title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1093 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Doing nothing and what it looks like: inactivity in fattening cattle link: https://peerj.com/articles/9395 last-modified: 2020-07-21 description: BackgroundAnimals kept in barren environments often show increased levels of inactivity and first studies indicate that inactive behaviour may reflect boredom or depression-like states. However, to date, knowledge of what inactivity looks like in different species is scarce and methods to precisely describe and analyse inactive behaviour are thus warranted.MethodsWe developed an Inactivity Ethogram including detailed information on the postures of different body parts (Standing/Lying, Head, Ears, Eyes, Tail) for fattening cattle, a farm animal category often kept in barren environments. The Inactivity Ethogram was applied to Austrian Fleckvieh heifers kept in intensive, semi-intensive and pasture-based husbandry systems to record inactive behaviour in a range of different contexts. Three farms per husbandry system were visited twice; once in the morning and once in the afternoon to cover most of the daylight hours. During each visit, 16 focal animals were continuously observed for 15 minutes each (96 heifers per husbandry system, 288 in total). Moreover, the focal animals’ groups were video recorded to later determine inactivity on the group level. Since our study was explorative in nature, we refrained from statistical hypothesis testing, but analysed both the individual- and group-level data descriptively. Moreover, simultaneous occurrences of postures of different body parts (Standing/Lying, Head, Ears and Eyes) were analysed using the machine learning algorithm cspade to provide insight into co-occurring postures of inactivity.ResultsInspection of graphs indicated that with increasing intensity of the husbandry system, more animals were inactive (group-level data) and the time the focal animals were inactive increased (individual-level data). Frequently co-occurring postures were generally similar between husbandry systems, but with subtle differences. The most frequently observed combination on farms with intensive and semi-intensive systems was lying with head up, ears backwards and eyes open whereas on pasture it was standing with head up, ears forwards and eyes open.ConclusionOur study is the first to explore inactive behaviour in cattle by applying a detailed description of postures from an Inactivity Ethogram and by using the machine learning algorithm cspade to identify frequently co-occurring posture combinations. Both the ethogram created in this study and the cspade algorithm may be valuable tools in future studies aiming to better understand different forms of inactivity and how they are associated with different affective states. creator: Sara Hintze creator: Freija Maulbetsch creator: Lucy Asher creator: Christoph Winckler uri: https://doi.org/10.7717/peerj.9395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hintze et al. title: An RNA-sequencing-based transcriptome for a significantly prognostic novel driver signature identification in bladder urothelial carcinoma link: https://peerj.com/articles/9422 last-modified: 2020-07-21 description: Bladder cancer (BC) is the ninth most common malignancy worldwide. Bladder urothelial carcinoma (BLCA) constitutes more than 90% of bladder cancer (BC). The five-year survival rate is 5–70%, and patients with BLCA have a poor clinical outcome. The identification of novel clinical molecular markers in BLCA is still urgent to allow for predicting clinical outcomes. This study aimed to identify a novel signature integrating the three-dimension transcriptome of protein coding genes, long non-coding RNAs, microRNAs that is related to the overall survival of patients with BLCA, contributing to earlier prediction and effective treatment selection, as well as to the verification of the established model in the subtypes identified. Gene expression profiling and the clinical information of 400 patients diagnosed with BLCA were retrieved from The Cancer Genome Atlas (TCGA) database. A univariate Cox regression analysis, robust likelihood-based survival modelling analysis and random forests for survival regression and classification algorithms were used to identify the critical biomarkers. A multivariate Cox regression analysis was utilized to construct a risk score formula with a maximum area under the curve (AUC = 0.7669 in the training set). The significant signature could classify patients into high-risk and low-risk groups with significant differences in overall survival time. Similar results were confirmed in the test set (AUC = 0.645) and in the entire set (AUC = 0.710). The multivariate Cox regression analysis indicated that the five-RNA signature was an independent predictive factor for patients with BLCA. Non-negative matrix factorization and a similarity network fusion algorithm were applied for identifying three molecular subtypes. The signature could separate patients in every subtype into high- and low- groups with a distinct difference. Gene set variation analysis of protein-coding genes associated with the five prognostic RNAs demonstrated that the co-expressed protein-coding genes were involved in the pathways and biological process of tumourigenesis. The five-RNA signature could serve as to some degree a reliable independent signature for predicting outcome in patients with BLCA. creator: Danqi Liu creator: Boting Zhou creator: Rangru Liu uri: https://doi.org/10.7717/peerj.9422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: School health assessment tools: a systematic review of measurement