title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2020-07 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Measurement properties of the Knee Injury and Osteoarthritis Outcome Score Patello-Femoral questionnaire in Saudi Arabians link: https://peerj.com/articles/9323 last-modified: 2020-07-31 description: BackgroundNo Arabic or its dialect questionnaire is available to evaluate the anterior knee pain in the Saudi Arabian religious population. This study aims to translate, adapt, and psychometrically validate the Knee Injury and Osteoarthritis Outcome Score (KOOS-PF) Patellofemoral scale in the Arabic language in Saudi Arabic dialect.MethodTranslation has been done as per standard guidelines. The questionnaire was administered to 95 patients to determine the psychometric properties including on two different occasions, with a 48-hour gap in-between; to ensure that their answers were reliable; 84 patients (88.4% compliance rate) responded for test and retest reliability, ceiling-floor effects, validity and other psychometric criteria.ResultsCronbach’s alpha (internal consistency) and test–retest reliability was good and excellent (∞ = 0.81; ICC > 0.95). None of the items showed >30% floor or ceiling effect and the minimal detectable change was within the acceptable range (<30%). The KOOS-PF subscale showed a moderate correlation (−0.568) with pain-visual analog scale for its construct validity.ConclusionThe Arabic dialect of KOOS-PFis reliable and valid to be used to evaluate isolated knee pain of patellofemoral origin in Muslim patients in Saudi Arabia. creator: Mahamed Ateef uri: https://doi.org/10.7717/peerj.9323 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ateef title: Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage link: https://peerj.com/articles/9523 last-modified: 2020-07-31 description: In the Caribbean Basin the distribution and diversity patterns of deep-sea scleractinian corals and stylasterid hydrocorals are poorly known compared to their shallow-water relatives. In this study, we examined species distribution and community assembly patterns of scleractinian and stylasterid corals on three high-profile seamounts within the Anegada Passage, a deep-water throughway linking the Caribbean Sea and western North Atlantic. Using remotely operated vehicle surveys conducted on the E/V Nautilus by the ROV Hercules in 2014, we characterized coral assemblages and seawater environmental variables between 162 and 2,157 m on Dog Seamount, Conrad Seamount, and Noroît Seamount. In all, 13 morphospecies of scleractinian and stylasterid corals were identified from video with stylasterids being numerically more abundant than both colonial and solitary scleractinians. Cosmopolitan framework-forming species including Madrepora oculata and Solenosmilia variabilis were present but occurred in patchy distributions among the three seamounts. Framework-forming species occurred at or above the depth of the aragonite saturation horizon with stylasterid hydrocorals being the only coral taxon observed below Ωarag values of 1. Coral assemblage variation was found to be strongly associated with depth and aragonite saturation state, while other environmental variables exerted less influence. This study enhances our understanding of the factors that regulate scleractinian and stylasterid coral distribution in an underreported marginal sea and establishes a baseline for monitoring future environmental changes due to ocean acidification and deoxygenation in the tropical western Atlantic. creator: Steven R. Auscavitch creator: Jay J. Lunden creator: Alexandria Barkman creator: Andrea M. Quattrini creator: Amanda W.J. Demopoulos creator: Erik E. Cordes uri: https://doi.org/10.7717/peerj.9523 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Auscavitch et al. title: Relationship between iron status markers and insulin resistance: an exploratory study in subjects with excess body weight link: https://peerj.com/articles/9528 last-modified: 2020-07-31 description: BackgroundControversy exists on the relationship between iron metabolism and cardiometabolic risk. The aim of this study was to determine if there is a link between dysmetabolic iron and cardiometabolic markers in subjects with excess body weight.MethodsCross-sectional study with fifty participants presenting overweight or obesity and at least another metabolic syndrome factor. Determinations: anthropometry, body composition, blood pressure, lipids, glucose, insulin, leptin, areas under the curve (AUC) for glucose and insulin after an oral glucose tolerance test, hs-C reactive protein (hs-CRP), blood count, ferritin, transferrin, transferrin saturation (TSAT), soluble transferrin receptor (sTfR). Gender-adjusted linear correlations and two independent samples t tests were used.ResultsFerritin was positively correlated with insulin-AUC (r = 0.547, p = 0.008) and TSAT was negatively correlated with waist-hip ratio (r =  − 0.385, p = 0.008), insulin (r =  − 0.551, p < 0.001), and insulin resistance (HOMA-IR, r =  − 0.586, p < 0.001). Subjects with TSAT ≤ 20% had higher insulin (p = 0.012) and HOMA-IR (p = 0.003) compared to those with TSAT > 20%. In conclusion, the observed results suggest that iron transport and storage are altered in subjects with overweight/obesity, at the same time that they exhibit the characteristic features of insulin resistance. Nevertheless, this occurs without iron overload or deficiency. These results should be validated in wider cohorts since they suggest that iron transport and storage should be assessed when performing the clinical evaluation of subjects with excess body weight. creator: M. Pilar Vaquero creator: Daniel Martínez-Maqueda creator: Angélica Gallego-Narbón creator: Belén Zapatera creator: Jara Pérez-Jiménez uri: https://doi.org/10.7717/peerj.9528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Vaquero et al. title: Heritability of the extra-pair mating behaviour of the pied flycatcher in Western Siberia link: https://peerj.com/articles/9571 last-modified: 2020-07-31 description: Males and females take part in extra-pair copulations in most socially monogamous bird species. The mechanisms leading to the frequent occurrence of extra-pair offspring in socially monogamous couples are strongly debated and unresolved, and they are often difficult to distinguish from one another. Most hypotheses explaining the evolution of extra-pair reproduction suggest selective and adaptive scenarios for their origination and persistence. Is extra-pair paternity a heritable trait? We evaluated the heritability of extra-pair paternity in the pied flycatcher (Ficedula hypoleuca) nesting in Western Siberia. Estimated heritability was low: depending on the model used, the point estimate of the heritability (mode) varied from 0.005 to 0.11, and the bounds of the 95% confidence interval are [0–0.16] in the widest range. Thus, it seems that extra-pair mating behaviour in the pied flycatchers is a plastic phenotypic mating tactic with a small or no genetic component. Our data can help to understand the evolution of extra-pair mating behaviour in socially monogamous species. creator: Vladimir G. Grinkov creator: Andreas Bauer creator: Helmut Sternberg creator: Michael Wink uri: https://doi.org/10.7717/peerj.9571 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Grinkov et al. title: Functional characterization of the chlorzoxazone 6-hydroxylation activity of human cytochrome P450 2E1 allelic variants in Han Chinese link: https://peerj.com/articles/9628 last-modified: 2020-07-31 description: BackgroundsCytochrome P450 (P450) 2E1 is one of the primary enzymes responsible for the metabolism of xenobiotics, such as drugs and environmental carcinogens. The genetic polymorphisms of the CYP2E1 gene in promoter and coding regions have been identified previously in the Han Chinese population from four different geographic areas of Mainland China.MethodsTo investigate whether genetic variants identified in the CYP2E1 coding region affect enzyme function, the enzymes of four single nucleotide polymorphism (SNP) variants in the coding region (novel c.1009C>T, causing p.Arg337X, where X represents the translational stop codon; c.227G>A, causing p.Arg76His; c.517G>A, yielding p.Gly173Ser; and c.1263C>T, presenting the highest allele frequency), two novel alleles (c.[227G>A;1263C>T] and c.[517G>A;1263C>T]), and the wild-type CYP2E1 were heterologously expressed in COS-7 cells and functionally characterized in terms of expression level and chlorzoxazone 6-hydroxylation activity. The impact of the CYP2E1 variant sequence on enzyme activity was predicted with three programs: Polyphen 2, PROVEAN and SIFT.ResultsThe prematurely terminated p.Arg337X variant enzyme was undetectable by western blotting and inactive toward chlorzoxazone 6-hydroxylation. The c.1263C>T and c.[517G>A;1263C>T] variant enzymes exhibited properties similar to those of the wild-type CYP2E1. The CYP2E1 variants c.227G>A and c.[227G>A;1263C>T] displayed significantly reduced enzyme activity relative to that of the wild-type enzyme (decreased by 42.8% and 32.8%, respectively; P < 0.01). The chlorzoxazone 6-hydroxylation activity of the c.517G>A transfectant was increased by 31% compared with the wild-type CYP2E1 enzyme (P < 0.01). Positive correlations were observed between the protein content and enzyme activity for CYP2E1 (P = 0.0005, r2 = 0.8833). The characterization of enzyme function allelic variants in vitro was consistent with the potentially deleterious effect of the amino acid changes as determined by prediction tools.ConclusionsThese findings indicate that the genetic polymorphisms of CYP2E1, i.e., c.1009C>T (p.Arg337X), c.227G>A (p.Arg76His), and c.517G>A (p.Gly173Ser), could influence the metabolism of CYP2E1 substrates, such as chlorzoxazone. creator: Ting Wang creator: Huihui Du creator: Jingsong Ma creator: Lu Shen creator: Muyun Wei creator: Xianglong Zhao creator: Luan Chen creator: Mo Li creator: Guorong Li creator: Qinghe Xing creator: Lin He creator: Shengying Qin uri: https://doi.org/10.7717/peerj.9628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Air quality improvement during triple-lockdown in the coastal city of Kannur, Kerala to combat Covid-19 transmission link: https://peerj.com/articles/9642 last-modified: 2020-07-31 description: The novel SARS-CoV-2 coronavirus that emerged in the city of Wuhan, China, last year has since become the COVID-19 pandemic across all continents. To restrict the spread of the virus pandemic, the Government of India imposed a lockdown from 25 March 2020. In India, Kannur district was identified as the first “hotspot” of virus transmission and a “triple-lockdown” was implemented for a span of twenty days from 20 April 2020. This article highlights the variations of surface O3, NO, NO2, CO, SO2, NH3, VOC’s, PM10, PM2.5 and meteorological parameters at the time of pre-lockdown, lockdown and triple-lockdown days at Kannur town in south India using ground-based analyzers. From pre-lockdown days to triple-lockdown days, surface O3 concentration was found to increase by 22% in this VOC limited environment. NO and NO2 concentrations were decreased by 61% and 71% respectively. The concentration of PM10 and PM2.5 were observed to decline significantly by 61% and 53% respectively. Reduction in PM10 during lockdown and triple-lockdown days enhanced the intensity of solar radiation reaching the lower troposphere, and increased air temperature and reduced the relative humidity. Owing to this, surface O3 production over Kannur was found to have increased during triple-lockdown days. The concentration of CO (67%), VOCs (61%), SO2 (62%) and NH3 (16%) were found to decrease significantly from pre-lockdown days to triple-lockdown days. The air quality index revealed that the air quality at the observational site was clean during the lockdown. creator: C.T. Resmi creator: T. Nishanth creator: M.K. Satheesh Kumar creator: M.G. Manoj creator: M. Balachandramohan creator: K.T. Valsaraj uri: https://doi.org/10.7717/peerj.9642 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Resmi et al. title: DNA from mollusc shell: a valuable and underutilised substrate for genetic analyses link: https://peerj.com/articles/9420 last-modified: 2020-07-30 description: Mollusc shells are an abundant resource that have been long used to predict the structures of ancient ecological communities, examine evolutionary processes, reconstruct paleoenvironmental conditions, track and predict responses to climatic change, and explore the movement of hominids across the globe. Despite the ubiquity of mollusc shell in many environments, it remains relatively unexplored as a substrate for molecular genetic analysis. Here we undertook a series of experiments using the New Zealand endemic greenshell mussel, Perna canaliculus, to explore the utility of fresh, aged, beach-cast and cooked mollusc shell for molecular genetic analyses. We find that reasonable quantities of DNA (0.002–21.48 ng/mg shell) can be derived from aged, beach-cast and cooked mussel shell and that this can routinely provide enough material to undertake PCR analyses of mitochondrial and nuclear gene fragments. Mitochondrial PCR amplification had an average success rate of 96.5% from shell tissue extracted thirteen months after the animal’s death. A success rate of 93.75% was obtained for cooked shells. Amplification of nuclear DNA (chitin synthase gene) was less successful (80% success from fresh shells, decreasing to 10% with time, and 75% from cooked shells). Our results demonstrate the promise of mollusc shell as a substrate for genetic analyses targeting both mitochondrial and nuclear genes. creator: Sara Ferreira creator: Rachael Ashby creator: Gert-Jan Jeunen creator: Kim Rutherford creator: Catherine Collins creator: Erica V. Todd creator: Neil J. Gemmell uri: https://doi.org/10.7717/peerj.9420 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ferreira et al. title: Semantic priming and schizotypal personality: reassessing the link between thought disorder and enhanced spreading of semantic activation link: https://peerj.com/articles/9511 last-modified: 2020-07-30 description: The term schizotypy refers to a group of stable personality traits with attributes similar to symptoms of schizophrenia, usually classified in terms of positive, negative or cognitive disorganization symptoms. The observation of increased spreading of semantic activation in individuals with schizotypal traits has led to the hypothesis that thought disorder, one of the characteristics of cognitive disorganization, stems from semantic disturbances. Nevertheless, it is still not clear under which specific circumstances (i.e., automatic or controlled processing, direct or indirect semantic relation) schizotypy affects semantic priming or whether it does affect it at all. We conducted two semantic priming studies with volunteers varying in schizotypy, one with directly related prime-target pairs and another with indirectly related pairs. Our participants completed a lexical decision task with related and unrelated pairs presented at short (250 ms) and long (750 ms) stimulus onset asynchronies (SOAs). Then, they responded to the brief versions of the Schizotypal Personality Questionnaire and the Oxford-Liverpool Inventory of Feelings and Experiences, both of which include measures of cognitive disorganization. Bayesian mixed-effects models indicated expected effects of SOA and semantic relatedness, as well as an interaction between relatedness and directness (greater priming effects for directly related pairs). Even though our analyses demonstrated good sensitivity, we observed no influence of cognitive disorganization over semantic priming. Our study provides no compelling evidence that schizotypal symptoms, specifically those associated with the cognitive disorganization dimension, are rooted in an increased spreading of semantic activation in priming tasks. creator: Javier Rodríguez-Ferreiro creator: Mari Aguilera creator: Rob Davies uri: https://doi.org/10.7717/peerj.9511 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Rodríguez-Ferreiro et al. title: Optimization of rain gauge sampling density for river discharge prediction using Bayesian calibration link: https://peerj.com/articles/9558 last-modified: 2020-07-30 description: River discharges are often predicted based on a calibrated rainfall-runoff model. The major sources of uncertainty, namely input, parameter and model structural uncertainty must all be taken into account to obtain realistic estimates of the accuracy of discharge predictions. Over the past years, Bayesian calibration has emerged as a suitable method for quantifying uncertainty in model parameters and model structure, where the latter is usually modelled by an additive or multiplicative stochastic term. Recently, much work has also been done to include input uncertainty in the Bayesian framework. However, the use of geostatistical methods for characterizing the prior distribution of the catchment rainfall is underexplored, particularly in combination with assessments of the influence of increasing or decreasing rain gauge network density on discharge prediction accuracy. In this article we integrate geostatistics and Bayesian calibration to analyze the effect of rain gauge density on river discharge prediction accuracy. We calibrated the HBV hydrological model while accounting for input, initial state, model parameter and model structural uncertainty, and also taking uncertainties in the discharge measurements into account. Results for the Thur basin in Switzerland showed that model parameter uncertainty was the main contributor to the joint posterior uncertainty. We also showed that a low rain gauge density is enough for the Bayesian calibration, and that increasing the number of rain gauges improved model prediction until reaching a density of one gauge per 340 km2. While the optimal rain gauge density is case-study specific, we make recommendations on how to handle input uncertainty in Bayesian calibration for river discharge prediction and present the methodology that may be used to carry out such experiments. creator: Alexandre M.J.-C. Wadoux creator: Gerard B.M. Heuvelink creator: Remko Uijlenhoet creator: Sytze de Bruin uri: https://doi.org/10.7717/peerj.9558 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wadoux et al. title: Gluconobacter dominates the gut microbiome of the Asian palm civet Paradoxurus hermaphroditus that produces kopi luwak link: https://peerj.com/articles/9579 last-modified: 2020-07-30 description: Coffee beans derived from feces of the civet cat are used to brew coffee known as kopi luwak (the Indonesian words for coffee and palm civet, respectively), which is one of the most expensive coffees in the world owing to its limited supply and strong market demand. Recent metabolomics studies have revealed that kopi luwak metabolites differ from metabolites found in other coffee beans. To produce kopi luwak, coffee beans are first eaten by civet cats. It has been proposed that fermentation inside the civet cat digestive tract may contribute to the distinctively smooth flavor of kopi luwak, but the biological basis has not been determined. Therefore, we characterized the microbiome of civet cat feces using 16S rRNA gene sequences to determine the bacterial taxa that may influence fermentation processes related to kopi luwak. Moreover, we compared this fecal microbiome with that of 14 other animals, revealing that Gluconobacter is a genus that is, uniquely found in feces of the civet cat. We also found that Gluconobacter species have a large number of cell motility genes, which may encode flagellar proteins allowing colonization of the civet gut. In addition, genes encoding enzymes involved in the metabolism of hydrogen sulfide and sulfur-containing amino acids were over-represented in Gluconobacter. These genes may contribute to the fermentation of coffee beans in the digestive tract of civet cats. creator: Hikaru Watanabe creator: Chong Han Ng creator: Vachiranee Limviphuvadh creator: Shinya Suzuki creator: Takuji Yamada uri: https://doi.org/10.7717/peerj.9579 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Watanabe et al. title: Genome‐wide identification of CpG island methylator phenotype related gene signature as a novel prognostic biomarker of gastric cancer link: https://peerj.com/articles/9624 last-modified: 2020-07-30 description: BackgroundGastric cancer (GC) is one of the most fatal cancers in the world. Results of previous studies on the association of the CpG island methylator phenotype (CIMP) with GC prognosis are conflicting and mainly based on selected CIMP markers. The current study attempted to comprehensively assess the association between CIMP status and GC survival and to develop a CIMP-related prognostic gene signature of GC.MethodsWe used a hierarchical clustering method based on 2,082 GC-related methylation sites to stratify GC patients from the cancer genome atlas into three different CIMP subgroups according to the CIMP status. Gene set enrichment analysis, tumor-infiltrating immune cells, and DNA somatic mutations analysis were conducted to reveal the genomic characteristics in different CIMP-related patients. Cox regression analysis and the least absolute shrinkage and selection operator were performed to develop a CIMP-related prognostic signature. Analyses involving a time-dependent receiver operating characteristic (ROC) curve and calibration plot were adopted to assess the performance of the prognostic signature.ResultsWe found a positive relationship between CIMP and prognosis in GC. Gene set enrichment analysis indicated that cancer-progression-related pathways were enriched in the CIMP-L group. High abundances of CD8+ T cells and M1 macrophages were found in the CIMP-H group, meanwhile more plasma cells, regulatory T cells and CD4+ memory resting T cells were detected in the CIMP-L group. The CIMP-H group showed higher tumor mutation burden, more microsatellite instability-H, less lymph node metastasis, and more somatic mutations favoring survival. We then established a CIMP-related prognostic gene signature comprising six genes (CST6, SLC7A2, RAB3B, IGFBP1, VSTM2L and EVX2). The signature was capable of classifying patients into high‐and low‐risk groups with significant difference in overall survival (OS; p < 0.0001). To assess performance of the prognostic signature, the area under the ROC curve (AUC) for OS was calculated as 0.664 at 1 year, 0.704 at 3 years and 0.667 at 5 years. When compared with previously published gene-based signatures, our CIMP-related signature was comparable or better at predicting prognosis. A multivariate Cox regression analysis indicated the CIMP-related prognostic gene signature was an independent prognostic indicator of GC. In addition, Gene ontology analysis indicated that keratinocyte differentiation and epidermis development were enriched in the high-risk group.ConclusionCollectively, we described a positive association between CIMP status and prognosis in GC and proposed a CIMP-related gene signature as a promising prognostic biomarker for GC. creator: Zhuo Zeng creator: Daxing Xie creator: Jianping Gong uri: https://doi.org/10.7717/peerj.9624 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zeng et al. title: The effect of lip closure on palatal growth in patients with unilateral clefts link: https://peerj.com/articles/9631 last-modified: 2020-07-30 description: ObjectivesThe objective of this study was to compare maxillary dimensions and growth in newborns with Complete Unilateral Cleft Lip and Palate (UCLP) to healthy newborns before and after cheiloplasty. Additionally, a palatal growth curve is constructed to give more information about the natural growth before surgical intervention.MethodsTwenty-eight newborns with complete UCLP were enrolled in this study. Multiple plaster-casts of each child during their first year were collected and grouped in before and after cheiloplasty. A previous developed semi-automatic segmentation tool was used to assess the maxillary dimensions and were compared to a healthy control group. Z-scores were calculated to indicate differences between the two populations and if cheiloplasty had influence on maxillary growth. Furthermore, the prediction model created in a previous study was used to indicate differences between predictions and the outcome in UCLP measurements. The analysis was tested for inter- and intra-observer variability.ResultsResults show differences in alveolar and palatal shape in UCLP patients in comparison with healthy controls. Prior to cheiloplasty an increased width and alveolar length was observed while the palatal depth was decreased. After cheiloplasty the widths moved towards normal but were still significantly larger.ConclusionInfants with unilateral cleft lip and palate show a wider maxillary arch in comparison with the control population. Initial treatment has most influence on the width of the arch, which decreased towards normal. creator: Robin Bruggink creator: Frank Baan creator: Gem Kramer creator: Colet Claessens creator: Anne Marie Kuijpers-Jagtman creator: Ewald M. Bronkhorst creator: Thomas J.J. Maal creator: Edwin Ongkosuwito uri: https://doi.org/10.7717/peerj.9631 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bruggink et al. title: A smartphone microscopic method for rapid screening of cloth facemask fabrics during pandemics link: https://peerj.com/articles/9647 last-modified: 2020-07-30 description: BackgroundIn pandemics, because of increased demand and subsequent shortage of commercial facemasks, people need to use cloth facemasks, although such masks are reported to provide reduced protection. These masks can be prepared in local levels from different fabric materials. In developing countries, cloth masks are preferable because of low cost and added advantages of reusability. The filtering performance of a cloth facemask depends on the facial fit and on the material properties of fabrics such as porosity, yarn spacing or packing, and pore size. In resource limited settings, an affordable and easy to implement method that can assess the surface properties of cloth facemask fabrics would be important.MethodsIn this work, we developed a smartphone microscopic method for rapid screening of fabric quality. We measured the field of view of the microscope and as a proof of concept, we implemented the method to examine surfaces of sixteen locally available cloth mask fabrics.ResultsOut of the 16 masks examined, we found very diverse yarn packing and pore morphology (pore size and shape) in the fabrics. The pore size ranged from ~80 to 720 μm; much larger than respiratory droplet and bio-aerosol. This observation partly explains why such cloth facemasks provide reduced protection to the user during pandemics. The performance of a cloth facemask partly depends on the material properties of fabric such as yarn packing, pore size, porosity. Therefore, the surface properties of fabrics obtained from the smartphone method can be used to get preliminary idea on the facemask quality. We believe that the method can be an affordable and rapid method for selection of better fabrics for cloth facemask during pandemics. creator: Bhanu B. Neupane creator: Ravindra K. Chaudhary creator: Amita Sharma uri: https://doi.org/10.7717/peerj.9647 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Neupane et al. title: A novel curation system to facilitate data integration across regional citizen science survey programs link: https://peerj.com/articles/9219 last-modified: 2020-07-29 description: Integrative modeling methods can now enable macrosystem-level understandings of biodiversity patterns, such as range changes resulting from shifts in climate or land use, by aggregating species-level data across multiple monitoring sources. This requires ensuring that taxon interpretations match up across different sources. While encouraging checklist standardization is certainly an option, coercing programs to change species lists they have used consistently for decades is rarely successful. Here we demonstrate a novel approach for tracking equivalent names and concepts, applied to a network of 10 regional programs that use the same protocols (so-called “Pollard walks”) to monitor butterflies across America north of Mexico. Our system involves, for each monitoring program, associating the taxonomic authority (in this case one of three North American butterfly fauna treatments: Pelham, 2014; North American Butterfly Association, Inc., 2016; Opler & Warren, 2003) that shares the most similar overall taxonomic interpretation to the program’s working species list. This allows us to define each term on each program’s list in the context of the appropriate authority’s species concept and curate the term alongside its authoritative concept. We then aligned the names representing equivalent taxonomic concepts among the three authorities. These stepping stones allow us to bridge a species concept from one program’s species list to the name of the equivalent in any other program, through the intermediary scaffolding of aligned authoritative taxon concepts. Using a software tool we developed to access our curation system, a user can link equivalent species concepts between data collecting agencies with no specialized knowledge of taxonomic complexities. creator: Dana L. Campbell creator: Anne E. Thessen creator: Leslie Ries uri: https://doi.org/10.7717/peerj.9219 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Campbell et al. title: Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae link: https://peerj.com/articles/9442 last-modified: 2020-07-29 description: The CRISPR system has become heavily utilized in biomedical research as a tool for genomic editing as well as for site-specific chromosomal localization of specific proteins. For example, we developed a CRISPR-based methodology for enriching a specific genomic locus of interest for proteomic analysis in Saccharomyces cerevisiae, which utilized a guide RNA-targeted, catalytically dead Cas9 (dCas9) as an affinity reagent. To more comprehensively evaluate the genomic specificity of using dCas9 as a site-specific tool for chromosomal studies, we performed dCas9-mediated locus enrichment followed by next-generation sequencing on a genome-wide scale. As a test locus, we used the ARS305 origin of replication on chromosome III in S. cerevisiae. We found that enrichment of this site is highly specific, with virtually no off-target enrichment of unique genomic sequences. The high specificity of genomic localization and enrichment suggests that dCas9-mediated technologies have promising potential for site-specific chromosomal studies in organisms with relatively small genomes such as yeasts. creator: Zachary J. Waldrip creator: Piroon Jenjaroenpun creator: Oktawia DeYoung creator: Intawat Nookaew creator: Sean D. Taverna creator: Kevin D. Raney creator: Alan J. Tackett uri: https://doi.org/10.7717/peerj.9442 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Waldrip et al. title: Evaluation of knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic link: https://peerj.com/articles/9575 last-modified: 2020-07-29 description: BackgroundThe novel coronavirus disease (COVID-19) is a new viral respiratory illness, first identified in Wuhan province, China. Dental professionals and dental students are at an increased risk for these viruses from dental patients, as dental practice involves face-to-face communication with the patients and frequent exposure to saliva, blood, and other body fluids. Dental education can play an important role in the training of dental students, adequate knowledge and adopting attitudes regarding infection control measures. The aim of this study was to evaluate knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic.MethodsA total of 355 pre-clinical and clinical dental students (242 and 113, respectively, comprising 190 females and 165 males) at Fırat University Dentistry Faculty, in Elazığ, Turkey answered an online questionnaire about the biosafety procedures for and their attitudes to and knowledge of COVID-19. The study was conducted in March 2020, Turkey. The data gained were analyzed using descriptive statistical methods and chi-square test.ResultsBoth the clinical and preclinical students were found to be afraid of infecting themselves and their environment with COVID-19, and the difference between them was statistically significant. Three quarters (74.9%) of the participants responded yes to the question of whether they thought that experiences related to COVID-19 affected them psychologically, with the differences between gender and clinical status were statistically significant. Responses to the question of which clinical rotation worried them more were 29.9% endodontics, 25.1% oral and maxillofacial surgery, 16.3% prosthesis, 15.2% periodontology, 6.8% restorative dentistry, 3.9% oral diagnosis and radiology, 1.7% pedodontics, and 1.1% orthodontics, with a significant difference between the preclinical and clinical students. Regarding the measures applied by the clinical students in their clinical rotation, the responses were 100% gloves and 100% mask (with 11.5% FFP3/N95 mask), 73.6% face protective shield and 37.1% safety glasses, and 49% bonnet and 16.8% disposable box, with 90.2% frequent hand washing, and 86.7% frequent hand antiseptic usage.ConclusionsWhile students gave good responses regarding the standard measures they take to protect against transmission of COVID-19, their knowledge and attitudes about the extra measures they can take should be improved. For students to be least affected by fears associated with the disease, dental faculties should be ready to provide psychological services to those in need. creator: Osman Ataş creator: Tuba Talo Yildirim uri: https://doi.org/10.7717/peerj.9575 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ataş and Talo Yildirim title: Altered gut microbiota associated with symptom severity in schizophrenia link: https://peerj.com/articles/9574 last-modified: 2020-07-29 description: BackgroundThe gut microbiome and microbiome-gut-brain (MGB) axis have been receiving increasing attention for their role in the regulation of mental behavior and possible biological basis of psychiatric disorders. With the advance of next-generation sequencing technology, characterization of the gut microbiota in schizophrenia (SZ) patients can provide rich clues for the diagnosis and prevention of SZ.MethodsIn this study, we compared the differences in the fecal microbiota between 82 SZ patients and 80 demographically matched normal controls (NCs) by 16S rRNA sequencing and analyzed the correlations between altered gut microbiota and symptom severity.ResultsThe alpha diversity showed no significant differences between the NC and SZ groups, but the beta diversity revealed significant community-level separation in microbiome composition between the two groups (pseudo-F =3.337, p < 0.001, uncorrected). At the phylum level, relatively more Actinobacteria and less Firmicutes (p < 0.05, FDR corrected) were found in the SZ group. At the genus level, the relative abundances of Collinsella, Lactobacillus, Succinivibrio, Mogibacterium, Corynebacterium, undefined Ruminococcus and undefined Eubacterium were significantly increased, whereas the abundances of Adlercreutzia, Anaerostipes, Ruminococcus and Faecalibacterium were decreased in the SZ group compared to the NC group (p < 0.05, FDR corrected). We performed PICRUSt analysis and found that several metabolic pathways differed significantly between the two groups, including the Polyketide sugar unit biosynthesis, Valine, Leucine and Isoleucine biosynthesis, Pantothenate and CoA biosynthesis, C5-Branched dibasic acid metabolism, Phenylpropanoid biosynthesis, Ascorbate and aldarate metabolism, Nucleotide metabolism and Propanoate metabolism pathways (p < 0.05, FDR corrected). Among the SZ group, the abundance of Succinivibrio was positively correlated with the total Positive and Negative Syndrome Scale (PANSS) scores (r = 0.24, p < 0.05, uncorrected) as well as the general PANSS scores (r = 0.22, p < 0.05, uncorrected); Corynebacterium was negatively related to the negative scores of PANSS (r = 0.22, p < 0.05, uncorrected).ConclusionsOur findings provided evidence of altered gut microbial composition in SZ group. In addition, we found that Succinvibrio and Corynebacterium were associated with the severity of symptoms for the first time, which may provide some new biomarkers for the diagnosis of SZ. creator: Shijia Li creator: Min Zhuo creator: Xia Huang creator: Yuanyuan Huang creator: Jing Zhou creator: Dongsheng Xiong creator: Jiahui Li creator: Ya Liu creator: Zhilin Pan creator: Hehua Li creator: Jun Chen creator: Xiaobo Li creator: Zhiming Xiang creator: Fengchun Wu creator: Kai Wu uri: https://doi.org/10.7717/peerj.9574 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing link: https://peerj.com/articles/9588 last-modified: 2020-07-29 description: BackgroundPlums are a kind of stone fruit, a category that includes peaches, cherries, apricots, and almonds. In Korea, Japanese plum trees are usually cultivated as they best suit the climate. To date, there have been few studies in Korea on viruses infecting plum trees compared to those infecting peach trees.MethodsTo identify viruses and viroids infecting plum trees, we collected leaf samples from six different plum cultivars and subjected them to RNA-sequencing (RNA-seq). Six different plum transcriptomes were de novo assembled using the Trinity assembler followed by BLAST searching against a viral reference database.ResultsWe identified hop stunt viroid (HSVd) and six viruses, including apple chlorotic leaf spot virus (ACLSV), little cherry virus-1 (LChV-1), peach virus D (PeVD), peach leaf pitting-associated virus (PLPaV), plum bark necrosis stem pitting-associated virus (PBNSPaV), and prunus necrotic ringspot virus (PNRSV), from six plum cultivars by RNA-seq. RT-PCR confirmed the infection of HSVd and three viruses—ACLSV, PBNSPaV, and PNRSV—in plum trees. However, RT-PCR demonstrated that plum trees in this study were not infected by LChV-1, PeVD, or PLPaV. It is likely that the three viruses LChV-1, PeVD, and PLPaV as identified by RNA-seq were contaminants from other peach libraries caused by index misassignment, which suggests that careful confirmation by other methods should be carried out in next-generation sequencing (NGS)-based virus identification. Taken together, we identified a viroid and three viruses infecting plum trees in Korea. creator: Yeonhwa Jo creator: Hoseong Choi creator: Sen Lian creator: Jin Kyong Cho creator: Hyosub Chu creator: Won Kyong Cho uri: https://doi.org/10.7717/peerj.9588 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jo et al. title: Assessment of productivity, nutrient uptake and economic benefits of rice under different nitrogen management strategies link: https://peerj.com/articles/9596 last-modified: 2020-07-29 description: BackgroundIntegrating a chemical nitrogen (N) fertilizer with an organic fertilizer and using slow-release mechanism are important N management strategies to increase the N utilization efficiency (NUE) and grain yield of rice. However, the performances of both N management strategies on the productivity, the nutrient absorption and utilization efficiency, and the economic benefits of rice have not yet been comprehensively evaluated.MethodsA 2-year field experiment was conducted with seven N management strategies without fertilizer (control), 100% conventional N fertilizer (conventional compound fertilizer and urea) (N100), 75% conventional N fertilizer with 25% organic–inorganic compound fertilizer (N75+OICF25), 50% conventional N fertilizer with 50% organic–inorganic compound fertilizer (N50+OICF50), 100% organic–inorganic compound fertilizer (OICF100), slow-release compound fertilizer with urea (SRCF+U), compound fertilizer with sulfur-coated urea (CF+SCU). The responses of the productivity, the nutrient absorption and utilization efficiency, and the economic benefits of rice to the different N management strategies were evaluated.ResultsCF+SCU performed comparably or better than N100, judging by the grain yield (GY), the N, phosphate (P) and potassium (K) agronomic efficiency (NAE, PAE and KAE), and the apparent N, P and K recovery efficiency (ANRE, APRE and AKRE). SRCF+U significantly increased the GY by an average of 7.7%, the NAE and the ANRE by 23.8 and 26.7%, the PAE and the APRE by 90.6 and 109.3%, and the KAE and the AKRE by 74.2 and 57.7%. The higher GY and nutrient utilization efficiency when using SRCF+U were attributed to the higher total biomass and total nutrient absorption. N75+OICF25 and N50+OICF50 produced a comparable grain yield than N100, whereas a significant yield reduction was observed when using OICF100. Compared with N100, N75+OICF25 resulted in a comparable or higher fertilizer use efficiency (0.3 and 4.7% for NAE and ANRE, 0.3 and 3.2% for PAE and APRE, 0.3 and −2.8% for KAE and AKRE). However, the fertilizer use efficiency when using N50+OICF50 and OICF100 were lower than with N100. The highest net return (NR) (5,845.03 yuan ha−1) and benefit to cost (B:C) ratio (0.34) were obtained when using SRCF+U. The NR and the B:C ratio when using N75+OICF25 were slightly higher than when using N100. However, N50+OICF50 and OICF100 significantly decreased the NR and the B:C ratio compared with N100 by 14.5 and 12.1% and by 35.1 and 29.0%, respectively.ConclusionsSRCF+U and CF+SCU enhanced the crop productivity, the nutrient uptake and utilization efficiency, and the economic benefits compared with N100. The comprehensive performance of SRCF+U was better than that of CF+SCU. N75+OICF25 produced almost similar productivity, nutrient uptake and use efficiency compared with N100. It demonstrated that N75+OICF25 stabilized the grain yield production of rice and reduced the input of chemical N fertilizer. creator: Guoying Yang creator: Hongting Ji creator: Hongjiang Liu creator: Yuefang Zhang creator: Liugen Chen creator: Jianchu Zheng creator: Zhi Guo creator: Jing Sheng uri: https://doi.org/10.7717/peerj.9596 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach link: https://peerj.com/articles/9606 last-modified: 2020-07-29 description: BackgroundThe Eurasian otter (Lutra lutra) underwent a strong decline in large areas of the Central-Western part of its distribution range, during the second half of the twentieth century. In Italy, only residual fragmented nuclei survive in the Central-Southern part of the peninsula. Nowadays, the otter is one of the most endangered mammals in Italy, and increasing the knowledge about the ecology of this species is a key step in defining fitting management strategies. Here we provide information about the diet of otter on the Agri river system, one of the most important presence sites in Italy, to understand both the species’ food requirements and the impact on fish communities.MethodsDNA metabarcoding and High Throughput Sequencing were used on DNA extracted from spraints. We amplified DNA with a primer set for vertebrates, focusing efforts on the bulk of the otter’s diet (fishes and amphibians).ResultsOur findings showed that the diet of the otter was dominated by cyprinids (97.77%, and 99.14% of fishes), while amphibians represented 0.85% of the sequences analyzed. Results are in general accordance with previous studies based on morphological characterization; however, molecular analyses allow the resolving of some morphological uncertainties. Although the study area offers a very wide range of available prey, the diet of the otters shows marked selectivity. We highlighted a variation in prey consumed, in accordance with the typology of water system (i.e., river, lake, tributary). Some of the preys found in the diet were alien species introduced by man for sport fishing. Our findings could help define strategies useful for the conservation of the otter population in Southern Italy, suggesting management actions directed at avoiding fish community alterations through illegal stockings without severe controls on their taxonomic status. These introductions could result in a general reduction in the diversity of the otter’s preys, affecting its predatory behavior. creator: Maria Buglione creator: Simona Petrelli creator: Claudia Troiano creator: Tommaso Notomista creator: Eleonora Rivieccio creator: Domenico Fulgione uri: https://doi.org/10.7717/peerj.9606 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Buglione et al. title: Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study link: https://peerj.com/articles/9623 last-modified: 2020-07-29 description: BackgroundMetagenome next-generation sequencing (mNGS) is a valuable diagnostic tool that can be used for the identification of early pathogens of acute respiratory distress syndrome (ARDS) in severe pneumonia. Little is known about the use of this technology in clinical application and the evaluation of the prognostic value of ARDS.MethodsWe performed a retrospective cohort study of patients with ARDS caused by severe pneumonia. Samples were collected from patients in the intensive care unit (ICU) of Jiangmen Central Hospital from January 2018 to August 2019. The no-next generation sequencing (NGS) group was composed of patients given conventional microbiological tests to examine sputum, blood, or bronchoalveolar lavage fluid. The NGS group was composed of patients tested using mNGS and conventional microbiological tests. We evaluated the etiological diagnostic effect and clinical prognostic value of mNGS in patients with ARDS caused by severe pneumonia.ResultsThe overall positive rate (91.1%) detected by the mNGS method was significantly higher than that of the culture method (62.2%, P = 0.001), and antibody plus polymerase chain reaction (28.9%, P < 0.001). Following adjustment of the treatment plan based on microbial testing results, the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score of the NGS group was lower than that of the no-NGS group 7 days after treatment (P < 0.05). The 28-day mortality rate of the NGS group was significantly lower than that of the no-NGS group (P < 0.05). Longer ICU stay, higher APACHE II score and sequential organ failure assessment score were risk factors for the death of ARDS, and adjusting the medication regimen based on mNGS results was a protective factor. The detection of mNGS can significantly shorten the ICU stay of immunosuppressed patients (P < 0.01), shorten the ventilation time (P < 0.01), and reduce the ICU hospitalization cost (P < 0.05).ConclusionsMetagenome next-generation sequencing is a valuable tool to determine the etiological value of ARDS caused by severe pneumonia to improve diagnostic accuracy and prognosis for this disease. For immunosuppressed patients, mNGS technology can be used in the early stage to provide more diagnostic evidence and guide medications. creator: Peng Zhang creator: Yan Chen creator: Shuyun Li creator: Chaoliang Li creator: Shuang Zhang creator: Weihao Zheng creator: Yantang Chen creator: Jie Ma creator: Xin Zhang creator: Yanming Huang creator: Shengming Liu uri: https://doi.org/10.7717/peerj.9623 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Spermatogenesis is normal in Tex33 knockout mice link: https://peerj.com/articles/9629 last-modified: 2020-07-29 description: Testis expressed gene 33 (Tex33) is a recently reported testis-specific gene and it is evolutionarily conserved in vertebrates. The Tex33 expression is found in cytoplasm of round spermatids in Mus musculus. However, the in vivo function of Tex33 remains unknown. In this study, we made a 62bp in frame deletion on Exon2 of Tex33 gene by CRISPR/Cas9 in C57B/L6 mouse, which cause frame shift mutation of Tex33 gene. Tex33-/-adult male were fertile, and there is no significant change on litter size compared with male wildtype (Tex33+/+) adult. Besides, no overt differences were found in testis/body weight ratios, testicular/epididymal tissue morphology, sperm counts, sperm morphology and spermatozoa