title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2020-11 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil link: https://peerj.com/articles/9680 last-modified: 2020-11-30 description: Forensic entomology is the study of insects and other arthropods used in the solution of crimes. Most of entomological evidences strongly depend on accurate species identification. Therefore, new methods are being developed due to difficulties in morphological identification, including molecular methods such as High-Resolution Melting. In this study, we reported a new HRM primer set to identify forensically important Calliphoridae (blowflies) from Brazil. For such purpose, Calliphoridae species of forensic importance in Brazil were listed and confirmed by specialists. Mitochondrial COI sequences of those species were downloaded from databases and aligned, and polymorphic variations were selected for distinction between species. Based on it, HRM primers were designed. Forty-three fly samples representing six species were tested in the HRM assay. All samples had the COI gene sequenced to validate the result. Identifying and differentiating the six species proposed using a combination of two amplicons was possible. The protocol was effective even for old insect specimens, collected and preserved dried for more than ten years, unlike the DNA sequencing technique that failed for those samples. The HRM technique proved to be an alternative tool to DNA sequencing, with advantage of amplifying degraded samples and being fast and cheaper than the sequencing technique. creator: Pablo Viana Oliveira creator: Francine Alves Nogueira de Almeida creator: Magda Delorence Lugon creator: Karolinni Bianchi Britto creator: Janyra Oliveira-Costa creator: Alexandre Rosa Santos creator: Greiciane Gaburro Paneto uri: https://doi.org/10.7717/peerj.9680 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Oliveira et al. title: Addition of L-cysteine to the N- or C-terminus of the all-D-enantiomer [D(KLAKLAK)2] increases antimicrobial activities against multidrug-resistant Pseudomonas aeruginosa, Acinetobacter baumannii and Escherichia coli link: https://peerj.com/articles/10176 last-modified: 2020-11-30 description: BackgroundAntimicrobial peptides have a broad spectrum of antimicrobial activities and are attracting attention as promising next-generation antibiotics against multidrug-resistant (MDR) bacteria. The all-d-enantiomer [D(KLAKLAK)2] has been reported to have antimicrobial activity against Escherichia coli and Pseudomonas aeruginosa, and to be resistant to protein degradation in bacteria because it is composed of D-enantiomer compounds. In this study, we demonstrated that modification of [D(KLAKLAK)2] by the addition of an L-cysteine residue to its N- or C- terminus markedly enhanced its antimicrobial activities against Gram-negative bacteria such as MDR Acinetobacter baumannii, E. coli, and P. aeruginosa.MethodsThe peptides [D(KLAKLAK)2] (DP), DP to which L-cysteine was added at the N-terminus C-DP, and DP to which L-cysteine was added at the C-terminus DP-C, were synthesized at >95% purity. The minimum inhibitory concentrations of peptides and antibiotics were determined by the broth microdilution method. The synergistic effects of the peptides and the antibiotics against MDR P. aeruginosa were evaluated using the checkerboard dilution method. In order to assess how these peptides affect the survival of human cells, cell viability was determined using a Cell Counting Kit-8.ResultsC-DP and DP-C enhanced the antimicrobial activities of the peptide against MDR Gram-negative bacteria, including A. baumannii, E. coli, and P. aeruginosa. The antimicrobial activity of DP-C was greater than that of C-DP, with these peptides also having antimicrobial activity against drug-susceptible P. aeruginosa and drug-resistant P. aeruginosa overexpressing the efflux pump components. C-DP and DP-C also showed antimicrobial activity against colistin-resistant E. coli harboring mcr-1, which encodes a lipid A modifying enzyme. DP-C showed synergistic antimicrobial activity against MDR P. aeruginosa when combined with colistin. The LD50 of DP-C against a human cell line HepG2 was six times higher than the MIC of DP-C against MDR P. aeruginosa. The LD50 of DP-C was not altered by incubation with low-dose colistin.ConclusionAttachment of an L-cysteine residue to the N- or C-terminus of [D(KLAKLAK)2] enhanced its antimicrobial activity against A. baumannii, E. coli, and P. aeruginosa. The combination of C-DP or DP-C and colistin had synergistic effects against MDR P. aeruginosa. In addition, DP-C and C-DP showed much stronger antimicrobial activity against MDR A. baumannii and E. coli than against P. aeruginosa. creator: Maki K. Ohno creator: Teruo Kirikae creator: Eisaku Yoshihara creator: Fumiko Kirikae creator: Isao Ishida uri: https://doi.org/10.7717/peerj.10176 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ohno et al. title: A Bayesian brain model of adaptive behavior: an application to the Wisconsin Card Sorting Task link: https://peerj.com/articles/10316 last-modified: 2020-11-30 description: Adaptive behavior emerges through a dynamic interaction between cognitive agents and changing environmental demands. The investigation of information processing underlying adaptive behavior relies on controlled experimental settings in which individuals are asked to accomplish demanding tasks whereby a hidden regularity or an abstract rule has to be learned dynamically. Although performance in such tasks is considered as a proxy for measuring high-level cognitive processes, the standard approach consists in summarizing observed response patterns by simple heuristic scoring measures. With this work, we propose and validate a new computational Bayesian model accounting for individual performance in the Wisconsin Card Sorting Test (WCST), a renowned clinical tool to measure set-shifting and deficient inhibitory processes on the basis of environmental feedback. We formalize the interaction between the task’s structure, the received feedback, and the agent’s behavior by building a model of the information processing mechanisms used to infer the hidden rules of the task environment. Furthermore, we embed the new model within the mathematical framework of the Bayesian Brain Theory (BBT), according to which beliefs about hidden environmental states are dynamically updated following the logic of Bayesian inference. Our computational model maps distinct cognitive processes into separable, neurobiologically plausible, information-theoretic constructs underlying observed response patterns. We assess model identification and expressiveness in accounting for meaningful human performance through extensive simulation studies. We then validate the model on real behavioral data in order to highlight the utility of the proposed model in recovering cognitive dynamics at an individual level. We highlight the potentials of our model in decomposing adaptive behavior in the WCST into several information-theoretic metrics revealing the trial-by-trial unfolding of information processing by focusing on two exemplary individuals whose behavior is examined in depth. Finally, we focus on the theoretical implications of our computational model by discussing the mapping between BBT constructs and functional neuroanatomical correlates of task performance. We further discuss the empirical benefit of recovering the assumed dynamics of information processing for both clinical and research practices, such as neurological assessment and model-based neuroscience. creator: Marco D’Alessandro creator: Stefan T. Radev creator: Andreas Voss creator: Luigi Lombardi uri: https://doi.org/10.7717/peerj.10316 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 D’Alessandro et al. title: Effects of food type and abundance on begging and sharing in Asian small-clawed otters (Aonyx cinereus) link: https://peerj.com/articles/10369 last-modified: 2020-11-30 description: Begging for food, a conspicuous solicitation display, is common in a variety of taxa, and it has received extensive research attention in a parent-offspring context. Both theoretical models and empirical evidence suggest that offspring begging can be an honest signal of hunger or a mediator of competition between siblings. At a behavioural mechanistic level, begging for food can be a form of harassment aimed at persuading those in possession of food to share. Food sharing, defined as the transfer of a defendable food item from one individual to another, can vary considerably between species, age-classes and food type and abundance. We investigated the determinants of begging and food-sharing behaviours in Asian small-clawed otters (Aonyx cinereus), a group-living species that commonly exhibits begging in captivity. We presented two captive otter populations with three food types that varied in exploitation complexity, in three different abundances. We predicted that begging rates would be highest when food was in lowest abundance and hardest to exploit, and that increased begging would lead to increased food sharing. We found that, over time, increased begging rates were indeed correlated with increased food transfers, but neither food type complexity nor abundance affected begging or sharing rates. However, age category was significantly associated with begging and food sharing rates: juvenile otters begged more and shared less than adult otters. The results from this first experimental study on begging and food sharing within the Mustelid family begin to reveal some of the drivers of these behaviours. creator: Madison Bowden-Parry creator: Erik Postma creator: Neeltje J. Boogert uri: https://doi.org/10.7717/peerj.10369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bowden-Parry et al. title: Effects of platelet-rich plasma on mesenchymal stem cells isolated from rat uterus link: https://peerj.com/articles/10415 last-modified: 2020-11-30 description: BackgroundPlatelet-rich plasma (PRP), which represents a valuable source of growth factors, is increasingly being applied in regenerative medicine. Recent findings suggest the feasibility of using PRP in the treatment of infertility secondary to refractory thin endometrium. Mesenchymal stem/stromal cells (MSCs) of the endometrium are an essential cellular component responsible for extracellular matrix remodeling, angiogenesis, cell-to-cell communication, and postmenstrual tissue repair. Using a rat model, we examine the effects of autologous PRP on MSCs isolated from the uterus and compare them with the effects of autologous ordinary plasma (OP) and complete growth medium.MethodsMSCs were isolated from uterine tissues via enzymatic disaggregation. Flow cytometry immunophenotyping of the primary cell cultures was complemented by immunocytochemistry for Ki-67 and vimentin. The ability of MSCs to differentiate in osteo-, chondro-, and adipogenic directions was assessed using differentiation-inducing media. The levels of autophagy and apoptosis markers, as well as the levels of matrix metalloproteinase 9 (MMP9) and estrogen receptor α, were assessed by western blotting.ResultsAfter 24 h incubation, the proliferation index of the PRP-treated MSC cultures was significantly higher than that of the MSC cultures treated with complete growth medium. PRP treatment elevated production of LC3B protein, an autophagy marker, while OP treatment upregulated the expression of stress-induced protein p53 and extracellular enzyme MMP9. The results indicate practical relevance and validity for PRP use in the treatment of infertility. creator: Polina Vishnyakova creator: Daria Artemova creator: Andrey Elchaninov creator: Zulfiia Efendieva creator: Inna Apolikhina creator: Gennady Sukhikh creator: Timur Fatkhudinov uri: https://doi.org/10.7717/peerj.10415 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Vishnyakova et al. title: Repurposing FDA-approved phytomedicines, natural products, antivirals and cell protectives against SARS-CoV-2 (COVID-19) RNA-dependent RNA polymerase link: https://peerj.com/articles/10480 last-modified: 2020-11-30 description: Following the recent emergence of SARS-CoV-2 or coronavirus disease 2019 (COVID-19), drug discovery and vaccine design to combat this fatal infection are critical. In this study, an essential enzyme in the SARS-CoV-2 replication machinery, RNA-dependent RNA polymerase (RDRP), is targeted in a virtual screening assay using a set of 1,664 FDA-approved drugs, including sets of botanical and synthetic derivatives. A set of 22 drugs showed a high docking score of >−7. Notably, approximately one-third of the top hits were either from natural products or biological molecules. The FDA-approved phytochemicals were sennosides, digoxin, asiaticoside, glycyrrhizin, neohesperidin, taxifolin, quercetin and aloin. These approved natural products and phytochemicals are used as general tonics, antioxidants, cell protectives, and immune stimulants (nadid, thymopentin, asiaticoside, glycyrrhizin) and in other miscellaneous systemic or topical applications. A comprehensive analysis was conducted on standard precision and extra precision docking, two-step molecular dynamics simulations, binding energy calculations and a post dynamics analysis. The results reveal that two drugs, docetaxel and neohesperidin, showed strong binding profiles with SARS CoV-2 RdRP. These results can be used as a primer for further drug discovery studies in the treatment of COVID-19. This initiative repurposes safe FDA-approved drugs against COVID-19 RdRP, providing a rapid channel for the discovery and application of new anti-CoV therapeutics. creator: Mahmoud Kandeel creator: Yukio Kitade creator: Abdullah Almubarak uri: https://doi.org/10.7717/peerj.10480 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kandeel et al. title: Molecular phylogeny and species delimitation of the freshwater prawn Macrobrachium pilimanus species group, with descriptions of three new species from Thailand link: https://peerj.com/articles/10137 last-modified: 2020-11-27 description: Specific status and species boundaries of several freshwater prawns in the Macrobrachium pilimanus species group remain ambiguous, despite the taxonomic re-description of type materials and additional specimens collected to expand the boundaries of some species. In this study, the “pilimanus” species group of Macrobrachium sensu Johnson (1958) was studied using specimens collected from montane streams of Thailand. Molecular phylogenetic analyses based on sequences of three molecular markers (COI, 16S and 18S rRNA) were performed. The phylogenetic results agreed with morphological identifications, and indicated the presence of at least nine putative taxa. Of these, six morphospecies were recognised as M. malayanum, M. forcipatum, M. dienbienphuense, M. hirsutimanus, M. eriocheirum, and M. sirindhorn. Furthermore, three morphologically and genetically distinct linages were detected, and are described herein as M. naiyanetri Siriwut sp. nov., M. palmopilosum Siriwut sp. nov. and M. puberimanus Siriwut sp. nov. The taxonomic comparison indicated wide morphological variation in several species and suggested additional diagnostic characters that are suitable for use in species diagnoses, such as the shape and orientation of fingers, the rostrum form, and the presence or absence of velvet pubescence hairs and tuberculated spinulation on each telopodite of the second pereiopods. The “pilimanus” species group was portrayed as non-monophyletic in both ML and BI analyses. The genetic structure of different geographical populations in Thailand was detected in some widespread species. The species delimitation based on the four delimitation methods (BIN, ABGD, PTP and GMYC) suggested high genetic diversity of the “pilimanus” species group and placed the candidate members much higher than in previous designations based on traditional morphology. This finding suggests that further investigation of morphological and genetic diversity of Southeast Asian freshwater prawns in the genus Macrobrachium is still required to provide a comprehensive species list to guide efforts in conservation and resource management. creator: Warut Siriwut creator: Ekgachai Jeratthitikul creator: Somsak Panha creator: Ratmanee Chanabun creator: Chirasak Sutcharit uri: https://doi.org/10.7717/peerj.10137 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Siriwut et al. title: Effectiveness of specific stabilization exercise compared with traditional trunk exercise in women with non-specific low back pain: a pilot randomized controlled trial link: https://peerj.com/articles/10304 last-modified: 2020-11-27 description: BackgroundNon-specific low back pain (LBP) is the leading cause of disability worldwide. The primary physiotherapeutic treatment for LBP is physical exercise, but evidence suggesting a specific exercise as most appropriate for any given case is limited.ObjectiveTo determine if specific stabilization exercise (SSE) is more effective than traditional trunk exercise (TTE) in reducing levels of pain, disability and inflammation in women with non-specific low back pain (LBP).DesignA pilot randomized controlled trial was conducted in Rovira i Virgili University, Catalonia.MethodsThirty-nine females experiencing non-specific LBP were included in two groups: the TTE program and SSE program, both were conducted by a physiotherapist during twenty sessions. The primary outcome was pain intensity (10-cm Visual Analogue Scale). Secondary outcomes were disability (Roland Morris Disability Questionnaire), and inflammation (IL-6 and TNF-α plasma levels). Measurements were taken at baseline, at half intervention, at post-intervention, and a month later.ResultsMean group differences in change from baseline to post-intervention for TTE were: −4.5 points (CI 3.3 to 5.6) for pain, −5.1 points (CI 3.0 to 7.3) for disability, 0.19 pg/mL (95% CI [−1.6–1.2]) for IL-6 levels, and 46.2 pg/mL (CI 13.0 to 85.3) for TNF-α levels. For SSE, differences were: −4.3 points (CI 3.1 to 5.6) for pain, −6.1 points (CI 3.7 to 8.6) for disability, 1.1 pg/mL (CI 0.0 to 2.1) for IL-6 levels , and 12.8 pg/mL (95% CI [−42.3–16.7]) for TNF-α levels. There were an insignificant effect size and no statistically significant overall mean differences between both groups.ConclusionThis study suggests that both interventions (traditional trunk and specific stabilization exercises) are effective in reducing pain and disability in non-specific LBP patients, but the two programs produce different degrees of inflammation change.Clinical trial registration numberNCT02103036. creator: Eduard Minobes-Molina creator: Maria Rosa Nogués creator: Montse Giralt creator: Carme Casajuana creator: Dyego Leandro Bezerra de Souza creator: Javier Jerez-Roig creator: Marta Romeu uri: https://doi.org/10.7717/peerj.10304 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Minobes-Molina et al. title: Eco-morphological diversity of larvae of soldier flies and their closest relatives in deep time link: https://peerj.com/articles/10356 last-modified: 2020-11-27 description: Stratiomyomorpha (soldier flies and allies) is an ingroup of Diptera, with a fossil record stretching back to the Early Cretaceous (the Barremian, about 125 MYA). Stratiomyomorpha includes at least 3,000 species in the modern fauna, with many species being crucial for ecosystem functions, especially as saprophages. Larvae of many stratiomyomorphans are especially important as scavengers and saproxyls in modern ecosystems. Yet, fossil larvae of the group are extremely scarce. Here we present 23 new records of fossil stratiomyomorphan larvae, representing six discrete morphotypes. Specimens originate from Cretaceous amber from Myanmar, Eocene Baltic amber, Miocene Dominican amber, and compression fossils from the Eocene of Messel (Germany) and the Miocene of Slovenia. We discuss the implications of these new records for our understanding of stratiomyomorphan ecomorphology in deep time as well as their palaeoecology. creator: Viktor A. Baranov creator: Yinan Wang creator: Rok Gašparič creator: Sonja Wedmann creator: Joachim T. Haug uri: https://doi.org/10.7717/peerj.10356 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Baranov et al. title: A diverse global fungal library for drug discovery link: https://peerj.com/articles/10392 last-modified: 2020-11-27 description: BackgroundSecondary fungal metabolites are important sources for new drugs against infectious diseases and cancers.MethodsTo obtain a library with enough diversity, we collected about 2,395 soil samples and 2,324 plant samples from 36 regions in Africa, Asia, and North America. The collection areas covered various climate zones in the world. We examined the usability of the global fungal extract library (GFEL) against parasitic malaria transmission, Gram-positive and negative bacterial pathogens, and leukemia cells.ResultsNearly ten thousand fungal strains were isolated. Sequences of nuclear ribosomal internal transcribed spacer (ITS) from 40 randomly selected strains showed that over 80% were unique. Screening GFEL, we found that the fungal extract from Penicillium thomii was able to block Plasmodium falciparum transmission to Anopheles gambiae, and the fungal extract from Tolypocladium album was able to kill myelogenous leukemia cell line K562. We also identified a set of candidate fungal extracts against bacterial pathogens. creator: Guodong Niu creator: Thirunavukkarasu Annamalai creator: Xiaohong Wang creator: Sheng Li creator: Stephen Munga creator: Guomin Niu creator: Yuk-Ching Tse-Dinh creator: Jun Li uri: https://doi.org/10.7717/peerj.10392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Niu et al. title: Data quantity is more important than its spatial bias for predictive species distribution modelling link: https://peerj.com/articles/10411 last-modified: 2020-11-27 description: Biological records are often the data of choice for training predictive species distribution models (SDMs), but spatial sampling bias is pervasive in biological records data at multiple spatial scales and is thought to impair the performance of SDMs. We simulated presences and absences of virtual species as well as the process of recording these species to evaluate the effect on species distribution model prediction performance of (1) spatial bias in training data, (2) sample size (the average number of observations per species), and (3) the choice of species distribution modelling method. Our approach is novel in quantifying and applying real-world spatial sampling biases to simulated data. Spatial bias in training data decreased species distribution model prediction performance, but sample size and the choice of modelling method were more important than spatial bias in determining the prediction performance of species distribution models. creator: Willson Gaul creator: Dinara Sadykova creator: Hannah J. White creator: Lupe Leon-Sanchez creator: Paul Caplat creator: Mark C. Emmerson creator: Jon M. Yearsley uri: https://doi.org/10.7717/peerj.10411 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gaul et al. title: Identification and prognostic value of DLGAP5 in endometrial cancer link: https://peerj.com/articles/10433 last-modified: 2020-11-27 description: BackgroundEndometrial cancer poses a serious threat to women’s health worldwide, and its pathogenesis, although actively explored, is not fully understood. DLGAP5 is a recently identified cell cycle-regulation gene not reported in endometrial cancer. This study was aiming to analyze the role of DLGAP5 in tumorigenesis and development and to investigate its prognostic significance of patients with endometrial cancer.MethodologyMicroarray datasets (GSE17025, GSE39099 and GSE63678) from the GEO database were used for comparative analysis, and their intersection was obtained by applying the Venn diagram, and DLGAP5 was selected as the target gene. Next, transcriptome data (n = 578) was downloaded from TCGA-UCEC to analyze the mRNA expression profile of DLGAP5. Then, immunohistochemical data provided by HPA were used to identify the different protein expression levels of DLGAP5 in tumor tissues and normal tissues. Subsequently, the prognostic meaning of DLGAP5 in patients with endometrial cancer was explored based on survival data from TCGA-UCEC (n = 541). Finally, the reliability of DLGAP5 expression was verified by RT-qPCR.ResultsTranscriptome data from TCGA-UCEC, immunohistochemical data from HPA, and RT-qPCR results from clinical samples were used for triple validation to confirm that the expression of DLGAP5 in endometrial cancer tissues was significantly higher than that in normal endometrial tissues. Kaplan–Meier survival analysis announced that the expression level of DLGAP5 was negatively correlated with the overall survival of patients with endometrial cancer.ConclusionsDLGAP5 is a potential oncogene with cell cycle regulation, and its overexpression can predict the poor prognosis of patients with endometrial cancer. As a candidate target for the diagnosis and treatment of endometrial cancer, it is worthwhile to make further study to reveal the carcinogenicity of DLGAP5 and the mechanism of its resistance of organisms. creator: Ruoyi Zheng creator: Zhengzheng Shi creator: Wenzhi Li creator: Jianqin Yu creator: Yuli Wang creator: Qing Zhou uri: https://doi.org/10.7717/peerj.10433 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zheng et al. title: The mRNA landscape profiling reveals potential biomarkers associated with acute kidney injury AKI after kidney transplantation link: https://peerj.com/articles/10441 last-modified: 2020-11-27 description: BackgroundThis study aims to identify potential biomarkers associated with acute kidney injury (AKI) post kidney transplantation.Material and MethodsTwo mRNA expression profiles from Gene Expression Omnibus repertory were downloaded, including 20 delayed graft function (DGF) and 68 immediate graft function (IGF) samples. Differentially expressed genes (DEGs) were identified between DGF and IGF group. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of DEGs were performed. Then, a protein-protein interaction analysis was performed to extract hub genes. The key genes were searched by literature retrieval and cross-validated based on the training dataset. An external dataset was used to validate the expression levels of key genes. Receiver operating characteristic curve analyses were performed to evaluate diagnostic performance of key genes for AKI.ResultsA total of 330 DEGs were identified between DGF and IGF samples, including 179 up-regulated and 151 down-regulated genes. Of these, OLIG3, EBF3 and ETV1 were transcription factor genes. Moreover, LEP, EIF4A3, WDR3, MC4R, PPP2CB, DDX21 and GPT served as hub genes in PPI network. EBF3 was significantly up-regulated in validation GSE139061 dataset, which was consistently with our initial gene differential expression analysis. Finally, we found that LEP had a great diagnostic value for AKI (AUC = 0.740).ConclusionEBF3 may be associated with the development of AKI following kidney transplantation. Furthermore, LEP had a good diagnostic value for AKI. These findings provide deeper insights into the diagnosis and management of AKI post renal transplantation. creator: Hui Bi creator: Min Zhang creator: Jialin Wang creator: Gang Long uri: https://doi.org/10.7717/peerj.10441 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Bi et al. title: Adaptive evolution at mRNA editing sites in soft-bodied cephalopods link: https://peerj.com/articles/10456 last-modified: 2020-11-27 description: BackgroundThe bulk of variability in mRNA sequence arises due to mutation—change in DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA can also be achieved by post-transcriptional modification including mRNA editing, changes in mRNA nucleotide sequence that mimic the effect of mutations. Such modifications are not inherited directly; however, as the processes affecting them are encoded in the genome, they have a heritable component, and therefore can be shaped by selection. In soft-bodied cephalopods, adenine-to-inosine RNA editing is very frequent, and much of it occurs at nonsynonymous sites, affecting the sequence of the encoded protein.MethodsWe study selection regimes at coleoid A-to-I editing sites, estimate the prevalence of positive selection, and analyze interdependencies between the editing level and contextual characteristics of editing site.ResultsHere, we show that mRNA editing of individual nonsynonymous sites in cephalopods originates in evolution through substitutions at regions adjacent to these sites. As such substitutions mimic the effect of the substitution at the edited site itself, we hypothesize that they are favored by selection if the inosine is selectively advantageous to adenine at the edited position. Consistent with this hypothesis, we show that edited adenines are more frequently substituted with guanine, an informational analog of inosine, in the course of evolution than their unedited counterparts, and for heavily edited adenines, these transitions are favored by positive selection. Our study shows that coleoid editing sites may enhance adaptation, which, together with recent observations on Drosophila and human editing sites, points at a general role of RNA editing in the molecular evolution of metazoans. creator: Mikhail Moldovan creator: Zoe Chervontseva creator: Georgii Bazykin creator: Mikhail S. Gelfand uri: https://doi.org/10.7717/peerj.10456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Moldovan et al. title: Invasion history of Harmonia axyridis (Pallas, 1773) (Coleoptera: Coccinellidae) in Ecuador link: https://peerj.com/articles/10461 last-modified: 2020-11-27 description: Harmonia axyridis is a ladybird extensively used around the world for biological control of agricultural pests. However, it has become invasive in several countries, producing negative ecological and socio-economic impacts. Herein, we review the invasion history of the Harlequin Ladybird Harmonia axyridis (Pallas, 1773) in Ecuador. Although first reported in Ecuador in 2012, museum specimens date back to 2004 and it is currently established across the country, especially along the Andean region. Due to its invasive nature, further studies are urgently needed to evaluate possible impacts of H. axyridis on the Ecuadorian biodiversity and agroindustry. creator: Diego F. Cisneros-Heredia creator: Emilia Peñaherrera-Romero uri: https://doi.org/10.7717/peerj.10461 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cisneros-Heredia and Peñaherrera-Romero title: Cumulative oxygen deficit is a novel predictor for the timing of invasive mechanical ventilation in COVID-19 patients with respiratory distress link: https://peerj.com/articles/10497 last-modified: 2020-11-27 description: Background and objectivesThe timing of invasive mechanical ventilation (IMV) is controversial in COVID-19 patients with acute respiratory hypoxemia. The study aimed to develop a novel predictor called cumulative oxygen deficit (COD) for the risk stratification.MethodsThe study was conducted in four designated hospitals for treating COVID-19 patients in Jingmen, Wuhan, from January to March 2020. COD was defined to account for both the magnitude and duration of hypoxemia. A higher value of COD indicated more oxygen deficit. The predictive performance of COD was calculated in multivariable Cox regression models.ResultsA number of 111 patients including 80 in the non-IMV group and 31 in the IMV group were included. Patients with IMV had substantially lower PaO2 (62 (49, 89) vs. 90.5 (68, 125.25) mmHg; p < 0.001), and higher COD (−6.87 (−29.36, 52.38) vs. −231.68 (−1040.78, 119.83) mmHg·day) than patients without IMV. As compared to patients with COD < 0, patients with COD > 30 mmHg·day had higher risk of fatality (HR: 3.79, 95% CI [2.57–16.93]; p = 0.037), and those with COD > 50 mmHg·day were 10 times more likely to die (HR: 10.45, 95% CI [1.28–85.37]; p = 0.029).ConclusionsThe study developed a novel predictor COD which considered both magnitude and duration of hypoxemia, to assist risk stratification of COVID-19 patients with acute respiratory distress. creator: Huiqing Ge creator: Jian-cang Zhou creator: FangFang Lv creator: Junli Zhang creator: Jun Yi creator: Changming Yang creator: Lingwei Zhang creator: Yuhan Zhou creator: Binbin Ren creator: Qing Pan creator: Zhongheng Zhang uri: https://doi.org/10.7717/peerj.10497 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ge et al. title: Early abolition of cough reflex predicts mortality in deeply sedated brain-injured patients link: https://peerj.com/articles/10326 last-modified: 2020-11-26 description: BackgroundDeep sedation may hamper the detection of neurological deterioration in brain-injured patients. Impaired brainstem reflexes within the first 24 h of deep sedation are associated with increased mortality in non-brain-injured patients. Our objective was to confirm this association in brain-injured patients.MethodsThis was an observational prospective multicenter cohort study involving four neuro-intensive care units. We included acute brain-injured patients requiring deep sedation, defined by a Richmond Assessment Sedation Scale (RASS) < −3. Neurological assessment was performed at day 1 and included pupillary diameter, pupillary light, corneal and cough reflexes, and grimace and motor response to noxious stimuli. Pre-sedation Glasgow Coma Scale (GCS) and Simplified Acute Physiology Score (SAPS-II) were collected, as well as the cause of death in the Intensive Care Unit (ICU).ResultsA total of 137 brain-injured patients were recruited, including 70 (51%) traumatic brain-injured patients, 40 (29%) vascular (subarachnoid hemorrhage or intracerebral hemorrhage). Thirty patients (22%) died in the ICU. At day 1, the corneal (OR 2.69, p = 0.034) and cough reflexes (OR 5.12, p = 0.0003) were more frequently abolished in patients that died in the ICU. In a multivariate analysis, abolished cough reflex was associated with ICU mortality after adjustment to pre-sedation GCS, SAPS-II, RASS (OR: 5.19, 95% CI [1.92–14.1], p = 0.001) or dose of sedatives (OR: 8.89, 95% CI [2.64–30.0], p = 0.0004).ConclusionEarly (day 1) cough reflex abolition is an independent predictor of mortality in deeply sedated brain-injured patients. Abolished cough reflex likely reflects a brainstem dysfunction that might result from the combination of primary and secondary neuro-inflammatory cerebral insults revealed and/or worsened by sedation. creator: Stanislas Kandelman creator: Jérémy Allary creator: Raphael Porcher creator: Cássia Righy creator: Clarissa Francisca Valdez creator: Frank Rasulo creator: Nicholas Heming creator: Guy Moneger creator: Eric Azabou creator: Guillaume Savary creator: Djillali Annane creator: Fabrice Chretien creator: Nicola Latronico creator: Fernando Augusto Bozza creator: Benjamin Rohaut creator: Tarek Sharshar uri: https://doi.org/10.7717/peerj.10326 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kandelman et al. title: Spatial and temporal activity patterns of Golden takin (Budorcas taxicolor bedfordi) recorded by camera trapping link: https://peerj.com/articles/10353 last-modified: 2020-11-26 description: Understanding animals’ migration, distribution and activity patterns is vital for the development of effective conservation action plans; however, such data for many species are lacking. In this study, we used camera trapping to document the spatial and temporal activity patterns of golden takins (Budorcas taxicolor bedfordi) in Changqing National Nature Reserve in the Qinling mountains, China, from April 2014 to October 2017. Our study obtained 3,323 independent detections (from a total of 12,351 detections) during a total camera trapping effort of 93,606 effective camera trap days at 573 sites. Results showed that: (1) the golden takin’s utilization distributions showed seasonal variation, with larger utilization distributions during spring and autumn compared to summer and winter; (2) the species was recorded at the highest elevations in July, and lowest elevations in December, with the species moving to higher-elevations in summer, lower-elevations in spring and autumn; (3) during all four seasons, golden takins showed bimodal activity peaks at dawn and dusk, with activity intensity higher in the second peak than the first, and overall low levels of activity recorded from 20:00–06:00; and (4) there were two annual activity peaks, the first being in April and the second in November, with camera capture rate during these two months higher than in other months, and activity levels in spring and autumn higher than in summer and winter. This study is the first application of camera traps to assess the spatial and temporal activity patterns of golden takins at a population level. Our findings suggest that the proposed national park should be designed to include golden takin habitat and that ongoing consistent monitoring efforts will be crucial to mitigating novel and ongoing threats to the species. creator: Jia Li creator: Yadong Xue creator: Yu Zhang creator: Wei Dong creator: Guoyu Shan creator: Ruiqian Sun creator: Charlotte Hacker creator: Bo Wu creator: Diqiang Li uri: https://doi.org/10.7717/peerj.10353 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: The m6A reader protein YTHDC2 is a potential biomarker and associated with immune infiltration in head and neck squamous cell carcinoma link: https://peerj.com/articles/10385 last-modified: 2020-11-26 description: Background Increasing evidence has shown that N6-methyladenosine (m6A) RNA methylation regulators have important biological functions in human cancers. However, there are few studies on the value of m6A reader protein YTHDC2 in the diagnosis and tumor-infiltrating of head and neck squamous cell carcinoma (HNSCC). Therefore, it is important to understand the potential clinical value of YTHDC2 in the prognosis and immune infiltration of HNSCC.MethodsIn this study, gene expression profiles and the corresponding clinical information of 270 HNSCC patients were downloaded from the Gene Expression Omnibus (GEO) database. The gene co-expression network was established to verify whether YTHDC2 was related to the prognosis of HNSCC and verified again in the public database. The correlations between YTHDC2 and immune infiltration was investigated via Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA).ResultsThe results showed that YTHDC2 appeared in the blue module related to survival time and survival state and had a close correlation with the prognosis and immune infiltration level of HNSCC in public database. Patients with low expression of YTHDC2 had poor overall survival (OS) and recurrence-free survival (RFS) than those with high expression. In addition, the expression of YTHDC2 was positively correlated with the level of CD4+ T cell subpopulations infiltration in HNSCC.ConclusionsThrough this study, we found that YTHDC2 is a tumor suppressor gene with high expression in normal tissues and low expression in tumor tissues. In addition, YTHDC2 is correlated with the immune infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, neutrophils, and dendritic cells in HNSCC, which may become a potential marker for prognosis and immune infiltration of HNSCC. creator: Yang Li creator: Ji-Na Zheng creator: En-Hao Wang creator: Chan-Juan Gong creator: Keng-Fu Lan creator: XiaoJun Ding uri: https://doi.org/10.7717/peerj.10385 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: A signature of tumor DNA repair genes associated with the prognosis of surgically-resected lung adenocarcinoma link: https://peerj.com/articles/10418 last-modified: 2020-11-26 description: BackgroundLung cancer has the highest morbidity and mortality of cancers worldwide. Lung adenocarcinoma (LUAD) is the most common pathological subtype of lung cancer and surgery is its most common treatment. The dysregulated expression of DNA repair genes is found in a variety of cancers and has been shown to affect the origin and progression of these diseases. However, the function of DNA repair genes in surgically-treated LUAD is unclear.MethodsWe sought to determine the association between the signature of DNA repair genes for patients with surgical LUAD and their overall prognosis. We obtained gene expression data and corresponding clinical information of LUAD from The Cancer Genome Atlas (TCGA) database. The differently expressed DNA repair genes of surgically-treated LUAD and normal tissues were identified using the Wilcoxon rank-sum test. We used uni- and multivariate Cox regression analyses to shrink the aberrantly expressed genes, which were then used to construct the prognostic signature and the risk score formula associated with the independent prognosis of surgically-treated LUAD. We used Kaplan–Meier and Cox hazard ratio analyses to confirm the diagnostic and prognostic roles. Two validation sets (GSE31210 and GSE37745) were downloaded from the Gene Expression Omnibus (GEO) and were used to externally verify the prognostic value of the signature. OSluca online database verifies the hazard ratio for the DNA repair genes by which the signature was constructed. We investigated the correlation between the signature of the DNA repair genes and the clinical parameters. The potential molecular mechanisms and pathways of the prognostic signature were explored using Gene Set Enrichment Analysis (GSEA).ResultsWe determined the prognostic signature based on six DNA repair genes (PLK1, FOXM1, PTTG1, CCNO, HIST3H2A, and BLM) and calculated the risk score based on this formula. Patients with surgically-treated LUAD were divided into high-risk and low-risk groups according to the median risk score. The high-risk group showed poorer overall survival than the low-risk group; the signature was used as an independent prognostic indicator and had a greater prognostic value in surgically-treated LUAD. The prognostic value was replicated in GSE31210 and GSE37745. OSluca online database analysis shows that six DNA repair genes were associated with poor prognosis in most lung cancer datasets. The prognostic signature risk score correlated with the pathological stage and smoking status in surgically-treated LUAD. The GSEA of the risk signature in high-risk patients showed pathways associated with the cell cycle, oocyte meiosis, mismatch repair, homologous recombination, and nucleotide excision repair.ConclusionsA six-DNA repair gene signature was determined using TCGA data mining and GEO data verification. The gene signature may serve as a novel prognostic biomarker and therapeutic target for surgically-treated LUAD. creator: Xiongtao Yang creator: Guohui Wang creator: Runchuan Gu creator: Xiaohong Xu creator: Guangying Zhu uri: https://doi.org/10.7717/peerj.10418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats link: https://peerj.com/articles/10434 last-modified: 2020-11-26 description: Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an evolutionary rate of 1.301 × 10−3, HPD (1.064 × 10−3–1.434 × 10−3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Merbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats; we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population. creator: Babatunde O. Motayo creator: Olukunle Oluwapamilerin Oluwasemowo creator: Paul A. Akinduti uri: https://doi.org/10.7717/peerj.10434 