in primary schools link: https://peerj.com/articles/9459 last-modified: 2020-07-21 description: Background This systematic review aimed to investigate the psychometric properties of the school health’s assessment tools in primary schools through COSMIN Risk of Bias checklist. We examined the studies that have addressed the measurement properties of school-health instruments to give a clear overview of the quality of all available tools measuring school health in primary schools. This systematic review was registered in PROPERO with the Registration ID: CRD42020158158.MethodDatabases of EBSCOhost, PubMed, ProQuest, Wily, PROSPERO, and OpenGrey were systematically searched without any time limitation to find all full-text English journal articles studied at least one of the COSMIN checklist measurement properties of a school-health assessment tool in primary schools. The instruments should be constructed based on a school health model. The eligible studies were assessed by COSMIN Risk of Bias checklist to report their quality of methodology for each measurement property and for the whole study by rating high, moderate or low quality.ResultsAt the final screening just seven studies remained for review. Four studies were tool development, three of them were rated as “adequate” and the other study as “very good”; five studies examined the content validity, three of them were appraised as “very good”, and the two remaining as “inadequate”. All seven studies measured structural validity, three of them were evaluated as “very good”, three other were scored as “adequate”, and the last study as “inadequate”. All the seven studies investigated the internal consistency, five of them were assessed as “very good”, one was rated as “doubtful”, and the last one as “inadequate”. Just one study examined the cross-cultural validity and was rated as “adequate”. Finally, all seven studies measured reliability, two of them were rated as “very good” and the rest five studies were appraised as “doubtful”. All rating was based on COSMIN checklist criteria for quality of measurement properties assessment.ConclusionThe number of studies addressing school health assessment tools was very low and therefore not sufficient. Hence, there is a serious need to investigate the psychometric properties of the available instruments measuring school health at primary schools. Moreover, the studies included in the present systematic review did not fulfill all the criteria of the COSMIN checklist for assessing measurement properties. We suggest that future studies consider these criteria for measuring psychometric properties and developing school health assessment tools. creator: Maryam Kazemitabar creator: Ali Moghadamzadeh creator: Mojtaba Habibi creator: Rezvan Hakimzadeh creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.9459 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kazemitabar et al. title: Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage link: https://peerj.com/articles/9484 last-modified: 2020-07-21 description: BackgroundBone marrow adipocyte (BMA), closely associated with bone degeneration, shares common progenitors with osteoblastic lineage. However, the intrinsic mechanism of cells fate commitment between BMA and osteogenic lineage remains unclear.MethodsGene Expression Omnibus (GEO) dataset GSE107789 publicly available was downloaded and analyzed. Differentially expressed genes (DEGs) were analyzed using GEO2R. Functional and pathway enrichment analyses of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were conducted by The Database for Annotation, Visualization and Integrated Discovery and Gene set enrichment analysis software. Protein–protein interactions (PPI) network was obtained using STRING database, visualized and clustered by Cytoscape software. Transcriptional levels of key genes were verified by real-time quantitative PCR in vitro in Bone marrow stromal cells (BMSCs) undergoing adipogenic differentiation at day 7 and in vivo in ovariectomized mice model.ResultsA total of 2,869 DEGs, including 1,357 up-regulated and 1,512 down-regulated ones, were screened out from transcriptional profile of human BMSCs undergoing adipogenic induction at day 7 vs. day 0. Functional and pathway enrichment analysis, combined with modules analysis of PPI network, highlighted ACSL1, sphingosine 1-phosphate receptors 3 (S1PR3), ZBTB16 and glypican 3 as key genes up-regulated at the early stage of BMSCs adipogenic differentiation. Furthermore, up-regulated mRNA expression levels of ACSL1, S1PR3 and ZBTB16 were confirmed both in vitro and in vivo.ConclusionACSL1, S1PR3 and ZBTB16 may play crucial roles in early regulation of BMSCs adipogenic differentiation creator: Pengyu Chen creator: Mingrui Song creator: Yutian Wang creator: Songyun Deng creator: Weisheng Hong creator: Xianrong Zhang creator: Bin Yu uri: https://doi.org/10.7717/peerj.9484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chen et al. title: Microbial and chemical dynamics of a toxic dinoflagellate bloom link: https://peerj.com/articles/9493 last-modified: 2020-07-21 description: Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration. creator: Nastassia V. Patin creator: Emily Brown creator: Gabriella Chebli creator: Claire Garfield creator: Julia Kubanek creator: Frank J. Stewart uri: https://doi.org/10.7717/peerj.9493 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Patin et al. title: Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam link: https://peerj.com/articles/9502 last-modified: 2020-07-21 description: BackgroundNeisseria meningitidis remains the main cause of sporadic meningitis and sepsis in military camps in Vietnam. Yet, very