motility in adult Tex33-/-male mice (N = 3), in comparison with Tex33+/+ adult (N = 3). TUNEL assay also indicates the germ cells apoptosis ratio was not significantly changed in adult Tex33-/- adult male mouse testis (N = 3), compared with adult Tex33+/+ male (N = 3). Importantly, the first wave of elongating spermatids formation happens in 5w old mice. We find that the first wave of spermiogenesis is not disrupted in both 5-week-old Tex33+/+ and Tex33-/-male mouse testes and three hallmarks of spermatogenesis, PLZF,γ-H2AX and TNP1, are all detectable in seminiferous tubule. All results indicate that Tex33 is a redundant gene to spermatogenesis. This study can help other researchers avoid repetitive works on redundant genes. creator: Zhendong Zhu creator: Xin Zhang creator: Wentao Zeng creator: Shuqin Zhao creator: Jianli Zhou creator: Zuomin Zhou creator: Mingxi Liu uri: https://doi.org/10.7717/peerj.9629 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhu et al. title: Five genes influenced by obesity may contribute to the development of thyroid cancer through the regulation of insulin levels link: https://peerj.com/articles/9302 last-modified: 2020-07-28 description: Previous studies indicate that obesity is an important contributor to the proceeding of thyroid cancer (TC) with limited knowledge of the underlying mechanism. Here, we hypothesize that molecules affected by obesity may play roles in the development of TC. To test the hypothesis above, we first conducted a large-scale literature-based data mining to identify genes influenced by obesity and genes related to TC. Then, a mega-analysis was conducted to study the expression changes of the obesity-specific genes in the case of TC, using 16 independent TC array-expression datasets (783 TC cases and 439 healthy controls). After that, pathway analysis was performed to explore the functional profile of the selected target genes and their potential connections with TC. We identified 1,036 genes associated with TC and 534 regulated by obesity, demonstrating a significant overlap (N = 176, p-value = 4.07e−112). Five out of the 358 obesity-specific genes, FABP4, CFD, GHR, TNFRSF11B, and LTF, presented significantly decreased expression in TC patients (LFC<−1.44; and p-value < 1e−7). Multiple literature-based pathways were identified where obesity could promote the pathologic development of TC through the regulation of these five genes and INS levels. The five obesity genes uncovered could be novel genes that play roles in the etiology of TC through the modulation of INS levels. creator: Jiaming Chen creator: Hongbao Cao creator: Meng Lian creator: Jugao Fang uri: https://doi.org/10.7717/peerj.9302 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Assessment of potato peel and agro-forestry biochars supplementation on in vitro ruminal fermentation link: https://peerj.com/articles/9488 last-modified: 2020-07-28 description: BackgroundThe awareness of environmental and socio-economic impacts caused by greenhouse gas emissions from the livestock sector leverages the adoption of strategies to counteract it. Feed supplements can play an important role in the reduction of the main greenhouse gas produced by ruminants—methane (CH4). In this context, this study aims to assess the effect of two biochar sources and inclusion levels on rumen fermentation parameters in vitro.MethodsTwo sources of biochar (agro-forestry residues, AFB, and potato peel, PPB) were added at two levels (5 and 10%, dry matter (DM) basis) to two basal substrates (haylage and corn silage) and incubated 24-h with rumen inocula to assess the effects on CH4 production and main rumen fermentation parameters in vitro.ResultsAFB and PPB were obtained at different carbonization conditions resulting in different apparent surface areas, ash content, pH at the point of zero charge (pHpzc), and elemental analysis. Relative to control (0% biochar), biochar supplementation kept unaffected total gas production and yield (mL and mL/g DM, p = 0.140 and p = 0.240, respectively) and fermentation pH (p = 0.666), increased CH4production and yield (mL and mL/g DM, respectively, p = 0.001) and ammonia-N (NH3-N, p = 0.040), and decreased total volatile fatty acids (VFA) production (p < 0.001) and H2 generated and consumed (p ≤ 0.001). Biochar sources and inclusion levels had no negative effect on most of the fermentation parameters and efficiency. Acetic:propionic acid ratio (p = 0.048) and H2 consumed (p = 0.019) were lower with AFB inclusion when compared to PPB. Biochar inclusion at 10% reduced H2 consumed (p < 0.001) and tended to reduce total gas production (p = 0.055). Total VFA production (p = 0.019), acetic acid proportion (p = 0.011) and H2 generated (p = 0.048) were the lowest with AFB supplemented at 10%, no differences being observed among the other treatments. The basal substrate affected most fermentation parameters independently of biochar source and level used.DiscussionBiochar supplementation increased NH3-N content, iso-butyric, iso-valeric and valeric acid proportions, and decreased VFA production suggesting a reduced energy supply for microbial growth, higher proteolysis and deamination of substrate N, and a decrease of NH3-N incorporation into microbial protein. No interaction was found between substrate and biochar source or level on any of the parameters measured. Although AFB and PPB had different textural and compositional characteristics, their effects on the rumen fermentation parameters were similar, the only observed effects being due to AFB included at 10%. Biochar supplementation promoted CH4 production regardless of the source and inclusion level, suggesting that there may be other effects beyond biomass and temperature of production of biochar, highlighting the need to consider other characteristics to better identify the mechanism by which biochar may influence CH4 production. creator: Ana R.F. Rodrigues creator: Margarida R.G. Maia creator: Ana R.J. Cabrita creator: Hugo M. Oliveira creator: Maria Bernardo creator: Nuno Lapa creator: Isabel Fonseca creator: Henrique Trindade creator: José L. Pereira creator: António J.M. Fonseca uri: https://doi.org/10.7717/peerj.9488 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rodrigues et al. title: Comparison of long-term changes in size and longevity of bee colonies in mid-west Japan and Maui with and without exposure to pesticide, cold winters, and mites link: https://peerj.com/articles/9505 last-modified: 2020-07-28 description: Four long-term field experiments in mid-west Japan (Shika) made it clear that extinction of colonies exposed to neonicotinoid was much higher than for colonies exposed to organophosphates. The incidence of hive death for of organophosphate-exposed and control (pesticide-free) colonies was similar. We conducted a field experiment in Maui for 271 days using the same pesticides (dinotefuran: 0.2 ppm, clothianidin: 0.08 ppm, fenitrothion: 1 ppm) as used in Shika with the honeybee, Apis mellifera, colonies without mites. Numbers of adult bees, capped brood, mites and other hive parameters were accurately counted on photographs of combs and on the inside of the hives. All six neonicotinoid (dinotefuran & clothianidin)-exposed colonies failed during the experiment. One of three organophosphate (fenitrothion)-exposed colonies and one of the three control colonies also failed. The findings from Maui, where colonies displayed no mites, provides evidence from Shika, with mites, that neonicotinoids are more hazardous to honeybee colonies than organophosphates. The apparent longevity of honeybee colonies on Maui was estimated by numbers of adult bees and capped brood using a mathematical model previously proposed. Seasonal changes in longevity on Maui differ greatly from changes at Shika, the latter showing distinct seasonal variation. Longevity on Maui remains nearly constant throughout the year with wide variations. At Shika, it increases drastically in winter, by six- to ten fold more than the other seasons. Differences seem to depend on the existence of cold winters and the length of flowering seasons. In a perpetually hospitable environment, small changes in conditions can be sensitively reflected in apparent longevity. Examining wide variations in apparent longevity that are seemingly incoherent, we recognized several differences in apparent longevity between neonicotinoid-exposed and organophosphate-exposed colonies: The colony that failed in after organophosphate-exposure colony group exhibited the longest apparent longevity and the fewest number of newly capped brood, as also was the case in control colonies. Extended longevity when few brood are newly produced is reasonable to maintain the colony from a physiological point of view. Extension of apparent longevity is not seen in neonicotinoid-exposed colonies when the number of newly capped brood is fewer. This finding suggests that neonicotinoid pesticides may inhibit normal apian physiology. creator: Toshiro Yamada creator: Kazuko Yamada uri: https://doi.org/10.7717/peerj.9505 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yamada and Yamada title: Mediterranean swordfish (Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas link: https://peerj.com/articles/9518 last-modified: 2020-07-28 description: BackgroundThe Mediterranean swordfish stock is overfished and considered not correctly managed. Elucidating the patterns of the Mediterranean swordfish population structure constitutes an essential prerequisite for effective management of this fishery resource. To date, few studies have investigated intra-Mediterranean swordfish population structure, and their conclusions are controversial.MethodsA panel of 20 microsatellites DNA was used to investigate fine-scale population structuring of swordfish from six main fishing areas of the Mediterranean Sea.ResultsThis study provides evidence to reject the hypothesis of a single swordfish population within the Mediterranean Sea. DAPC analysis revealed the presence of three genetic clusters and a high level of admixture within the Mediterranean Sea. Genetic structure was supported by significant FST values while mixing was endorsed by the heterozygosity deficit observed in sampling localities indicative of a possible Wahlund effect, by sampling admixture individuals. Overall, our tests reject the hypothesis of a single swordfish population within the Mediterranean Sea. Homing towards the Mediterranean breeding areas may have generated a weak degree of genetic differentiation between populations even at the intra-basin scale. creator: Tommaso Righi creator: Andrea Splendiani creator: Tatiana Fioravanti creator: Andrea Petetta creator: Michela Candelma creator: Giorgia Gioacchini creator: Kyle Gillespie creator: Alex Hanke creator: Oliana Carnevali creator: Vincenzo Caputo Barucchi uri: https://doi.org/10.7717/peerj.9518 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Righi et al. title: Proteomic analysis of human cervical adenocarcinoma mucus to identify potential protein biomarkers link: https://peerj.com/articles/9527 last-modified: 2020-07-28 description: BackgroundCervical cancer is the most common gynecological cancer, encompassing cervical squamous cell carcinoma, adenocarcinoma, and other epithelial tumors. There are many diagnostic methods to detect cervical cancers but no precision screening tool for cervical adenocarcinoma at present.Material and methodsThe cervical mucus from three normal cervices (Ctrl), three endocervical adenocarcinoma (EA), and three cervical adenocarcinoma in situ (AIS) was collected for proteomic analysis. The proteins were screened using liquid chromatography-mass spectrometry analysis (LC-MS). The biological function of the differently expressed proteins were predicted by Gene Ontology (GO).ResultsA total of 711 proteins were identified, including 237 differently expressed proteins identified in EA/Ctrl comparison, 256 differently expressed proteins identified in AIS/Ctrl comparison, and 242 differently expressed proteins identified in AIS/EA comparison (up-regulate ≥ 1.5 or down-regulate ≤ 0.67). Functional annotation was performed using GO analysis on 1,056 differently expressed proteins to identify those that may impact cervical cancer, such as heme protein myeloperoxidase, which is involved in the immune process, and APOA1, which is associated with lipid metabolism.ConclusionWe used proteomic analysis to screen out differently expressed proteins from normal cervical mucus and cervical adenocarcinoma mucus samples. These differently expressed proteins may be potential biomarkers for the diagnosis and treatment of cervical adenocarcinoma but require additional study. creator: Zhifang Ma creator: Jie Chen creator: Ting Luan creator: Chengzhuo Chu creator: Wangfei Wu creator: Yichao Zhu creator: Yun Gu uri: https://doi.org/10.7717/peerj.9527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ma et al. title: Predatory functional response and fitness parameters of Orius strigicollis Poppius when fed Bemisia tabaci and Trialeurodes vaporariorum as determined by age-stage, two-sex life table link: https://peerj.com/articles/9540 last-modified: 2020-07-28 description: BackgroundThe polyphagous predatory bug O. strigicollis is an active predator used to control thrips and aphids. The whitefly species Bemisia tabaci and Trialeurodes vaporariorum are voracious pests of different economic agricultural crops and vegetables.MethodIn this study, the Holling disc equation and the age-stage, two-sex life table technique were used to investigate the functional response and biological traits of third instar nymphs and adult female O. strigicollis when presented third instar nymphs of both whitefly species as prey.ResultsThe results showed a type II functional response for each life stage of O. strigicollis when fed each whitefly species. The calculated prey handling time for different O. strigicollis life stages were shorter when fed T. vaporariorum than when fed B. tabaci nymphs. In contrast, the nymphal development of O. strigicollis was significantly shorter when fed B. tabaci than T. vaporariorum nymphs. Additionally, the total pre-oviposition period of adult females was statistically shorter when fed B. tabaci nymphs than T. vaporariorum nymphs. Furthermore, the survival rates and total fecundity of O. strigicollis were higher when fed B. tabaci than T. vaporariorum. There were no significant differences in any population parameters of O. strigicollis when fed either whitefly species. These results show that O. strigicollis could survive and maintain its populations on both species of whitefly and could therefore serve as a biological control agent in integrated pest management (IPM). creator: Shakeel Ur Rehman creator: Xingmiao Zhou creator: Shahzaib Ali creator: Muhammad Asim Rasheed creator: Yasir Islam creator: Muhammad Hafeez creator: Muhammad Aamir Sohail creator: Haris Khurram uri: https://doi.org/10.7717/peerj.9540 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rehman et al. title: Comparative proteome analysis reveals VPS28 regulates milk fat synthesis through ubiquitylation in bovine mammary epithelial cells link: https://peerj.com/articles/9542 last-modified: 2020-07-28 description: In our previous study, we found that VPS28 (vacuolar protein sorting 28 homolog) could alter ubiquitylation level to regulate milk fat synthesis in bovine primary mammary epithelial cells (BMECs). While the information on the regulation of VPS28 on proteome of milk fat synthesis is less known, we explored its effect on milk fat synthesis using isobaric tags for relative and absolute quantitation assay after knocking down VPS28 in BMECs. A total of 2,773 proteins in three biological replicates with a false discovery rate of less than 1.2% were identified and quantified. Among them, a subset of 203 proteins were screened as significantly down-(111) and up-(92) regulated in VPS28 knockdown BMECs compared with the control groups. According to Gene Ontology analysis, the differentially expressed proteins were enriched in the “proteasome,” “ubiquitylation,” “metabolism of fatty acids,” “phosphorylation,” and “ribosome.” Meanwhile, some changes occurred in the morphology of BMECs and an accumulation of TG (triglyceride) and dysfunction of proteasome were identified, and a series of genes associated with milk fat synthesis, ubiquitylation and proteasome pathways were analyzed by quantitative real-time PCR. The results of this study suggested VPS28 regulated milk fat synthesis was mediated by ubiquitylation; it could be an important new area of study for milk fat synthesis and other milk fat content traits in bovine. creator: Lily Liu creator: Qin Zhang uri: https://doi.org/10.7717/peerj.9542 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liu and Zhang title: Arabidopsis thaliana exudates induce growth and proteomic changes in Gluconacetobacter diazotrophicus link: https://peerj.com/articles/9600 last-modified: 2020-07-28 description: BackgroundPlants interact with a variety of microorganisms during their life cycle, among which beneficial bacteria deserve special attention. Gluconacetobacter diazotrophicus is a beneficial bacterium able to fix nitrogen and promote plant growth. Despite its biotechnological potential, the mechanisms regulating the interaction between G. diazotrophicus and host plants remain unclear.MethodsWe analyzed the response of G. diazotrophicus to cocultivation with Arabidopsis thaliana seedlings. Bacterial growth in response to cocultivation and plant exudates was analyzed. Through comparative proteomic analysis, G. diazotrophicus proteins regulated during cocultivation were investigated. Finally, the role of some up-accumulated proteins in the response G. diazotrophicus to cocultivation was analyzed by reverse genetics, using insertion mutants.ResultsOur results revealed the induction of bacterial growth in response to cocultivation. Comparative proteomic analysis identified 450 bacterial proteins, with 39 up-accumulated, and 12 down-accumulated in response to cocultivation. Among the up-accumulated pathways, the metabolism of pentoses and protein synthesis were highlighted. Proteins potentially relevant to bacterial growth response such as ABC-F-Etta, ClpX, Zwf, MetE, AcnA, IlvC, and AccC were also increased. Reverse genetics analysis, using insertion mutants, revealed that the lack of ABC-F-Etta and AccC proteins severely affects G. diazotrophicus response to cocultivation. Our data demonstrated that specific mechanisms are activated in the bacterial response to plant exudates, indicating the essential role of “ribosomal activity” and “fatty acid biosynthesis” in such a process. This is the first study to demonstrate the participation of EttA and AccC proteins in plant-bacteria interactions, and open new perspectives for understanding the initial steps of such associations. creator: Tamires Cruz dos Santos creator: Mariana Ramos Leandro creator: Clara Yohana Maia creator: Patrícia Rangel creator: Fabiano S. Soares creator: Ricardo Reis creator: Lucas Passamani creator: Vanildo Silveira creator: Gonçalo Apolinário de Souza Filho uri: https://doi.org/10.7717/peerj.9600 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 dos Santos et al. title: Energy balance of food in a detrito-bryophagous groundhopper (Orthoptera: Tetrigidae) link: https://peerj.com/articles/9603 last-modified: 2020-07-28 description: Detritus (decaying organic matter) and phyllodes of mosses are two main components in the diet of groundhoppers (Orthoptera: Tetrigidae). We studied the energy balance of consumed food under laboratory conditions in the detrito-bryophagous groundhopper, Tetrix subulata (Linnaeus, 1758). The results indicated that the energy food budget of this detrito-bryophagous groundhopper was comparable to those of small herbivorous grasshoppers (Acrididae: Gomphocerinae, Melanoplinae), which have a similar energy food budget of approximately 800–1,100 J/g. T. subulata consumed four times more detritus than mosses, although both components provided similar amounts of energy (ca. 15–16 kJ/g). However, in contrast with detritus, moss fragments passed through the digestive tract without a distinct change in their mass or a loss in their energy value. We assume that moss may cause the longer retention of semifluid mass of partly digested food in the alimentary tract; hence, the digestion and efficiency of nutrient absorption from detritus could be more effective. creator: Kateřina Kuřavová creator: Jan Šipoš creator: Petr Kočárek uri: https://doi.org/10.7717/peerj.9603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kuřavová et al. title: Testing pterosaur ingroup relationships through broader sampling of avemetatarsalian taxa and characters and a range of phylogenetic analysis techniques link: https://peerj.com/articles/9604 last-modified: 2020-07-28 description: The pterosaurs first appear in the fossil record in the middle of the Late Triassic. Their earliest representatives are known from Northern Hemisphere localities but, by the end of the Jurassic Period, this clade of flying reptiles achieved a global distribution, as well as high levels of diversity and disparity. Our understanding of early pterosaur evolution and the fundamental interrelationships within Pterosauria has improved dramatically in recent decades. However, there is still debate about how the various pterosaur subgroups relate to one another and about which taxa comprise these. Many recent phylogenetic analyses, while sampling well from among the known Triassic and Early Jurassic pterosaurs, have not included many non-pterosaurian ornithodirans or other avemetatarsalians. Given the close relationship between these groups of archosaurs, the omission of other ornithodirans and avemetatarsalians has the potential to adversely affect the results of phylogenetic analyses, in terms of character optimisation and ingroup relationships recovered. This study has addressed this issue and tests the relationships between the early diverging pterosaur taxa following the addition of avemetatarsalian taxa and anatomical characters to an existing early pterosaur dataset. This study has, for the first time, included taxa that represent the aphanosaurs, lagerpetids, silesaurids and dinosaurs, in addition to early pterosaurs. Anatomical characters used in other recent studies of archosaurs and early dinosaurs have also been incorporated. By expanding the outgroup taxa and anatomical character coverage in this pterosaur dataset, better resolution between the taxa within certain early pterosaur subclades has been achieved and stronger support for some existing clades has been found; other purported clades of early pterosaurs have not been found in this analysis—for example there is no support for a monophyletic Eopterosauria or Eudimorphodontidae. Further support has been found for a sister-taxon relationship between Peteinosaurus zambelli and Macronychoptera, a clade here named Zambellisauria (clade nov.), as well as for a monophyletic and early diverging Preondactylia. Some analyses also support the existence of a clade that falls as sister-taxon to the zambellisaurs, here named Caviramidae (clade nov.). Furthermore, some support has been found for a monophyletic Austriadraconidae at the base of Pterosauria. Somewhat surprisingly, Lagerpetidae is recovered outside of Ornithodira sensu stricto, meaning that, based upon current definitions at least, pterosaurs fall within Dinosauromorpha in this analysis. However, fundamental ornithodiran interrelationships were not the focus of this study and this particular result should be treated with caution for now. However, these results do further highlight the need for broader taxon and character sampling in phylogenetic analyses, and the effects of outgroup choice on determining ingroup relationships. creator: Matthew G. Baron uri: https://doi.org/10.7717/peerj.9604 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Baron title: Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome link: https://peerj.com/articles/9608 last-modified: 2020-07-28 description: Sugarcane contributes 80% of global sugar production and to bioethanol generation for the bioenergy industry. Its productivity is threatened by drought that can cause up to 60% yield loss. This study used RNA-Seq to gain a better understanding of the underlying mechanism by which drought-tolerant sugarcane copes with water stress. We compared gene expression in KPS01-12 (drought-tolerant genotype) and UT12 (drought-sensitive genotype) that have significantly different yield loss rates under drought conditions. We treated KPS01-12 and UT12 with mild and moderate water stress and found differentially expressed genes in various biological processes. KPS01-12 had higher expression of genes that were involved in water retention, antioxidant secondary metabolite biosynthesis, and oxidative and osmotic stress response than UT12. In contrast, the sensitive genotype had more down-regulated genes that were involved in photosynthesis, carbon fixation and Calvin cycle than the tolerant genotype. Our obtained expression profiles suggest that the tolerant sugarcane has a more effective genetic response than the sensitive genotype at the initiation of drought stress. The knowledge gained from this study may be applied in breeding programs to improve sugarcane production in drought conditions. creator: Wanapinun Nawae creator: Jeremy R. Shearman creator: Sithichoke Tangphatsornruang creator: Prapat Punpee creator: Thippawan Yoocha creator: Duangjai Sangsrakru creator: Chaiwat Naktang creator: Chutima Sonthirod creator: Warodom Wirojsirasak creator: Kittipat Ukoskit creator: Klanarong Sriroth creator: Peeraya Klomsa-ard creator: Wirulda Pootakham uri: https://doi.org/10.7717/peerj.9608 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nawae et al. title: Ancient globetrotters—connectivity and putative native ranges of two cosmopolitan biofouling amphipods link: https://peerj.com/articles/9613 last-modified: 2020-07-28 description: The geographic distributions of some coastal marine species have appeared as cosmopolitan ever since they were first scientifically documented. In particular, for many benthic species that are associated with anthropogenic substrata, there is much speculation as to whether or not their broad distributions can be explained by natural mechanisms of dispersal. Here, we focused on two congeneric coastal crustaceans with cosmopolitan distributions—the tube-dwelling amphipods Jassa marmorata and Jassa slatteryi. Both species are common elements of marine biofouling on nearly all kinds of artificial hard substrata in temperate to warm seas. We hypothesized that the two species’ modern occurrences across the oceans are the result of human shipping activities that started centuries ago. Mitochondrial DNA sequences of the CO1 fragment of specimens from distinct marine regions around the world were analysed, evaluating genetic structure and migration models and making inferences on putative native ranges of the two Jassa species. Populations of both species exhibited considerable genetic diversity with differing levels of geographic structure. For both species, at least two dominant haplotypes were shared among several geographic populations. Rapid demographic expansion and high migration rates between geographically distant regions support a scenario of ongoing dispersal all over the world. Our findings indicate that the likely former native range of J. marmorata is the Northwest Atlantic, whereas the likely former native range of J. slatteryi is the Northern Pacific region. As corroborated by the genetic connectivity between populations, shipping still appears to be the more successful vector of the two species’ dispersal when compared to natural mechanisms. Historical invasion events that likely started centuries ago, along with current ongoing dispersal, confirm these species’ identities as true “neocosmopolitans”. creator: Jan Beermann creator: Allison K. Hall-Mullen creator: Charlotte Havermans creator: Joop WP Coolen creator: Richard PMA Crooijmans creator: Bert Dibbits creator: Christoph Held creator: Andrea Desiderato uri: https://doi.org/10.7717/peerj.9613 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Beermann et al. title: Toxicity thresholds of three insecticides and two fungicides to larvae of the coral Acropora tenuis link: https://peerj.com/articles/9615 last-modified: 2020-07-28 description: Tropical marine ecosystems, such as coral reefs, face several threats to their health and resilience, including poor water quality. Previous studies on the risks posed by pesticides have focused on five priority herbicides; however, as the number of pesticides applied in coastal agriculture increases, a suite of ‘alternative’ pesticides is being detected in tropical nearshore waters. To improve our understanding of the risks posed by alternative pesticides to tropical marine organisms, the effects of three insecticides (diazinon, fipronil, imidacloprid) and two fungicides (chlorothalonil, propiconazole) were tested on larval metamorphosis of the coral Acropora tenuis. A. tenuis larvae were affected by all five pesticides and the reference toxicant copper. The no effect concentration (NEC) and the 10% and 50% effect concentrations (EC10 and EC50, respectively) for larval metamorphosis were estimated from concentration-response curves after 48 h exposure. The NEC, EC10 and EC50 (in µg L−1), respectively, of each pesticide were as follows: chlorothalonil (2.4, 2.8, 6.0); fipronil (12.3, 13.9, 29.1); diazinon (38.0, 40.8, 54.7); imidacloprid (263, 273, 347); and propiconazole (269, 330, 1008). These toxicity thresholds are higher than reported concentrations in monitoring programs; however, these data will contribute to improving water quality guideline values, which inform the total risk assessments posed by complex contaminant mixtures to which these pesticides contribute. creator: Florita Flores creator: Sarit Kaserzon creator: Gabriele Elisei creator: Gerard Ricardo creator: Andrew P. Negri uri: https://doi.org/10.7717/peerj.9615 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Flores et al. title: Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis link: https://peerj.com/articles/9633 last-modified: 2020-07-28 description: BackgroundColorectal cancer (CRC) is the third most common cancer in the world. The present study is aimed at identifying hub genes associated with the progression of CRC.MethodThe data of the patients with CRC were obtained from the Gene Expression Omnibus (GEO) database and assessed by weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses performed in R by WGCNA, several hub genes that regulate the mechanism of tumorigenesis in CRC were identified. Differentially expressed genes in the data sets GSE28000 and GSE42284 were used to construct a co-expression network for WGCNA. The yellow, black and blue modules associated with CRC level were filtered. Combining the co-expression network and the PPI network, 15 candidate hub genes were screened.ResultsAfter validation using the TCGA-COAD dataset, a total of 10 hub genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. The expressions of MT1G, CXCL8, IL1B, CXCL5, CXCL11 and GZMB in CRC tissues were higher than normal tissues (p-value < 0.05). The expressions of MT1X, MT2A, IL10RA and KIT in CRC tissues were lower than normal tissues (p-value < 0.05).ConclusionsBy combinating with a series of methods including GO enrichment analysis, KEGG pathway analysis, PPI network analysis and gene co-expression network analysis, we identified 10 hub genes that were associated with the progression of CRC. creator: Jie Meng creator: Rui Su creator: Yun Liao creator: Yanyan Li creator: Ling Li uri: https://doi.org/10.7717/peerj.9633 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Meng et al. title: Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes link: https://peerj.com/articles/9648 last-modified: 2020-07-28 description: BackgroundSARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission.MethodsWe used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variations. These frequencies were compared with relative substitutions frequencies between SARS-CoV-2 and related animal coronaviruses. A similar analysis was performed for human coronaviruses SARS-CoV and HKU1.ResultsWe found a 9-fold excess of G–U transversions among SARS-CoV-2 mutations over relative substitution frequencies between SARS-CoV-2 and a close relative coronavirus from bats (RaTG13). This suggests that mutation patterns of SARS-CoV-2 have changed after transmission to humans. The excess of G–U transversions was much smaller in a similar analysis for SARS-CoV and non-existent for HKU1. Remarkably, we did not find a similar excess of complementary C–A mutations in SARS-CoV-2. We discuss possible explanations for these observations. creator: Alexander Y. Panchin creator: Yuri V. Panchin uri: https://doi.org/10.7717/peerj.9648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Panchin and Panchin title: Change of direction asymmetry across different age categories in youth soccer link: https://peerj.com/articles/9486 last-modified: 2020-07-27 description: BackgroundIn youth, the development of change of direction (COD) and sprint performance is a key component for successfully competing in soccer across age. During a COD, the presence of directional asymmetries may be detrimental due to the unpredictable nature of the sport. Therefore, the aims of the study were to investigate asymmetries in COD ability and to examine the differences in COD and sprint performance across age in young soccer players.MethodsSixty-eight sub-elite soccer players of different age categories (U18, U17, U16, U15) were tested on a 10-m linear sprint test and 90°COD (5-m entry and exit) test in both directions. Asymmetric index (AI) of COD deficit was obtained for dominant (fastest) and non-dominant directions (slowest).ResultsThe results showed that U16 were more asymmetrical than U18, U17, and U15 from large to moderate effects. The sprint time improved linearly across age with U18 and U15 displaying the fastest and slowest 10-m sprint performance (p < 0.01), respectively. Moreover, COD ability measured by COD deficit did not change across age (p > 0.05).ConclusionGiven the results of this study, practitioners are encouraged to assess asymmetries between dominant and non-dominant directions rather than solely players’ COD ability in young soccer players. creator: Athos Trecroci creator: Alessio Rossi creator: Thomas Dos’Santos creator: Damiano Formenti creator: Luca Cavaggioni creator: Stefano Longo creator: F. Marcello Iaia creator: Giampietro Alberti uri: https://doi.org/10.7717/peerj.9486 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Trecroci et al. title: Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: an in silico approach link: https://peerj.com/articles/9572 last-modified: 2020-07-27 description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19. creator: M. Shaminur Rahman creator: M. Nazmul Hoque creator: M. Rafiul Islam creator: Salma Akter creator: A. S. M. Rubayet Ul Alam creator: Mohammad Anwar Siddique creator: Otun Saha creator: Md. Mizanur Rahaman creator: Munawar Sultana creator: Keith A. Crandall creator: M. Anwar Hossain uri: https://doi.org/10.7717/peerj.9572 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rahman et al. title: Exploring the socio-economic and environmental components of infectious diseases using multivariate geovisualization: West Nile Virus link: https://peerj.com/articles/9577 last-modified: 2020-07-27 description: BackgroundThis study postulates that underlying environmental conditions and a susceptible population’s socio-economic status should be explored simultaneously to adequately understand a vector borne disease infection risk. Here we focus on West Nile Virus (WNV), a mosquito borne pathogen, as a case study for spatial data visualization of environmental characteristics of a vector’s habitat alongside human demographic composition for understanding potential public health risks of infectious disease. Multiple efforts have attempted to predict WNV environmental risk, while others have documented factors related to human vulnerability to the disease. However, analytical modeling that combines the two is difficult due to the number of potential explanatory variables, varying spatial resolutions of available data, and differing research questions that drove the initial data collection. We propose that the use of geovisualization may provide a glimpse into the large number of potential variables influencing the disease and help distill them into a smaller number that might reveal hidden and unknown patterns. This geovisual look at the data might then guide development of analytical models that can combine environmental and socio-economic data.MethodsGeovisualization was used to integrate an environmental model of the disease vector’s habitat alongside human risk factors derived from socio-economic variables. County level WNV incidence rates from California, USA, were used to define a geographically constrained study area where environmental and socio-economic data were extracted from 1,133 census tracts. A previously developed mosquito habitat model that was significantly related to WNV infected dead birds was used to describe the environmental components of the study area. Self-organizing maps found 49 clusters, each of which contained census tracts that were more similar to each other in terms of WNV environmental and socio-economic data. Parallel coordinate plots permitted visualization of each cluster’s data, uncovering patterns that allowed final census tract mapping exposing complex spatial patterns contained within the clusters.ResultsOur results suggest that simultaneously visualizing environmental and socio-economic data supports a fuller understanding of the underlying spatial processes for risks to vector-borne disease. Unexpected patterns were revealed in our study that would be useful for developing future multilevel analytical models. For example, when the cluster that contained census tracts with the highest median age was examined, it was determined that those census tracts only contained moderate mosquito habitat risk. Likewise, the cluster that contained census tracts with the highest mosquito habitat risk had populations with moderate median age. Finally, the cluster that contained census tracts with the highest WNV human incidence rates had unexpectedly low mosquito habitat risk. creator: Abhishek K. Kala creator: Samuel F. Atkinson creator: Chetan Tiwari uri: https://doi.org/10.7717/peerj.9577 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kala et al. title: Viable bacterial communities on hospital window components in patient rooms link: https://peerj.com/articles/9580 last-modified: 2020-07-27 description: Previous studies demonstrate an exchange of bacteria between hospital room surfaces and patients, and a reduction in survival of microorganisms in dust inside buildings from sunlight exposure. While the transmission of microorganisms between humans and their local environment is a continuous exchange which generally does not raise cause for alarm, in a hospital setting with immunocompromised patients, these building-source microbial reservoirs may pose a risk. Window glass is often neglected during hospital disinfection protocols, and the microbial communities found there have not previously been examined. This pilot study examined whether living bacterial communities, and specifically the pathogens Methicillin-resistant Staphylococcus aureus (MRSA) and Clostridioides difficile (C. difficile), were present on window components of exterior-facing windows inside patient rooms, and whether relative light exposure (direct or indirect) was associated with changes in bacterial communities on those hospital surfaces. Environmental samples were collected from 30 patient rooms in a single ward at Oregon Health & Science University (OHSU) in Portland, Oregon, USA. Sampling locations within each room included the window glass surface, both sides of the window curtain, two surfaces of the window frame, and the air return grille. Viable bacterial abundances were quantified using qPCR, and community composition was assessed using Illumina MiSeq sequencing of the 16S rRNA gene V3/V4 region. Viable bacteria occupied all sampled locations, but was not associated with a specific hospital surface or relative sunlight exposure. Bacterial communities were similar between window glass and the rest of the room, but had significantly lower Shannon Diversity, theorized to be related to low nutrient density and resistance to bacterial attachment of glass compared to other surface materials. Rooms with windows that were facing west demonstrated a higher abundance of viable bacteria than those facing other directions, potentially because at the time of sampling (morning) west-facing rooms had not yet been exposed to sunlight that day. Viable C. difficile was not detected and viable MRSA was detected at very low abundance. Bacterial abundance was negatively correlated with distance from the central staff area containing the break room and nursing station. In the present study, it can be assumed that there is more human traffic in the center of the ward, and is likely responsible for the observed gradient of total abundance in rooms along the ward, as healthcare staff both deposit more bacteria during activities and affect microbial transit indoors. Overall, hospital window components possess similar microbial communities to other previously identified room locations known to act as reservoirs for microbial agents of hospital-associated infections. creator: Patrick F. Horve creator: Leslie G. Dietz creator: Suzanne L. Ishaq creator: Jeff Kline creator: Mark Fretz creator: Kevin G. Van Den Wymelenberg uri: https://doi.org/10.7717/peerj.9580 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Horve et al. title: Food sources of energy and nutrients among Canadian adults following a gluten-free diet link: https://peerj.com/articles/9590 last-modified: 2020-07-27 description: BackgroundThe gluten-free diet (GFD) involves the elimination of wheat and related grains. Wheat is a key fortification vehicle for nutrients such as iron and B vitamins. While there is growing evidence of low nutrients intake and poor diet quality amongst people following long-term GFD, few studies have used a dietary pattern approach to analyse top food sources of nutrients in today’s complex food environment. Thus, the purpose of this study was to identify food sources of energy and nutrients from previously collected diet records of adults following a GFD.MethodsThree, 3-day food records were collected from 35 participants in a lifestyle intervention study (n = 240 records). All food items were categorised according to the Bureau of Nutritional Sciences Food Group Codes. Percentages of total dietary intakes from food groups were ranked.ResultsMean intakes of dietary fibre, calcium and iron (females) were lower than recommended, with half the sample consuming below the recommended proportion of energy as carbohydrate. Meat, poultry and fish were the top source of energy (19.5%) in the diet. Gluten-free (GF) grain products were the top source of carbohydrate, fibre and iron and second greatest source of energy. Amongst grains, breakfast/hot cereals, yeast breads, and mixed grain dishes were the greatest nutrient contributors, despite most commercial cereals and breads (65%) being unenriched. Legumes were not frequently consumed.ConclusionsGF grains were the top food source of carbohydrate, fibre and iron, despite few brands being enriched or fortified. It is a challenge to assess and monitor nutrient intakes on GFD due to the lack of nutrient composition data for B vitamins and minerals (other than iron). Dietary planning guidance for the appropriate replacement of nutrients provided by wheat is warranted. creator: Jennifer A. Jamieson creator: Anna Neufeld uri: https://doi.org/10.7717/peerj.9590 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jamieson and Neufeld title: An analysis of the perceived causes leading to task-failure in resistance-exercises link: https://peerj.com/articles/9611 last-modified: 2020-07-27 description: BackgroundWhile reaching task-failure in resistance-exercises is a topic that attracts scientific and applied interest, the underlying perceived reasons leading to task-failure remain underexplored. Here, we examined the reasons subjects attribute to task-failure as they performed resistance-exercises using different loads.MethodsTwenty-two resistance-trained subjects (11-females) completed one Repetition-Maximum (RM) tests in the barbell squat and bench-press. Then, in the next two counterbalanced sessions, subjects performed two sets to task-failure in both exercises, using either 70% or 83% of 1RM. Approximately 30 seconds after set-completion, subjects verbally reported the reasons they perceived to have caused them to reach task-failure. Their answers were recorded, transcribed, and thematically analyzed. The differences between the frequencies of the identified categories were then tested using a mixed logistic regression model.ResultsThe most commonly reported reason was muscle fatigue (54%, p < 0.001), mostly of the target muscles involved in each exercise. However, remote muscles involved to a lesser extent in each exercise were also reported. Approximately half of the remaining reasons included general fatigue (26%), pain (12%), cardiovascular strain (11%), and negative affect (10%), with the latter three reported more often in the squat (p = 0.022).ConclusionsIn contrast to our expectations, task-failure was perceived to be caused by a range of limiting factors other than fatigue of the target muscles. It now remains to be established whether different perceived limiting factors of resistance-exercises lead to different adaptations, such as muscular strength and hypertrophy. creator: Aviv Emanuel creator: Isaac Isur Rozen Smukas creator: Israel Halperin uri: https://doi.org/10.7717/peerj.9611 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Emanuel et al. title: Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam link: https://peerj.com/articles/9612 last-modified: 2020-07-27 description: This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams. creator: Tong Jia creator: Tingyan Guo creator: Baofeng Chai uri: https://doi.org/10.7717/peerj.9612 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jia et al. title: How “dirty” is the Dark Triad? Dark character profiles, swearing, and sociosexuality link: https://peerj.com/articles/9620 last-modified: 2020-07-27 description: Malevolent character traits (i.e., the Dark Triad: Machiavellianism, narcissism, and psychopathy) are associated to emotional frigidity, antagonism, immoral strategic thinking, betrayal, exploitation, and sexual promiscuity. Despite the fact that character is a complex adaptive system, almost every study has solely investigated the linear association between malevolent character and attitudes towards both swearing and sociosexual orientation (i.e., behavior, attitude, and desire regarding promiscuous sexual behavior). In contrast, the aim in this set of studies was to evaluate these associations in relation to specific profiles of malevolent character (i.e., the Dark Cube). In two studies participants responded to the Dark Triad Dirty Dozen, the Taboo Words’ Offensiveness and Usage Inventories (i.e., attitudes towards 30 swear words’ level of offensiveness and usage) (Study 1: N1 = 1,000) and the Sociosexual Orientation Inventory Revised (Study 2: N2 = 309). Participants were clustered according to all eight possible combinations based on their dark trait scores (M/m = high/low Machiavellianism; N/n = high/low narcissism; P/p = high/low psychopathy). The results of this nonlinear approach suggested that the frequent usage, not level of offensiveness, of swear words was associated to Machiavellianism and narcissism. In other words, individuals with high levels in these traits might swear and are verbally offensive often, because they do not see swearing as offensive (cf. with the attitude-behavior-cognition-hypothesis of taboo words; Rosenberg, Sikström & Garcia, 2017). Moreover, promiscuous sociosexual attitude and desire were related to each dark trait only when the other two were low. Additionally, promiscuous sociosexual behavior was not associated to these malevolent character traits. That is, individuals high in the dark traits are willing to and have the desire to engage in sexual relations without closeness, commitment, and other indicators of emotional bonding. However, they do not report high levels of previous sexual experience, relationships, and infidelity. Hence, they approve and desire for it, but they are not actually doing it. The use of person-centered and non-linear methods, such as the Dark Character Cube, seem helpful in the advancement of a coherent theory of a biopsychosocial model of dark character. creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.9620 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Garcia title: Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy link: https://peerj.com/articles/9621 last-modified: 2020-07-27 description: We aimed to identify prognostic signature based on autophagy-related genes (ARGs) for breast cancer patients. The datasets of breast cancer were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Least absolute shrinkage and selection operator (LASSO) Cox regression was conducted to construct multiple-ARG risk signature. In total, 32 ARGs were identified as differentially expressed between tumors and adjacent normal tissues based on TCGA. Six ARGs (IFNG, TP63, PPP1R15A, PTK6, EIF4EBP1 and NKX2-3) with non-zero coefficient were selected from the 32 ARGs using LASSO regression. The 6-ARG signature divided patients into high-and low-risk group. Survival analysis indicated that low-risk group had longer survival time than high-risk group. We further validated the 6-ARG signature using dataset from GEO and found similar results. We analyzed the associations between ARGs and breast cancer survival in TCGA and nine GEO datasets, and obtained 170 ARGs with significant associations. EIF4EBP1, FOS and FAS were the top three ARGs with highest numbers of significant associations. EIF4EBP1 may be a key ARG which had a higher expression level in patients with more malignant molecular subtypes and higher grade breast cancer. In conclusion, our 6-ARG signature was of significance in predicting of overall survival of patients with breast cancer. EIF4EBP1 may be a key ARG associated with breast cancer survival. creator: Shanliang Zhong creator: Huanwen Chen creator: Sujin Yang creator: Jifeng Feng creator: Siying Zhou uri: https://doi.org/10.7717/peerj.9621 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhong et al. title: Auditory processing in the zebra finch midbrain: single unit responses and effect of rearing experience link: https://peerj.com/articles/9363 last-modified: 2020-07-24 description: In birds the auditory system plays a key role in providing the sensory input used to discriminate between conspecific and heterospecific vocal signals. In those species that are known to learn their vocalizations, for example, songbirds, it is generally considered that this ability arises and is manifest in the forebrain, although there is no a priori reason why brainstem components of the auditory system could not also play an important part. To test this assumption, we used groups of normal reared and cross-fostered zebra finches that had previously been shown in behavioural experiments to reduce their preference for conspecific songs subsequent to cross fostering experience with Bengalese finches, a related species with a distinctly different song. The question we asked, therefore, is whether this experiential change also changes the bias in favour of conspecific song displayed by auditory midbrain units of normally raised zebra finches. By recording the responses of single units in MLd to a variety of zebra finch and Bengalese finch songs in both normally reared and cross-fostered zebra finches, we provide a positive answer to this question. That is, the difference in response to conspecific and heterospecific songs seen in normal reared zebra finches is reduced following cross-fostering. In birds the virtual absence of mammalian-like cortical projections upon auditory brainstem nuclei argues against the interpretation that MLd units change, as observed in the present experiments, as a result of top-down influences on sensory processing. Instead, it appears that MLd units can be influenced significantly by sensory inputs arising directly from a change in auditory experience during development. creator: Priscilla Logerot creator: Paul F. Smith creator: Martin Wild creator: M. Fabiana Kubke uri: https://doi.org/10.7717/peerj.9363 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Logerot et al. title: The effects of humic substances on DNA isolation from soils link: https://peerj.com/articles/9378 last-modified: 2020-07-24 description: BackgroundHumic substances (HS) are compounds with a complicated structure, present in the humus soil layer, water, lake sediments, peat, brown coal and shales. Due to their similar physicochemical properties to DNA, they may have an adverse effect on the subsequent use of the isolated material. The main aim of this research was to examine the effect of HS on DNA isolation depending on the soil type and land use, taking into account the spectroscopic full characteristics of HS fractions.MethodsThe research was conducted on eight types of soil sample. Soils represented the most important Soil Reference Groups for temperate climates: Fluvisols, Regosols, Cambisols, Arenosols, Histosols and Luvisols. Soil samples were also collected from areas diversified in terms of use: arable land, grassland and forest. The extraction of HS fractions was performed using the procedure recommended by the International HS Society. The fractional composition of HS was characterized by UV–Vis and fluorescence methods. Soil DNA is extracted by direct cell lysis in the using a CTAB-based method with a commonly-used commercial soil DNA isolation kit. The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms.ResultsBased on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. Despite the differentiation of the internal structure of HS fractions, the decisive factor in the efficiency of DNA isolation from soil samples was the total carbon content in HS. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for metagenomic analysis, especially from humus-rich soils. creator: Ewa Wnuk creator: Adam Waśko creator: Anna Walkiewicz creator: Piotr Bartmiński creator: Romualda Bejger creator: Lilla Mielnik creator: Andrzej Bieganowski uri: https://doi.org/10.7717/peerj.9378 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wnuk et al. title: Effectiveness of non-lethal predator deterrents to reduce livestock losses to leopard attacks within a multiple-use landscape of the Himalayan region link: https://peerj.com/articles/9544 last-modified: 2020-07-24 description: Lethal measures are widely adopted by local communities and governments to manage human-wildlife conflicts. Such measures lead to large scale decline of carnivore populations globally with trophic cascades on ecosystems and questionable impacts on human-wildlife conflicts. Mitigating human-carnivore conflicts through non-lethal measures will protect endangered predators and secure livelihoods. However, information on the effectiveness of such measures are extremely limited and hence cannot be applied in developing scientific evidence. Further to develop human-carnivore coexistence models, it is important for local community members, biologists and wildlife managers to actively participate in conservation programs. We evaluated the response of a non-lethal visual deterrent (i.e. fox lights) to deter leopard attacks on livestock within a multiple-use landscape of western Himalaya through community engagement. We monitored 16 experimental sites and 17 control sites within 27 villages and recorded data on livestock depredation by leopards between April 2018 to April 2019. A multivariate analysis was conducted to determine the influence of landscape predictors and animal husbandry practices on livestock depredation by leopards within the vicinity of human settlements. We found that visual deterrents discouraged common leopards to predate on livestock (cows and goats). We also demonstrated that community based conservation initiatives are successful in mitigating human-carnivore conflicts within large semi-natural landscapes. We suggest developing site specific coexistence strategies and adopting non-lethal measures to safeguard carnivores, livestock and humans within shared landscapes. creator: Dipanjan Naha creator: Pooja Chaudhary creator: Gaurav Sonker creator: Sambandam Sathyakumar uri: https://doi.org/10.7717/peerj.9544 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Naha et al. title: A cross-sectional assessment of the relationship between sedative medication and anticholinergic medication use and the movement behaviour of older adults living in residential aged care link: https://peerj.com/articles/9605 last-modified: 2020-07-24 description: ObjectivesMedications with anticholinergic or sedative effects are frequently used by older people but can increase risk of falls and adverse events; however, less is known about their effect on movement behaviour. Here we examine the cross-sectional association between medication use and movement behaviour in older adults living in residential aged care.Materials and MethodsTwenty-eight older adults living in residential aged care in metropolitan Australia participated. Medication data were collected from participants’ medical charts and sedative load and anticholinergic burden were determined. Seven-day movement behaviour was objectively assessed by a wrist-worn triaxial accelerometer. Raw accelerations were converted to sleep, sedentary time, and time in light, moderate, and moderate-to-vigorous physical activity. To explore the relationship between medication and movement behaviour, Spearman’s Rho correlations were conducted, as the data were not normally distributed.ResultsAnalyses indicated that while anticholinergic burden was not associated with movement behaviour, sedative load was negatively correlated with a number of variables, accounting for 14% variance in moderate-to-vigorous physical activity (MVPA), and 17% in the bout length of MVPA (p < .02).ConclusionThe findings of this study showed a negative association between sedative load, due to medicines, and an individual’s movement behaviour. The impact of this could be a reduction in the ability of this population to maintain or improve their functional mobility, which may overshadow any benefits of the medicine in some circumstances. creator: Gaynor Parfitt creator: Dannielle Post creator: Lisa Kalisch Ellett creator: Renly Lim creator: Alison Penington creator: Megan Corlis creator: Elizabeth Roughead uri: https://doi.org/10.7717/peerj.9605 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Parfitt et al. title: Disentangling biological variability and taphonomy: shape analysis of the limb long bones of the sauropodomorph dinosaur Plateosaurus link: https://peerj.com/articles/9359 last-modified: 2020-07-23 description: Sauropodomorph dinosaurs constitute a well-studied clade of dinosaurs, notably because of the acquisition of gigantism within this group. The genus Plateosaurus is one of the best-known sauropodomorphs, with numerous remains from various localities. Its tumultuous taxonomic history suggests the relevance of addressing its intrageneric shape variability, mixed with taphonomic modifications of the original bone shape. Here we investigate quantitatively the morphological variation of Plateosaurus occurring at the genus level by studying the shape variation of a sample of limb long bones. By means of 3D geometric morphometrics, the analysis of the uncorrelated variation permits separation of the variation estimated as obviously taphonomically influenced from the more biologically plausible variation. Beyond the dominant taphonomic signal, our approach permits interpretation of the most biologically plausible features, even on anatomical parts influenced by taphonomic deformations. Those features are thus found on a quantitative basis from the variation of samples containing fossil specimens, by taking the impact of taphonomy into account, which is paramount in order to avoid making biologically ambiguous interpretations. creator: Rémi Lefebvre creator: Ronan Allain creator: Alexandra Houssaye creator: Raphaël Cornette uri: https://doi.org/10.7717/peerj.9359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lefebvre et al. title: Morphological changes in the lower Lancang River due to extensive human activities link: https://peerj.com/articles/9471 last-modified: 2020-07-23 description: BackgroundMorphological changes in river beds determine the risk for soil erosion within floodplain areas. At present, little is known about river morphological changes in high-altitude mountainous area influenced by extensive human activities. The study has important reference value for clarifying the morphological changes of mountainous rivers due to extensive human activities.MethodsBased on the long-term multi-source remote sensing image data, we analyzed morphological changes in the lower Lancang River (LCR) in Southwest China at regional and local scales, and determined their influencing factors. Visual interpretation is used to extract the information and unify the interpretation standards of various localities, mainly including water bodies, sandbars, shorelines and beaches. Based on high-resolution remote sensing images, we analyzed the planforms, erosion and accretion conditions in Jinghongba (JHB) reach and Ganlanba (GLB) reach.ResultsOur results showed that: (1) during 1993–2016, the planforms of Jinghongba and Ganlanba in the wide valley of the lower LCR changed significantly, (2) In the interval 1993 to 2016, the JHB reach exhibited extensive erosion, with the right bank more eroded seriously than the left bank, and an erosion area of 0.36 km2. The erosion area of the GLB reach was 0.33 km2, with accretion area of 0.61 km2. The right bank was dominated by erosion, while the left bank by sedimentation; (3) Morphological changes in JHB and GLB reches were the result of the combined effects of cascade hydropower development, river regulation, and sand-mining in the river. The results improved the understanding of riverbed evolution, and could help guide sediment management in mountainous areas influenced by extensive human activities. creator: Peijia Wang creator: Kaidao Fu creator: Jiangcheng Huang creator: Xingwu Duan creator: Zaizhi Yang uri: https://doi.org/10.7717/peerj.9471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: The rule-based insensitivity effect: a systematic review link: https://peerj.com/articles/9496 last-modified: 2020-07-23 description: BackgroundAdherence to inaccurate rules has been viewed as a characteristic of human rule-following (i.e., the rule-based insensitivity effect; RBIE) and has been thought to be exacerbated in individuals suffering from clinical conditions. This review intended to systematically examine these claims in adult populations.MethodologyWe screened 1464 records which resulted in 21 studies that were deemed eligible for inclusion. Each of these studies was examined to determine: (1) if there is evidence for the RBIE in adults and (2) if this effect is larger in those suffering from psychological problems compared to their non-suffering counterparts. In addition, we investigated how (3) different operationalizations of the RBIE, and (4) the external validity and risks of bias of the experimental work investigating this effect, might influence the conclusions that can be drawn from the current systematic review.Results(1) Out of the 20 studies that were relevant for examining if evidence exists for the RBIE in adults, only 11 were eligible for vote counting. Results showed that after the contingency change, the rule groups were more inclined to demonstrate behavior that was reinforced before the change, compared to their non-instructed counterparts. Critically, however, none of these studies examined if their no-instructions group was an adequate comparison group. As a result, this made it difficult to determine whether the effects that were observed in the rule groups could be attributed to the rules or instructions that were manipulated in those experiments. (2) The single study that was relevant for examining if adults suffering from psychological problems demonstrated larger levels of the RBIE, compared to their non-clinical counterparts, was not eligible for vote counting. As a result, no conclusions could be drawn about the extent to which psychological problems moderated the RBIE in that study. (3) Similar procedures and tasks have been used to examine the RBIE, but their precise parameters differ across studies; and (4) most studies report insufficient information to evaluate all relevant aspects affecting their external validity and risks of bias.ConclusionsDespite the widespread appeal that the RBIE has enjoyed, this systematic review indicates that, at present, only preliminary evidence exists for the idea that adults demonstrate the RBIE and no evidence is available to assume that psychological problems exacerbate the RBIE in adults.The systematic review was registered in PROSPERO (CRD42018088210). creator: Ama Kissi creator: Colin Harte creator: Sean Hughes creator: Jan De Houwer creator: Geert Crombez uri: https://doi.org/10.7717/peerj.9496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kissi et al. title: Analysis of prognostic genes in the tumor microenvironment of lung adenocarcinoma link: https://peerj.com/articles/9530 last-modified: 2020-07-23 description: BackgroundPrognostic genes in the tumor microenvironment play an important role in immune biological processes and the response of cancer to immunotherapy. Thus, we aimed to assess new biomarkers that are associated with immune/stromal cells in lung adenocarcinomas (LUAD) using the ESTIMATE algorithm, which also significantly affects the prognosis of cancer.MethodsThe RNA sequencing (RNA-Seq) and clinical data of LUAD were downloaded from the the Cancer Genome Atlas (TCGA ). The immune and stromal scores were calculated for each sample using the ESTIMATE algorithm. The LUAD gene chip expression profile data and the clinical data (GSE37745, GSE11969, and GSE50081) were downloaded from the Gene Expression Omnibus (GEO) for subsequent validation analysis. Differentially expressed genes were calculated between high and low score groups. Univariate Cox regression analysis was performed on differentially expressed genes (DEGs) between the two groups to obtain initial prognosis genes. These were verified by three independent LUAD cohorts from the GEO database. Multivariate Cox regression was used to identify overall survival-related DEGs. UALCAN and the Human Protein Atlas were used to analyze the mRNA /protein expression levels of the target genes. Immune cell infiltration was evaluated using the Tumor Immune Estimation Resource (TIMER) and CIBERSORT methods, and stromal cell infiltration was assessed using xCell.ResultsIn this study, immune scores and stromal scores are significantly associated with the clinical characteristics of LUAD, including T stage, M stage, pathological stage, and overall survival time. 530 DEGs (18 upregulated and 512 downregulated) were found to coexist in the difference analysis with the immune scores and stromal scores subgroup. Univariate Cox regression analysis showed that 286 of the 530 DEGs were survival-related genes (p < 0.05). Of the 286 genes initially identified, nine prognosis-related genes (CSF2RB, ITK, FLT3, CD79A, CCR4, CCR6, DOK2, AMPD1, and IGJ) were validated from three separate LUAD cohorts. In addition, functional analysis of DEGs also showed that various immunoregulatory molecular pathways, including regulation of immune response and the chemokine signaling pathways, were involved. Five genes (CCR6, ITK, CCR4, DOK2, and AMPD1) were identified as independent prognostic indicators of LUAD in specific data sets. The relationship between the expression levels of these genes and immune genes was assessed. We found that CCR6 mRNA and protein expression levels of LUAD were greater than in normal tissues. We evaluated the infiltration of immune cells and stromal cells in groups with high and low levels of expression of CCR6 in the TCGA LUAD cohort. In summary, we found a series of prognosis-related genes that were associated with the LUAD tumor microenvironment. creator: Zhan-yu Xu creator: Mengli Zhao creator: Wenjie Chen creator: Kun Li creator: Fanglu Qin creator: Wei-wei Xiang creator: Yu Sun creator: Jiangbo Wei creator: Li-qiang Yuan creator: Shi-kang Li creator: Sheng-hua Lin uri: https://doi.org/10.7717/peerj.9530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xu et al. title: Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) link: https://peerj.com/articles/9552 last-modified: 2020-07-23 description: Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323–25,369 bp each) separated by a large single-copy (LSC) region (86,510–86,716 bp) and a small single-copy (SSC) region (18,441–18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65–0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species. creator: Furrukh Mehmood creator: Abdullah creator: Zartasha Ubaid creator: Iram Shahzadi creator: Ibrar Ahmed creator: Mohammad Tahir Waheed creator: Peter Poczai creator: Bushra Mirza uri: https://doi.org/10.7717/peerj.9552 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mehmood et al. title: Outstanding performance of an invasive alien tree Bischofia javanica relative to native tree species and implications for management of insular primary forests link: https://peerj.com/articles/9573 last-modified: 2020-07-23 description: Invasive alien tree species can exert severe impacts, especially in insular biodiversity hotspots, but have been inadequately studied. Knowledge of the life history and population trends of an invasive alien tree species is essential for appropriate ecosystem management. The invasive tree Bischofia javanica has overwhelmed native trees on Haha-jima Island in the Ogasawara Islands, Japan. We explored forest community dynamics 2 years after a typhoon damaged the Sekimon primary forests on Haha-jima Island, and predicted the rate of population increase of B. javanica using a logistic model from forest dynamics data for 19 years. During the 2 years after the typhoon, only B. javanica increased in population size, whereas populations of native tree species decreased. Stem diameter growth of B. javanica was more rapid than that of other tree species, including native pioneer trees. Among the understory stems below canopy trees of other species, B. javanica grew most rapidly and B. javanica canopy trees decreased growth of the dominant native Ardisia sieboldii. These competitive advantages were indicated to be the main mechanism by which B. javanica replaces native trees. The logistic model predicted that B. javanica would reach 30% of the total basal area between 2017 (in the eastern plot adjacent to a former B. javanica plantation) and 2057 (in the western plot distant from the plantation site), which is a maximum percentage allowing to eradicate under the present guideline of the National Forest. The results suggest immediate removal of B. javanica is required to preserve native biodiversity in these forests. creator: Tetsuto Abe creator: Nobuyuki Tanaka creator: Yoshikazu Shimizu uri: https://doi.org/10.7717/peerj.9573 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abe et al. title: WHONDRS-GUI: a web application for global survey of surface water metabolites link: https://peerj.com/articles/9277 last-modified: 2020-07-22 description: BackgroundThe Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created.ResultsThe web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811, which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server (https://xmlin.shinyapps.io/whondrs/). creator: Xinming Lin creator: Huiying Ren creator: Amy E. Goldman creator: James C. Stegen creator: Timothy D. Scheibe uri: https://doi.org/10.7717/peerj.9277 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Battelle Memorial Institute title: Antimicrobial stewardship in remote primary healthcare across northern Australia link: https://peerj.com/articles/9409 last-modified: 2020-07-22 description: BackgroundThe high burden of infectious disease and associated antimicrobial use likely contribute to the emergence of antimicrobial resistance in remote Australian Aboriginal communities. We aimed to develop and apply context-specific tools to audit antimicrobial use in the remote primary healthcare setting.MethodsWe adapted the General Practice version of the National Antimicrobial Prescribing Survey (GP NAPS) tool to audit antimicrobial use over 2–3 weeks in 15 remote primary healthcare clinics across the Kimberley region of Western Australia (03/2018–06/2018), Top End of the Northern Territory (08/2017–09/2017) and far north Queensland (05/2018–06/2018). At each clinic we reviewed consecutive clinic presentations until 30 presentations where antimicrobials had been used were included in the audit. Data recorded included the antimicrobials used, indications and treating health professional. We assessed the appropriateness of antimicrobial use and functionality of the tool.ResultsWe audited the use of 668 antimicrobials. Skin and soft tissue infections were the dominant treatment indications (WA: 35%; NT: 29%; QLD: 40%). Compared with other settings in Australia, narrow spectrum antimicrobials like benzathine benzylpenicillin were commonly given and the appropriateness of use was high (WA: 91%; NT: 82%; QLD: 65%). While the audit was informative, non-integration with practice software made the process manually intensive.ConclusionsPatterns of antimicrobial use in remote primary care are different from other settings in Australia. The adapted GP NAPS tool functioned well in this pilot study and has the potential for integration into clinical care. Regular stewardship audits would be facilitated by improved data extraction systems. creator: Will Cuningham creator: Lorraine Anderson creator: Asha C. Bowen creator: Kirsty Buising creator: Christine Connors creator: Kathryn Daveson creator: Joanna Martin creator: Stacey McNamara creator: Bhavini Patel creator: Rodney James creator: John Shanks creator: Kerr Wright creator: Trent Yarwood creator: Steven YC Tong creator: Jodie McVernon uri: https://doi.org/10.7717/peerj.9409 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cuningham et al. title: Salivary proteome of a Neotropical primate: potential roles in host defense and oral food perception link: https://peerj.com/articles/9489 last-modified: 2020-07-22 description: BackgroundSaliva contains a very complex mixture of proteins for defense against microbiological pathogens and for oral food perception. Howler monkeys are Neotropical primates that can consume a mostly leaf diet. They are well known to thrive in highly disturbed habitats where they may cope with a diversity of dietary challenges and infection risks. We aimed to describe the salivary proteome of howlers to contribute to better understanding of their physiology.MethodsWe analyzed the salivary proteins of wild black howler monkeys (Alouatta pigra), by SDS-PAGE-1-D and Nano LC-MS/MS and categorized them by their function involved in host defense and oral food perception.ResultsOur proteomic analysis identified 156 proteins in howler saliva including a number of host defense peptides that are the first line of defense in mammals, such as defensin, cathelicidin, dermcidin, and lactotransferrin, and proteins with anti-bacterial, anti-fungal, and anti-viral capacity, such as IgA, IgG, IgM, BPI, salivary heat shock 70 kDa protein, beta-2-microbulin, and protein S-100. We also identified key proteins necessary for taste perception, including salivary carbonic anhydrase VI, cystatin D, IgA, and fatty acid-binding protein. Proteins to detect astringent foods were identifying, including four members of cystatins (A, B, C and D), lactoperoxidase, and histidine-rich proteins. No chitinase and amylase were identified as would be expected because howlers do not eat insects and little starch. These findings provide basic information to future studies in oral biology, ingestive physiology, and physiological ecology of mammals and non-human primates. creator: Fabiola Carolina Espinosa-Gómez creator: Eliel Ruíz-May creator: Juan Carlos Serio-Silva creator: Colin A. Chapman uri: https://doi.org/10.7717/peerj.9489 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Espinosa-Gómez et al. title: Description of two new species of the genus Heterochelamon Türkay & Dai, 1997 (Crustacea: Decapoda: Brachyura: Potamidae), from southern China link: https://peerj.com/articles/9565 last-modified: 2020-07-22 description: This study describes two new species of freshwater crab of the genus HeterochelamonTürkay & Dai, 1997 from southern China, H. huidongense from Guangdong Province and H. jinxiuense from Guangxi Zhuang Autonomous Region. The two new species can be differentiated from congeners by characters derived from the shape of the epibranchial tooth, external orbital angle, cheliped proportions and structure of the male first gonopod. The present study brings the number of Heterochelamon species to seven. We used the mitochondrial 16S rRNA gene for a molecular analysis and the results are consistent with the morphological features that support the recognition of two new taxa. creator: Song-Bo Wang creator: Yi-Yang Xu creator: Jie-Xin Zou uri: https://doi.org/10.7717/peerj.9565 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: An overview of biomass conversion: exploring new opportunities link: https://peerj.com/articles/9586 last-modified: 2020-07-22 description: Recycling biomass is indispensable these days not only because fossil energy sources are gradually depleted, but also because pollution of the environment, caused by the increasing use of energy, must be reduced. This article intends to overview the results of plant biomass processing methods that are currently in use. Our aim was also to review published methods that are not currently in use. It is intended to explore the possibilities of new methods and enzymes to be used in biomass recycling. The results of this overview are perplexing in almost every area. Advances have been made in the pre-treatment of biomass and in the diversity and applications of the enzymes utilized. Based on molecular modeling, very little progress has been made in the modification of existing enzymes for altered function and adaptation for the environmental conditions during the processing of biomass. There are hardly any publications in which molecular modeling techniques are used to improve enzyme function and to adapt enzymes to various environmental conditions. Our view is that using modern computational, biochemical, and biotechnological methods would enable the purposeful design of enzymes that are more efficient and suitable for biomass processing. creator: László Fülöp creator: János Ecker uri: https://doi.org/10.7717/peerj.9586 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fülöp and Ecker title: Role of methyltransferase-like enzyme 3 and methyltransferase-like enzyme 14 in urological cancers link: https://peerj.com/articles/9589 last-modified: 2020-07-22 description: N6-methyladenosine (m6A) modifications can be found in eukaryotic messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA). Several studies have demonstrated a close relationship between m6A modifications and cancer cells. Methyltransferase-like enzyme 3 (METTL3) and methyltransferase-like enzyme 14 (METTL14) are two major enzymes involved in m6A modifications that play vital roles in various cancers. However, the roles and regulatory mechanisms of METTL3 and METTL14 in urological cancers are largely unknown. In this review, we summarize the current research results for METTL3 and METTL14 and identify potential pathways involving these enzymes in kidney, bladder, prostate, and testicular cancer. We found that METTL3 and METTL14 have different expression patterns in four types of urological cancers. METTL3 is highly expressed in bladder and prostate cancer and plays an oncogenic role on cancer cells; however, its expression and role are opposite in kidney cancer. METTL14 is expressed at low levels in kidney and bladder cancer, where it has a tumor suppressive role. Low METTL3 or METTL14 expression in cancer cells negatively regulates cell growth-related pathways (e.g., mTOR, EMT, and P2XR6) but positively regulates cell death-related pathways (e.g., P53, PTEN, and Notch1). When METTL3 is highly expressed, it positively regulates the NF-kB and SHH-GL1pathways but negatively regulates PTEN. These results suggest that although METTL3 and METTL14 have different expression levels and regulatory mechanisms in urological cancers, they control cancer cell fate via cell growth- and cell death-related pathways. These findings suggest that m6A modification may be a potential new therapeutic target in urological cancer. creator: Zijia Tao creator: Yiqiao Zhao creator: Xiaonan Chen uri: https://doi.org/10.7717/peerj.9589 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tao et al. 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. title: Prediction of human fetal–maternal blood concentration ratio of chemicals link: https://peerj.com/articles/9562 last-modified: 2020-07-21 description: BackgroundThe measurement of human fetal-maternal blood concentration ratio (logFM) of chemicals is critical for the risk assessment of chemical-induced developmental toxicity. While a few in vitro and ex vivo experimental methods were developed for predicting logFM of chemicals, the obtained experimental results are not able to directly predict in vivo outcomes.MethodsA total of 55 chemicals with logFM values representing in vivo fetal-maternal blood ratio were divided into training and test datasets. An interpretable linear regression model was developed along with feature selection methods. Cross-validation on training dataset and prediction on independent test dataset were conducted to validate the prediction model.ResultsThis study presents the first valid quantitative structure-activity relationship model following the Organisation for Economic Co-operation and Development (OECD) guidelines based on multiple linear regression for predicting in vivo logFM values. The autocorrelation descriptor AATSC1c and information content descriptor ZMIC1 were identified as informative features for predicting logFM. After the adjustment of the applicability domain, the developed model performs well with correlation coefficients of 0.875, 0.850 and 0.847 for model fitting, leave-one-out cross-validation and independent test, respectively. The model is expected to be useful for assessing human transplacental exposure. creator: Chia-Chi Wang creator: Pinpin Lin creator: Che-Yu Chou creator: Shan-Shan Wang creator: Chun-Wei Tung uri: https://doi.org/10.7717/peerj.9562 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: The effects of “Fangcang, Huoshenshan, and Leishenshan” hospitals and environmental factors on the mortality of COVID-19 link: https://peerj.com/articles/9578 last-modified: 2020-07-21 description: BackgroundIn December 2019, a novel coronavirus disease (COVID-19) broke out in Wuhan, China; however, the factors affecting the mortality of COVID-19 remain unclear.MethodsThirty-two days of data (the growth rate/mortality of COVID-19 cases) that were shared by Chinese National Health Commission and Chinese Weather Net were collected by two authors independently. Student’s t-test or Mann-Whitney U test was used to test the difference in the mortality of confirmed/severe cases before and after the use of “Fangcang, Huoshenshan, and Leishenshan” makeshift hospitals (MSHs). We also studied whether the above outcomes of COVID-19 cases were related to air temperature (AT), relative humidity (RH), or air quality index (AQI) by performing Pearson’s analysis or Spearman’s analysis.ResultsEight days after the use of MSHs, the mortality of confirmed cases was significantly decreased both in Wuhan (t = 4.5, P < 0.001) and Hubei (U = 0, P < 0.001), (t and U are the test statistic used to test the significance of the difference). In contrast, the mortality of confirmed cases remained unchanged in non-Hubei regions (U = 76, P = 0.106). While on day 12 and day 16 after the use of MSHs, the reduce in mortality was still significant both in Wuhan and Hubei; but in non-Hubei regions, the reduce also became significant this time (U = 123, P = 0.036; U = 171, P = 0.015, respectively). Mortality of confirmed cases was found to be negatively correlated with AT both in Wuhan (r =  − 0.441, P = 0.012) and Hubei (r =  − 0.440, P = 0.012). Also, both the growth rate and the mortality of COVID-19 cases were found to be significantly correlated with AQI in Wuhan and Hubei. However, no significant correlation between RH and the growth rate/mortality of COVID-19 cases was found in our study.ConclusionsOur findings indicated that both the use of MSHs, the rise of AT, and the improvement of air quality were beneficial to the survival of COVID-19 patients. creator: Yuwen Cai creator: Tianlun Huang creator: Xin Liu creator: Gaosi Xu uri: https://doi.org/10.7717/peerj.9578 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cai et al. title: Identification and expression pattern of chemosensory genes in the transcriptome of Propsilocerus akamusi link: https://peerj.com/articles/9584 last-modified: 2020-07-21 description: Chironomidae is the most ecologically diverse insects in aquatic and semi-aquatic habitats. Propsilocerus akamusi (Tokunaga) is a dominant and ubiquitous chironomid species in Eastern Asia and its morphologically unique larvae are also considered as indicator organisms to detect water contamination, potential toxicity and waterborne pathogens. Since few studies to date have focused on the olfactory system of P. akamusi, our study aims to elucidate the potential functions of chemosensory genes in P. akamusi. In our study, we found that although signals released from male groups might attract female swarmers, it was a completely male-dominated mating process. Sequencing the transcriptome of P. akamusi on an Illumina HiSeq platform generated 4.42, 4.46 and 4.53 Gb of clean reads for heads, legs, and antennae, respectively. 27,609 unigenes, 20,379 coding sequences (CDSs), and 8,073 simple sequence repeats were finally obtained. The gene-level differential expression analysis demonstrated variants among three different tissues, including 2,019 genes specifically expressed in heads, 1,540 genes in legs, and 2,071 genes in antennae. Additionally, we identified an assortment of putative olfactory genes consisting of 34 odorant binding proteins, 17 odorant receptors, 32 gustatory receptors, 22 ionotropic receptors, six chemosensory proteins as well as 3 sensory neuron membrane proteins; their relative abundances in the above three tissues were also determined by RT-qPCR. Our finding could allow a more plausible understanding of certain olfaction-mediated behaviors in groups of this macroinvertebrate. creator: Chuncai Yan creator: Xiaoya Sun creator: Wei Cao creator: Ruoqun Li creator: Cong Zhao creator: Zeyang Sun creator: Wenbin Liu creator: Lina Pan uri: https://doi.org/10.7717/peerj.9584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yan et al. title: RdRp mutations are associated with SARS-CoV-2 genome evolution link: https://peerj.com/articles/9587 last-modified: 2020-07-21 description: COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral genome over time as it spread across the world. An important question that still needs to be answered is whether any of the common mutations affect the viral properties, and therefore the disease characteristics. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C>T mutation, on mutation rate and viral spread. By focusing on mutations in the slowly evolving M or E genes, we aimed to minimize the effects of selective pressure. Our results indicate that 14408C>T mutation increases the mutation rate, while the third-most common RdRp mutation, 15324C>T, has the opposite effect. It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere. creator: Doğa Eskier creator: Gökhan Karakülah creator: Aslı Suner creator: Yavuz Oktay uri: https://doi.org/10.7717/peerj.9587 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Eskier et al. title: Pedagogic prestidigitation: using magic tricks to enhance educational videos link: https://peerj.com/articles/9610 last-modified: 2020-07-21 description: Previous research suggests that magic tricks can be employed within an educational context to enhance attention, engagement, critical thinking and recall. This study builds on this work by examining the impact of incorporating magic tricks into an online educational video. Adult participants (N = 198) completed a need for cognition scale and then watched a video containing either several bespoke card tricks that had been specially devised to help tell the story of the Apollo Moon landings (Magic Video), or an almost identical video that did not contain any magic tricks (Control Video). All participants rated their levels of engagement, absorption and recall. Compared to the Control Video, the Magic Video was rated as significantly more interesting, informative and absorbing. There was no difference between the groups for recall. There was a positive correlation between participants’ need for cognition scores, and the degree to which they found the Magic Video interesting, and were willing to share it with others. The theoretical, methodological and practical implications of these results are discussed, along with recommendations for future work. creator: Richard Wiseman creator: William Houstoun creator: Caroline Watt uri: https://doi.org/10.7717/peerj.9610 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wiseman et al. title: The timing mega-study: comparing a range of experiment generators, both lab-based and online link: https://peerj.com/articles/9414 last-modified: 2020-07-20 description: Many researchers in the behavioral sciences depend on research software that presents stimuli, and records response times, with sub-millisecond precision. There are a large number of software packages with which to conduct these behavioral experiments and measure response times and performance of participants. Very little information is available, however, on what timing performance they achieve in practice. Here we report a wide-ranging study looking at the precision and accuracy of visual and auditory stimulus timing and response times, measured with a Black Box Toolkit. We compared a range of popular packages: PsychoPy, E-Prime®, NBS Presentation®, Psychophysics Toolbox, OpenSesame, Expyriment, Gorilla, jsPsych, Lab.js and Testable. Where possible, the packages were tested on Windows, macOS, and Ubuntu, and in a range of browsers for the online studies, to try to identify common patterns in performance. Among the lab-based experiments, Psychtoolbox, PsychoPy, Presentation and E-Prime provided the best timing, all with mean precision under 1 millisecond across the visual, audio and response measures. OpenSesame had slightly less precision across the board, but most notably in audio stimuli and Expyriment had rather poor precision. Across operating systems, the pattern was that precision was generally very slightly better under Ubuntu than Windows, and that macOS was the worst, at least for visual stimuli, for all packages. Online studies did not deliver the same level of precision as lab-based systems, with slightly more variability in all measurements. That said, PsychoPy and Gorilla, broadly the best performers, were achieving very close to millisecond precision on several browser/operating system combinations. For response times (measured using a high-performance button box), most of the packages achieved precision at least under 10 ms in all browsers, with PsychoPy achieving a precision under 3.5 ms in all. There was considerable variability between OS/browser combinations, especially in audio-visual synchrony which is the least precise aspect of the browser-based experiments. Nonetheless, the data indicate that online methods can be suitable for a wide range of studies, with due thought about the sources of variability that result. The results, from over 110,000 trials, highlight the wide range of timing qualities that can occur even in these dedicated software packages for the task. We stress the importance of scientists making their own timing validation measurements for their own stimuli and computer configuration. creator: David Bridges creator: Alain Pitiot creator: Michael R. MacAskill creator: Jonathan W. Peirce uri: https://doi.org/10.7717/peerj.9414 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bridges et al. title: Raccoon roundworm prevalence (Baylisascaris procyonis) at the North Carolina Zoo, USA link: https://peerj.com/articles/9426 last-modified: 2020-07-20 description: Baylisascaris procyonis is an important zoonotic nematode of raccoons (Procyon lotor). Infection with this parasite has important health implications for humans, zoo animals, and free-ranging wildlife. As a large, natural habitat zoo, the North Carolina Zoo (NC Zoo) coexists with native wildlife. Raccoons are abundant at the NC Zoo and the prevalence of B. procyonis is unknown. Raccoon latrines were located through employee reporting and systematic searching throughout the zoo and sampled for B. procyonis in October and November of 2018 and 2019. Parasite prevalence, latrine location, substrate category and latrine persistence were recorded. Thirty-three latrines were located in 2018 and eight new latrines in 2019 while four latrines from the prior year were no longer available to be sampled. Of the 29 latrines sampled over the two years, 16 (55%) persisted for at least one year. The majority of the latrines were found on natural substrate with rock showing the highest preference. Just over half (n = 21 of 41 total) of the active latrines in the study were in or immediately adjacent to animal enclosures. Two latrines were found in public areas including one contaminating children’s play equipment. Additionally, fresh fecal samples were collected from five adult raccoons presented to the zoo’s veterinary clinic in 2018 and 2019. All fecal samples tested by centrifugal flotation for both years were negative for B. procyonis. The results of this study show the value of field sampling to properly assess risk and enable informed decision-making regarding public health and wildlife management. creator: Meghan M. Louis creator: Larry J. Minter creator: James R. Flowers creator: Michael K. Stoskopf creator: Suzanne Kennedy-Stoskopf uri: https://doi.org/10.7717/peerj.9426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Louis et al. title: Detecting the outbreak of influenza based on the shortest path of dynamic city network link: https://peerj.com/articles/9432 last-modified: 2020-07-20 description: The influenza pandemic causes a large number of hospitalizations and even deaths. There is an urgent need for an efficient and effective method for detecting the outbreak of influenza so that timely, appropriate interventions can be made to prevent or at least prepare for catastrophic epidemics. In this study, we proposed a computational method, the shortest-path-based dynamical network marker (SP-DNM), to detect the pre-outbreak state of influenza epidemics by monitoring