title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1094 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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.