limited molecular data of their genotypic and epidemiological characteristics are available from Vietnam, and particularly the military environment. Whole genome sequencing (WGS) has proven useful for meningococcal disease surveillance and guiding preventative vaccination programs. Previously, we characterized key genetic and epidemiological features of an invasive N. meningitidis B isolate from a military unit in Vietnam. Here, we extend these findings by sequencing two additional invasive N. meningitidis B isolated from cerebrospinal fluid (CSF) of two meningitis cases at another military unit and compared their genomic sequences and features. We also report the sequence types and antigenic profiles of 25 historical and more recently emerged N. meningitidis isolates from these units and other units in proximity.MethodsStrains were sequenced using the Illumina HiSeq platform, de novo assembled and annotated. Genomes were compared within and between military units, as well as against the global N. meningitidis collection and other isolates from the Southeast Asia region using PubMLST. Variations at the nucleotide level were determined, and phylogenetic relationships were estimated. Antigenic genotypes and vaccine coverage were analyzed using gMATS and PubMLST. Susceptibility of isolates against commonly used antibiotic agents was examined using E-test.ResultsGenome comparison revealed a high level of similarity among isolates both within and between units. All isolates showed resistance to chloramphenicol and carried identical catP gene with other Southeast Asian isolates, suggesting a common lineage. Their antigenic genotypes predicted no coverage by either Bexsero®or Trumenba®, and nucleotide variation analysis revealed diverse new, unassigned alleles at multiple virulence loci of all strains. Groups of singleton and unique novel sequence types extending beyond individual camps were found from epidemiological data of 25 other isolates. Our results add to the sparse published molecular data of N. meningitidis in the military units in Vietnam, highlight their diversity, distinct genetic features and antibiotic resistance pattern, and emphasize the need for further studies on the molecular characteristics of N. meningitidis in Vietnam. creator: Trang Thu Le creator: Thach Xuan Tran creator: Long Phi Trieu creator: Christopher M. Austin creator: Huong Minh Nguyen creator: Dong Van Quyen uri: https://doi.org/10.7717/peerj.9502 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Le et al. title: Habitat preferences rather than morphological traits affect the recovery process of Collembola (Arthropoda, Hexapoda) on a bare saline–alkaline land link: https://peerj.com/articles/9519 last-modified: 2020-07-21 description: The Songnen Plain of China was once an important grassland used for sheep grazing, but it has largely been degraded to bare saline-alkaline land (BSAL). BSAL consists of plant-free areas characterized by high soil pH values (up to 10) and salt and alkali (e.g., Na+ and Ca2+) contents, as well as low soil organic matter and water contents; thus, very few soil faunal species can survive on BSAL. The recovery of degraded ecosystems provides a great opportunity to investigate the reconstruction of belowground soil faunal communities. Collembola are a class of widespread and abundant soil fauna that can colonize this harsh environment. Habitat changes on BSAL promote aboveground revegetation, which greatly facilitates the recovery of Collembola. A soil transfer experiment on the BSAL of the Songnen Plain was conducted to study the effects of habitat and Collembola morphological traits on the recovery process of Collembola. Defaunated and with-fauna soil blocks were transferred among three habitats: BSAL, reclaimed arable land, and naturally revegetated grassland. The recovered Collembola in the transferred soil blocks were compared two, seven, and 12 weeks after the start of the experiment. The results showed that (1) the majority of the Collembola, regardless of their morphological traits, recovered in the defaunated soil blocks within 2 weeks; (2) generalists and habitat-preferring species recovered faster than specialists; (3) the average total abundance, species richness, and community composition of Collembola recovered to the natural levels in 2 weeks; and (4) 12 weeks after replacement, the highest average total abundance and species richness of Collembola were found in the arable land. Our results indicate that the majority of Collembola in this study, regardless of their dispersal type, which is related to their morphological traits, are fast dispersers, and their recovery speeds are mainly affected by habitat preferences. We suggest that the reclamation of BSAL to arable land rather than its natural recovery to grassland aids in the recovery of Collembola in degraded grassland systems. creator: Zhen Ni creator: Xiumin Yan creator: Liang Chang creator: Xin Sun creator: Donghui Wu creator: Bing Zhang uri: https://doi.org/10.7717/peerj.9519 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ni et al. title: Quantifying uncertainty in annual runoff due to missing data link: https://peerj.com/articles/9531 last-modified: 2020-07-21 description: Long-term streamflow datasets inevitably include gaps, which must be filled to allow estimates of runoff and ultimately catchment water budgets. Uncertainty introduced by filling gaps in discharge records is rarely, if ever, reported. We characterized the uncertainty due to streamflow gaps in a reference watershed at the Hubbard Brook Experimental Forest (HBEF) from 1996 to 2009 by simulating artificial gaps of varying duration and flow rate, with the objective