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Motayo et al. title: Partial restoration of normal intestinal microbiota in morbidly obese women six months after bariatric surgery link: https://peerj.com/articles/10442 last-modified: 2020-11-26 description: We studied the impact of bariatric surgery on the intestinal microbiota of morbidly obese study subjects. A total of 13 morbidly obese women (five of which had type 2 diabetes) and 14 healthy age- and gender-matched controls were recruited and the microbiota composition of fecal samples were determined by using a phylogenetic microarray. Sampling of the patients took place just one month before and 6 months after the operation. Within six months after bariatric surgery, the obese subjects had lost on average a quarter of their weight whereas four of the five of the diabetic subjects were in remission. Bariatric surgery was associated with an increased microbial community richness and Bacteroidetes/Firmicutes ratio. In addition, we observed an increased relative abundance of facultative anaerobes, such as Streptococcus spp., and a reduction in specific butyrate-producing Firmicutes. The observed postoperative alterations in intestinal microbiota reflect adaptation to the changing conditions in the gastrointestinal tract, such as energy restriction and the inability to process fiber-rich foods after bariatric surgery. creator: Jukka Koffert creator: Leo Lahti creator: Lotta Nylund creator: Seppo Salminen creator: Jarna C. Hannukainen creator: Paulina Salminen creator: Willem M. de Vos creator: Pirjo Nuutila uri: https://doi.org/10.7717/peerj.10442 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Koffert et al. title: Characteristics and outcomes of hemodialysis patients with COVID-19: a retrospective single center study link: https://peerj.com/articles/10459 last-modified: 2020-11-26 description: BackgroundThe coronavirus 19 (COVID-19) pandemic has heightened the threat to the health and lives of patients with comorbid diseases. Infection by COVID-19 is especially detrimental to patients on hemodialysis. In this study, we evaluated the clinical characteristics, laboratory findings, treatments and prognoses of hemodialysis patients with COVID-19.MethodsA total of 16 hemodialysis patients with COVID-19 were recruited from Wuhan Fourth Hospital from 5 February to 20 March 2020 for a retrospective, single-center study. A total of 62 non-dialysis patients with COVID-19 were the control group. We collected data on the clinical characteristics, laboratory findings, treatments, and clinical outcomes of patients affected by the virus.ResultsHemodialysis patients with COVID-19 had a lower incidence of fever (P = 0.001) and relatively higher incidence of pre-admission comorbidities and shortness of breath than non-dialysis patients with COVID-19 (75% vs. 61%, P = 0.467 50% vs. 33.87%, P = 0.248 ). Hemodialysis patients had lower levels of hemoglobin (P < 0.001), white blood cell counts (P = 0.015), neutrophils (P = 0.016), AST (P = 0.037), ALT (P < 0.001) and procalcitonin (P < 0.001), and higher levels of D-dimer (P < 0.001) and thrombin time (P < 0.001). Hemodialysis patients had a higher incidence of pulmonary effusion, cord-like high-density shadows, pleural thickening, and atelectasis (P < 0.05). Hemodialysis patients also had relatively higher rates of mortality and prolonged hospital stays compared with the control group.ConclusionsHemodialysis patients typically present with multiple comorbidities and are considered to be a high-risk group for COVID-19 infections. Hemodialysis patients with COVID-19 may have prolonged hospital stays and unfavorable prognoses and should be closely monitored. creator: Yongwen Luo creator: Junli Li creator: Zhifen Liu creator: Heping Yu creator: Xiang Peng creator: Cheng’an Cao uri: https://doi.org/10.7717/peerj.10459 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Luo et al. title: Chimpanzees’ (Pan troglodytes) problem-solving skills are influenced by housing facility and captive care duration link: https://peerj.com/articles/10263 last-modified: 2020-11-25 description: Although a large body of primate cognition research is done in captive institutions, little is known about how much individuals from different facilities vary in their experiences and cognitive skills. Here we present the results of an experimental study investigating how physical cognitive skills vary between chimpanzees in relation to captive settings and their time in captivity. We tested 59 chimpanzees housed at two different captive facilities (a rehabilitation center (sanctuary) and a zoo) in three problem-solving tasks. Our results showed that chimpanzees at the two housing facilities significantly differed in overall task performance. On average, the sanctuary chimpanzees outperformed the chimpanzees housed at the zoo in the detour reaching task and the honey trap task. However, the zoo chimpanzees performed slightly better on average in the learning task. We propose that, for this particular sample, the documented differences result from a combination of factors, such as prior experience with cognitive testing, motivation levels and varying degrees of human exposure. Within the sanctuary sample, we found that chimpanzees who arrived at an earlier age at the sanctuary and had therefore spent a larger percentage of their lives in a captive environment, were better problem-solvers than those that arrived at a later age to the sanctuary. Thus, rehabilitation and time in captivity contributed to improved physical cognitive skills in sanctuary chimpanzees. Our results highlight the importance of studying intraspecific variation and the effect that previous experience and living conditions might have on physical cognitive skills in non-human apes. Accordingly, we should be cautious when extrapolating findings of cognitive studies from one population to the species as a whole. creator: Sofia Forss creator: Alba Motes-Rodrigo creator: Christine Hrubesch creator: Claudio Tennie uri: https://doi.org/10.7717/peerj.10263 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Forss et al. title: A morphological and molecular study of Hydrodynastes gigas (Serpentes, Dipsadidae), a widespread species from South America link: https://peerj.com/articles/10073 last-modified: 2020-11-25 description: BackgroundStudies with integrative approaches (based on different lines of evidence) are fundamental for understanding the diversity of organisms. Different data sources can improve the understanding of the taxonomy and evolution of snakes. We used this integrative approach to verify the taxonomic status of Hydrodynastes gigas (Duméril, Bibron & Duméril, 1854), given its wide distribution throughout South America, including the validity of the recently described Hydrodynastes melanogigasFranco, Fernandes & Bentim, 2007.MethodsWe performed a phylogenetic analysis of Bayesian Inference with mtDNA 16S and Cytb, and nuDNA Cmos and NT3 concatenated (1,902 bp). In addition, we performed traditional morphometric analyses, meristic, hemipenis morphology and coloration pattern of H. gigas and H. melanogigas.ResultsAccording to molecular and morphological characters, H. gigas is widely distributed throughout South America. We found no evidence to support that H. gigas and H. melanogigas species are distinct lineages, therefore, H. melanogigas is a junior synonym of H. gigas. Thus, the melanic pattern of H. melanogigas is the result of a polymorphism of H. gigas. Melanic populations of H. gigas can be found in the Tocantins-Araguaia basin. creator: Priscila S. Carvalho creator: Hussam Zaher creator: Nelson J. da Silva Jr creator: Diego J. Santana uri: https://doi.org/10.7717/peerj.10073 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Carvalho et al. title: Remote sensing inversion and spatial variation of land surface temperature over mining areas of Jixi, Heilongjiang, China link: https://peerj.com/articles/10257 last-modified: 2020-11-25 description: BackgroundJixi is a typical mining city in China that has undergone dramatic changes in its land-use pattern of mining areas over the development of its coal resources. The impacts of coal mining activities have greatly affected the regional land surface temperature and ecological system.MethodsThe Landsat 8 Operational Land Imager (OLI) data from 2015 and 2019 were used from the Jiguan, Didao, and Chengzihe District of Jixi in Heilongjiang, China as the study area. The calculations to determine the land-use classification, vegetation coverage, and land surface temperature (LST) were performed using ArcGIS10.5 and ENVI 5.3 software packages. A correlation analysis revealed the impact of land-use type, vegetation coverage, and coal mining activities on LSTs.ResultsThe results show significant spatial differentiation in the LSTs of Jixi City. The LSTs for various land-use types were ranked from high to low as follows: mining land > construction land > grassland > cultivated land > forest land > water area. The LST was lower in areas with high vegetation coverage than in other areas. For every 0.1 increase in vegetation coverage, the LST is expected to drop by approximately 0.75 °C. An analysis of mining land patches indicates that the patch area of mining lands has a significant positive correlation with both the average and maximum patch temperatures. The average patch temperature shows a logarithmic increase with the growth of the patch area, and within 200,000 m2, the average patch temperature increases significantly. The maximum patch temperature shows a linear increase with the patch area growth, and for every 100,000 m2 increase in the patch area of mining lands, the maximum patch temperature increases by approximately 0.81 °C. The higher the average patch temperature of mining land, the higher the temperature in its buffer zone, and the greater its influence scope. This study provides a useful reference for exploring the warming effects caused by coal mining activities and the definition of its influence scope. creator: Jia-shuo Cao creator: Zheng-yu Deng creator: Wen Li creator: Yuan-dong Hu uri: https://doi.org/10.7717/peerj.10257 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cao et al. title: Pro-inflammatory response ensured by LPS and Pam3CSK4 in RAW 264.7 cells did not improve a fungistatic effect on Cryptococcus gattii infection link: https://peerj.com/articles/10295 last-modified: 2020-11-25 description: BackgroundThe macrophage lineage is characterized by plasticity due to the acquisition of distinct functional phenotypes, and two major subsets are evaluated; classical M1 activation (strong microbicidal activity) and alternative M2 activation (immunoregulatory functions). The M1 subset expresses inducible nitric oxide synthase (iNOS), which is a primary marker to identify these cells, whereas M2 macrophages are characterized by expression of Arginase-1, found in inflammatory zone 1 (Fizz1), chitinase-like molecule (Ym-1), and CD206. The micro-environmental stimuli and signals in tissues are critical in the macrophage polarization. Toll-like receptors (TLR) ligands, such as lipopolysaccharide (LPS), palmitoyl-3-cysteine-serine-lysine-4 (Pam3CSK4), and ArtinM (mannose-binding lectin) are inductors of M1 subset. The impact of TLR2 and TLR4 signals to fight against Cryptococcus gattii infection is unknown, which is a fungal pathogen that preferentially infects the lung of immunocompetent individuals. The macrophages initiate an immune response to combat the C. gattii, then we evaluated in RAW 264.7 cell the effect of TLR2 and TLR4 agonists on the macrophage polarization dynamic and the impact on the growth of C. gattii.Methods and ResultsWe demonstrated that P3C4, LPS, and ArtinM induced an increase in the levels of iNOS transcripts in RAW 264.7 cells, whereas the relative expression of arginase-1, Ym-1, and Fizz1 was significantly increased in the presence of IL-4 alone. The effects of TLR2 and TLR4 agonists on repolarization from the M2 to M1 subset was evaluated, and the first stimulus was composed of IL-4 and, after 24 h of incubation, the cells were submitted to a second stimulus of P3C4, LPS, ArtinM, or Medium. These TLR agonists induced the production of TNF-α in polarized RAW 264.7 cells to the M2 subset, moreover the measurement of M1/M2 markers using qRT-PCR demonstrated that a second stimulus with LPS for 24 h induced a significant augmentation of levels of iNOS mRNA. This impact of TLR2 and TLR4 agonists in the activation of the RAW 264.7 macrophage was assayed in the presence of C. gattii, the macrophages stimulated with TLR2 and TLR4 agonists for 24 h and co-cultured with C. gattii, as a second stimulus, reached high levels of TNF-α even after incubation with different concentrations of C. gattii. The activation of RAW 264.7 cells induced by TLR2 and TLR4 agonists favored the phagocytosis of C. gattii and inhibited the growth of yeast in the early period of infection. However, RAW 264.7 cells incubated with C. gattii in the presence of TLR2 and TLR4 agonists did not result a significant difference in the colony forming unit (CFU) assay in the early period of C. gattii infection, compared to negative control.ConclusionPolarized RAW 264.7 cells to the M1 subset with TLR2 and TLR4 agonists did not inhibit the growth of C. gattii, whereas robust immunity was identified that could dysregulate host tolerance to this pathogen. creator: Gabriela Yamazaki de Campos creator: Raquel Amorim Oliveira creator: Patrícia Kellen Martins Oliveira-Brito creator: Maria Cristina Roque-Barreira creator: Thiago Aparecido da Silva uri: https://doi.org/10.7717/peerj.10295 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 de Campos et al. title: Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect link: https://peerj.com/articles/10312 last-modified: 2020-11-25 description: Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a “CAU” anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family. creator: Ting-Ting Zhang creator: Yi-Kun Hou creator: Ting Yang creator: Shu-Ya Zhang creator: Ming Yue creator: Jianni Liu creator: Zhonghu Li uri: https://doi.org/10.7717/peerj.10312 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Three new deep-sea species of Thyasiridae (Mollusca: Bivalvia) from the abyssal plain of the northwestern Pacific Ocean and hadal depths of the Kuril-Kamchatka Trench link: https://peerj.com/articles/10405 last-modified: 2020-11-25 description: The Thyasiridae is the most species-rich family of bivalves in the abyssal and hadal zones of the northwestern Pacific Ocean. In recent years, with at least 14 thyasirid species found in that region at depths exceeding 3,000 m. Some of them are the numerically dominant species in bottom communities. However, all members in that family have not yet been identified to the species level. Based on the material collected from 1953 to 2016 by five deep-sea expeditions, three new species of Thyasiridae (Mollusca: Bivalvia) are described from the abyssal and hadal zones of the northwestern Pacific. “Axinulus” roseus sp. nov. was found in the Kuril-Kamchatka Trench at 9,000–9,583 m depth. This species has a large rhomboidal shell with strong commarginal sculpture, a well defined, long and deep lunule and escutcheon without an auricle, a ctenidium consisting of a single demibranch, extensively lobed lateral pouches, and a large prodissoconch with specific sculpture. It is one of the dominant species in terms of abundance in macrobenthic communities in the deepest basin of the Kuril-Kamchatka Trench with a population density of up to 396 ind. m−2. The species has a shell length of up to 9.0 mm and it is the largest thyasirid with a single demibranch. “Axinulus” oliveri sp. nov. was found in a vast region of the northwestern Pacific on the abyssal plain adjacent to the Kuril-Kamchatka Trench, on the abyssal slope of the Kuril Islands, and in the Kuril-Kamchatka Trench at 4,648–6,168 m depth. This species is characterized by its ovate-rhomboidal shell, a well defined, deep and long escutcheon with a distinct auricle, a ctenidium with a single demibranch, and extensively lobed lateral pouches. It is widespread in the northwestern Pacific and forms populations with a density of up to 36 ind. m−2. Scanning electron microscopic observation of the gills of “A.” roseus sp. nov. and “A.” oliveri sp. nov. revealed that these species are not chemosymbiotic. “Axinulus” roseus sp. nov. and “A.” oliveri sp. nov. are provisionally assigned to the genus Axinulus, because they differ from the type species of the genus in a number of morphological and anatomical features. Parathyasira fragilis sp. nov. was found on the abyssal plain adjacent to the Kuril-Kamchatka Trench at 5,249–5,399 m depth. This species is distinguished by its very thin, fragile, dorsoventrally elongated, rhomboidal shell with very long anterodorsal margin and a long, wide, flat lunule. The taxonomic position of the new species is discussed. creator: Gennady M. Kamenev uri: https://doi.org/10.7717/peerj.10405 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kamenev title: Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results link: https://peerj.com/articles/10410 last-modified: 2020-11-25 description: Water fleas (Crustacea: Cladocera) are among the most intensively studied freshwater invertebrates. However, ecologically important daphniids that live on the surface layer (neuston) remain taxonomically confused. Here we attempt to reconcile genetic and morphological information for the neustonic genus Scapholeberis Schoedler, 1858 (Cladocera: Daphniidae) and present the first revision of the Scapholeberis kingii species group. We analyzed new and existing mitochondrial DNA sequences (сytochrome C oxidase subunit I gene region) together with morphology for all but one of the known species of the neustonic daphniids. Morphological comparisons of available populations, belonging to the Scapholeberis kingii species group from several Australian, Asian and African localities, revealed, that they are almost identical according to parthenogenetic females. However, Australian populations can be reliably distinguished from Asian ones based on the morphology of gamogenetic females. Mitochondrial DNA data analyses revealed divergent lineages (>17% for the DNA barcoding COI region) for the three different species (Australia, Asia and Africa). Based on this set of data, we redescribed S. kingii Sars, 1888 from Australia, its terra typica, and described a new species, S. smirnovisp.nov. from the Russian Far East, Korea and Japan. The status of populations from Ethiopia and the Republic of South Africa remained unclear, because in the African material and the putative type material, we found only parthenogenetic females. Our results provide an integrative revision of the S. kingii species group and improve the taxonomic scaffold used for barcoding and genomics for the remaining species groups in the daphniid genus Scapholeberis. creator: Petr G. Garibian creator: Anna N. Neretina creator: Derek J. Taylor creator: Alexey A. Kotov uri: https://doi.org/10.7717/peerj.10410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Garibian et al. title: Antibacterial activity of human defensins against Staphylococcus aureus and Escherichia coli link: https://peerj.com/articles/10455 last-modified: 2020-11-25 description: BackgroundThe global problem of antibiotic resistance requires the search for and development of new methods of treatment. One of the promising strategies is the use of low doses of antimicrobial peptides, in particular, human defensins HNP-1, hBD-1, and hBD-3, in combination with antibacterial drugs already used in clinical practice. This approach may be used to increase the effectiveness of conventional antibiotics. However, this requires thorough study of the effectiveness of defensins in combination with antibiotics against a large number of bacterial strains with known phenotypes of antibiotic resistance. The aim of this work was to study the antibacterial effect of HNP-1, hBD-1 and hBD-3 in combination with rifampicin or amikacin against clinical isolates of Staphylococcus aureus (n = 27) and Escherichia coli (n = 24) collected from hospitalized patients.MethodsThe standard checkerboard assay was used to determine minimum inhibitory concentrations (MICs) of antimicrobials. The combined microbicidal effects of two substances (defensin + conventional antibiotic) were assessed by the fractional inhibitory concentration index (FICI).ResultsThe highest anti-staphylococcal activity (including methicillin-resistant strains) among defensins was demonstrated by hBD-3 that had MIC of 1 (0.5–4) mg/L (hereinafter, MIC values are presented as median and interquartile range). The MIC of HNP-1 against S. aureus was 4 (2–8) mg/L; the MIC of hBD-1 was 8 (4–8) mg/L. Against E. coli, the most effective was also found to be hBD-3 that had MIC of 4 (4–8) mg/L; the MIC of HNP-1 was 12 (4–32) mg/L. The combinations of HNP-1 + rifampicin and hBD-3 + rifampicin demonstrated synergistic effects against S. aureus. Against E. coli, combinations of HNP-1 + amikacin and hBD-3 + amikacin also showed synergy of action. creator: Albert Bolatchiev uri: https://doi.org/10.7717/peerj.10455 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bolatchiev title: miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2 link: https://peerj.com/articles/9704 last-modified: 2020-11-24 description: BackgroundThe present study is to screen lymph node metastasis-related microRNAs (miRNAs) in lung adenocarcinoma (LUAD) and uncover their underlying mechanisms.MethodsThe miRNA microarray dataset was collected from the Gene Expression Omnibus database under accession number GSE64859. The differentially expressed miRNAs (DEMs) were identified using a t-test. Target genes of DEMs were predicted through the miRWalk2.0 database. The function of these target genes was annotated with the clusterProfiler and the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools. Protein-protein interaction network was established using the STRING database to extract hub target genes. The expressions and associations with survival and lymph node metastasis of miRNAs and target genes were validated by analysis of The Cancer Genome Atlas (TCGA) dataset.ResultsEight DEMs were identified between lymph node metastasis and non-metastasis samples of GSE64859 dataset. miRNA-target gene pairs were predicted between six DEMs and 251 target genes (i.e. hsa-miR-224-PRPF4B, hsa-miR-147b-WDR82 and hsa-miR-31-NR3C2). The clusterProfiler analysis showed WDR82 was involved in the mRNA surveillance pathway, while the GO enrichment analysis using the DAVID database indicated PRPF4B participated in the protein phosphorylation and NR3C2 was related with the transcription, DNA-templated. WDR82 and PRPF4B may be hub genes because they could interact with others. Two DEMs (miR-31-5p and miR-31-3p) and 45 target genes (including PRPF4B and NR3C2) were significantly associated with overall survival. The expressions of miR-224 and miR-147b were validated to be upregulated, while WDR82, PRPF4B and NR3C2 were downregulated in lymph node metastasis samples of TCGA datasets compared with non-metastasis samples. Also, there were significantly negative expression correlations between miR-147b and WDR82, between miR-224 and PRPF4B, as well as between miR-31 and NR3C2 in LUAD samples.ConclusionsThe present study identified several crucial miRNA-mRNA interaction pairs, which may provide novel explanations for the lymph node metastasis and poor prognosis for LUAD patients. creator: Yan Wang creator: Shengtao Shang creator: Kun Yu creator: Hongbin Sun creator: Wenduan Ma creator: Wei Zhao uri: https://doi.org/10.7717/peerj.9704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: The Italian record of the Cretaceous shark, Ptychodus latissimus Agassiz, 1835 (Chondrichthyes; Elasmobranchii) link: https://peerj.com/articles/10167 last-modified: 2020-11-24 description: Associated and isolated teeth of the extinct elasmobranch Ptychodus latissimusAgassiz, 1835 from the Upper Cretaceous Scaglia Rossa pelagic limestone of northern Italy are described and discussed here in detail for the first time. The dentition of this widely distributed species consists of low-crowned molariform teeth that exhibit marked and strong occlusal ornamentations suitable for crushing hard-shelled prey. The associated tooth sets and isolated teeth analyzed here are heterogeneous in size and crown outline, but unambiguously belong to a single species. Re-examination of this Italian material consisting of ca. 30 specimens mostly coming from historical collections allows for a rigorous assessment of the intraspecific variability of P. latissimus, including the identification of three different tooth “morphotypes” based on their positions within the jaws. The relatively flat crowns and occlusal sharp and thick ridges indicate a high adaptation for crushing hard-shelled prey in P. latissimus indicating that the durophagous adaptations of this species were certainly more pronounced than in all other species of Ptychodus. We hypothesize that P. latissimus was a third-level predator occupying habitats with abundant thick-shelled prey, such as inoceramid bivalves and ammonites. creator: Manuel Amadori creator: Jacopo Amalfitano creator: Luca Giusberti creator: Eliana Fornaciari creator: Giorgio Carnevale creator: Juergen Kriwet uri: https://doi.org/10.7717/peerj.10167 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Amadori et al. title: Hissing of geese: caller identity encoded in a non-vocal acoustic signal link: https://peerj.com/articles/10197 last-modified: 2020-11-24 description: Non-vocal, or unvoiced, signals surprisingly have received very little attention until recently especially when compared to other acoustic signals. Some sounds made by terrestrial vertebrates are produced not only by the larynx but also by the syrinx. Furthermore, some birds are known to produce several types of non-syrinx sounds. Besides mechanical sounds produced by feathers, bills and/or wings, sounds can be also produced by constriction, anywhere along the pathway from the lungs to the lips or nostrils (in mammals), or to the bill (in birds), resulting in turbulent, aerodynamic sounds. These noises often emulate whispering, snorting or hissing. Even though hissing sounds have been studied in mammals and reptiles, only a few studies have analyzed hissing sounds in birds. Presently, only the hissing of small, nesting passerines as a defense against their respective predators have been studied. We studied hissing in domestic goose. This bird represents a ground nesting non-passerine bird which frequently produces hissing out of the nest in comparison to passerines producing hissing during nesting in holes e.g., parids. Compared to vocally produced alarm calls, almost nothing is known about how non-vocal hissing sounds potentially encode information about a caller’s identity. Therefore, we aimed to test whether non-vocal air expirations can encode an individual’s identity similar to those sounds generated by the syrinx or the larynx. We analyzed 217 hissing sounds from 22 individual geese. We calculated the Potential for Individual Coding (PIC) comparing the coefficient of variation both within and among individuals. In addition, we conducted a series of 15 a stepwise discriminant function analysis (DFA) models. All 16 acoustic variables showed a higher coefficient of variation among individuals. Twelve DFA models revealed 51.2–54.4% classification result (cross-validated output) and all 15 models showed 60.8–68.2% classification output based on conventional DFA in comparison to a 4.5% success rate when classification by chance. This indicates the stability of the DFA results even when using different combinations of variables. Our findings showed that an individual’s identity could be encoded with respect to the energy distribution at the beginning of a signal and the lowest frequencies. Body weight did not influence an individual’s sound expression. Recognition of hissing mates in dangerous situations could increase the probability of their surviving via a more efficient anti-predator response. creator: Richard Policht creator: Artur Kowalczyk creator: Ewa Łukaszewicz creator: Vlastimil Hart uri: https://doi.org/10.7717/peerj.10197 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Policht et al. title: Habitat conditions strongly affect macro- and microelement concentrations in Taraxacum microspecies growing on coastal meadows along a soil salinity gradient link: https://peerj.com/articles/10233 last-modified: 2020-11-24 description: Wild greens can contribute to the human diet as an important source of essential nutrients and drugs. Since environmental factors, including soil properties, may affect the chemical composition of plants, it is necessary among others to assess various habitats in terms of their usefulness for wild plant harvesting and to study impact of environmental factors on the qualitative and quantitative chemical composition of plants. This study was aimed at (1) examining the mineral composition of leaves of three dandelion microspecies, (2) determining the variability of macro- and microelement concentrations in dandelion leaves from populations growing on salty, brackish and non-saline coastal meadows, and (3) assessing the effects of different habitat conditions on the mineral composition of dandelion leaves. It was hypothesized that dandelion microspecies would differ significantly in the mineral composition of leaves. It was also expected that soil conditions would significantly affect nutrient concentrations in dandelion leaves, with soil salinity being the most important factor that differentiated studied populations. Leaves of three dandelion microspecies (Taraxacum balticum, T. nordstedtii, T. haematicum) were harvested in Baltic costal grasslands, along the soil salinity gradient, to determine macro- and microelement concentrations. Soil samples collected in the closest vicinity of the harvested plants showed the study sites to differ significantly in their soil properties. Moderately saline and organic soils, rich in potassium (K), magnesium (Mg), and calcium (Ca), supported T. balticum. Moderately or weakly saline and non-saline, organic or mineral soils, with lower median values of K, Mg, and Ca, were typical of T. nordstedtii sites, while the lowest median values of all the soil properties studied were found for T. haematicum sites. Our results proved that dandelion microspecies differ significantly in the mineral composition of their leaves. The between-microspecies differences were significant for all the macroelements except magnesium and all the microelements except molybdenum. Most of the macro- and microelements in leaves of the dandelion microspecies correlated positively and significantly with the soil properties, the strongest correlations being found for soil salinity and the leaf Na, Mn, Ca, Fe, K and Zn contents, followed by soil pH and the leaf Na, Mn, Fe, K, Ca, Zn and Mg. Moreover, the impact of soil properties on the mineral contents in leaves of the dandelions we examined seems to be stronger than the genetic differences between dandelion microspecies. Results of our studies on mineral composition of dandelion leaves lend support to the contention that wild greens provide essential mineral nutrients to the diet. Coastal meadows, fed by the brackish water of the Baltic Sea and free of anthropogenic pollution, are a good habitat to collect wild greens from. creator: Beata Bosiacka creator: Monika Myśliwy creator: Mateusz Bosiacki uri: https://doi.org/10.7717/peerj.10233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bosiacka et al. title: Spatially resolved dendritic integration: towards a functional classification of neurons link: https://peerj.com/articles/10250 last-modified: 2020-11-24 description: The vast tree-like dendritic structure of neurons allows them to receive and integrate input from many neurons. A wide variety of neuronal morphologies exist, however, their role in dendritic integration, and how it shapes the response of the neuron, is not yet fully understood. Here, we study the evolution and interactions of dendritic spikes in excitable neurons with complex real branch structures. We focus on dozens of digitally reconstructed illustrative neurons from the online repository NeuroMorpho.org, which contains over 130,000 neurons. Yet, our methods can be promptly extended to any other neuron. This approach allows us to estimate and map specific and heterogeneous patterns of activity observed across extensive dendritic trees with thousands of compartments. We propose a classification of neurons based on the location of the soma (centrality) and the number of branches connected to the soma. These are key topological factors in determining the neuron’s energy consumption, firing rate, and the dynamic range, which quantifies the range in synaptic input rate that can be reliably encoded by the neuron’s firing rate. Moreover, we find that bifurcations, the structural building blocks of complex dendrites, play a major role in increasing the dynamic range of neurons. Our results provide a better understanding of the effects of neuronal morphology in the diversity of neuronal dynamics and function. creator: Christoph Kirch creator: Leonardo L. Gollo uri: https://doi.org/10.7717/peerj.10250 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kirch and Gollo title: DPM1 expression as a potential prognostic tumor marker in hepatocellular carcinoma link: https://peerj.com/articles/10307 last-modified: 2020-11-24 description: BackgroundAltered glycosylation of proteins contributes to tumor progression. Dolichol phosphate mannose synthase (DPMS), an essential mannosyltransferase, plays a central role in post-translational modification of proteins, including N-linked glycoproteins, O-mannosylation, C-mannosylation and glycosylphosphatidylinositol anchors synthesis. Little is known about the function of DPMS in liver cancer.MethodsThe study explored the roles of DPMS in the prognosis of hepatocellular carcinoma using UALCAN, Human Protein Atlas, GEPIA, cBioPortal and Metascape databases. The mRNA expressions of DPM1/2/3 also were detected by quantitative real-time PCR experiments in vitro.ResultsThe transcriptional and proteinic expressions of DPM1/2/3 were both over-expressed in patients with hepatocellular carcinoma. Over-expressions of DPMS were discovered to be dramatically associated with clinical cancer stages and pathological tumor grades in hepatocellular carcinoma patients. In addition, higher mRNA expressions of DPM1/2/3 were found to be significantly related to shorter overall survival in liver cancer patients. Futhermore, high genetic alteration rate of DPMS (41%) was also observed in patients with liver cancer, and genetic alteration in DPMS was associated with shorter overall survival in hepatocellular carcinoma patients. We also performed quantitative real-time PCR experiments in human normal hepatocytes and hepatoma cells to verify the expressions of DPM1/2/3 and results showed that the expression of DPM1 was significantly increased in hepatoma cells SMMC-7721 and HepG2.ConclusionsTaken together, these results suggested that DPM1 could be a potential prognostic biomarker for survivals of hepatocellular carcinoma patients. creator: Ming Li creator: Shengli Xia creator: Ping Shi uri: https://doi.org/10.7717/peerj.10307 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: HIV-1 promoter is gradually silenced when integrated into BACH2 in Jurkat T-cells link: https://peerj.com/articles/10321 last-modified: 2020-11-24 description: BackgroundThe persistence of the latent HIV-1 reservoir is a major obstacle to curing HIV-1 infection. HIV-1 integrates into the cellular genome and some targeted genomic loci are frequently detected in clonally expanded latently HIV-1 infected cells, for instance, the gene BTB domain and CNC homology 2 (BACH2).MethodsWe investigated HIV-1 promoter activity after integration into specific sites in BACH2 in Jurkat T-cells. The HIV-1-based vector LTatCL[M] contains two fluorophores: (1) Cerulean, which reports the activity of the HIV-1 promoter and (2) mCherry driven by a constitutive promotor and flanked by genetic insulators. This vector was inserted into introns 2 and 5 of BACH2 of Jurkat T-cells via CRISPR/Cas9 technology in the same and convergent transcriptional orientation of BACH2, and into the genomic safe harbour AAVS1. Single cell clones representing active (Cerulean+/mCherry+) and inactive (Cerulean–/mCherry+) HIV-1 promoters were characterised.ResultsUpon targeted integration of the 5.3 kb vector LTatCL[M] into BACH2, the HIV-1 promoter was gradually silenced as reflected by the decrease in Cerulean expression over a period of 162 days. Silenced HIV-1 promoters could be reactivated by TNF-α and Romidepsin. This observation was independent of the targeted intron and the transcriptional orientation. BACH2 mRNA and protein expression was not impaired by mono-allelic integration of LTatCL[M].ConclusionSuccessful targeted integration of the HIV-1-based vector LTatCL[M] allows longitudinal analyses of HIV-1 promoter activity. creator: Anne Inderbitzin creator: Yik Lim Kok creator: Lisa Jörimann creator: Audrey Kelley creator: Kathrin Neumann creator: Daniel Heinzer creator: Toni Cathomen creator: Karin J. Metzner uri: https://doi.org/10.7717/peerj.10321 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Inderbitzin et al. title: Wnt16 signaling promotes osteoblast differentiation of periosteal derived cells in vitro and in vivo link: https://peerj.com/articles/10374 last-modified: 2020-11-24 description: BackgroundPeriosteum plays critical roles in de novo bone formation and fracture repair. Wnt16 has been regarded as a key regulator in periosteum bone formation. However, the role of Wnt16 in periosteum derived cells (PDCs) osteogenic differentiation remains unclear. The study goal is to uncover whether and how Wnt16 acts on the osteogenesis of PDCs.MethodsWe detected the variation of Wnt16 mRNA expression in PDCs, which were isolated from mouse femur and identified by flow cytometry, cultured in osteogenic medium for 14 days, then knocked down and over-expressed Wnt16 in PDCs to analysis its effects in osteogenesis. Further, we seeded PDCs (Wnt16 over-expressed/vector) in β-tricalcium phosphate cubes, and transplanted this complex into a critical size calvarial defect. Lastly, we used immunofluorescence, Topflash and NFAT luciferase reporter assay to study the possible downstream signaling pathway of Wnt16.ResultsWnt16 mRNA expression showed an increasing trend in PDCs under osteogenic induction for 14 days. Wnt16 shRNA reduced mRNA expression of Runx2, collage type I (Col-1) and osteocalcin (OCN) after 7 days of osteogenic induction, as well as alizarin red staining intensity after 21days. Wnt16 also increased the mRNA expression of Runx2 and OCN and the protein production of Runx2 and Col-1 after 2 days of osteogenic stimulation. In the orthotopic transplantation assay, more bone volume, trabecula number and less trabecula space were found in Wnt16 over-expressed group. Besides, in the newly formed tissue Brdu positive area was smaller and Col-1 was larger in Wnt16 over-expressed group compared to the control group. Finally, Wnt16 upregulated CTNNB1/β-catenin expression and its nuclear translocation in PDCs, also increased Topflash reporter luciferase activity. By contrast, Wnt16 failed to increase NFAT reporter luciferase activity.ConclusionTogether, Wnt16 plays a positive role in regulating PDCs osteogenesis, and Wnt16 may have a potential use in improving bone regeneration. creator: Ying Jin creator: Xiaoyan Sun creator: Fang Pei creator: Zhihe Zhao creator: Jeremy Mao uri: https://doi.org/10.7717/peerj.10374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jin et al. title: Modelling the effects of Spartina alterniflora invasion on the landscape succession of Yancheng coastal natural wetlands, China link: https://peerj.com/articles/10400 last-modified: 2020-11-24 description: BackgroundThe Yancheng coastal natural wetlands (YCNR) are well-preserved silty tidal flat wetlands in China. Due to the severe invasion of Spartina alterniflora, the native ecosystem has undergone great changes. The successful invasion of S. alterniflora reduced the biodiversity of the YCNR, changed the structure and function of the local ecosystem, and eventually led to the degradation of the ecosystem and the loss of ecosystem function and service. Fully understanding the impact of an alien species invasion on YCNR succession is an important prerequisite for protecting and restoring the wetlands.MethodsIn this study, remote sensing, GIS technology, and a cellular-automaton Markov model were used to simulate the natural succession process of native ecosystems without being affected by alien species. By comparing the landscape of the YCNR with the model simulation results, we gained a better understanding of how alien species affect native landscape-scale ecosystems.ResultsDuring the natural succession of the coastal native wetland ecosystem in the YCNR, the pioneer species S. alterniflora occupied the mudflats and expanded seaward. The whole area expanded and moved seaward with an average annual movement of 58.23 m. Phragmites australis seemed to dominate the competition with S. salsa communities, and the area gradually expanded with an average annual movement of 39.89 m. The invasion of S. alterniflora changed the native ecosystem’s spatial succession process, causing the S. salsa ecosystem to be stressed by ecosystems on the side of the sea (S. alterniflora) and that of land (P. australis). The area of the seaward-expanding P. australis ecosystem has been declining. Under a reasonable protected area policy, human activities have enhanced the succession rate of the P. australis ecosystem and have had a small impact on the ecological spatial succession of S. salsa and S. alterniflora. creator: Lingjun Dai creator: Hongyu Liu creator: Gang Wang creator: Cheng Wang creator: Ziru Guo creator: Yi Zhou creator: Yufeng Li uri: https://doi.org/10.7717/peerj.10400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dai et al. title: The paleobiology and paleoecology of South African Lystrosaurus link: https://peerj.com/articles/10408 last-modified: 2020-11-24 description: Lystrosaurus was one of the few tetrapods to survive the end-Permian mass extinction (EPME), the most catastrophic biotic crisis in Phanerozoic history. The significant increased abundance of this genus during the post-extinction Early Triassic recovery period has made Lystrosaurus an iconic survivor taxon globally and ideal for studying changes in growth dynamics during a mass extinction. There is potential evidence of a Lilliput effect in Lystrosaurus in South Africa as the two Triassic species that became highly abundant after the EPME are relatively smaller than the two Permian species. In order to test this hypothesis a detailed examination of the body size and life history of Permo-Triassic Lystrosaurus is required. In this study, the basal skull length and growth patterns of the four South African Lystrosaurus species from the Karoo Basin, L. maccaigi, L. curvatus, L. murrayi and L. declivis, were examined using cranial measurements