title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=393 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Validating a re-implementation of an algorithm to integrate transcriptome and ChIP-seq data link: https://peerj.com/articles/16318 last-modified: 2023-10-20 description: Transcription factor binding to a gene regulatory region induces or represses its expression. Binding and expression target analysis (BETA) integrates the binding and gene expression data to predict this function. First, the regulatory potential of the factor is modeled based on the distance of its binding sites from the transcription start sites in a decay function. Then the differential expression statistics from an experiment where this factor was perturbed represent the binding effect. The rank product of the two values is employed to order in importance. This algorithm was originally implemented in Python. We reimplemented the algorithm in R to take advantage of existing data structures and other tools for downstream analyses. Here, we attempted to replicate the findings in the original BETA paper. We applied the new implementation to the same datasets using default and varying inputs and cutoffs. We successfully replicated the original results. Moreover, we showed that the method was appropriately influenced by varying the input and was robust to choices of cutoffs in statistical testing. creator: Mahmoud Ahmed creator: Deok Ryong Kim uri: https://doi.org/10.7717/peerj.16318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ahmed and Kim title: Analysis of the apoplast fluid proteome during the induction of systemic acquired resistance in Arabidopsis thaliana link: https://peerj.com/articles/16324 last-modified: 2023-10-20 description: BackgroundPlant-pathogen interactions occur in the apoplast comprising the cell wall matrix and the fluid in the extracellular space outside the plasma membrane. However, little is known regarding the contribution of the apoplastic proteome to systemic acquired resistance (SAR).MethodsSpecifically, SAR was induced by inoculating plants with Pst DC3000 avrRps4. The apoplast washing fluid (AWF) was collected from the systemic leaves of the SAR-induced or mock-treated plants. A label free quantitative proteomic analysis was performed to identified the proteins related to SAR in AWF.ResultsA total of 117 proteins were designated as differentially accumulated proteins (DAPs), including numerous pathogenesis-related proteins, kinases, glycosyl hydrolases, and redox-related proteins. Functional enrichment analyses shown that these DAPs were mainly enriched in carbohydrate metabolic process, cell wall organization, hydrogen peroxide catabolic process, and positive regulation of catalytic activity. Comparative analysis of proteome data indicated that these DAPs were selectively enriched in the apoplast during the induction of SAR.ConclusionsThe findings of this study indicate the apoplastic proteome is involved in SAR. The data presented herein may be useful for future investigations on the molecular mechanism mediating the establishment of SAR. creator: Shuna Jiang creator: Liying Pan creator: Qingfeng Zhou creator: Wenjie Xu creator: Fuge He creator: Lei Zhang creator: Hang Gao uri: https://doi.org/10.7717/peerj.16324 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jiang et al. title: Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens link: https://peerj.com/articles/15746 last-modified: 2023-10-19 description: BackgroundThe Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species.MethodsBlood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14× and ~10× coverage, respectively) from Dachigam National Park.ResultsThe annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species. creator: Khursheed Ahmad creator: Ankit Shankar Pacha creator: Rashid Yahya Naqash creator: Sathish Kumar Peddamma creator: Srinivas Yellapu creator: Shenu Hudson creator: Dushyant Singh Baghel creator: Parag Nigam creator: Samrat Mondol uri: https://doi.org/10.7717/peerj.15746 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ahmad et al. title: Assessment tools and incidence of hospital-associated disability in older adults: a rapid systematic review link: https://peerj.com/articles/16036 last-modified: 2023-10-19 description: BackgroundDuring hospitalization older adults have a high risk of developing functional impairments unrelated to the reasons for their admission. This is termed hospital-associated disability (HAD). This systematic review aimed to assess the incidence of HAD in older adults admitted to acute care with two outcomes: firstly in at least one activity of daily living from a set of functional tasks (e.g., Katz Index) and secondly the incidence