ACKR1 and SFRP4 expression levels could help predict the prognosis of patients with cervical cancer.ConclusionsIn this study, we selected the top 10 DEGs which were down-regulated in cervical cancer tissues. All of them had dramatically diagnostic value. APOD, ACKR1 and SFRP4 were associated with the survivals of cervical cancer. C1QTNF7, HSPB6, GSTM5, IGFBP6 and F10 were first reported to be candidate genes of cervical carcinoma. creator: Jia Xu creator: Wen Yang creator: Xiufeng Xie creator: Chenglei Gu creator: Luyang Zhao creator: Feng Liu creator: Nina Zhang creator: Yuge Bai creator: Dan Liu creator: Hainan Liu creator: Xiangshu Jin creator: Yuanguang Meng uri: https://doi.org/10.7717/peerj.18157 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Xu et al. title: The effect of post-activation enhancement on the performance of Chinese national skeleton athletes in the “ice push sled”-a first cross-sectional study link: https://peerj.com/articles/18271 last-modified: 2024-10-02 description: ObjectiveTo investigate the impact of post-activation potentiation (PAP) induced by resisted sled sprint at different loads on the subsequent 30 m ice push sled performance of Chinese skeleton athletes, and to identify the resisted sled sprint load that most effectively enhances PAP for Chinese skeleton athletes.MethodsSeven elite athletes from the Chinese skeleton team participated in four tests with more than 48 h intervals. During the tests, on the first test, athletes completed a 40 min standard warm-up, rested for 6 min, and then performed a 30 m test. On the second, third, and fourth test, athletes completed the standard warm-up, then performed 20 m sprints with resisted sled (RS) at 75%, 50%, and 25% of body mass (BM), respectively, rested for 6 min, and then performed the 30 m test.ResultsNo significant differences were found in morning pulse, blood urea, and creatine kinase levels among four tests. The percentage of maximum heart rate (%HRmax) within different intensity ranges showed no significant differences among four tests. However, significant differences were observed in ice push sled performance among four tests (No BMRS: 5.08 ± 0.27; 25% BMRS: 5.05 ± 0.29; 50% BMRS: 5.02 ± 0.27; 75% BMRS: 5.04 ± 0.28). Post hoc analyses revealed that the 50% BMRS test had faster speed compared to the no resistance (p < 0.05), the 25% BMRS (p < 0.05), and the 75% BMRS (p < 0.05) tests. Additionally, the 75% BMRS test had faster speed than the no resistance test (p < 0.05).ConclusionA 20 m sprint with 50% BMRS effectively enhances the PAP effect in skeleton athletes, improving their ice push sled performance. Coaches can incorporate this resisted sled sprint in athletes’ training routines for performance enhancement in both daily training and pre-competition preparations. creator: Guang Tian creator: Haojie Li creator: Huan Zhu creator: Binghong Gao uri: https://doi.org/10.7717/peerj.18271 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tian et al. title: Unveiling the impact of organically activated biochar on physiological, biochemical, and yield attributes of maize under varied field moisture conditions link: https://peerj.com/articles/17883 last-modified: 2024-10-01 description: Water deficiency in semiarid regions is a limiting factor that affects crop quality and yield. In Punjab, Pakistan, a 27% decline in maize yield was detected over the past two decades just because of water scarcity. Currently, no studies have reported the effects of organically activated biochar (AB) on crop productivity under natural field conditions. For this purpose, a field experiment in a split-split-plot design was conducted with three amendment levels (0, 2, and 4 tonnes ac−1), and three maize hybrids (DK-9108, DK-6321, and Sarhaab) under 100%, 70%, and 50% irrigation water (IW) of crop evapotranspiration (ETc). The AB significantly improved the soil’s physical and chemical properties, and maximum improvement was recorded in 4 tonnes ac−1 AB amendment in organic matter (16.6%), total organic carbon (17%), phosphorus (11.43%), and available potassium (29.27%). The 4 tonnes ac−1AB amendment in soil had a significant impact on total chlorophyll content (0.3–1-fold in DK-6321), carotenoid content (3.9–4.4-fold in Sarhaab), and relative water content (30% and 21% in Sarhaab) under 50% irrigation water (IW) of ETc at V14th and R3 stages, respectively. Moreover, a