and bone histology. The basal skull length measurements show that the Triassic species are smaller than the Permian species and supports previous studies. The osteohistology examination of all four species reveal rapidly forming fibrolamellar bone tissues during early to mid-ontogeny. Growth marks are common in L. maccaigi and L. curvatus, but rare and inconsistent in the purely Triassic L. murrayi and L. declivis. The inconsistency of the growth marks in these latter two taxa suggests the presence of developmental plasticity. This feature may have been advantageous in allowing these species to alter their growth patterns in response to environmental cues in the post-extinction Early Triassic climate. An overall transition to slower forming parallel-fibered bone is observed in the largest individuals of L. maccaigi, but absent from the limb bones of the other species. The absence of such bone tissue or outer circumferential lamellae in L. curvatus, L. murrayi and L. declivis indicates that even the largest collected specimens do not represent fully grown individuals. Although L. murrayi and L. declivis are smaller in size, the lack of a growth asymptote in the largest specimens indicates that adult individuals would have been notably larger and may have been similar in size to large L. maccaigi and L. curvatus when fully grown. Thus, the previously described Lilliput effect, recognized by some authors in the Karoo fossil record (such as the therocephalian Moschorhinus kitchingi), may be a product of high juvenile excess mortality in the Triassic rather than a strict “dwarfing” of Lystrosaurus species. The lifestyle of Lystrosaurus was also re-examined. Although previous studies have proposed an aquatic lifestyle for the genus, the similar morphology and bone microanatomy to several other large terrestrial Permo-Triassic dicynodonts supports a fully terrestrial mode of life. creator: Jennifer Botha uri: https://doi.org/10.7717/peerj.10408 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Botha title: Classification of ovarian cancer associated with BRCA1 mutations, immune checkpoints, and tumor microenvironment based on immunogenomic profiling link: https://peerj.com/articles/10414 last-modified: 2020-11-24 description: BackgroundOvarian cancer is a highly fatal gynecological malignancy and new, more effective treatments are needed. Immunotherapy is gaining attention from researchers worldwide, although it has not proven to be consistently effective in the treatment of ovarian cancer. We studied the immune landscape of ovarian cancer patients to improve the efficacy of immunotherapy as a treatment option.MethodsWe obtained expression profiles, somatic mutation data, and clinical information from The Cancer Genome Atlas. Ovarian cancer was classified based on 29 immune-associated gene sets, which represented different immune cell types, functions, and pathways. Single-sample gene set enrichment (ssGSEA) was used to quantify the activity or enrichment levels of the gene sets in ovarian cancer, and the unsupervised machine learning method was used sort the classifications. Our classifications were validated using Gene Expression Omnibus datasets.ResultsWe divided ovarian cancer into three subtypes according to the ssGSEA score: subtype 1 (low immunity), subtype 2 (median immunity), and subtype 3 (high immunity). Most tumor-infiltrating immune cells and immune checkpoint molecules were upgraded in subtype 3 compared with those in the other subtypes. The tumor mutation burden (TMB) was not significantly different among the three subtypes. However, patients with BRCA1 mutations were consistently detected in subtype 3. Furthermore, most immune signature pathways were hyperactivated in subtype 3, including T and B cell receptor signaling pathways, PD-L1 expression and PD-1 checkpoint pathway the NF-κB signaling pathway, Th17 cell differentiation and interleukin-17 signaling pathways, and the TNF signaling pathway.ConclusionOvarian cancer subtypes that are based on immune biosignatures may contribute to the development of novel therapeutic treatment strategies for ovarian cancer. creator: Yousheng Wei creator: Tingyu Ou creator: Yan Lu creator: Guangteng Wu creator: Ying Long creator: Xinbin Pan creator: Desheng Yao uri: https://doi.org/10.7717/peerj.10414 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wei et al. title: The pandemic paradox: domestic violence and happiness of women link: https://peerj.com/articles/10472 last-modified: 2020-11-24 description: BackgroundAcross the globe, lockdowns have been enforced as a pandemic response to COVID-19. Such lockdown coupled with school closures and stay-at-home orders made women more vulnerable in terms of higher responsibility and spending more time with an abusive partner, if any.MethodsThis study investigates the situation of women during COVID-19 induced lockdown by focusing on their happiness and inquiring about the incidence of violence. Using the zero-inflated negative binomial model, our findings ascertained that family settings, type of relationship with a spouse, and age significantly affects the positive count of violence during the lockdown. We further estimated the determinants of happiness and found that years of schooling, the role of women in household decision making, and feeling empowered is affecting their happiness.ResultsWomen having higher education have more odds of zero violence. Unemployed women and women who are not working have higher odds of zero violence as compared to women who are working. During this lockdown after the COVID-19 pandemic, women living in urban areas, having higher education, having an adequate household income to meet the expenditures, having lesser anxiety, not facing violence, feeling empowered when their husband is around, and have higher decision-making power are happier.Discussion and conclusionThe study is important in the context of happiness and violence inflicted on women during the lockdown and provides the basis to improve the pandemic response policy. The inclusion of women’s safety and happiness in pandemic response policy is important to ensure the well-being of women and to devise better health and economic policy. Our estimates suggest higher education results in less incidence of violence which could be argued as desirable outcomes for building healthy, productive, and happy communities. In addition to this, as pandemic induced lock-down is likely to result in higher unemployment across the globe including Pakistan, therefore, in light of our estimates pertaining to the role of unemployment in the incidence of violence, policymakers should deploy more resources to enhance income and to combat the rising unemployment. As a counter-intuitive outcome of these policy interventions, incidence of violence will be dampened, educational attainment and women empowerment will be increased which will certainly increase happiness. creator: Wajiha Haq creator: Syed Hassan Raza creator: Tahir Mahmood uri: https://doi.org/10.7717/peerj.10472 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Haq et al. title: Two new species of Tardigrada from moss cushions (Grimmia sp.) in a xerothermic habitat in northeast Tennessee (USA, North America), with the first identification of males in the genus Viridiscus link: https://peerj.com/articles/10251 last-modified: 2020-11-23 description: BackgroundThe phylum Tardigrada consists of over 1,300 species that inhabit terrestrial, freshwater and marine environments throughout the world. In terrestrial habitats they live primarily in mosses, lichens, leaf litter and soil, whereas tardigrades in freshwater and marine environments are mainly found in sediments and on aquatic plants. More than 65 species have been previously reported in the state of Tennessee, USA.MethodsTardigrades present in moss cushions (Grimmia sp.) collected from a xerothermic habitat on the East Tennessee State University campus, Johnson City, TN, USA, were extracted, mounted on slides, identified, and counted. Additional samples of fresh dried moss were used for integrative analyses, including morphological analysis with phase contrast (PCM) and scanning electron microscopy (SEM), as well as molecular analyses of COI, 18S rRNA, 28S rRNA, and ITS-2 of the Macrobiotus and Milnesium species.ResultsFive species were found, including two species new to science: Viridiscus miraviridis sp. nov. and Macrobiotus basiatus sp. nov. Viridiscus miraviridis sp. nov. differs from other members of the genus mainly by having a different type of dorsal cuticle and some other, more subtle, morphometric characters. In addition to the two new species, Viridiscus perviridis and Viridiscus viridissimus were present, and males of Vir. viridissimus were found for the first time, the first record of males in the genus Viridiscus. Macrobiotus basiatus sp. nov. is most similar to Macrobiotus nelsonae, but it differs from Mac. nelsonae mainly by the stylet supports being situated in a more anterior position, shorter and narrower egg processes, and a smaller number of areoles around the egg processes. Moreover, the identification of Milnesium inceptum was confirmed as the first record for the USA by analysis of COI. creator: Diane R. Nelson creator: Rebecca Adkins Fletcher creator: Roberto Guidetti creator: Milena Roszkowska creator: Daria Grobys creator: Łukasz Kaczmarek uri: https://doi.org/10.7717/peerj.10251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nelson et al. title: Comprehensive genomic analysis of microenvironment phenotypes in ovarian cancer link: https://peerj.com/articles/10255 last-modified: 2020-11-23 description: BackgroundOvarian cancer is one of the leading causes of cancer-related death in women. The incidence of ovarian cancer is insidious, and the recurrence rate is high. The survival rate of ovarian cancer has not significantly improved over the past decade. Recently, immune checkpoint inhibitors such as those targeting CTLA-4, PD-1, or PD-L1 have been used to treat ovarian cancer. Therefore, a full analysis of the immune biomarkers associated with this malignancy is necessary.MethodsIn this study, we used data from The Cancer Genome Atlas (TCGA) database to analyze the infiltration patterns of specific immune cell types in tumor samples. Data from the Gene Expression Omnibus (GEO) database was used for external validation. According to the invasion patterns of immune cells, we divided the ovarian cancer microenvironment into two clusters: A and B. These tumor microenvironment (TME) subtypes were associated with genomic and clinicopathological characteristics. Subsequently, a random forest classification model was established. Differential genomic features, functional enrichment, and DNA methylation were analyzed between the two clusters. The characteristics of immune cell infiltration and the expression of immune-related cytokines or markers were analyzed. Somatic mutation analysis was also performed between clusters A and B. Finally, multivariate Cox analysis was used to analyze independent prognostic factors.ResultsThe ovarian cancer TME cluster A was characterized by less infiltration of immune cells and sparse distribution and low expression of immunomodulators. In contrast, cytotoxic T cells and immunosuppressive cells were significantly increased in the ovarian cancer TME cluster B. Additionally, immune-related cytokines or markers, including IFN-γ and TNF-β, were also expressed in large quantities. In total, 35 differentially methylated and expressed genes (DMEGs) were identified. Functional enrichment analyses revealed that the DMEGs in cluster B participated in important biological processes and immune-related pathways. The mutation load in cluster B was insignificantly higher than that of cluster A (p = 0.076). Multivariate Cox analysis showed that TME was an independent prognostic factor for ovarian cancer (hazard ratio: 1.33, 95% confidence interval: 1.01–1.75, p = 0.041).ConclusionThis study described and classified basic information about the immune invasion pattern of ovarian cancer and integrated biomarkers related to different immunophenotypes to reveal interactions between ovarian cancer and the immune system. creator: Jingshu Wang creator: Tingting Zhang creator: Lina Yang creator: Gong Yang uri: https://doi.org/10.7717/peerj.10255 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Exposure to low concentrations of pesticide stimulates ecological functioning in the dung beetle Onthophagus nuchicornis link: https://peerj.com/articles/10359 last-modified: 2020-11-23 description: Body-size is an important trait for predicting how species contribute to ecosystem functions and respond to environmental stress. Using the dung beetle Onthophagus nuchicornis (Coleoptera: Scarabaeidae), we explored how variation in body-size affected ecosystem functioning (dung burial) and sensitivity to an environmental stressor (exposure to the veterinary anthelmintic ivermectin). We found that large beetles buried nearly 1.5-fold more dung than small beetles, but that mortality from exposure to a range of concentrations of ivermectin did not differ between large and small beetles. Unexpectedly, we found that exposure to low concentrations of ivermectin (0.01⁠–1 mg ivermectin per kg dung) stimulated dung burial in both small and large beetles. Our results provide evidence of ecological functioning hormesis stemming from exposure to low amounts of a chemical stressor that causes mortality at high doses. creator: Paul Manning creator: G. Christopher Cutler uri: https://doi.org/10.7717/peerj.10359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Manning and Cutler title: Determination of the reference genes for qRT-PCR normalization and expression levels of MAT genes under various conditions in Ulocladium link: https://peerj.com/articles/10379 last-modified: 2020-11-23 description: The genus Ulocladium is thought to be strictly asexual. One of the possible reasons for the lack of sexuality in Ulocladium species is the absence of the stimulus of environmental factors. Sexual reproduction in ascomycetes is controlled by a specific region in the genome referred to as mating-type locus (MAT) that consists of two dissimilar DNA sequences in the mating partners, termed MAT1-1 and MAT1-2 idiomorphs. To identify the response of MAT loci to environmental conditions, the mRNA transcription level of MAT1-1-1 and MAT1-2-1 genes was tested using qRT-PCR under different temperatures (−20 °C, −10 °C, 0 °C, 10 °C, 20 °C, 30 °C and 40 °C), culture medias (CM, OA, HAY, PCA, PDA and V8), photoperiods (24 h light, 24 h dark, 12 h light/12 h dark, 10 h light/14 h dark and 8 h light/16 h dark), and CO2 concentrations (0.03%, 0.5%, 1%, 5%, 10%, 15% and 20%). For obtaining reliable results from qRT-PCR, the most stable internal control gene and optimal number of reference genes for normalization were determined under different treatments. The results showed that there is no universal internal control gene that is expressed at a constant level under different experimental treatments. In comparison to various incubation conditions, the relative expression levels of both MAT genes were significantly increased when fungal mycelia were grown on HAY culture media at 0–10 °C with a light/dark cycle, indicating that temperature, culture media, and light might be the key environmental factors for regulating the sexuality in Ulocladium. Moreover, MAT1-1-1 and MAT1-2-1 genes showed similar expression patterns under different treatments, suggesting that the two MAT genes might play an equally important role in the sexual evolutionary process. creator: Li-Guo Ma creator: Yun Geng uri: https://doi.org/10.7717/peerj.10379 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ma and Geng title: Effects of whole-body vibrations on neuromuscular fatigue: a study with sets of different durations link: https://peerj.com/articles/10388 last-modified: 2020-11-23 description: BackgroundWhole body vibrations have been used as an exercise modality or as a tool to study neuromuscular integration. There is increasing evidence that longer WBV exposures (up to 10 minutes) induce an acute impairment in neuromuscular function. However, the magnitude and origin of WBV induced fatigue is poorly understood.PurposeThe study aimed to investigate the magnitude and origin of neuromuscular fatigue induced by half-squat long-exposure whole-body vibration intervention (WBV) with sets of different duration and compare it to non-vibration (SHAM) conditions.MethodsTen young, recreationally trained adults participated in six fatiguing trials, each consisting of maintaining a squatting position for several sets of the duration of 30, 60 or 180 seconds. The static squatting was superimposed with vibrations (WBV30, WBV60, WBV180) or without vibrations (SHAM30, SHAM60, SHAM180) for a total exercise exposure of 9-minutes in each trial. Maximum voluntary contraction (MVC), level of voluntary activation (%VA), low- (T20) and high-frequency (T100) doublets, low-to-high-frequency fatigue ratio (T20/100) and single twitch peak torque (TWPT) were assessed before, immediately after, then 15 and 30 minutes after each fatiguing protocol.ResultInferential statistics using RM ANOVA and post hoc tests revealed statistically significant declines from baseline values in MVC, T20, T100, T20/100 and TWPT in all trials, but not in %VA. No significant differences were found between WBV and SHAM conditions.ConclusionOur findings suggest that the origin of fatigue induced by WBV is not significantly different compared to control conditions without vibrations. The lack of significant differences in %VA and the significant decline in other assessed parameters suggest that fatiguing protocols used in this study induced peripheral fatigue of a similar magnitude in all trials. creator: Miloš Kalc creator: Ramona Ritzmann creator: Vojko Strojnik uri: https://doi.org/10.7717/peerj.10388 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kalc et al. title: The use of artificial substrate units to improve inventories of cryptic crustacean species on Caribbean coral reefs link: https://peerj.com/articles/10389 last-modified: 2020-11-23 description: Motile cryptofauna inhabiting coral reefs are complex assemblages that utilize the space available among dead coral stands and the surrounding coral rubble substrate. They comprise a group of organisms largely overlooked in biodiversity estimates because they are hard to collect and identify, and their collection causes disturbance that is unsustainable in light of widespread reef degradation. Artificial substrate units (ASUs) provide a better sampling alternative and have the potential to enhance biodiversity estimates. The present study examines the effectiveness of ASUs made with defaunated coral rubble to estimate the diversity of motile cryptic crustaceans in the back-reef zone of the Puerto Morelos Reef National Park, Mexico. Species richness, Simpson’s diversity index, Shannon–Wiener index and the composition of assemblages were compared between ASUs and samples from the surrounding coral rubble substrate. A combined total of 2,740 specimens of 178 different species, belonging to five orders of Crustacea (Amphipoda, Cumacea, Isopoda, Tanaidacea and Decapoda) were collected. Species richness was higher in the surrounding coral rubble and Shannon–Wiener and Simpson indexes were higher in ASUs. Species composition differed between methods, with only 71 species being shared among sampling methods. Decapoda was more speciose in ASUs and Peracarids in the surrounding coral rubble. Combining the use of ASUs with surrounding rubble provided a better inventory of motile cryptic crustacean biodiversity, as 65% of the species were represented by one or two specimens. creator: Luz Verónica Monroy-Velázquez creator: Rosa E. Rodríguez-Martínez creator: Paul Blanchon creator: Fernando Alvarez uri: https://doi.org/10.7717/peerj.10389 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Monroy-Velázquez et al. title: Sensation of the tiniest kind: the antennal sensilla of the smallest free-living insect Scydosella musawasensis (Coleoptera: Ptiliidae) link: https://peerj.com/articles/10401 last-modified: 2020-11-23 description: Miniaturization is a major evolutionary trend prominent in insects, which has resulted in the existence of insects comparable in size to some unicellular protists. The adaptation of the complex antennal multisensory systems to extreme miniaturization is a fascinating problem, which remains almost unexplored. We studied the antennal sensilla of Scydosella musawasensisHall, 1999 (Coleoptera: Ptiliidae), the smallest free-living insect, using scanning electron microscopy. The antenna of S. musawasensis bears 131 sensilla; no intraspecific variation in the number or position of the sensilla has been revealed. Nine different morphological types of sensilla are described according to their external morphological features and distribution: four types of sensilla trichodea, one type of sensilla chaetica, two types of sensilla styloconica, and two types of sensilla basiconica. Morphometric analysis of the sensilla of S. musawasensis, based on measurements of the lengths and diameters of sensilla and their location and number, showed the absence of significant differences between females and males. Comparative allometric analysis of S. musawasensis and larger Coleoptera showed that the number of sensilla and the size of sensilla chaetica decrease with decreasing body size. However, the number of the types of sensilla and the length and diameter of the multiporous sensilla basiconica revealed no correlation with the body size. Comparison of the acquired data with the results of our earlier study of the antennal sensilla of some of the smallest parasitic wasps is used to put forward hypotheses on the common principles of miniaturization of the antennal sensory systems of insects. creator: Anna V. Diakova creator: Alexey A. Polilov uri: https://doi.org/10.7717/peerj.10401 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Diakova and Polilov title: Identifying MMP14 and COL12A1 as a potential combination of prognostic biomarkers in pancreatic ductal adenocarcinoma using integrated bioinformatics analysis link: https://peerj.com/articles/10419 last-modified: 2020-11-23 description: BackgroundPancreatic ductal adenocarcinoma (PDAC) is a fatal malignant neoplasm. It is necessary to improve the understanding of the underlying molecular mechanisms and identify the key genes and signaling pathways involved in PDAC.MethodsThe microarray datasets GSE28735, GSE62165, and GSE91035 were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified by integrated bioinformatics analysis, including protein–protein interaction (PPI) network, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The PPI network was established using the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. GO functional annotation and KEGG pathway analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. Hub genes were validated via the Gene Expression Profiling Interactive Analysis tool (GEPIA) and the Human Protein Atlas (HPA) website.ResultsA total of 263 DEGs (167 upregulated and 96 downregulated) were common to the three datasets. We used STRING and Cytoscape software to establish the PPI network and then identified key modules. From the PPI network, 225 nodes and 803 edges were selected. The most significant module, which comprised 11 DEGs, was identified using the Molecular Complex Detection plugin. The top 20 hub genes, which were filtered by the CytoHubba plugin, comprised FN1, COL1A1, COL3A1, BGN, POSTN, FBN1, COL5A2, COL12A1, THBS2, COL6A3, VCAN, CDH11, MMP14, LTBP1, IGFBP5, ALB, CXCL12, FAP, MATN3, and COL8A1. These genes were validated using The Cancer Genome Atlas (TCGA) and Genotype–Tissue Expression (GTEx) databases, and the encoded proteins were subsequently validated using the HPA website. The GO analysis results showed that the most significantly enriched biological process, cellular component, and molecular function terms among the 20 hub genes were cell adhesion, proteinaceous extracellular matrix, and calcium ion binding, respectively. The KEGG pathway analysis showed that the 20 hub genes were mainly enriched in ECM–receptor interaction, focal adhesion, PI3K-Akt signaling pathway, and protein digestion and absorption. These findings indicated that FBN1 and COL8A1 appear to be involved in the progression of PDAC. Moreover, patient survival analysis performed via the GEPIA using TCGA and GTEx databases demonstrated that the expression levels of COL12A1 and MMP14 were correlated with a poor prognosis in PDAC patients (p < 0.05).ConclusionsThe results demonstrated that upregulation of MMP14 and COL12A1 is associated with poor overall survival, and these might be a combination of prognostic biomarkers in PDAC. creator: Jingyi Ding creator: Yanxi Liu creator: Yu Lai uri: https://doi.org/10.7717/peerj.10419 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ding et al. title: A meta-analysis contrasting active versus passive restoration practices in dryland agricultural ecosystems link: https://peerj.com/articles/10428 last-modified: 2020-11-23 description: Restoration of agricultural drylands globally, here farmlands and grazing lands, is a priority for ecosystem function and biodiversity preservation. Natural areas in drylands are recognized as biodiversity hotspots and face continued human impacts. Global water shortages are driving increased agricultural land retirement providing the opportunity to reclaim some of these lands for natural habitat. We used meta-analysis to contrast different classes of dryland restoration practices. All interventions were categorized as active and passive for the analyses of efficacy in dryland agricultural ecosystems. We evaluated the impact of 19 specific restoration practices from 42 studies on soil, plant, animal, and general habitat targets across 16 countries, for a total of 1,427 independent observations. Passive vegetation restoration and grazing exclusion led to net positive restoration outcomes. Passive restoration practices were more variable and less effective than active restoration practices. Furthermore, passive soil restoration led to net negative restoration outcomes. Active restoration practices consistently led to positive outcomes for soil, plant, and habitat targets. Water supplementation was the most effective restoration practice. These findings suggest that active interventions are necessary and critical in most instances for dryland agricultural ecosystems likely because of severe anthropogenic pressures and concurrent environmental stressors—both past and present. creator: M. Florencia Miguel creator: H. Scott Butterfield creator: Christopher J. Lortie uri: https://doi.org/10.7717/peerj.10428 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Miguel et al. title: Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana link: https://peerj.com/articles/10256 last-modified: 2020-11-20 description: Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response. creator: Lauren K. Hudson creator: Lisha Constantine-Renna creator: Linda Thomas creator: Christina Moore creator: Xiaorong Qian creator: Katie Garman creator: John R. Dunn creator: Thomas G. Denes uri: https://doi.org/10.7717/peerj.10256 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hudson et al. title: Morph-specific seasonal variation of aggressive behaviour in a polymorphic lizard species link: https://peerj.com/articles/10268 last-modified: 2020-11-20 description: The persistence of colour polymorphism (CP) within a given population is generally associated with the coexistence of alternative reproductive strategies, each one involving specific trade-offs among behavioural, morphological, physiological, and other life histories. Common wall lizard (Podarcis muralis), is a medium-sized diurnal lizard, showing CP in three main colours (yellow, white, and red) on throat and belly, and a morph-specific pattern for both immunocompetence and seasonal variation of T levels. Yellow males show low stamina with high plasma T levels at the beginning of the season, while white males show high stamina with a higher plasma T levels at the end of the season. We hypothesised the presence of two strategies: a risky one, characterised by high aggressiveness played by yellow-morph, and a conservative one by white morph with low aggressiveness. Thus, we tested the aggressive response to conspecifics of yellow and white morphs using a mirror inserted into their cage, mimicking an intrusion of a stranger in their territories, throughout the breeding season (from April to July, 117 trials). We considered three types of aggressive response, with different levels of aggressiveness: (i) bite against the image reflected in the mirror, (ii) seconds spent by the individuals into the half mirrored cage, and (iii) number of times the lizard entered the half mirrored cage. We also considered the number of tongue flicking as explorative behaviour variable. All lizards were tested after a period of acclimatisation to the captivity conditions. Results demonstrate that yellow males showed a higher aggressive response in the early season and a decrease aggressive response towards the end, whereas white males showed an opposite pattern. creator: Alan Jioele Coladonato creator: Marco Mangiacotti creator: Stefano Scali creator: Marco A. L. Zuffi creator: Carlotta Pasquariello creator: Cristian Matellini creator: Simone Buratti creator: Mara Battaiola creator: Roberto Sacchi uri: https://doi.org/10.7717/peerj.10268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Coladonato et al. title: Identification of hub genes associated with the pathogenesis of diffuse large B-cell lymphoma subtype one characterized by host response via integrated bioinformatic analyses link: https://peerj.com/articles/10269 last-modified: 2020-11-20 description: BackgroundHost response diffuse large B-cell lymphoma (HR DLBCL) shares features of histologically defined T-cell/histiocyte-rich B-cell lymphoma, including fewer genetic abnormalities, frequent splenic and bone marrow involvement, and younger age at presentation. HR DLBCL is inherently less responsive to the standard treatment for DLBCL. Moreover, the mechanism of infiltration of HR DLBCL with preexisting abundant T-cells and dendritic cells is unknown, and their associated underlying immune responses incompletely defined. Here, hub genes and pathogenesis associated with HR DLBCL were explored to reveal molecular mechanisms and treatment targets.MethodsDifferentially expressed genes were identified in three datasets (GSE25638, GSE44337, GSE56315). The expression profile of the genes in the GSE53786 dataset was used to constructed a co-expression network. Protein-protein interactions analysis in the modules of interest identified candidate hub genes. Then screening of real hub genes was carried out by survival analysis within the GSE53786 and GSE10846 datasets. Expression of hub genes was validated in the Gene expression profiling interactive analysis, Oncomine databases and human tissue specimens. Functional enrichment analysis and Gene set enrichment analysis were utilized to investigate the potential mechanisms. Tumor Immune Estimation Resource and The Cancer Genome Atlas were used to mine the association of the hub gene with tumor immunity, potential upstream regulators were predicted using bioinformatics tools.ResultsA total of 274 common differentially expressed genes were identified. Within the key module, we identified CXCL10 as a real hub gene. The validation of upregulated expression level of CXCL10 was consistent with our study. CXCL10 might have a regulatory effect on tumor immunity. The predicted miRNA (hsa-mir-6849-3p) and transcription factor (IRF9) might regulate gene expression in the hub module. creator: Lingna Zhou creator: Liya Ding creator: Yuqi Gong creator: Jing Zhao creator: Gong Xin creator: Ren Zhou creator: Wei Zhang uri: https://doi.org/10.7717/peerj.10269 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhou et al. title: The cranial morphology of Tanystropheus hydroides (Tanystropheidae, Archosauromorpha) as revealed by synchrotron microtomography link: https://peerj.com/articles/10299 last-modified: 2020-11-20 description: The postcranial morphology of the extremely long-necked Tanystropheus hydroides is well-known, but observations of skull morphology were previously limited due to compression of the known specimens. Here we provide a detailed description of the skull of PIMUZ T 2790, including a partial endocast and endosseous labyrinth, based on synchrotron microtomographic data, and compare its morphology to that of other early Archosauromorpha. In many features, such as the wide and flattened snout and the configuration of the temporal and palatal regions, Tanystropheus hydroides differs strongly from other early archosauromorphs. The braincase possesses a combination of derived archosaur traits, such as the presence of a laterosphenoid and the ossification of the lateral wall of the braincase, but also differs from archosauriforms in the morphology of the ventral ramus of the opisthotic, the horizontal orientation of the parabasisphenoid, and the absence of a clearly defined crista prootica. Tanystropheus hydroides was a ram-feeder that likely caught its prey through a laterally directed snapping bite. Although the cranial morphology of other archosauromorph lineages is relatively well-represented, the skulls of most tanystropheid taxa remain poorly understood due to compressed and often fragmentary specimens. The recent descriptions of the skulls of Macrocnemus bassanii and now Tanystropheus hydroides reveal a large cranial disparity in the clade, reflecting wide ecological diversity, and highlighting the importance of non-archosauriform Archosauromorpha to both terrestrial and aquatic ecosystems during the Triassic. creator: Stephan N.F. Spiekman creator: James M. Neenan creator: Nicholas C. Fraser creator: Vincent Fernandez creator: Olivier Rieppel creator: Stefania Nosotti creator: Torsten M. Scheyer uri: https://doi.org/10.7717/peerj.10299 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Spiekman et al. title: Translocation of an arctic seashore plant reveals signs of maladaptation to altered climatic conditions link: https://peerj.com/articles/10357 last-modified: 2020-11-20 description: Ongoing anthropogenic climate change alters the local climatic conditions to which species may be adapted. Information on species’ climatic requirements and their intraspecific variation is necessary for predicting the effects of climate change on biodiversity. We used a climatic gradient to test whether populations of two allopatric varieties of an arctic seashore herb (Primula nutans ssp. finmarchica) show adaptation to their local climates and how a future warmer climate may affect them. Our experimental set-up combined a reciprocal translocation within the distribution range of the species with an experiment testing the performance of the sampled populations in warmer climatic conditions south of their range. We monitored survival, size, and flowering over four growing seasons as measures of performance and, thus, proxies of fitness. We found that both varieties performed better in experimental gardens towards the north. Interestingly, highest up in the north, the southern variety outperformed the northern one. Supported by weather data, this suggests that the climatic optima of both varieties have moved at least partly outside their current range. Further warming would make the current environments of both varieties even less suitable. We conclude that Primula nutans ssp. finmarchica is already suffering from adaptational lag due to climate change, and that further warming may increase this maladaptation, especially for the northern variety. The study also highlights that it is not sufficient to run only reciprocal translocation experiments. Climate change is already shifting the optimum conditions for many species and adaptation needs also to be tested outside the current range of the focal taxon in order to include both historic conditions and future conditions. creator: Maria Hällfors creator: Susanna Lehvävirta creator: Tone Aandahl creator: Iida-Maria Lehtimäki creator: Lars Ola Nilsson creator: Anna Ruotsalainen creator: Leif E. Schulman creator: Marko T. Hyvärinen uri: https://doi.org/10.7717/peerj.10357 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Hällfors et al. title: Genome-wide identification and analysis of the thiolase family in insects link: https://peerj.com/articles/10393 last-modified: 2020-11-20 description: Thiolases are important enzymes involved in lipid metabolism in both prokaryotes and eukaryotes, and are essential for a range of metabolic pathways, while, little is known for this important family in insects. To shed light on the evolutionary models and functional diversities of the thiolase family, 137 thiolase genes were identified in 20 representative insect genomes. They were mainly classified into five classes, namely cytosolic thiolase (CT-thiolase), T1-thiolase, T2-thiolase, trifunctional enzyme thiolase (TFE-thiolase), and sterol carrier protein 2 thiolase (SCP2-thiolase). The intron number and exon/intron structures of the thiolase genes reserve large diversification. Subcellular localization prediction indicated that all the thiolase proteins were mitochondrial, cytosolic, or peroxisomal enzymes. Four highly conserved sequence fingerprints were found in the insect thiolase proteins, including CxS-, NEAF-, GHP-, and CxGGGxG-motifs. Homology modeling indicated that insect thiolases share similar 3D structures with mammals, fishes, and microorganisms. In Bombyx mori, microarray data and reverse transcription-polymerase chain reaction (RT-PCR) analysis suggested that some thiolases might be involved in steroid metabolism, juvenile hormone (JH), and sex pheromone biosynthesis pathways. In general, sequence and structural characteristics were relatively conserved among insects, bacteria and vertebrates, while different classes of thiolases might have differentiation in specific functions and physiological processes. These results will provide an important foundation for future functional validation of insect thiolases. creator: Shou-Min Fang uri: https://doi.org/10.7717/peerj.10393 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Fang title: Response of Bolivian gray titi monkeys (Plecturocebus donacophilus) to an anthropogenic noise gradient: behavioral and hormonal correlates link: https://peerj.com/articles/10417 last-modified: 2020-11-20 description: Worldwide urban expansion and deforestation have caused a rapid decline of non-human primates in recent decades. Yet, little is known to what extent these animals can tolerate anthropogenic noise arising from roadway traffic and human presence in their habitat. We studied six family groups of titis residing at increasing distances from a busy highway, in a park promoting ecotourism near Santa Cruz de la Sierra, Bolivia. We mapped group movements, sampled the titis’ behavior, collected fecal samples from each study group and conducted experiments in which we used a mannequin simulating a human intrusion in their home range. We hypothesized that groups of titi monkeys exposed to higher levels of anthropogenic noise and human presence would react weakly to the mannequin and show higher concentrations of fecal cortisol compared with groups in least perturbed areas. Sound pressure measurements and systematic monitoring of soundscape inside the titis’ home ranges confirmed the presence of a noise gradient, best characterized by the root-mean-square (RMS) and median amplitude (M) acoustic indices; importantly, both anthropogenic noise and human presence co-varied. Study groups resided in small, overlapping home ranges and they spent most of their time resting and preferentially used the lower forest stratum for traveling and the higher levels for foraging. Focal sampling analysis revealed that the time spent moving by adult pairs was inversely correlated with noise, the behavioral change occurring within a gradient of minimum sound pressures ranging from 44 dB(A) to 52 dB(A). Validated enzyme-immunoassays of fecal samples however detected surprisingly low cortisol concentrations, unrelated to the changes observed in the RMS and M indices. Finally, titis’ response to the mannequin varied according to our expectation, with alarm calling being greater in distant groups relative to highway. Our study thus indicates reduced alarm calling through habituation to human presence and suggests a titis’ resilience to anthropogenic noise with little evidence of physiological stress. creator: Lucero M. Hernani Lineros creator: Amélie Chimènes creator: Audrey Maille creator: Kimberly Dingess creator: Damián I. Rumiz creator: Patrice Adret uri: https://doi.org/10.7717/peerj.10417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hernani Lineros et al. title: Loss of HOXB3 correlates with the development of hormone receptor negative breast cancer link: https://peerj.com/articles/10421 last-modified: 2020-11-20 description: BackgroundThe homeobox gene family, encoding a specific nuclear protein, is essential for embryonic development, differentiation, and homeostasis. The role of the HOXB3 protein varies in different tumors. This study aims to explore the role of the HOXB3 gene in breast cancer.MethodDifferentially expressed genes were screened by analyzing metastatic breast cancer gene chip data from TCGA and GEO databases. The function of the selected HOXB3 gene was also analyzed in different databases and through molecular biology methods, such as qRT-PCR, western blot and IF to verify bioinformatics findings.ResultsBoth bioinformatics analyses and western blot showed that HOXB3 was lost in breast cancer compared to normal breast tissue. Survival analysis also showed that lower expression of HOXB3 was associated with poor prognosis. Bioinformatics analyses further showed that HOXB3 was positively correlated with hormone receptors. Metascape for GO analysis of GEO data provided possible mechanisms that HOXB3 could positively regulate cell adhesion, inhibit cell proliferation and activate immune response in breast cancer; moreover, GSEA included several cancer-associated pathways.ConclusionIn summary, HOXB3 expression was decreased in breast cancer, and it was associated with poor prognosis. It might become a new biomarker to predict prognosis of breast cancer. creator: Lizhe Zhu creator: Shibo Yu creator: Siyuan Jiang creator: Guanqun Ge creator: Yu Yan creator: Yuhui Zhou creator: Ligang Niu creator: Jianjun He creator: Yu Ren creator: Bin Wang uri: https://doi.org/10.7717/peerj.10421 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhu et al. title: Freeze-like responses to pain in humans and its modulation by social context link: https://peerj.com/articles/10094 last-modified: 2020-11-19 description: BackgroundMaladaptive defensive responses such as excessive avoidance behavior have received increasing attention as a main mechanism for the development and maintenance of chronic pain complaints. However, another defensive response which is commonly studied in animals as a proxy for fear is freezing behavior. No research to date has investigated human freezing