title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1368 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands link: https://peerj.com/articles/6800 last-modified: 2019-04-25 description: Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and ‘universal’ gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The ‘VirION’ (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature. creator: Joanna Warwick-Dugdale creator: Natalie Solonenko creator: Karen Moore creator: Lauren Chittick creator: Ann C. Gregory creator: Michael J. Allen creator: Matthew B. Sullivan creator: Ben Temperton uri: https://doi.org/10.7717/peerj.6800 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Warwick-Dugdale et al. title: Forensic characteristics and population genetics of Chinese Kazakh ethnic minority with an efficient STR panel link: https://peerj.com/articles/6802 last-modified: 2019-04-25 description: On the purpose of enhancing the forensic efficiency of CODIS STR loci, new STR loci have been gradually discovered and developed into some commercial multiplex systems. Recently, 22 STR loci including 18 non-CODIS STR loci and four CODIS STR loci were investigated in 501 unrelated healthy individuals of Kazakh ethnic group. Seven to 20 alleles at the different loci were identified and altogether 276 alleles for 22 selected loci were detected with the corresponding allelic frequencies ranging from 0.0010 to 0.3623. No significant deviation was observed from the Hardy–Weinberg equilibrium test for any of the 22 STRs. The value of cumulative power of discrimination in Kazakh group was 1-1.00E−28. Analyses of population differentiations and genetic distances between Kazakh and other Chinese groups presented that the Kazakh group with the Uygur group. These 22 STR loci evenly distributed on 22 different autosomal chromosomes were characterized by high genetic diversities and therefore could be utilized in the forensic cases to further increase the discrimination performance. creator: Chong Chen creator: Yuxin Guo creator: Xiaoye Jin creator: Wei Cui creator: Yuanyuan Wei creator: Yating Fang creator: Qiong Lan creator: Tingting Kong creator: Tong Xie creator: Bofeng Zhu uri: https://doi.org/10.7717/peerj.6802 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Beliefs are multidimensional and vary in stability over time - psychometric properties of the Beliefs and Values Inventory (BVI) link: https://peerj.com/articles/6819 last-modified: 2019-04-25 description: The cognitive processes underlying belief are still obscure. Understanding these processes may lead to more targeted treatment to better address functional impairment, such as occurs with delusions. One way in which this might be accomplished is to understand healthy, everyday beliefs, and how these may relate to characteristics observed in delusions. As yet, no such measure exists to accurately measure belief across a range of themes and dimensions. This paper outlines two studies documenting the creation and psychometric properties of a novel measure assessing three different dimensions of belief across themes of politics, science, the paranormal, religion, and morality in UK samples (n = 1, 673 total). Reliability estimates suggested good to excellent consistency (alpha > 0.8 per theme) with moderate to excellent reliability at 48 h (ICC = 0.61 –0.96) and 3.5 months (ICC = 0.61 –0.89). Factor analyses suggested good support for our five chosen themes of belief, suggesting they are distinct topic areas. Correlations across theme and dimension suggested dissociable characteristics within themes. These results have implications for 1. understanding the stability and relationship between themes of belief in a population and, 2. exploring how beliefs may change over time or as a result of an intervention. Full analysis code and data are available from the Open Science Framework (https://osf.io/hzvwr/). creator: Joseph M. Barnby creator: Vaughan Bell creator: Luke Sheridan Rains creator: Mitul A. Mehta creator: Quinton Deeley uri: https://doi.org/10.7717/peerj.6819 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Barnby et al. title: Hand hygiene knowledge and attitude of medical students in western Saudi Arabia link: https://peerj.com/articles/6823 last-modified: 2019-04-25 description: BackgroundThe practice of hand hygiene (HH) has prime importance among Health Care Professionals (HCPs) and non-compliance could cause adverse consequences. By keeping the importance of HH in mind, this study aims at investigating the knowledge and attitudes towards HH among medical students and interns at King Abdulaziz University (KAU), Jeddah, Saudi Arabia (SA).MethodsThe study includes 453 medical students and interns (189 males & 264 females). This study was completed in three months; from September to November 2017. The World Health Organization (WHO) HH questionnaire was used and data were analyzed on SPSS-21.ResultsTwo-third of the participants 292 (64.2%) had formal training in HH in the last three years. Almost half of the participants 254 (56.1%) had correct knowledge regarding the major course of transmission of potentially detrimental microbes among patients in the healthcare premises. Just 124 (27.4%) of the respondents had the correct knowledge about the most common basis of germs accountable for healthcare-related infections. Females had significantly better knowledge than males regarding the type of HH technique needed before palpation of the abdomen (177(54%) Vs. 151(46%); P < 0.002), before an injection (175(54.5%) Vs. 146(45.5%); P < 0.007), after emptying a bedpan (207(64.7%) Vs. 113(35.3%); P < 0.001), following discarding examination gloves (256(60.4% Vs. 168(39.6%); P < 0.001] and after exposure to blood (200(64.1%) Vs. 112(35.