of functional decline in an individual functional task (e.g., bathing), and to identify any tools or functional tasks used to assess activities of daily living (ADL) in hospitalized older patients.MethodsA rapid systematic review was performed according to the recommendations of the Cochrane Rapid Reviews Methods Group and reported the data according the PRISMA statement. A literature search was performed in Medline (via Ovid), EMBASE, and Cochrane Central Register of Controlled Trials databases on 26 August 2021. Inclusion criteria: older adults (≥65 years), assessment of individual items of activities of daily living at baseline and discharge. Exclusion criterion: studies investigating a specific condition that could affect functional decline and studies that primarily examined a population with cognitive impairment. The protocol was registered on OSF registries (https://osf.io/9jez4/) identifier: DOI 10.17605/OSF.IO/9JEZ4.ResultsTen studies were included in the final review. Incidence of HAD (overall score) was 37% (95% CI 0.30–0.43). Insufficient data prevented meta-analysis of the individual items. One study provided sufficient data to calculate incidence, with the following values for patients’ self-reported dependencies: 32% for bathing, 27% for dressing, 27% for toileting, 30% for eating and 27% for transferring. The proxy reported the following values for patients’ dependencies: 70% for bathing, 66% for dressing, 70% for toileting, 61% for eating and 59% for transferring. The review identified four assessment tools, two sets of tasks, and individual items assessing activities of daily living in such patients.ConclusionsIncidence of hospital-associated disability in older patients might be overestimated, due to the combination of disease-related disability and hospital-associated disability. The tools used to assess these patients presented some limitations. These results should be interpreted with caution as only one study reported adequate information to assess the HAD incidence. At the item level, the latter was higher when disability was reported by the proxies than when it was reported by patients. This review highlights the lack of systematic reporting of data used to calculate HAD incidence. The methodological quality and the risk of bias in the included studies raised some concerns. creator: Katia Giacomino creator: Roger Hilfiker creator: David Beckwée creator: Jan Taeymans creator: Karl Martin Sattelmayer uri: https://doi.org/10.7717/peerj.16036 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Giacomino et al. title: Differences in lumbar spine intradiscal pressure between standing and sitting postures: a comprehensive literature review link: https://peerj.com/articles/16176 last-modified: 2023-10-19 description: BackgroundMusculoskeletal disorders (MSDs), especially in the lumbar spine, are a leading concern in occupational health. Work activities associated with excessive exposure are a source of risk for MSDs. The optimal design of workplaces requires changes in both sitting and standing postures. In order to secure such a design scientifically proved quantitative data are needed that would allow for the assessment of differences in spine load due to body posture and/or exerted force. Intradiscal pressure (IP) measurement in the lumbar spine is the most direct method of estimating spinal loads. Hence, this study aims at the quantitative evaluation of differences in lumbar spine load due to body posture and exerted forces, based on IP reported in publications obtained from a comprehensive review of the available literature.MethodologyIn order to collect data from studies measuring IP in the lumbar spine, three databases were searched. Studies with IP for living adults, measured in various sitting and standing postures, where one of these was standing upright, were included in the analysis. For data to be comparable between studies, the IP for each position was referenced to upright standing. Where different studies presented IP for the same postures, those relative IPs (rIP) were merged. Then, an analysis of the respective outcomes was conducted to find the possible relationship of IPs dependent on a specific posture.ResultsA preliminary analysis of the reviewed papers returned nine items fulfilling the inclusion and exclusion criteria. After merging relative IPs from different studies, rIP for 27 sitting and 26 standing postures was yielded. Some of the data were useful for deriving mathematical equations expressing rIP as a function of back flexion angle and exerted force in the form of a second degree polynomial equation for the standing and sitting positions. The equations showed that for the standing posture, the increase in IP with