the dynamical change of the shortest path in a city network. Specifically, by mapping the real-time information to a properly constructed city network, our method detects the early-warning signal prior to the influenza outbreak in both Tokyo and Hokkaido for consecutive 9 years, which demonstrate the effectiveness and robustness of the proposed method. creator: Yingqi Chen creator: Kun Yang creator: Jialiu Xie creator: Rong Xie creator: Zhengrong Liu creator: Rui Liu creator: Pei Chen uri: https://doi.org/10.7717/peerj.9432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Quantifying local ecological knowledge to model historical abundance of long-lived, heavily-exploited fauna link: https://peerj.com/articles/9494 last-modified: 2020-07-20 description: Deriving robust historical population trends for long-lived species subject to human exploitation is challenging in scenarios where long-term scientific data are scarce or unavailable, as often occurs for species affected by small-scale fisheries and subsistence hunting. The importance of Local Ecological Knowledge (LEK) in data-poor scenarios is increasingly recognized in conservation, both in terms of uncovering historical trends and for engaging community stewardship of historic information. Building on previous work in marine historical ecology and local ecological knowledge, we propose a mixed socio-ecological framework to reliably document and quantify LEK to reconstruct historical population trends. Our method can be adapted by interdisciplinary teams to study various long-lived taxa with a history of human use. We demonstrate the validity of our approach by reconstructing long-term abundance data for the heavily-exploited East Pacific green turtle (Chelonia mydas) in Baja California, Mexico, which was driven to near extinction by a largely unregulated fishery from the early 1950s to the 1980s. No scientific baseline abundance data were available for this time-frame because recent biological surveys started in 1995 after all green turtle fisheries in the area were closed. To fill this data gap, we documented LEK among local fishers using ethnographic methods and obtained verified, qualitative data to understand the socio-environmental complexity of the green turtle fishery. We then established an iterative framework to synthesize and quantify LEK using generalized linear models (GLMs) and nonlinear regression (NLR) to generate a standardized, LEK-derived catch-per-unit-effort (CPUE) time-series. CPUE is an index of abundance that is compatible with contemporary scientific survey data. We confirmed the accuracy of LEK-derived CPUE estimates via comparisons with fisheries statistics available for 1962–1982. We then modeled LEK-derived abundance trends prior to 1995 using NLR. Our model established baseline abundance and described historical declines, revealing that the most critical (exponential) decline occurred between 1960 and 1980. This robust integration of LEK data with ecological science is of critical value for conservation and management, as it contributes to a holistic view of a species’ historic and contemporary conservation status. creator: Michelle-María Early-Capistrán creator: Elena Solana-Arellano creator: F. Alberto Abreu-Grobois creator: Nemer E. Narchi creator: Gerardo Garibay-Melo creator: Jeffrey A. Seminoff creator: Volker Koch creator: Andrea Saenz-Arroyo uri: https://doi.org/10.7717/peerj.9494 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Early-Capistrán et al. title: Engineering of HN3 increases the tumor targeting specificity of exosomes and upgrade the anti-tumor effect of sorafenib on HuH-7 cells link: https://peerj.com/articles/9524 last-modified: 2020-07-20 description: Safe, efficient and cancer cell targeted delivery of CRISPR/Cas9 is important to increase the effectiveness of available cancer treatments. Although cancer derived exosomes offer significant advantages, the fact that it carries cancer related/inducing signaling molecules impedes them from being used as a reliable drug delivery vehicle. In this study, we report that normal epithelial cell-derived exosomes engineered to have HN3 (HN3LC9-293exo), target tumor cells as efficiently as that of the cancer cell-derived exosomes (C9HuH-7exo). HN3LC9-293exo were quickly absorbed by the recipient cancer cell in vitro. Anchoring HN3 to the membrane of the exosomes using LAMP2, made HN3LC9-293exo to specifically enter the GPC3+ HuH-7 cancer cells than the GPC3− LO2 cells in a co-culture model. Further, sgIQ 1.1 plasmids were loaded to exosomes and surprisingly, in combination with sorafenib, synergistic anti-proliferative and apoptotic effect of loaded HN3LC9-293exo was more than the loaded C9HuH-7exo. While cancer-derived exosomes might induce the drug resistance and tumor progression, normal HEK-293 cells-derived exosomes with modifications for precise cancer cell targeting like HN3LC9-293exo can act as better, safe and natural delivery systems to improve the efficacy of the cancer treatments. creator: Cong He creator: Doulathunnisa Jaffar Ali creator: Yumin Li creator: Yanliang Zhu creator: Bo Sun creator: Zhongdang Xiao uri: https://doi.org/10.7717/peerj.9524 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 He et al. title: The importance of open science for biological assessment of aquatic environments link: https://peerj.com/articles/9539 last-modified: 2020-07-20 description: Open science principles that seek to improve science can effectively bridge the gap between researchers and environmental managers. However, widespread adoption has yet to gain traction for the development and application of bioassessment products. At the core of this philosophy is the concept that research should be reproducible and transparent, in addition to having long-term value through effective data preservation and sharing. In this article, we review core open science concepts that have recently been adopted in the ecological sciences and emphasize how adoption can benefit the field of bioassessment for both prescriptive condition assessments and proactive applications that inform environmental management. An example from the state of California demonstrates effective adoption of open science principles through data stewardship, reproducible research, and engagement of stakeholders with multimedia applications. We also discuss technical, sociocultural, and institutional challenges for adopting open science, including practical approaches for overcoming these hurdles in bioassessment applications. creator: Marcus W. Beck creator: Casey O’Hara creator: Julia S. Stewart Lowndes creator: Raphael D. Mazor creator: Susanna Theroux creator: David J. Gillett creator: Belize Lane creator: Gregory Gearheart uri: https://doi.org/10.7717/peerj.9539 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Beck et al. title: Application of material from used car tyres in geotechnics—an environmental impact analysis link: https://peerj.com/articles/9546 last-modified: 2020-07-20 description: This work begins with a literature-based discussion of the hazardous-waste problem represented by car tyres as hazardous waste, along with possible ways in which they might be utilised or managed. The impact of the material on the environment is characterised in the process, not least in the context of pollutants leached to the aquatic environment. Input in terms of new research results concerns the impact on water and soil of material from used car tyres being used in geotechnics. Specifically, tyre bales comprising 100–140 car vehicle tyres compressed into a lightweight block and secured by galvanised steel tie wires running around the length and depth of the bale, were researched, having been immersed in basins with alkaline and acidic water following initial preparation and pre-washing. The aim was to in some sense simulate—respectively—conditions in which rain and surface/ground water are involved, or else acid rain. To do that, the tyre bales were placed in the water for 120 days, with emerging leachate analysed after set intervals of time, with a view to changes in key physicochemical parameters of water being noted, as well as signs of the leaching of both undesirable components and priority substances, from tyres into the aqueous medium. Washing of the tyre bales was shown to induce slight pollution of water, with limited exceedance of normative values in respect of OWO content. However, this increase was not due to leaching of the Persistent Organic Pollutants tested for, but may rather have reflected contamination of tyres used, e.g., of soil at the place of previous storage. In general, waste water arising does not therefore contain substances that would stand in the way (legally) of its being discharged into a combined sewer system. Similar conclusions were arrived at through analysis of the leaching of pollutants from tyre bales exposed in the aforementioned pools of water of neutral and acidic reaction. Wastewater arising was not enriched significantly in impurities (be these metals, PAHs, phthalates, selected anions or cations), and there were therefore no exceedances of standards imposed for wastewater discharged to either waters or soil. creator: Aleksander Duda creator: Małgorzata Kida creator: Sabina Ziembowicz creator: Piotr Koszelnik uri: https://doi.org/10.7717/peerj.9546 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Duda et al. title: Pots vs trammel nets: a catch comparison study in a Mediterranean small-scale fishery link: https://peerj.com/articles/9287 last-modified: 2020-07-17 description: Passive bottom-set nets are the most widely used fishing gears in Mediterranean small-scale fisheries (SSFs). Trammel nets, in particular, have key advantages such as their ease of use and handling and high capture efficiency for numerous commercial species. However, they entail high discard rates (5–44% of the total catch) connected to high mortality, thus exerting an adverse impact on benthic communities, besides catching individuals of commercial species under the minimum conservation reference size (MCRS) and specimens of protected species. Fish pots are seen as alternative and a more sustainable gear type that allow reducing discards in SSFs. In this study, a collapsible pot was tested at three coastal sites in the north-western Adriatic Sea (GFCM GSA 17) to compare its catch efficiency with that of the local traditional trammel nets. Data analysis demonstrated a similar catch efficiency for the commercial species, both among sites and as a whole. Moreover, the trammel net caught a larger amount of discards, both in terms of species number and of CPUEW. The catch comparison study involved the two most abundant landed species, common cuttlefish Sepia officinalis and annular sea bream Diplodus annularis. The pots were more effective for S. officinalis, whereas the trammel net was more effective for the shorter length classes for D. annularis, which were mostly under the MCRS (12 cm). The innovative pots could provide a valuable alternative to the trammel nets traditionally used in the Adriatic Sea, at least in certain areas and periods. Their main advantages include that they do not require a different rigging and they can be used without bait, while their foldable design allows large numbers to be easily loaded on board SSF vessels. The results of this pilot study indicate that pots can achieve the objectives of reducing discards and bycatch in SSFs without penalizing the catch of commercial species. creator: Andrea Petetta creator: Claudio Vasapollo creator: Massimo Virgili creator: Giada Bargione creator: Alessandro Lucchetti uri: https://doi.org/10.7717/peerj.9287 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Petetta et al. title: Variation of soil nutrients and bacterial community diversity of different land utilization types in Yangtze River Basin, Chongqing Municipality link: https://peerj.com/articles/9386 last-modified: 2020-07-17 description: The diversity and community distribution of soil bacteria in different land use types in Yangtze River Basin, Chongqing Municipality were studied by using Illumina MiSeq analysis methods. Soil physical and chemical properties were determined, and correlation analyses were performed to identify the key factors affecting bacterial numbers and α-diversity in these soils. The results showed that the soil physical and chemical properties of different land use types decrease in the order: mixed forest (M2) > pure forest (P1) > grassland (G3) > bare land (B4). There were significant differences in bacterial diversity and communities of different land use types. The diversity of different land use types showed the same sequence with the soil physical and chemical properties. The abundance and diversity of bacterial in M2 and P1 soils was significantly higher than that in G3 and B4 soils. At phylum level, G3 and B4 soils were rich in only Proteobacteria and Actinobacteria, whereas M2 and P1 soils were rich in Proteobacteria, Actinobacteria and Firmicutes. At genus level, Faecalibacterium and Agathobacter were the most abundant populations in M2 soil and were not found in other soils. Pearson correlation analysis showed that soil moisture content, pH, AN, AP, AK and soil enzyme activity were significantly related to bacterial numbers, diversity and community distribution. creator: Yanlin Li creator: Chunmei Zeng creator: Meijun Long uri: https://doi.org/10.7717/peerj.9386 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Biodiversity of carapace epibiont diatoms in loggerhead sea turtles (Caretta caretta Linnaeus 1758) in the Aegean Sea Turkish coast link: https://peerj.com/articles/9406 last-modified: 2020-07-17 description: BackgroundThe Aegean Sea coast of Turkey hosts one of the most important nesting grounds for loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea. Previous studies have revealed that the sea turtle carapace provides favourable conditions for various epibiontic organisms. Epibionts occurring on the carapace have been examined from different locations in the oceans.MethodsThis is the first time such a high number (39) of samples collected from nesting turtles during such a long time period (extending from 2011 to 2018) has been used for the study of the diatom component of the microbiome on the turtle carapaces. A total of 33 samples were investigated in terms of light microscopy (LM) and scanning electron microscopy (SEM). Six unprocessed biofilm fragments were subject to SEM observations.ResultsA total of 457 epizoic diatom taxa belonging to 86 genera were identified. Epizoic forms, e.g., Achnanthes spp., Chelonicola spp. or Tripterion spp. (also identified by SEM observations of the undisturbed pieces of the microbiome) dominated in terms of relative abundance, but the highest numbers of taxa were ubiquitously represented by Navicula (79), Nitzschia (45), Amphora (40), Cocconeis (32), Diploneis (25) and Mastogloia (23). Navicula perminuta and Delphineis australis were the most frequent taxa, present in 65% of the samples, both with an average relative abundance of 10%. The results of our study revealed that diatoms are an essential component of the loggerhead sea turtles’ microbiome, in terms of high biodiversity and abundance. Although strict epibionts provide a signature of the turtle microbiome, the carapace as a solid substrate attracts numerous benthic diatom species which are considered opportunistic forms and can be found in the surrounding benthic habitats of the vast ocean littoral space. creator: Aydın Kaleli creator: Ana Car creator: Andrzej Witkowski creator: Marta Krzywda creator: Catherine Riaux-Gobin creator: Cüneyt Nadir Solak creator: Yakup Kaska creator: Izabela Zgłobicka creator: Tomasz Płociński creator: Rafał Wróbel creator: Krzysztof Kurzydłowski uri: https://doi.org/10.7717/peerj.9406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kaleli et al. title: An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications link: https://peerj.com/articles/9424 last-modified: 2020-07-17 description: BackgroundLake Sinai Viruses (LSV) are common RNA viruses of honey bees (Apis mellifera) that frequently reach high abundance but are not linked to overt disease. LSVs are genetically heterogeneous and collectively widespread, but despite frequent detection in surveys, the ecological and geographic factors structuring their distribution in A. mellifera are not understood. Even less is known about their distribution in other species. Better understanding of LSV prevalence and ecology have been hampered by high sequence diversity within the LSV clade.MethodsHere we report a new polymerase chain reaction (PCR) assay that is compatible with currently known lineages with minimal primer degeneracy, producing an expected 365 bp amplicon suitable for end-point PCR and metagenetic sequencing. Using the Illumina MiSeq platform, we performed pilot metagenetic assessments of three sample sets, each representing a distinct variable that might structure LSV diversity (geography, tissue, and species).ResultsThe first sample set in our pilot assessment compared cDNA pools from managed A. mellifera hives in California (n = 8) and Maryland (n = 6) that had previously been evaluated for LSV2, confirming that the primers co-amplify divergent lineages in real-world samples. The second sample set included cDNA pools derived from different tissues (thorax vs. abdomen, n = 24 paired samples), collected from managed A. mellifera hives in North Dakota. End-point detection of LSV frequently differed between the two tissue types; LSV metagenetic composition was similar in one pair of sequenced samples but divergent in a second pair. Overall, LSV1 and intermediate lineages were common in these samples whereas variants clustering with LSV2 were rare. The third sample set included cDNA from individual pollinator specimens collected from diverse landscapes in the vicinity of Lincoln, Nebraska. We detected LSV in the bee Halictus ligatus (four of 63 specimens tested, 6.3%) at a similar rate as A. mellifera (nine of 115 specimens, 7.8%), but only one H. ligatus sequencing library yielded sufficient data for compositional analysis. Sequenced samples often contained multiple divergent LSV lineages, including individual specimens. While these studies were exploratory rather than statistically powerful tests of hypotheses, they illustrate the utility of high-throughput sequencing for understanding LSV transmission within and among species. creator: Deborah D. Iwanowicz creator: Judy Y. Wu-Smart creator: Tugce Olgun creator: Autumn H. Smart creator: Clint R.V. Otto creator: Dawn Lopez creator: Jay D. Evans creator: Robert Cornman uri: https://doi.org/10.7717/peerj.9424 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Iwanowicz et al. title: Mesozooplankton grazing minimally impacts phytoplankton abundance during spring in the western North Atlantic link: https://peerj.com/articles/9430 last-modified: 2020-07-17 description: The impacts of grazing by meso- and microzooplankton on phytoplankton primary production (PP) was investigated in the surface layer of the western North Atlantic during spring. Shipboard experiments were performed on a latitudinal transect at three stations that differed in mixed layer depth, temperature, and mesozooplankton taxonomic composition. The mesozooplankton community was numerically dominated by Calanus finmarchicus at the northern and central station, with Calanus hyperboreus also present at the northern station. The southern station was >10 °C warmer than the other stations and had the most diverse mesozooplankton assemblage, dominated by small copepods including Paracalanus spp. Microzooplankton grazing was detected only at the northern station, where it removed 97% of PP. Estimated clearance rates by C. hyperboreus and C. finmarchicus suggested that at in-situ abundance these mesozooplankton were not likely to have a major impact on phytoplankton abundance, unless locally aggregated. Although mesozooplankton grazing impact on total phytoplankton was minimal, these grazers completely removed the numerically scarce > 10 µm particles, altering the particle-size spectrum. At the southern station, grazing by the whole mesozooplankton assemblage resulted in a removal of 14% of PP, and its effect on net phytoplankton growth rate was similar irrespective of ambient light. In contrast, reduction in light availability had an approximately 3-fold greater impact on net phytoplankton growth rate than mesozooplankton grazing pressure. The low mesozooplankton grazing impact across stations suggests limited mesozooplankton-mediated vertical export of phytoplankton production. The constraints provided here on trophic transfer, as well as quantitative estimates of the relative contribution of light and grazer controls of PP and of grazer-induced shifts in particle size spectra, illuminate food web dynamics and aid in parameterizing modeling-frameworks assessing global elemental fluxes and carbon export. creator: Francoise Morison creator: James Joseph Pierson creator: Andreas Oikonomou creator: Susanne Menden-Deuer uri: https://doi.org/10.7717/peerj.9430 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Morison et al. title: The switch from one substance-of-abuse to another: illicit drug substitution behaviors in a sample of high-risk drug users link: https://peerj.com/articles/9461 last-modified: 2020-07-17 description: BackgroundSubstitution can be defined as the consciously motivated choice to use one drug, either licit or illicit, instead of another, due to perceptions of cost, availability, safety, legality, substance characteristics, and substance attributions. Substitution represents a potential risk to drug users, mainly when substitutes are of higher potency and toxicity. This study offers a basic conceptualization of illicit substitution behavior and describes substitution patterns among users of two highly prevalent drugs of abuse—heroin and cannabis.MethodsHere, 592 high-risk drug users undergoing pharmacological and psycho-social treatment were interviewed. Patients were asked questions about current drug use, lifetime substitution, and substitution patterns. Descriptive statistics, chi-square tests of independence, and multinomial logistic regressions were used to identify and test correlates of substitution patterns for heroin and cannabis.ResultsOf the 592 drug users interviewed, 448 subjects (75.7%) reported having substituted their preferred drug for another illicit substance. Interviews yielded a total of 275 substitution events reported by users of cannabis, and 351 substitution events reported by users of heroin. The most frequently reported substitution substances for responders who preferred heroin were illicit non-prescribed “street” methadone (35.9%), followed by oral and transdermal prescription opioids (17.7%). For responders who preferred cannabis, substitution for synthetic cannabinoid receptor agonists (33.5%) followed by alcohol (16.0%) were the most commonly reported. Age at onset–of–use (p < 0.005), population group (p = 0.008), and attending treatment for the first time (p = 0.026) were significantly associated with reported lifetime substitution. Past-year use of stimulants, heroin, hallucinogens, methylenedioxymethamphetamine (MDMA), and novel psychoactive substances were—at the 95% confidence level—also significantly associated with reported lifetime substitution. In multivariate analysis, the odds for methadone substitution among heroin users were significantly affected by age at onset-of-use, type of treatment center, and education. Odds for substitution for synthetic cannabinoid receptor agonists among cannabis users were significantly affected by age, population group, type of treatment center, and education.ConclusionSelf-substitution behavior should be considered by clinicians and policymakers as a common practice among most drugusers. Substitution for street methadone provides evidence for the ongoing diversion of this substance from Opioid Maintenance Treatment Centers, while the prominence of substitution of synthetic cannabinoids among dual-diagnosis patients should be regarded as an ongoing risk to patients that needs to be addressed by clinicians. Analysis of additional substitution patterns should provide further valuable insights into the behavior of drugusers. creator: Barak Shapira creator: Paola Rosca creator: Ronny Berkovitz creator: Igor Gorjaltsan creator: Yehuda Neumark uri: https://doi.org/10.7717/peerj.9461 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shapira et al. title: Mechanisms behind bottom-up effects: eutrophication increases fecundity by shortening the interspawning interval in stickleback link: https://peerj.com/articles/9521 last-modified: 2020-07-17 description: Anthropogenic eutrophication is altering aquatic environments by promoting primary production. This influences the population dynamics of consumers through bottom-up effects, but the underlying mechanisms and pathways are not always clear. To evaluate and mitigate effects of eutrophication on ecological communities, more research is needed on the underlying factors. Here we show that anthropogenic eutrophication increases population fecundity in the threespine stickleback (Gasterosteus aculeatus) by increasing the number of times females reproduce—lifetime fecundity—rather than instantaneous fecundity. When we exposed females to nutrient-enriched waters with enhanced algal growth, their interspawning interval shortened but the size of their egg clutches, or the size of their eggs, did not change. The shortening of the interspawning interval was probably caused by higher food intake, as algae growth promotes the growth of preferred prey populations. Enhanced female lifetime fecundity could increase offspring production and, hence, influence population dynamics. In support of this, earlier studies show that more offspring are emerging in habitats with denser algae growth. Thus, our results stress the importance of considering lifetime fecundity, in addition to instantaneous fecundity, when investigating the impact of human-induced eutrophication on population processes. At a broader level, our results highlight the importance of following individuals over longer time spans when evaluating the pathways and processes through which environmental changes influence individual fitness and population processes. creator: Anne Saarinen creator: Ulrika Candolin uri: https://doi.org/10.7717/peerj.9521 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Saarinen and Candolin title: Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays link: https://peerj.com/articles/9551 last-modified: 2020-07-17 description: The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize. creator: Lidong Hao creator: Shubing Shi creator: Haibin Guo creator: Ming Li creator: Pan Hu creator: Yadong Wei creator: Yanfei Feng uri: https://doi.org/10.7717/peerj.9551 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hao et al. title: Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2 link: https://peerj.com/articles/9576 last-modified: 2020-07-17 description: Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment. creator: Arohi Parlikar creator: Kishan Kalia creator: Shruti Sinha creator: Sucheta Patnaik creator: Neeraj Sharma creator: Sai Gayatri Vemuri creator: Gaurav Sharma uri: https://doi.org/10.7717/peerj.9576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Parlikar et al. title: Assessment of biomass potentials of microalgal communities in open pond raceways using mass cultivation link: https://peerj.com/articles/9418 last-modified: 2020-07-16 description: Metagenome studies have provided us with insights into the complex interactions of microorganisms with their environments and hosts. Few studies have focused on microalgae-associated metagenomes, and no study has addressed aquatic microalgae and their bacterial communities in open pond raceways (OPRs). This study explored the possibility of using microalgal biomasses from OPRs for biodiesel and biofertilizer production. The fatty acid profiles of the biomasses and the physical and chemical properties of derived fuels were evaluated. In addition, the phenotype-based environmental adaptation ability of soybean plants was assessed. The growth rate, biomass, and lipid productivity of microalgae were also examined during mass cultivation from April to November 2017. Metagenomics analysis using MiSeq identified ∼127 eukaryotic phylotypes following mass cultivation with (OPR 1) or without (OPR 3) a semitransparent film. Of these, ∼80 phylotypes were found in both OPRs, while 23 and 24 phylotypes were identified in OPRs 1 and 3, respectively. The phylotypes belonged to various genera, such as Desmodesmus, Pseudopediastrum, Tetradesmus, and Chlorella, of which, the dominant microalgal species was Desmodesmus sp. On average, OPRs 1 and 3 produced ∼8.6 and 9.9 g m−2 d−1 (0.307 and 0.309 DW L−1) of total biomass, respectively, of which 14.0 and 13.3 wt% respectively, was lipid content. Fatty acid profiling revealed that total saturated fatty acids (mainly C16:0) of biodiesel obtained from the microalgal biomasses in OPRs 1 and 3 were 34.93% and 32.85%, respectively; total monounsaturated fatty acids (C16:1 and C18:1) were 32.40% and 31.64%, respectively; and polyunsaturated fatty acids (including C18:3) were 32.68% and 35.50%, respectively. Fuel properties determined by empirical equations were within the limits of biodiesel standards ASTM D6751 and EN 14214. Culture solutions with or without microalgal biomasses enhanced the environmental adaptation ability of soybean plants, increasing their seed production. Therefore, microalgal biomass produced through mass cultivation is excellent feedstock for producing high-quality biodiesel and biofertilizer. creator: Seung-Woo Jo creator: Jeong-Mi Do creator: Ho Na creator: Ji Won Hong creator: Il-Sup Kim creator: Ho-Sung Yoon uri: https://doi.org/10.7717/peerj.9418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jo et al. title: Subcellular compartmentalization of the plant antioxidant system: an integrated overview link: https://peerj.com/articles/9451 last-modified: 2020-07-16 description: The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g., ascorbate, glutathione, and their oxidized forms) and thioredoxin/glutaredoxin systems which can serve as reducing agents for antioxidant enzymes. The number of genes encoding AOS enzymes varies between classes, and same class enzymes encoded by different gene copies may have different subcellular localizations, functional loads and modes of evolution. These facts hereafter reinforce the complex nature of AOS regulation and functioning. Further studies can describe new trends in the behavior and functioning of systems components, and provide new fundamental knowledge about systems regulation. The system is revealed to have a lot of interactions and interplay pathways between its components at the subcellular level (antioxidants, enzymes, ROS level, and hormonal and transcriptional regulation). These facts should be taken into account in further studies during the AOS modeling by describing the main pathways of generating and utilizing ROS, as well as the associated signaling processes and regulation of the system on cellular and organelle levels, which is a complicated and ambitious task. Another objective for studying the phenomenon of the AOS is related to the influence of cell dynamics and circadian rhythms on it. Therefore, the AOS requires an integrated and multi-level approach to study. We focused this review on the existing scientific background and experimental data used for the systems biology research of the plant AOS. creator: Aleksandr Bobrovskikh creator: Ulyana Zubairova creator: Alexey Kolodkin creator: Alexey Doroshkov uri: https://doi.org/10.7717/peerj.9451 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bobrovskikh et al. title: The chemotactic swimming behavior of bird schistosome miracidia in the presence of compatible and incompatible snail hosts link: https://peerj.com/articles/9487 last-modified: 2020-07-16 description: No effective method has yet been developed to prevent the threat posed by the emerging disease—cercarial dermatitis (swimmer’s itch), caused by infective cercariae of bird schistosomes (Digenea: Schistosomatidae). In our previous studies, the New Zealand mud snail—Potamopyrgus antipodarum (Gray, 1853; Gastropoda, Tateidae)—was used as a barrier between the miracidia of Trichobilharzia regenti and the target snails Radix balthica. Since the presence of non-indigenous snails reduced the parasite prevalence under laboratory conditions, we posed three new research questions: (1) Do bird schistosomes show totally perfect efficacy for chemotactic swimming behavior? (2) Do the larvae respond to substances emitted by incompatible snail species? (3) Do the excretory-secretory products of incompatible snail species interfere with the search for a compatible snail host? The experiments were carried out in choice-chambers for the miracidia of T. regenti and T. szidati. The arms of the chambers, depending on the variant, were filled with water conditioned by P. antipodarum, water conditioned by lymnaeid hosts, and dechlorinated tap water. Miracidia of both bird schistosome species chose more frequently the water conditioned by snails—including the water conditioned by the incompatible lymnaeid host and the alien species, P. antipodarum. However, species-specific differences were noticed in the behavior of miracidia. T. regenti remained more often inside the base arm rather than in the arm filled with water conditioned by P. antipodarum or the control arm. T. szidati, however, usually left the base arm and moved to the arm filled with water conditioned by P. antipodarum. In conclusion, the non-host snail excretory-secretory products may interfere with the snail host-finding behavior of bird schistosome miracidia and therefore they may reduce the risk of swimmer’s itch. creator: Anna Marszewska creator: Anna Cichy creator: Jana Bulantová creator: Petr Horák creator: Elżbieta Żbikowska uri: https://doi.org/10.7717/peerj.9487 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Marszewska et al. title: Review of the genus Loimia Malmgren, 1866 (Annelida, Terebellidae) from China seas with recognition of two new species based on integrative taxonomy link: https://peerj.com/articles/9491 last-modified: 2020-07-16 description: Specimens of the genus Loimia (Annelida, Terebellidae) deposited in the Marine Biological Museum of the Chinese Academy of Sciences (MBMCAS) together with materials newly collected from China seas were examined. Based on morphological comparisons and molecular analysis, some specimens collected from the coasts of Shandong province and Guangxi province were confirmed as two new Loimia species respectively (Loimia borealis sp. n. and Loimia macrobranchia sp. n.). Morphologically, L. borealis sp. n. is distinguished from previously known species of this genus by having seven equal sized ventral shields, with length five times the width; this species was retrieved as sister to the clades of Loimia arboreaMoore, 1903 and Loimia banderaHutchings, 1990 in the phylogenetic tree, which was reconstructed based on mitochondrial COI gene. Loimia macrobranchia sp. n. differs from congeners by the large size of its first pair of branchiae with a thick main stem and about 18 dendritic branches arranged in two levels. A key to identifying Loimia species found in Chinese seas is given. creator: Weina Wang creator: Jixing Sui creator: Qi Kou creator: Xin-Zheng Li uri: https://doi.org/10.7717/peerj.9491 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Light dependent courtship behavior in Drosophila simulans and D. melanogaster link: https://peerj.com/articles/9499 last-modified: 2020-07-16 description: Differences in courtship signals and perception are well-known among Drosophila species. One such described difference is the dependency on light, and thus presumably vision, for copulation success. Many studies have described a difference in light-dependent copulation success between D. melanogaster and D. simulans, identifying D. simulans as a light-dependent species, and D. melanogaster as a light-independent one. However, many of these studies use assays of varying design and few strains to represent the entire species. Here, we attempt to better characterize this purported difference using 11 strains of each species, paired by collection location, in behavioral assays conducted at two different exposure times. We show that, while there is a species-wide difference in magnitude of light-dependent copulation success, D. melanogaster copulation success is, on average, still impaired in the dark at both exposure times we measured. Additionally, there is significant variation in strain-specific ability to copulate in the dark in both species across two different exposure times. We find that this variation correlates strongly with longitude in D. melanogaster, but not in D. simulans. We hypothesize that differences in species history and demography may explain behavioral variation. Finally, we use courtship assays to show that light-dependent copulation success in one D. simulans strain is driven in part by both males and females. We discuss potential differences in courtship signals and/or signal importance between these species and potential for further comparative studies for functional characterization. creator: Michael P. Shahandeh creator: Cameryn Brock creator: Thomas L. Turner uri: https://doi.org/10.7717/peerj.9499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shahandeh et al. title: Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China link: https://peerj.com/articles/9500 last-modified: 2020-07-16 description: Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks. creator: Xiaojuan Chen creator: Da He creator: Lianfeng Zhou creator: Yankun Cao creator: Zhanjing Li uri: https://doi.org/10.7717/peerj.9500 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chen et al. title: Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context link: https://peerj.com/articles/9517 last-modified: 2020-07-16 description: Quaternary climate and associated vegetational changes affected the fauna of the Chilean Mediterranean ecosystem. Here we studied the genetic variation of the long-haired mouse, Abrothrix longipilis, a sigmodontine rodent endemic to this area. Within an environmentally explicit context, we examined the geographic distribution of the genetic diversity and demographic history of the species based on sequences of the mitochondrial Cytochrome-b gene of 50 individuals from 13 localities and a large panel of single nucleotide polymorphisms of 17 individuals from 6 localities. The gene genealogy of A. longipilis revealed three intraspecific lineages that are allopatric and latitudinally segregated (northern, central, and southern lineages) with an estimated crown age for the whole species clade of 552.3 kyr B.P. A principal component analysis based on 336,596 SNP loci is in line with the information given by the the mitochondrial gene genealogy. Along its complete distributional range, A. longipilis showed patterns of isolation by distance and also isolation by environment. The general pattern of historical demography showed stability for most intraspecific lineages of A. longipilis. Northern and central lineages showed signals of historical demographic stability, while the southern lineage showed contrasting signals. In agreement with this, the niche models performed showed that in the northern range of A. longipilis, areas of high suitability for this species increased towards the present time; areas of central range would have remained relatively stable, while southern areas would have experienced more change through time. In summary, our study shows three distinct allopatric lineages of A. longipilis, each showing slightly different demographic history. creator: Lourdes Valdez creator: Marcial Quiroga-Carmona creator: Guillermo D’Elía uri: https://doi.org/10.7717/peerj.9517 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Valdez et al. title: Diagnostic and prognostic values of upregulated SPC25 in patients with hepatocellular carcinoma link: https://peerj.com/articles/9535 last-modified: 2020-07-16 description: BackgroundSpindle pole body component 25 (SPC25) plays a vital role in many cellular processes, such as tumorigenesis. However, the clinical significance of SPC25 in hepatocellular carcinoma (HCC) has not been investigated. This study aimed to explore the expression patterns of SPC25 in HCC and non-neoplastic tissues and to investigate the diagnostic and prognostic values of SPC25.MethodThe expression of SPC25 was examined in 374 HCC issues and 50 non-neoplastic tissues from The Cancer Genome Atlas (TCGA) cohort. The diagnostic and prognostic values of SPC25 were analyzed via receiver operating characteristic (ROC) curve and survival analyses, respectively. Univariate and multivariate Cox regression analyses were used to identify the prognostic factors and to establish a nomogram. The diagnostic and prognostic values were further validated in an external cohort from the International Cancer Genome Consortium (ICGC) database.ResultsThe expression of SPC25 in HCC tissues was significantly higher than that in normal tissues in both cohorts (all P < 0.001). The ROC curve analysis indicated that SPC25 expression has high diagnostic value in HCC with area under the curve (AUC) value of 0.969 (95% confidence interval [CI] [0.948–0.984]) and 0.945 (95% CI [0.920–0.965]) for TCGA and ICGC cohorts, respectively. Patients with HCC exhibiting high SPC25 expression were associated with worse prognosis than those exhibiting low SPC25 expression in both cohorts (all P < 0.001). SPC25 was independently associated with overall survival in both cohorts (all P < 0.001). The concordance indices of the nomogram for predicting overall survival in TCGA and ICGC cohorts were 0.647 and 0.805, respectively, which were higher than those of the American Joint Committee on Cancer (AJCC) staging system.ConclusionSPC25 was upregulated in HCC and independently predicted poor overall survival of patients with HCC. Therefore, SPC25 is an effective diagnostic and prognostic biomarker for HCC. An SPC25-based nomogram was more accurate and useful than the AJCC staging system to predict prognosis of HCC. creator: Xiaolin Yang creator: Hongzhi Sun creator: Ying Song creator: Li Yang creator: Haibo Liu uri: https://doi.org/10.7717/peerj.9535 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition link: https://peerj.com/articles/9538 last-modified: 2020-07-16 description: This study investigates the isolated decomposition of spruce and lodgepole conifer needles to enhance our understanding of how needle litter impacts near-surface terrestrial biogeochemical processes. Harvested needles were exported to a subalpine meadow to enable a discrete analysis of the decomposition processes over 2 years. Initial chemistry revealed the lodgepole needles to be less recalcitrant with a lower carbon to nitrogen (C:N) ratio. Total C and N fundamentally shifted within needle species over time with decreased C:N ratios for spruce and increased ratios for lodgepole. Differences in chemistry correlated with CO2 production and soil microbial communities. The most pronounced trends were associated with lodgepole needles in comparison to the spruce and needle-free controls. Increased organic carbon and nitrogen concentrations associated with needle presence in soil extractions further corroborate the results with clear biogeochemical signatures in association with needle chemistry. Interestingly, no clear differentiation was observed as a function of bark beetle impacted spruce needles vs those derived from healthy spruce trees despite initial differences in needle chemistry. These results reveal that the inherent chemistry associated with tree species has a greater impact on soil biogeochemical signatures during isolated needle decomposition. By extension, biogeochemical shifts associated with bark beetle infestation are likely driven more by changes such as the cessation of rhizospheric processes than by needle litter decomposition. creator: Laura T. Leonard creator: Kristin Mikkelson creator: Zhao Hao creator: Eoin L. Brodie creator: Kenneth H. Williams creator: Jonathan O. Sharp uri: https://doi.org/10.7717/peerj.9538 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Leonard et al. title: Endophytic Burkholderia sp. SSG as a potential biofertilizer promoting boxwood growth link: https://peerj.com/articles/9547 last-modified: 2020-07-16 description: BackgroundBurkholderia sp. SSG is a bacterial endophyte isolated from boxwood leaves showing a resistant response to infection by the boxwood blight pathogen Calonectria pseudonaviculata. SSG acted as a protective and curative biocontrol agent for boxwood blight and as a bio-sanitizer of disease inoculum in the field. Many gene clusters involved in antibiotic production and plant growth promotion (PGP) were found in the genome, giving this endophyte great application potential as a treatment for plant protection. However, the PGP features have not been documented. This study investigated the plant growth promotion activity of SSG in boxwood.MethodsTo determine whether SSG is a plant growth promoting bacterium, four PGP traits, auxin and siderophore production, nitrogen fixation and phosphate solubilization, were examined in the laboratory with colorimetric or agar plate assays. The plant growth promoting activity of SSG was tested on three boxwood varieties characterized by slow, intermediate and fast growth rates, namely Justin Brouwers, Buddy and Winter Gem, respectively. These plants were drenched with an SSG cell suspension or water and washed plant weight was compared before and after treatment to determine growth changes after 10 months.ResultsThe SSG culture was sustainable on nitrogen free media, suggesting that SSG may fix atmospheric nitrogen. It was also a strong phosphate solubilizer and a potent siderophore and indole-3-acetic acid (IAA) producer. Significant growth promotion was observed on boxwood cultivars Justin Brouwers, Buddy and Winter Gem 10 months after plant roots were drenched with SSG cells. The growth rate of treated plants was 76.1, 58.3, and 37.3% higher than that of the control, respectively. The degree of growth promotion was significantly different among plant varieties, notably more pronounced with the slow and intermediate growers. This study demonstrates that the SSG bacterium has multiple PGP traits and is a prospective plant biofertilizer. creator: Ping Kong creator: Chuanxue Hong uri: https://doi.org/10.7717/peerj.9547 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kong and Hong title: Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey link: https://peerj.com/articles/9569 last-modified: 2020-07-16 description: Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia. creator: Osman İbiş uri: https://doi.org/10.7717/peerj.9569 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 İbiş title: Chlorine-based DUWL disinfectant leads to a different microbial composition of water derived biofilms compared to H2O2-based chemical disinfectants in vitro link: https://peerj.com/articles/9503 last-modified: 2020-07-15 description: BackgroundBiofilm formation in dental unit waterlines (DUWL) may lead to health risks for dental staff and patients. Therefore, dental unit waterlines need to be disinfected, for instance by using chemical disinfectants. However, the application of chemical disinfectants may lead to the selection of specific microorganisms. Therefore, the aim of our study was to assess the microbial composition of water-derived biofilms, after a continuous exposure to maintenance doses of commercially available chemical disinfectants, in vitro.MethodsThe AAA-model was used to grow water derived biofilms. The biofilms were subjected to the maintenance dose of each disinfectant. To determine the microbial composition, the V4 hypervariable