behavior in the context of pain. In addition, there is an increasing realization that social context can affect pain-relevant processes such as pain experience and pain behavior but less is known about the effects of social context on defensive responses to pain. Hence, this study investigated freezing behavior and facial pain expression in the context of pain, and their modulation by social context.MethodsHealthy, pain-free participants (N = 39) stood on a stabilometric force platform in a threatening or safe social context, which was manipulated using angry or happy facial stimuli. In some trials, an auditory cue (conditioned stimulus; CS) predicted the occurrence of painful electrocutaneous stimulus (unconditioned stimulus; pain-US). We assessed body sway (an index of freezing), heart rate, facial pain expression, self-reported pain intensity, unpleasantness, and pain-US expectancy during the CS and the context alone (no CS).ResultsThe results were mixed. Neither the anticipation of pain, nor social context affected body sway. Heart rate and painful facial expression were reduced in the threatening social context at high anxiety levels. A threatening social context also elicited higher pain-US expectancy ratings. In sum, a threatening social context increases the expectation of pain, but reduces the facial expression of pain and lowers heart rate in highly anxious individuals. creator: Kai Karos creator: Ann Meulders creator: Tine Leyssen creator: Johan W. Vlaeyen uri: https://doi.org/10.7717/peerj.10094 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Karos et al. title: High-dose testosterone supplementation disturbs liver pro-oxidant/antioxidant balance and function in adolescent male Wistar rats undergoing moderate-intensity endurance training link: https://peerj.com/articles/10228 last-modified: 2020-11-19 description: In some countries, anabolic-androgenic steroid abuse is rampant among adolescent boys and young men, including some of those seeking physical fitness and/or pleasing appearance through various exercise types. This tactic carries the risk of severe harmful health effects, including liver injury. Most anabolic-androgenic steroid stacking protocols employed are based on the use of the ‘prototypic’ anabolic-androgenic steroid testosterone and/or its esters. There is a vast body of data on the effects of anabolic-androgenic steroids’ abuse combined with physical exercise training on the liver antioxidant barrier in adult subjects, whereas those concerning adolescents are scant. This study aimed to assess, in adolescent male Wistar rats undergoing a 6-week moderate-intensity endurance training (treadmill running), the influence of concurrent weekly supplementation with intramuscular testosterone enanthate (TE, 8 or 80 mg/kg body weight/week) on selected indices of liver status and oxidative stress. The rats were sacrificed, and their livers and blood samples were harvested two days after the last training session. High-dose TE treatment significantly reduced body and liver weight gains. Neither low-dose nor high-dose TE treatment affected liver α-tocopherol or γ-tocopherol content, whereas low-dose TE treatment significantly lowered hepatic reduced glutathione content. TE treatment significantly elevated liver thiobarbituric acid-reactive substances content and blood activities of alkaline phosphatase and γ-glutamyltransferase, but not of aspartate aminotransferase or alanine aminotransferase. Liver catalase activity was lowered by >50% in both TE-treated groups, while superoxide dismutase activity was significantly but slightly affected (−15%) only by the high-dose TE treatment. Glutathione peroxidase and glutathione reductase activities were not significantly altered. TE treatment significantly increased liver thiobarbituric acid-reactive substances content and lowered blood HDL-cholesterol, but did not significantly affect LDL-cholesterol or triglycerides level. In conclusion, high-dose TE treatment significantly disturbed liver antioxidant barrier and prooxidative-antioxidative balance and hence counteracted favorable effects of concurrent moderate-intensity endurance training in adolescent male rats. creator: Ewa Sadowska-Krępa creator: Barbara Kłapcińska creator: Anna Nowara creator: Sławomir Jagsz creator: Izabela Szołtysek-Bołdys creator: Małgorzata Chalimoniuk creator: Józef Langfort creator: Stanisław J. Chrapusta uri: https://doi.org/10.7717/peerj.10228 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sadowska-Krępa et al. title: Comprehensive analysis and identification of key genes and signaling pathways in the occurrence and metastasis of cutaneous melanoma link: https://peerj.com/articles/10265 last-modified: 2020-11-19 description: BackgroundMelanoma is a malignant tumor of melanocytes, and the incidence has increased faster than any other cancer over the past half century. Most primary melanoma can be cured by local excision, but metastatic melanoma has a poor prognosis. Cutaneous melanoma (CM) is prone to metastasis, so the research on the mechanism of melanoma occurrence and metastasis will be beneficial to diagnose early, improve treatment, and prolong life survival. In this study, we compared the gene expression of normal skin (N), primary cutaneous melanoma (PM) and metastatic cutaneous melanoma (MM) in the Gene Expression Omnibus (GEO) database. Then we identified the key genes and molecular pathways that may be involved in the development and metastasis of cutaneous melanoma, thus to discover potential markers or therapeutic targets.MethodsThree gene expression profiles (GSE7553, GSE15605 and GSE46517) were downloaded from the GEO database, which contained 225 tissue samples. R software identified the differentially expressed genes (DEGs) between pairs of N, PM and MM samples in the three sets of data. Subsequently, we analyzed the gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of the DEGs, and constructed a protein-protein interaction (PPI) network. MCODE was used to seek the most important modules in PPI network, and then the GO function and KEGG pathway of them were analyzed. Finally, the hub genes were calculated by the cytoHubba in Cytoscape software. The Cancer Genome Atlas (TCGA) data were analyzed using UALCAN and GEPIA to validate the hub genes and analyze the prognosis of patients.ResultsA total of 134, 317 and 147 DEGs were identified between N, PM and MM in pair. GO functions and KEGG pathways analysis results showed that the upregulated DEGs mainly concentrated in cell division, spindle microtubule, protein kinase activity and the pathway of transcriptional misregulation in cancer. The downregulated DEGs occurred in epidermis development, extracellular exosome, structural molecule activity, metabolic pathways and p53 signaling pathway. The PPI network obtained the most important module, whose GO function and KEGG pathway were enriched in oxidoreductase activity, cell division, cell exosomes, protein binding, structural molecule activity, and metabolic pathways. 14, 18 and 18 DEGs were identified respectively as the hub genes between N, PM and MM, and TCGA data confirmed the expression differences of hub genes. In addition, the overall survival curve of hub genes showed that the differences in these genes may lead to a significant decrease in overall survival of melanoma patients.ConclusionsIn this study, several hub genes were found from normal skin, primary melanoma and metastatic melanoma samples. These hub genes may play an important role in the production, invasion, recurrence or death of CM, and may provide new ideas and potential targets for its diagnosis or treatment. creator: Hanying Dai creator: Lihuang Guo creator: Mingyue Lin creator: Zhenbo Cheng creator: Jiancheng Li creator: Jinxia Tang creator: Xisha Huan creator: Yue Huang creator: Keqian Xu uri: https://doi.org/10.7717/peerj.10265 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dai et al. title: Wing morphological responses to latitude and colonisation in a range expanding butterfly link: https://peerj.com/articles/10352 last-modified: 2020-11-19 description: Populations undergoing rapid climate-driven range expansion experience distinct selection regimes dominated both by increased dispersal at the leading edges and steep environmental gradients. Characterisation of traits associated with such expansions provides insight into the selection pressures and evolutionary constraints that shape demographic and evolutionary responses. Here we investigate patterns in three components of wing morphology (size, shape, colour) often linked to dispersal ability and thermoregulation, along latitudinal gradients of range expansion in the Speckled Wood butterfly (Pararge aegeria) in Britain (two regions of expansion in England and Scotland). We measured 774 males from 54 sites spanning 799 km with a 10-year mean average temperature gradient of 4 °C. A geometric morphometric method was used to investigate variation in size and shape of forewings and hindwings; colour, pattern, and contrast of the wings were examined using a measure of lightness (inverse degree of melanism). Overall, wing size increased with latitude by ∼2% per 100 km, consistent with Bergmann’s rule. Forewings became more rounded and hindwings more elongated with history of colonisation, possibly reflecting selection for increased dispersal ability. Contrary to thermal melanism expectations, wing colour was lighter where larvae developed at cooler temperatures and unrelated to long-term temperature. Changes in wing spot pattern were also detected. High heterogeneity in variance among sites for all of the traits studied may reflect evolutionary time-lags and genetic drift due to colonisation of new habitats. Our study suggests that temperature-sensitive plastic responses for size and colour interact with selection for dispersal traits (wing size and shape). Whilst the plastic and evolutionary responses may in some cases act antagonistically, the rapid expansion of P. aegeria implies an overall reinforcing effect between these two mechanisms. creator: Evelyn D. Taylor-Cox creator: Callum J. Macgregor creator: Amy Corthine creator: Jane K. Hill creator: Jenny A. Hodgson creator: Ilik J. Saccheri uri: https://doi.org/10.7717/peerj.10352 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Taylor-Cox et al. title: Oxytocin weakens self-other distinction in males during empathic responses to sadness: an event-related potentials study link: https://peerj.com/articles/10384 last-modified: 2020-11-19 description: By making use of event-related potential (ERP) technology, a randomized, double-blind, between-subject design study was performed in order to investigate whether OXT can weaken men’s self-other distinction during empathic responses to sad expressions. In the two experimental tasks, 39 male subjects were asked to either evaluate the emotional state shown in a facial stimulus (other-task) or to evaluate their own emotional responses (self-task). The results revealed that OXT reduced the differences in P2 (150–200 ms) amplitudes between sad and neutral expressions in the self-task but enhanced P2 to sad expressions in the other-task, indicating OXT’s role in integrating the self with others instead of separating them. In addition, OXT also reduced the LPC (400–600 ms) amplitudes between sad-neutral expressions in the self-task, implying that OXT’s weakening effects on the self-other distinction could occur at both the early and late cognitive control stages of the empathic response. creator: Tong Yue creator: Ying Xu creator: Liming Xue creator: Xiting Huang uri: https://doi.org/10.7717/peerj.10384 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yue et al. title: High cytoplasmic YAP1 expression predicts a poor prognosis in patients with colorectal cancer link: https://peerj.com/articles/10397 last-modified: 2020-11-19 description: PurposeYes associated protein 1 (YAP1), which is a standout amongst the most essential effectors of the Hippo pathway, assumes a vital part in a few kinds of cancer. However, whether YAP1 is an oncogene in CRC (colorectal cancer) remains controversial, and the association between the subcellular localization of YAP1 and clinical implications in CRC remains unknown.Patients and methodsIn this study, we investigated the subcellular localization of YAP1 in CRC cells by immunohistochemistry and then associate these findings with clinical information in a large CRC cohort with 919 CRC patients.ResultsThe results show that CRC tissues has a significant higher expression of cytoplasmic YAP1 compared to adjacent normal tissues (all P < 0.001). Cytoplasmic YAP1 expression was significantly associated with the number of lymph nodes removed and differentiation grade (all P < 0.001). Furthermore, after correcting confounding variables, for example, TNM stage and differentiation grade, the multivariate Cox analysis confirmed cytoplasmic YAP1-high subgroup had a significant shorter DFS (HR = 3.255; 95% CI [2.290–4.627]; P < 0.001) and DSS (HR = 4.049; 95% CI [2.400–6.830]; P < 0.001) than cytoplasmic YAP1-low subgroup. High cytoplasmic YAP1 expression is associated with a worse survival in stage III CRC patients who received chemotherapy.ConclusionCytoplasmic YAP1 could be could be utilized as a prognosis factor in CRC patients, and may be an indicator of whether certain patients population could benefit from postoperative chemotherapy. creator: Tianqi Dong creator: Yuncang Yuan creator: Xudong Xiang creator: Shuping Sang creator: Hao Shen creator: Lei Wang creator: Chunyan Yang creator: Fangfang Li creator: Hongliang Li creator: Shangyong Zheng uri: https://doi.org/10.7717/peerj.10397 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dong et al. title: Four sesquiterpene glycosides from loquat (Eriobotrya japonica) leaf ameliorates palmitic acid-induced insulin resistance and lipid accumulation in HepG2 Cells via AMPK signaling pathway link: https://peerj.com/articles/10413 last-modified: 2020-11-19 description: Insulin resistance (IR), caused by impaired insulin signal and decreased insulin sensitivity, is generally responsible for the pathophysiology of type 2 diabetes mellitus (T2DM). Sesquiterpene glycosides (SGs), the exclusive natural products from loquat leaf, have been regarded as potential lead compounds owing to their high efficacy in hypoglycemia and hypolipidemia. Here, we evaluated the beneficial effects of four single SGs isolated from loquat leaf, including SG1, SG2, SG3 and one novel compound SG4 against palmitic acid-induced insulin resistance in HepG2 cells. SG1, SG3 and SG4 could significantly enhance glucose uptake of insulin-resistant HepG2 cells at non-cytotoxic concentration. Meanwhile, Oil Red O staining showed the decrease of both total cholesterol and triglyceride content, suggesting the amelioration of lipid accumulation by SGs in insulin-resistant HepG2 cells. Further investigations found that the expression levels of phosphorylated AMPK, ACC, IRS-1, and Akt were significantly up-regulated after SGs treatment, on the contrary, the expression levels of SREBP-1 and FAS were significantly down-regulated. Notably, AMPK inhibitor Compound C (CC) blocked the regulative effects, while AMPK activator AICAR mimicked the effects of SGs in PA-treated insulin-resistant HepG2 cells. In conclusion, SGs (SG4>SG1≈SG3>SG2) improved lipid accumulation in insulin-resistant HepG2 cells through the AMPK signaling pathway. creator: Jiawei Li creator: Xiaoqin Ding creator: Tunyu Jian creator: Han Lü creator: Lei Zhao creator: Jing Li creator: Yan Liu creator: Bingru Ren creator: Jian Chen uri: https://doi.org/10.7717/peerj.10413 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Vascular plant species diversity of Mt. Etna (Sicily): endemicity, insularity and spatial patterns along the altitudinal gradient of the highest active volcano in Europe link: https://peerj.com/articles/9875 last-modified: 2020-11-18 description: BackgroundAltitudinal variation in vascular plant richness and endemism is crucial for the conservation of biodiversity. Territories featured by a high species richness may have a low number of endemic species, but not necessarily in a coherent pattern. The main aim of our research is to perform an in-depth survey on the distribution patterns of vascular plant species richness and endemism along the elevation gradient of Mt. Etna, the highest active volcano in Europe.MethodsWe used all the available data (literature, herbarium and seed collections), plus hundreds of original (G Giusso, P Minissale, S Sciandrello, pers. obs., 2010–2020) on the occurrence of the Etna plant species. Mt. Etna (highest peak at 3,328 mt a.s.l.) was divided into 33 belts 100 m wide and the species richness of each altitudinal range was calculated as the total number of species per interval. In order to identify areas with high plant conservation priority, 29 narrow endemic species (EE) were investigated through hot spot analysis using the “Optimized Hot Spot Analysis” tool available in the ESRI ArcGIS software package.ResultsOverall against a floristic richness of about 1,055 taxa, 92 taxa are endemic, of which 29 taxa are exclusive (EE) of Mt. Etna, 27 endemic of Sicily (ES) and 35 taxa endemic of Italy (EI). Plant species richness slowly grows up to 1,000 m, then decreases with increasing altitude, while endemic richness shows an increasing percentage incidence along the altitudinal gradient (attributed to the increased isolation of higher elevation). The highest endemic richness is recorded from 2,000 up to 2,800 m a.s.l., while the highest narrow endemic richness (EE) ranges from 2,500 up to 2,800 m a.s.l. Life-form patterns clearly change along altitudinal gradient. In regard to the life-form of the endemics, the most represented are the hemicryptophytes, annual plants (therophytes) are prevailing at lower altitudes and show a decreasing trend with increasing elevation, while chamaephytes are featured by an increasing trend up to 3,100 m of altitude. Furthermore, the results of the hotspot analysis emphasize the high plant conservation priority areas localized in oro-mediterranean (1,800–2,400 m s.l.m.) and cryo-mediterranean (2,400–2,800 m) bioclimatic belts, in correspondence of the oldest substrates of the volcano.ConclusionsHigh plant speciation rate caused by increasing isolation with elevation is the most plausible explanation for the largest active volcano in Europe. The high degree of endemic species on Mt. Etna is linked to its geographical, geological and climatic isolation, all important drivers of speciation acting on the population gene flows. The hot spot map obtained represents a useful support for help environmental decision makers to identify priority areas for plant conservation. creator: Saverio Sciandrello creator: Pietro Minissale creator: Gianpietro Giusso del Galdo uri: https://doi.org/10.7717/peerj.9875 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sciandrello et al. title: Evidence of facultative parthenogenesis in three Neotropical pitviper species of the Bothrops atrox group link: https://peerj.com/articles/10097 last-modified: 2020-11-18 description: We examined four suspected cases of facultative parthenogenesis in three species of a neotropical lineage of pitvipers of the Bothrops atrox group. Reproduction without mating was observed in captive females of B. atrox, B. moojeni and B. leucurus housed alone for seven years (the two former species) and nine years (the latter one). In addition to the observation of captivity data, we investigated molecularly this phenomenon using heterologous microsatellites. DNA was extracted from the mothers’ scales or liver, from embryo and newborn fragments, and yolked ova. Four of the microsatellites showed good amplification using Polymerase Chain Reaction and informative band segregation patterns among each mother and respective offspring. Captivity information, litter characteristics (comparison of the number of newborns, embryos and yolked ova) and molecular data altogether agreed with facultative parthenogenesis predictions in at least three out of the four mothers studied: B. atrox (ID#933) was heterozygous for three out of the four markers, and the sons S1 and S2 were homozygous; B. moojeni (BUT86) was heterozygous for two out of four markers, offspring S1, S3, E2, and E4, and O1 to O6 were homozygous; and B. leucurus (MJJS503) was heterozygous for three out of four markers, and son E1 and O1 were homozygous. B. moojeni (BUT44) was homozygous for all loci analyzed in the mother and offspring, which although not informative is also consistent with parthenogenesis. This study represents the first molecular confirmation of different pitviper species undergoing facultative parthenogenesis among Neotropical endemic snakes. creator: Sergio D. Cubides-Cubillos creator: José S.L. Patané creator: Karina Maria Pereira da Silva creator: Selma Maria Almeida-Santos creator: Denise S. Polydoro creator: Guilherme Guidolin Galassi creator: Silvia Regina Travaglia Cardoso creator: Maria José de J. Silva uri: https://doi.org/10.7717/peerj.10097 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cubides-Cubillos et al. title: Seed morphology and sculpture of invasive Impatiens capensis Meerb. from different habitats link: https://peerj.com/articles/10156 last-modified: 2020-11-18 description: Impatiens capensis is an annual plant native to eastern North America that is currently spreading across Europe. In Poland, due to this plant’s rapid spread in the secondary range and high competitiveness in relation to native species, it is considered a locally invasive species. The microstructure of seeds is an important tool for solving various taxonomic problems and also provides data useful for determining the impact of various environmental factors on the phenotypic variability of species. This issue is particularly important in regard to invasive species which occupy a wide range of habitats in the invaded range. There are few reports on seed size and thus far no descriptions of the seed ultrastructure of I. capensis in the analyzed literature. We present new data on the seed morphology of I. capensis growing in different habitats and conditions in the secondary range of the species. The studied populations differed significantly in each of the investigated traits (seed length, width, circumference, area, roundness, and mass). Our findings showed that anthropogenic disturbances in habitats and some soil parameters (presence of carbonates, potassium, loose sand, and moisture) were statistically significant with various seed sizes and morphology in the studied populations of I. capensis. Moreover, our studies showed maximum seed length (5.74 mm) and width (3.21 mm) exceeding those values given in the available literature. For the first time, we also provide a detailed SEM study of the ultrastructure of the seed coat of I. capensis. There are two types of epidermal cells on the seeds: (a) between the ribs (elongated with straight anticlinal walls, slightly concave outer periclinal walls, and micropapillate secondary sculpture on the edges with anticyclic walls), and (b) on the ribs (isodiametric cells with straight anticlinal walls and concave outer periclinal walls). Unlike the variability of size and weight of seeds, the coat ornamentation has turned out to be a steady feature within the studied secondary range of I. capensis. creator: Agnieszka Rewicz creator: Monika Myśliwy creator: Wojciech Adamowski creator: Marek Podlasiński creator: Anna Bomanowska uri: https://doi.org/10.7717/peerj.10156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rewicz et al. title: Changes and sex- and age-related differences in the expression of drug metabolizing enzymes in a KRAS-mutant mouse model of lung cancer link: https://peerj.com/articles/10182 last-modified: 2020-11-18 description: BackgroundThis study aimed to systematically profile the alterations and sex- and age-related differences in the drug metabolizing enzymes (DMEs) in a KRAS-mutant mouse model of lung cancer (KRAS mice).MethodologyIn this study, the LC-MS/MS approach and a probe substrate method were used to detect the alterations in 21 isoforms of DMEs, as well as the enzymatic activities of five isoforms, respectively. Western blotting was applied to study the protein expression of four related receptors.ResultsThe proteins contents of CYP2C29 and CYP3A11, were significantly downregulated in the livers of male KRAS mice at 26 weeks (3.7- and 4.4-fold, respectively, p < 0.05). SULT1A1 and SULT1D1 were upregulated by 1.8- to 7.0- fold at 20 (p = 0.015 and 0.017, respectively) and 26 weeks (p = 0.055 and 0.031, respectively). There were positive correlations between protein expression and enzyme activity for CYP2E1, UGT1A9, SULT1A1 and SULT1D1 (r2 ≥ 0.5, p < 0.001). Western blotting analysis revealed the downregulation of AHR, FXR and PPARα protein expression in male KRAS mice at 26 weeks. For sex-related differences, CYP2E1 was male-predominant and UGT1A2 was female-predominant in the kidney. UGT1A1 and UGT1A5 expression was female-predominant, whereas UGT2B1 exhibited male-predominant expression in liver tissue. For the tissue distribution of DMEs, 21 subtypes of DMEs were all expressed in liver tissue. In the intestine, the expression levels of CYP2C29, CYP27A1, UGT1A2, 1A5, 1A6a, 1A9, 2B1, 2B5 and 2B36 were under the limitation of quantification. The subtypes of CYP7A1, 1B1, 2E1 and UGT1A1, 2A3, 2B34 were detected in kidney tissue.ConclusionsThis study, for the first time, unveils the variations and sex- and age-related differences in DMEs in C57 BL/6 (WT) mice and KRAS mice. creator: Xiaoyan Li creator: Yiyan Lu creator: Xiaojun Ou creator: Sijing Zeng creator: Ying Wang creator: Xiaoxiao Qi creator: Lijun Zhu creator: Zhongqiu Liu uri: https://doi.org/10.7717/peerj.10182 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Adaptive divergence, neutral panmixia, and algal symbiont population structure in the temperate coral Astrangia poculata along the Mid-Atlantic United States link: https://peerj.com/articles/10201 last-modified: 2020-11-18 description: Astrangia poculata is a temperate scleractinian coral that exists in facultative symbiosis with the dinoflagellate alga Breviolum psygmophilum across a range spanning the Gulf of Mexico to Cape Cod, Massachusetts. Our previous work on metabolic thermal performance of Virginia (VA) and Rhode Island (RI) populations of A. poculata revealed physiological signatures of cold (RI) and warm (VA) adaptation of these populations to their respective local thermal environments. Here, we used whole-transcriptome sequencing (mRNA-Seq) to evaluate genetic differences and identify potential loci involved in the adaptive signature of VA and RI populations. Sequencing data from 40 A. poculata individuals, including 10 colonies from each population and symbiotic state (VA-white, VA-brown, RI-white, and RI-brown), yielded a total of 1,808 host-associated and 59 algal symbiont-associated single nucleotide polymorphisms (SNPs) post filtration. Fst outlier analysis identified 66 putative high outlier SNPs in the coral host and 4 in the algal symbiont. Differentiation of VA and RI populations in the coral host was driven by putatively adaptive loci, not neutral divergence (Fst = 0.16, p = 0.001 and Fst = 0.002, p = 0.269 for outlier and neutral SNPs respectively). In contrast, we found evidence of neutral population differentiation in B. psygmophilum (Fst = 0.093, p = 0.001). Several putatively adaptive host loci occur on genes previously associated with the coral stress response. In the symbiont, three of four putatively adaptive loci are associated with photosystem proteins. The opposing pattern of neutral differentiation in B. psygmophilum, but not the A. poculata host, reflects the contrasting dynamics of coral host and algal symbiont population connectivity, dispersal, and gene by environment interactions. creator: Hannah E. Aichelman creator: Daniel J. Barshis uri: https://doi.org/10.7717/peerj.10201 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Aichelman and Barshis title: Machine learning prediction of motor response after deep brain stimulation in Parkinson’s disease—proof of principle in a retrospective cohort link: https://peerj.com/articles/10317 last-modified: 2020-11-18 description: IntroductionDespite careful patient selection for subthalamic nucleus deep brain stimulation (STN DBS), some Parkinson’s disease patients show limited improvement of motor disability. Innovative predictive analysing methods hold potential to develop a tool for clinicians that reliably predicts individual postoperative motor response, by only regarding clinical preoperative variables. The main aim of preoperative prediction would be to improve preoperative patient counselling, expectation management, and postoperative patient satisfaction.MethodsWe developed a machine learning logistic regression prediction model which generates probabilities for experiencing weak motor response one year after surgery. The model analyses preoperative variables and is trained on 89 patients using a five-fold cross-validation. Imaging and neurophysiology data are left out intentionally to ensure usability in the preoperative clinical practice. Weak responders (n = 30) were defined as patients who fail to show clinically relevant improvement on Unified Parkinson Disease Rating Scale II, III or IV.ResultsThe model predicts weak responders with an average area under the curve of the receiver operating characteristic of 0.79 (standard deviation: 0.08), a true positive rate of 0.80 and a false positive rate of 0.24, and a diagnostic accuracy of 78%. The reported influences of individual preoperative variables are useful for clinical interpretation of the model, but cannot been interpreted separately regardless of the other variables in the model.ConclusionThe model’s diagnostic accuracy confirms the utility of machine learning based motor response prediction based on clinical preoperative variables. After reproduction and validation in a larger and prospective cohort, this prediction model holds potential to support clinicians during preoperative patient counseling. creator: Jeroen G.V. Habets creator: Marcus L.F. Janssen creator: Annelien A. Duits creator: Laura C.J. Sijben creator: Anne E.P. Mulders creator: Bianca De Greef creator: Yasin Temel creator: Mark L. Kuijf creator: Pieter L. Kubben creator: Christian Herff uri: https://doi.org/10.7717/peerj.10317 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Habets et al. title: Stem cell imaging through convolutional neural networks: current issues and future directions in artificial intelligence technology link: https://peerj.com/articles/10346 last-modified: 2020-11-18 description: Stem cells are primitive and precursor cells with the potential to reproduce into diverse mature and functional cell types in the body throughout the developmental stages of life. Their remarkable potential has led to numerous medical discoveries and breakthroughs in science. As a result, stem cell–based therapy has emerged as a new subspecialty in medicine. One promising stem cell being investigated is the induced pluripotent stem cell (iPSC), which is obtained by genetically reprogramming mature cells to convert them into embryonic-like stem cells. These iPSCs are used to study the onset of disease, drug development, and medical therapies. However, functional studies on iPSCs involve the analysis of iPSC-derived colonies through manual identification, which is time-consuming, error-prone, and training-dependent. Thus, an automated instrument for the analysis of iPSC colonies is needed. Recently, artificial intelligence (AI) has emerged as a novel technology to tackle this challenge. In particular, deep learning, a subfield of AI, offers an automated platform for analyzing iPSC colonies and other colony-forming stem cells. Deep learning rectifies data features using a convolutional neural network (CNN), a type of multi-layered neural network that can play an innovative role in image recognition. CNNs are able to distinguish cells with high accuracy based on morphologic and textural changes. Therefore, CNNs have the potential to create a future field of deep learning tasks aimed at solving various challenges in stem cell studies. This review discusses the progress and future of CNNs in stem cell imaging for therapy and research. creator: Ramanaesh Rao Ramakrishna creator: Zariyantey Abd Hamid creator: Wan Mimi Diyana Wan Zaki creator: Aqilah Baseri Huddin creator: Ramya Mathialagan uri: https://doi.org/10.7717/peerj.10346 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ramakrishna et al. title: Prevalence of eimeriosis in the one-humped camels (Camelus dromedarius) from Riyadh and Al-Qassim, Saudi Arabia link: https://peerj.com/articles/10347 last-modified: 2020-11-18 description: BackgroundThe one-humped camels are economically important for several countries in Africa, Asia, and the Arabian Peninsula. Coccidiosis causes significant economic impact. Studies on coccidian parasite species causing such infections are limited. The present study aimed to carry out a survey of Eimeria spp. in camels from Riyadh and Al-Qassim, Saudi Arabia.MethodsA total of 209 fecal samples from Camelus (C.) dromedarius slaughtered in West Abattoir in Riyadh and Onaizah Modern abattoir in Al-Qassim were collected. Samples were examined by flotation methods and oocyst sporulation.ResultsOf the 209 examined fecal samples, 75 were positive for Eimeria spp..The prevalence of oocysts in Riyadh and Al-Qassim were 33.89% (40/118) and 38.46% (35/92), respectively. The prevalence in young male camels was 41.02% (32/78) and 39.62% (21/53), respectively and in adult males was 19.35% (6/31) and 36% (9/25), respectively. Adult females displayed a prevalence of 22.22% (2/9) and 38.46% (5/13) in Riyadh and Al-Qassim, respectively. Three Eimeria spp. were identified; E. cameli, E. rajasthani, and E. pellerdyi. The presence of E. pellerdyi is considered the first record in Saudi Arabia. creator: Dina M. Metwally creator: Tahani T. Al-Otaibi creator: Shurug A. Albasyouni creator: Manal F. El-Khadragy creator: Reem A. Alajmi uri: https://doi.org/10.7717/peerj.10347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Metwally et al. title: Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas link: https://peerj.com/articles/10348 last-modified: 2020-11-18 description: There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time. creator: Austin S. Chipps creator: Amanda M. Hale creator: Sara P. Weaver creator: Dean A. Williams uri: https://doi.org/10.7717/peerj.10348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chipps et al. title: Kinematic effects of the circle with and without rider in walking horses link: https://peerj.com/articles/10354 last-modified: 2020-11-18 description: BackgroundBiomechanical studies of walk, especially walk on the circle, are scarce, while circles or curved tracks are frequently used during equestrian activities. To study horse–rider–circle interactions on the circle, the first steps would be to investigate how the unridden, freely walking horse is influenced by circular movement, and then add a rider. The aim was to study horse vertical trunk movements, and sagittal cannon angles (protraction–retraction) during walk in straight-line and on the circle without rider, and on the circle with a rider using minimal influence.MethodsTen horses were ridden by five riders, summing to 14 trials. Each trial included straight walk unridden (on concrete), and walk on 10 m diameter circles (left and right on soft surface) first lunged (unridden) and then ridden with minimal rider influence. Inertial measurement units (100 Hz) were positioned on the withers, third sacral vertebra (S3) and laterally on metacarpal and metatarsal bones (using self-adhesive bandage). Selected data were split in steps (withers and S3 vertical translations) or strides (cannon protraction–retraction) at maximum hind limb protraction, and range of motion (ROM), minima and maxima, and their timing, were extracted. Data were analyzed using mixed models with inner/outer/straight nested within unridden/ridden as fixed effect, and controlling for stride duration. Differences between: inner vs outer steps/limbs; the same step/limb unridden vs ridden; and the same step/limb straight vs inner/outer unridden; were examined for statistical significance at p < 0.05.ResultsInner limbs had smaller cannon ROM than outer limbs, for example, forelimbs when ridden (inner vs outer 62° vs 63°) and hind limbs when unridden (53° vs 56°). Forelimb cannon ROM was the largest for straight (65°). Hind limb ROM for straight walk (55°) was in-between inner (52–53°) and outer hind limbs (56–57°). Vertical ROM of S3 was larger during the inner (unridden/ridden 0.050/0.052 m) vs the outer step (unridden/ridden 0.049/0.051 m). Inner (0.050 m) and outer steps (0.049 m) unridden had smaller S3 ROM compared to straight steps (unridden, 0.054 m). Compared to when unridden, withers ROM was smaller when ridden: inner hind steps unridden/ridden 0.020 vs 0.015 m and outer hind steps 0.020 vs 0.013 m. When ridden, withers ROM was larger during the inner hind step vs the outer.ConclusionThe outer hind limb had greater cannon pro-retraction ROM, compared to the inner limb. Larger croup ROM during the inner step appears to be coupled to increased retraction of the outer hind limb. Knowledge of magnitudes and timing of the horse’s movements on the circle in unridden and ridden walk may stimulate riders to educate eye and feel in analyzing the execution of circles, and stimulate further studies of the walk, for example, on interactions with rider influence, natural horse asymmetries, or lameness. creator: Agneta Egenvall creator: Hanna Engström creator: Anna Byström uri: https://doi.org/10.7717/peerj.10354 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Egenvall et al. title: Solid state fermentation of Moringa oleifera leaf meal by mixed strains for the protein enrichment and the improvement of nutritional value link: https://peerj.com/articles/10358 last-modified: 2020-11-18 description: Moringa oleifera Lam. (MO) is a fast-growing multi-purpose deciduous tree with high biomass and nutritional value. However, the presence of antinutritional factors, poor palatability, and indigestibility of Moringa oleifera leaf meal (MOLM) restrict its application to animal feed. This study aimed to obtain high-quality protein feeds via solid-state fermentation (SSF) of MOLM. The process conditions for increasing the true protein (TP) content using Aspergillus niger, Candida utilis and Bacillus subtilis co-cultures were optimized, and the chemical composition of MOLM was compared before and after fermentation. The results of this study showed that the highest TP content could be obtained through mixed-strain culture of A. niger, C. utilis and B. subtilis at a ratio of 1:1:2. The MOLM was inoculated with A. niger, followed by C. utilis and B. subtilis 24 h later. The optimized co-culture parameters were as follows: total inoculation size, 24%; temperature, 32 °C; fermentation time, 6.5 days; and initial water content, 60%. The maximum TP yield was 28.37%. Notably, in the fermented MOLM (FMOLM), the content of nutrients such as crude protein (CP), small peptides, and total amino acids (AAs) were significantly increased relative to unfermented MOLM, whereas the contents of crude fiber (CF), tannin, and phytic acid were significantly decreased. MOLM analysis using scanning electron microscopy (SEM) revealed that SSF disrupted the surface structure of MOLM, and sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) indicated that macromolecular proteins were degraded. The in vitro protein digestibility (IVPD) of FMOLM was also improved significantly. Our findings suggest that multi-strain fermentation with A. niger, C. utilis and B. subtilis improves the nutritional quality of MOLM, rendering it a viable functional feedstuff for use in livestock industries in the future. creator: Honghui Shi creator: Bin Su creator: Xiaoyang Chen creator: Ruiqi Pian uri: https://doi.org/10.7717/peerj.10358 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shi et al. title: Processing moving visual scenes during upright stance in elderly patients with mild cognitive impairment link: https://peerj.com/articles/10363 last-modified: 2020-11-18 description: BackgroundThe ability to maintain balance in an upright stance gradually worsens with age and is even more difficult for patients with cognitive disorders. Cognitive impairment plays a probable role in the worsening of stability. The purpose of this study was to expose subjects with mild cognitive impairment (MCI) and healthy, age-matched controls to moving visual scenes in order to examine their postural adaptation abilities.MethodsWe observed postural responses to moving visual stimulation while subjects stood on a force platform. The visual disturbance was created by interposing a moving picture in four directions (forward, backward, right, and left). The pre-stimulus (a static scene for 10 s), stimulus (a dynamic visual scene for 20 seconds) and post-stimulus (a static scene for 20 seconds) periods were evaluated. We separately analyzed the total path (TP) of the center of pressure (COP) and the root mean square (RMS) of the COP displacement in all four directions.ResultsWe found differences in the TP of the COP during the post-stimulus period for all stimulus directions except in motion towards the subject (left p = 0.006, right p = 0.004, and away from the subject p = 0.009). Significant RMS differences between groups were also observed during the post-stimulus period in all directions except when directed towards the subject (left p = 0.002, right p = 0.007, and away from the subject p = 0.014).ConclusionExposing subjects to a moving visual scene induced greater destabilization in MCI subjects compared to healthy elderly controls. Surprisingly, the moving visual scene also induced significant aftereffects in the MCI group. Our findings indicate that the MCI group had diminished adaptation to the dynamic visual scene and recovery. These results suggest that even mild cognitive deficits can impair sensory information integration and alter the sensory re-weighing process. creator: Martin Kucharik creator: Zuzana Kosutzka creator: Jozef Pucik creator: Michal Hajduk creator: Marian Saling uri: https://doi.org/10.7717/peerj.10363 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kucharik et al. title: Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology link: https://peerj.com/articles/10364 last-modified: 2020-11-18 description: In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini. creator: Natalia I. Abramson creator: Fedor N. Golenishchev creator: Semen Yu. Bodrov creator: Olga V. Bondareva creator: Evgeny A. Genelt-Yanovskiy creator: Tatyana V. Petrova uri: https://doi.org/10.7717/peerj.10364 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Abramson et al. title: Temporal trend of cardiorespiratory endurance in urban Catalan high school students over a 20 year period link: https://peerj.com/articles/10365 last-modified: 2020-11-18 description: BackgroundPhysical fitness is considered an important indicator of health in adolescents. However, in recent years several studies in the scientific