increasing back flexion angle is steeper when applying an external force than when maintaining body position only. In a sitting position with the back flexed at 20°, adding 10 kg to each hand increases the IP by about 50%. According to the equations developed, for back flexion angles less than 20°, the IP is greater in sitting than in standing. When the angle is greater than 20°, the IP in the sitting position is less than in the standing position at the same angle of back flexion.ConclusionsAnalysis of the data from the reviewed papers showed that: sitting without support increases IP by about 30% in relation to upright standing; a polynomial of the second degree defines changes in IP as a function of back flexion for for both postures. There are differences in the pattern of changes in IP with a back flexion angle between sitting and standing postures, as back flexion in standing increases IP more than in sitting. creator: Danuta Roman-Liu creator: Joanna Kamińska creator: Tomasz Tokarski uri: https://doi.org/10.7717/peerj.16176 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Roman-Liu et al. title: Transcriptome analysis reveals the mechanism of pyroptosis-related genes in septic cardiomyopathy link: https://peerj.com/articles/16214 last-modified: 2023-10-19 description: BackgroundSeptic cardiomyopathy (SC) is characterized by myocardial dysfunction caused by sepsis and constitutes one of the serious complications of sepsis. Pyroptosis is a unique proinflammatory programmed cell death process. However, the role of pyroptosis in the development of SC remains unclear, and further study is required. The purpose of this study is to identify pyroptosis-related genes (PRGs) in SC and explore the mechanism of pyroptosis involved in the regulation of SC formation and progression.MethodsDifferential expression analysis and enrichment analysis were performed on the SC-related dataset GSE79962 to identify differentially expressed genes (DEGs). PRGs were screened by intersecting genes associated with pyroptosis in previous studies with the DEGs obtained from GSE79962. The expression pattern of them was studied based on their raw expression data. Additionally, corresponding online databases were used to predict miRNAs, transcription factors (TFs) and therapeutic agents of PRGs. Lipopolysaccharide (LPS)-induced cell damage models in H9C2 and AC16 cell lines were constructed, cell activity was detected by CCK-8 and cell pyroptosis were detected by Hoechst33342/PI staining. Furthermore, these PRGs were verified in the external datasets (GSE53007 and GSE142615) and LPS-induced cell damage model. Finally, the effect of siRNA-mediated PRGs knockdown on the pyroptosis phenotype was examined.ResultsA total of 1,206 DEGs were screened, consisting of 663 high-expressed genes and 543 low-expressed genes. Among them, ten PRGs (SOD2, GJA1, TIMP3, TAP1, TIMP1, NOD1, TP53, CPTP, CASP1 and SAT1) were identified, and they were mainly enriched in “Pyroptosis”, “Ferroptosis”, “Longevity regulating pathway”, and “NOD-like receptor signaling pathway”. A total of 147 miRNAs, 31 TFs and 13 therapeutic drugs were predicted targeting the PRGs. The expression trends of SOD2 were confirmed in both the external datasets and LPS-induced cell damage models. Knockdown of SOD2 induced increased pyroptosis in the AC16 LPS-induced cell damage model.ConclusionsIn this study, we demonstrated that SOD2 is highly expressed in both the SC and LPS-induced cell damage models. Knockdown of SOD2 led to a significant increase in pyroptosis in the AC16 LPS-induced cell damage model. These findings suggest that SOD2 may serve as a potential target for the diagnosis and treatment of SC. creator: Haoyan Zhu creator: Jiahe Wu creator: Chenze Li creator: Ziyue Zeng creator: Tianwen He creator: Xin Liu creator: Qiongxin Wang creator: Xiaorong Hu creator: Zhibing Lu creator: Huanhuan Cai uri: https://doi.org/10.7717/peerj.16214 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhu et al. title: Fishery catch records support machine learning-based prediction of illegal fishing off US West Coast link: https://peerj.com/articles/16215 last-modified: 2023-10-19 description: Illegal, unreported, and unregulated (IUU) fishing is a major problem worldwide, often made more challenging by a lack of at-sea and shoreside monitoring of commercial fishery catches. Off the US West Coast, as in many places, a primary concern for enforcement and management is whether vessels are illegally fishing in locations where they are not permitted to fish. We explored the use of supervised machine learning analysis in a partially observed fishery to identify potentially illicit behaviors when vessels did not have observers on board. We built