region of the 16S rRNA gene was sequenced. The sequences were clustered in operational taxonomic units (OTUs).ResultsThe bacterial composition of biofilms in all treatment groups differed significantly (PERMANOVA F = 4.441, p = 0.001). Pairwise comparisons revealed Anoxyl treated biofilms were significantly different from all groups (p = 0.0001). In the Anoxyl-treated biofilms, the relative abundance of Comamonadaceae and Sphingopyxis was high compared to the Dentosept, Green and Clean and Oxygenal groups.ConclusionWe concluded that exposure to low doses of the chlorine-based chemical disinfectant Anoxyl led to a substantially different composition of water derived biofilms compared to biofilms exposed to H2O2-based chemical disinfectants. creator: Charifa Zemouri creator: Alexa M.G.A. Laheij creator: Catherine M.C. Volgenant creator: Bernd W. Brandt creator: Wim Crielaard creator: Mark J. Buijs creator: Egija Zaura creator: Johannes J. de Soet uri: https://doi.org/10.7717/peerj.9503 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zemouri et al. title: Decomposition of dinosaurian remains inferred by invertebrate traces on vertebrate bone reveal new insights into Late Jurassic ecology, decay, and climate in western Colorado link: https://peerj.com/articles/9510 last-modified: 2020-07-15 description: A survey of 2,368 vertebrate fossils from the Upper Jurassic Mygatt-Moore Quarry (MMQ) (Morrison Formation, Brushy Basin Member) in western Colorado revealed 2,161 bone surface modifications on 884 specimens. This is the largest, site-wide bone surface modification survey of any Jurassic locality. Traces made by invertebrate actors were common in the assemblage, second in observed frequency after vertebrate bite marks. Invertebrate traces are found on 16.174% of the total surveyed material and comprise 20.148% of all identified traces. Six distinct invertebrate trace types were identified, including pits and furrows, rosettes, two types of bioglyph scrapes, bore holes and chambers. A minimum of four trace makers are indicated by the types, sizes and morphologies of the traces. Potential trace makers are inferred to be dermestid or clerid beetles, gastropods, an unknown necrophagous insect, and an unknown osteophagus insect. Of these, only gastropods are preserved at the site as body fossils. The remaining potential trace makers are part of the hidden paleodiversity from the North American Late Jurassic Period, revealed only through this ichnologic and taphonomic analysis. Site taphonomy suggests variable, but generally slow burial rates that range from months up to 6 years, while invertebrate traces on exposed elements indicate a minimum residence time of five months for carcasses with even few preserved invertebrate traces. These traces provide insight into the paleoecology, paleoclimate, and site formation of the MMQ, especially with regards to residence times of the skeletal remains on the paleolandscape. Comprehensive taphonomic studies, like this survey, are useful in exploring patterns of paleoecology and site formation, but they are also rare in Mesozoic assemblages. Additional work is required to determine if 16.174% is typical of bulk-collected fossils from Jurassic ecosystems in North America, or if the MMQ represents an unusual locality. creator: Julia B. McHugh creator: Stephanie K. Drumheller creator: Anja Riedel creator: Miriam Kane uri: https://doi.org/10.7717/peerj.9510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 McHugh et al. title: Canine SOD1 harboring E40K or T18S mutations promotes protein aggregation without reducing the global structural stability link: https://peerj.com/articles/9512 last-modified: 2020-07-15 description: Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease associated with aggregation of superoxide dismutase 1 (SOD1) protein. More than 160 mutations in human SOD1 have been identified in familial ALS and extensively characterized in previous studies. Here, we investigated the effects of T18S and E40K mutations on protein aggregation of canine SOD1. These two mutations are exclusively found in canine degenerative myelopathy (an ALS-like neurodegenerative disease in dogs), whose phenotype is unknown at the level of protein folding. Interestingly, the T18S and E40K mutations did not alter far-UV CD spectrum, enzymatic activity, or global structural stability of canine SOD1. However, thioflavin-T assay and transmission electron microscopy analysis revealed that these mutations promote formation of fibrous aggregates, in particular in the Cu2+/Zn2+-unbound state. These evidence suggested that the T18S and E40K mutations promote protein aggregation through a unique mechanism, possibly involving destabilization of the local structure, reduction of net negative charge, or production of disulfide-linked oligomers. creator: Shintaro Kimura creator: Yuji O. Kamatari creator: Yukina Kuwahara creator: Hideaki Hara creator: Osamu Yamato creator: Sadatoshi Maeda creator: Hiroaki Kamishina creator: Ryo Honda uri: https://doi.org/10.7717/peerj.9512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kimura et al. title: Craniofacial characteristics of Syrian adolescents with Class II division 1 malocclusion: a retrospective study link: https://peerj.com/articles/9545 last-modified: 2020-07-15 description: BackgroundMalocclusion characteristics vary across different ethnic groups and populations. Limited data are available regarding the characteristics of Syrian adolescents with Class II division 1 (Class II-1) malocclusion, and the recent inflow of Syrian refugees and immigrants into Europe and many areas worldwide demonstrate the need for updated studies to discover the craniofacial characteristics of these new immigrants.ObjectivesThe present compound cephalometric and tooth-size study sought to assess the dentofacial morphology, upper-airway dimensions, and tooth-size characteristics of Syrian adolescents with Class II-1 malocclusion and compare the results with established Syrian population norms.Materials and MethodsThe study sample consisted of 43 Syrian patients including 24 females and 19 males with Class II-1 malocclusion (age: 14.3 (±1.5) years, mean (±SD)). Cephalometric radiographs and orthodontic casts were analyzed using special orthodontic software (OnyxCeph3™) and a universal digital caliper, respectively. Statistics were calculated using the SPSS software.ResultsIn Syrian adolescents with Class II-1 malocclusion, the position of the mandible relative to the nasion perpendicular (mean (95% confidence interval)) was −11.01 (−12.45, −9.57) mm. Facial axis angle showed a negative value: −6.25 (−7.65, −4.85) degrees. An obtuse nasolabial angle was observed: 104.05 (101.77, 106.33) degrees. The average width of the upper pharynx was 11.50 (10.53, 12.47) mm; however, there was no prevalence of an upper-pharyngeal width of 5 mm or less. The average value of the anterior tooth-size ratio was 80.69 (79.85, 81.53) percent. In total, 39.5% of the investigated subjects had anterior ratios outside two standard deviations from Bolton’s norm, while 25.6% of the investigated subjects had anterior ratios outside two standard deviations from Syrian population norm.ConclusionsIn this study, the inter-maxillary discrepancy of Class II-1 Syrian adolescents was a consequence of their hyperdivergent facial pattern. The observed small pharyngeal widths were not clinically significant, while the anterior tooth-size discrepancy might be clinically relevant. creator: Alaa Al Ayoubi creator: Daniel Dalla Torre creator: Melinda Madléna uri: https://doi.org/10.7717/peerj.9545 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Al Ayoubi et al. title: Biofilm released cells can easily be obtained in a fed-batch system using ica+ but not with ica- isolates link: https://peerj.com/articles/9549 last-modified: 2020-07-15 description: Staphylococcus epidermidis is one of the major opportunistic bacterial pathogens in healthcare facilities, mainly due to its strong ability to form biofilms in the surface of indwelling medical devices. To study biofilms under in vitro conditions, both fed-batch and flow systems are widely used, with the first being the most frequent due to their low cost and ease of use.AimTo assess if a fed-batch system previously developed to obtain biofilm released cells (Brc) from strong biofilm producing S. epidermidis isolates could also be used to obtain and characterize Brc from isolates with lower abilities to form biofilms.MethodologyThe applicability of a fed-batch system to obtain Brc from biofilms of 3 ica+ and 3 ica− isolates was assessed by quantifying the biofilm and Brc biomass by optical density (OD) and colony-forming units (CFU) measurements. The effect of media replacement procedures of fed-batch systems on the amount of biofilm was determined by quantifying the biofilm and biofilm bulk fluid, by CFU, after consecutive washing steps.ResultsThe fed-batch model was appropriate to obtain Brc from ica+ isolates, that presented a greater ability to form biofilms and release cells. However, the same was not true for ica− isolates, mainly because the washing procedure would physically remove a significant number of cells from the biofilm.ConclusionsThis study demonstrates that a fed-batch system is only feasible to be used to obtain Brc from S. epidermidis when studying strong and cohesive biofilm-forming isolates. creator: Vânia Gaio creator: Nuno Cerca uri: https://doi.org/10.7717/peerj.9549 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gaio and Cerca title: Changes of diazotrophic communities in response to cropping systems in a Mollisol of Northeast China link: https://peerj.com/articles/9550 last-modified: 2020-07-15 description: Nitrogen-fixing microorganisms play important roles in N cycling. However, knowledge related to the changes in the diazotrophic community in response to cropping systems is still rudimentary. In this study, the nifH gene was used to reveal the abundance and community compositions of diazotrophs in the cropping systems of continuous cropping of corn (CC) and soybean (SS) and soybean-corn rotation for growing corn (CSC) and soybean (SCS) in a black soil of Northeast China. The results showed that the abundance of the nifH gene was significantly higher in cropping soybean than in cropping corn under the same cropping system, while remarkably increased in the rotation system under the same crop. The Shannon index in the CC treatment was significantly higher than that in the other treatments, but the OTU number and Chao1 index had no significant change among the four treatments. Bradyrhizobium japonicum was the dominant diazotrophic species, and its relative abundance was at the lowest value in the CC treatment. In contrast, Skermanella sp. had the highest relative abundance in the CC treatment. A PCoA showed that the diazotrophic communities were separated between different cropping systems, and the variation caused by continuous corn cropping was the largest. Among the tested soil properties, the soil available phosphorus was a primary factor in determining diazotrophic community compositions. Overall, the findings of this study highlighted that the diazotrophic communities in black soils are very sensitive to cropping systems. creator: Jiaxun Zou creator: Qin Yao creator: Junjie Liu creator: Yansheng Li creator: Fuqiang Song creator: Xiaobing Liu creator: Guanghua Wang uri: https://doi.org/10.7717/peerj.9550 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zou et al. title: Beyond loot boxes: a variety of gambling-like practices in video games are linked to both problem gambling and disordered gaming link: https://peerj.com/articles/9466 last-modified: 2020-07-14 description: A variety of practices have recently emerged which relate to both video games and gambling. These range from opening loot boxes, to esports betting, real-money video gaming, token wagering, and social casino spending. It is unknown either how harmful or how widespread many of these activities are. A sample of 1,081 adults from the UK aged 18+ was therefore recruited. This sample was purposively recruited via quota sampling to represent the UK population in terms of sex, age, and ethnicity. Engagement in all forms of gaming-related practices were significantly associated with both problem gambling and disordered gaming. A total of 18.5% of the sample had engaged in these activities at least once in the new year. These results suggest a convergent ecosystem of practices that relate to both video games and gambling. Engagement in each of these activities is linked to problem gambling. However, it remains unclear whether engagement in these activities causes problem gambling. creator: David Zendle uri: https://doi.org/10.7717/peerj.9466 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zendle title: Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods link: https://peerj.com/articles/9174 last-modified: 2020-07-14 description: BackgroundAlternative splicing (AS) is an important mechanism for regulating gene expression and proteome diversity. Tumor-alternative splicing can reveal a large class of new splicing-associated potential new antigens that may affect the immune response and can be used for immunotherapy.MethodsThe RNA-seq transcriptome data and clinical information of stomach adenocarcinoma (STAD) cohort were downloaded from The Cancer Genome Atlas (TCGA) database data portal, and data of splicing events were obtained from the SpliceSeq database. Predicting genes were validated by Asian cancer research group (ACRG) cohort and Oncomine database. RT-qPCR was used to analysis the expression of ECT2 in STAD.ResultsA total of 32,166 AS events were identified, among which 2,042 AS events were significantly associated with patients survival. Biological pathway analysis indicated that these genes play an important role in regulating gastric cancer-related processes such as GTPase activity and PI3K-Akt signaling pathway. Next, we derived a risk signature, using alternate acceptor, that is an independent prognostic marker. Moreover, high ECT2 expression was associated with poorer prognosis in STAD. Multivariate survival analysis demonstrated that high ECT2 expression was an independent risk factor for overall survival. Gene set enrichment analysis revealed that high ECT2 expression was enriched for hallmarks of malignant tumors. The ACRG cohort and Oncomine also showed that high ECT2 expression was associated with poorer prognosis in gastric cancer patients. Finally, RT-qPCR showed ECT2 expression was higher in STAD compared to the normal tissues.ConclusionThis study excavated the alternative splicing events in gastric cancer, and found ECT2 might be a biomarkers for diagnosis and prognosis. creator: Jie Liu creator: Miao Zhou creator: Yangyang Ouyang creator: Laifeng Du creator: Lingbo Xu creator: Hongyun Li uri: https://doi.org/10.7717/peerj.9174 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Establishment and characterization of fantail goldfish fin (FtGF) cell line from goldfish, Carassius auratus for in vitro propagation of Cyprinid herpes virus-2 (CyHV-2) link: https://peerj.com/articles/9373 last-modified: 2020-07-14 description: BackgroundHerpesviral hematopoietic necrosis disease, caused by cyprinid herpesvirus-2 (CyHV-2), is responsible for massive mortalities in the aquaculture of goldfish, Carassius auratus. Permissive cell lines for the isolation and propagation of CyHV-2 have been established from various goldfish tissues by sacrificing the fish. Here, we report the development of a cell line, FtGF (Fantail Goldfish Fin), from caudal fin of goldfish using non-lethal sampling. We also describe a simple protocol for successful establishment and characterization of a permissive cell line through explant method and continuous propagation of CyHV-2 with high viral titer using this cell line.MethodsCaudal fin tissue samples were collected from goldfish without killing the fish. Cell culture of goldfish caudal fin cells was carried out using Leibovitz’s L-15 (L-15) medium containing 20% FBS and 1X concentration of antibiotic antimycotic solution, incubated at 28 °C. Cells were characterized and origin of the cells was confirmed by sequencing fragments of the 16S rRNA and COI genes. CyHV-2 was grown in the FtGF cells and passaged continuously 20 times. The infectivity of the CyHV-2 isolated using FtGF cells was confirmed by experimental infection of naïve goldfish.ResultsThe cell line has been passaged up to 56 times in L-15 with 10% FBS. Karyotyping of FtGF cells at 30th, 40th and 56th passage indicated that modal chromosome number was 2n = 104. Species authentication of FtGF was performed by sequencing of the 16S rRNA and COI genes. The cell line was used for continuous propagation of CyHV-2 over 20 passages with high viral titer of 107.8±0.26 TCID50/mL. Following inoculation of CyHV-2 positive tissue homogenate, FtGF cells showed cytopathic effect by 2nd day post-inoculation (dpi) and complete destruction of cells was observed by the 10th dpi. An experimental infection of naïve goldfish using supernatant from infected FtGF cells caused 100% mortality and CyHV-2 infection in the challenged fish was confirmed by the amplification of DNA polymerase gene, histopathology and transmission electron microscopy. These findings provide confirmation that the FtGF cell line is highly permissive to the propagation of CyHV-2. creator: Arathi Dharmaratnam creator: Raj Kumar creator: Basheer Saidmuhammed Valaparambil creator: Neeraj Sood creator: Pravata Kumar Pradhan creator: Sweta Das creator: T. Raja Swaminathan uri: https://doi.org/10.7717/peerj.9373 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dharmaratnam et al. title: The validity of activity trackers is affected by walking speed: the criterion validity of Garmin Vivosmart® HR and StepWatch™ 3 for measuring steps at various walking speeds under controlled conditions link: https://peerj.com/articles/9381 last-modified: 2020-07-14 description: IntroductionThe use of activity trackers has increased both among private consumers and in healthcare. It is therefore relevant to consider whether a consumer-graded activity tracker is comparable to or may substitute a research-graded activity tracker, which could further increase the use of activity trackers in healthcare and rehabilitation. Such use will require knowledge of their accuracy as the clinical implications may be significant. Studies have indicated that activity trackers are not sufficiently accurate, especially at lower walking speeds. The present study seeks to inform decision makers and healthcare personnel considering implementing physical activity trackers in clinical practice. This study investigates the criterion validity of the consumer-graded Garmin Vivosmart® HR and the research-graded StepWatch™ 3 compared with manual step count (gold standard) at different walking speeds under controlled conditions.MethodsThirty participants, wearing Garmin Vivosmart® HR at the wrist and StepWatch™ 3 at the ankle, completed six trials on a treadmill at different walking speeds: 1.6 km/h, 2.4 km/h, 3.2 km/h, 4.0 km/h, 4.8 km/h, and 5.6 km/h. The participants were video recorded, and steps were registered by manual step count. Medians and inter-quartile ranges (IQR) were calculated for steps and differences in steps between manually counted steps and the two devices. In order to assess the clinical relevance of the tested devices, the mean absolute percentage error (MAPE) was determined at each speed. A MAPE ≤3% was considered to be clinically irrelevant. Furthermore, differences between manually counted steps and steps recorded by the two devices were presented in Bland–Altman style plots.ResultsThe median of differences in steps between Garmin Vivosmart® HR and manual step count ranged from −49.5 (IQR = 101) at 1.6 km/h to −1 (IQR = 4) at 4.0 km/h. The median of differences in steps between StepWatch™ 3 and manual step count were 4 (IQR = 14) at 1.6 km/h and 0 (IQR = 1) at all other walking speeds. The results of the MAPE showed that differences in steps counted by Garmin Vivosmart® HR were clinically irrelevant at walking speeds 3.2–4.8 km/h (MAPE: 0.61–1.27%) as the values were below 3%. Differences in steps counted by StepWatch™ 3 were clinically irrelevant at walking speeds 2.4–5.6 km/h (MAPE: 0.08–0.35%).ConclusionGarmin Vivosmart® HR tended to undercount steps compared with the manual step count, and StepWatch™ 3 slightly overcounted steps compared with the manual step count. Both the consumer-graded activity tracker (Garmin Vivosmart® HR) and the research-graded (StepWatch™ 3) are valid in detecting steps at selected walking speeds in healthy adults under controlled conditions. However, both activity trackers miscount steps at slow walking speeds, and the consumer graded activity tracker also miscounts steps at fast walking speeds. creator: Frederik Rose Svarre creator: Mads Møller Jensen creator: Josephine Nielsen creator: Morten Villumsen uri: https://doi.org/10.7717/peerj.9381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Svarre et al. title: Targeting secretory leukocyte protease inhibitor (SLPI) inhibits colorectal cancer cell growth, migration and invasion via downregulation of AKT link: https://peerj.com/articles/9400 last-modified: 2020-07-14 description: The secretory leukocyte protease inhibitor (SLPI) is a serine protease inhibitor which plays important role in bacterial infection, inflammation, wound healing and epithelial proliferation. Dysregulation of SLPI has been reported in a variety of human cancers including glioblastoma, lung, breast, ovarian and colorectal carcinomas and is associated with tumor aggressiveness and metastatic potential. However, the pathogenic role of SLPI in colorectal cancer is still unclear. Here we showed that SLPI mRNA level was significantly upregulated in colorectal cancer tissues compared to adjacent normal controls. Targeting SLPI by siRNA inhibited proliferation, migration and invasion of colorectal cancer cells lines HT29 and HT116 in vitro. Mechanistically, blockage of cancer cell growth and metastasis after SLPI knockdown was associated with down-regulation of AKT signaling. In conclusion, SLPI regulated colorectal cell growth and metastasis via AKT signaling. SLPI may be a novel biomarker and therapeutic target for colorectal cancer. Targeting AKT signaling may be effective for colorectal cancer treatment. creator: Zhijiang Wei creator: Guiying Liu creator: Rufu Jia creator: Wei Zhang creator: Li Li creator: Yuanyuan Zhang creator: Zhijing Wang creator: Xiyong Bai uri: https://doi.org/10.7717/peerj.9400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wei et al. title: Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities link: https://peerj.com/articles/9403 last-modified: 2020-07-14 description: Paenibacillus triticisoli BJ-18, a N2-fixing bacterium, is able to promote plant growth, but the secondary metabolites that may play a role in promoting plant growth have never been characterized. In this study, untargeted metabolomics profiling of P. triticisoli BJ-18 indicated the existence of 101 known compounds, including N2-acetyl ornithine, which is the precursor of siderophores, plant growth regulators such as trehalose 6-phosphate, betaine and trigonelline, and other bioactive molecules such as oxymatrine, diosmetin, luotonin A, (-)-caryophyllene oxide and tetrahydrocurcumin. In addition, six compounds were also isolated from P. triticisoli BJ-18 using a combination of silica gel chromatography, sephadex LH-20, octadecyl silane (ODS), and high-performance liquid chromatography (HPLC). The compound structures were further analyzed by Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and Electronic Circular Dichroism (ECD). The six compounds included three classical siderophore fusarinines identified as deshydroxylferritriacetylfusigen, desferritriacetylfusigen, and triacetylfusigen, and three indolic acids identified as paenibacillic acid A, 3-indoleacetic acid (IAA), and 3-indolepropionic acid (IPA). Both deshydroxylferritriacetylfusigen and paenibacillic acid A have new structures. Fusarinines, which normally occur in fungi, were isolated from bacterium for the first time in this study. Both siderophores (compounds 1 and 2) showed antimicrobial activity against Escherichia coli, Staphylococcus aureus and Bacillus subtilis, but did not show obvious inhibitory activity against yeast Candida albicans, whereas triacetylfusigen (compound 3) showed no antibiosis activity against these test microorganisms. Paenibacillic acid A, IAA, and IPA were shown to promote the growth of plant shoots and roots, and paenibacillic acid A also showed antimicrobial activity against S. aureus. Our study demonstrates that siderophores and indolic acids may play an important role in plant growth promotion by P. triticisoli BJ-18. creator: Yunzhi Zhang creator: Jinwei Ren creator: Wenzhao Wang creator: Baosong Chen creator: Erwei Li creator: Sanfeng Chen uri: https://doi.org/10.7717/peerj.9403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Utilization of brewery wastes in food industry link: https://peerj.com/articles/9427 last-modified: 2020-07-14 description: Beer is the most popular low-alcohol beverage consumed in large amounts in many countries each year. The brewing industry is an important global business with huge annual revenues. It is profitable and important for the economies of many countries around the world. The brewing process involves several steps, which lead to fermentation of sugars contained in malt and conversion thereof into alcohol and carbon dioxide by yeasts. Beer brewing generates substantial amounts of by-products. The three main brewing industry wastes include brewer’s spent grain, hot trub, and residual brewer’s yeast. Proper management of these wastes may bring economical benefits and help to protect the environment from pollution caused by their excessive accumulation. The disposal of these wastes is cumbersome for the producers, however they are suitable for reuse in the food industry. Given their composition, they can serve as a low-cost and highly nutritional source of feed and food additives. They also have a potential to be a cheap material for extraction of compounds valuable for the food industry and a component of media used in biotechnological processes aimed at production of compounds and enzymes relevant for the food industry. creator: Kamila Rachwał creator: Adam Waśko creator: Klaudia Gustaw creator: Magdalena Polak-Berecka uri: https://doi.org/10.7717/peerj.9427 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rachwałet al. title: Correlation between emotional regulation and peripheral lymphocyte counts in colorectal cancer patients link: https://peerj.com/articles/9475 last-modified: 2020-07-14 description: BackgroundColorectal cancer is one of the most common cancers worldwide. Psychological morbidity has an important impact on quality of life and major clinical outcomes. Several data have shown that the immune system may be a key player on the relation between psychological features and cancer outcomes. Natural Killer (NK) cells have been shown to be influenced by psychological factors. The aim of this investigation was to assess the impact of anxiety, depression, and anger state, trait, and expression on the immune response, particularly, their effect on NK cells and CD8+ T cells in surgical colorectal cancer patients.MethodsWe studied 54 surgical colorectal cancer patients and assessed patients pre-surgically, post-surgically, and 12 months after surgery (follow-up). We applied the Hospital Anxiety and Depression Scale and the State-Trait Anger Expression Inventory and measured peripheral T cells, CD8+ T cells, and NK cells. We did a cross-sectional analysis as well as a longitudinal assessment of the variables during the follow-up period.ResultsPre-surgical assessment: Trait anger, angry reaction, and anger-out had a significant negative correlation with NK cells. The lymphocytes values were unaffected by the presence of clinical anxiety or depression. Post-surgical assessment: Patients without clinical anxiety had higher levels of T cells. Angry reaction was negatively correlated with NK cells. Lymphocytes values were unaffected by the presence of clinical depression. Follow-up assessment: Patients without clinical depression had higher T cell counts. Trait anger and angry reaction were negatively correlated with the levels of NK cells. The lymphocytes values were unaffected by the presence of clinical anxiety. Longitudinal assessment: Angry-temperament, anger expression, and anger-in reduced significantly from the first to the second assessment. Anxiety, state anger, and trait anger significantly diminished from the pre-surgical to the follow-up assessment. Depression levels did not alter during the follow-up period. The lymphocyte count, and particularly T cells and CD8+ T cells, was significantly higher in the follow-up when compared with the pre-surgical assessment.ConclusionOur study suggests the existence of a relation between psychological response and immune response in colorectal cancer patients. We identified the importance of emotional regulation as a potential modulator for NK cell counts. Higher values of propensity to experience anger states and express them outwards seem to be associated with lower NK cell counts. creator: Estela Kakoo Brioso creator: Sérgio Ferreira Cristina creator: Luis Costa creator: Silvia Ouakinin uri: https://doi.org/10.7717/peerj.9475 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kakoo Brioso et al. title: Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding link: https://peerj.com/articles/9508 last-modified: 2020-07-14 description: Environmental DNA (eDNA) metabarcoding is a cost-effective novel approach to estimate biodiversity in an ecosystem. In this study, the MiFish pipeline was employed to test if the system methodology is sufficiently reliable to estimate fish biodiversity in Korean rivers. A total of 125 unique haplotypes and 73 species were identified at the species level from 16 water samples collected from a single survey in four Korean rivers (Hyeongsan, Taehwa, Seomjin, and Nakdong). Among the four rivers, the highest species richness was recorded in the Seomjin River (52 species), followed by the Taehwa (42 species) and Hyeongsan (40 species) rivers. The Nakdong River (26 species) presented the lowest species richness and number of endemic species, presumably due to its metropolitan location and anthropogenic impacts, such as dams or weirs. We were also able to detect that five exotic species (Carassius cuvieri, Cyprinus carpio, Cyprinus megalophthalmus, Lepomis macrochirus, and Micropterus salmoides) are widely distributed in all surveyed rivers, a situation that might be problematic in terms of conservation. Our findings indicate that the eDNA metabarcoding technique is one of the most cost-effective scientific tools available for the management and conservation of the freshwater fish resources available in Korea. However, the low number of 12S sequences of endemic species in the database and low resolution of the MiFish region for differentiating several taxa should be upgraded for their wide use. creator: Md Jobaidul Alam creator: Nack-Keun Kim creator: Sapto Andriyono creator: Hee-kyu Choi creator: Ji-Hyun Lee creator: Hyun-Woo Kim uri: https://doi.org/10.7717/peerj.9508 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Alam et al. title: A novel histozoic myxosporean, Enteromyxum caesio n. sp., infecting the redbelly yellowtail fusilier, Caesio cuning, with the creation of the Enteromyxidae n. fam., to formally accommodate this commercially important genus link: https://peerj.com/articles/9529 last-modified: 2020-07-14 description: Gastrointestinal myxosporean parasites from the genus Enteromyxum are known to cause severe disease, resulting in high mortalities in numerous species of cultured marine fishes globally. Originally described as Myxidium spp., they were transferred to a new genus, Enteromyxum, to emphasize their novel characteristics. Their retention in the family Myxidiidae at the time was warranted, but more comprehensive phylogenetic analyses have since demonstrated the need for a new family for these parasites. We discovered a novel Enteromyxum in wild fish from Malaysia and herein describe the fourth species in the genus and erect a new family, the Enteromyxidae n. fam., to accommodate them. Enteromyxum caesio n. sp. is described infecting the tissues of the stomach in the redbelly yellowtail fusilier, Caesio cuning, from Malaysia. The new species is distinct from all others in the genus, as the myxospores although morphologically similar, are significantly smaller in size. Furthermore, small subunit ribosomal DNA sequence data reveal that E. caesio is <84% similar to others in the genus, but collectively they form a robust and discrete clade, the Enteromyxidae n. fam., which is placed as a sister taxon to other histozoic marine myxosporeans. In addition, we describe, using transmission electron microscopy, the epicellular stages of Enteromyxum fugu and show a scanning electron micrograph of a mature myxospore of E. caesio detailing the otherwise indistinct sutural line, features of the polar capsules and spore valve ridges. The Enteromyxidae n. fam. is a commercially important group of parasites infecting the gastrointestinal tract of marine fishes and the histozoic species can cause the disease enteromyxosis in intensive finfish aquaculture facilities. Epicellular and sloughed histozoic stages are responsible for fish-to-fish transmission in net pen aquaculture systems but actinospores from an annelid host are thought to be necessary for transmission to fish in the wild. creator: Mark A. Freeman creator: Tetsuya Yanagida creator: Àrni Kristmundsson uri: https://doi.org/10.7717/peerj.9529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Freeman et al. title: Soil macro-fauna respond to environmental variations along a coastal-inland gradient link: https://peerj.com/articles/9532 last-modified: 2020-07-14 description: Varied environmental conditions in coastal-inland zones tend to influence soil faunal communities. However, few studies have focused on the responses of soil fauna to environmental variations along the coastal-inland gradient. In order to better understand the aforementioned responses, a total of 80 soil macro-faunal samples were collected at the five different distances from the coastline of China’s Bohai Bay. The results revealed that the compositions, structural characteristics and diversity of the soil macro-fauna varied among the different habitats. With the increases in the distance from the sea, the individual density, richness and diversity levels of the soil macro-fauna all first increased and then decreased. The individual density, richness and diversity values were all at their maximum at 30 km from the sea. The Edge effect promoted unique and rare soil macro-faunal taxa. Formicidae, Curculionidae and Aphodiidae were found to be the edge taxa. Agelenidae, Liocranidae and Nematocera were considered to be indicator taxa of severe sea effects. Paradoxosomatidae was an indicator taxon of slight effects. Overall, the environmental variations along the coastal-inland gradient were found to have the potential to affect the soil macro-faunal communities, and the different taxa of the soil macro-fauna responded to those variations in different ways. This study further revealed the processes and mechanisms of the sea influencing the soil macro-faunal communities, which had been caused by the coastal-inland gradient. The results of this study also provided a theoretical basis for developing future biodiversity guidelines for coastal ecosystems. creator: Xiaoxue Zheng creator: Yan Tao creator: Zhongqiang Wang creator: Chen Ma creator: Hong He creator: Xiuqin Yin uri: https://doi.org/10.7717/peerj.9532 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zheng et al. title: Predictive values of stool-based tests for mucosal healing among Taiwanese patients with ulcerative colitis: a retrospective cohort analysis link: https://peerj.com/articles/9537 last-modified: 2020-07-14 description: Background/PurposeOver the past two decades, ulcerative colitis (UC) has emerged in the Asia Pacific area, and its treatment goal has shifted from symptom relief to endoscopic remission. Endoscopy is the gold standard for the assessment of mucosal healing; however, it is an invasive method. Fecal calprotectin (FC) is a non-invasive stool-based inflammatory marker which has been used to monitor mucosal healing status, but it is expensive. By contrast, the immune fecal occult blood test (iFOBT) is a widely utilized stool-based screening tool for colorectal cancer. In this study, we compared the predictive values of iFOBT and FC for mucosal healing in Taiwanese patients with UC.MethodsA total of 50 patients with UC identified via the electronic clinical database of Changhua Christian Hospital, Taiwan, were retrospectively enrolled from January 2018 to July 2019. Results of iFOBT, FC level, and blood tests as well as Mayo scores were reviewed and analyzed. Colonic mucosa was evaluated using the endoscopic Mayo subscore.ResultsThe average age of the patients was 46 years, and 62% of the patients were men. Disease distribution was as follows: E1 (26%), E2 (40%), and E3 (34%). Complete mucosal healing (Mayo score = 0) was observed in 30% of patients. Endoscopic mucosal healing with a Mayo score of 0 or 1 was observed in 62% of the patients. Results of FC and iFOBT were compared among patients with and without mucosal healing. Predictive cutoff values were analyzed using receiver operating characteristics curves. iFOBT and FC had similar area under the curve for both complete mucosal healing (0.813 vs. 0.769, respectively, p = 0.5581) and endoscopic mucosal healing (0.906 vs. 0.812, respectively, p = 0.1207).ConclusionIn daily clinical practice, FC and iFOBT do not differ in terms of predictive values for mucosal healing among Taiwanese patients with UC. creator: Hsu-Heng Yen creator: Mei-Wen Chen creator: Yu-Yao Chang creator: Hsuan-Yuan Huang creator: Tsui-Chun Hsu creator: Yang-Yuan Chen uri: https://doi.org/10.7717/peerj.9537 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yen et al. title: Bioinformatics analysis and identification of circular RNAs promoting the osteogenic differentiation of human bone marrow mesenchymal stem cells on titanium treated by surface mechanical attrition link: https://peerj.com/articles/9292 last-modified: 2020-07-13 description: BackgroundTo analyze and identify the circular RNAs (circRNAs) involved in promoting the osteogenic differentiation of human bone mesenchymal stem cells (hBMSCs) on titanium by surface mechanical attrition treatment (SMAT).MethodsThe experimental material was SMAT titanium and the control material was annealed titanium. Cell Counting Kits-8 (CCK-8) was used to detect the proliferation of hBMSCs, and alkaline phosphatase (ALP) activity and alizarin red staining were used to detect the osteogenic differentiation of hBMSCs on the sample surfaces. The bioinformatics prediction software miwalk3.0 was used to construct competing endogenous RNA (ceRNA) networks by predicting circRNAs with osteogenesis-related messenger RNAs (mRNAs) and microRNAs (miRNAs). The circRNAs located at the key positions in the networks were selected and analyzed by quantitative real-time PCR (QRT-PCR).ResultsCompared with annealed titanium, SMAT titanium could promote the proliferation and osteogenic differentiation of hBMSCs. The total number of predicted circRNAs was 51. Among these, 30 circRNAs and 8 miRNAs constituted 6 ceRNA networks. Circ-LTBP2 was selected for verification. QRT-PCR results showed that the expression levels of hsa_circ_0032599, hsa_circ_0032600 and hsa_circ_0032601 were upregulated in the experimental group compared with those in the control group; the differential expression of hsa_circ_0032600 was the most obvious and statistically significant, with a fold change (FC) = 4.25 ± 1.60, p-values (p) < 0.05. creator: Shanshan Zhu creator: Yuhe Zhu creator: Zhenbo Wang creator: Chen Liang creator: Nanjue Cao creator: Ming Yan creator: Fei Gao creator: Jie Liu creator: Wei Wang uri: https://doi.org/10.7717/peerj.9292 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhu et al. title: High frequency direct shoot regeneration from Kazakh commercial potato cultivars link: https://peerj.com/articles/9447 last-modified: 2020-07-13 description: Potato (Solanum tuberosum L.) is the third most economically important crop in the world and has a high nutritional value. In this study, the in vitro culture response of four widely grown in Kazakhstan potato cultivars, Astanalyk, Monument Kunaev, Tokhtar, and Aksor, was investigated using stem and leaf explants. Published protocols were evaluated and optimized to develop a more efficient protocol for the regeneration of plants from local potato cultivars in tissue culture, which is a prerequisite to facilitate potato genome modification. The explants were cultured on solid Murashige and Skoog medium supplemented with different concentrations and combinations of zeatin, 6-benzylaminopurine (BAP), gibberellic acid (GA3), 1-naphthaleneacetic acid (NAA) and indole-3-acetic acid (IAA). The maximum regeneration was induced from the stem internodal explants. A significant effect of the explant source on direct regeneration was confirmed with statistical analysis. The number of shoots obtained from the internode was 10.0 from cv. Aksor followed by cvs. Tokhtar and Astanalyk. The medium DRM-VIII with 1 mg/l zeatin, 0.1 mg/l IAA and 7.0 mg/l GA3 was considered the best for direct shoot regeneration and multiple shoot formation from all cultivars. To conclude, we outline a protocol for direct plant regeneration from four potato cultivars. Our findings suggest commercial cultivars Astanalyk and Aksor are good candidates for developing the genome-edited plants through direct shoot regeneration. creator: Laura S. Abeuova creator: Balnur R. Kali creator: Aizhan O. Rakhimzhanova creator: Sara S. Bekkuzhina creator: Shuga A. Manabayeva uri: https://doi.org/10.7717/peerj.9447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abeuova et al. title: Plastome comparative genomics in maples resolves the infrageneric backbone relationships link: https://peerj.com/articles/9483 last-modified: 2020-07-13 description: Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples. creator: Fabiola Areces-Berazain creator: Yixi Wang creator: Damien D. Hinsinger creator: Joeri S. Strijk uri: https://doi.org/10.7717/peerj.9483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Areces-Berazain et al. title: Evolutionary history of a Scottish harbour seal population link: https://peerj.com/articles/9167 last-modified: 2020-07-10 description: Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area. creator: Natacha Nikolic creator: Paul Thompson creator: Mark de Bruyn creator: Matthias Macé creator: Claude Chevalet uri: https://doi.org/10.7717/peerj.9167 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nikolic et al. title: First report of begomoviruses infecting Cucumis sativus L. in North America and identification of a proposed new begomovirus species link: https://peerj.com/articles/9245 last-modified: 2020-07-10 description: BackgroundMembers of the Begomovirus genus are phytopathogens that infect dicotyledonous plants, producing economic losses in tropical and subtropical regions. To date, only seven species of begomoviruses (BGVs) infecting cucumber have been described. Most cucumber infections were reported in South Asia. In the Americas, begomoviral infections affecting cucumber are scarce; just one report of begomovirus has been described in South America. The presence of whitefly and typical symptoms of viral infections observed in a cucumber field in Colima, Mexico, suggested that plants in this field were affected by BGVs.MethodsTo identify the BGVs infecting cucumber, we performed a high-throughput sequencing and compared the assembled contigs against the GenBank nucleic acid sequence database. To confirm the presence of viruses in cucumber samples, we performed a PCR detection using specific oligonucleotides. We cloned and sequenced by Sanger method the complete genome of a potential new begomovirus. Begomovirus species demarcation was performed according to the International Committee on Taxonomy of Viruses. The evolutionary relationship of the new virus was inferred using phylogenetic and recombination analyses.ResultsWe identified five species of begomovirus infecting plants in a field. None of these have been previously reported infecting cucumber. One of the five species of viruses here reported is a new begomovirus species. Cucumber chlorotic leaf virus, the new species, is a bipartite begomovirus that has distinctive features of viruses belonging to the squash leaf curl virus clade.ConclusionsThe findings here described represent the first report of begomoviral infection affecting cucumber plants in North America. Previous to this report, only seven begomovirus species have been reported in the world, here we found five species infecting cucumber plants in a small sample suggesting that cucumber is vulnerable to BGVs. One of these viruses is a new species of begomovirus which is the first begomovirus originally isolated from the cucumber. The findings of this report could help to develop strategies to fight the begomoviral infections that affect cucumber crops. creator: Sarahi Sanchez-Chavez creator: Carlos Fernando Regla-Marquez creator: Zugey Elizabeth Cardenas-Conejo creator: Daniel Alejandro Garcia-Rodriguez creator: Sara Centeno-Leija creator: Hugo Serrano-Posada creator: Andromeda Liñan-Rico creator: Brenda Lizet Partida-Palacios creator: Yair Cardenas-Conejo uri: https://doi.org/10.7717/peerj.9245 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sanchez-Chavez et al. title: Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching link: https://peerj.com/articles/9347 last-modified: 2020-07-10 description: MicroRNAs (miRNAs) are important regulators that fine-tune diverse cellular activities. Cynomolgus macaques (Macaca fascicularis) are used extensively in biomedical and pharmaceutical research; however, substantially fewer miRNAs have been identified in this species than in humans. Consequently, we investigated conserved miRNA profiles in cynomolgus macaques by homology searching and small RNA sequencing. In total, 1,455 high-confidence miRNA gene loci were identified, 408 of which were also confirmed by RNA sequencing, including 73 new miRNA loci reported in cynomolgus macaques for the first time. Comparing miRNA expression with age, we found a positive correlation between sequence conservation and expression levels during miRNA evolution. Additionally, we found that the miRNA gene locations in cynomolgus macaque genome were very flexible. Most were embedded in intergenic spaces or introns and clustered together. Several miRNAs were found in certain gene locations, including 64 exon-resident miRNAs, six splice-site-overlapping miRNAs (SO-miRNAs), and two pairs of distinct mirror miRNAs. We also identified 78 miRNA clusters, 68 of which were conserved in the human genome, including 10 large miRNA clusters predicted to regulate diverse developmental and cellular processes in cynomolgus macaque. Thus, this study not only expands the number of identified miRNAs in cynomolgus macaques but also provides clues for future research on the differences in miRNA repertoire between macaques and humans. creator: Xia Huang creator: Shijia Li creator: Xiaoming Liu creator: Shuting Huang creator: Shuang Li creator: Min Zhuo uri: https://doi.org/10.7717/peerj.9347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Analysis of factors contributing to postoperative body weight change in patients with gastric cancer: based on generalized estimation equation link: https://peerj.com/articles/9390 last-modified: 2020-07-10 description: AimsThe study aimed to explore