%); P < 0.001). Female participants had better knowledge than males regarding the type of HH actions. Females also had a significantly better attitude towards the importance of HH than males (240(62.5%) Vs. 144(37.5%); P < 0.001).ConclusionThe majority of the participants’ knowledge regarding HH was not up to the mark; however, female students had better knowledge compared to male students. The medical students and interns’ knowledge and positive attitude towards HH can play a pivotal role in preventing HCPs associated infections and it would overall decrease the infection-related burden on the hospital and governmental budgets. It is suggested that multi-dimensional plans are required to change this low compliance to a higher rate. creator: Marwan A. Bakarman creator: Mukhtiar Baig creator: Ahmad A. Malik creator: Zohair J. Gazzaz creator: Mostafa M. Mostafa creator: Mohamed A. Zayed creator: Abdulaziz S. Balubaid creator: Ahmed K. Alzahrani uri: https://doi.org/10.7717/peerj.6823 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bakarman et al. title: Bibliometric analysis of scientific publications in rheumatology journals from China and other top-ranking countries between 2007 and 2017 link: https://peerj.com/articles/6825 last-modified: 2019-04-25 description: ObjectivesRheumatology-related diseases remain a significant burden worldwide. However, little is known about the comparative status of rheumatology research between Mainland China (MC) and the world’s leading countries. The aim of this study is to compare the quantity and quality of research output in the field of rheumatology that were written by researchers from MC, the USA, the UK, the Netherlands and France.MethodsBetween 2007 and 2017, all articles published in 30 rheumatology journals were identified via Science Citation Index Expanded database. The number of total and annual articles, article types (randomized controlled trials (RCTs), reviews, case reports, clinical trials and meta-analysis), impact factor (IF), citations, h-index and articles in the high-impact journals were collected for quantity and quality comparisons. The correlation of socioeconomic factors and annual publications was also analyzed.ResultsFrom 2007 to 2017, there were 53,439 articles published in rheumatology journals, of which researchers from the USA published 13,391 articles, followed by the UK, the Netherlands, France and MC with 6,179, 4,310, 4,066 and 2,898 articles, respectively. Publications from MC represented the ninth, but the number is growing rapidly. For total and average citations, MC still lags behind the other four countries in the study. Similar trends were observed in average IF, h-index and articles in the high-impact journals. In terms of article types, the USA occupies the dominant place, except for meta-analysis. The annual numbers of articles from MC and the USA were positively correlated with gross domestic product (p < 0.05).ConclusionsThe USA has played predominant role in rheumatology research for the last 11 years. The annual number of published articles from MC has increased notably from 2007 to 2017. Although MC has made progress in the number of published articles over the past decade, it still lags far behind the highly developed countries in most bibliometric indicators. Thus, the general quality of publications from MC needs further improvement. creator: Chen Zhang creator: Xinzhe Feng creator: Chen Wang creator: Denghui Liu creator: Chongru He creator: Weidong Xu uri: https://doi.org/10.7717/peerj.6825 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Evolution of digestive enzymes and dietary diversification in birds link: https://peerj.com/articles/6840 last-modified: 2019-04-25 description: As the most species-rich class of tetrapod vertebrates, Aves possesses diverse feeding habits, with multiple origins of insectivory, carnivory, frugivory, nectarivory, granivory and omnivory. Since digestive enzymes mediate and limit energy and nutrient uptake, we hypothesized that genes encoding digestive enzymes have undergone adaptive evolution in birds. To test this general hypothesis, we identified 16 digestive enzyme genes (including seven carbohydrase genes (hepatic amy, pancreatic amy, salivary amy, agl, g6pc, gaa and gck), three lipase genes (cyp7a1, lipf and pnlip), two protease genes (ctrc and pgc), two lysozyme genes (lyz and lyg) and two chitinase genes (chia and chit1)) from the available genomes of 48 bird species. Among these 16 genes, three (salivary amy, lipf and chit1) were not found in all 48 avian genomes, which was further supported by