classification models (random forest and gradient boosting ensemble tree estimators) using labeled data from nearly 10,000 fishing trips for which we had landing records (i.e., catch data) and observer data. We identified a set of variables related to catch (e.g., catch weights and species) and delivery port that could predict, with 97% accuracy, whether vessels fished in state versus federal waters. Notably, our model performances were robust to inter-annual variability in the fishery environments during recent anomalously warm years. We applied these models to nearly 60,000 unobserved landing records and identified more than 500 instances in which vessels may have illegally fished in federal waters. This project was developed at the request of fisheries enforcement investigators, and now an automated system analyzes all new unobserved landings records to identify those in need of additional investigation for potential violations. Similar approaches informed by the spatial preferences of species landed may support monitoring and enforcement efforts in any number of partially observed, or even totally unobserved, fisheries globally. creator: Jordan T. Watson creator: Robert Ames creator: Brett Holycross creator: Jenny Suter creator: Kayleigh Somers creator: Camille Kohler creator: Brian Corrigan uri: https://doi.org/10.7717/peerj.16215 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Watson et al. title: Response of soil extracellular enzyme activity and stoichiometry to short-term warming and phosphorus addition in desert steppe link: https://peerj.com/articles/16227 last-modified: 2023-10-19 description: BackgroundPhosphorus (P) is regarded as one of the major limiting factors in grassland ecosystems. Soil available phosphorus deficiency could affect soil extracellular enzyme activity, which is essential for microbial metabolism. Yet it is still unclear how soil available phosphorus affects soil extracellular enzyme activity and microbial nutrient limitation of desert steppe in the context of climate warming.MethodsThis study carried out a short-term open-top chambers (OTCs) experiment in a desert steppe to examine the effects of warming, P addition, and their interaction on soil properties, the activities of soil extracellular enzymes, and stoichiometries.ResultsThe findings demonstrated that soil acquisition enzyme stoichiometry of C: N: P was 1.2:1:1.5 in this experiment region, which deviated from the global mean scale (1:1:1). Warming increased soil AN (ammonium nitrogen and nitrate nitrogen) contents and decreased microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). Phosphorus addition raised soil available phosphorus and microbial biomass phosphorus (MBP) contents. Soil extracellular enzyme activities and stoichiometries in desert steppe are largely impacted by soil AN, MBC: MBP, and MBN: MBP. These results revealed that the changes of soil available nutrients and stoichiometries induced by short-term warming and P addition could influence soil microbial activities and alleviate soil microbial carbon and phosphorus limitation. Our findings highlight that soil available phosphorus played a critical role in regulating soil extracellular enzyme activity and microbial nutrient limitation of desert steppe. Further research on soil microbial communities should explore the microbiological mechanisms underlying these findings. creator: Lingxia Feng creator: Bing Cao creator: Xiaojia Wang uri: https://doi.org/10.7717/peerj.16227 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Feng et al. title: Similarities and differences in the microbial structure of surface soils of different vegetation types link: https://peerj.com/articles/16260 last-modified: 2023-10-19 description: BackgroundSoil microbial community diversity serves as a highly sensitive indicator for assessing the response of terrestrial ecosystems to various changes, and it holds significant ecological relevance in terms of indicating ecological alterations. At the global scale, vegetation type acts as a major driving force behind the diversity of soil microbial communities, encompassing both bacterial and fungal components. Modifications in vegetation type not only induce transformations in the visual appearance of land, but also influence the soil ecosystem’s material cycle and energy flow, resulting in substantial impacts on the composition and performance of soil microbes.MethodsIn order to examine the disparities in the structure and diversity of soil microbial communities across distinct vegetation types, we opted to utilize sample plots representing four specific vegetation types. These included a woodland with the dominant tree species Drypetes perreticulata, a woodland with the dominant