factors contributing to body weight change over time in gastric cancer patients after gastrectomy, in order to find risk factors to implement nutritional intervention beforehand.MethodsA cohort of gastric cancer patients who were treated with gastrectomy from January to March 2019 at a university affiliated hospital in Shanghai were consecutively identified in this study. Demographics, disease related information, nutrition knowledge, attitude, and practice score were collected before gastrectomy. In addition, body weight before surgery (T0), body weight at one month (T1), two months (T2), and three months (T3) after gastrectomy were recorded. Generalized estimation equation was used to describe body weight change and analyze factors contributing to body weight change after surgery.ResultsThere were 49 patients recruited in the study. Patient body weight decreased by 9.2% at T1 (Wald χ = 271.173, P <0.001), 11.0% at T2 (Wald χ2 = 277.267, P <0.001), and 11.4% at T3 compared to baseline at T0 (Wald χ = 284.076, P <0.001). The results of GEE for multivariable analysis showed that surgery type (Wald χ = 6.027, P = 0.014) and preoperative BMI (Wald χ = 12.662, P = 0.005) were contributing factors of body weight change. Compared with distal gastrectomy patients, total gastrectomy patients experienced greater body weight loss (β = 2.8%, P = 0.014). Compared with patients with BMI&λτ; 18.5 kg/m2, patients with BMI ≥ 25 kg/m2experienced greater body weight loss (β = 4.5% P = 0.026).ConclusionGastric cancer patients experienced significant weight loss during 3 months after gastrectomy. Total gastrectomy and BMI ≥ 25 kg/m2were risk factors to postoperative body weight loss for GC patients. The results suggested hinted that clinician should pay attention to postoperative nutrition status of patient undergoing total gastrectomy and obesity patients. creator: Qiuju Tian creator: Liyuan Qin creator: Weiyi Zhu creator: Shaojie Xiong creator: Beiwen Wu uri: https://doi.org/10.7717/peerj.9390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tian et al. title: Effect of sodium (S)-2-hydroxyglutarate in male, and succinic acid in female Wistar rats against renal ischemia-reperfusion injury, suggesting a role of the HIF-1 pathway link: https://peerj.com/articles/9438 last-modified: 2020-07-10 description: BackgroundIschemia–reperfusion (IR) injury is the main cause of delayed graft function in solid organ transplantation. Hypoxia-inducible factors (HIFs) control the expression of genes related to preconditioning against IR injury. During normoxia, HIF-α subunits are marked for degradation by the egg-laying defective nine homolog (EGLN) family of prolyl-4-hydroxylases. The inhibition of EGLN stabilizes HIFs and protects against IR injury. The aim of this study was to determine whether the EGLN inhibitors sodium (S)-2-hydroxyglutarate [(S)-2HG] and succinic acid (SA) have a nephroprotective effect against renal IR injury in Wistar rats.Methods(S)-2HG was synthesized in a 22.96% yield from commercially available L-glutamic acid in a two-step methodology (diazotization/alkaline hydrolysis), and its structure was confirmed by nuclear magnetic resonance and polarimetry. SA was acquired commercially. (S)-2HG and SA were independently evaluated in male and female Wistar rats respectively after renal IR injury. Rats were divided into the following groups: sham (SH), nontoxicity [(S)-2HG: 12.5 or 25 mg/kg; SA: 12.5, 25, or 50 mg/kg], IR, and compound+IR [(S)-2HG: 12.5 or 25 mg/kg; SA: 12.5, 25, or 50 mg/kg]; independent SH and IR groups were used for each assessed compound. Markers of kidney injury (BUN, creatinine, glucose, and uric acid) and liver function (ALT, AST, ALP, LDH, serum proteins, and albumin), proinflammatory cytokines (IL-1β, IL-6, and TNF-α), oxidative stress biomarkers (malondialdehyde and superoxide dismutase), and histological parameters (tubular necrosis, acidophilic casts, and vascular congestion) were assessed. Tissue HIF-1α was measured by ELISA and Western blot, and the expression of Hmox1 was assessed by RT-qPCR.Results(S)-2HG had a dose-dependent nephroprotective effect, as evidenced by a significant reduction in the changes in the BUN, creatinine, ALP, AST, and LDH levels compared with the IR group. Tissue HIF-1α was only increased in the IR group compared to SH; however, (S)-2HG caused a significant increase in the expression of Hmox1, suggesting an early accumulation of HIF-1α in the (S)-2HG-treated groups. There were no significant effects on the other biomarkers. SA did not show a nephroprotective effect; the only changes were a decrease in creatinine level at 12.5 mg/kg and increased IR injury at 50 mg/kg. There were no effects on the other biochemical, proinflammatory, or oxidative stress biomarkers.ConclusionNone of the compounds were hepatotoxic at the tested doses. (S)-2HG showed a dose-dependent nephroprotective effect at the evaluated doses, which involved an increase in the expression of Hmox1, suggesting stabilization of HIF-1α. SA did not show a nephroprotective effect but tended to increase IR injury when given at high doses. creator: Eduardo Cienfuegos-Pecina creator: Tannya R. Ibarra-Rivera creator: Alma L. Saucedo creator: Luis A. Ramírez-Martínez creator: Deanna Esquivel-Figueroa creator: Ixel Domínguez-Vázquez creator: Karina J. Alcántara-Solano creator: Diana P. Moreno-Peña creator: Gabriela Alarcon-Galvan creator: Diana Raquel Rodríguez-Rodríguez creator: Liliana Torres-González creator: Linda E. Muñoz-Espinosa creator: Edelmiro Pérez-Rodríguez creator: Paula Cordero-Pérez uri: https://doi.org/10.7717/peerj.9438 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cienfuegos-Pecina et al. title: Impact of homocysteine levels on clinical outcome in patients with acute ischemic stroke receiving intravenous thrombolysis therapy link: https://peerj.com/articles/9474 last-modified: 2020-07-10 description: BackgroundThe purpose of this study was to retrospectively assess the potential correlation between clinical outcomes and homocysteine (Hcy) levels in acute ischemic stroke (AIS) patients after recombinant tissue plasminogen activator (rtPA) treatment.MethodsAIS patients treated by rtPA were enrolled between September 2018 and March 2019 in the Stroke Center (Department of Neurology and Neurosurgery), Shanghai Tenth People’s Hospital, Tongji University School of Medicine. Demographics, baseline and clinical characteristics, and modified Rankin Scale (mRS) score after three months from the onset were retrospectively analyzed. Then we compared data about demographics, baseline and clinical characteristics between patients with favorable (mRS score 0–2) and unfavorable (mRS score 3–6) outcomes.ResultsAmong 141 patients, 36 patients had poor outcome, for an incidence of 25.53%. Univariate analysis showed that higher Hcy levels (OR = 1.07, 95% CI [1.02–1.12]), older age (OR = 1.06, 95% CI [1.02–1.10]), longer door to needle time (DNT) (OR = 1.03, 95% CI [1.01–1.05]), higher D-Dimer levels (OR = 1.33, 95% CI [1.03–1.71]), and higher National Institutes of Health Stroke Scale (NIHSS) score before treatment (OR = 1.21, 95% CI [1.08–1.35]) were each associated with poor outcome. Also, without internal carotid artery plaque (OR = 0.30, 95% CI [0.10–0.92]) showed a protective effect on patients’ clinical outcome. Patients with higher levels of Hcy decline also showed an increased risk of poor outcome for AIS patients obtaining rtPA treatment (Non-adjusted: OR = 1.07, 95% CI [1.02–1.12]; Adjust model I adjusts for demographics (age, male): OR = 1.06, 95% CI [1.02–1.11]; Adjust model II adjusts for hospital care factors (onset to treatment, DNT): OR = 1.08, 95% CI [1.03–1.13]; Adjust model III adjusts for health and stroke factors (INR, D-Dimer, HGB, NIHSS score before treatment, smoking, drinking, hypertension, diabetes, coronary disease, hyperlipidemia, previous stroke, atrial fibrillation, hemorrhagic transformation, internal carotid artery plaque): OR = 1.06, 95% CI [1.02–1.11]). The results are very stable in all three models constructed.ConclusionThe results of this study indicate that increased Hcy level independently predicts unfavorable outcome in AIS patients accepting thrombolytic therapy. However, the contribution of Hcy to the outcome, although significant, is relatively small and perhaps not clinically significant when all the other confounders are considered. creator: Lei Li creator: Xiaoye Ma creator: Li Zeng creator: Sajan Pandey creator: Ronghao Wan creator: Rui Shen creator: Quanbin Zhang uri: https://doi.org/10.7717/peerj.9474 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Cellular heterogeneity map of diverse immune and stromal phenotypes within breast tumor microenvironment link: https://peerj.com/articles/9478 last-modified: 2020-07-10 description: BackgroundCellular heterogeneity within the tumor microenvironment is essential to tumorigenesis and tumor development. A high-resolution global view of the tumor-infiltrating immune and stromal cells in breast tumors is needed.MethodsxCell was used to create a cellular heterogeneity map of 64 cell types in 1,092 breast tumor and adjacent normal tissues. xCell digitally dissects tissue cellular heterogeneity based on gene expression. Integrated statistical analyses were then performed.ResultsThere were noticeable differences between the cell fractions in tumor tissues and normal tissues. Tumors displayed higher proportions of immune cells, including CD4+ Tem, CD8+ naïve T cells, and CD8+ Tcm compared with normal tissues. Immune inhibitory receptors (PD1, CTLA4, LAG3 and TIM3) were co-expressed on certain subtypes of T cells in breast tumors, and PD1 and CTLA4 were both positively correlated with CD8+ Tcm and CD8+ T cells. 28 cell types were significantly associated with overall survival in univariate analysis. CD4+ Tem, CD8+ Tcm, CD8+ T-cells, CD8+ naive T-cells, and B cells were positive prognostic factors but CD4+ naive T-cells were negative prognostic factors for breast cancer patients. TDRD6 and TTK are promising T cell and B cell targets for tumor vaccines. Endothelial cells and fibroblasts were significantly less prevalent in tumor tissues; astrocytes and mesangial cells were negatively correlated with the T stage. Mesangial cells and keratinocytes were found to be favorable prognostic factors and myocytes were negative prognostic factors. Five cell types were found to be independent prognostic factors and we used these to create a reliable prognostic model for breast cancer patients. Cellular heterogeneity was discovered among different breast cancer subtypes by Her2, ER, and PR status. Tri-negative patients had the highest fraction of immune cells while luminal type patients had the lowest. The various cells may have diverse or opposing roles in the prognosis of breast cancer patients.ConclusionsWe created a uniquecellular map for the diverse heterogeneity of immune and stromal phenotypes within the breast tumor microenvironment. This map may lead to potential therapeutic targets and biomarkers with prognostic utility. creator: Yuan Li creator: Zuhua Chen creator: Long Wu creator: Junjie Ye creator: Weiping Tao uri: https://doi.org/10.7717/peerj.9478 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Association between individual retinal layer thickness and visual acuity in patients with epiretinal membrane: a pilot study link: https://peerj.com/articles/9481 last-modified: 2020-07-10 description: PurposeWe investigated the correlation between visual acuity (VA) and individual retinal layer thickness in the foveal, parafoveal, and perifoveal regions of patients with an idiopathic epiretinal membrane (ERM).MethodsOne hundred and five subjects presenting with unilateral idiopathic ERM were included in this study. We segmented each patient’s optical coherence tomography (OCT) image into seven layers and calculated the mean layer thickness in the foveal, parafoveal, and perifoveal regions using the Iowa Reference Algorithm. In 105 patients with ERM, we detected correlations between their macular regions’ individual retinal layer thickness and their best corrected VA. Thirty-one of the 105 patients with ERM underwent vitrectomy and completed six months of follow-up. We then compared the 31 surgical patients’ preoperative and postoperative individual retinal layer thickness in each macular region. Additionally, the association between preoperative individual retinal layer thickness in each macular region and VA six months post-surgery in patients with ≥ two Snellen lines of visual improvement was determined.ResultsMultiple linear regression analysis showed that the inner nuclear layer (INL) thickness in the foveal, parafoveal, and perifoveal region were all associated with VA in the 105 patients (R2 = 0.344, P < 0.001; R2 = 0.427, P < 0.001; and R2 = 0.340, P < 0.001, respectively). Thirty-one surgical patients 6 months post-surgery showed significantly decreased thicknesses (P ≤ 0.012) of the foveal INL, inner plexiform layer (IPL), and outer nuclear layer (ONL); the parafoveal retina nerve fiber layer (RNFL), IPL, INL, and ONL; and the perifoveal RNFL, IPL, INL, ganglion cell layer (GCL), outer plexiform layer (OPL), and photoreceptor layer (PRL). We found a weak correlation between postoperative VA and preoperative foveal and perifoveal RNFL thickness (r = 0.404 and r = 0.359, respectively), and a moderate correlation between postoperative VA and preoperative foveal and parafoveal INL thickness (r = 0.529 and r = 0.583, respectively) in the 31 surgical patients (P ≤ 0.047). The preoperative INL thickness in the foveal, parafoveal, and perifoveal regions showed a moderate to strong correlation (r = 0.507, 0.644, and 0.548, respectively), with postoperative VA in patients with ≥ 2 lines of visual improvement (P ≤ 0.038).ConclusionWe detected a correlation between retinal damage and VA in the parafoveal, perifoveal, and foveal regions. Our results suggest that INL thickness in all macular regions may be a prognostic factor for postoperative VA in ERM patients. creator: Jing Zou creator: Wei Tan creator: Wenlong Huang creator: Kangcheng Liu creator: Fangling Li creator: Huizhuo Xu uri: https://doi.org/10.7717/peerj.9481 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zou et al. title: Methylobacterium, a major component of the culturable bacterial endophyte community of wild Brassica seed link: https://peerj.com/articles/9514 last-modified: 2020-07-10 description: BackgroundPlants are commonly colonized by a wide diversity of microbial species and the relationships created can range from mutualistic through to parasitic. Microorganisms that typically form symptomless associations with internal plant tissues are termed endophytes. Endophytes associate with most plant species found in natural and managed ecosystems. They are extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Plant domestication has reduced endophyte diversity and therefore the wild relatives of many crop species remain untapped reservoirs of beneficial microbes. Brassica species display immense diversity and consequently provide the greatest assortment of products used by humans from a single plant genus important for agriculture, horticulture, bioremediation, medicine, soil conditioners, composting crops, and in the production of edible and industrial oils. Many endophytes are horizontally transmitted, but some can colonize the plant’s reproductive tissues, and this gives these symbionts an efficient mechanism of propagation via plant seed (termed vertical transmission).MethodsThis study surveyed 83 wild and landrace Brassica accessions composed of 14 different species with a worldwide distribution for seed-originating bacterial endophytes. Seed was stringently disinfected, sown within sterile tissue culture pots within a sterile environment and incubated. After approximately 1-month, direct isolation techniques were used to recover bacterial endophytes from roots and shoots of symptomless plants. Bacteria were identified based on the PCR amplification of partial 16S rDNA gene sequences and annotated using the BLASTn program against the NCBI rRNA database. A diversity index was used as a quantitative measure to reflect how many different bacterial species there were in the seed-originating microbial community of the Brassica accessions sampled.ResultsBacterial endophytes were recovered from the majority of the Brassica accessions screened. 16S rDNA gene sequencing identified 19 different bacterial species belonging to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria with the most frequently isolated species being Methylobacterium fujisawaense, Stenotrophomonas rhizophila and Pseudomonas lactis. Methylobacterium was the dominant genus composing 56% of the culturable isolated bacterial community and was common in 77% of accessions possessing culturable bacterial endophytes. Two selected isolates of Methylobacterium significantly promoted plant growth when inoculated into a cultivar of oilseed rape and inhibited the growth of the pathogen Leptosphaeria maculans in dual culture. This is the first report that investigates the seed-originating endophytic microorganisms of wild Brassica species and highlights the Brassica microbiome as a resource for plant growth promoting bacteria and biological control agents. creator: Davood Roodi creator: James P. Millner creator: Craig McGill creator: Richard D. Johnson creator: Ruy Jauregui creator: Stuart D. Card uri: https://doi.org/10.7717/peerj.9514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Roodi et al. title: In or out: Response slowing across housing conditions as a measure of affect in three Western lowland gorillas (Gorilla gorilla gorilla) link: https://peerj.com/articles/9525 last-modified: 2020-07-10 description: BackgroundIndividuals experiencing negative affect have shown response slowing, a longer latency to respond in relation to baseline, when presented with aversive stimuli. We assessed response slowing in three male gorillas housed in a bachelor group as a function of daytime and nighttime housing arrangements.MethodsIn both experiments, three gorillas were rewarded for touching a single image (baseline, non-threatening gorilla or threatening gorilla) on a touchscreen. In Experiment One, they completed 48 50-trial sessions across combinations of three nested daytime and three nighttime conditions. In Experiment Two, they completed eight 50-trial sessions with novel stimuli across two daytime conditions, which were nested within two nighttime conditions. Housing conditions represented different amounts of space and degree of choice. We predicted that the gorillas would show response slowing to threatening stimuli when space and choice were restricted.ResultsWe did not observe response slowing in Experiment One, although daytime and nighttime conditions interacted to predict response latencies. The gorillas responded more slowly when they had access to indoors and outdoors overnight compared to when they were in their stalls or together in an indoor habitat, but only if they had been given access to both indoors and outdoors or locked in the indoor habitat the day before. In Experiment Two, the gorillas did show response slowing to threatening stimuli, but this pattern did not interact with housing conditions. Our results, although limited by a small sample, are somewhat consistent with those of a previous study that did not find significant response slowing for apes as a function of aversive testing conditions, although the procedure has been effective in identifying dysregulated fear (high fear in low threat conditions) in macaques. The utility of this paradigm for testing affect in apes awaits further evaluation. creator: Molly McGuire creator: Jennifer M. Vonk uri: https://doi.org/10.7717/peerj.9525 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 McGuire and Vonk title: Arthropod IGF, relaxin and gonadulin, putative orthologs of Drosophila insulin-like peptides 6, 7 and 8, likely originated from an ancient gene triplication link: https://peerj.com/articles/9534 last-modified: 2020-07-10 description: BackgroundInsects have several genes coding for insulin-like peptides and they have been particularly well studied in Drosophila. Some of these hormones function as growth hormones and are produced by the fat body and the brain. These act through a typical insulin receptor tyrosine kinase. Two other Drosophila insulin-like hormones are either known or suspected to act through a G-protein coupled receptor. Although insulin-related peptides are known from other insect species, Drosophila insulin-like peptide 8, one that uses a G-protein coupled receptor, has so far only been identified from Drosophila and other flies. However, its receptor is widespread within arthropods and hence it should have orthologs. Such putative orthologs were recently identified in decapods and have been called gonadulins.MethodologyIn an effort to identify gonadulins in other arthropods public genome assemblies and short-read archives from insects and other arthropods were explored for the presence of genes and transcripts coding insulin-like peptides and their putative receptors.ResultsGonadulins were detected in a number of arthropods. In those species for which transcriptome data from the gonads is available insect gonadulin genes are expressed in the ovaries and at least in some species also in the testes. In some insects differences in gonadulin expression in the ovary between actively reproducing and non-reproducing females differs more than 100-fold. Putative orthologs of Drosophila ilp 6 were also identified. In several non-Dipteran insects these peptides have C-terminally extensions that are alternatively spliced. The predicted peptides have been called arthropod insulin-like growth factors. In cockroaches, termites and stick insects genes coding for the arthropod insulin-like growth factors, gonadulin and relaxin, a third insulin-like peptide, are encoded by genes that are next to one another suggesting that they are the result of a local gene triplication. Such a close chromosomal association was also found for the arthropod insulin-like growth factor and gonadulin genes in spiders. Phylogenetic tree analysis of the typical insulin receptor tyrosine kinases from insects, decapods and chelicerates shows that the insulin signaling pathway evolved differently in these three groups. The G-protein coupled receptors that are related to the Drosophila ilp 8 receptor similarly show significant differences between those groups.ConclusionA local gene triplication in an early ancestor likely yielded three genes coding gonadulin, arthropod insulin-like growth factor and relaxin. Orthologs of these genes are now commonly present in arthropods and almost certainly include the Drosophila insulin-like peptides 6, 7 and 8. creator: Jan A. Veenstra uri: https://doi.org/10.7717/peerj.9534 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Veenstra title: From the index case to global spread: the global mobility based modelling of the COVID-19 pandemic implies higher infection rate and lower detection ratio than current estimates link: https://peerj.com/articles/9548 last-modified: 2020-07-10 description: BackgroundSince the outbreak of the COVID-19 pandemic, multiple efforts of modelling of the geo-temporal transmissibility of the virus have been undertaken, but none describes the pandemic spread at the global level. The aim of this research is to provide a high-resolution global model of the pandemic that overcomes the problem of biased country-level data on the number of infected cases. To achieve this we propose a novel SIR-type metapopulation transmission model and a set of analytically derived model parameters. We used them to perform a simulation of the disease spread with help of the Global Epidemic and Mobility (GLEAM) framework embedding actual population densities, commute patterns and long-range travel networks. The simulation starts on 17 November 2019 with the index case (presymptomatic, yet infectious) in Wuhan, China, and results in an accurate prediction of the number of diagnosed cases after 154 days in multiple countries across five continents. In addition, the model outcome shows high compliance with the results of a random screening test conducted on pregnant women in the New York area.MethodsWe have built a modified SIR metapopulation transmission model and parameterized it analytically either by setting the values of the parameters based on the literature, or by assuming their plausible values. We compared our results with the number of diagnosed cases in twenty selected countries, ones which provide reliable statistics but differ substantially in terms of strength and speed of undertaken Non-Drug Interventions. The obtained 95% confidence intervals for the predictions are in agreement with the empirical data.ResultsThe parameters that successfully model the pandemic are: the basic reproduction number R0, 4.4; a latent non-infectious period of 1.1. days followed by 4.6 days of the presymptomatic infectious period; the probability of developing severe symptoms, 0.01; the probability of being diagnosed when presenting severe symptoms of 0.6; the probability of diagnosis for cases with mild symptoms or asymptomatic, 0.001.DiscussionParameters that successfully reproduce the observed number of cases indicate that both R0 and the prevalence of the virus might be underestimated. This is in concordance with the newest research on undocumented COVID-19 cases. Consequently, the actual mortality rate is putatively lower than estimated. Confirmation of the pandemic characteristic by further refinement of the model and screening tests is crucial for developing an effective strategy for the global epidemiological crisis. creator: Marian Siwiak creator: Pawel Szczesny creator: Marlena Siwiak uri: https://doi.org/10.7717/peerj.9548 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Siwiak et al. title: Identifying hub genes of papillary thyroid carcinoma in the TCGA and GEO database using bioinformatics analysis link: https://peerj.com/articles/9120 last-modified: 2020-07-09 description: BackgroundThyroid carcinoma (THCA) is a common endocrine malignant tumor. Papillary carcinoma with low degree of malignancy and good prognosis is the most common. It can occur at any age, but it is more common in young adults. Although the mortality rate is decreased due to early diagnosis, the survival rate varies depending on the type of tumor. Therefore, the purpose of this study is to identify hub biomarkers and novel therapeutic targets for THCA.MethodsThe GSE3467, GSE3678, GSE33630 and GSE53157 were obtained from the GEO database, including 100 thyroid tumors and 64 normal tissues to obtain the intersection of differentially expressed genes, and a protein-protein interaction network was constructed to obtain the HUB gene. The corresponding overall survival information from The Cancer Genome Atlas Project-THCA was then included in this research. The signature mechanism was studied by analyzing the gene ontology and the Kyoto Encyclopedia of Genes and Genome database.ResultsIn this research, we identified eight candidate genes (FN1, CCND1, CDH2, CXCL12, MET, IRS1, DCN and FMOD) from the network. Also, expression verification and survival analysis of these candidate genes based on the TCGA database indicate the robustness of the above results. Finally, our hospital samples validated the expression levels of these genes.ConclusionThe research identified eight mRNA (four up–regulated and four down–regulated) which serve as signatures and could be a potential prognostic marker of THCA. creator: Ying Wan creator: Xiaolian Zhang creator: Huilin Leng creator: Weihua Yin creator: Wenxing Zeng creator: Congling Zhang uri: https://doi.org/10.7717/peerj.9120 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wan et al. title: Environmentally relevant levels of four psychoactive compounds vary in their effects on freshwater fish condition: a brain concentration evidence approach link: https://peerj.com/articles/9356 last-modified: 2020-07-09 description: BackgroundThe aquatic environment has been contaminated with various anthropogenic pollutants, including psychoactive compounds that may alter the physiology and behavior of free-living organisms. The present study focused on the condition and related mortality of the juvenile chub (Squalius cephalus). The aim of the study was to test whether the adverse effects of the antidepressants sertraline and citalopram, the analgesic tramadol and the illicit drug methamphetamine, on fish condition exist under environmentally relevant concentrations and whether these effects persist after a depuration period. Innovative analyses of the fish brain concentrations of these compounds were performed with the aim to show relationship between compound brain tissue concentration and fish condition.MethodsThe laboratory experiment consisted of 42 days of exposure and a subsequent 14-day depuration period with regular monitoring of the condition and mortality of exposed and control fish. Identical methodology, including individual brain concentration analyses for the tested compounds, was applied for all substances. Additional study on feeding under sertraline exposure was also conducted. The feeding was measured from the 28th day of the exposure, three times in a week, by observation of food intake during 15 minutes in social environment.ResultsThe effects of particular psychoactive compounds on chub condition varied. While sertraline induced a lower condition and increased mortality, the effects of methamphetamine were inverse, and tramadol and citalopram had no significant effect at all. Individual brain concentrations of the tested compounds showed that the effects of sertraline and methamphetamine on fish condition were increased with brain concentration increases. Additionally, the food intake was reduced in case of sertraline. In contrast, there was no relationship between tramadol and citalopram brain tissue concentration and fish condition, suggesting that the concentration-dependent effect is strongly compound-specific. Methamphetamine was the only compound with a persistent effect after the depuration period. Our results demonstrate the suitability of the brain concentration evidence approach and suggest that changes in fish condition and other related parameters can be expected in freshwater ecosystems polluted with specific psychoactive compounds. creator: Pavla Hubená creator: Pavel Horký creator: Roman Grabic creator: Kateřina Grabicová creator: Ondřej Slavík creator: Tomáš Randák uri: https://doi.org/10.7717/peerj.9356 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hubená et al. title: Access to scientific literature by the conservation community link: https://peerj.com/articles/9404 last-modified: 2020-07-09 description: Access to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ∼97% need to use the scientific literature in order to support their IUCN-related conservation work, with ∼50% needing to do so at least once per week. The crux of the survey revolved around the question, “How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?” and revealed that roughly half (49%) of the respondents find it not easy or not at all easy to access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and sex (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ∼50% in Asia and Latin America, and ∼40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent’s IUCN-related work were Conservation Biology, Biological Conservation, Nature, and Science. The majority prefer to read journal articles on screen but books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide. creator: Daisy Larios creator: Thomas M. Brooks creator: Nicholas B.W. Macfarlane creator: Sugoto Roy uri: https://doi.org/10.7717/peerj.9404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Larios et al. title: Molecular phylogenetics and evolutionary history of the endemic land snail genus Everettia in northern Borneo link: https://peerj.com/articles/9416 last-modified: 2020-07-09 description: Borneo has gone through dramatic changes in geology and topography from the early Eocene until the early Pliocene and experienced climatic cycling during the Pleistocene. However, how these changes have shaped the present-day patterns of high diversity and complex distribution are still poorly understood. In this study, we use integrative approaches by estimating phylogenetic relationships, divergence time, and current and past niche suitability for the Bornean endemic land snail genus Everettia to provide additional insight into the evolutionary history of this genus in northern Borneo in the light of the geological vicariance events and climatic fluctuations in the Pleistocene. Our results show that northern Borneo Everettia species belong to two deeply divergent lineages: one contains the species that inhabit high elevation at the central mountain range, while the other contains lowland species. Species diversification in these lineages has taken place before the Pliocene. Climate changes during the Pleistocene did not play a significant role in species diversification but could have shaped contemporary species distribution patterns. Our results also show that the species-rich highland habitats have acted as interglacial refugia for highland species. This study of a relatively sedentary invertebrate supports and enhances the growing understanding of the evolutionary history of Borneo. Species diversification in Everettia is caused by geological vicariance events between the early Miocene and the Pliocene, and the distribution patterns were subsequently determined by climatic fluctuations in the Pleistocene. creator: Thor-Seng Liew creator: Mohammad Effendi Marzuki creator: Menno Schilthuizen creator: Yansen Chen creator: Jaap J. Vermeulen creator: Jayasilan Mohd-Azlan uri: https://doi.org/10.7717/peerj.9416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Liew et al. title: A collection of hexactinellids (Porifera) from the deep South Atlantic and North Pacific: new genus, new species and new records link: https://peerj.com/articles/9431 last-modified: 2020-07-09 description: This article describes or redescribes four hexactinellid sponges, namely Poliopogon amadou, Euplectella sanctipauli sp. nov., Bolosoma perezi sp. nov. and Advhena magnifica gen. et sp. nov. P. amadou, E. sanctipauli sp. nov. and B. perezi sp. nov. represent new findings for the South Atlantic deep-sea fauna, including the first record of Bolosoma for this ocean. Advhena magnifica gen. et sp. nov., on the other hand, was collected by NOAA oceanographic expeditions in the North Pacific (Pigafetta Guyot). creator: Cristiana Castello-Branco creator: Allen G. Collins creator: Eduardo Hajdu uri: https://doi.org/10.7717/peerj.9431 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Castello-Branco et al. title: Sharing for science: high-resolution trophic interactions revealed rapidly by social media link: https://peerj.com/articles/9485 last-modified: 2020-07-09 description: Discrete, ephemeral natural phenomena with low spatial or temporal predictability are incredibly challenging to study systematically. In ecology, species interactions, which constitute the functional backbone of ecological communities, can be notoriously difficult to characterise especially when taxa are inconspicuous and the interactions of interest (e.g., trophic events) occur infrequently, rapidly, or variably in space and time. Overcoming such issues has historically required significant time and resource investment to collect sufficient data, precluding the answering of many ecological and evolutionary questions. Here, we show the utility of social media for rapidly collecting observations of ephemeral ecological phenomena with low spatial and temporal predictability by using a Facebook group dedicated to collecting predation events involving reptiles and amphibians in sub-Saharan Africa. We collected over 1900 independent feeding observations using Facebook from 2015 to 2019 involving 83 families of predators and 129 families of prey. Feeding events by snakes were particularly well-represented with close to 1,100 feeding observations recorded. Relative to an extensive literature review spanning 226 sources and 138 years, we found that social media has provided snake dietary records faster than ever before in history with prey being identified to a finer taxonomic resolution and showing only modest concordance with the literature due to the number of novel interactions that were detected. Finally, we demonstrate that social media can outperform other citizen science image-based approaches (iNaturalist and Google Images) highlighting the versatility of social media and its ability to function as a citizen science platform. creator: Robin A. Maritz creator: Bryan Maritz uri: https://doi.org/10.7717/peerj.9485 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Maritz and Maritz title: Prognostic value of complementary biomarkers of neurodegeneration in a mixed memory clinic cohort link: https://peerj.com/articles/9498 last-modified: 2020-07-09 description: BackgroundBiomarkers of neurodegeneration, e.g. MRI brain atrophy and [18F]FDG-PET hypometabolism, are often evaluated in patients suspected of neurodegenerative disease.ObjectiveOur primary objective was to investigate prognostic properties of atrophy and hypometabolism.MethodsFrom March 2015-June 2016, 149 patients referred to a university hospital memory clinic were included. The primary outcome was progression/stable disease course as assessed by a clinician at 12 months follow-up. Intracohort defined z-scores of baseline MRI automatic quantified volume and [18F]FDG-PET standardized uptake value ratios were calculated for all unilaterally defined brain lobes and dichotomized as pronounced atrophy (+A)/ pronounced hypometabolism (+H) at z-score <0. A logistic regression model with progression status as the outcome was carried out with number of lobes with the patterns +A/-H, -A/+H, +A/+H respectively as predictors. The model was mutually adjusted along with adjustment for age and sex. A sensitivity analysis with a z-score dichotomization at −0.1 and −0.5 and dichotomization regarding number of lobes affected at one and three lobes was done.ResultsMedian follow-up time was 420 days [IQR: 387-461 days] and 50 patients progressed. Patients with two or more lobes affected by the pattern +A/+H compared to patients with 0–1 lobes affected had a statistically significant increased risk of progression (odds ratio, 95 % confidence interval: 4.33, 1.90–9.86) in a multivariable model. The model was partially robust to the applied sensitivity analysis.ConclusionCombined atrophy and hypometabolism as assessed by MRI and [18F]FDG-PET in patients under suspicion of neurodegenerative disease predicts progression over 1 year. creator: Mathias Holsey Gramkow creator: Le Gjerum creator: Juha Koikkalainen creator: Jyrki Lötjönen creator: Ian Law creator: Steen Gregers Hasselbalch creator: Gunhild Waldemar creator: Kristian Steen Frederiksen uri: https://doi.org/10.7717/peerj.9498 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gramkow et al. title: Very few sites can reshape the inferred phylogenetic tree link: https://peerj.com/articles/8865 last-modified: 2020-07-08 description: The history of animal evolution, and the relative placement of extant animal phyla in this history is, in principle, testable from phylogenies derived from molecular sequence data. Though datasets have increased in size and quality in the past years, the contribution of individual genes (and ultimately amino acid sites) to the final phylogeny is unequal across genes. Here we demonstrate that removing a small fraction of sites strongly favoring one topology can produce a highly-supported tree of an alternate topology. We explore this approach using a dataset for animal phylogeny, and create a highly-supported tree with a monophyletic group of sponges and ctenophores, a topology not usually recovered. Because of the high sensitivity of such an analysis to gene selection, and because most gene sets are neither standardized nor representative of the entire genome, researchers should be diligent about making intermediate analyses available with their phylogenetic studies. Effort is needed to ensure these datasets are maximally informative, by ensuring all genes are systematically sampled across relevant species. From there, it could be determined whether any gene or gene sets introduce bias, and then deal with those biases appropriately. creator: Warren R. Francis creator: Donald E. Canfield uri: https://doi.org/10.7717/peerj.8865 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Francis and Canfield title: Effect of predation risk and ectoparasitic louse flies on physiological stress condition of the red-tailed tropicbird (Phaethon rubricauda) from Rapa Nui and Salas & Gómez islands link: https://peerj.com/articles/9088 last-modified: 2020-07-08 description: BackgroundIntroduced predators at seabird colonies and parasites may have lethal and/or sub-lethal consequences for bird populations. We assessed the potential sub-lethal negative effects of these stressors in a native seabird listed as vulnerable in its south-eastern pacific distribution. This study was conducted in two red-tailed tropicbird (Phaethon rubricauda) colonies, one located in Rapa Nui Island, which is threatened by the presence of introduced predators, and the other located in Salas & Gómez Island, which has no introduced predators, but birds are infested by ectoparasitic louse flies.MethodsThe effects on physiological stress traits of both, predation risk on different nest types (protected and exposed) on Rapa Nui, and different levels of louse flies’ parasitic loads on Salas & Gómez were studied. Three variables were analyzed: the heterophil/lymphocyte (H/L) ratio, the transcriptional levels of mRNA HSP70 in blood, and the body condition. These stress indicators and leukocyte counts were compared between colonies.ResultsNo significant differences were found in any stress indicator between different nest types within Rapa Nui, showing that the effect of predator’s presence was the same for adults nesting in both, protected and exposed nests. No significant correlation was found between louse flies’ parasitic loads and any stress indicators in the birds of Salas & Gómez. Also, there was no difference in any stress indicator between islands. However, a significant opposite trend between islands was found in the eosinophil, lymphocyte, and monocyte counts when related to body condition.ConclusionsWe found a lack of significant differentiation in all the stress level indicators assessed within and between islands. The presence of louse flies in Salas & Gómez vs. the absence of this parasite at Rapa Nui may be the cause for the significant difference in the trend of eosinophil, lymphocyte and monocyte counts between the islands. However, further studies are necessary to elucidate the reason for this difference and to better investigate the lethal effects of introduced predators on the Rapa Nui colony to evaluate appropriate conservation measures for this native seabird. creator: Nicolas Luna creator: Andrea I. Varela creator: Guillermo Luna-Jorquera creator: Katherina Brokordt uri: https://doi.org/10.7717/peerj.9088 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Luna et al. title: Low frequencies in the display vocalization of the Western Capercaillie (Tetrao urogallus) link: https://peerj.com/articles/9189 last-modified: 2020-07-08 description: Only a few bird species are known to produce low-frequency vocalizations. We analyzed the display vocalizations of Western Capercaillie males kept in breeding centers and identified harmonically structured signals with a fundamental frequency of 28.7 ± 1.2 Hz (25.6–31.6 Hz). These low-frequency components temporally overlap with the Whetting phase (96% of its duration) and they significantly contribute to the distinct vocal expression between individuals. The resulting model of discrimination analysis classified 67.6% vocalizations (63%, cross-validated result) correctly to the specific individual in comparison to the probability by chance of 12.5%. We discuss a possible function of low-frequency components that remains unclear. The occurrence of such low frequencies is surprising as this grouse is substantially smaller than cassowaries (Southern cassowary Casuarius casuarius and Dwarf cassowary Casuarius bennetti) , the species that produces similarly low frequencies. Because these low frequency components temporarily overlap with the Whetting phase, they are hardly audible from a distance larger than several meters. creator: Vlastimil Hart creator: Richard Policht creator: Vojtěch Jandák creator: Marek Brothánek creator: Hynek Burda uri: https://doi.org/10.7717/peerj.9189 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hart et al. title: ?Amphictis (Carnivora, Ailuridae) from the Belgrade Formation of North Carolina, USA link: https://peerj.com/articles/9284 last-modified: 2020-07-08 description: Miocene terrestrial mammals are poorly known from the Atlantic Coastal Plain. Fossils of the Order Carnivora from this time and region are especially rare. We describe a carnivoran mandible with a p4 from the late Oligocene or early early Miocene Belgrade Formation in Jones County, North Carolina. Comparisons are made with carnivoran jaws with similar premolar and molar lengths from the late Oligocene and Miocene of North America and Eurasia. These indicate that the North Carolina jaw is assignable to the Ailuridae, a family whose only living member is the red panda. The jaw is tentatively referred to Amphictis, a genus known elsewhere from the late Oligocene and early Miocene of Europe and the early Miocene (Hemingfordian) of North America.The North Carolina mandible compares best with the late Oligocene (MP 28) Amphictis ambiguus from Pech du Fraysse, France, the oldest known member of the Family Ailuridae, and with the early Miocene (MN 1–MN 2a) A. schlosseri from southwestern Germany. This identification is compatible with a late late Arikareean (Ar4, early Miocene, MN 2-3 equivalent) age assignment for the other terrestrial mammals of the Belgrade Formation. creator: Jon Baskin creator: Edwin Dickinson creator: John DuBois creator: Henry Galiano creator: Adam Hartstone-Rose uri: https://doi.org/10.7717/peerj.9284 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Baskin et al. title: The metabolic profile of Asinara (albino) and Sardo donkeys (pigmented) (Equus asinus L., 1758) points to unequivocal breed assignment of individuals link: https://peerj.com/articles/9297 last-modified: 2020-07-08 description: This study pointed to explore if variations in circulating levels of metabolites in the blood stream of no. 25 feral donkeys occur in view of the different coat color between specimens of Asinara (albino, no. 8) vs. Sardo (dun-grey, no. 17) breed. All individuals involved in this investigation are living in the nature, at Mediterranean latitudes and roam in the same areas all over the National Park of Capo Caccia, where they feed on spontaneous vegetation sources. The study was conducted during the positive photoperiod of the boreal hemisphere (peak in the month of June, 2019) to maximize the effect of exposure to the natural sun radiation and thus elicit the coping ability of albino (Asinara) in comparison with pigmented donkeys (Sardo). The biochemical profile of all donkeys was used in a Discriminant Analysis (DA) to explore if circulating levels of metabolites could point to metabolic markers for breed assignment of individuals following a canonical discriminant analysis (CANDISC). The biochemical investigation included also the determination of the circulating Vitamin E (alpha tocopherol, α-TOH), as an essential biologically active compound involved in antioxidant mechanisms, and its respective status (circulating α-TOH to total triglycerides and total cholesterol ratio). In the CANDISC, the distance between the two breeds