our synteny analysis. Of the remaining 13 genes, eight were single-copy and five (chia, gaa, lyz, lyg and pgc) were multi-copy. Moreover, the multi-copy genes gaa, lyg and pgc were predicted to exhibit functional divergence among copies. Positively selected sites were detected in all of the analyzed digestive enzyme genes, except agl, g6pc, gaa and gck, suggesting that different diets may have favored differences in catalytic capacities of these enzymes. Furthermore, the analysis also revealed that the pancreatic amylase gene and one of the lipase genes (cyp7a1) have higher ω (the ratio of nonsynonymous to the synonymous substitution rates) values in species consuming a larger amount of seeds and meat, respectively, indicating an intense selection. In addition, the gck carbohydrase gene in species consuming a smaller amount of seeds, fruits or nectar, and a lipase gene (pnlip) in species consuming less meat were found to be under relaxed selection. Thus, gene loss, gene duplication, functional divergence, positive selection and relaxed selection have collectively shaped the evolution of digestive enzymes in birds, and the evolutionary flexibility of these enzymes may have facilitated their dietary diversification. creator: Yan-Hong Chen creator: Huabin Zhao uri: https://doi.org/10.7717/peerj.6840 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen and Zhao title: Training-induced increase in Achilles tendon stiffness affects tendon strain pattern during running link: https://peerj.com/articles/6764 last-modified: 2019-04-24 description: BackgroundDuring the stance phase of running, the elasticity of the Achilles tendon enables the utilisation of elastic energy and allows beneficial contractile conditions for the triceps surae muscles. However, the effect of changes in tendon mechanical properties induced by chronic loading is still poorly understood. We tested the hypothesis that a training-induced increase in Achilles tendon stiffness would result in reduced tendon strain during the stance phase of running, which would reduce fascicle strains in the triceps surae muscles, particularly in the mono-articular soleus.MethodsEleven subjects were assigned to a training group performing isometric single-leg plantarflexion contractions three times per week for ten weeks, and another ten subjects formed a control group. Before and after the training period, Achilles tendon stiffness was estimated, and muscle-tendon mechanics were assessed during running at preferred speed using ultrasonography, kinematics and kinetics.ResultsAchilles tendon stiffness increased by 18% (P < 0.01) in the training group, but the associated reduction in strain seen during isometric contractions was not statistically significant. Tendon elongation during the stance phase of running was similar after training, but tendon recoil was reduced by 30% (P < 0.01), while estimated tendon force remained unchanged. Neither gastrocnemius medialis nor soleus fascicle shortening during stance was affected by training.DiscussionThese results show that a training-induced increase in Achilles tendon stiffness altered tendon behaviour during running. Despite training-induced changes in tendon mechanical properties and recoil behaviour, the data suggest that fascicle shortening patterns were preserved for the running speed that we examined. The asymmetrical changes in tendon strain patterns supports the notion that simple in-series models do not fully explain the mechanical output of the muscle-tendon unit during a complex task like running. creator: Amelie Werkhausen creator: Neil J. Cronin creator: Kirsten Albracht creator: Gøran Paulsen creator: Askild V. Larsen creator: Jens Bojsen-Møller creator: Olivier R. Seynnes uri: https://doi.org/10.7717/peerj.6764 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Werkhausen et al. title: Likes, comments, and shares of marine organism imagery on Facebook link: https://peerj.com/articles/6795 last-modified: 2019-04-24 description: Several calls to action urge scientists and science communicators to engage more with online communities. While these calls have been answered by a high percentage of scientists and science communicators online, it often remains unclear what are the best models for effective communication. Best practices and methods for online science communication can benefit from experimental and quantitative research addressing how and when users engage with online content. This study addresses with quantitative and predictive models a key question for the popular, but often-ignored in science communication, social media platform Facebook. Specifically, this study examines the impact of imagery through quantification of likes, comments, and shares on Facebook posts. Here, I show that a basic quantitative model can be useful in predicting response to marine organism imagery on Facebook. The results of this online experiment suggest image type, novelty, and aesthetics impact the number of likes, shares, and comments on a post. In addition, the likes, shares, and comments on images did not follow traditional definitions of “charismatic megafauna”, with cephalopods and bony fishes receiving more