literature have shown a considerable lower trend and an alarming worsening of the current adolescents’ physical condition when comparing with previous decades, especially in urban populations. The aim of the current study was to analyse the temporal trend in cardiorespiratory endurance (CRE) in urban Catalan adolescents over a 20-year period (1999–2019).MethodsA cross-sectional analysis study considering the 20-m Shuttle Run test (SRT) results obtained in the last 20 years was carried out. 1,701 adolescents between 15 and 16 years old (914 boys and 787 girls) were divided into four groups, corresponding to consecutive periods of five years (Group 1: 1999–2004; Group 2: 2005–2009; Group 3: 2010–2014 and Group 4: 2015–2019). ANOVA was used to test the period effect on CRE and post hoc Bonferroni analysis was performed to test pairwise differences between groups (p < 0.05).ResultsResults showed a significantly lower performance in CRE in both sexes. The percentual negative difference was 0.67%, 9.6% and 7% for boys and 5.06%, 14.97% and 9.41% for girls, when comparing the performance in 20-m Shuttle Run test for the first period, respectively.ConclusionsResults suggest that the physical fitness of Catalan urban adolescents is lower in both sexes when comparing the different analysed periods of time. Therefore, CRE adolescents should be improved in order to help to protect against cardiovascular disease and other health risks in adulthood. creator: Jordi Arboix-Alió creator: Bernat Buscà creator: Enric M. Sebastiani creator: Joan Aguilera-Castells creator: Sergio Marcaida creator: Luis Garcia Eroles creator: María José Sánchez López uri: https://doi.org/10.7717/peerj.10365 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Arboix-Alió et al. title: Indomethacin augments lipopolysaccharide-induced expression of inflammatory molecules in the mouse brain link: https://peerj.com/articles/10391 last-modified: 2020-11-18 description: Indomethacin and other non-steroidal anti-inflammatory drugs (NSAIDs) are used to relieve pain and fever including during infections. However, some studies suggest that NSAIDs protect against neuroinflammation, while some find no effects or worsening of neuroinflammation. We evaluated the effect of indomethacin alone on in combination with minocycline, a drug that inhibits neuroinflammation, on the expression of transcripts of neuroinflammatory molecules-induced by lipopolysaccharide (LPS) in the brain of mice. Inoculation of male BALB/c mice with LPS induced the expression of the microglia marker ionized calcium binding adaptor molecule protein, mRNA expression of the genes for cytokines interleukin-1beta (Il1b) and tumor necrosis factor-alpha (Tnf) and inducible nitric oxide synthase gene (Nos2), but not Il10, in the brain. Treatment with indomethacin had no significant effect on the cytokines or Nos2 mRNA expression in naïve animals. However, pretreatment with indomethacin increased LPS-induced Nos2 mRNA and inducible nitric oxide (iNOS) protein expression, but had no significant effect on LPS-induced mRNA expression of the cytokines. Minocycline reduced LPS-induced Il1b and Tnf, but not Nos2, mRNA expression. Treatment with indomethacin plus minocycline had no effect on LPS-induced Il1b, Tnf and Nos2 mRNA expression. In conclusion these results show that indomethacin significantly augments LPS-induced Nos2 mRNA and iNOS protein expression in the brain. In the presence of indomethacin, minocycline could not inhibit LPS-induced pro-inflammatory cytokine expression. Thus, indomethacin could exacerbate neuroinflammation by increasing the expression of iNOS and also block the anti-inflammatory effects of minocycline. creator: Mona Yasin Mohamed creator: Willias Masocha uri: https://doi.org/10.7717/peerj.10391 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Mohamed and Masocha title: Behavioural patterns of free roaming wild boar in a spatiotemporal context link: https://peerj.com/articles/10409 last-modified: 2020-11-18 description: Although the almost worldwide distributed wild boar Sus scrofa is a well-studied species, little is known about the behaviour of autochthonous, free living wild boar in a spatiotemporal context which can help to better understand wild boar in conflict terms with humans and to find solutions. The use of camera traps is a favourable and non-invasive method to study them. To observe natural behaviour, 60 camera traps were placed for three months in a state forest of 17.8 km2 in the region of the Luneburg Heath in northern Germany. In this area wild boar, roe deer, red deer, wolves and humans are common. The cameras recorded 20 s length video clips when animals passed the detection zone and could be triggered again immediately afterwards. In total 38 distinct behavioural elements were observed, which were assigned to one of seven behavioural categories. The occurrence of the behavioural categories per day was evaluated to compare their frequencies and see which are more essential than others. Generalised Additive Models were used to analyse the occurrence of each behaviour in relation to habitat and activity time. The results show that essential behavioural categories like foraging behaviour, locomotion and vigilance behaviour occurred more frequently than behaviour that “just” served for the well-being of wild boar. These three behavioural categories could be observed together mostly in the night in broad-leaved forests with a herb layer of 50–100%, comfort behaviour occurred mostly at the ponds in coniferous forest. It is also observable that the behavioural categories foraging and comfort behaviour alternated several times during the night which offers the hypothesis that foraging is mostly followed by comfort behaviour. These findings pave the way towards implementing effective control strategies in the wild and animal welfare in captivity. creator: Dana Erdtmann creator: Oliver Keuling uri: https://doi.org/10.7717/peerj.10409 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Erdtmann and Keuling title: Tropical peatlands and their conservation are important in the context of COVID-19 and potential future (zoonotic) disease pandemics link: https://peerj.com/articles/10283 last-modified: 2020-11-17 description: The COVID-19 pandemic has caused global disruption, with the emergence of this and other pandemics having been linked to habitat encroachment and/or wildlife exploitation. High impacts of COVID-19 are apparent in some countries with large tropical peatland areas, some of which are relatively poorly resourced to tackle disease pandemics. Despite this, no previous investigation has considered tropical peatlands in the context of emerging infectious diseases (EIDs). Here, we review: (i) the potential for future EIDs arising from tropical peatlands; (ii) potential threats to tropical peatland conservation and local communities from COVID-19; and (iii) potential steps to help mitigate these risks. We find that high biodiversity in tropical peat-swamp forests, including presence of many potential vertebrate and invertebrate vectors, combined, in places, with high levels of habitat disruption and wildlife harvesting represent suitable conditions for potential zoonotic EID (re-)emergence. Although impossible to predict precisely, we identify numerous potential threats to tropical peatland conservation and local communities from the COVID-19 pandemic. This includes impacts on public health, with the potential for haze pollution from peatland fires to increase COVID-19 susceptibility a noted concern; and on local economies, livelihoods and food security, where impacts will likely be greater in remote communities with limited/no medical facilities that depend heavily on external trade. Research, training, education, conservation and restoration activities are also being affected, particularly those involving physical groupings and international travel, some of which may result in increased habitat encroachment, wildlife harvesting or fire, and may therefore precipitate longer-term negative impacts, including those relating to disease pandemics. We conclude that sustainable management of tropical peatlands and their wildlife is important for mitigating impacts of the COVID-19 pandemic, and reducing the potential for future zoonotic EID emergence and severity, thus strengthening arguments for their conservation and restoration. To support this, we list seven specific recommendations relating to sustainable management of tropical peatlands in the context of COVID-19/disease pandemics, plus mitigating the current impacts of COVID-19 and reducing potential future zoonotic EID risk in these localities. Our discussion and many of the issues raised should also be relevant for non-tropical peatland areas and in relation to other (pandemic-related) sudden socio-economic shocks that may occur in future. creator: Mark E. Harrison creator: Lahiru S. Wijedasa creator: Lydia E.S. Cole creator: Susan M. Cheyne creator: Shofwan Al Banna Choiruzzad creator: Liana Chua creator: Greta C. Dargie creator: Corneille E.N. Ewango creator: Euridice N. Honorio Coronado creator: Suspense A. Ifo creator: Muhammad Ali Imron creator: Dianna Kopansky creator: Trilianty Lestarisa creator: Patrick J. O’Reilly creator: Julie Van Offelen creator: Johannes Refisch creator: Katherine Roucoux creator: Jito Sugardjito creator: Sara A. Thornton creator: Caroline Upton creator: Susan Page uri: https://doi.org/10.7717/peerj.10283 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Harrison et al. title: Use and effectiveness of dapagliflozin in patients with type 2 diabetes mellitus: a multicenter retrospective study in Taiwan link: https://peerj.com/articles/9998 last-modified: 2020-11-17 description: Aims/IntroductionTo investigate the clinical outcomes of patients with type 2 diabetes mellitus (T2DM) who initiated dapagliflozin in real-world practice in Taiwan.Materials and MethodsIn this multicenter retrospective study, adult patients with T2DM who initiated dapagliflozin after May 1st 2016 either as add-on or switch therapy were included. Changes in clinical and laboratory parameters were evaluated at 3 and 6 months. Baseline factors associated with dapagliflozin response in glycated hemoglobin (HbA1c) were analyzed by univariate and multivariate logistic regression.ResultsA total of 1,960 patients were eligible. At 6 months, significant changes were observed: HbA1c by −0.73% (95% confidence interval [CI] −0.80, −0.67), body weight was -1.61 kg (95% CI −1.79, −1.42), and systolic/diastolic blood pressure by −3.6/−1.4 mmHg. Add-on dapagliflozin showed significantly greater HbA1c reduction (−0.82%) than switched therapy (−0.66%) (p = 0.002). The proportion of patients achieving HbA1c <7% target increased from 6% at baseline to 19% at Month 6. Almost 80% of patients experienced at least 1% reduction in HbA1c, and 65% of patients showed both weight loss and reduction in HbA1c. Around 37% of patients had at least 3% weight loss. Multivariate logistic regression analysis indicated patients with higher baseline HbA1c and those who initiated dapagliflozin as add-on therapy were associated with a greater reduction in HbA1c.ConclusionsIn this real-world study with the highest patient number of Chinese population to date, the use of dapagliflozin was associated with significant improvement in glycemic control, body weight, and blood pressure in patients with T2DM. Initiating dapagliflozin as add-on therapy showed better glycemic control than as switch therapy. creator: Jung-Fu Chen creator: Yun-Shing Peng creator: Chung-Sen Chen creator: Chin-Hsiao Tseng creator: Pei-Chi Chen creator: Ting-I Lee creator: Yung-Chuan Lu creator: Yi-Sun Yang creator: Ching-Ling Lin creator: Yi-Jen Hung creator: Szu-Ta Chen creator: Chieh-Hsiang Lu creator: Chwen-Yi Yang creator: Ching-Chu Chen creator: Chun-Chuan Lee creator: Pi-Jung Hsiao creator: Ju-Ying Jiang creator: Shih-Te Tu uri: https://doi.org/10.7717/peerj.9998 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Anti-Streptococcus mutans and anti-biofilm activities of dextranase and its encapsulation in alginate beads for application in toothpaste link: https://peerj.com/articles/10165 last-modified: 2020-11-17 description: BackgroundThe accumulation of plaque causes oral diseases. Dental plaque is formed on teeth surfaces by oral bacterial pathogens, particularly Streptococcus mutans, in the oral cavity. Dextranase is one of the enzymes involved in antiplaque accumulation as it can prevent dental caries by the degradation of dextran, which is a component of plaque biofilm. This led to the idea of creating toothpaste containing dextranase for preventing oral diseases. However, the dextranase enzyme must be stable in the product; therefore, encapsulation is an attractive way to increase the stability of this enzyme.MethodsThe activity of food-grade fungal dextranase was measured on the basis of increasing ratio of reducing sugar concentration, determined by the reaction with 3, 5-dinitrosalicylic acid reagent. The efficiency of the dextranase enzyme was investigated based on its minimal inhibitory concentration (MIC) against biofilm formation by S. mutans ATCC 25175. Box-Behnken design (BBD) was used to study the three factors affecting encapsulation: pH, calcium chloride concentration, and sodium alginate concentration. Encapsulation efficiency (% EE) and the activity of dextranase enzyme trapped in alginate beads were determined. Then, the encapsulated dextranase in alginate beads was added to toothpaste base, and the stability of the enzyme was examined. Finally, sensory test and safety evaluation of toothpaste containing encapsulated dextranase were done.ResultsThe highest activity of the dextranase enzyme was 4401.71 unit/g at a pH of 6 and 37 °C. The dextranase at its MIC (4.5 unit/g) showed strong inhibition against the growth of S. mutans. This enzyme at 1/2 MIC also showed a remarkable decrease in biofilm formation by S. mutans. The most effective condition of dextranase encapsulation was at a pH of 7, 20% w/v calcium chloride and 0.85% w/v sodium alginate. Toothpaste containing encapsulated dextranase alginate beads produced under suitable condition was stable after 3 months of storage, while the sensory test of the product was accepted at level 3 (like slightly), and it was safe.ConclusionThis research achieved an alternative health product for oral care by formulating toothpaste with dextranase encapsulated in effective alginate beads to act against cariogenic bacteria, like S. mutants, by preventing dental plaque. creator: Nucharee Juntarachot creator: Sasithorn Sirilun creator: Duangporn Kantachote creator: Phakkharawat Sittiprapaporn creator: Piyachat Tongpong creator: Sartjin Peerajan creator: Chaiyavat Chaiyasut uri: https://doi.org/10.7717/peerj.10165 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Juntarachot et al. title: A valid and reliable measure of nothing: disentangling the “Gavagai effect” in survey data link: https://peerj.com/articles/10209 last-modified: 2020-11-17 description: BackgroundIn three recent studies, Maul demonstrated that sets of nonsense items can acquire excellent psychometric properties. Our aim was to find out why responses to nonsense items acquire a well-defined structure and high internal consistency.MethodWe designed two studies. In the first study, 610 participants responded to eight items where the central term (intelligence) was replaced by the term “gavagai”. In the second study, 548 participants responded to seven items whose content was totally invented. We asked the participants if they gave any meaning to “gavagai”, and conducted analyses aimed at uncovering the most suitable structure for modeling responses to meaningless items.ResultsIn the first study, 81.3% of the sample gave “gavagai” meaning, while 18.7% showed they had given it no interpretation. The factorial structures of the two groups were very different from each other. In the second study, the factorial model fitted almost perfectly. However, further analysis revealed that the structure of the data was not continuous but categorical with three unordered classes very similar to midpoint, disacquiescent, and random response styles.DiscussionApparently good psychometric properties on meaningless scales may be due to (a) respondents actually giving an interpretation to the item and responding according to that interpretation, or (b) a false positive because the statistical fit of the factorial model is not sensitive to cases where the actual structure of the data does not come from a common factor. In conclusion, the problem is not in factor analysis, but in the ability of the researcher to elaborate substantive hypotheses about the structure of the data, to employ analytical procedures congruent with those hypotheses, and to understand that a good fit in factor analysis does not have a univocal interpretation and is not sufficient evidence of either validity nor good psychometric properties. creator: Victor B. Arias creator: Fernando P. Ponce creator: Martin Bruggeman creator: Noelia Flores creator: Cristina Jenaro uri: https://doi.org/10.7717/peerj.10209 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Arias et al. title: The neuropsychological profile of professional action video game players link: https://peerj.com/articles/10211 last-modified: 2020-11-17 description: In the past 20 years, there has been growing research interest in the association between video games and cognition. Although many studies have found that video game players are better than non-players in multiple cognitive domains, other studies failed to replicate these results. Until now, the vast majority of studies defined video game players based on the number of hours an individual spent playing video games, with relatively few studies focusing on video game expertise using performance criteria. In the current study, we sought to examine whether individuals who play video games at a professional level in the esports industry differ from amateur video game players in their cognitive and learning abilities. We assessed 14 video game players who play in a competitive league (Professional) and 16 casual video game players (Amateur) on set of standard neuropsychological tests evaluating processing speed, attention, memory, executive functions, and manual dexterity. We also examined participants’ ability to improve performance on a dynamic visual attention task that required tracking multiple objects in three-dimensions (3D-MOT) over five sessions. Professional players showed the largest performance advantage relative to Amateur players in a test of visual spatial memory (Spatial Span), with more modest benefits in a test of selective and sustained attention (d2 Test of Attention), and test of auditory working memory (Digit Span). Professional players also showed better speed thresholds in the 3D-MOT task overall, but the rate of improvement with training did not differ in the two groups. Future longitudinal studies of elite video game experts are required to determine whether the observed performance benefits of professional gamers may be due to their greater engagement in video game play, or due to pre-existing differences that promote achievement of high performance in action video games. creator: Julie Justine Benoit creator: Eugenie Roudaia creator: Taylor Johnson creator: Trevor Love creator: Jocelyn Faubert uri: https://doi.org/10.7717/peerj.10211 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Benoit et al. title: Short stature and SHOX (Short stature homeobox) variants—efficacy of screening using various strategies link: https://peerj.com/articles/10236 last-modified: 2020-11-17 description: BackgroundSHOX mutations have previously been described as causes of Léri-Weill dyschondrosteosis (LWD), Langer mesomelic dysplasia (LMD), and idiopathic short stature. The loss of X chromosome—Turner syndrome or mosaic 45,X/46,XX or 46,XY—also leads to the heterozygous loss of SHOX in patients with short stature only or with features similar to LWD. The aim of this study was to assess the efficacy of the targeted screening for SHOX variants, which involved different methods in the laboratory analysis of short stature. We determined the significance and positive predictive value of short stature for the detection of SHOX variants.MethodsTargeted screening for variants in SHOX involving MLPA, sequencing, karyotyping and FISH was performed in the short stature cohort (N = 174) and control cohort (N = 91). The significance of short stature and particular characteristics for the detection of SHOX variants was determined by Fisher’s exact test, and the probability of SHOX mutation occurrence was calculated using a forward/stepwise logistic regression model.ResultsIn total, 27 and 15 variants influencing SHOX were detected in the short stature and control cohorts, respectively (p > 0.01). Sex chromosome aberrations and pathogenic CNV resulting in diagnosis were detected in eight (4.6%) and five (2.9%) patients of the short stature group and three (3.3%) and one (1.1%) individuals of the control group. VUS variants were discovered in 14 (8.0%) and 11 (12.1%) individuals of the short stature and control groups, respectively. MLPA demonstrated the detection rate of 13.22%, and it can be used as a frontline method for detection of aberrations involving SHOX. However, only mosaicism of monosomy X with a higher frequency of monosomic cells could be reliably discovered by this method. Karyotyping and FISH can compensate for this limitation; their detection rates in short stature group were 3.55% and 13.46% (N = 52), respectively. FISH proved to be more effective than karyotyping in the study as it could reveal cryptic mosaics in some cases where karyotyping initially failed to detect such a clone. We suggest adding FISH on different tissue than peripheral blood to verify sex-chromosome constitution, especially in cases with karyotypes: 45,X; mosaic 45,X/46,XX or 46,XY; 46,Xidic(Y) detected from blood; in children, where mosaic 45,X was detected prenatally but was not confirmed from peripheral blood. The correlation of short stature with the occurrence of SHOX mutations was insignificant and short stature demonstrates a low positive predictive value-15.5% as unique indicator for SHOX mutations. The typical skeletal signs of LWD, including Madelung deformity and disproportionate growth, positively correlate with the findings of pathogenic SHOX variants (p < 0.01) by Fisher’s exact test but not with the findings of VUS variants in SHOX which are more prevalent in the individuals with idiopathic short stature or in the individuals with normal height. creator: Pavlina Capkova creator: Zuzana Capkova creator: Peter Rohon creator: Katerina Adamová creator: Jirina Zapletalova uri: https://doi.org/10.7717/peerj.10236 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Capkova et al. title: Assessing anthropogenic risk to sea otters (Enhydra lutris nereis) for reintroduction into San Francisco Bay link: https://peerj.com/articles/10241 last-modified: 2020-11-17 description: Southern sea otters have been actively managed for their conservation and recovery since listing on the federal Endangered Species Act in 1977. Still, they remain constrained to a geographically small area on the central coast of California relative to their former coast-wide range, with population numbers far below those of the estimated optimal sustainable population size. Species managers have discussed reintroducing southern sea otters into parts of their historic range to facilitate sustained population growth and geographic range expansion. San Francisco Bay (SFB), historically home to several thousand sea otters, is one location identified as a candidate release site for these reintroductions. The return of sea otters to SFB could bring benefits to local ecosystem restoration and tourism, in addition to spurring sea otter population growth to meet recovery goals. However, this is a highly urbanized estuary, so sea otters could also be exposed to serious anthropogenic threats that would challenge a successful reintroduction. In light of these potential detriments we performed a spatially-explicit risk assessment to analyze the suitability of SFB for southern sea otter reintroduction. We looked at threats to sea otters specific to SFB, including: the impacts of vessel traffic from commercial shipping, high-speed ferries, and recreational vessels; environmental contaminants of methylmercury and polychlorinated biphenyls; major oil spills; and commercial fishing. Factors that influenced the relative threat imposed by each stressor included the spatio-temporal extent and intensity of the stressor and its mitigation potential. Our analysis revealed the complex spatial and temporal variation in risk distribution across the SFB. The type and magnitude of anthropogenic risk was not uniformly distributed across the study area. For example, the central SFB housed the greatest cumulative risk, where a high degree of vessel traffic and other stressors occurred in conjunction. The individual stressors that contributed to this risk score varied across different parts of the study area as well. Whereas vessel traffic, particularly of fast ferries, was a high scoring risk factor in in the north and central bay, in the south bay it was environmental contaminants that caused greater risk potential. To help identify areas within the study area that managers might want to target for release efforts, the spatially-explicit risk map revealed pockets of SFB that could provide both suitable habitat and relatively low overall risk. However in some cases these were adjacent or in close proximity to identified high-risk portions of habitat in SFB. This predictive suitability and risk assessment can be used by managers to consider the spatial distribution of potential threats, and risk abatement that may be necessary for sea otters to re-occupy their historic home range in SFB. creator: Jane Rudebusch creator: Brent B. Hughes creator: Katharyn E. Boyer creator: Ellen Hines uri: https://doi.org/10.7717/peerj.10241 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rudebusch et al. title: Predicting disease occurrence of cabbage Verticillium wilt in monoculture using species distribution modeling link: https://peerj.com/articles/10290 last-modified: 2020-11-17 description: BackgroundAlthough integrated pest management (IPM) is essential for conservation agriculture, this method can be inadequate for severely infected fields. The ability to predict the potential occurrence of severe infestation of soil-borne disease would enable farmers to adopt suitable methods for high-risk areas, such as soil disinfestation, and apply other options for lower risk areas. Recently, researchers have used species distribution modeling (SDM) to predict the occurrence of target plant and animal species based on various environmental variables. In this study, we applied this technique to predict and map the occurrence probability of a soil-borne disease, Verticillium wilt, using cabbage as a case study.MethodsA disease survey assessing the distribution of Verticillium wilt in cabbage fields in Tsumagoi village (central Honshu, Japan) was conducted two or three times annually from 1997 to 2013. Road density, elevation and topographic wetness index (TWI) were selected as explanatory variables for disease occurrence potential. A model of occurrence probability of Verticillium wilt was constructed using the MaxEnt software for SDM analysis. As the disease survey was mainly conducted in an agricultural area, the area was weighted as “Bias Grid” and area except for the agricultural area was set as background.ResultsGrids with disease occurrence showed a high degree of coincidence with those with a high probability occurrence. The highest contribution to the prediction of disease occurrence was the variable road density at 97.1%, followed by TWI at 2.3%, and elevation at 0.5%. The highest permutation importance was road density at 93.0%, followed by TWI at 7.0%, while the variable elevation at 0.0%. This method of predicting disease probability occurrence can help with disease monitoring in areas with high probability occurrence and inform farmers about the selection of control measures. creator: Kentaro Ikeda creator: Takeshi Osawa uri: https://doi.org/10.7717/peerj.10290 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ikeda and Osawa title: Analysis of genes and underlying mechanisms involved in foam cells formation and atherosclerosis development link: https://peerj.com/articles/10336 last-modified: 2020-11-17 description: BackgroundFoam cells (FCs) play crucial roles in the process of all stages of atherosclerosis. Smooth muscle cells (SMCs) and macrophages are the major sources of FCs. This study aimed to identify the common molecular mechanism in these two types of FCs.MethodsGSE28829, GSE43292, GSE68021, and GSE54666 were included to identify the differentially expressed genes (DEGs) associated with FCs derived from SMCs and macrophages. Gene Ontology biological process (GO-BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed by using the DAVID database. The co-regulated genes associated with the two origins of FCs were validated (GSE9874), and their expression in vulnerable atherosclerosis plaques (GSE120521 and GSE41571) was assessed.ResultsA total of 432 genes associated with FCs derived from SMCs (SMC-FCs) and 81 genes associated with FCs derived from macrophages (M-FCs) were identified, and they were mainly involved in lipid metabolism, inflammation, cell cycle/apoptosis. Furthermore, three co-regulated genes associated with FCs were identified: GLRX, RNF13, and ABCA1. These three common genes showed an increased tendency in unstable or ruptured plaques, although in some cases, no statistically significant difference was found.ConclusionsDEGs related to FCs derived from SMCs and macrophages have contributed to the understanding of the molecular mechanism underlying the formation of FCs and atherosclerosis. GLRX, RNF13, and ABCA1 might be potential targets for atherosclerosis treatment. creator: Kai Zhang creator: Xianyu Qin creator: Xianwu Zhou creator: Jianrong Zhou creator: Pengju Wen creator: Shaoxian Chen creator: Min Wu creator: Yueheng Wu creator: Jian Zhuang uri: https://doi.org/10.7717/peerj.10336 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Third molar agenesis in modern humans with and without agenesis of other teeth link: https://peerj.com/articles/10367 last-modified: 2020-11-17 description: BackgroundThe number of teeth in the human dentition is of interest both from developmental and evolutionary aspects. The present case-control study focused on the formation of third molars in modern humans aiming to shed more light on the most variable tooth class in the dentition.Materials and MethodsFor this reason, we investigated third molar formation in a sample of 303 individuals with agenesis of teeth other than third molars (agenesis group) and compared it to a sex and age matched control group of 303 individuals without agenesis of teeth other than third molars.ResultsThe prevalence of third molar agenesis in the agenesis group was 50.8%, which is significantly higher than the 20.5% in the control group (p < 0.001). The chance of a missing third molar in the agenesis group was increased by 38.3% (p < 0.001), after controlling for the agenesis in other teeth factor. When considering the amount of missing third molars per individual, a clear tendency towards more missing third molars was evident in the agenesis group compared to the control group. The frequency of bilaterally missing third molars in the agenesis group was 29% in the maxilla, as well as in the mandible, which is about three times higher than the frequency of unilaterally missing third molars (p < 0.001). In the control group, bilaterally missing third molars occurred in 8.6% in the maxilla and 8.9% in the mandible.ConclusionThe present results indicate that genetic factors involved in tooth agenesis affect also the dentition as a whole. Furthermore, the third molars are more vulnerable to factors involved in agenesis of other teeth and they are more often affected as a whole. These findings seem to be associated with the evolutionary trend in humans towards reduced molar number. creator: Maya Scheiwiller creator: Elias S. Oeschger creator: Nikolaos Gkantidis uri: https://doi.org/10.7717/peerj.10367 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Scheiwiller et al. title: Increased copy number of syncytin-1 in the trophectoderm is associated with implantation of the blastocyst link: https://peerj.com/articles/10368 last-modified: 2020-11-17 description: BackgroundA key step in embryo implantation is the adhesion to and invasion of the endometrium by the blastocyst trophectoderm. The envelope proteins of HERV-W and -FRD (human endogenous retrovirus-W and -FRD), syncytin-1 and syncytin-2, are mainly distributed in the placenta, and play important roles in the development of the placenta. The placenta originates from the trophectoderm of the blastocyst. It is unclear whether the envelope proteins of HERV-W and -FRD have an effect on the development of the trophectoderm and whether they have any association with the implantation of the blastocyst.MethodsThe whole-genome amplification products of the human blastocyst trophectoderm were used to measure the copy number of syncytin-1 and syncytin-2 using real time qPCR. In addition, clinical data associated with the outcome of pregnancies was collected, and included age, body mass index (BMI), basic follicle stimulating hormone(bFSH), rate of primary infertility and oligo-astheno-teratospermia, the thickness of the endometrium on the day of endometrial transformation, the levels of estrogen and progestin on the transfer day, the days and the morphological scores of the blastocysts. The expression of mRNA and the copy numbers of syncytin-1 and syncytin-2 in H1 stem cells, and in differentiated H1 cells, induced by BMP4, were measured using real time qPCR.ResultsThe relative copy number of syncytin-1 in the pregnant group (median: 424%, quartile: 232%–463%, p < 0.05) was significantly higher than in the non-pregnant group (median: 100%, quartile: 81%–163%). There was a correlation (rs = 0.681, p < 0.001) between the copy number of syncytin-1 and blastocyst implantation after embryo transfer. As the stem cells differentiated, the expression of NANOG mRNA decreased, and the expression of caudal type homeobox 2(CDX2) and β-human chorionic gonadotropin (β-hCG) mRNAs increased. Compared to the undifferentiated cells, the relative expression of the syncytin-1 mRNA was 1.63 (quartile: 0.59–6.37, p > 0.05), 3.36 (quartile: 0.85–14.80, p > 0.05), 10.85 (quartile: 3.39–24.46, p < 0.05) and 67.81 (quartile: 54.07–85.48, p < 0.05) on day 1, 3, 5 and 7, respectively, after the differentiation. The relative expression of syncytin-2 was 5.34 (quartile: 4.50–10.30), 7.90 (quartile: 2.46–14.01), 57.44 (quartile: 38.35–103.87) and 344.76 (quartile: 267.72–440.10) on day 1, 3, 5 and 7, respectively, after the differentiation (p < 0.05). The copy number of syncytin-1 increased significantly during differentiation.ConclusionPreceding the transfer of frozen embryos, the increased copy number of syncytin-1 in the blastocyst trophectoderm was associated with good outcomes of pregnancies. creator: Luyan Guo creator: Fang Gu creator: Yan Xu creator: Canquan Zhou uri: https://doi.org/10.7717/peerj.10368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: MiR-26a-5p inhibits GSK3β expression and promotes cardiac hypertrophy in vitro link: https://peerj.com/articles/10371 last-modified: 2020-11-17 description: BackgroundThe role of miR-26a-5p expression in cardiac hypertrophy remains unclear. Herein, the effect of miR-26a-5p on cardiac hypertrophy was investigated using phenylephrine (PE)-induced cardiac hypertrophy in vitro and in a rat model of hypertension-induced hypertrophy in vivo.MethodsThe PE-induced cardiac hypertrophy models in vitro and vivo were established. To investigate the effect of miR-26a-5p activation on autophagy, the protein expression of autophagosome marker (LC3) and p62 was detected by western blot analysis. To explore the effect of miR-26a-5p activation on cardiac hypertrophy, the relative mRNA expression of cardiac hypertrophy related mark GSK3β was detected by qRT-PCR in vitro and vivo. In addition, immunofluorescence staining was used to detect cardiac hypertrophy related mark α-actinin. The cell surface area was measured by immunofluorescence staining. The direct target relationship between miR-26a-5p and GSK3β was confirmed by dual luciferase report.ResultsMiR-26a-5p was highly expressed in PE-induced cardiac hypertrophy. MiR-26a-5p promoted LC3II and decreased p62 expression in PE-induced cardiac hypertrophy in the presence or absence of lysosomal inhibitor. Furthermore, miR-26a-5p significantly inhibited GSK3β expression in vitro and in vivo. Dual luciferase report results confirmed that miR-26a-5p could directly target GSK3β. GSK3β overexpression significantly reversed the expression of cardiac hypertrophy-related markers including ANP, ACTA1 and MYH7. Immunofluorescence staining results demonstrated that miR-26a-5p promoted cardiac hypertrophy related protein α-actinin expression, and increased cell surface area in vitro and in vivo.ConclusionOur study revealed that miR-26a-5p promotes myocardial cell autophagy activation and cardiac hypertrophy by regulating GSK3β, which needs further research. creator: Liqun Tang creator: Jianhong Xie creator: Xiaoqin Yu creator: Yangyang Zheng uri: https://doi.org/10.7717/peerj.10371 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tang et al. title: Different analysis strategies of 16S rRNA gene data from rodent studies generate contrasting views of gut bacterial communities associated with diet, health and obesity link: https://peerj.com/articles/10372 last-modified: 2020-11-17 description: BackgroundOne of the main functions of diet is to nurture the gut microbiota and this relationship affects the health of the host. However, different analysis strategies can generate different views on the relative abundance of each microbial taxon, which can affect our conclusions about the significance of diet to gut health in lean and obese subjects. Here we explored the impact of using different analysis strategies to study the gut microbiota in a context of diet, health and obesity.MethodsOver 15 million 16S rRNA gene sequences from published studies involving dietary interventions in obese laboratory rodents were analyzed. Three strategies were used to assign the 16S sequences to Operational Taxonomic Units (OTUs) based on the GreenGenes reference OTU sequence files clustered at 97% and 99% similarity.ResultsDifferent strategies to select OTUs influenced the relative abundance of all bacterial taxa, but the magnitude of this phenomenon showed a strong study effect. Different taxa showed up to 20% difference in relative abundance within the same study, depending on the analysis strategy. Very few OTUs were shared among the samples. ANOSIM test on unweighted UniFrac distances showed that study, sequencing technique, animal model, and dietary treatment (in that order) were the most important factors explaining the differences in bacterial communities. Except for obesity status, the contribution of diet and other factors to explain the variability in bacterial communities was lower when using weighted UniFrac distances. Predicted functional profile and high-level phenotypes of the microbiota showed that each study was associated with unique features and patterns.ConclusionsThe results confirm previous findings showing a strong study effect on gut microbial composition and raise concerns about the impact of analysis strategies on the membership and composition of the gut microbiota. This study may be helpful to guide future research aiming to investigate the relationship between diet, health, and the gut microbiota. creator: Jose F. Garcia-Mazcorro creator: Jorge R. Kawas creator: Cuauhtemoc Licona Cassani creator: Susanne Mertens-Talcott creator: Giuliana Noratto uri: https://doi.org/10.7717/peerj.10372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Garcia-Mazcorro et al. title: Investigation of acute-phase proteins and cytokines response in goats with contagious caprine pleuropneumonia with special reference to their diagnostic accuracy link: https://peerj.com/articles/10394 last-modified: 2020-11-17 description: Acute-phase proteins (APPs) have always had valued diagnostic potentialities in response to infection. This study aimed to evaluate the diagnostic accuracy of selected APPs and proinflammatory cytokines (PIC) in goats with contagious caprine pleuropneumonia (CCPP) under field conditions. Moreover, to highlight the role of tested biomarkers in CCPP pathogenesis. Fifty-eight goats (38 confirmed cases with CCPP and 20 healthy controls) were involved in this investigation. C-reactive protein (CRP), procalcitonin (PCT), haptoglobin (HP), fibrinogen (Fb), serum amyloid A (SAA), selected PIC (IL1-α, IL1-β, IL-6, interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α)) levels were investigated in serum samples from all goats under investigation. Latex agglutination test was used for diagnosis of goats with CCPP. For microbiological investigations, nasopharyngeal swabs (from all goats), lung tissues and pleural fluids (from only necropsied goats) were collected. This study revealed that all tested parameters have a high to moderate degree of diagnostic performance for CCPP. Magnitudes of increase in levels of APPs (CRP, HP and SAA) were stronger than PIC, IFN-γ, Fb and PCT. All tested parameters showed high diagnostic accuracy (AUROC >90%), except HP (AUROC = 87.3%) and IFN-γ (AUROC = 78.8%) showed moderate accuracy in differentiation of goats with and without CCPP infection. For detecting goats with and without CCPP infection, HP had the lowest sensitivity (Se = 81.6%) and Fb had the lowest specificity (Sp = 85.0%) among the APPs parameters tested. However, PCT showed the highest Se (100%) and Sp (95.0%) to detect goats with and without CCPP infection among tested parameters. Conclusively, this study endorses the significance of selected APPs and PIC as additional screening diagnostic parameters for naturally occurring CCPP in goats. However, it does not replace traditional methods for diagnosis of CCPP in goats. Furthermore, APPs and PIC have an important role in disease pathogenesis in goats. creator: Wael El-Deeb creator: Mahmoud Fayez creator: Ibrahim Elsohaby creator: Mohamed Salem creator: Abdulrhman Alhaider creator: Mahmoud Kandeel uri: https://doi.org/10.7717/peerj.10394 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 El-Deeb et al. title: The easternmost occurrence of Mammut pacificus (Proboscidea: Mammutidae), based on a partial skull from eastern Montana, USA link: https://peerj.com/articles/10030 last-modified: 2020-11-16 description: Mammut pacificus is a recently described species of mastodon from the Pleistocene of California and Idaho. We report the easternmost occurrence of this taxon based upon the palate with right and left M3 of an adult male from the Irvingtonian of eastern Montana. The undamaged right M3 exhibits the extreme narrowness that characterizes M. pacificus