was not significant. However, it pointed to different metabolites (UREA, total protein, total triglycerides, Zn) capable of describing biochemical patterns on each respective breed (Asinara vs. Sardo). The multivariate analysis DA carried out using 22 metabolites correctly assigned individuals to the two breeds in the 100% of cases. In view of such metabolic background, circulating α-TOH found in the bloodstream of Asinara vs. Sardo donkeys under free grazing conditions turned out to reach similar values (2.114 vs. 1.872 µg/ml, respectively, p = 0.676). It is worth noting that significant differences were observed as to circulating lactate dehydrogenase (LDH, p = 0.022) levels, in association with increased creatine phosphokinase (CPK, p = 0.076), both above the upper limit of the physiological range reported in other donkey breeds, and found in the totality of Asinara (albino) donkeys solely, still apparently clinically healthy. creator: Maria Grazia Cappai creator: Corrado Dimauro creator: Giovanni Paolo Biggio creator: Raffaele Cherchi creator: Francesca Accioni creator: Flavia Pudda creator: Gianpiero Boatto creator: Walter Pinna uri: https://doi.org/10.7717/peerj.9297 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cappai et al. title: pulseTD: RNA life cycle dynamics analysis based on pulse model of 4sU-seq time course sequencing data link: https://peerj.com/articles/9371 last-modified: 2020-07-08 description: The life cycle of intracellular RNA mainly involves transcriptional production, splicing maturation and degradation processes. Their dynamic changes are termed as RNA life cycle dynamics (RLCD). It is still challenging for the accurate and robust identification of RLCD under unknow the functional form of RLCD. By using the pulse model, we developed an R package named pulseTD to identify RLCD by integrating 4sU-seq and RNA-seq data, and it provides flexible functions to capture continuous changes in RCLD rates. More importantly, it also can predict the trend of RNA transcription and expression changes in future time points. The pulseTD shows better accuracy and robustness than some other methods, and it is available on the GitHub repository (https://github.com/bioWzz/pulseTD_0.2.0). creator: Xin Wang creator: Siyu He creator: Jian Li creator: Jun Wang creator: Chengyi Wang creator: Mingwei Wang creator: Danni He creator: Xingfeng Lv creator: Qiuyan Zhong creator: Hongjiu Wang creator: Zhenzhen Wang uri: https://doi.org/10.7717/peerj.9371 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Open Access uptake by universities worldwide link: https://peerj.com/articles/9410 last-modified: 2020-07-08 description: The implementation of policies promoting the adoption of an open science (OS) culture must be accompanied by indicators that allow monitoring the uptake of such policies and their potential effects on research publishing and sharing practices. This study presents indicators of open access (OA) at the institutional level for universities worldwide. By combining data from Web of Science, Unpaywall and the Leiden Ranking disambiguation of institutions, we track OA coverage of universities’ output for 963 institutions. This paper presents the methodological challenges, conceptual discrepancies and limitations and discusses further steps needed to move forward the discussion on fostering OA and OS practices and policies. creator: Nicolas Robinson-Garcia creator: Rodrigo Costas creator: Thed N. van Leeuwen uri: https://doi.org/10.7717/peerj.9410 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Robinson-Garcia et al. title: Exceptionally preserved ‘skin’ in an Early Cretaceous fish from Colombia link: https://peerj.com/articles/9479 last-modified: 2020-07-08 description: Studies of soft tissue, cells and original biomolecular constituents preserved in fossil vertebrates have increased greatly in recent years. Here we report preservation of ‘skin’ with chemical and molecular characterization from a three-dimensionally preserved caudal portion of an aspidorhynchid Cretaceous fish from the equatorial Barremian of Colombia, increasing the number of localities for which exceptional preservation is known. We applied several analytical techniques including SEM-EDS, FTIR and ToF-SIMS to characterize the micromorphology and molecular and elemental composition of this fossil. Here, we show that the fossilized ‘skin’ exhibits similarities with those from extant fish, including the wrinkles after suffering compression stress and flexibility, as well as architectural and tissue aspects of the two main layers (epidermis and dermis). This similarity extends also to the molecular level, with the demonstrated preservation of potential residues of original proteins not consistent with a bacterial source. Our results show a potential preservation mechanism where scales may have acted as an external barrier and together with an internal phosphate layer resulting from the degradation of the dermis itself creating an encapsulated environment for the integument. creator: Andrés Alfonso-Rojas creator: Edwin-Alberto Cadena uri: https://doi.org/10.7717/peerj.9479 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Alfonso-Rojas and Cadena title: Successful promotion of physical activity among students of medicine through motivational interview and Web-based intervention link: https://peerj.com/articles/9495 last-modified: 2020-07-08 description: BackgroundRegular physical activity supports healthy behavior and contributes to the reduction of preventable diseases. Students in their social transition period are the ideal groups for interventions. The higher education period, associated with demanding changes and poor time management, results in a low level of physical activity. In this age, social media usually are a suitable channel of communication and multicomponent interventions are the most desirable. It has not been sufficiently investigated how effective a Web-based approach is among university students when it comes to physical activity in the long-term period. We combined a Web-based approach with motivational interviews and tested these two interventions together and separate to assess their impact on improving the physical activity of medical students 1 year after the intervention.MethodsAll 514 first-year students at the Faculty of Medicine in Belgrade were invited to fill in a baseline questionnaire. Also, they underwent measurement of weight, height and waist circumference. After that, students selected a 6 months intervention according to their preference: Intervention through social media (Facebook) (Group 1) or combined with a motivational interview (Group 2). Group 3 consisted of students without any intervention. One year after completion of the 6 months intervention period, all students were invited to a second comprehensive assessment. Analyses were performed employing a wide range of statistical testing, including direct logistic regression, to identify determinants of increased physical activity measured by an average change of Metabolic Equivalent of Task (MET). This outcome measure was defined as the difference between the values at baseline and one year after completion of the 6 months intervention period.ResultsDue to a large number of potential determinants of the change of MET, three logistic regression models considered three groups of independent variables: basic socio-demographic and anthropometric data, intervention and willingness for change, and health status with life choices. The only significant model comprised parameters related to the interventions (p < 0.001). It accurately classified 73.5% of cases. There is a highly significant overall effect for type of intervention (Wald = 19.5, df = 2, p < 0.001) with high odds for the increase of physical activity. Significant relationship between time and type of intervention also existed (F = 7.33, p < 0.001, partial η2 = 0.091). The influence of both factors (time and interventions) led to a change (increase) in the dependent variable MET.ConclusionOur study confirmed the presence of low-level physical activity among students of medicine and showed that multicomponent interventions have significant potential for positive change. The desirable effects of the Web-based intervention are higher if an additional booster is involved, such as a motivational interview. creator: Dubravka Mandic creator: Vesna Bjegovic-Mikanovic creator: Dejana Vukovic creator: Bosiljka Djikanovic creator: Zeljka Stamenkovic creator: Nebojsa M. Lalic uri: https://doi.org/10.7717/peerj.9495 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Mandic et al. title: The effects of knee extensor moment biofeedback on gait biomechanics and quadriceps contractile behavior link: https://peerj.com/articles/9509 last-modified: 2020-07-08 description: Individuals with knee joint pathologies exhibit quadriceps dysfunction that, during walking, manifests as smaller peak knee extensor moment (pKEM) and reduced knee flexion excursion. These changes persist despite muscle strengthening and may alter stance phase knee joint loading considered relevant to osteoarthritis risk. Novel rehabilitation strategies that more directly augment quadriceps mechanical output during functional movements are needed to reduce this risk. As an important first step, we tested the efficacy of real-time biofeedback during walking to prescribe changes of ±20% and ±40% of normal walking pKEM values in 11 uninjured young adults. We simultaneously recorded knee joint kinematics, ground reaction forces, and, via ultrasound, vastus lateralis (VL) fascicle length change behavior. Participants successfully responded to real-time biofeedback and averaged up to 55% larger and 51% smaller than normal pKEM values with concomitant and potentially favorable changes in knee flexion excursion. While the VL muscle-tendon unit (MTU) lengthened, VL fascicles accommodated weight acceptance during walking largely through isometric, or even slight concentric, rather than eccentric action as is commonly presumed. Targeted pKEM biofeedback may be a useful rehabilitative and/or scientific tool to elicit desirable changes in knee joint biomechanics considered relevant to the development of osteoarthritis. creator: Amanda E. Munsch creator: Brian Pietrosimone creator: Jason R. Franz uri: https://doi.org/10.7717/peerj.9509 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Munsch et al. title: Motor expertise affects the unconscious processing of geometric forms link: https://peerj.com/articles/9520 last-modified: 2020-07-08 description: BackgroundThe unconscious processing of information is an important skill used by competitive athletes to handle the rapidly changing movements of opponents and equipment. Previous studies have shown that unconscious information processing among athletes is better than that among non-athletes in the sports-specific domain. However, it is not yet clear whether athletes also show superior unconscious information processing in the general cognitive domain.MethodsTwenty-five competitive table tennis players (athletes) and 26 aged-matched non-athletic college students (non-athlete controls) were recruited for this study. Participants first performed a masked priming task that used geometric shapes as primes and targets to examine unconscious information processing in the general cognitive domain. As a control, participants then completed a prime identification task to determine whether they could consciously detect the priming geometric forms. Reaction times and error rates were analyzed to examine whether motor expertise influenced unconscious information processing in the general domain. Nineteen athletes and 17 non-athletes from our present study, which used general stimuli, also participated in our previous study, which used sport-specific stimuli. The strength of the unconscious response priming effect was analyzed to examine whether the effect of motor expertise on unconscious processing could be transferred from a sports-specific domain to a general domain.ResultsSignal detection analyses indicated that neither athletes nor non-athletes could consciously perceive the priming stimuli. Two-way repeated-measures analyses of variance followed by simple main effects analyses of the masked priming performance, indicating that athletes responded faster and committed fewer errors when the priming stimulus was congruent with the target stimulus. These results suggested that athletes exhibited a significant unconscious response priming effect of geometric forms. By contrast, non-athletes did not respond faster or commit fewer errors for congruent vs. incongruent conditions. No significant difference was detected between athletes and non-athletes in error rates for congruent trials, but athletes committed significantly more errors than non-athletes on incongruent trials. The strength of the unconscious response priming effect that athletes exhibited was greater than that for non-athletes, both in the present study with general stimuli and in our previous study with sport-specific stimuli.ConclusionThe results indicated that motor expertise facilitated the unconscious processing of geometric forms, suggesting that the influence of motor expertise on unconscious information processing occurs not only for the sports-specific domain but also transfers to the general cognitive domain. creator: Jiaxian Geng creator: Fanying Meng creator: Chao Wang creator: Hanna Haponenko creator: Anmin Li uri: https://doi.org/10.7717/peerj.9520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Geng et al. title: Metoprolol rescues endothelial progenitor cell dysfunction in diabetes link: https://peerj.com/articles/9306 last-modified: 2020-07-07 description: Added risk portended by diabetes in addition to hypertension has been related to an amplification of endothelial dysfunction. β-blockers are widely used for cardiovascular diseases and improve the endothelial function compared with a placebo. However, the effect of β-blockers on the endothelial progenitor cells (EPCs) function in diabetes is still unknown. Five β-blockers (metoprolol, atenolol, propranolol, bisoprolol, and nebivolol) were tested in EPC functional screening. Metoprolol improved EPC function significantly among the five β-blockers and was chosen for the in vivo tests in STZ induced diabetic mice. Reactive hyperemia peripheral arterial tonometry (RH-PAT) measurements were performed using the Endo-PAT2000 device in diabetic patients. Metoprolol, but not other β-blockers, improved EPC function in both tube formation and migration assay. EPC function was significantly decreased in diabetic mice, and metoprolol treatment restored damaged EPC migration capabilities and circulation EPC number. Metoprolol treatment promoted wound healing and stimulated angiogenesis in diabetic mice. Furthermore, metoprolol significantly enhanced eNOS phosphorylation and decreased O2− levels in EPCs of diabetic mice. In clinical trials, the RH-PAT index was significantly higher in metoprolol-treated versus bisoprolol-treated diabetics. Metoprolol could accelerate wound healing in diabetic mice and improve endothelial function in diabetic subjects, which may be mediated in part by improving impaired EPC function. creator: Lang Yan creator: Yi-fan Dong creator: Tao-lin Qing creator: Ya-ping Deng creator: Xue Han creator: Wen-jing Shi creator: Jin-feng Li creator: Fang-yuan Gao creator: Xiao-fang Zhang creator: Yi-jun Tian creator: Xiao-yu Dai creator: Jiang-bo Zhu creator: Ji-kuai Chen uri: https://doi.org/10.7717/peerj.9306 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yan et al. title: Three-dimensional thoracic and pelvic kinematics and arm swing maximum velocity in older adults using inertial sensor system link: https://peerj.com/articles/9329 last-modified: 2020-07-07 description: Understanding characteristics of torso motion and arm swing of older adults is important. A comprehensive database of three-dimensional thoracic and pelvic kinematics and arm swing maximum velocity of older adults during overground walking is still lacking. Moreover, the relationships between these variables are not fully understood. Therefore, we investigated age and gender effects of three-dimensional thoracic and pelvic ranges of motion and arm swing maximum velocity in 113 healthy old adults (aged 60–89 years) in a 2-min walk test using APDM Movement Monitoring inertial sensor system by two-way ANOVA, and post hoc Bonferroni correction was applied for multiple comparisons between age groups. A paired t-test was used to study the side preference of arm swing maximum velocity. The relationships between variables were investigated via multiple linear regression models. In general, thoracic and pelvic motions showed reduced amplitude with aging. Gait speed, pelvis coronal plane motion and arm swing maximum velocity significantly declined with age. Only the pelvic sagittal plane motion showed a gender main effect. Coronal plane motions of the thorax and pelvis were closely associated, as were sagittal plane motions. Thoracic coronal plane motion was the significant variable influencing pelvic transverse plane motion and vice versa. Gait speed, pelvic coronal and transverse plane motions and thorax sagittal plane motion were significant independent variables that influenced dominant arm maximum velocity. A larger maximum velocity was seen in the left arm. This investigation is valuable for better understanding of gait phenomena and will contribute to identification of gait dysfunction and development of rehabilitation measures. creator: Xin Fang creator: Zhongli Jiang uri: https://doi.org/10.7717/peerj.9329 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fang and Jiang title: Universality vs experience: a cross-cultural pilot study on the consonance effect in music at different altitudes link: https://peerj.com/articles/9344 last-modified: 2020-07-07 description: BackgroundPrevious studies have shown that music preferences are influenced by cultural “rules”, and some others have suggested a universal preference for some features over others.MethodsWe investigated cultural differences on the “consonance effect”, consisting in higher pleasantness judgments for consonant compared to dissonant chords—according to the Western definition of music: Italian and Himalayan participants were asked to express pleasantness judgments for consonant and dissonant chords. An Italian and a Nepalese sample were tested both at 1,450 m and at 4,750 m of altitude, with the further aim to evaluate the effect of hypoxia on this task. A third sample consisted of two subgroups of Sherpas: lowlanders (1,450 m of altitude), often exposed to Western music, and highlanders (3,427 m of altitude), less exposed to Western music. All Sherpas were tested where they lived.ResultsIndependently from the altitude, results confirmed the consonance effect in the Italian sample, and the absence of such effect in the Nepalese sample. Lowlander Sherpas revealed the consonance effect, but highlander Sherpas did not show this effect.ConclusionsResults of this pilot study show that neither hypoxia (altitude), nor demographic features (age, schooling, or playing music), nor ethnicity per se influence the consonance effect. We conclude that music preferences are attributable to music exposure. creator: Giulia Prete creator: Danilo Bondi creator: Vittore Verratti creator: Anna Maria Aloisi creator: Prabin Rai creator: Luca Tommasi uri: https://doi.org/10.7717/peerj.9344 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Prete et al. title: Integrating population genetic structure, microbiome, and pathogens presence data in Dermacentor variabilis link: https://peerj.com/articles/9367 last-modified: 2020-07-07 description: Tick-borne diseases (TBDs) continue to emerge and re-emerge in several regions of the world, highlighting the need for novel and effective control strategies. The development of effective strategies requires a better understanding of TBDs ecology, and given the complexity of these systems, interdisciplinary approaches are required. In recent years, the microbiome of vectors has received much attention, mainly because associations between native microbes and pathogens may provide a new promising path towards the disruption of pathogen transmission. However, we still do not fully understand how host genetics and environmental factors interact to shape the microbiome of organisms, or how pathogenic microorganisms affect the microbiome and vice versa. The integration of different lines of evidence may be the key to improve our understanding of TBDs ecology. In that context, we generated microbiome and pathogen presence data for Dermacentor variabilis, and integrated those data sets with population genetic data, and metadata for the same individual tick specimens. Clustering and multivariate statistical methods were used to combine, analyze, and visualize data sets. Interpretation of the results is challenging, likely due to the low levels of genetic diversity and the high abundance of a few taxa in the microbiome. Francisella was dominant in almost all ticks, regardless of geography or sex. Nevertheless, our results showed that, overall, ticks from different geographic regions differ in their microbiome composition. Additionally, DNA of Rickettsia rhipicephali, R. montanensis, R. bellii, and Anaplasma spp., was detected in D. variabilis specimens. This is the first study that successfully generated microbiome, population genetics, and pathogen presence data from the same individual ticks, and that attempted to combine the different lines of evidence. The approaches and pre-processing steps used can be applied to a variety of taxa, and help better understand ecological processes in biological systems. creator: Paula Lado creator: Bo Luan creator: Michelle E.J. Allerdice creator: Christopher D. Paddock creator: Sandor E. Karpathy creator: Hans Klompen uri: https://doi.org/10.7717/peerj.9367 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Lado et al. title: Reliability and validity of an equanimity questionnaire: the two-factor equanimity scale (EQUA-S) link: https://peerj.com/articles/9405 last-modified: 2020-07-07 description: BackgroundMany studies have revealed the positive impact of mindfulness training on mental health and proposed equanimity as a general outcome in contemplative research. Despite recent interest, relatively few studies have empirically examined equanimity and measurement instruments are still lacking. The main goal of this study was to develop an Equanimity Scale (the EQUA-S) in a Western population with or without meditation experience, based on previous definitions of equanimity, in order to investigate its relations with the relevant psychological constructs and health outcomes.MethodsAdults from the general population (N = 265; Mage = 34.81) completed various measures: the EQUA-S, mindfulness, hyper-sensitivity, avoidance and fusion, impulsivity, personality, alexithymia, sensitivity to punishment and reward and frequency of problematic addictive behaviors. The dimensionality of the EQUA-S was examined using Factor Analyses. The convergent validity of this new scale was investigated using Pearson’s Correlations.ResultsThe results of a factor analysis revealed two dimensions of equanimity: an even-minded state of mind (E-MSM) and a hedonic independence (HI) component. While the E-MSM was positively related to emotional stability, adaptive emotional regulation and several mindfulness-related abilities, HI was found to correlate negatively with addictive issues.DiscussionThe relations with personality constructs and possible related cognitive processes are discussed. creator: Catherine Juneau creator: Nicolas Pellerin creator: Elliott Trives creator: Matthieu Ricard creator: Rébecca Shankland creator: Michael Dambrun uri: https://doi.org/10.7717/peerj.9405 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Juneau et al. title: Molecular, physiological, and biochemical characterization of extracellular lipase production by Aspergillus niger using submerged fermentation link: https://peerj.com/articles/9425 last-modified: 2020-07-07 description: BackgroundExtracellular production of fungal lipases especially the lipases obtained from the Aspergilli has gained immense interest in recent years due to its diverse biotechnological applications. In this study, we focused on determining the fermentation parameters required for the optimal lipase production.MethodsA total of 256 fungal isolates were obtained from oil seeds. From each genus, one isolate was selected to evaluate lipase production using phenol red and tributyrin plate assays. Lipase activity was estimated using the spectrophotometric pNPP hydrolysis assay. The highest lipase producer isolates were identified using 18S ribosomal RNA gene sequencing. The genetic variability was determined by random amplified polymorphic DNA (RAPD) analysis and the dendrogram was constructed using the unweighted pair group method with arithmetic averages method. The isolates were examined in a submerged fermentation culture (Smf) to measure the effect of temperature, pH, incubation time, carbon source, nitrogen source, inoculum volume, and lipid source on lipase production.ResultsEleven isolates belonging to the genus Aspergillus were analyzed for lipase production where they were found to be the highest lipase producers among various fungal genera. All the tested isolates were identified as A. niger using 18s rRNA sequencing. Genetic diversity was evaluated among all of the studied A. niger isolates using RAPD primers. The RAPD primers were used to amplify 285 loci, of which five were polymorphic (1.75%) and seven were monomorphic (2.45%). Thus, a high level of genetic diversity was observed among all isolates. The tributyrin test and the lipase activity assay identified five strains of A. niger as high lipase producers, and their optimal enzyme activities were 709.74, 532.54, 735.64, 794.62, and 787.69 U/ml. The optimal conditions for lipase production were as follows: 40 °C, pH 7.5, 1% fructose as the carbon source, 1% yeast extract as the nitrogen source, 2% palm oil, 2.5 × 107 spores/ml suspension, and 3 days of incubation.ConclusionsThe current study provides a comprehensive characterization of the optimal conditions, which are essential to enhance lipase production in five A. niger isolates. creator: Amira Hassan Alabdalall creator: Norah Ayad ALanazi creator: Sumayh A. Aldakeel creator: Sayed AbdulAzeez creator: J. Francis Borgio uri: https://doi.org/10.7717/peerj.9425 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Alabdalall et al. title: Modifying effects of leaf litter extracts from invasive versus native tree species on copper-induced responses in Lemna minor link: https://peerj.com/articles/9444 last-modified: 2020-07-07 description: Invasive plant species tend to migrate from their native habitats under favourable climatic conditions; therefore, trophic and other relationships in ecosystems are changing. To investigate the effect of natural organic matter derived from native Alnus glutinosa tree species and from invasive in Lithuania Acer negundo tree species on copper toxicity in Lemna minor, we analysed the dynamics of Cu binding in aqueous leaf litter extracts (LLE) and plant accumulation, morphophysiological parameters, and antioxidative response. The results revealed that A. glutinosa LLE contained polyphenols (49 mg pyrogallol acid equivalent (PAE)/g DM) and tannins (7.5 mg PAE/g DM), while A. negundo LLE contained only polyphenols (23 mg PAE/g DM). The ability of LLE to bind Cu increased rapidly over 1.5–3 h to 61% and 49% of the total Cu concentration (6.0 ± 0.9 mg/L), respectively for A. glutinosa (AG) and A. negundo (AN), then remained relatively stable until 48 h. At the same time, L. minor accumulated 384, 241 or 188 µg Cu/g FW when plants were exposed to Cu (100 µM CuSO4), Cu with 100 mg/L dissolved organic carbon (DOC) from either AG LLE or AN LLE, accordingly. Catalase (CAT) and guaiacol peroxidase (POD) played a dominant role in hydrogen peroxide scavenging when plants were exposed to Cu and 10 or 100 mg/L DOCAG mixtures in both the first (up to 6h) and the second (6–48 h) response phases. Due to functioning of oxidative stress enzymes, the levels of the lipid peroxidation product malondialdehyde (MDA) reduced in concentration-dependent manner, compared to Cu treatment. When combining Cu and DOCAN treatments, the most sensitive enzymes were POD, ascorbate peroxidase and glutathione reductase. Their activities collectively with CAT were sufficient to reduce MDA levels to Cu-induced in the initial, but not the second response phase. These data suggest that leaf litter extracts of different phenolic compositions elicited different antioxidant response profiles resulting in different reductions of Cu stress, thus effecting L. minor frond and root development observed after seven days. The complex data from this study may be useful in modelling the response of the aquatic ecosystem to a changing environment. creator: Rolandas Karitonas creator: Sigita Jurkonienė creator: Kazys Sadauskas creator: Jūratė Vaičiūnienė creator: Levonas Manusadžianas uri: https://doi.org/10.7717/peerj.9444 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Karitonas et al. title: Transcriptome analysis reveals a reprogramming energy metabolism-related signature to improve prognosis in colon cancer link: https://peerj.com/articles/9458 last-modified: 2020-07-07 description: Although much progress has been made to improve treatment, colon cancer remains a leading cause of cancer death worldwide. Metabolic reprogramming is a significant ability of cancer cells to ensure the necessary energy supply in uncontrolled proliferation. Since reprogramming energy metabolism has emerged as a new hallmark of cancer cells, accumulating evidences have suggested that metabolism-related genes may serve as key regulators of tumorigenesis and potential biomarkers. In this study, we analyzed a set of reprogramming energy metabolism-related genes by transcriptome analysis in colon cancer and revealed a five-gene signature that could significantly predict the overall survival. The reprogramming energy metabolism-related signature could distinguish patients into high-risk and low-risk groups with significantly different survival times (P = 0.0011; HR = 1.92; 95% CI [1.29–2.87]). Its prognostic value was confirmed in another two independent colon cancer cohorts (P = 5.2e–04; HR = 2.09, 95%; CI [1.37–3.2] for GSE17538 and P = 3.8e−04; HR = 2.08, 95% CI [1.37–3.16] for GSE41258). By multivariable analysis, we found that the signature was independent of clinicopathological features. Its power in promoting risk stratification of the current clinical stage was then evaluated by stratified analysis. Moreover, the signature could improve the power of the TNM stage for the prediction of overall survival and could be used in patients who received adjuvant chemotherapy. Overall, our results demonstrated the important role of the reprogramming energy metabolism-related signature in promoting stratification of high-risk patients, which could be diagnostic of adjuvant therapy benefit. creator: Xinxin Zhang creator: Jinyuan Xu creator: Yujia Lan creator: Fenghua Guo creator: Yun Xiao creator: Yixue Li creator: Xia Li uri: https://doi.org/10.7717/peerj.9458 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Consolidation chemotherapy may improve pathological complete response for locally advanced rectal cancer after neoadjuvant chemoradiotherapy: a retrospective study link: https://peerj.com/articles/9513 last-modified: 2020-07-07 description: BackgroundPatients with locally advanced rectal cancer (LARC) have an improved prognosis if achieved a pathological complete response (pCR) on account of neoadjuvant chemoradiation therapy (nCRT). However, the proportion of patients achieving pCR is only 8–24%. The purpose of this study was to explore whether the addition of consolidation chemotherapy to nCRT could improve pCR rate in patients with LARC.Materials and MethodsThe subjects were 144 individuals with clinical stage II (T3–4, N0) or III (any T, N1–2) LARC who had received neoadjuvant CRT followed by total mesorectal excision (TME). Eighty-three patients in the consolidation chemotherapy group received two cycles XELOX between CRT and TME, while 61 patients in the standard treatment group without consolidation chemotherapy. The pCR (ypT0N0), tumor downstaging (ypT0-2N0) after TME and adverse events (AEs) during and post treatment were compared between the treatment groups using multivariable logistic regression analysis. To adjust the unbalanced variables for the primary endpoint, logistic regression analysis and stratified analysis were performed.ResultsThe consolidation chemotherapy group improved pCR rate (19.3% vs 4.9%, p = 0.01) and tumor downstaging rate (45.8% vs 24.6%, p = 0.009) compared to the standard treatment group. After adjustment for clinical tumor stage, clinical nodal stage and time interval to surgery, patients with consolidation chemotherapy were more likely to reach pCR (adjusted odds ratio 4.91, 95% CI [1.01–23.79], p = 0.048). AEs during and post treatment in the two groups were 54.1% vs 49.3% (p = 0.57), respectively. In addition, the incidence of any grade 1–2 AEs in the two groups was 93.4% vs 95.1% (p = 0.93), while the incidence of grade 3 AEs was 1.6% versus 2.4% (p = 0.74), respectively. No grade 4 AEs occurred in two groups.ConclusionsThe addition of neoadjuvant consolidation chemotherapy after CRT significantly increased the pCR rate and did not increase the AEs during and post treatment and in patients with LARC. creator: Jin Cui creator: Xue Dou creator: Yanlai Sun creator: Jinbo Yue uri: https://doi.org/10.7717/peerj.9513 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cui et al. title: Safety evaluation of four faba bean extracts used as dietary supplements in grass carp culture based on hematological indices, hepatopancreatic function and nutritional condition link: https://peerj.com/articles/9516 last-modified: 2020-07-07 description: Faba bean (Vicia faba, FB) is known to improve the texture of fish meat but retards growth possibly by inducing hemolysis, hepatopancreas damage, and metabolic disorder. In this study, we used ultrasonic processing to isolate four FB extracts (water extract, alcohol extract, proteins and residues) and examined their beneficial and detrimental effects. These extracts were separately mixed with commercial feed and fed to grass carp (Ctenopharyngodon idellus) using whole FB and commercial feed as controls. After fish were fed one of the six experimental diets for 50 d and 100 d, we evaluated the growth and hematological parameters, activities of metabolic enzymes, hepatopancreatic histology and oxidative response, and lipid metabolism. Results showed that both whole FB and FB residues caused growth retardation and hepatopancreas damage (P < 0.05), whereas growth performance was improved in the FB water and alcohol extract groups compared to the whole FB group. Although the FB water extract negatively affected the number and morphological parameters of red blood cells (P < 0.05), the hematological damage was less pronounced than that of the whole FB group. Excessive hepatopancreatic fat accumulation was found in the whole FB, FB alcohol extract and FB residues groups. Moreover, serious hepatopancreas damages were observed in the FB residues group. These results suggest that the beneficial and detrimental components of FB were successfully separated in the four extracts, and the FB water extract would be the best choice for grass carp culture in terms of growth performance and health. The safety evaluation of the four FB extracts would facilitate further application of FB in aquatic feed. creator: Lingling Ma creator: Gen Kaneko creator: Jun Xie creator: Guangjun Wang creator: Zhifei Li creator: Jingjing Tian creator: Kai Zhang creator: Yun Xia creator: Wangbao Gong creator: Haihang Li creator: Ermeng Yu uri: https://doi.org/10.7717/peerj.9516 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ma et al. title: Small molecule therapeutics for COVID-19: repurposing of inhaled furosemide link: https://peerj.com/articles/9533 last-modified: 2020-07-07 description: The novel coronavirus SARS-CoV-2 has become a global health concern. The morbidity and mortality of the potentially lethal infection caused by this virus arise from the initial viral infection and the subsequent host inflammatory response. The latter may lead to excessive release of pro-inflammatory cytokines, IL-6 and IL-8, as well as TNF-α ultimately culminating in hypercytokinemia (“cytokine storm”). To address this immuno-inflammatory pathogenesis, multiple clinical trials have been proposed to evaluate anti-inflammatory biologic therapies targeting specific cytokines. However, despite the obvious clinical utility of such biologics, their specific applicability to COVID-19 has multiple drawbacks, including they target only one of the multiple cytokines involved in COVID-19’s immunopathy. Therefore, we set out to identify a small molecule with broad-spectrum anti-inflammatory mechanism of action targeting multiple cytokines of innate immunity. In this study, a library of small molecules endogenous to the human body was assembled, subjected to in silico molecular docking simulations and a focused in vitro screen to identify anti-pro-inflammatory activity via interleukin inhibition. This has enabled us to identify the loop diuretic furosemide as a candidate molecule. To pre-clinically evaluate furosemide as a putative COVID-19 therapeutic, we studied its anti-inflammatory activity on RAW264.7, THP-1 and SIM-A9 cell lines stimulated by lipopolysaccharide (LPS). Upon treatment with furosemide, LPS-induced production of pro-inflammatory cytokines was reduced, indicating that furosemide suppresses the M1 polarization, including IL-6 and TNF-α release. In addition, we found that furosemide promotes the production of anti-inflammatory cytokine products (IL-1RA, arginase), indicating M2 polarization. Accordingly, we conclude that furosemide is a reasonably potent inhibitor of IL-6 and TNF-α that is also safe, inexpensive and well-studied. Our pre-clinical data suggest that it may be a candidate for repurposing as an inhaled therapy against COVID-19. creator: Zhiyu Wang creator: Yanfei Wang creator: Prachi Vilekar creator: Seung-Pil Yang creator: Mayuri Gupta creator: Myong In Oh creator: Autumn Meek creator: Lisa Doyle creator: Laura Villar creator: Anja Brennecke creator: Imindu Liyanage creator: Mark Reed creator: Christopher Barden creator: Donald F. Weaver uri: https://doi.org/10.7717/peerj.9533 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Intermittent theta burst stimulation facilitates functional connectivity from the dorsal premotor cortex to primary motor cortex link: https://peerj.com/articles/9253 last-modified: 2020-07-06 description: BackgroundMotor information in the brain is transmitted from the dorsal premotor cortex (PMd) to the primary motor cortex (M1), where it is further processed and relayed to the spinal cord to eventually generate muscle movement. However, how information from the PMd affects M1 processing and the final output is unclear. Here, we applied intermittent theta burst stimulation (iTBS) to the PMd to alter cortical excitability not only at the application site but also at the PMd projection site of M1. We aimed to determine how PMd iTBS–altered information changed M1 processing and the corticospinal output.MethodsIn total, 16 young, healthy participants underwent PMd iTBS with 600 pulses (iTBS600) or sham-iTBS600. Corticospinal excitability, short-interval intracortical inhibition (SICI), and intracortical facilitation (ICF) were measured using transcranial magnetic stimulation before and up to 60 min after stimulation.ResultsCorticospinal excitability in M1 was significantly greater 15 min after PMd iTBS600 than that after sham-iTBS600 (p = 0.012). Compared with that after sham-iTBS600, at 0 (p = 0.014) and 15 (p = 0.037) min after iTBS600, SICI in M1 was significantly decreased, whereas 15 min after iTBS600, ICF in M1 was significantly increased (p = 0.033).ConclusionOur results suggested that projections from the PMd to M1 facilitated M1 corticospinal output and that this facilitation may be attributable in part to decreased intracortical inhibition and increased intracortical facilitation in M1. Such a facilitatory network may inform future understanding of the allocation of resources to achieve optimal motion output. creator: Hai-Jiang Meng creator: Na Cao creator: Jian Zhang creator: Yan-Ling Pi uri: https://doi.org/10.7717/peerj.9253 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Meng et al. title: Melatonin improves the germination rate of cotton seeds under drought stress by opening pores in the seed coat link: https://peerj.com/articles/9450 last-modified: 2020-07-06 description: The germination of cotton (Gossypium hirsutum L.) seeds is affected by drought stress; however, little is known about the physiological mechanism affecting germination and the effect of melatonin (MT) on cotton seed germination under drought stress. Therefore, we studied the effects of exogenous MT on the antioxidant capacity and epidermal microstructure of cotton under drought stress. The results demonstrated a retarded water absorption capacity of testa under drought stress, significantly inhibiting germination and growth in cotton seeds. Drought stress led to the accumulation of reactive oxygen species (ROS), malondialdehyde (MDA), and osmoregulatory substances (e.g., proline, soluble protein, and soluble sugars); it also decreased the activity of antioxidant enzymes and α-amylase. Drought stress inhibited gibberellin acid (GA3) synthesis and increased abscisic acid (ABA) content, seriously affecting seed germination. However, seeds pre-soaked with MT (100 µM) showed a positive regulation in the number and opening of stomata in cotton testa. The exogenous application of MT increased the germination rate, germination potential, radical length, and fresh weight, as well as the activities of superoxide dismutase (SOD), peroxidase (POD), and α-amylase. In addition, MT application increased the contents of organic osmotic substances by decreasing the hydrogen peroxide (H2O2), superoxide anion (O2-), and MDA levels under drought stress. Further analysis demonstrated that seeds pre-soaked with MT alleviated drought stress by affecting the ABA and GA3 contents. Our findings show that MT plays a positive role in protecting cotton seeds from drought stress. creator: Yandan Bai creator: Shuang Xiao creator: Zichen Zhang creator: Yongjiang Zhang creator: Hongchun Sun creator: Ke Zhang creator: Xiaodan Wang creator: Zhiying Bai creator: Cundong Li creator: Liantao Liu uri: https://doi.org/10.7717/peerj.9450 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bai et al. title: Rodents’ responses to manipulated plant litter and seed densities: implications for restoration link: https://peerj.com/articles/9465 last-modified: 2020-07-06 description: Rodent populations in arid grasslands do not always track seed production, possibly due to high levels of plant litter. When natural disturbances are suppressed, litter accumulates becoming physically complex, causing rodents to harvest fewer seeds per equivalent time foraging. It also alters security from predation. Restoring natural disturbances may be an important element in conserving rodent communities. The aim of this study was to assess the influence of two levels of plant litter cover and seed densities on nocturnal rodent population characteristics in a semiarid grassland. Specifically, I hypothesized that kangaroo rats, pocket mice, grasshopper mice, and total rodents would be higher in the sparse plant litter treatment than dense litter, whereas deer mice would be lower in sparse plots. I further hypothesized that kangaroo rats and deer mice would be higher in the seed augmented treatment compared to the unseeded treatment. A prescribed fire removed litter in four of eight plots prior to sowing native seeds 1 year postfire into two burned and two unburned plots. Rodents were live-trapped during spring and fall 1 year. Sparse litter treatment had higher total rodent abundance, biomass, and frequency of offspring compared to dense plots indicating use of stored seeds. Banner-tailed kangaroo rats had higher abundance, implying reduced predation risk. Pocket mice body mass was greater in dense plots. After winter, seeded plots had higher kangaroo rat body mass and grasshopper mice abundance than unseeded, reflecting the use of stored seeds. These short term results demonstrate litter’s physical complexity may be equivalent to seed pulses on the responses of nocturnal rodents. Managers might positively influence grassland rodents by providing a mosaic of varying levels of plant litter. creator: Nancy Nicolai uri: https://doi.org/10.7717/peerj.9465 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nicolai title: Predicting the effect of variants on splicing using Convolutional Neural Networks link: https://peerj.com/articles/9470 last-modified: 2020-07-06 description: Mutations that cause an error in the splicing of a messenger RNA (mRNA) can lead to diseases in humans. Various computational models have been developed to recognize the sequence pattern of the splice sites. In recent studies, Convolutional Neural Network (CNN) architectures were shown to outperform other existing models in predicting the splice sites. However, an insufficient effort has been put into extending the CNN model to predict the effect of the genomic variants on the splicing of mRNAs. This study proposes a framework to elaborate on the utility of CNNs to assess the effect of splice variants on the identification of potential disease-causing variants that disrupt the RNA splicing process. Five models, including three CNN-based and two non-CNN machine learning based, were trained and compared using two existing splice site datasets, Genome Wide Human splice sites (GWH) and a dataset provided at the Deep Learning and Artificial Intelligence winter school 2018 (DLAI). The donor sites were also used to test on the HSplice tool to evaluate the predictive models. To improve the effectiveness of predictive models, two datasets were combined. The CNN model with four convolutional layers showed the best splice site prediction performance with an AUPRC of 93.4% and 88.8% for donor and acceptor sites, respectively. The effects of variants on splicing were estimated by applying the best model on variant data from the ClinVar database. Based on the estimation, the framework could effectively differentiate pathogenic variants from the benign variants (p = 5.9 × 10−7). These promising results support that the proposed framework could be applied in future genetic studies to identify disease causing loci involving the splicing mechanism. The datasets and Python scripts used in this study are available on the GitHub repository at https://github.com/smiile8888/rna-splice-sites-recognition. creator: Thanyathorn Thanapattheerakul creator: Worrawat Engchuan creator: Jonathan H. Chan uri: https://doi.org/10.7717/peerj.9470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Thanapattheerakul et al. title: Evaluation of psychological stress in scientific researchers during the 2019–2020 COVID-19 outbreak in China link: https://peerj.com/articles/9497 last-modified: 2020-07-06 description: BackgroundBeginning in December 2019, coronavirus disease 2019 (COVID-19) caused an outbreak of infectious pneumonia. The Chinese government introduced a series of grounding measures to prevent the spread of COVID-19. The living and working patterns of many scientific researchers also underwent significant changes during this period.MethodsAn opportunity sample (n = 251) was obtained in China using a questionnaire with 42 questions on scientific research progress and psychological stress during the COVID-19 epidemic.ResultsOf the 251 participants, 76.9% indicated that their research was affected by the COVID-19 outbreak, and participants who were affected by the outbreak had higher stress levels than those who were not affected. Participants who conducted COVID-19 research and indicated concern that they would fail to finish the research on time were more likely to indicate high levels of stress. Respondents indicated that extending deadlines (64.1%), receiving support from superiors for research (51.8%), and increasing benefits for researchers (51.0%) would likely relieve outbreak-related stress.ConclusionThe COVID-19 outbreak had a major impact on the experiments of researchers in the life sciences, especially in basic and clinical medicine. It has also caused high levels of psychological stress in these populations. Measures should be taken to relieve psychological pressure on basic medical researchers and students who will soon complete their degrees (e.g., Master’s and PhD candidates in graduation years). creator: Xueyan Zhang creator: Xinyu Li creator: Zhenxin Liao creator: Mingyi Zhao creator: Quan Zhuang uri: https://doi.org/10.7717/peerj.9497 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Novel circulating protein biomarkers for thyroid cancer determined through data-independent acquisition mass spectrometry link: https://peerj.com/articles/9507 last-modified: 2020-07-06 description: BackgroundDistinguishing between different types of thyroid cancers (TC) remains challenging in clinical laboratories. As different tumor types require different clinical interventions, it is necessary to establish new methods for accurate diagnosis of TC.MethodsProteomic analysis of the human serum was performed through data-independent acquisition mass spectrometry for 29 patients with TC (stages I–IV): 13 cases of papillary TC (PTC), 10 cases of medullary TC (MTC), and six cases follicular TC (FTC). In addition, 15 patients with benign thyroid nodules (TNs) and 10 healthy controls (HCs) were included in this study. Subsequently, 17 differentially expressed proteins were identified in 291 patients with TC, including 247 with PTC, 38 with MTC, and six with FTC, and 69 patients with benign TNs and 176 with HC, using enzyme-linked immunosorbent assays.ResultsIn total, 517 proteins were detected in the serum samples using an Orbitrap Q-Exactive-plus mass spectrometer. The amyloid beta A4 protein, apolipoprotein A-IV, gelsolin, contactin-1, gamma-glutamyl hydrolase, and complement factor H-related protein 1 (CFHR1) were selected for further analysis. The median serum CFHR1 levels were significantly higher in the MTC and FTC groups than in the PTC and control groups (P < 0.001). CFHR1 exhibited higher diagnostic performance in distinguishing patients with MTC from those with PTC (P < 0.001), with a sensitivity of 100.0%, specificity of 85.08%, area under the curve of 0.93, and detection cut-off of 0.92 ng/mL.ConclusionCFHR1 may serve as a novel biomarker to distinguish PTC from MTC with high sensitivity and specificity. creator: Dandan Li creator: Jie Wu creator: Zhongjuan Liu creator: Ling Qiu creator: Yimin Zhang uri: https://doi.org/10.7717/peerj.9507 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Association between the number and size of intrapulmonary lymph nodes and chronic obstructive pulmonary disease severity link: https://peerj.com/articles/9166 last-modified: 2020-07-03 description: PurposeOne of the main pathophysiological mechanisms of chronic obstructive pulmonary disease is inflammation, which has been associated with lymphadenopathy. Intrapulmonary lymph nodes can be identified on CT as perifissural nodules (PFN). We investigated the association between the number and size of PFNs and measures of COPD severity.Materials and MethodsCT images were obtained from COPDGene. 