of quantifying their contribution to uncertainty in annual streamflow. Gaps were filled using an ensemble of regressions relating discharge from nearby streams, and the predicted flow was compared to the actual flow. Differences between the predicted and actual runoff increased with both gap length and flow rate, averaging 2.8% of the runoff during the gap. At the HBEF, the sum of gaps averaged 22 days per year, with the lowest and highest annual uncertainties due to gaps ranging from 1.5 mm (95% confidence interval surrounding mean runoff) to 21.1 mm. As a percentage of annual runoff, uncertainty due to gap filling ranged from 0.2–2.1%, depending on the year. Uncertainty in annual runoff due to gaps was small at the HBEF, where infilling models are based on multiple similar catchments in close proximity to the catchment of interest. The method demonstrated here can be used to quantify uncertainty due to gaps in any long-term streamflow data set, regardless of the gap-filling model applied. creator: Craig R. See creator: Mark B. Green creator: Ruth D. Yanai creator: Amey S. Bailey creator: John L. Campbell creator: Jeremy Hayward uri: https://doi.org/10.7717/peerj.9531 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes link: https://peerj.com/articles/9554 last-modified: 2020-07-21 description: The development of explanatory models of protein sequence evolution has broad implications for our understanding of cellular biology, population history, and disease etiology. Here we analyze the GTEx transcriptome resource to quantify the effect of the transcriptome on protein sequence evolution in a multi-tissue framework. We find substantial variation among the central nervous system tissues in the effect of expression variance on evolutionary rate, with highly variable genes in the cortex showing significantly greater purifying selection than highly variable genes in subcortical regions (Mann–Whitney U p = 1.4 × 10−4). The remaining tissues cluster in observed expression correlation with evolutionary rate, enabling evolutionary analysis of genes in diverse physiological systems, including digestive, reproductive, and immune systems. Importantly, the tissue in which a gene attains its maximum expression variance significantly varies (p = 5.55 × 10−284) with evolutionary rate, suggesting a tissue-anchored model of protein sequence evolution. Using a large-scale reference resource, we show that the tissue-anchored model provides a transcriptome-based approach to predicting the primary affected tissue of developmental disorders. Using gradient boosted regression trees to model evolutionary rate under a range of model parameters, selected features explain up to 62% of the variation in evolutionary rate and provide additional support for the tissue model. Finally, we investigate several methodological implications, including the importance of evolutionary-rate-aware gene expression imputation models using genetic data for improved search for disease-associated genes in transcriptome-wide association studies. Collectively, this study presents a comprehensive transcriptome-based analysis of a range of factors that may constrain molecular evolution and proposes a novel framework for the study of gene function and disease mechanism. creator: Patrick Evans creator: Nancy J. Cox creator: Eric R. Gamazon uri: https://doi.org/10.7717/peerj.9554 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Evans et al. title: Ethyl pyruvate inhibits glioblastoma cells migration and invasion through modulation of NF-κB and ERK-mediated EMT link: https://peerj.com/articles/9559 last-modified: 2020-07-21 description: BackgroundGlioblastoma is a grade IV glioma with the highest degree of malignancy and extremely high incidence. Because of the poor therapeutic effect of surgery and radiochemotherapy, glioblastoma has a high recurrence rate and lethality, and is one of the most challenging tumors in the field of oncology. Ethyl pyruvate (EP), a stable lipophilic pyruvic acid derivative, has anti-inflammatory, antioxidant, immunomodulatory and other cellular protective effects. It has been reported that EP has potent anti-tumor effects on many types of tumors, including pancreatic cancer, prostate cancer, liver cancer, gastric cancer. However, whether EP has anti-tumor effect on glioblastoma or not is still unclear.MethodsGlioblastoma U87 and U251 cells were treated with different concentrations of EP for 24 h or 48 h. CCK8 assay and Colony-Formation assay were performed to test the viability and proliferation. Wound-healing assay and Transwell assay were carried out to measure cell invasion and migration. Western blot was not only used to detect the protein expression of epithelial-mesenchymal transition (EMT)-related molecules, but also to detect the expression and activation levels of NF-κB (p65) and Extracellular Signal Regulated Kinase (ERK).ResultsIn glioblastoma U87 and U251 cells treated with EP, the viability, proliferation, migration, invasion abilities were inhibited in a dose-dependent manner. EP inhibited EMT and the activation of NF-κB (p65) and ERK. With NF-κB (p65) and ERK activated, EMT, migration and invasion of U87 and U251 cells were promoted. However the activation of NF-κB (p65) and ERK were decreased, EMT, migration and invasion abilities were inhibited in U87 and U251 cells treated with EP.ConclusionEP inhibits glioblastoma cells migration and invasion by blocking NF-κB and ERK-mediated EMT. creator: Qing Huang creator: Yongming Fu creator: Shan Zhang creator: Youxiang Zhang creator: Simin Chen creator: Zuping Zhang uri: https://doi.org/10.7717/peerj.9559 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Huang et al.