rather than M. americanum. The Montana specimen dates to an interglacial interval between pre-Illinoian and Illinoian glaciation, perhaps indicating that M. pacificus was extirpated in the region due to habitat shifts associated with glacial encroachment. creator: Andrew T. McDonald creator: Amy L. Atwater creator: Alton C. Dooley Jr creator: Charlotte J.H. Hohman uri: https://doi.org/10.7717/peerj.10030 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 McDonald et al. title: Acetate correlates with disability and immune response in multiple sclerosis link: https://peerj.com/articles/10220 last-modified: 2020-11-16 description: BackgroundGut microbiota has been related to multiple sclerosis (MS) etiopathogenesis. Short-chain fatty acids (SCFA) are compounds derived from microbial metabolism that have a role in gut-brain axis.ObjectivesTo analyse SCFA levels in plasma of MS patients and healthy donors (HD), and the possible link between these levels and both clinical data and immune cell populations.MethodsNinety-five MS patients and 54 HD were recruited. Patients were selected according to their score in the Expanded Disability Status Scale (EDSS) (49 EDSS ≤ 1.5, 46 EDSS ≥ 5.0). SCFA were studied in plasma samples by liquid chromatography-mass spectrometry. Peripheral blood mononuclear cells were studied by flow cytometry. Gender, age, treatments, EDSS and Multiple Sclerosis Severity Score (MSSS) were evaluated at the recruitment.ResultsPlasma acetate levels were higher in patients than in HD (p = 0.003). Patients with EDSS ≥ 5.0 had higher acetate levels than those with EDSS≤ 1.5 (p = 0.029), and HD (p = 2.97e–4). Acetate levels correlated with EDSS (r = 0.387; p = 1.08e–4) and MSSS (r = 0.265; p = 0.011). In untreated MS patients, acetate levels correlated inversely with CD4+ naïve T cells (r =  − 0.550, p = 0.001) and directly with CD8+ IL-17+ cells (r = 0.557; p = 0.001).ConclusionsPlasma acetate levels are higher in MS patients than in HD. In MS there exists a correlation between plasma acetate levels, EDSS and increased IL-17+ T cells. Future studies will elucidate the role of SCFA in the disease. creator: Silvia Pérez-Pérez creator: María Inmaculada Domínguez-Mozo creator: Aitana Alonso-Gómez creator: Silvia Medina creator: Noelia Villarrubia creator: Jose Ignacio Fernández-Velasco creator: María Ángel García-Martínez creator: Estefanía García-Calvo creator: Héctor Estévez creator: Lucienne Costa-Frossard creator: Jose C. Alvarez-Cermeño creator: Jose L. Luque-Garcia creator: Rafael Arroyo creator: Luisa M. Villar creator: Roberto Alvarez-Lafuente uri: https://doi.org/10.7717/peerj.10220 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pérez-Pérez et al. title: Diversity of edible insects in a Natural World Heritage Site of India: entomophagy attitudes and implications for food security in the region link: https://peerj.com/articles/10248 last-modified: 2020-11-16 description: Insects not only play a significant role in the ecological process of nature but since pre-historic times have also formed a part of the human diet. With a still growing population and skewed demographic structures across most societies of the world, their role as nutrient-rich food has been increasingly advocated by researchers and policymakers globally. In this study, we examine the edible insect diversity and entomophagy attitudes of ethnic people in Manas National Park, a UNESCO Natural World Heritage Site, located in Assam (India). The study involved a field investigation through which the pattern of entomophagy and the attitude towards insect-eating was studied. Following this, we examined the edible insect diversity and abundance at different sampling points. A total of 22 species of edible insects belonging to fifteen families and eight orders were recorded from different habitat types. Out of these 22 species, Orthopterans showed a maximum number of eight species followed by Hymenoptera (four), Hemiptera (three), Lepidoptera (two), Blattodea (two) and one species each from Coleoptera, Odonata, and Mantodea. Dominance, diversity, and equitability indices were computed along with the relative abundance of the insects concerning four habitat types. Aspects of the economic significance of entomophagy were also observed during the field investigation. To manage insects in the interest of food security, more attention should be given to sustainable collecting and rearing methods emphasizing their economic, nutritional, and ecological advantages. creator: Jayanta Kr Das creator: Arup Kumar Hazarika creator: Unmilan Kalita creator: Subhash Khanna creator: Tarali Kalita creator: Sangeeta Choudhury uri: https://doi.org/10.7717/peerj.10248 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Das et al. title: Nitrogen fertilization affects maize grain yield through regulating nitrogen uptake, radiation and water use efficiency, photosynthesis and root distribution link: https://peerj.com/articles/10291 last-modified: 2020-11-16 description: High external nitrogen (N) inputs can maximize maize yield but can cause a subsequent reduction in N use efficiency (NUE). Thus, it is necessary to identify the minimum effective N fertilizer input that does not affect maize grain yield (GY) and to investigate the photosynthetic and root system consequences of this optimal dose. We conducted a 4-year field experiment from 2014 to 2017 with four N application rates: 300 (N300), 225 (N225), 150 (N150), and 0 Kg ha−1 (N0) in the Northwest of China. GY was assessed by measuring the photosynthetic capacity and root system (root volume, surface area, length density and distribution). Grain yield decreased by −3%, 7.7%, and 21.9% when the N application rates decreased by 25%, 50%, and 100% from 300 Kg ha−1. We found that yield reduction driven by N reduction was primarily due to decreased radiation use efficiency (RUE) and WUE instead of intercepted photosynthetically active radiation and evapotranspiration. In the N225 treatment, GY, WUE, and RUE were not significantly reduced, or in some cases, were greater than those of the N300 treatment. This pattern was also observed with relevant photosynthetic and root attributes (i.e., high net photosynthetic rate, stomatal conductance, and root weight, as well as deep root distribution). Our results suggest that application of N at 225 Kg ha−1 can increased yield by improving the RUE, WUE, and NUE in semi-arid regions. creator: Wennan Su creator: Shakeel Ahmad creator: Irshad Ahmad creator: Qingfang Han uri: https://doi.org/10.7717/peerj.10291 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Su et al. title: Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes link: https://peerj.com/articles/10343 last-modified: 2020-11-16 description: BackgroundCassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes.MethodsA novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms.ResultsAnalysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T). creator: Pattsarun Cheawchanlertfa creator: Sawannee Sutheeworapong creator: Piroon Jenjaroenpun creator: Thidathip Wongsurawat creator: Intawat Nookaew creator: Supapon Cheevadhanarak creator: Akihiko Kosugi creator: Patthra Pason creator: Rattiya Waeonukul creator: Khanok Ratanakhanokchai creator: Chakrit Tachaapaikoon uri: https://doi.org/10.7717/peerj.10343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cheawchanlertfa et al. title: Effects of microhabitat on rodent-mediated seed removal of endangered Kmeria septentrionalis in the karst habitat link: https://peerj.com/articles/10378 last-modified: 2020-11-16 description: Seed removal behaviors of rodents are largely influenced by microhabitat. Although the karst ecosystem is composed of a broad variety of microhabitats, we have no information on how they affect such behaviors. We investigated rodents’ seed removal behaviors in four karst microhabitats (stone cavern, stone groove, stone surface, and soil surface) using three types of Kmeria septentrionalis seeds: fresh, black (intact seeds with black aril that dehydrates and darkens), and exposed (clean seeds without the aril). We show that Rattus norvegicus, Leopoldamys edwardsi and Rattus flavipectus were the predominant seed predators. Even though all seed types experienced a high removal rate in all four microhabitats, but rodents preferentially removed seeds from the three stone microhabitats (stone caves: 69.71 ± 2.74%; stone surface: 60.53 ± 2.90%; stone groove: 56.94 ± 2.91%) compared to the soil surface (53.90 ± 2.92%). Seeds that had been altered by being exposed to the environment were more attractive to rodents than fresh seeds (76.25 ± 2.20% versus 36.18 ± 2.29%). The seed removal behavior of rodents was significantly affected by the microhabitat and seed type. Finally, seeds that had fallen on the soil surface microhabitat incurred a lower predation risk than seeds fallen on other microhabitats, which increased their probability to germinate. Our results indicate that the lower predation rate of seeds from the endangered K. septentrionalis dropped on the soil surface increases trees’ likelihood of survival. creator: Guohai Wang creator: Yang Pan creator: Guole Qin creator: Weining Tan creator: Changhu Lu uri: https://doi.org/10.7717/peerj.10378 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation link: https://peerj.com/articles/10075 last-modified: 2020-11-13 description: BackgroundHuman embryonic stem cells (hESC) have been an invaluable research tool to study motor neuron development and disorders. However, transcriptional regulation of multiple temporal stages from ESCs to spinal motor neurons (MNs) has not yet been fully elucidated. Thus, the goals of this study were to profile the time-course expression patterns of lncRNAs during MN differentiation of ESCs and to clarify the potential mechanisms of the lncRNAs that are related to MN differentiation.MethodsWe utilized our previous protocol which can harvest motor neuron in more than 90% purity from hESCs. Then, differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) during MN differentiation were identified through RNA sequencing. Bioinformatic analyses were performed to assess potential biological functions of genes. We also performed qRT-PCR to validate the DElncRNAs and DEmRNAs.ResultsA total of 441 lncRNAs and 1,068 mRNAs at day 6, 443 and 1,175 at day 12, and 338 lncRNAs and 68 mRNAs at day 18 were differentially expressed compared with day 0. Bioinformatic analyses identified that several key regulatory genes including POU5F1, TDGF1, SOX17, LEFTY2 and ZSCAN10, which involved in the regulation of embryonic development. We also predicted 283 target genes of DElncRNAs, in which 6 mRNAs were differentially expressed. Significant fold changes in lncRNAs (NCAM1-AS) and mRNAs (HOXA3) were confirmed by qRT-PCR. Then, through predicted overlapped miRNA verification, we constructed a lncRNA NCAM1-AS-miRNA-HOXA3 network. creator: Xue-Jiao Sun creator: Ming-Xing Li creator: Chen-Zi Gong creator: Jing Chen creator: Mohammad Nasb creator: Sayed Zulfiqar Ali Shah creator: Muhammad Rehan creator: Ya-Jie Li creator: Hong Chen uri: https://doi.org/10.7717/peerj.10075 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: Regional infectious risk prediction of COVID-19 based on geo-spatial data link: https://peerj.com/articles/10139 last-modified: 2020-11-13 description: After the first confirmed case of the novel coronavirus disease (COVID-19) was found, it is of considerable significance to divide the risk levels of various provinces or provincial municipalities in Mainland China and predict the spatial distribution characteristics of infectious diseases. In this paper, we predict the epidemic risk of each province based on geographical proximity information, spatial inverse distance information, economic distance and Baidu migration index. A simulation study revealed that the information based on geographical economy matrix and migration index could well predict the spatial spread of the epidemic. The results reveal that the accuracy rate of the prediction is over 87.10% with a rank difference of 3.1. The results based on prior information will guide government agencies and medical and health institutions to implement responses to major public health emergencies when facing the epidemic situation. creator: Xuewei Cheng creator: Zhaozhou Han creator: Badamasi Abba creator: Hong Wang uri: https://doi.org/10.7717/peerj.10139 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cheng et al. title: Identification of L-asparaginases from Streptomyces strains with competitive activity and immunogenic profiles: a bioinformatic approach link: https://peerj.com/articles/10276 last-modified: 2020-11-13 description: The enzyme L-asparaginase from Escherichia coli is a therapeutic enzyme that has been a cornerstone in the clinical treatment of acute lymphoblastic leukemia for the last decades. However, treatment effectiveness is limited by the highly immunogenic nature of the protein and its cross-reactivity towards L-glutamine. In this work, a bioinformatic approach was used to identify, select and computationally characterize L-asparaginases from Streptomyces through sequence-based screening analyses, immunoinformatics, homology modeling, and molecular docking studies. Based on its predicted low immunogenicity and excellent enzymatic activity, we selected a previously uncharacterized L-asparaginase from Streptomyces scabrisporus. Furthermore, two putative asparaginase binding sites were identified and a 3D model is proposed. These promising features allow us to propose L-asparaginase from S. scabrisporus as an alternative for the treatment of acute lymphocytic leukemia. creator: Iván González-Torres creator: Ernesto Perez-Rueda creator: Zahaed Evangelista-Martínez creator: Andrés Zárate-Romero creator: Angélica Moreno-Enríquez creator: Alejandro Huerta-Saquero uri: https://doi.org/10.7717/peerj.10276 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 González-Torres et al. title: The optimal platelet concentration in platelet-rich plasma for proliferation of human cells in vitro—diversity, biases, and possible basic experimental principles for further research in the field: A review link: https://peerj.com/articles/10303 last-modified: 2020-11-13 description: BackgroundIn the last decades, several in vitro studies have tested the effect of plate-rich plasma (PRP) on the proliferation of human cells in search of a wizard for the use of PRP in a clinical setting. However, the literature displays striking differences regarding this question despite the relatively similar experimental design. The aim of this review is twofold: describe and explain this diversity and suggest basic principles for further in vitro studies in the field. The optimal platelet concentration in vivo will also be discussed.MethodsA search in mainly EMBASE and PubMed was performed to identify in vitro studies that investigate the effect of different PRP concentrations on human cell proliferation. The assessment of bias was based on the principles of “Good Cell Culture Practice” and adapted.ResultsIn total, 965 in vitro studies were detected. After the initial screening, 31 studies remained for full-text screening. A total of 16 studies met the criteria of final inclusion and appeared relatively sound. In general, the studies state consistently that PRP stimulates the proliferation of the human cell. Two main types of experimental techniques were detected: 1. The Fixed PRP Concentration Group using a fixed PRP concentration throughout the experiment, which leads to a substantial decrease in nutrition available at higher concentrations. 2. The Fixed PRP Volume Group using a fixed PRP-to-media ratio (Vol/Vol) throughout the experiment. A general tendency was observed in both groups: when the PRP to media ratio increased (Vol/Vol), the proliferation rate decreased. Further, The Low Leukocyte group observed a substantial higher optimal PRP concentration than The High leukocyte group. No prominent tendencies was seen regarding anticoagulants, activation methods, and blood donor (age or sex).DiscussionTwo major biases regarding optimal proliferation in vitro is pointed out: 1. Too high PRP volume. It is speculated that the techniques used by some studies led to an adverse growth condition and even cell starvation at higher concentrations. 2. High leukocyte levels. Reduced proliferation rate due to proinflammatory substances released during degranulation of leukocytes.ConclusionsThe two main biases may explain the bell-shaped effect of PRP and the detrimental effects at higher platelet concentrations observed in several studies. These biases may also explain the low optimal PRP concentration observed in some studies. Even if one universal optimal PRP concentration does not exist, the review indicates that PRP concentrations in the upper parts of the scale is optimal or at least beneficial. Finally, following basic experimental principles are suggested. 1: The PRP/media ratio (Vol/Vol) should be kept as constant. 2: The PRP/media ratio should provide a sufficient nutrition supply, that is, PRP ≤ 10% (Vol/Vol). 3: The cell density per well (cells/mL) should be defined. 4: Leukocyte level should be kept low, preferable depleted (< 0.1 PLT/µL). creator: Olav K. Straum uri: https://doi.org/10.7717/peerj.10303 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Straum title: Cytokine RT-qPCR and ddPCR for immunological investigations of the endangered Australian sea lion (Neophoca cinerea) and other mammals link: https://peerj.com/articles/10306 last-modified: 2020-11-13 description: Measurement of cytokine gene expression by reverse transcription quantitative polymerase chain reaction (RT-qPCR) is used widely to assess the immune system of animals and to identify biomarkers of disease, but its application is limited in wildlife species due to a lack of species-specific reagents. The free-ranging endangered Australian sea lion (Neophoca cinerea) experiences significant clinical disease and high pup mortality due to intestinal hookworm infection. Developing immunological tools specific to the species will aid in the assessment of drivers of disease and its impact in population demographics. This study describes the development and validation of cross-reactive RT-qPCR assays to measure five important cytokines involved in innate and Th1/Th2 responses (IL-6, TNFα, IFNγ, IL-4 and IL-10) in unstimulated blood samples from a range of different mammalian species including the Australian sea lion. All RT-qPCR assays efficiencies ranged between 87% (Ovis aries TNFα) and 111% (Bos taurus IL-10) and had strong linearity (R2). IL-4 and IFNγ gene expression for N. cinerea fell below the dynamic range (and therefore quantifiable limits) of RT-qPCR assays but were able to be quantified using the novel droplet digital PCR (ddPCR). This study delivers new immunological tools for eco-immunologists studying cytokine gene expression in wildlife species and is to our knowledge, the first cytokine ddPCR approach to be reported in a pinniped species. creator: María-Ignacia Meza Cerda creator: Rachael Gray creator: Damien P. Higgins uri: https://doi.org/10.7717/peerj.10306 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Meza Cerda et al. title: Combined application of biochar and nitrogen fertilizer improves rice yield, microbial activity and N-metabolism in a pot experiment link: https://peerj.com/articles/10311 last-modified: 2020-11-13 description: The excessive use of synthetic nitrogen (N) fertilizers in rice (Oryza sativa L.) has resulted in high N loss, soil degradation, and environmental pollution in a changing climate. Soil biochar amendment is proposed as a climate change mitigation tool that supports carbon sequestration and reduces N losses and greenhouse gas (GHG) emissions from the soil. The current study evaluated the impact of four different rates of biochar (B) (C/B0-0 t ha−1, B1-20 t ha−1, B2-40 t ha−1, and B3-60 t ha−1) and two N levels (N1; low (270 kg N ha−1) and N2; high (360 kg N ha−1)), on rice (cultivar Zhenguiai) grown in pots. Significant increases in the average soil microbial biomass N (SMBN) (88%) and carbon (87%) were recorded at the highest rate of 60-ton ha−1B and 360 kg N ha−1 compared to the control (N1C) during both seasons (S1 and S2). The photochemical efficiency (Fv/Fm), quantum yield of the photosystem (PS) II (ΦPS II), electron transport rate (ETR), and photochemical quenching (qP) were enhanced at low rates of biochar applications (20 to 40 t B ha−1) for high and low N rates across the seasons. Nitrate reductase (NR), glutamine synthetase (GS), and glutamine 2-oxoglutarate aminotransferase (GOGAT) activity were, on average, 39%, 55%, and 63% higher in the N1B3, N2B2, and N2B3 treatments, respectively than the N1C. The grain quality was higher in the N1B3 treatment than the N1C, i.e., the protein content (PC), amylose content (AC), percent brown rice (BRP), and percent milled rice (MRP) were, on average, 16%, 28%, 4.6%, and 5% higher, respectively in both seasons. The results of this study indicated that biochar addition to the soil in combination with N fertilizers increased the dry matter (DM) content, N uptake, and grain yield of rice by 24%, 27%, and 64%, respectively, compared to the N1C. creator: Izhar Ali creator: Saif Ullah creator: Liang He creator: Quan Zhao creator: Anas Iqbal creator: Shangqing Wei creator: Tariq Shah creator: Niyaz Ali creator: Yan Bo creator: Muhammad Adnan creator: Amanullah creator: Ligeng Jiang uri: https://doi.org/10.7717/peerj.10311 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ali et al. title: Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform link: https://peerj.com/articles/10340 last-modified: 2020-11-13 description: Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform. creator: Pacharaporn Angthong creator: Tanaporn Uengwetwanit creator: Wirulda Pootakham creator: Kanchana Sittikankaew creator: Chutima Sonthirod creator: Duangjai Sangsrakru creator: Thippawan Yoocha creator: Intawat Nookaew creator: Thidathip Wongsurawat creator: Piroon Jenjaroenpun creator: Wanilada Rungrassamee creator: Nitsara Karoonuthaisiri uri: https://doi.org/10.7717/peerj.10340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Angthong et al. title: Identification of the important environmental factors influencing natural vegetation succession following cropland abandonment on the Loess Plateau, China link: https://peerj.com/articles/10349 last-modified: 2020-11-13 description: Identification of typical vegetation succession types and their important influencing factors is an important prerequisite to implement differential vegetation and soil management after land abandonment on the Loess Plateau, China. However, there is no reported study specifically on the identification of vegetation types and their important factors as well as the thresholds of the important factors for classification of the vegetation types, based on the medium- to long-term succession of natural vegetation after cropland abandonment. We collected vegetation and soil data on the natural vegetation with the longest 60-year-old forest communities that developed after cropland abandonment and analyzed the data using two-way indicator species analysis, detrended correspondence analysis, direct canonical correspondence analysis and classification tree model. The vegetation communities were classified into five distinct vegetation types, including Artemisia scoparia, Lespedeza davurica and Stipa bungeana, Artemisia giraldii pamp, Sophora viciifolia, Quercus liaotungensis and Biota orientalis. The years after cropland abandonment and soil C/N were further identified as important factors determining the types of vegetation. Likewise, it was observed that most of the investigated soil nutrient variables and soil texture-related variables improved with the vegetation succession while soil water in the surface layers showed a decreasing trend. These findings may provide an ecological basis for site-specific management of vegetation types after cropland abandonment in the medium-long term on the Loess Plateau. Our results encourage further exploration of vegetation succession and their important factors based on longer periods of vegetation succession after cropland abandonment under more soil and climatic conditions on the mountainous areas as the Loess Plateau. creator: Zhenguo Zhang creator: Mingming Wang creator: Jikai Liu creator: Xinwei Li uri: https://doi.org/10.7717/peerj.10349 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Clinical impact of lenvatinib in patients with unresectable hepatocellular carcinoma who received sorafenib link: https://peerj.com/articles/10382 last-modified: 2020-11-13 description: BackgroundLenvatinib has been approved for use in the systemic treatment for unresectable hepatocellular carcinoma (HCC). This study aimed to investigate the efficacy and safety of lenvatinib in patients with unresectable HCC who received sorafenib.MethodsA total of 40 patients who received lenvatinib after sorafenib were retrospectively identified: as second line in 20 patients, third line in 10 patients, and fourth line and later lines in 10 patients. The treatment response to lenvatinib was determined in accordance with the guidelines of the modified Response Evaluation Criteria in Solid Tumors (mRECIST) every 2–3 months after commencement of lenvatinib.ResultsMedian progression-free survival (PFS) and median overall survival (OS) of the whole population were 3.3 and 9.8 months, respectively. The objective response rate was 27.5%. Univariate and multivariate analyses showed that alpha-fetoprotein level >400 ng/mL was an independent prognostic factor of worse PFS and OS. The clinical outcomes of lenvatinib therapy as second-line, third-line, or fourth line and later line treatment were similar, and previous response to sorafenib could predict the response to subsequent lenvatinib. Most adverse events were grades 1–2, and the majority of patients tolerated the side effects. Our study confirms the efficacy and safety of lenvatinib as second-line and later line treatment for patients with unresectable HCC who received sorafenib in clinical practice. creator: Yen-Yang Chen creator: Chih-Chi Wang creator: Yueh-Wei Liu creator: Wei-Feng Li creator: Yen-Hao Chen uri: https://doi.org/10.7717/peerj.10382 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: A new species of the large-headed coastal marine turtle Solnhofia (Testudinata, Thalassochelydia) from the Late Jurassic of NW Switzerland link: https://peerj.com/articles/9931 last-modified: 2020-11-12 description: BackgroundThe large-headed turtle Solnhofia parsonsi is known by a handful of specimens from the Late Jurassic of Germany and Switzerland (maybe also France). Solnhofia parsonsi is traditionally regarded as a “eurysternid” Thalassochelydia, a group of small to medium sized, mostly lagoonal or marginal turtles found almost exclusively in the Late Jurassic of Europe. More recently, Solnhofia parsonsi has been proposed to be a close relative of Sandownidae, an enigmatic group of Cretaceous to Paleogene turtles characterized by a derived cranial anatomy and a wider geographical distribution. Sandownids may therefore have evolved from thalassochelydian ancestors such as Solnhofia parsonsi.MethodsWe herein describe new material of Solnhofia from the Kimmeridgian (Late Jurassic) of Porrentruy, NW Switzerland. The bulk of the material consists of an association of a cranium and over 180 shell bones found together in a block of marly limestone. A second cranium and a mandible from slightly younger, but nearby localities are also described.ResultsWe refer the new material to Solnhofia brachyrhyncha n. sp. The new species shares with Solnhofia parsonsi a relatively large head, an extensive secondary palate formed primarily by the maxillae, a greatly developed processus trochlearis oticum with a contribution from the parietal and quadratojugal, a large jugal-palatine contact in the floor of the fossa orbitalis, and a posteromedial process of the jugal running on the dorsal surface of the maxilla and pterygoid. Some of these characteristics are also present in sandownids, but our morphological study clearly shows that Solnhofia brachyrhyncha is closer to Solnhofia parsonsi than to any sandownids.DiscussionSolnhofia brachyrhyncha differs from Solnhofia parsonsi in many aspects, notably: a shortened and broader cranium, a shorter and posteriorly broader upper triturating surface with a slightly sinusoidal lateral margin and without contribution from the palatine, a processus trochlearis oticum more oblique in dorsal or ventral view and less concave in anterior view, choanae that do not extend posteriorly on the pterygoids, a more developed processus pterygoideus externus, a condylus mandibularis situated anterior to the level of the occipital plane, a greater ventral exposure of the parabasisphenoid, a mandible about as wide as long, a relatively short symphysis, a lower triturating surface widened posterolaterally thanks to the presence of large laterally projecting dentary tubercles, a stouter and shorter coronoid process, a splenial positioned more anteriorly along the mandibular ramus, costo-peripheral fontanelles extending more anteriorly and posteriorly along the costal series, and an escutcheon shaped central plastral fontanelle formed mostly by the hypoplastra. In addition to the morphology of the new species, we also briefly discuss about observable ontogenetic variations and possible taphonomic origin of the assemblage. creator: Jérémy Anquetin creator: Christian Püntener uri: https://doi.org/10.7717/peerj.9931 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Anquetin and Püntener title: A combination of two ELISA tests for nasopharyngeal carcinoma screening in endemic areas based on a case-control study link: https://peerj.com/articles/10254 last-modified: 2020-11-12 description: For populations with a high risk of nasopharyngeal carcinoma (NPC) in Guangdong province in southern China, mass screening is the first choice to prevent death from NPC. To improve the performance of NPC screening, we used a combination based on the IgA antibody against the Epstein-Barr virus (EBV) capsid antigen (VCA-IgA) and the IgA antibody against Epstein-Barr virus nuclear antigen 1 (EBNA1-IgA) to NPC screening by enzyme-linked immunosorbent assay (ELISA). A multiplication model was applied to measure the level of the combination. We evaluated the NPC screening effect of the markers.A case-control study was performed to assess the NPC screening effect of the markers. A total of 10,894 serum specimens were collected, including 554 samples from NPC patients and 10,340 samples from healthy controls. In the training stage, 640 subjects were randomly selected, including 320 NPC cases and 320 healthy controls. In the verification stage, 10,254 subjects were used to verify the NPC screening effect of the combination. Receiver operating characteristic (ROC) analysis was performed. In the verification stage, the combination achieved an sensitivity of 91.45%, a specificity of 93.45%, and an area under the ROC curve (AUC) of 0.978 (95% CI [0.968–0.987]). Compared with VCA-IgA and EBNA1-IgA individually, the combination had an improved screening performance. A probability (PROB) calculated by logistic regression model based on VCA-IgA and EBNA1-IgA was applied to NPC screening by ELISA in China. The AUC of the combination was a little bit larger than the PROB. There was a slight increase (3.13%) in the sensitivity of the combination compared to the sensitivity of the PROB, while the specificity was lower for the combination (92.50%) than for the PROB (95.94%). We successfully applied a combination of two ELISA tests based on VCA-IgA and EBNA1-IgA for NPC screening by using a multiplication model. The results suggested that the combination was effective and can be an option for NPC screening. creator: Dongping Rao creator: Meiqin Fu creator: Yingjie Chen creator: Qing Liu creator: Lin Xiao creator: Xin Zhang creator: Zhongxiao Li creator: Haitao Li creator: Yongyi He creator: Yongxing Chen creator: Jieying Chen creator: Jin Hu creator: Yanming Huang uri: https://doi.org/10.7717/peerj.10254 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rao et al. title: Effects of diet and gizzard muscularity on grit use in domestic chickens link: https://peerj.com/articles/10277 last-modified: 2020-11-12 description: The gizzard is the only gastrointestinal organ for mechanical processing in birds. Many birds use grit in the gizzard to enhance mechanical processing efficiency. We conducted an experiment to test the factors that affect chicken grit use in 68 male layer chicks of Gallus gallus domesticus, which were divided into two different groups in gizzard muscularity (high and low). Within each muscularity group, two different diets were provided (herbivory and non-herbivory) to test whether diet and gizzard muscularity affect grit characteristics including amount, size, and shape (circularity, roundness, and solidity) at different stages of digestion (ingested grit, grit in gizzard, and excreted grit). All animals ingested more grit than they excreted, possibly because excreted grit was below the detection size limit of 0.5 mm of the present study. The amounts of grit ingested and remained in the gizzard were larger in herbivorous groups, but these groups excreted less grit. Larger, rougher grit was selectively ingested by all chicks, but size preferences were especially pronounced in the herbivorous groups. Grit in the gizzard tended to be larger in herbivorous groups, but the grit in excreta was smaller, whereas the size of excreted grit was larger in groups with less muscular gizzards. Grit in the gizzard was much smoother than the offered and ingested grit, especially in the herbivorous, muscular gizzard groups. Excreted grit in all groups was smoother than the offered grit. These results show that diet affects the characteristics of ingested grit, grit in the gizzard, and excreted grit, whereas gizzard muscularity affects the characteristics of grit in the gizzard and excreted grit. The use of larger sizes and amounts of grit by herbivorous groups may be a response to the needs of digesting hard, coarse materials. The recovered behavioral flexibility of grit use might reflect the omnivorous nature of Gallus gallus domesticus and may aid smooth dietary shifts. The results also show that the shape of grit remaining in the gizzard does not reflect the initial shape of ingested grit, in contrast to previously published ideas. Instead, the shape of grit in the gizzard more closely reflects the diet and gizzard muscularity of chicks. creator: Ryuji Takasaki creator: Yoshitsugu Kobayashi uri: https://doi.org/10.7717/peerj.10277 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Takasaki and Kobayashi title: High-quality genome assembly of Metaphire vulgaris link: https://peerj.com/articles/10313 last-modified: 2020-11-12 description: Earthworms enrich the soil and protect the health of their ecological environment. Previous studies on these invertebrates determined their protein content, hormone secretions, medicinal value, and ecological habits, but their whole genomic sequence remains incomplete. We performed whole genome sequencing of Metaphire vulgaris (Chen, 1930), which belongs to the genus Metaphire of the family Megascolecidae. The genome assembly was 729 Mb, with a N50 contig size of 4.2 Mb. In total, 559 contigs were anchored to 41 chromosomes according to the results of Hi-C (High-throughput Chromosome Conformation Capture) technology, which was confirmed by karyological analysis. A comparison of the genomic sequences and genes indicated that there was a whole-genome duplication in M. vulgaris followed by several chromosome fusion events. Hox genes and lumbrokinase genes were identified as partial clusters surrounding the genome. Our high-quality genome assembly of M. vulgaris will provide valuable information for gene function and evolutionary studies in earthworms. creator: Feng Jin creator: Zhaoli Zhou creator: Qi Guo creator: Zhenwen Liang creator: Ruoyu Yang creator: Jibao Jiang creator: Yanlin He creator: Qi Zhao creator: Qiang Zhao uri: https://doi.org/10.7717/peerj.10313 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jin et al. title: Radon and thoron exhalation rate, emanation factor and radioactivity risks of building materials of the Iberian Peninsula link: https://peerj.com/articles/10331 last-modified: 2020-11-12 description: Radon (222Rn) and thoron (220Rn) are radioactive gases emanating from geological materials. Inhalation of these gases is closely related to an increase in the probability of lung cancer if the levels are high. The majority of studies focus on radon, and the thoron is normally ignored because of its short half-life (55.6 s). However, thoron decay products can also cause a significant increase in dose. In buildings with high radon levels, the main mechanism for entry of radon is pressure-driven flow of soil gas through cracks in the floor. Both radon and thoron can also be released from building materials to the indoor atmosphere. In this work, we study the radon and thoron exhalation and emanation properties of an extended variety of common building materials manufactured in the Iberian Peninsula (Portugal and Spain) but exported and used in all countries of the world. Radon and thoron emission from samples collected in the closed chamber was measured by an active method that uses a continuous radon/thoron monitor. The correlations between exhalation rates of these gases and their parent nuclide exhalation (radium/thorium) concentrations were examined. Finally, indoor radon and thoron and the annual effective dose were calculated from radon/thoron concentrations in the closed chamber. Zircon is the material with the highest concentration values of 226Ra and 232Th and the exhalation and emanation rates. Also in the case of zircon and some granites, the annual effective dose was higher than the annual exposure limit for the general public of 1 mSv y−1, recommended by the European regulations. creator: Samuel Frutos-Puerto creator: Eduardo Pinilla-Gil creator: Eva Andrade creator: Mário Reis creator: María José Madruga creator: Conrado Miró Rodríguez uri: https://doi.org/10.7717/peerj.10331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Frutos-Puerto et al. title: The rs78378222 prevalence and the copy loss of the protective allele A in the tumor tissue of diffuse large B-cell lymphoma link: https://peerj.com/articles/10335 last-modified: 2020-11-12 description: BackgroundRare single nucleotide polymorphisms (SNPs) are likely to be a crucial genetic factor for human diseases, including cancer. rs78378222 is rare SNP in 3′-untranslated region (UTR) of TP53 gene leading to disturbance of 3′-end mRNA processing. The frequency of rs78378222 varies in several studied populations. The meta-analysis of 34 genome-wide association studies indicated that rs78378222 was significantly associated with an increased risk of cancer overall. Bioinformatic analysis indicates that somatic loss of the protective A allele of rs78378222 occurs in the tumor tissue of some malignant. The goal of the current study is to document the rs78378222 prevalence and evaluate the copy loss status of the protective allele A in the tumor tissue of patients with diffuse large B-cell lymphoma (DLBCL).MethodsTotal DNA was isolated from FFPE-samples and peripheral blood of patients with DLBCL and comparable in age and sex controls. rs78378222 genotyping was performed by the PCR-RFLP method using restriction endonuclease HindIII. Direct Sanger’s sequencing was used to confirm the presence of C allele of the rs78378222. The search for TP53 gene mutations was carried out by Sanger’s direct sequencing method, according to the IARC protocol.ResultsThe result of genotyping of 136 DNA samples from DLBCL tumor tissue suggested that frequency of the rs78378222 was 11/136 (8.1%). Rare allele C frequency was 11/272 (4.2%). A total of 5/11 DLBCL rs78378222 heterozygous samples had the heterozygosity loss in the TP53 gene. Only one of these cases was combined with TP53 gene mutations which have proven oncogenic potential—p.Arg196Gln, other four cases have not mutations in the coding regions of gene.ConclusionsAt the stages of DLBCL initiation or progression a loss of the protective allele A of rs78378222 occurs. Further efforts are needed to study possible molecular mechanisms underlying somatic alterations in DLBCL in this region of the TP53 3′-UTR as well as functional studies to illustrate how the presents of rs78378222 may affect tumor progression of lymphoma. creator: Elena N. Voropaeva creator: Yuriy L. Orlov creator: Tatiana I. Pospelova creator: Anna A. Gurageva creator: Mikhail I. Voevoda creator: Vladimir N. Maksimov creator: Olga B. Seregina creator: Maria I. Churkina uri: https://doi.org/10.7717/peerj.10335 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Voropaeva et al. title: A comparison between predetermined and self-selected approaches in resistance training: effects on power performance and psychological outcomes among elite youth athletes link: https://peerj.com/articles/10361 last-modified: 2020-11-12 description: BackgroundThe aim of this study was to investigate if choice over resistance training exercise order affects motor performance and psychological outcomes among elite youth hockey players.MethodsSeventeen elite hockey players (male, n = 14; female, n = 3, age: 15.1 ± 1.1 years) participated in this study. In the first session, individual optimum power loads were calculated in the back squat, jump squat, bench press and bench throw exercises. Then, in four counterbalanced sessions, participants completed three sets of six repetitions in the same exercises loaded with their optimum power loads. In two sessions, athletes used a self-selected order of exercises, while in other two sessions the order was predetermined. Power outputs were estimated with a linear position transducer. Fatigue and enjoyment were measured during and after the sessions using standardized questionnaires. Repeated measures analyses of variance and a paired-sample t-test were used to compare the effects between conditions.ResultsWe observed trivial to small differences between conditions in power outputs (p ≥ 0.07; ES ≤ 0.21), fatigue (p ≥ 0.42; ES ≤ 0.33) and enjoyment (p = 0.72; ES = 0.05).ConclusionGiven the comparable effects between approaches, both can be used when coaching youth athletes. Self-selecting the order of exercises based on preferences is a feasible and practical coaching option when working with youth athletes. creator: Kevin Watson creator: Israel Halperin creator: Joan Aguilera-Castells creator: Antonio Dello Iacono uri: https://doi.org/10.7717/peerj.10361 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Watson et al. title: Effects of personality on the developmental trajectories of academic burnout among Korean medical students link: https://peerj.com/articles/10362 last-modified: 2020-11-12 description: BackgroundMedical students have a high risk of burnout from tremendous academic stress, and previous cross-sectional studies have explained this risk from the personality perspective. However, the relationship between complex personality profiles and developmental