50 subjects were randomly selected per GOLD stage (0 to 4), GOLD-unclassified, and never-smoker groups and allocated to either “Healthy,” “Mild,” or “Moderate/severe” groups. 26/350 (7.4%) subjects had missing images and were excluded. Supported by computer-aided detection, a trained researcher prelocated non-calcified opacities larger than 3 mm in diameter. Included lung opacities were classified independently by two radiologists as either “PFN,” “not a PFN,” “calcified,” or “not a nodule”; disagreements were arbitrated by a third radiologist. Ordinal logistic regression was performed as the main statistical test.ResultsA total of 592 opacities were included in the observer study. A total of 163/592 classifications (27.5%) required arbitration. A total of 17/592 opacities (2.9%) were excluded from the analysis because they were not considered nodular, were calcified, or all three radiologists disagreed. A total of 366/575 accepted nodules (63.7%) were considered PFNs. A maximum of 10 PFNs were found in one image; 154/324 (47.5%) contained no PFNs. The number of PFNs per subject did not differ between COPD severity groups (p = 0.50). PFN short-axis diameter could significantly distinguish between the Mild and Moderate/severe groups, but not between the Healthy and Mild groups (p = 0.021).ConclusionsThere is no relationship between PFN count and COPD severity. There may be a weak trend of larger intrapulmonary lymph nodes among patients with more advanced stages of COPD. creator: Anton Schreuder creator: Colin Jacobs creator: Ernst T. Scholten creator: Mathias Prokop creator: Bram van Ginneken creator: David A. Lynch creator: Cornelia M. Schaefer-Prokop uri: https://doi.org/10.7717/peerj.9166 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Schreuder et al. title: Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papaya L.) link: https://peerj.com/articles/9319 last-modified: 2020-07-03 description: The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene structures and protein motifs according to analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLHs varied from one to 10 with an average of five. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of CpbHLHs. creator: Min Yang creator: Chenping Zhou creator: Hu Yang creator: Ruibin Kuang creator: Bingxiong Huang creator: Yuerong Wei uri: https://doi.org/10.7717/peerj.9319 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships link: https://peerj.com/articles/9389 last-modified: 2020-07-03 description: Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable results. These poorly resolved relationships may be the product of methodological shortcomings or of an evolutionary history that did not generate the signal traits needed for its eventual reconstruction. Relationships within the euteleost fish family Salmonidae have proven challenging to resolve in molecular phylogenetics studies in part due to ancestral autopolyploidy contributing to conflicting gene trees. We examine a sequence capture dataset from salmonids and use alternative strategies to accommodate the effects of gene tree conflict based on aspects of salmonid genome history and the multispecies coalescent. We investigate in detail three uncertain relationships: (1) subfamily branching, (2) monophyly of Coregonus and (3) placement of Parahucho. Coregoninae and Thymallinae are resolved as sister taxa, although conflicting topologies are found across analytical strategies. We find inconsistent and generally low support for the monophyly of Coregonus, including in results of analyses with the most extensive dataset and complex model. The most consistent placement of Parahucho is as sister lineage of Salmo. creator: Matthew A. Campbell creator: Thaddaeus J. Buser creator: Michael E. Alfaro creator: J. Andrés López uri: https://doi.org/10.7717/peerj.9389 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Campbell et al. title: A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae) link: https://peerj.com/articles/9411 last-modified: 2020-07-03 description: Frogs of the genus Microhyla include some of the world’s smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla—Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene—early Miocene that coincides with an onset of seasonally dry climates in South Asia. Body size evolution modeling suggests that four groups of Microhyla have independently achieved extreme miniaturization with adult body size below 15 mm. Three of the five smallest Microhyla species are obligate phytotelm-breeders and we argue that their peculiar reproductive biology may be a factor involved in miniaturization. Body size increases in Microhyla—Glyphoglossus seem to be associated with a burrowing adaptation to seasonally dry habitats. Species delimitation analyses suggest a vast underestimation of species richness and diversity in Microhyla and reveal 15–33 undescribed species. We revalidate M. nepenthicola, synonymize M. pulverata with M. marmorata, and provide insights on taxonomic statuses of a number of poorly known species. Further integrative studies, combining evidence from phylogeny, morphology, advertisement calls, and behavior will result in a better systematic understanding of this morphologically cryptic radiation of Asian frogs. creator: Vladislav A. Gorin creator: Evgeniya N. Solovyeva creator: Mahmudul Hasan creator: Hisanori Okamiya creator: D.M.S. Suranjan Karunarathna creator: Parinya Pawangkhanant creator: Anslem de Silva creator: Watinee Juthong creator: Konstantin D. Milto creator: Luan Thanh Nguyen creator: Chatmongkon Suwannapoom creator: Alexander Haas creator: David P. Bickford creator: Indraneil Das creator: Nikolay A. Poyarkov uri: https://doi.org/10.7717/peerj.9411 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gorin et al. title: The impact of short-term exposure to near shore stressors on the early life stages of the reef building coral Montipora capitata link: https://peerj.com/articles/9415 last-modified: 2020-07-03 description: Successful reproduction and survival are crucial to the continuation and resilience of corals globally. As reef waters warm due to climate change, episodic largescale tropical storms are becoming more frequent, drastically altering the near shore water quality for short periods of time. Therefore, it is critical that we understand the effects warming waters, fresh water input, and run-off have on sexual reproduction of coral. To better understand the effects of these near shore stressors on Hawaiian coral, laboratory experiments were conducted at the Institute of Marine Biology to determine the independent effects of suspended sediment concentrations (100 mg l−1 and 200 mg l−1), lowered salinity (28‰), and elevated temperature (31 °C) on the successful fertilization, larval survival, and settlement of the scleractinian coral Montipora capitata. In the present study, early developmental stages of coral were exposed to one of three near shore stressors for a period of 24 h and the immediate (fertilization) and latent effects (larval survival and settlement) were observed and measured. Fertilization success and settlement were not affected by any of the treatments; however, larval survival was negatively affected by all of the treatments by 50% or greater (p > 0.05). These data show that early life stages of M. capitata may be impacted by near shore stressors associated with warming and more frequent storm events. creator: Claire V.A. Lager creator: Mary Hagedorn creator: Kuʻulei S. Rodgers creator: Paul L. Jokiel uri: https://doi.org/10.7717/peerj.9415 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lager et al. title: A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains link: https://peerj.com/articles/9448 last-modified: 2020-07-03 description: BackgroundChrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology.MethodsThe chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe.ResultsThe sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species. creator: Swati Tyagi creator: Jae-A Jung creator: Jung Sun Kim creator: So Youn Won uri: https://doi.org/10.7717/peerj.9448 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tyagi et al. title: Treating coral bleaching as weather: a framework to validate and optimize prediction skill link: https://peerj.com/articles/9449 last-modified: 2020-07-03 description: Few coral reefs remain unscathed by mass bleaching over the past several decades, and much of the coral reef science conducted today relates in some way to the causes, consequences, or recovery pathways of bleaching events. Most studies portray a simple cause and effect relationship between anomalously high summer temperatures and bleaching, which is understandable given that bleaching rarely occurs outside these unusually warm times. However, the statistical skill with which temperature captures bleaching is hampered by many “false alarms”, times when temperatures reached nominal bleaching levels, but bleaching did not occur. While these false alarms are often not included in global bleaching assessments, they offer valuable opportunities to improve predictive skill, and therefore understanding, of coral bleaching events. Here, I show how a statistical framework adopted from weather forecasting can optimize bleaching predictions and validate which environmental factors play a role in bleaching susceptibility. Removing the 1 °C above the maximum monthly mean cutoff in the typical degree heating weeks (DHW) definition, adjusting the DHW window from 12 to 9 weeks, using regional-specific DHW thresholds, and including an El Niño threshold already improves the model skill by 45%. Most importantly, this framework enables hypothesis testing of other factors or metrics that may improve our ability to forecast coral bleaching events. creator: Thomas M. DeCarlo uri: https://doi.org/10.7717/peerj.9449 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 DeCarlo title: Preservation of latest Cretaceous (Maastrichtian)—Paleocene frogs (Eorubeta nevadensis) of the Sheep Pass Formation of east-central Nevada and implications for paleogeography of the Nevadaplano link: https://peerj.com/articles/9455 last-modified: 2020-07-03 description: Here we report on exceptional preservation of remains of the frog Eorubeta nevadensis in deposits of the Sheep Pass Formation, ranging from Late Cretaceous to Eocene, in the south Egan Range, Nevada. This formation represents a lacustrine basin within the Sevier retroarc hinterland. The formation is subdivided into six members (A–F); of interest here are members B and C. The base of member B is ?uppermost Cretaceous-Paleocene, while member C is Paleocene. Member B frogs are preserved in three taphonomic modes. Mode 1 frogs are nearly complete and accumulated under attritional processes, with frogs settling on microbial mats, as evidenced by crenulated fabric of entombing limestone. Mode 2 involves accumulation of frogs as a result of attritional processes. These frogs are mostly complete with some showing evidence of invertebrate scavenging. Possible scavengers are gastropods, ostracods, and decapods. Mode 3 is represented by isolated, reworked remains of frogs as a result of storm activity, supported by the association of elements with disarticulated bivalves and mud rip-up clasts. Member C preserves frogs in two taphonomic modes. Mode 4 are nearly complete frogs that accumulated during discrete mass mortality events. Numerous individuals are preserved along bedding planes in identical preservational states. Mode 5 is beds of frog bone hash, which represent increased energy to the depositional system (likely tempestites) and reworking of previously buried frog remains. Taphonomy of the frogs, along with the associated fauna and flora, are consistent with preservation in a cool, temperate lake basin, supporting previous interpretations that the Nevadaplano was an elevated plateau during the late Cretaceous through the Eocene. This is a period of time coincident with a climatic thermal optimum, thus the most parsimonious explanation for a temperate lake at the latitude of east-central Nevada is to invoke high elevation, which is consistent with independent structural and clumped stable isotope studies. creator: Joshua W. Bonde creator: Peter A. Druschke creator: Richard P. Hilton creator: Amy C. Henrici creator: Stephen M. Rowland uri: https://doi.org/10.7717/peerj.9455 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bonde et al. title: Selection of Beauveria bassiana (Hypocreales: Cordycipitaceae) strains to control Xyleborus affinis (Curculionidae: Scolytinae) females link: https://peerj.com/articles/9472 last-modified: 2020-07-03 description: BackgroundXyleborus affinis Eichhoff (Coleoptera: Curculionidae) is an ambrosia beetle reported to affect avocado trees (Persea americana Mill.). The use of the entomopathogenic fungus (EPF) Beauveria bassiana (Bals.-Criv.) Vuill. for ambrosia beetle control represents an alternative to insecticides.MethodsThis study was designed in two stages to select B. bassiana strains with potential to control X. affinis females. In the first stage, 19 B. bassiana Mexican strains from EPF collection, isolated from Coleoptera (CHE-CNRCB, http://www.gob.mx/senasica/documentos/coleccion-de-hongos-entomopatogenos), were tested. Analyses included radial growth rate, conidial yield, spore germination, and germ tube length. Results were analysed by Principal Component Analysis (PCA) to identify clusters within favourable growth phenotypes. For the second stage, 10 selected strains were re-analysed for virulence-related metabolic characteristic, including cell wall-bound cuticle-degrading enzymes–Pr1-like proteases and β-N-acetyl glucosaminidases (NAGase) chitinases, conidial hydrophobicity and monopolar germination parameters. A second PCA analysis was run for those virulence parameters analysed, and upon results strains CHE-CNRCB 44, 171, 431 and 485 were selected and tested against X. affinis females. Females were treated with a 1 × 108 conidia mL−1 suspension (recommended rate), using a Potter Tower.ResultsAll strains showed insecticidal activity, inducing up to 58% mortality; about 30% dead beetles developed aerial mycelia (CHE-CNRCB 485) and the fastest mortality rate was t0 = 1.95 (CHE-CNRCB 44).ConclusionSince all selected strains showed virulence against X. affinis females, results indicated the possibility of selecting B. bassiana strains based on multiple metabolic attributes, as a preliminary test to perform bioassays against order-related target insects. creator: Jesús E. Castrejón-Antonio creator: Patricia Tamez-Guerra creator: Roberto Montesinos-Matías creator: Maria J. Ek-Ramos creator: Paul M. Garza-López creator: Hugo C. Arredondo-Bernal uri: https://doi.org/10.7717/peerj.9472 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Castrejón-Antonio et al. title: Diminishing returns as a function of disturbance link: https://peerj.com/articles/9490 last-modified: 2020-07-03 description: According to Spearman’s law of diminishing returns (SLODR), IQ test scores are more g saturated among those with low, compared to those with high, ability. The present simulation shows that such difference in saturation can be observed if test scores are affected by a disturbing factor, for example, low motivation, illness, or linguistic confusion, that varies in magnitude between individuals. More contemporary criteria of SLODR can also be satisfied if test scores are affected by disturbance, especially if the disturbance variable is negatively skewed. This indicates a possible threat against the validity of findings supporting SLODR and points at the importance for researchers to try to eliminate the influence of such disturbing factors from their studies. creator: Kimmo Sorjonen creator: Bo Melin uri: https://doi.org/10.7717/peerj.9490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sorjonen and Melin title: Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure link: https://peerj.com/articles/9492 last-modified: 2020-07-03 description: The rapid development of the SARS-CoV-2 mediated COVID-19 pandemic has been the cause of significant health concern, highlighting the immediate need for effective antivirals. SARS-CoV-2 is an RNA virus that has an inherently high mutation rate. These mutations drive viral evolution and genome variability, thereby facilitating viruses to have rapid antigenic shifting to evade host immunity and to develop drug resistance. Viral RNA-dependent RNA polymerases (RdRp) perform viral genome duplication and RNA synthesis. Therefore, we compared the available RdRp sequences of SARS-CoV-2 from Indian isolates and the ‘Wuhan wet sea food market virus’ sequence to identify, if any, variation between them. Our data revealed the occurrence of seven mutations in Indian isolates of SARS-CoV-2. The secondary structure prediction analysis of these seven mutations shows that three of them cause alteration in the structure of RdRp. Furthermore, we did protein modelling studies to show that these mutations can potentially alter the stability of the RdRp protein. Therefore, we propose that RdRp mutations in Indian SARS-CoV-2 isolates might have functional consequences that can interfere with RdRp targeting pharmacological agents. creator: Gyanendra Bahadur Chand creator: Atanu Banerjee creator: Gajendra Kumar Azad uri: https://doi.org/10.7717/peerj.9492 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chand et al. title: Contextual violence and its link to social aggression: a study of community violence in Juárez link: https://peerj.com/articles/9162 last-modified: 2020-07-02 description: The city of Juárez, Mexico has been immersed in an atmosphere of violence and danger for more than a decade. Due to this violence, residents of Juárez may be at risk of severe contextual victimization, which occurs when individuals are indirectly affected by the physical and socio-cultural conditions of their violent communities through second-hand information (e.g., witnessing or hearing about violent acts in their everyday life). The objective of this study was to explore the effects of contextual victimization on variables related to community violence such as aggression, post-traumatic stress disorder (PTSD), and acceptance of violence. Data were collected from a sample of university students in Juárez (n = 298) using the Aggression Questionnaire (AQ), the Acceptance of Violence Scale (AVS), Checklist for PTSD Traits scale, and the Contextual Victimization by Community Violence scale (CVCV). Participants’ responses were analyzed in structural equation models (SEM) to uncover the latent variables behind each scale and test the hypothesized effects of CVCV on PTSD, AQ and AVS. Good validity indexes and internal consistency of all instruments were confirmed. SEM show significant positive effects of contextual violence on PTSD and PTSD on the disposition to aggression, but not on the acceptance of violence. Also, the variance explained of PTSD and AQ found in the sample of women (20% of PTSD and 23% of AQ) is almost twice than in men’s sample (9% for PTSD and 14% for AQ). creator: Jaime Martín del Campo-Ríos creator: Christian Enrique Cruz-Torres uri: https://doi.org/10.7717/peerj.9162 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Martín del Campo-Ríos and Cruz-Torres title: Foliar application of abscisic acid mitigates cadmium stress and increases food safety of cadmium-sensitive lettuce (Lactuca sativa L.) genotype link: https://peerj.com/articles/9270 last-modified: 2020-07-02 description: Cadmium (Cd2 +) is among the toxic non-essential heavy metals that adversely affect plants metabolic processes and the safety of produce. However, plant hormones can improve plant’s tolerance to various stresses. This study investigated the effect of exogenous abscisic acid (ABA) on the biochemical and physiological processes and food safety of cadmium (Cd2 +)-sensitive lettuce genotype (Lüsu). Seedlings were subjected to five treatments: [(i) Control (untreated plants), (ii) 100 µM CdCl2, (iii) 100 µM CdCl2+10 µg L−1 ABA (iv) 10 µg L−1 ABA, and (v) 0.01 g L−1 ABA-inhibitor (fluridone)] for fourteen days in hydroponic system. The 100 µM CdCl2 increased the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA), decreased photosynthesis and plant biomass. Moreover, it decreased the contents of essential nutrients (except copper) in the leaves but increased the contents of toxic Cd2 + in the leaves and roots of the plants. Foliar application of fluridone (0.01 g L−1) also caused oxidative stress by increasing the contents of H2O2 and MDA. It also decreased the contents of nutrient elements in the leaves of the plants. However, exogenous ABA (10 µg L−1) mitigated the Cd2 +-induced stress, increased antioxidant enzymes activities, photosynthesis and plant biomass under CdCl2 treatment. Remarkably, exogenous ABA increased the contents of essential nutrient elements but decreased the Cd2 + content in leaves under the CdCl2 treatment. Our results have demonstrated that foliar application of ABA mitigates Cd2 + stress and increases the nutritional quality and food safety of Cd2 +-sensitive lettuce genotype under CdCl2 treatment. creator: Mohammed Mujitaba Dawuda creator: Weibiao Liao creator: Linli Hu creator: Jihua Yu creator: Jianming Xie creator: Alejandro Calderón-Urrea creator: Yue Wu creator: Zhongqi Tang uri: https://doi.org/10.7717/peerj.9270 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dawuda et al. title: Association of retinal nerve fiber abnormalities with serum CNTF and cognitive functions in schizophrenia patients link: https://peerj.com/articles/9279 last-modified: 2020-07-02 description: BackgroundRecent studies have reported reductions in retinal nerve fiber layers (RNFL) in schizophrenia. Ciliary neurotrophic factor (CNTF) has shown protective effects on both the neurogenesis and retina. This study aimed at investigating retinal abnormalities and establishing their correlation with serum CNTF and cognitive impairments in schizophrenic Chinese patients.MethodsIn total, 221 patients diagnosed with schizophrenia and 149 healthy controls were enrolled. Serum CNTF and clinical features of patients were investigated. Cognitive functions were evaluated with Repeatable Battery for the Assessment of Neuropsychology Status (RBANS). RNFL thickness and macular thickness (MT) of both eyes were measured with optical coherence tomography (OCT). T-tests and analysis of covariance were used to compare the variables between the patient and control groups, while multiple linear regression analysis was performed to determine the associations of RNFL thickness, CNTF and cognitive impairments.ResultsRNFL was found thinner in patients than in healthy controls (right: 88.18 ± 25.84 µm vs.102.13 ± 14.32 µm, p = 0.001; left: 92.84 ± 13.54 µm vs.103.71 ± 11.94 µm, p < 0.001). CNTF was lower in the schizophrenia group (1755.45 ± 375.73 pg/ml vs. 1909.99 ± 368.08 pg/ml, p = 0.001). Decline in RNFL thickness was found correlated with course of illness and serum CNTF in patients (all p < 0.05). Similarly, cognitive functions such as immediate memory and visuospatial functions were also found correlated with decline in RNFL thickness.ConclusionDecline in RNFL thickness was associated with cognitive impairments of schizophrenia and CNFT serum concentration. The possibility of reduction in RNFL thickness as a biomarker for schizophrenia needs to be further examined. creator: Yanhong Liu creator: Lvzhen Huang creator: Yongsheng Tong creator: Jingxu Chen creator: Dongfang Gao creator: Fude Yang uri: https://doi.org/10.7717/peerj.9279 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: SSREnricher: a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis link: https://peerj.com/articles/9372 last-modified: 2020-07-02 description: Microsatellite (SSR) markers are the most popular markers for genetic analyses and molecular selective breeding in plants and animals. However, the currently available methods to develop SSRs are relatively time-consuming and expensive. One of the most factors is low frequency of polymorphic SSRs. In this study, we developed a software, SSREnricher, which composes of six core analysis procedures, including SSR mining, sequence clustering, sequence modification, enrichment containing polymorphic SSR sequences, false-positive removal and results output and multiple sequence alignment. After running of transcriptome sequences on this software, a mass of polymorphic SSRs can be identified. The validation experiments showed almost all markers (>90%) that were identified by the SSREnricher as putative polymorphic markers were indeed polymorphic. The frequency of polymorphic SSRs identified by SSREnricher was significantly higher (P < 0.05) than that of traditional and HTS approaches. The software package is publicly accessible on GitHub (https://github.com/byemaxx/SSREnricher). creator: Wei Luo creator: Qing Wu creator: Lan Yang creator: Pengyu Chen creator: Siqi Yang creator: Tianzhu Wang creator: Yan Wang creator: Zongjun Du uri: https://doi.org/10.7717/peerj.9372 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Luo et al. title: Elephants in the neighborhood: patterns of crop-raiding by Asian elephants within a fragmented landscape of Eastern India link: https://peerj.com/articles/9399 last-modified: 2020-07-02 description: Loss of forest cover, rise in human populations and fragmentation of habitats leads to decline in biodiversity and extinction of large mammals globally. Elephants, being the largest of terrestrial mammals, symbolize global conservation programs and co-occur with humans within multiple-use landscapes of Asia and Africa. Within such shared landscapes, poaching, habitat loss and extent of human–elephant conflicts (HEC) affect survival and conservation of elephants. HEC are severe in South Asia with increasing attacks on humans, crop depredation and property damage. Such incidents reduce societal tolerance towards elephants and increase the risk of retaliation by local communities. We analyzed a 2-year dataset on crop depredation by Asian elephants (N = 380) events in North Bengal (eastern India). We also explored the effect of landscape, anthropogenic factors (area of forest, agriculture, distance to protected area, area of human settlements, riverine patches and human density) on the spatial occurrence of such incidents.Crop depredation showed a distinct nocturnal pattern (22.00–06:00) and majority of the incidents were recorded in the monsoon and post-monsoon seasons. Results of our spatial analysis suggest that crop depredation increased with an increase in the area of forest patches, agriculture, presence of riverine patches and human density. Probability of crop depredation further increased with decreasing distance from protected areas. Villages within 1.5 km of a forest patch were most affected. Crop raiding incidents suggest a deviation from the “high-risk high-gain male biased” foraging behavior and involved proportionately more mixed groups (57%) than lone bulls (43%). Demographic data suggest that mixed groups comprised an average of 23 individuals with adult and sub adult females, bulls and calves. Crop depredation and fatal elephant attacks on humans were spatially clustered with eastern, central and western parts of North Bengal identified as hotspots of HEC. Our results will help to prioritize mitigation measures such as prohibition of alcohol production within villages, improving condition of riverine patches, changing crop composition, fencing agriculture fields, implement early warning systems around protected areas and training local people on how to prevent conflicts. creator: Dipanjan Naha creator: Suraj Kumar Dash creator: Abhisek Chettri creator: Akashdeep Roy creator: Sambandam Sathyakumar uri: https://doi.org/10.7717/peerj.9399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Naha et al. title: TAPB and RSB protects cardiac diastolic function in elderly patients undergoing abdominopelvic surgery: a retrospective cohort study link: https://peerj.com/articles/9441 last-modified: 2020-07-02 description: BackgroundDiastolic dysfunction, an early manifestation and clinical symptom of heart failure with preserved ejection fraction, can be influenced by various anesthesia management strategies. Trans-esophageal echocardiography was used to undertake to assess left ventricular diastolic function during anesthesia maintenance using sevoflurane alone and sevoflurane combining with transversus abdominis plane block and rectus sheath block in elderly patients with diastolic dysfunction undergoing abdominopelvic surgery.MethodsThirty-eight patients were divided into two groups in this retrospective study, sevoflurane and sevoflurane combining with TAPB and RSB according to employing different anesthesia maintenance schemes. The parameters HR, MAP, CVP, E, A, E/A, e, a, e/a, and E/a were obtained immediately after anesthesia induction hemodynamics stability (HR1, MAP1, CVP1, E1, A1, E1/A1, e1, a1, e1/a1, and E1/a1) and 1 hour later (HR2, MAP2, CVP2, E2, A2, E2/A2, e2, a2, e2/a2, and E2/a2).ResultsTransmitral diastolic Doppler flow characteristics illustrated E/A significant decreases in the S group but increases in the ST group (p = 0.02 < 0.05) 1 hour after anesthesia induction hemodynamic stability. Tissue Doppler imaging characteristics showed a more significant increase e/a (P = 0.005 < 0.05) and decreases in a value (p = 0.009 < 0.05) in the ST group 1 hour after anesthesia induction hemodynamics stability.ConclusionsMaintaining anesthesia with sevoflurane combining with TAPB and RSB was more suitable for protecting cardiac diastolic function than sevoflurane alone in elderly patients with diastolic dysfunction undergoing open abdominal and pelvic surgery. creator: Chao Gong creator: Shitong Li creator: Xiaojing Huang creator: Lianhua Chen uri: https://doi.org/10.7717/peerj.9441 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gong et al. title: Effects of vegetation restoration on soil quality in fragile karst ecosystems of southwest China link: https://peerj.com/articles/9456 last-modified: 2020-07-02 description: Soil quality assessment is important for karst ecosystems where soil erosion is significant. A large amount of vegetation restoration has been implemented since the early 21st century in degraded karst areas across southwestern China. However, the impacts on soil quality of different restoration types rarely have been compared systematically. In the current study, we investigated the soil quality after a number of vegetation restoration projects as well as their adjacent cropland by analyzing soil samples. Six vegetation restoration types were evaluated, including one natural restoration (natural shrubland, protected for 13 years), three economic forests (4 years Eucalyptus robusta, 4 years Prunus salicina and 6 years Zenia insignis) and two mixed forests (1 year Juglans regia–crop and 13 years Toona sinensis-Pennisetum purpureum ). We evaluated the benefits of different restoration types more accurately by setting each adjacent cropland as the control and setting the variation between the corresponding restored and control site as the evaluation object so that the background differences of six sites could be eliminated. The results indicated that natural shrubland, Toona sinensis-Pennisetum purpureum and Zenia insignis were effective in improving soil quality index (SQI) in degraded karst cropland largely due to their higher SOC and TN content. The variation of SQI (VSQI) of natural shrubland was significantly higher than that in Eucalyptus robusta, Prunus salicina and Juglans regia-crop in total soil layer (0–30 cm) (P < 0.05), indicating natural shrubland had better capacity to improve soil quality. The boosting regression tree model revealed that vegetation restoration type explained 73.49% and restoration time explained 10.30% of the variation in VSQI, which confirmed that vegetation restoration type and restoration time are critical for achieving soil reserves. Therefore, it is vital to select appropriate vegetation type in restoration projects and recovery for a long time in order to achieve better soil quality. The current study provides a theoretical basis on which to assess the effects of different vegetation restoration types on the heterogeneous degraded karst areas. creator: Huiling Guan creator: Jiangwen Fan uri: https://doi.org/10.7717/peerj.9456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Guan and Fan title: Effects of microbial evolution dominate those of experimental host-mediated indirect selection link: https://peerj.com/articles/9350 last-modified: 2020-07-01 description: Microbes ubiquitously inhabit animals and plants, often affecting their host’s phenotype. As a result, even in a constant genetic background, the host’s phenotype may evolve through indirect selection on the microbiome. ‘Microbiome engineering’ offers a promising novel approach for attaining desired host traits but has been attempted only a few times. Building on the known role of the microbiome on development in fruit flies, we attempted to evolve earlier-eclosing flies by selecting on microbes in the growth media. We carried out parallel evolution experiments in no- and high-sugar diets by transferring media associated with fast-developing fly lines over the course of four selection cycles. In each cycle, we used sterile eggs from the same inbred population, and assayed mean fly eclosion times. Ultimately, flies eclosed seven to twelve hours earlier, depending on the diet, but microbiome engineering had no effect relative to a random-selection control treatment. 16S rRNA gene sequencing showed that the microbiome did evolve, particularly in the no sugar diet, with an increase in Shannon diversity over time. Thus, while microbiome evolution did affect host eclosion times, these effects were incidental. Instead, any experimentally enforced selection effects were swamped by uncontrolled microbial evolution, likely resulting in its adaptation to the media. These results imply that selection on host phenotypes must be strong enough to overcome other selection pressures simultaneously operating on the microbiome. The independent evolutionary trajectories of the host and the microbiome may limit the extent to which indirect selection on the microbiome can ultimately affect host phenotype. Random-selection lines accounting for independent microbial evolution are essential for experimental microbiome engineering studies. creator: Jigyasa Arora creator: Margaret A. Mars Brisbin creator: Alexander S. Mikheyev uri: https://doi.org/10.7717/peerj.9350 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Arora et al. title: Spawning of French grunts, Haemulon flavolineatum, in recirculating aquarium systems link: https://peerj.com/articles/9417 last-modified: 2020-07-01 description: BackgroundBecause the French grunt, Haemulon flavolineatum, is an ecologically important reef fish prized by both recreational anglers and public aquariums, the wild population requires limits on harvests. Yet, the environmental conditions conducive for French grunt spawning in aquarium settings is not well understood. Therefore, the goal of this study was to document the conditions leading to voluntary spawning and the number of eggs produced by French grunts without the use of hormones or artificial insemination.MethodsWe hypothesized and verified that it is possible for French grunts to spontaneously spawn in human care. Forty individuals were collected around the Florida Keys and haphazardly stocked in five recirculating seawater systems each containing two 250-L circular tanks. Over the course of 87 days, eggs were collected daily from each system and environmental parameters were monitored.ResultsTotal daily number of eggs released ranged from 0 to 207,644 eggs. Of the observed environmental parameters, temperature and alkalinity had the greatest impact on number of eggs released. This study demonstrates that it is possible for French grunts to reproduce in captivity with little environmental manipulation, thus an ideal candidate to culture for the zoo/aquarium industry. creator: Leah Maurer creator: Matthew Dawson creator: Larry Boles creator: Stacy Knight creator: Andrew Stamper uri: https://doi.org/10.7717/peerj.9417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Maurer et al. title: Habitat association in the critically endangered Mangshan pit viper (Protobothrops mangshanensis), a species endemic to China link: https://peerj.com/articles/9439 last-modified: 2020-07-01 description: Habitat directly affects the population size and geographical distribution of wildlife species, including the Mangshan pit viper (Protobothrops mangshanensis), a critically endangered snake species endemic to China. We searched for Mangshan pit viper using randomly arranged transects in their area of distribution and assessed their habitat association using plots, with the goals of gaining a better understanding of the habitat features associated with P. mangshanensis detection and determining if the association with these features varies across season. We conducted transect surveys, found 48 individual snakes, and measured 11 habitat variables seasonally in used and random plots in Hunan Mangshan National Nature Reserve over a period of 5 years (2012–2016). The important habitat variables for predicting Mangshan pit viper detection were fallen log density, shrub density, leaf litter cover, herb cover and distance to water. In spring, summer and autumn, Mangshan pit viper detection was always positively associated with fallen log density. In summer, Mangshan pit viper detection was related to such habitats with high canopy cover, high shrub density and high herb cover. In autumn, snakes generally occurred in habitats near water in areas with high fallen log density and tall shrubs height. Our study is the first to demonstrate the relationship between Mangshan pit viper detection and specific habitat components. Mangshan pit viper detection was associated with habitat features such as with a relatively high fallen log density and shrub density, moderately high leaf litter cover, sites near stream, and with lower herb cover. The pattern of the relationship between snakes and habitats was not consistent across the seasons. Identifying the habitat features associated with Mangshan pit viper detection can better inform the forestry department on managing natural reserves to meet the habitat requirements for this critically endangered snake species. creator: Bing Zhang creator: Bingxian Wu creator: Daode Yang creator: Xiaqiu Tao creator: Mu Zhang creator: Shousheng Hu creator: Jun Chen creator: Ming Zheng uri: https://doi.org/10.7717/peerj.9439 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Bioindicator potential of Ricinus communis to simulated rainfall containing potassium fluoride link: https://peerj.com/articles/9445 last-modified: 2020-07-01 description: BackgroundFluoride pollution is a global problem because of its high phytotoxicity. Fluoride is released in air, water and soil through industrial processes, where it damages various plant species. Ricinus communis is widely distributed in Brazil, India and China and has been extensively used as a phytoremediation species in heavy metal-contaminated soils. However, few studies regarding the effect of air pollutants on R. communis have been published, and no information about the exposure of this species to fluoride is available. Therefore, the aim of the present study was to investigate the effects of fluoride on R. communis morphoanatomical and physiological responses using simulated rainfall containing potassium fluoride (KF).MethodsYoung plants at approximately 10 days after emergence were treated daily with KF using simulated rainfall at 0, 1.5, 3.0 and 4.5 mg L−1, for 37 consecutive days. Chlorophyll a fluorescence, gas exchange, anatomical characteristics and fluoride accumulation in the roots and leaves were evaluated after this period.ResultsNo visual or anatomical symptoms were observed for the first three treatments. Necrosis and chlorosis were visually evident after the 37th day of KF application at 4.5 mg L−1, followed by changes in parenchyma tissues, cell collapse and phenolic compound accumulation at the end of the experiment. No damage was observed in terms of photosynthetic photochemical and biochemical stages. Maintenance of physiological characteristics in the presence of fluoride accumulation in roots and leaves were shown to be important fluoride biomarkers. These characteristics suggest that R. communis is tolerant to 1.5 and 3.0 mg L−1 KF, and is anatomically sensitive at 4.5 mg L−1 KF. creator: Douglas Almeida Rodrigues creator: Juliana de Fátima Sales creator: Sebastião Carvalho Vasconcelos Filho creator: Arthur Almeida Rodrigues creator: Eduardo Matheus Guimarães Teles creator: Alan Carlos Costa creator: Efraim Lázaro Reis creator: Thais Andrade de Carvalho Silva creator: Caroline Müller uri: https://doi.org/10.7717/peerj.9445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Rodrigues et al. title: A novel bamboo sheet chair and its influence on sitting comfort link: https://peerj.com/articles/9476 last-modified: 2020-07-01 description: BackgroundIn today’s economy, workers spend increasingly more time in seated positions, leading to a growing scientific interest in chair design. In this study we used body pressure distribution tests to compare a novel bamboo chair with unique structural features to other commonly-used chairs. We studied the bamboo sheet chair’s physical characteristics and comfort to provide a scientific theoretical basis for common use seat design.MethodsA total of 25 (14 male and 11 female) subjects participated in the study. Subjects were divided into six groups according to their body characteristics parameters included stature, weight, shoulder breadth, hip breadth, waist width, popliteal height, buttocks-popliteal length, and buttock-abdomen depth, with three groups for males and three groups for females. Each subject was required to complete specified body pressure tests for three different experimental chairs for three minutes and subjective comfort evaluations were also administered. The pressure indexes were measured from the seat pan and backrest and calculated with MATLAB 2015b, which mainly included maximum pressure (Pm), average pressure (Pa), pressure exponent (Pe) and contact area index (PAI). Three pressure threshold limits of 0.67 kPa, 4.00 kPa and 9.33 kPa and four contact surface indexes were used in the experiment to reflect the contact area between human and chair.ResultsThe contact areas in the backrest (52.96 ± 32.94 cm2) and seat pan (307.75 ± 90.31 cm2) in the middle-to-high threshold pressure range, and the contact areas of the backrest (4.34 ± 5.95 cm2) in the high threshold pressure range of bamboo sheet chair were smaller than the corresponding indexes of the common office chair (81.430 ± 45.04 cm2, p = 0.00; 394.39 ± 98.99 cm2, p = 0.02; 13.54 ± 12.00 cm2, p = 0.00, respectively). The pressure index (2.68 ± 0.88 kPa), maximum pressure (6.66 ± 2.05 kPa), and average pressure (2.42 ± 0.59 kPa) values of the bamboo sheet chair backrest were also found to be lower than those of the office chair (4.32 ± 1.62 kPa, p = 0.00; 10.50 ± 3.88 kPa, p = 0.00; 3.43 ± 0.97 kPa, p = 0.00, respectively). The average pressure on the seat pan was greater than 4 kPa for all subjects, while the average pressure on the seat pan was greater than 9.33 kPa for male subjects with a body mass index (BMI) of 27.48.DiscussionThe bamboo sheet chair’s contact areas within the middle-to-high and high-pressure threshold ranges of the backrest and seat pan were smaller than those of the office chair, indicating that the bamboo sheet chair is effective at relieving pressure. Human body characteristics must be considered in the design of seat functional size. Buttocks-popliteal length, weight, body mass index, body shape and weight distribution, all have important effects on the distribution of body pressure at the human-chair interface. creator: Fangcheng Yuan creator: Yong Guo creator: Yunjiao Shi creator: Kaiting Zhang creator: Zhenzhen Zhu creator: Yuxia Chen uri: https://doi.org/10.7717/peerj.9476 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yuan et al.