interactions than cartilaginous fishes and marine mammals. Length and quality of caption did not significantly impact likes, comments, or shares. This study provides one of the first quantitative analysis of virality of scientific images via social media. The results challenge previously held conceptions of social media scientific outreach including increasing emphasis on imagery selection and curation, notions of which taxa the public connect with, and role of captions for imagery. creator: Craig R. McClain uri: https://doi.org/10.7717/peerj.6795 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 McClain title: Transcriptional analysis reveals the metabolic state of Burkholderia zhejiangensis CEIB S4-3 during methyl parathion degradation link: https://peerj.com/articles/6822 last-modified: 2019-04-24 description: Burkholderia zhejiangensis CEIB S4-3 has the ability to degrade methyl parathion (MP) and its main hydrolysis byproduct p-nitrophenol (PNP). According to genomic data, several genes related with metabolism of MP and PNP were identified in this strain. However, the metabolic state of the strain during the MP degradation has not been evaluated. In the present study, we analyzed gene expression changes during MP hydrolysis and PNP degradation through a transcriptomic approach. The transcriptional analysis revealed differential changes in the expression of genes involved in important cellular processes, such as energy production and conversion, transcription, amino acid transport and metabolism, translation, ribosomal structure and biogenesis, among others. Transcriptomic data also exhibited the overexpression of both PNP-catabolic gene clusters (pnpABA′E1E2FDC and pnpE1E2FDC) present in the strain. We found and validated by quantitative reverse transcription polymerase chain reaction the expression of the methyl parathion degrading gene, as well as the genes responsible for PNP degradation contained in two clusters. This proves the MP degradation pathway by the strain tested in this work. The exposure to PNP activates, in the first instance, the expression of the transcriptional regulators multiple antibiotic resistance regulator and Isocitrate Lyase Regulator (IclR), which are important in the regulation of genes from aromatic compound catabolism, as well as the expression of genes that encode transporters, permeases, efflux pumps, and porins related to the resistance to multidrugs and other xenobiotics. In the presence of the pesticide, 997 differentially expressed genes grouped in 104 metabolic pathways were observed. This report is the first to describe the transcriptomic analysis of a strain of B. zhejiangensis during the biodegradation of PNP. creator: María Luisa Castrejón-Godínez creator: Ma. Laura Ortiz-Hernández creator: Emmanuel Salazar creator: Sergio Encarnación creator: Patricia Mussali-Galante creator: Efraín Tovar-Sánchez creator: Enrique Sánchez-Salinas creator: Alexis Rodríguez uri: https://doi.org/10.7717/peerj.6822 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Castrejón-Godínez et al. title: A fixed agreement—consequences of brood size manipulation on alternation in blue tits link: https://peerj.com/articles/6826 last-modified: 2019-04-24 description: Recent studies have proposed that conditional cooperation may resolve sexual conflict over the amount of care provided by each parent. Such conditional cooperation may allow parents to equalize their investment by alternating their provisioning visits. This alternated pattern of male and female visits, that is, alternation, is thought to stimulate each other’s investment leading to higher levels of provisioning and potential benefits for offspring development. However, experimental studies testing the role of alternation as an adaptive parental strategy to negotiate the level of investment are still absent. Therefore, we manipulated blue tit (Cyanistes caeruleus) parents by temporarily changing their brood sizes to induce changes in demand and thus visit rates. Parents were expected to visit more—assuming that prey sizes were constant—and alternate at higher levels when confronted with an enlarged brood given the greater potential for sexual conflict. In contrast, in reduced broods visit rates and alternation may become lower due to the smaller investment that is needed for reduced broods. We show that the level of alternation did not differ in response to the manipulated brood sizes, despite a directional change in visit rates for enlarged and reduced broods as expected. Nestlings did not benefit from high levels of alternation as no effects on nestling mass gain were present in either of the different manipulations. These findings indicate that alternation does not serve as a mechanism to motivate each other to feed at higher rates. Parents hence appeared to be inflexible in their level of alternation. We therefore suggest that the level of alternation might reflect a fixed agreement about the relative investment by each of the caring parents. creator: Maaike Griffioen creator: Wendt Müller creator: Arne Iserbyt uri: https://doi.org/10.7717/peerj.6826 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Griffioen et al.