trajectory of burnout has not been delineated yet.MethodsThe longitudinal changes in burnout were measured by the Maslach Burnout Inventory-Student Survey (MBI-SS) at baseline (1st week), mid-term (9th week), and end-term (17th week), and personality was examined at baseline using the Temperament and Character Inventory (TCI). Latent trajectory groups based on the MBI-SS total scores were extracted using the General Growth Mixture Model (GGMM), and significant differences in personality profiles among the latent groups were identified using profile analysis and Analysis of Variance.ResultsThree burnout trajectory groups of high-increasing (HI), moderate-increasing (MI), and low-stable (LS) were identified, and these groups had significantly different TCI subscale profiles. The HI group had the highest score in Harm-Avoidance (HA) and lowest score in Self-Directedness (SD), and the MI group had a higher score in HA and lower scores in SD and Cooperativeness (CO) when compared to the LS group with the lowest score in HA and highest scores in SD and CO.ConclusionThe current study showed that the HA, SD, and CO subscales of the TCI might explain the longitudinal development of academic burnout in medical students. Prevention of burnout and promotion of well-being in medical education concerning personality are discussed. creator: Han Chae creator: C. Robert Cloninger creator: Soo Jin Lee uri: https://doi.org/10.7717/peerj.10362 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chae et al. title: Using the FRAIL scale to compare pre-existing demographic lifestyle and medical risk factors between non-frail, pre-frail and frail older adults accessing primary health care: a cross-sectional study link: https://peerj.com/articles/10380 last-modified: 2020-11-12 description: BackgroundFew studies in the scientific literature have analyzed frailty status as an ordinal variable (non-frail, pre-frail and frail) rather than as a binary variable (frail vs non-frail). These studies have found that pre-frailty behaves differently from frailty (no ordinality in the variable). However, although the comparison between pre-frail and frail individuals is clinically relevant to understanding how to treat pre-frailty, this comparison was not performed in previous studies.Materials and MethodsA cross-sectional observational study was designed with 621 older individuals aged ≥60 years in Spain in 2017–2018, determining factors associated with a higher frailty stage (non-frail, pre-frail and frail) and undertaking this comparison, in addition to measuring non-frailty. The factors assessed through a multinominal regression model were: age, sex, living alone, recent loss of the partner, income and total comorbidities.ResultsOf the total participants, 285 were non-frail (45.9%), 210 were pre-frail (33.8%) and 126 were frail (20.3%). Compared to non-frail individuals, pre-frail individuals were older, with more comorbidities and a lower income. Compared to non-frail individuals, frail individuals were more likely to be female, older, with more comorbidities and a lower income. Compared to pre-frail individuals, frail individuals were more likely to be female, older and with more comorbidities.ConclusionComparison between the pre-frail and frail groups showed that frail persons were more likely to have a lower income, be female, older and have a higher number of comorbidities. creator: Vanessa Aznar-Tortonda creator: Antonio Palazón-Bru creator: Vicente Francisco Gil-Guillén uri: https://doi.org/10.7717/peerj.10380 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Aznar-Tortonda et al. title: The frequency of combined IFITM3 haplotype involving the reference alleles of both rs12252 and rs34481144 is in line with COVID-19 standardized mortality ratio of ethnic groups in England link: https://peerj.com/articles/10402 last-modified: 2020-11-12 description: Evidence was brought forward in England and the USA that Black, Asian, Latino and Minority Ethnic people exhibit higher mortality risk from COVID-19 than White people. While socioeconomic factors were suggested to contribute to this trend, they arguably do not explain the range of the differences observed, allowing for possible genetic implications. Almost concurrently, the analysis of a cohort in Chinese COVID-19 patients proposed an association between the severity of the disease and the presence of the minor allele of rs12252 of the Interferon-induced transmembrane protein 3 (IFITM3) gene. This SNP, together with rs34481144, are the two most studied polymorphisms of IFITM3 and have been associated in the past with increased severity in Influenza, Dengue, Ebola, and HIV viruses. IFITM3 is an immune effector protein that is pivotal for the restriction of viral replication, but also for the regulation of cytokine production. Following up on these two developments in the ongoing SARS-CoV-2 pandemic, the present study investigates a possible association between the differences in mortality of ethnic groups in England and the combined haplotypes of rs12252 and rs34481144. The respective allele frequencies were collected for 26 populations from the 1000 Genomes Project and subgroups were pooled wherever possible to create correspondences with ethnic groups in England. A significant correlation (r = 0.9687, p = 0.0003) and a striking agreement was observed between the reported Standardized Mortality Ratios and the frequency of the combined haplotype of both reference alleles, suggesting that the combination of the reference alleles of the specific SNPs may be implicated in more severe outcomes of COVID-19. This study calls for further focus on the role of IFITM3 variants in the mechanism of cellular invasion of SARS-CoV-2, their impact in COVID-19 severity and their possible implications in vaccination efficacy. creator: Dimitris Nikoloudis creator: Dimitrios Kountouras creator: Asimina Hiona uri: https://doi.org/10.7717/peerj.10402 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nikoloudis et al. title: Definition and review on a category of long non-coding RNA: Atherosclerosis-associated circulating lncRNA (ASCLncRNA) link: https://peerj.com/articles/10001 last-modified: 2020-11-11 description: Atherosclerosis (AS) is one of the most common cardiovascular system diseases which seriously affects public health in modern society. Finding potential biomarkers in the complicated pathological progression of AS is of great significance for the prevention and treatment of AS. Studies have shown that long noncoding RNAs (lncRNAs) can be widely involved in the regulation of many physiological processes, and have important roles in different stages of AS formation. LncRNAs can be secreted into the circulatory system through exosomes, microvesicles, and apoptotic bodies. Recently, increasing studies have been focused on the relationships between circulating lncRNAs and AS development. The lncRNAs in circulating blood are expected to be new non-invasive diagnostic markers for monitoring the progression of AS. We briefly reviewed the previously reported lncRNA transcripts which related to AS development and detectable in circulating blood, including ANRIL, SENCR, CoroMarker, LIPCAR, HIF1α-AS1, LncRNA H19, APPAT, KCNQ1OT1, LncPPARδ, LincRNA-p21, MALAT1, MIAT, and UCA1. Further researches and a definition of atherosclerosis-associated circulating lncRNA (ASCLncRNA) were also discussed. creator: Shanshan Lu creator: Qin Liang creator: Yanqing Huang creator: Fanming Meng creator: Junwen Liu uri: https://doi.org/10.7717/peerj.10001 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lu et al. title: The complete mitochondrial genome of Gyps coprotheres (Aves, Accipitridae, Accipitriformes): phylogenetic analysis of mitogenome among raptors link: https://peerj.com/articles/10034 last-modified: 2020-11-11 description: Three species of Old World vultures on the Asian peninsula are slowly recovering from the lethal consequences of diclofenac. At present the reason for species sensitivity to diclofenac is unknown. Furthermore, it has since been demonstrated that other Old World vultures like the Cape (Gyps coprotheres; CGV) and griffon (G. fulvus) vultures are also susceptible to diclofenac toxicity. Oddly, the New World Turkey vulture (Cathartes aura) and pied crow (Corvus albus) are not susceptible to diclofenac toxicity. As a result of the latter, we postulate an evolutionary link to toxicity. As a first step in understanding the susceptibility to diclofenac toxicity, we use the CGV as a model species for phylogenetic evaluations, by comparing the relatedness of various raptor species known to be susceptible, non-susceptible and suspected by their relationship to the Cape vulture mitogenome. This was achieved by next generation sequencing and assembly. The Cape vulture mitogenome had a genome size of 16,908 bp. The mitogenome phylogenetic analysis indicated a close evolutionary relationship between Old World vultures and other members of the Accipitridae as indicated by bootstrap value of 100% on the phylogenetic trees. Based on this, we postulate that the other species could also be sensitive to the toxic effects of diclofenac. This warrants further investigations. creator: Emmanuel Oluwasegun Adawaren creator: Morne Du Plessis creator: Essa Suleman creator: Duodane Kindler creator: Almero O. Oosthuizen creator: Lillian Mukandiwa creator: Vinny Naidoo uri: https://doi.org/10.7717/peerj.10034 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Adawaren et al. title: Fire weather effects on flammability of indigenous and invasive alien plants in coastal fynbos and thicket shrublands (Cape Floristic Region) link: https://peerj.com/articles/10161 last-modified: 2020-11-11 description: BackgroundGlobally, and in the Cape Floristic Region of South Africa, extreme fires have become more common in recent years. Such fires pose societal and ecological threats and have inter alia been attributed to climate change and modification of fuels due to alien plant invasions. Understanding the flammability of different types of indigenous and invasive alien vegetation is essential to develop fire risk prevention and mitigation strategies. We assessed the flammability of 30 species of indigenous and invasive alien plants commonly occurring in coastal fynbos and thicket shrublands in relation to varying fire weather conditions.MethodsFresh plant shoots were sampled and burnt experimentally across diverse fire weather conditions to measure flammability in relation to fire weather conditions, live fuel moisture, fuel load and vegetation grouping (fynbos, thicket and invasive alien plants). Flammability measures considered were: burn intensity, completeness of burn, time-to-ignition, and the likelihood of spontaneous ignition. We also investigated whether the drying of plant shoots (simulating drought conditions) differentially affected the flammability of vegetation groups.ResultsFire weather conditions enhanced all measures of flammability, whereas live fuel moisture reduced burn intensity and completeness of burn. Live fuel moisture was not significantly correlated with fire weather, suggesting that the mechanism through which fire weather enhances flammability is not live fuel moisture. It furthermore implies that the importance of live fuel moisture for flammability of evergreen shrublands rests on inter-specific and inter-vegetation type differences in fuel moisture, rather than short-term intra-specific fluctuation in live fuel moisture in response to weather conditions. Fuel load significantly increased burn intensity, while reducing ignitability. Although fire weather, live fuel moisture, and fuel load had significant effects on flammability measures, vegetation and species differences accounted for most of the variation. Flammability was generally highest in invasive alien plants, intermediate in fynbos, and lowest in thicket. Fynbos ignited rapidly and burnt completely, whereas thicket was slow to ignite and burnt incompletely. Invasive alien plants were slow to ignite, but burnt with the highest intensity, potentially due to volatile organic composition. The drying of samples resulted in increases in all measures of flammability that were comparable among vegetation groups. Flammability, and by implication fire risk, should thus not increase disproportionately in one vegetation group compared to another under drought conditions—unless the production of dead fuels is disproportionate among vegetation groups. Thus, we suggest that the dead:live fuel ratio is a potentially useful indicator of flammability of evergreen shrublands and that proxies for this ratio need to be investigated for incorporation into fire danger indices. creator: Samukelisiwe T. Msweli creator: Alastair J. Potts creator: Herve Fritz creator: Tineke Kraaij uri: https://doi.org/10.7717/peerj.10161 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Msweli et al. title: Chemical analysis of callus extracts from toxic and non-toxic varieties of Jatropha curcas L. link: https://peerj.com/articles/10172 last-modified: 2020-11-11 description: Jatropha curcas L. belongs to Euphorbiaceae family, and it synthesizes flavonoid and diterpene compounds that have showed antioxidant, anti-inflammatory, anticancer, antiviral, antimicrobial, antifungal and insecticide activity. Seeds of this plant accumulate phorbol esters, which are tigliane type diterpenes, reported as toxic and, depending on its concentration, toxic and non-toxic varieties has been identified. The aim of this work was to characterize the chemical profile of the extracts from seeds, leaves and callus of both varieties (toxic and non-toxic) of Jatropha curcas, to verify the presence of important compounds in dedifferentiated cells and consider the possibility of using these cultures for the massive production of metabolites. Callus induction was obtained using NAA (1.5 mg L−1) and BAP (1.5 mg L−1) after 21 d for both varieties. Thin layer chromatography analysis showed differences in compounds accumulation in callus from non-toxic variety throughout the time of culture, diterpenes showed an increase along the time, in contrast with flavonoids which decreased. Based on the results obtained through microQTOF-QII spectrometer it is suggested a higher accumulation of phorbol esters, derived from 12-deoxy-16-hydroxy-phorbol (m/z 365 [M+H]+), in callus of 38 d than those of 14 d culture, from both varieties. Unlike flavonoids accumulation, the MS chromatograms analysis allowed to suggest lower accumulation of flavonoids as the culture time progresses, in callus from both varieties. The presence of six glycosylated flavonoids is also suggested in leaf and callus extracts derived from both varieties (toxic and non-toxic), including: apigenin 6-C-α-L-arabinopyranosyl-8-C-β-D-xylopyranoside (m/z 535 [M+H]+), apigenin 4′-O-rhamnoside (m/z 417 [M+H]+), vitexin (m/z 433 [M+H]+), vitexin 4′-O-glucoside-2″-O-rhamnoside (m/z 741 [M+H]+), vicenin-2 (m/z 595 [M+H]+), and vicenin-2,6″-O-glucoside (m/z 757 [M+H]+). creator: Gerardo Leyva-Padrón creator: Pablo Emilio Vanegas-Espinoza creator: Silvia Evangelista-Lozano creator: Alma Angélica Del Villar-Martínez creator: Crescencio Bazaldúa uri: https://doi.org/10.7717/peerj.10172 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Leyva-Padrón et al. title: Variation in female reproductive tract morphology across the reproductive cycle in the zebra finch link: https://peerj.com/articles/10195 last-modified: 2020-11-11 description: BackgroundIn seasonally breeding birds, the reproductive tract undergoes a dramatic circannual cycle of recrudescence and regression, with oviduct size increasing 5–220 fold from the non-breeding to the breeding state. Opportunistically breeding birds can produce multiple clutches sequentially across an extended period in response primarily to environmental rather than seasonal cues. In the zebra finch, it has been shown that there is a significant reduction in gonadal morphology in non-breeding females. However, the scale of recrudescence and regression of reproductive tissue within a single breeding cycle is unknown and yet important to understand the cost of breeding, and the physiological readiness to breed in such flexible breeders.MethodsWe examined the reproductive tissue of breeding female zebra finches at six stages in the nesting cycle from pre-breeding to fledging offspring. We quantified the wet mass of the oviduct, the volume of the largest pre-ovulatory follicle, and the total number of pre-ovulatory follicles present on the ovary.ResultsMeasures of the female reproductive tract were highest during nesting and laying stages and declined significantly in the later stages of the breeding cycle. Importantly, we found that the mass of reproductive tissue changes as much across a single reproductive event as that previously characterized between birds categorized as breeding and non-breeding. However, the regression of the ovary is less dramatic than that seen in seasonal breeders. This could reflect low-level maintenance of reproductive tissues in opportunistic breeders, but needs to be confirmed in wild non-breeding birds. creator: Laura L. Hurley creator: Ondi L. Crino creator: Melissah Rowe creator: Simon C. Griffith uri: https://doi.org/10.7717/peerj.10195 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hurley et al. title: Cathepsin D in prawn reproductive system: its localization and function in actin degradation link: https://peerj.com/articles/10218 last-modified: 2020-11-11 description: Cathepsin D (CAT-D) is a well-known aspartic protease that serves a function as house-keeping lysosomal enzyme in all somatic cells. Its existence in reproductive tissues is highly variable, even in the somatic derived epithelial cells of reproductive tract. In Macrobrachium rosenbergii, existence of MrCAT-D and its translational product was detected in both somatic cells (Sertoli-like supporting cells) and developing spermatogenic cells as well as along accessory spermatic ducts. Specifically, MrCAT-D was localized onto the sperm surface rather than within the acrosomal matrix, as evident by similar staining pattern of anti-CAT-D on live and aldehyde fixed sperm. MrCAT-D in testicular extracts and sperm isolates showed active enzyme activities towards its specific fluorogenic substrate (MCA-Gly-Lys-Pro-Ile-Leu-Phe-Phe-Arg-Leu-Lys (Dnp)-D-Arg-NH2). MrCAT-D also exerted its function towards hydrolyzing filamentous actin, the meshwork of which is shown to be localized at the junction between germ cells and supporting cells and spermatogonia in M. rosenbergii testicular epithelium. Together, we have localized MrCAT-D transcript and its translational product in both supporting and germ cells of testis and claimed its enzymatic function towards actin degradation, which may be related to sperm release from the epithelial cell interaction. creator: Chompoonut Sukonset creator: Piyaporn Surinlert creator: Orawan Thongsum creator: Atthaboon Watthammawut creator: Monsicha Somrit creator: Jirasuda Nakeim creator: Wattana Weerachatyanukul creator: Somluk Asuvapongpatana uri: https://doi.org/10.7717/peerj.10218 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sukonset et al. title: Emerging roles of APLN and APELA in the physiology and pathology of the female reproductive system link: https://peerj.com/articles/10245 last-modified: 2020-11-11 description: APLN, APELA and their common receptor APLNR (composing the apelinergic axis) have been described in various species with extensive body distribution and multiple physiological functions. Recent studies have witnessed emerging intracellular cascades triggered by APLN and APELA which play crucial roles in female reproductive organs, including hypothalamus-pituitary-gonadal axis, ovary, oviduct, uterus and placenta. However, a comprehensive summary of APLN and APELA roles in physiology and pathology of female reproductive system has not been reported to date. In this review, we aim to concentrate on the general characteristics of APLN and APELA, as well as their specific physiological roles in female reproductive system. Meanwhile, the pathological contexts of apelinergic axis dysregulation in the obstetrics and gynecology are also summarized here, suggesting its potential prospect as a diagnostic biomarker and/or therapeutic intervention in the polycystic ovary syndrome, ovarian cancer, preeclampsia and gestational diabetes mellitus. creator: Xueying Wang creator: Xiaofei Liu creator: Zifan Song creator: Xin Shen creator: Siying Lu creator: Yan Ling creator: Haibin Kuang uri: https://doi.org/10.7717/peerj.10245 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Improving decolorization of dyes by laccase from Bacillus licheniformis by random and site-directed mutagenesis link: https://peerj.com/articles/10267 last-modified: 2020-11-11 description: BackgroundDye wastewater increases cancer risk in humans. For the treatment of dyestuffs, biodegradation has the advantages of economy, high efficiency, and environmental protection compared with traditional physical and chemical methods. Laccase is the best candidate for dye degradation because of its multiple substrates and pollution-free products.MethodsHere, we modified the laccase gene of Bacillus licheniformis by error-prone PCR and site-directed mutagenesis and expressed in E. coli. The protein was purified by His-tagged protein purification kit. We tested the enzymatic properties of wild type and mutant laccase by single factor test, and further evaluated the decolorization ability of laccase to acid violet, alphazurine A, and methyl orange by spectrophotometry.ResultsMutant laccase Lacep69and D500G were superior to wild type laccase in enzyme activity, stability, and decolorization ability. Moreover, the laccase D500G obtained by site-directed mutagenesis had higher enzyme activity in both, and the specific activity of the purified enzyme was as high as 426.13 U/mg. Also, D500G has a higher optimum temperature of 70 °C and temperature stability, while it has a more neutral pH 4.5 and pH stability. D500G had the maximum enzyme activity at a copper ion concentration of 12 mM. The results of decolorization experiments showed that D500G had a strong overall decolorization ability, with a lower decolorization rate of 18% for methyl orange and a higher decolorization rate of 78% for acid violet.ConclusionCompared with the wild type laccase, the enzyme activity of D500G was significantly increased. At the same time, it has obvious advantages in the decolorization effect of different dyes. Also, the advantages of temperature and pH stability increase its tolerance to the environment of dye wastewater. creator: Tongliang Bu creator: Rui Yang creator: YanJun Zhang creator: Yuntao Cai creator: Zizhong Tang creator: Chenglei Li creator: Qi Wu creator: Hui Chen uri: https://doi.org/10.7717/peerj.10267 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bu et al. title: Forelimb joints contribute to locomotor performance in reindeer (Rangifer tarandus) by maintaining stability and storing energy link: https://peerj.com/articles/10278 last-modified: 2020-11-11 description: Reindeer (Rangifer tarandus) have lengthy seasonal migrations on land and their feet possess excellent locomotor characteristics that can adapt to complex terrains. In this study, the kinematics and vertical ground reaction force (GRF) of reindeer forelimb joints (interphalangeal joint b, metacarpophalangeal joint c, and wrist joint d) under walk, trot 1, and trot 2 were measured using a motion tracking system and Footscan pressure plates. Significant differences among different locomotor activities were observed in the joint angles, but not in changes of the joint angles (αb, αc, αd) during the stance phase. Peak vertical GRF increased as locomotor speed increased. Net joint moment, power, and work at the forelimb joints were calculated via inverse dynamics. The peak joint moment and net joint power related to the vertical GRF increased as locomotor speed increased. The feet absorbed and generated more energy at the joints. During different locomotor activities, the contribution of work of the forelimbs changed with both gait and speed. In the stance phase, the metacarpophalangeal joint absorbed more energy than the other two joints while trotting and thus performed better in elastic energy storage. The joint angles changed very little (∼5°) from 0 to 75% of the stance phase, which reflected the stability of reindeer wrist joints. Compared to typical ungulates, reindeer toe joints are more stable and the stability and energy storage of forelimb joints contribute to locomotor performance in reindeer. creator: Guoyu Li creator: Rui Zhang creator: Dianlei Han creator: Hao Pang creator: Guolong Yu creator: Qingqiu Cao creator: Chen Wang creator: Lingxi Kong creator: Wang Chengjin creator: Wenchao Dong creator: Tao Li creator: Jianqiao Li uri: https://doi.org/10.7717/peerj.10278 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Gene signature for prognosis in comparison of pancreatic cancer patients with diabetes and non-diabetes link: https://peerj.com/articles/10297 last-modified: 2020-11-11 description: BackgroundPancreatic cancer (PC) has much weaker prognosis, which can be divided into diabetes and non-diabetes. PC patients with diabetes mellitus will have more opportunities for physical examination due to diabetes, while pancreatic cancer patients without diabetes tend to have higher risk. Identification of prognostic markers for diabetic and non-diabetic pancreatic cancer can improve the prognosis of patients with both types of pancreatic cancer.MethodsBoth types of PC patients perform differently at the clinical and molecular levels. The Cancer Genome Atlas (TCGA) is employed in this study. The gene expression of the PC with diabetes and non-diabetes is used for predicting their prognosis by LASSO (Least Absolute Shrinkage and Selection Operator) Cox regression. Furthermore, the results are validated by exchanging gene biomarker with each other and verified by the independent Gene Expression Omnibus (GEO) and the International Cancer Genome Consortium (ICGC). The prognostic index (PI) is generated by a combination of genetic biomarkers that are used to rank the patient’s risk ratio. Survival analysis is applied to test significant difference between high-risk group and low-risk group.ResultsAn integrated gene prognostic biomarker consisted by 14 low-risk genes and six high-risk genes in PC with non-diabetes. Meanwhile, and another integrated gene prognostic biomarker consisted by five low-risk genes and three high-risk genes in PC with diabetes. Therefore, the prognostic value of gene biomarker in PC with non-diabetes and diabetes are all greater than clinical traits (HR = 1.102, P-value < 0.0001; HR = 1.212, P-value < 0.0001). Gene signature in PC with non-diabetes was validated in two independent datasets.ConclusionsThe conclusion of this study indicated that the prognostic value of genetic biomarkers in PCs with non-diabetes and diabetes. The gene signature was validated in two independent databases. Therefore, this study is expected to provide a novel gene biomarker for predicting prognosis of PC with non-diabetes and diabetes and improving clinical decision. creator: Mingjun Yang creator: Boni Song creator: Juxiang Liu creator: Zhitong Bing creator: Yonggang Wang creator: Linmiao Yu uri: https://doi.org/10.7717/peerj.10297 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Development and validation of Egyptian developmental screening chart for children from birth up to 30 months link: https://peerj.com/articles/10301 last-modified: 2020-11-11 description: BackgroundDetecting developmental delay in children is an ongoing world commitment, especially for those below three years. To accurately assess the development of children; a culturally appropriate screening tool must be used. Egypt lacks such tool and multiple studies have shown that western tools are not suitable in other cultures.ObjectivesTo develop and validate an easy, rapid, culturally appropriate and applicable screening chart for early detection of developmental delay among Egyptian children from birth up to 30 months and develop a Z-score chart for motor and mental development follow up based on our Egyptian screening chart.MethodsA cross sectional randomized study was carried out on 1503 Egyptian children of both genders aged from birth up to 30 months assumed to have normal development according to the inclusion and exclusion criteria. They were selected from vaccination centers and well-baby clinics. Developmental milestones from Baroda development screening test (BDST) were applied on them after items were translated and adapted to Egyptian culture. Egyptian children developmental milestones scores were analyzed and carefully prepared in tables and charts. A 97% pass level of developmental achievements represents the threshold below which children are considered delayed. A Z-score chart for motor and mental development follow up was designed by calculating each age group achievement. The developed Egyptian developmental screening chart (EDSC) was validated against Ages and Stages Questionnaires (ASQ-3) as a reference standard in another different sample of 337 children in different age groups.ResultsThe developed EDSC is represented in a chart format with two curves 50% and 97% pass level. Children considered delayed when the score below 97% pass level. Results revealed a statistically significant difference between EDSC and BDST at 50% and 97% pass levels. A Z-score chart for motor and mental development follow up was designed by calculating each age group achievement. EDSC sensitivity and specificity were calculated 84.38 (95% CI [67.21%–94.72%]) and 98.36 (95% CI [96.22%–99.47%]) respectively with an overall test accuracy 97.03 (95% CI [94.61%–98.57%]) (p ≤ .001). Agreement between EDSC and ASQ-3 was high (kappa score was 0.827) with negative and positive agreement 98.36 and 84.38, respectively.ConclusionsExtensive revision of the BDST was needed in order to create and validate a more culturally appropriate Egyptian screening chart. This is the first study to create and validate an Egyptian-specific screening tool, to be rapid and easy to use in Egypt for early detection of developmental delay and enabling early intervention practices. A Z-score curve is reliable for follow up motor and mental development by calculating each age group achievement. creator: Ali M. El Shafie creator: Zein A.L. Omar creator: Mai M. Bashir creator: Sorour F. Mahmoud creator: Elsayedamr M. Basma creator: Ahmed E. Hussein creator: Alaa Mosad Mostafa creator: Wael A. Bahbah uri: https://doi.org/10.7717/peerj.10301 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 El Shafie et al. title: Maternal sitagliptin treatment attenuates offspring glucose metabolism and intestinal proinflammatory cytokines IL-6 and TNF-α expression in male rats link: https://peerj.com/articles/10310 last-modified: 2020-11-11 description: Increasing evidence shows that maternal overnutrition may increase the risk of diabetes in offspring. We hypothesized that maternal sitagliptin intervention may improve glucose intolerance through gut targeting. Female Sprague-Dawley (SD) rats were fed a normal diet (ND) or a high-fat diet (HFD) for 4 weeks before mating. ND pregnant rats were divided into two subgroups: ND group (ND alone) and the ND-sitagliptin group (ND combined with 10 mg/kg/day sitagliptin treatment). HFD pregnant rats were randomized to one of two groups: HFD group (HFD alone) and the HFD-sitagliptin group (HFD combined with 10 mg/kg/day sitagliptin treatment) during pregnancy and lactation. Glucose metabolism was assessed in offspring at weaning. Intestinal gene expression levels were investigated. Maternal sitagliptin intervention moderated glucose intolerance and insulin resistance in male pups. Moreover, maternal sitagliptin treatment inhibited offspring disordered intestinal expression of proinflammatory markers, including interleukin-6 (Il6), ll1b, and tumor necrosis factor (Tnf), at weaning and reduced intestinal IL-6, TNF-α expression by immunohistochemical staining and serum IL-6, TNF-α levels. However, maternal sitagliptin intervention did not affect offspring serum anti-inflammatory cytokine IL-10 level. Our results are the first to show that maternal sitagliptin intervention moderated glucose metabolism in male offspring. It may be involved with moderating intestinal IL-6 and TNF-α expression in male rat offspring. creator: Qian Zhang creator: Xinhua Xiao creator: Jia Zheng creator: Ming Li creator: Miao Yu creator: Fan Ping creator: Tong Wang creator: Xiaojing Wang uri: https://doi.org/10.7717/peerj.10310 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: High ecological resilience of the sea fan Gorgonia ventalina during two severe hurricanes link: https://peerj.com/articles/10315 last-modified: 2020-11-11 description: Since about the turn of the millennium, octocorals have been increasing in abundance on Caribbean reefs. The mechanisms underlying this trend have not been resolved, but the emergent species assemblage appears to be more resilient than the scleractinians they are replacing. The sea fan Gorgonia ventalina is an iconic species in the contemporary octocoral fauna, and here its population dynamics are described from St. John, US Virgin Islands, from 2013 to 2019. Mean densities of G. ventalina at Yawzi Point (9-m depth) varied from 1.4–1.5 colonies m−2, and their mean heights from 24–30 cm; nearby at Tektite (14-m depth), they varied from 0.6–0.8 colonies m−2 and from 25–33 cm. These reefs were impacted by two Category 5 hurricanes in 2017, but neither the density of G. ventalina, the density of their recruits (< 5-cm tall), nor the height of colonies, differed among years, although growth was depressed after the hurricanes. Nevertheless, at Tektite, colony height trended upwards over time, in part because colonies 10.1–20 cm tall were reduced in abundance after the hurricanes. These trends were sustained without density-associated effects mediating recruitment or self-thinning of adults. The dynamics of G. ventalina over seven years reveals the high resilience of this species that will contribute to the persistence of octocorals as a dominant state on Caribbean reefs. creator: Peter J. Edmunds uri: https://doi.org/10.7717/peerj.10315 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Edmunds title: Age relationships with telomere length, body weight and body length in wild dugong (Dugong dugon) link: https://peerj.com/articles/10319 last-modified: 2020-11-11 description: The ability to estimate age and determine the growth status of free-ranging dugongs (Dugong dugon) is vital to providing insight into the basic biology of this endangered species. Currently, age estimation in dugong carcasses relies on counting dentin growth layer groups (GLGs) in tusks, but a disadvantage is they need to be intact. We explored whether measures of telomere length could be used as an alternative approach to age estimation in dugongs given that in other species, telomere length and age are inversely related. In this study, relative telomere length (rTL) was measured by qPCR in skin samples from 24 dugongs of varying ages determined by counts of GLGs. In addition, relationships between age by GLG counts and body weight and length and were examined. Our findings indicate that age estimated by GLGs was negatively correlated with telomere length using the logistic formula with a rate of telomere attrition of approximately 0.036 rTL/year between the ages of 5–20 years. By comparison, both body weight and length were positively correlated with GLG-based age, with growth rates of ~8.8 kg/year for weight and ~3.58 cm/year for length, respectively. After that, growth rates slowed substantially and then plateaued. The results suggest that physical maturity in dugongs occurs at 20 years of age and that measures of rTL might serve as a tool for age estimation in dugongs, living and deceased. creator: Phaothep Cherdsukjai creator: Kittisak Buddhachat creator: Janine Brown creator: Manthanee Kaewkool creator: Anocha Poommouang creator: Patcharaporn Kaewmong creator: Kongkiat Kittiwattanawong creator: Korakot Nganvongpanit uri: https://doi.org/10.7717/peerj.10319 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cherdsukjai et al. title: An in vitro ovarian explant culture system to examine sex change in a hermaphroditic fish link: https://peerj.com/articles/10323 last-modified: 2020-11-11 description: Many teleost fishes undergo natural sex change, and elucidating the physiological and molecular controls of this process offers unique opportunities not only to develop methods of controlling sex in aquaculture settings, but to better understand vertebrate sexual development more broadly. Induction of sex change in some sequentially hermaphroditic or gonochoristic fish can be achieved in vivo through social manipulation, inhibition of aromatase activity, or steroid treatment. However, the induction of sex change in vitro has been largely unexplored. In this study, we established an in vitro culture system for ovarian explants in serum-free medium for a model sequential hermaphrodite, the New Zealand spotty wrasse (Notolabrus celidotus). This culture technique enabled evaluating the effect of various treatments with 17β-estradiol (E2), 11-ketotestosterone (11KT) or cortisol (CORT) on spotty wrasse ovarian architecture for 21 days. A quantitative approach to measuring the degree of ovarian atresia within histological images was also developed, using pixel-based machine learning software. Ovarian atresia likely due to culture was observed across all treatments including no-hormone controls, but was minimised with treatment of at least 10 ng/mL E2. Neither 11KT nor CORT administration induced proliferation of spermatogonia (i.e., sex change) in the cultured ovaries indicating culture beyond 21 days may be needed to induce sex change in vitro. The in vitro gonadal culture and analysis systems established here enable future studies investigating the paracrine role of sex steroids, glucocorticoids and a variety of other factors during gonadal sex change in fish. creator: Alexander Goikoetxea creator: Erin L. Damsteegt creator: Erica V. Todd creator: Andrew McNaughton creator: Neil J. Gemmell creator: P. Mark Lokman uri: https://doi.org/10.7717/peerj.10323 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Goikoetxea et al. title: Deregulation of lysophosphatidic acid metabolism in oral cancer promotes cell migration via the up-regulation of COX-2 link: https://peerj.com/articles/10328 last-modified: 2020-11-11 description: Oral squamous cell carcinoma (OSCC) is the sixth most common cancer worldwide and accounts for 300,000 new cases yearly. The five-year survival rate is approximately 50% and the major challenges to improving patient prognosis include late presentation, treatment resistance, second primary tumours and the lack of targeted therapies. Therefore, there is a compelling need to develop novel therapeutic strategies. In this study, we have examined the effect of lysophosphatidic acid (LPA) on OSCC cell migration, invasion and response to radiation, and investigated the contribution of cyclooxygenase-2 (COX-2) in mediating the tumour promoting effects of LPA. Using the TCGA data set, we show that the expression of the lipid phosphate phosphatases (LPP), LPP1 and LPP3, was significantly down-regulated in OSCC tissues. There was no significant difference in the expression of the ENPP2 gene, which encodes for the enzyme autotaxin (ATX) that produces LPA, between OSCCs and control tissues but ENPP2 levels were elevated in a subgroup of OSCCs. To explore the phenotypic effects of LPA, we treated OSCC cell lines with LPA and showed that the lipid enhanced migration and invasion as well as suppressed the response of the cells to irradiation. We also show that LPA increased COX-2 mRNA and protein levels in OSCC cell lines and inhibition of COX-2 activity with the COX-2 inhibitor, NS398, attenuated LPA-induced OSCC cell migration. Collectively, our data show for the first time that COX-2 mediates some of the pro-tumorigenic effects of LPA in OSCC and identifies the ATX-LPP-LPA-COX-2 pathway as a potential therapeutic target for this disease. creator: Mariati Abdul Rahman creator: May Leng Tan creator: Steven P. Johnson creator: Robert J. Hollows creator: Wen Lin Chai creator: Jason P. Mansell creator: Lee Fah Yap creator: Ian C. Paterson uri: https://doi.org/10.7717/peerj.10328 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abdul Rahman et al. title: Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci link: https://peerj.com/articles/10327 last-modified: 2020-11-11 description: Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies. creator: Ricardo M. Landínez-García creator: Juan Carlos Narváez creator: Edna J. Márquez uri: https://doi.org/10.7717/peerj.10327 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Landínez-García et al. title: A forecast model for prevention of foodborne outbreaks of non-typhoidal salmonellosis link: https://peerj.com/articles/10009 last-modified: 2020-11-10 description: BackgroundThis work presents a forecast model for non-typhoidal salmonellosis outbreaks.MethodThis forecast model is based on fitted values of multivariate regression time series that consider diagnosis and estimation of different parameters, through a very flexible statistical treatment called generalized auto-regressive and moving average models (GSARIMA).ResultsThe forecast model was validated by analyzing the cases of Salmonella enterica serovar Enteritidis in Sydney Australia (2014–2016), the environmental conditions and the consumption of high-risk food as predictive variables.ConclusionsThe prediction of cases of Salmonella enterica serovar Enteritidis infections are included in a forecast model based on fitted values of time series modeled by GSARIMA, for an early alert of future outbreaks caused by this pathogen, and associated to high-risk food. In this context, the decision makers in the epidemiology field can led to preventive actions using the proposed model. creator: Fernando Rojas creator: Claudia Ibacache-Quiroga uri: https://doi.org/10.7717/peerj.10009 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rojas and Ibacache-Quiroga title: Spectroscopic and electrochemical study of interactions between DNA and different salts of 1,4-dihydropyridine AV-153 link: https://peerj.com/articles/10061 last-modified: 2020-11-10 description: 1,4-dihydropyridines (1,4-DHP) possess important biochemical and pharmacological properties, including antimutagenic and DNA-binding activity. The latter activity was first described for water-soluble 1,4-DHP with carboxylic group in position 4, the sodium salt of the 1,4-DHP derivative AV-153 among others. Some data show the modification of physicochemical properties and biological activities of organic compounds by metal ions that form the salts. We demonstrated the different affinity to DNA and DNA-protecting capacity of AV-153 salts, depending on the salt-forming ion (Na, K, Li, Rb, Ca, Mg). This study aimed to use different approaches to collate data on the DNA-binding mode of AV-153-Na and five other AV-153 salts. All the AV-153 salts in this study quenched the ethidium bromide and DNA complex