tree species Horsfieldia hainanensis, a Zea mays farmland and a Citrus reticulata fields. Through the application of high-throughput sequencing, the 16S V3_V4 region of soil bacteria and the ITS region of fungi were sequenced in this experiment. Subsequently, a comparative analysis was conducted to explore and assess the structure and dissimilarities of soil bacterial and fungal communities of the four vegetation types were analyzed comparatively.ResultsOur findings indicated that woodland soil exhibit a higher richness of microbial diversity compared to farmland soils. There were significant differences between woodland and farmland soil microbial community composition. However, all four dominant phyla of soil fungi were Ascomycota across the four vegetation types, but the bacterial dominant phyla were different in the two-farmland soil microbial communities with the highest similarity. Furthermore, we established a significant correlation between the nutrient content of different vegetation types and the relative abundance of soil microorganisms at both phyla and genus levels. This experiment serves as a crucial step towards unraveling the intricate relationships between plants, soil microbes, and soil, as well as understanding the underlying driving mechanism. creator: Yong Jiang creator: Wenxu Zhu creator: Keye Zhu creator: Yang Ge creator: Wuzheng Li creator: Nanyan Liao uri: https://doi.org/10.7717/peerj.16260 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jiang et al. title: Association between sports expertise and visual attention in male and female soccer players link: https://peerj.com/articles/16286 last-modified: 2023-10-19 description: BackgroundVisual attention plays a crucial role in daily living and in sports, affecting an athlete’s performance and thus, potentially, the outcome of a match. However, studies assessing the association between the level of sports expertise and visual attention have yielded mixed results. This study was conducted to examine whether visual attention could be developed with increased sports expertise, and whether visual attention differed between male athletes and female athletes.MethodsA total of 128 participants were included in this study: 64 first-level national soccer athletes recruited from college soccer teams (considered elite athletes; 32 men and 32 women with similar soccer performance requirements and training experience), and 64 physical education college students with limited soccer experience (considered novice athletes; 32 men and 32 women with matched soccer experience). To assess visual attention, we used a multiple object tracking (MOT) task with four targets among a total of 10 objects moving at a fixed speed of 10°/s in random directions across a computer monitor screen. Tracking accuracy on the MOT task was calculated for each participant as the proportion of correctly selected targets. A univariate analysis of variance was performed, with group (expert, novice) and sex (male, female) as independent variables, and tracking accuracy on the MOT task as the dependent variable to assess whether sports expertise or sex influenced visual attention. Simple effects tests followed by comparisons with Bonferroni corrections were used, and effect size calculations were performed using Cohen’s f statistic.ResultsTracking accuracy on the MOT task was significantly affected by sports expertise (F(1,124) = 91.732, p < 0.001, ηP2 = 0.425), with accuracy among expert soccer athletes superior to that among novice soccer athletes. Moreover, a statistically significant interaction between sports expertise and sex was detected (F(1,124) = 7.046, p = 0.009, ηP2= 0.054). Better tracking performance was observed for male soccer players (mean [SD], 0.39 [0.12]) than for female soccer players (mean [SD], 0.27 [0.08]); p < 0.01; d=1.17; r = 0.51) but only in the novice group. No significant sex difference was detected in tracking performance between elite male soccer athletes (mean [SD], 0.51 [0.09]) and elite female soccer athletes (mean [SD], 0.49 [0.11]).ConclusionThese findings confirm previous results indicating that long-term extensive sports training develops visual attention as assessed by MOT performance and extend previous findings to include soccer athletes. The findings of a sex difference in visual attention among novice soccer players but not among elite soccer athletes who had similar performance requirements and training experience suggest that long-term extensive training may minimize the sex difference in visual attention. creator: Peng Jin creator: Zheqi Ji creator: Tianyi Wang creator: Xiaomin Zhu uri: https://doi.org/10.7717/peerj.16286 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jin et al.