significant decline in stress markers (proline content and sugar content) was detected at both growth stages in all maize hybrids in AB amended soil. The analysis of plant metabolites indicated increased intensities of phenolics, alkyl esters, and carbohydrates by 2.5–7%, 17–80%, and 40–43% in DK-6321 under 50% IW in 2–4 tonnes ac−1 AB amended soil, respectively. The highest improvement in growth and yield attributes among maize hybrids was detected in the order DK-6321¿DK-9108¿Sarhaab in 2–4 tonnes ac−1AB amended soil under 70% and 50% IW of ETc, respectively. Hence, this research might help to develop an effective soil amendment to restore degraded soils and improve maize growth under arid climatic conditions. creator: Hajra Iqbal creator: Summera Jahan creator: Muhammad Akbar creator: Atif Kamran creator: Fahd Rasul creator: Sobia Shahzad creator: Manzer H. Siddiqui creator: Saud Alamri uri: https://doi.org/10.7717/peerj.17883 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Iqbal et al. title: Knowledge, attitude, and practice toward hyperuricemia among healthcare workers in Shandong, China link: https://peerj.com/articles/17926 last-modified: 2024-10-01 description: BackgroundHyperuricemia is a relatively common condition, with a prevalence of over 20% among the general population. Also, most patients initially present no symptoms. This study aimed to investigate the knowledge, attitude, and practice (KAP) toward hyperuricemia among healthcare workers in Shandong, China.MethodsHealthcare workers were recruited in this cross-sectional study conducted in Shandong in December 2022. A self-designed questionnaire was used to collect demographic information and KAP data.ResultsA total of 372 questionnaires were distributed, and 216 (58.06%) valid questionnaires were collected from 131 physicians, 80 nurses, and five other healthcare workers. The participants had a mean score of 10.76 ± 2.53 (possible range: 0–14, 76.9%) and 31.94 ± 2.58 (possible range: 0–40, 79.9%) in knowledge and attitude, respectively. The physicians’ and nurses’ practice scores were 47.57 ± 5.34 (possible range: 0–55, 86.5%) and 30.06 ± 4.11 (possible range: 0–35, 85.9%), respectively. The attitude scores were independently associated with proactive practice in both physicians (P < 0.001) and nurses (P = 0.046).ConclusionThis study found that healthcare workers in Shandong had adequate knowledge, positive attitudes, and proactive practices towards hyperuricemia. However, there is room for improvement in the attitudes of both physicians and nurses to achieve better practice. creator: Honghai Peng creator: Ke Zhang creator: Chunxue Zhang creator: Jun Gao uri: https://doi.org/10.7717/peerj.17926 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Peng et al. title: Prognostic value of a modified pathological staging system for gastric cancer based on the number of retrieved lymph nodes and metastatic lymph node ratio link: https://peerj.com/articles/18165 last-modified: 2024-10-01 description: AimThe prognosis for gastric cancer (GC) remains grim, underscoring the importance of accurate staging and treatment. Given the potential benefits of using lymph node ratio (LNR) for improved prognostication and treatment planning, it is critical to incorporate examined lymph nodes (ELN) count in an integrated GC staging system.MethodsPatients data from the Surveillance, Epidemiology, and End Results (SEER) database between 2010 and 2015 was utilized as training set. The Mantel-Cox survival test was used to calculate chi-square values for 40 LNR segments with a 0.025 interval, defining a novel LNR-based N (rN) classification based on the cutoff points. A revised AJCC (rAJCC) staging system was established by replacing the 8th AJCC N staging with a rN classification. The relationship between the ELN count and prognosis or positive lymph node detection was conducted by using multivariable models. The series of the odds ratios and hazard ratios were fitted with a locally weighted scatterplot smoothing (LOWESS) smoother, and the structural break points were determined by Chow test to clarify an optimal minimum ELN count. The integrated GC staging system incorporated both rAJCC system and the ideal ELN count. Discriminatory ability and prognostic homogeneity of the rAJCC and integrated staging system was compared with AJCC staging system in the SEER validation set (2016–2017), the Cancer Genome Atlas Program (TCGA) database, and the Third Affiliated Hospital of Sun Yat-sen University database.ResultsThe current study found that LNR and ELN count are both significantly associated with the prognosis of GC patients (HR = 0.98, p < 0.001 and HR = 2.51, p < 0.001). Four peaks of the chi-square value were identified as LNR cut-off points at 0.025, 0.175, 0.45 and 0.6 to define a novel rN stage. In comparison to the 8th AJCC staging system, the rAJCC staging system demonstrated significant prognostic advantages and discriminatory ability in the training set (5-Y OS AUC: 71.7 vs. 73.0; AIC: 57,290.7 vs. 57,054.9). The superiority of the rAJCC staging system was confirmed in all validation sets. Using a LOWESS smoother and Chow test, a threshold ELN count of 30 was determined to maximum improvement in the prognosis of node-negative patients without downgrading due to potential metastasis, while also maximizing the detection efficiency of at least one involved lymph node. The integrated staging system, combining the refined rAJCC classification with an optimized ELN count threshold, has demonstrated superior discriminatory performance compared to the standalone rAJCC or the traditional AJCC system.ConclusionThe development of a novel GC staging system, which integrated the LNR-based N classification and the minimum ELN count, has exhibited superior prognostic accuracy, holding promise as a valuable asset in the clinical management of GC. However, it is crucial to recognize the limitations from the retrospective database, which should be addressed in subsequent analyses. creator: Guiru Jia creator: Dagui Zhou creator: Xiao Tang creator: Jianpei Liu creator: Purun Lei uri: https://doi.org/10.7717/peerj.18165 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jia et al. title: Changes of collagen content in lung tissues of plateau yak and its mechanism of adaptation to hypoxia link: https://peerj.com/articles/18250 last-modified: 2024-10-01 description: Collagen is crucial for tissue structure, functional maintenance, and cellular processes such as proliferation and differentiation. However, the specific changes in collagen expression and its associated genes in the lung tissues of yaks at high altitudes and their relationship with environmental adaptation remain poorly understood. Studying differences in the content of collagen fibers and gene expression between yaks at high (4,500 m) and low (2,600 m) altitudes, as well as between cattle at low altitudes (2,600 m). Using Masson staining, we found that the collagen fiber content in the lung tissues of yaks at low altitude was significantly higher compared to yaks at high altitude and cattle at the same altitude (P < 0.05). It was revealed through transcriptomic analyses that genes differentially expressed between high and low altitude yaks, as well as between low altitude yaks and cattle, were notably enriched in pathways related to cell adhesion, collagen synthesis, focal adhesion, and ECM-receptor interactions. Specifically, genes involved in mesenchymal collagen synthesis (e.g., COL1A1, COL1A2, COL3A1), basement membrane collagen synthesis (e.g., COL4A1, COL4A2, COL4A4, COL4A6), and peripheral collagen synthesis (e.g., COL5A1, COL6A1, COL6A2, COL6A3) were significantly upregulated in the lung tissues of yaks at low altitude compared to their high altitude counterparts and cattle (P < 0.05). In conclusion, yaks at lower altitudes exhibit increased collagen synthesis by upregulating collagen gene expression, which contributes to maintaining alveolar stability and septal flexibility. Conversely, the expression of collagen genes in yak lung tissues was down-regulated with the increase in altitude, and it was speculated that the decrease in collagen may be used to constrain the function of elastic fibers that are more abundant at high altitude, so as to enable them to adapt to the harsh environment with hypoxia and high altitude. This adaptation mechanism highlights the role of collagen in environmental acclimatization and contributes to our understanding of how altitude and species influence collagen-related physiological processes in yaks. creator: Jingyi Li creator: Nating Huang creator: Xun Zhang creator: Ci Sun creator: Jiarui Chen creator: Qing Wei uri: https://doi.org/10.7717/peerj.18250 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al.