fluorescence, which points to an intercalation binding mode. For some of them, the intercalation binding was confirmed using cyclic voltammetry and circular dichroism spectroscopy. It was shown that in vitro all AV-153 salts can interact with four DNA bases. The FTIR spectroscopy data showed the interaction of AV-153 salts with both DNA bases and phosphate groups. A preference for base interaction was observed as the AV-153 salts interacted mostly with G and C bases. However, the highest differences were detected in the spectral region assigned to phosphate groups, which might indicate either conformational changes of DNA molecule (B form to A or H form) or partial denaturation of the molecule. According to the UV/VIS spectroscopy data, the salts also interact with the human telomere repeat, both in guanine quadruplex (G4) and single-stranded form; Na and K salts manifested higher affinity to G4, Li and Rb –to single-stranded DNA. creator: Elina Leonova creator: Karlis Shvirksts creator: Vitalijs Borisovs creator: Edgars Smelovs creator: Jelizaveta Sokolovska creator: Egils Bisenieks creator: Gunars Duburs creator: Mara Grube creator: Nikolajs Sjakste uri: https://doi.org/10.7717/peerj.10061 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Leonova et al. title: A new genus of oryzomyine rodents (Cricetidae, Sigmodontinae) with three new species from montane cloud forests, western Andean cordillera of Colombia and Ecuador link: https://peerj.com/articles/10247 last-modified: 2020-11-10 description: The Andean cloud forests of western Colombia and Ecuador are home to several endemic mammals; members of the Oryzomyini, the largest Sigmodontinae tribe, are extensively represented in the region. However, our knowledge about this diversity is still incomplete, as evidenced by several new taxa that have been described in recent years. Extensive field work in two protected areas enclosing remnants of Chocó montane forest recovered a high diversity of small mammals. Among them, a medium-sized oryzomyine is here described as a new genus having at least three new species, two of them are named and diagnosed. Although externally similar to members of the genera Nephelomys and Tanyuromys, the new genus has a unique molar pattern within the tribe, being characterized by a noticeable degree of hypsodonty, simplification, lamination, and third molar compression. A phylogeny based on a combination of molecular markers, including nuclear and mitochondrial genes, and morphological data recovered the new genus as sister to Mindomys, and sequentially to Nephelomys. The new genus seems to be another example of a sigmodontine rodent unique to the Chocó biogeographic region. Its type species inhabits cloud forest between 1,600 and 2,300 m in northernmost Ecuador (Carchi Province); a second species is restricted to lower montane forest, 1,200 m, in northern Ecuador (Imbabura Province); a third putative species, here highlighted exclusively by molecular evidence from one immature specimen, is recorded in the montane forest of Reserva Otonga, northern Ecuador (Cotopaxi Province). Finally, the new genus is also recorded in southernmost Colombia (Nariño Department), probably represented there also by a new species. These species are spatially separated by deep river canyons through Andean forests, resulting in marked environmental discontinuities. Unfortunately, Colombian and Ecuadorian Pacific cloud forests are under rapid anthropic transformation. Although the populations of the type species are moderately abundant and occur in protected areas, the other two persist in threatened forest fragments. creator: Jorge Brito creator: Claudia Koch creator: Alexandre R. Percequillo creator: Nicolás Tinoco creator: Marcelo Weksler creator: C. Miguel Pinto creator: Ulyses F. J. Pardiñas uri: https://doi.org/10.7717/peerj.10247 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Brito et al. title: Genetic loci determining potato starch yield and granule morphology revealed by genome-wide association study (GWAS) link: https://peerj.com/articles/10286 last-modified: 2020-11-10 description: BackgroundIt is well-documented that (bio)chemical reaction capacity of raw potato starch depends on crystallinity, morphology and other chemical and physical properties of starch granules, and these properties are closely related to gene functions. Preparative yield, amylose/amylopectin content, and phosphorylation of potato tuber starch are starch-related traits studied at the genetic level. In this paper, we perform a genome-wide association study using a 22K SNP potato array to identify for the first time genomic regions associated with starch granule morphology and to increase number of known genome loci associated with potato starch yield.MethodsA set of 90 potato (Solanum tuberosum L.) varieties from the ICG “GenAgro” collection (Novosibirsk, Russia) was harvested, 90 samples of raw tuber starch were obtained, and DNA samples were isolated from the skin of the tubers. Morphology of potato tuber starch granules was evaluated by optical microscopy and subsequent computer image analysis. A set of 15,214 scorable SNPs was used for the genome-wide analysis. In total, 53 SNPs were found to be significantly associated with potato starch morphology traits (aspect ratio, roundness, circularity, and the first bicomponent) and starch yield-related traits.ResultsA total of 53 novel SNPs was identified on potato chromosomes 1, 2, 4, 5, 6, 7, 9, 11 and 12; these SNPs are associated with tuber starch preparative yield and granule morphology. Eight SNPs are situated close to each other on the chromosome 1 and 19 SNPs—on the chromosome 2, forming two DNA regions—potential QTLs, regulating aspect ratio and roundness of the starch granules. Thirty-seven of 53 SNPs are located in protein-coding regions. There are indications that granule shape may depend on starch phosphorylation processes. The GWD gene, which is known to regulate starch phosphorylation—dephosphorylation, participates in the regulation of a number of morphological traits, rather than one specific trait. Some significant SNPs are associated with membrane and plastid proteins, as well as DNA transcription and binding regulators. Other SNPs are related to low-molecular-weight metabolite synthesis, and may be associated with flavonoid biosynthesis and circadian rhythm-related metabolic processes. The preparative yield of tuber starch is a polygenic trait that is associated with a number of SNPs from various regions and chromosomes in the potato genome. creator: Vadim K. Khlestkin creator: Tatyana V. Erst creator: Irina V. Rozanova creator: Vadim M. Efimov creator: Elena K. Khlestkina uri: https://doi.org/10.7717/peerj.10286 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Khlestkin et al. title: Differential effects of cotreatment of the antibiotic rifampin with host-directed therapeutics in reducing intracellular Staphylococcus aureus infection link: https://peerj.com/articles/10330 last-modified: 2020-11-10 description: BackgroundChronic infection by Staphylococcus aureus drives pathogenesis in important clinical settings, such as recurrent pulmonary infection in cystic fibrosis and relapsing infection in osteomyelitis. Treatment options for intracellular S. aureus infection are limited. Rifampin, a lipophilic antibiotic, readily penetrates host cell membranes, yet monotherapy is associated with rapid antibiotic resistance and development of severe adverse events. Antibiotic cotreatment can reduce this progression, yet efficacy diminishes as antibiotic resistance develops. ML141 and simvastatin inhibit S. aureus invasion through host-directed rather than bactericidal mechanisms.ObjectiveTo determine whether cotreatment of ML141 or of simvastatin with rifampin would enhance rifampin efficacy.MethodsAssays to assess host cell invasion, host cell viability, host cell membrane permeability, and bactericidal activity were performed using the human embryonic kidney (HEK) 293-A cell line infected with S. aureus (29213) and treated with vehicle control, simvastatin, ML141, rifampin, or cotreatment of simvastatin or ML141 with rifampin.ResultsWe found cotreatment of ML141 with rifampin reduced intracellular infection nearly 85% when compared to the no treatment control. This decrease more than doubled the average 40% reduction in response to rifampin monotherapy. In contrast, cotreatment of simvastatin with rifampin failed to improve rifampin efficacy. Also, in contrast to ML141, simvastatin increased propidium iodide (PI) positive cells, from an average of 10% in control HEK 293-A cells to nearly 20% in simvastatin-treated cells, indicating an increase in host cell membrane permeability. The simvastatin-induced increase was reversed to control levels by cotreatment of simvastatin with rifampin.ConclusionTaken together, rifampin efficacy is increased through host-directed inhibition of S. aureus invasion by ML141, while efficacy is not increased by simvastatin. Considerations regarding novel therapeutic approaches may be dependent on underlying differences in pharmacology. creator: Melissa D. Evans creator: Robert Sammelson creator: Susan McDowell uri: https://doi.org/10.7717/peerj.10330 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Evans et al. title: Hypoxia and metabolic inhibitors alter the intracellular ATP:ADP ratio and membrane potential in human coronary artery smooth muscle cells link: https://peerj.com/articles/10344 last-modified: 2020-11-10 description: ATP-sensitive potassium (KATP) channels couple cellular metabolism to excitability, making them ideal candidate sensors for hypoxic vasodilation. However, it is still unknown whether cellular nucleotide levels are affected sufficiently to activate vascular KATP channels during hypoxia. To address this fundamental issue, we measured changes in the intracellular ATP:ADP ratio using the biosensors Perceval/PercevalHR, and membrane potential using the fluorescent probe DiBAC4(3) in human coronary artery smooth muscle cells (HCASMCs). ATP:ADP ratio was significantly reduced by exposure to hypoxia. Application of metabolic inhibitors for oxidative phosphorylation also reduced ATP:ADP ratio. Hyperpolarization caused by inhibiting oxidative phosphorylation was blocked by either 10 µM glibenclamide or 60 mM K+. Hyperpolarization caused by hypoxia was abolished by 60 mM K+ but not by individual K+ channel inhibitors. Taken together, these results suggest hypoxia causes hyperpolarization in part by modulating K+ channels in SMCs. creator: Mingming Yang creator: Caroline Dart creator: Tomoko Kamishima creator: John M. Quayle uri: https://doi.org/10.7717/peerj.10344 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Exogenous Fe2+ alleviated the toxicity of CuO nanoparticles on Pseudomonas tolaasii Y-11 under different nitrogen sources link: https://peerj.com/articles/10351 last-modified: 2020-11-10 description: Extensive use of CuO nanoparticles (CuO-NPs ) inevitably leads to their accumulation in wastewater and toxicity to microorganisms that effectively treat nitrogen pollution. Due to the effects of different mediums, the sources of CuO-NPs-induced toxicity to microorganisms and methods to mitigating the toxicity are still unclear. In this study, CuO-NPs were found to impact the nitrate reduction of Pseudomonas tolaasii Y-11 mainly through the action of NPs themselves while inhibiting the ammonium transformation of strain Y-11 through releasing Cu2+. As the content of CuO-NPs increased from 0 to 20 mg/L, the removal efficiency of NO3− and NH4+ decreased from 42.29% and 29.83% to 2.05% and 2.33%, respectively. Exogenous Fe2+ significantly promoted the aggregation of CuO-NPs, reduced the possibility of contact with bacteria, and slowed down the damage of CuO-NPs to strain Y-11. When 0.01 mol/L Fe2+ was added to 0, 1, 5, 10 and 20 mg/L CuO-NPs treatment, the removal efficiencies of NO3- were 69.77%, 88.93%, 80.51%, 36.17% and 2.47%, respectively; the removal efficiencies of NH4+ were 55.95%, 96.71%, 38.11%, 20.71% and 7.43%, respectively. This study provides a method for mitigating the toxicity of CuO-NPs on functional microorganisms. creator: Yuran Yang creator: Can Zhang creator: Xuejiao Huang creator: Xuwei Gui creator: Yifang Luo creator: Zhenlun Li uri: https://doi.org/10.7717/peerj.10351 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Effects of rhodioloside on the neurological functions of rats with total cerebral ischemia/reperfusion and cone neuron injury in the hippocampal CA1 region link: https://peerj.com/articles/10056 last-modified: 2020-11-09 description: Rhodioloside, the main effective constituent of Rhodiola rosea, demonstrates antiaging and antioxidative stress functions and inhibits calcium overloading in cells. These functions imply that rhodioloside may exert protective effects on hippocampal neurons after total cerebral ischemia/reperfusion injury. In this study, male Wistar rat models of total cerebral ischemia were constructed and randomly divided into four groups: sham-operation, ischemia/reperfusion, low-dosage, and high-dosage groups. The result showed that rhodioloside treatment reduced the apoptosis rates of hippocampal neurons and the histological grades of cone cells in the hippocampal CA1 region, but neuronal density was significantly increased. Besides, the protein expressions of Bcl-2/Bax and p53 were measured and found Bcl-2/Bax was increased and p53 protein level was reduced. Therefore, rhodioloside might have protective effects on rats with ischemia/reperfusion brain injury. creator: Yue Zhang creator: Xinqing Guo creator: Guohua Wang creator: Jidan Liu creator: Peiyu Liang creator: Huan Wang creator: Chunyan Zhu creator: Qiong Wu uri: https://doi.org/10.7717/peerj.10056 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: The land flatworm Amaga expatria (Geoplanidae) in Guadeloupe and Martinique: new reports and molecular characterization including complete mitogenome link: https://peerj.com/articles/10098 last-modified: 2020-11-09 description: BackgroundThe land flatworm Amaga expatriaJones & Sterrer, 2005 (Geoplanidae) was described from two specimens collected in Bermuda in 1963 and 1988 and not recorded since.MethodsOn the basis of a citizen science project, we received observations in the field, photographs and specimens from non-professionals and local scientists in Martinique and Guadeloupe. We barcoded (COI) specimens from both islands and studied the histology of the reproductive organs of one specimen. Based on Next Generation Sequencing, we obtained the complete mitogenome of A. expatria and some information on its prey from contaminating DNA.ResultsWe add records from 2006 to 2019 in two French islands of the Caribbean arc, Guadeloupe (six records) and Martinique (14 records), based on photographs obtained from citizen science and specimens examined. A specimen from Martinique was studied for histology of the copulatory organs and barcoded for the COI gene; its anatomy was similar to the holotype, therefore confirming species identification. The COI gene was identical for several specimens from Martinique and Guadeloupe and differed from the closest species by more than 10%; molecular characterisation of the species is thus possible by standard molecular barcoding techniques. The mitogenome is 14,962 bp in length and contains 12 protein coding genes, two rRNA genes and 22 tRNA genes; for two protein genes it was not possible to determine the start codon. The mitogenome was compared with the few available mitogenomes from geoplanids and the most similar was Obama nungara, a species from South America. An analysis of contaminating DNA in the digestive system suggests that A. expatria preys on terrestrial molluscs, and citizen science observations in the field suggest that prey include molluscs and earthworms; the species thus could be a threat to biodiversity of soil animals in the Caribbean. creator: Jean-Lou Justine creator: Delphine Gey creator: Jessica Thévenot creator: Romain Gastineau creator: Hugh D. Jones uri: https://doi.org/10.7717/peerj.10098 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Justine et al. title: Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats link: https://peerj.com/articles/10217 last-modified: 2020-11-09 description: Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database. creator: Xuefeng Fu creator: Bingru Zhao creator: Kechuan Tian creator: Yujiang Wu creator: Langda Suo creator: Gui Ba creator: Deji Ciren creator: Ji De creator: Cuoji Awang creator: Shuangbao Gun creator: Bohui Yang uri: https://doi.org/10.7717/peerj.10217 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Fu et al. title: Loading history changes the morphology and compressive force-induced expression of receptor activator of nuclear factor kappa B ligand/osteoprotegerin in MLO-Y4 osteocytes link: https://peerj.com/articles/10244 last-modified: 2020-11-09 description: BackgroundIn this study, we investigated the effect of the mechanical loading history on the expression of receptor activator of nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG) in MLO-Y4 osteocyte-like cells.MethodsThree hours after MLO-Y4 osteocytes were seeded, a continuous compressive force (CCF) of 31 dynes/cm2 with or without additional CCF (32 dynes/cm2) was loaded onto the osteocytes. After 36 h, the additional CCF (loading history) was removed for a recovery period of 10 h. The expression of RANKL, OPG, RANKL/OPG ratio, cell numbers, viability and morphology were time-dependently examined at 0, 3, 6 and 10 h. Then, the same additional CCF was applied again for 1 h to all osteocytes with or without the gap junction inhibitor to examine the expression of RANKL, OPG, the RANKL/OPG ratio and other genes that essential to characterize the phenotype of MLO-Y4 cells. Fluorescence recovery after photobleaching technique was also applied to test the differences of gap-junctional intercellular communications (GJIC) among MLO-Y4 cells.ResultsThe expression of RANKL and OPG by MLO-Y4 osteocytes without a loading history was dramatically decreased and increased, respectively, in response to the 1-h loading of additional weight. However, the expression of RANKL, OPG and the RANKL/OPG ratio were maintained at the same level as in the control group in the MLO-Y4 osteocytes with a loading history but without gap junction inhibitor treatment. Treatment of loading history significantly changed the capacity of GJIC and protein expression of connexin 43 (Cx43) but not the mRNA expression of Cx43. No significant difference was observed in the cell number or viability between the MLO-Y4 osteocyte-like cells with and without a loading history or among different time checkpoints during the recovery period. The cell morphology showed significant changes and was correlated with the expression of OPG, Gja1 and Dmp1 during the recovery period.ConclusionOur findings indicated that the compressive force-induced changes in the RANKL/OPG expression could be habituated within at least 11 h by 36-h CCF exposure. GJIC and cell morphology may play roles in response to loading history in MLO-Y4 osteocyte-like cells. creator: Ziyi Wang creator: Yao Weng creator: Yoshihito Ishihara creator: Naoya Odagaki creator: Ei Ei Hsu Hlaing creator: Takashi Izawa creator: Hirohiko Okamura creator: Hiroshi Kamioka uri: https://doi.org/10.7717/peerj.10244 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information link: https://peerj.com/articles/10264 last-modified: 2020-11-09 description: The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a breadth of plant biology inquiries. Data and code are available at GitHub: https://github.com/eporetsky/MutRank. creator: Elly Poretsky creator: Alisa Huffaker uri: https://doi.org/10.7717/peerj.10264 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Poretsky and Huffaker title: Effects of substrate and water depth of a eutrophic pond on the physiological status of a submerged plant, Vallisneria natans link: https://peerj.com/articles/10273 last-modified: 2020-11-09 description: Effects of substrate and water depth on the physiological status of a submerged macrophyte, Vallisneria natans (Lour.) H. Hara, were determined by measuring biomarkers in leaves and roots, to understand factors limiting the re-establishment of V. natans in urban eutrophic ponds. Ramets of V. natans were grown in the laboratory using aquaria containing water and bottom mud from a eutrophic pond and maintained under sufficient light in an incubator. The growth and chlorophyll-a (Chl-a) content of leaves were greater in aquaria with mud than in those with sand, which was used as the reference substrate. The contents of a peroxidation product (malondialdehyde (MDA)) and three antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD)) in leaves and roots, used as stress biomarkers, changed during the experiment, although differences in these contents between mud and sand were not consistent across the experimental days. To control water depth in the field, ramets of V. natans were grown in cages with different substrates (mud and sand) installed at different depths (0.5, 1.2, and 2.0 m) in the pond. The mean light quantum during the experiment decreased with increasing depth, from 79.3 μmol/m2 s at 0.5 m to 7.9 μmol/m2 s at 2.0 m. The Chl-a content in leaves decreased, whereas the MDA content in both leaves and roots increased with increasing water depth. All enzyme activities increased at the beginning and then decreased to the end of the experiment at 2.0 m depth, suggesting deterioration of enzyme activities due to depth-related stress. The MDA content and CAT activity were higher for sand than for mud, whereas the difference in the growth and the leaf Chl-a content between substrates remained unclear in the pond. On comparing the laboratory and field experiments, the leaf Chl-a content was found to be lower and the MDA content and enzyme activities exhibited sharp increase for ramets grown in the pond, even at 0.5 m depth, when compared with those grown in the aquaria. Our results suggest that the bottom mud of the pond is not the major limiting factor in the re-establishment of V. natans. Because water depth and light attenuation exerted strong stress on V. natans, shallow areas or measures to improve water transparency are required to promote the introduction of V. natans in eutrophic ponds for successful restoration in urban areas. creator: Aimin Hao creator: Sohei Kobayashi creator: Huilin Huang creator: Qi Mi creator: Yasushi Iseri uri: https://doi.org/10.7717/peerj.10273 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hao et al. title: The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species link: https://peerj.com/articles/10274 last-modified: 2020-11-09 description: BackgroundTwo endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies.MethodsThe genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated.ResultsThe sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species. creator: Mirella Pupo Santos creator: João V.S. Rabelo Araujo creator: Arthur V. Sant’anna Lopes creator: Julio Cesar Fiorio Vettorazzi creator: Marcela Santana Bastos Boechat creator: Fernanda AbreuSantana Arêdes creator: Naiara Viana Campos creator: Emiliano Nicolas Calderon creator: Fernando M. Gomes Santos creator: Tais Nogueira Fernandes creator: Rodrigo Nunes da Fonseca creator: Messias Gonzaga Pereira creator: Guilherme Oliveira creator: Daniel Basilio Zandonadi creator: RodrigoLemes Martins creator: Francisco de Assis Esteves uri: https://doi.org/10.7717/peerj.10274 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Santos et al. title: Foraging efficiency, social status and body condition in group-living horses and ponies link: https://peerj.com/articles/10305 last-modified: 2020-11-09 description: Individual animals experience different costs and benefits associated with group living, which may impact on their foraging efficiency in ways not yet well specified. This study investigated associations between social dominance, body condition and interruptions to foraging behaviour in a cross-sectional study of 116 domestic horses and ponies, kept in 20 discrete herds. Social dominance was measured for each individual alongside observations of winter foraging behaviour. During bouts of foraging, the duration, frequency and category (vigilance, movement, social displacements given and received, scratching and startle responses) of interruptions were recorded, with total interruption time taken as a proxy measure of foraging efficiency. Total foraging time was not influenced by body condition or social dominance. Body condition was associated with social dominance, but more strongly associated with foraging efficiency. Specifically, lower body condition was associated with greater vigilance. This demonstrates that factors other than social dominance can result in stable differences in winter body condition. creator: Sarah L. Giles creator: Pat Harris creator: Sean A. Rands creator: Christine J. Nicol uri: https://doi.org/10.7717/peerj.10305 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Giles et al. title: COVID-19 infection: Disease detection and mobile technology link: https://peerj.com/articles/10345 last-modified: 2020-11-09 description: BackgroundA pneumonia outbreak of unknown etiology took place in Wuhan, Hubei province, China and spread quickly worldwide in December 2019. Chinese Center for Disease Control and Prevention identified a novel beta-coronavirus called 2019-nCoV, now officially known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) that is responsible for the pandemic. The coronavirus COVID-19 affected 215 countries and territories around the world and more than 99 hundred thousand people at present (Nature Nanotechnology, 2020). At present, there are no specific vaccines or treatments available for COVID-19. However, there are many ongoing clinical trials evaluating potential treatments. At this time the experts recommend precautions such as social distancing, hand washing, and wearing face masks to reduce disease transmission. This review article aims to improve the readers’ awareness towards the important role of mobile technology for SARS-CoV-2.MethodologyTo achieve this objective, we performed a COVID-19 literature review from various sources that include data from the published articles as well as World Health Organization reports on coronavirus disease and how mobile technology is useful to fight against this disease.ResultsMobile technology can be helpful in mapping disease spread and provides an easy way to provide awareness that promotes safety and adoption of necessary precautions to mitigate and stop community transmission.ConclusionThe spread rate of COVID-19 is very high and until now no vaccines are available to control this disease. To this end we should leverage other avenues such as digital technologies to protect ourselves from this disease. Mobile technology such as smartphones are playing an important role in this pandemic, by launching apps to track coronavirus infected people. These apps are very easy to use and provide self-isolation guidelines as well as other safety tips. creator: Jaya Verma creator: Amar Shankar Mishra uri: https://doi.org/10.7717/peerj.10345 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Verma and Mishra title: De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis link: https://peerj.com/articles/10157 last-modified: 2020-11-06 description: Cnidium monnieri (L.) Cuss (C. monnieri) is one of the most widely used traditional herbal medicines, exhibiting a wide range of pharmacological functions for treating asynodia, trichomonas vaginitis, and osphyalgia. Its important medicinal value comes from its abundance of coumarins. To identify genes involved in coumarin biosynthesis and accumulation, we analyzed transcriptome data from flower, leaf, root and stem tissues of C. monnieri. A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of these, 119,177 unigenes were annotated in public databases. We identified differentially expressed genes (DEGs) based on expression profile analysis. These DEGs exhibited higher expression levels in flower tissue than in leaf, stem or root tissues. We identified and analyzed numerous genes encoding enzymes involved in coumarin biosynthesis, and verified genes encoding key enzymes using quantitative real-time PCR. Our transcriptome data will make great contributions to research on C. monnieri and provide clues for identifying candidate genes involved in coumarin metabolic pathways. creator: Yuanyuan Shi creator: Shengxiang Zhang creator: Daiyin Peng creator: Chunmiao Shan creator: Liqiang Zhao creator: Bin Wang creator: Jiawen Wu uri: https://doi.org/10.7717/peerj.10157 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shi et al. title: Dependence structure analysis of multisite river inflow data using vine copula-CEEMDAN based hybrid model link: https://peerj.com/articles/10285 last-modified: 2020-11-06 description: Several data-driven and hybrid models are univariate and not considered the dependance structure of multivariate random variables, especially the multi-site river inflow data, which requires the joint distribution of the same river basin system. In this paper, we proposed a Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN) Vine copula-based approach to address this issue. The proposed hybrid model comprised on two stages: In the first stage, the CEEMDAN is used to extract the high dimensional multi-scale features. Further, the multiple models are used to predict multi-scale components and residuals. In the second stage, the residuals obtained from the first stage are used to model the joint uncertainty of multi-site river inflow data by using Canonical Vine. For the application of the proposed two-step architecture, daily river inflow data of the Indus River Basin is used. The proposed two-stage methodology is compared with only the first stage proposed model, Vector Autoregressive and copula-based Autoregressive Integrated Moving Average models. The four evaluation measures, that is, Mean Absolute Relative Error (MARE), Mean Absolute Deviation (MAD), Nash-Sutcliffe Efficiency (NSE) and Mean Square Error (MSE), are used to observe the prediction performance. The results demonstrated that the proposed model outperforms significantly with minimum MARE, MAD, NSE, and MSE for two case studies having significant joint dependance. Therefore, it is concluded that the prediction can be improved by appropriately modeling the dependance structure of the multi-site river inflow data. creator: Hafiza Mamona Nazir creator: Ijaz Hussain creator: Muhammad Faisal creator: Alaa Mohamd Shoukry creator: Mohammed Abdel Wahab Sharkawy creator: Fares Fawzi Al-Deek creator: Muhammad Ismail uri: https://doi.org/10.7717/peerj.10285 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nazir et al. title: No conclusive evidence that difficult general knowledge questions cause a “Google Stroop effect”. A replication study link: https://peerj.com/articles/10325 last-modified: 2020-11-06 description: Access to the digital “all-knowing cloud” has become an integral part of our daily lives. It has been suggested that the increasing offloading of information and information processing services to the cloud will alter human cognition and metacognition in the short and long term. A much-cited study published in Science in 2011 provided first behavioral evidence for such changes in human cognition. Participants had to answer difficult trivia questions, and subsequently showed longer response times in a variant of the Stroop task with internet-related words (“Google Stroop effect”). The authors of this study concluded that the concept of the Internet is automatically activated in situations where information is missing (e.g., because we might feel the urge to “google” the information). However, the “Google Stroop effect” could not be replicated in two recent replication attempts as part of a large replicability project. After the failed replication was published in 2018, the first author of the original study pointed out some problems with the design of the failed replication. In our study, we therefore aimed to replicate the “Google Stroop effect” with a research design closer to the original experiment. Our results revealed no conclusive evidence in favor of the notion that the concept of the Internet or internet access (via computers or smartphones) is automatically activated when participants are faced with hard trivia questions. We provide recommendations for follow-up research. creator: Guido Hesselmann uri: https://doi.org/10.7717/peerj.10325 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hesselmann title: Deep learning prediction of likelihood of ICU admission and mortality in COVID-19 patients using clinical variables link: https://peerj.com/articles/10337 last-modified: 2020-11-06 description: BackgroundThis study aimed to develop a deep-learning model and a risk-score system using clinical variables to predict intensive care unit (ICU) admission and in-hospital mortality in COVID-19 patients.MethodsThis retrospective study consisted of 5,766 persons-under-investigation for COVID-19 between 7 February 2020 and 4 May 2020. Demographics, chronic comorbidities, vital signs, symptoms and laboratory tests at admission were collected. A deep neural network model and a risk-score system were constructed to predict ICU admission and in-hospital mortality. Prediction performance used the receiver operating characteristic area under the curve (AUC).ResultsThe top ICU predictors were procalcitonin, lactate dehydrogenase, C-reactive protein, ferritin and oxygen saturation. The top mortality predictors were age, lactate dehydrogenase, procalcitonin, cardiac troponin, C-reactive protein and oxygen saturation. Age and troponin were unique top predictors for mortality but not ICU admission. The deep-learning model predicted ICU admission and mortality with an AUC of 0.780 (95% CI [0.760–0.785]) and 0.844 (95% CI [0.839–0.848]), respectively. The corresponding risk scores yielded an AUC of 0.728 (95% CI [0.726–0.729]) and 0.848 (95% CI [0.847–0.849]), respectively.ConclusionsDeep learning and the resultant risk score have the potential to provide frontline physicians with quantitative tools to stratify patients more effectively in time-sensitive and resource-constrained circumstances. creator: Xiaoran Li creator: Peilin Ge creator: Jocelyn Zhu creator: Haifang Li creator: James Graham creator: Adam Singer creator: Paul S. Richman creator: Tim Q. Duong uri: https://doi.org/10.7717/peerj.10337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Transmissibility of coronavirus disease 2019 in Chinese cities with different dynamics of imported cases link: https://peerj.com/articles/10350 last-modified: 2020-11-06 description: BackgroundMonitoring the reproduction number (Rt) of the disease could help determine whether there is sustained transmission in a population, but areas with similar epidemic trends could have different transmission dynamics given the risk from imported cases varied across regions. In this study, we examined the Rt of coronavirus disease 2019 (COVID-19) by taking different dynamics of imported cases into account and compared the transmissibility of COVID-19 at different intervention periods in Hangzhou and Shenzhen.MethodsWe obtained the daily aggregated counts of laboratory-confirmed imported and local cases of COVID-19 infections in Hangzhou and Shenzhen from January 1 to March 13, 2020. Daily Rt and piecewise Rt before and after Wuhan lockdown were estimated, accounting for imported cases.ResultsSince the epidemic of COVID-19 in Shenzhen was dominated by imported cases, Rt was around 0.1 to 0.7 before the Wuhan lockdown. After the lockdown of Wuhan and the initialization of measures in response to the outbreak, local transmission was well-controlled as indicated by a low estimated value of piecewise Rt, 0.15 (95% CI [0.09–0.21]). On the contrary, Rt obtained for Hangzhou ranged from 1.2 to 4.9 with a piecewise Rt of 2.55 (95% CI [2.13–2.97]) before the lockdown of Wuhan due to the surge in local cases. Because of the Wuhan lockdown and other outbreak response measures, Rt dropped below unity in mid-February.ConclusionsEven though Shenzhen had more cases than Hangzhou, local transmission did not sustain probably due to limited transmission from imported cases owing to the reduction in local susceptibles as residents left the city during Chunyun. The lockdown measures and local outbreak responses helped reduce the local transmissibility. creator: Ka Chun Chong creator: Wei Cheng creator: Shi Zhao creator: Feng Ling creator: Kirran N. Mohammad creator: Maggie Wang creator: Benny CY Zee creator: Lai Wei creator: Xi Xiong creator: Hengyan Liu creator: Jingxuan Wang creator: Enfu Chen uri: https://doi.org/10.7717/peerj.10350 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chong et al. title: BiSCoT: improving large eukaryotic genome assemblies with optical maps link: https://peerj.com/articles/10150 last-modified: 2020-11-05 description: MotivationLong read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and organization of contigs into scaffolds is not always optimal.ResultsWe developed BiSCoT (Bionano SCaffolding COrrection Tool), a tool that post-processes files generated during a Bionano scaffolding in order to produce an assembly of greater contiguity and quality. BiSCoT was tested on a human genome and four publicly available plant genomes sequenced with Nanopore long reads and improved significantly the contiguity and quality of the assemblies. BiSCoT generates a fasta file of the assembly as well as an AGP file which describes the new organization of the input assembly.AvailabilityBiSCoT and improved assemblies are freely available on GitHub at http://www.genoscope.cns.fr/biscot and Pypi at https://pypi.org/project/biscot/. creator: Benjamin Istace creator: Caroline Belser creator: Jean-Marc Aury uri: https://doi.org/10.7717/peerj.10150 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Istace et al. title: Diversity of the gut microbiome in three grasshopper species using 16S rRNA and determination of cellulose digestibility link: https://peerj.com/articles/10194 last-modified: 2020-11-05 description: BackgroundGrasshoppers are typical phytophagous pests, and they have large appetites with high utilization of plants fibers, the digestion of which may depend on the microorganisms in their intestines. Grasshoppers have the potential to be utilized in bioreactors, which could improve straw utilization efficiency in the future. In this study, we describe the gut microbiome in three species of grasshoppers, Oedaleus decorus asiaticus, Aiolopus tamulus and Shirakiacris shirakii, by constructing a 16S rDNA gene library and analyzed the digestibility of cellulose and hemicellulose in the grasshoppers by using moss black phenol colorimetry and anthrone colorimetry.ResultsThere were 509,436 bacterial OTUs (Operational Taxonomic Units) detected in the guts of all the grasshoppers sampled. Among them, Proteobacteria and Firmicutes were the most common, Aiolopus tamulus had the highest bacterial diversity, and Shirakiacris shirakii had the highest bacterial species richness. The intestinal microflora structure varied between the different species of grasshopper, with Aiolopus tamulus and Shirakiacris shirakii being the most similar. Meanwhile, the time at which grasshopper specimens were collected also led to changes in the intestinal microflora structure in the same species of grasshoppers. Klebsiella may form the core elements of the microflora in the grasshopper intestinal tract. The digestibility of cellulose/hemicellulose among the three species grasshoppers varied (38.01/24.99%, 43.95/17.21% and 44.12/47.62%). LEfSe analysis and Spearman correlation coefficients showed that the hemicellulosic digestibility of Shirakiacris shirakii was significantly higher than that of the other two species of grasshopper, which may be related to the presence of Pseudomonas, Stenotrophomonas, Glutamicibacter, Corynebacterium, and Brachybacterium in Shirakiacris shirakii intestinal tract.ConclusionThe intestinal microbial communities of the three grasshoppers species are similar on phylum level, but the dominant genera of different species grasshoppers are different. The cellulose digestibility of the three species of grasshoppers is relatively high, which may be correlated with the presence of some gut microbiome. Increasing the understanding of the structure and function of the grasshopper intestinal microflora will facilitate further research and the utilization of intestinal microorganisms in the future. creator: Jian-Mei Wang creator: Jing Bai creator: Fang-Yuan Zheng creator: Yao Ling creator: Xiang Li creator: Jing Wang creator: Yong-Chao Zhi creator: Xin-Jiang Li uri: https://doi.org/10.7717/peerj.10194 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Characterizing carbonyl compounds and their sources in Fuzhou ambient air, southeast of China link: https://peerj.com/articles/10227 last-modified: 2020-11-05 description: In recent years, ozone (O3) concentrations in the southeastern coastal areas of China have shown a gradual upward trend. As precursors and intermediates in the formation of O3, carbonyl compounds play key roles in the atmospheric photochemical oxidation cycle. To explore the main pollution characteristics of carbonyl compounds in a typical coastal city in southeast China, ambient samples were collected in Fuzhou (the provincial capital of Fujian province, located on the southeast coast of China) and analyzed using high-performance liquid chromatography with ultraviolet detection. The study was continuously carried out at an urban site (Jinjishan) and a suburban site (Gushan) in Fuzhou from May 8 to 20, 2018. The total concentration of 16 carbonyl compounds at the urban site was 15.45 ± 11.18 ppbv, and the total concentration at the suburban site was 17.57 ± 12.77 ppbv. Formaldehyde (HCHO), acetaldehyde, and acetone were the main species detected in the samples, and acetone had the highest concentration among the species detected. The suburban site had a higher formaldehyde/acetaldehyde ratio and lower acetaldehyde/propionaldehyde ratio than the urban site, implying that biogenic sources potentially contributed to the carbonyl compound concentrations at the suburban site. The results of an observation-based model showed that anthropogenic hydrocarbons promoted HCHO production on May 17 at the urban site. Compared to biogenic emissions, anthropogenic activity is a more important source of carbonyl compounds. creator: Zhen He creator: Xin Zhang creator: Yunfeng Li creator: Xuefen Zhong creator: Hong Li creator: Rui Gao creator: Jinjuan Li uri: https://doi.org/10.7717/peerj.10227 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 He et al. title: Nuclear microsatellites reveal population genetic structuring and fine-scale pattern of hybridization in the Japanese mantis shrimp Oratosquilla oratoria link: https://peerj.com/articles/10270 last-modified: 2020-11-05 description: The interplay between historical and contemporary processes can produce complex patterns of genetic differentiation in the marine realm. Recent mitochondrial and nuclear sequence analyses revealed cryptic speciation in the Japanese mantis shrimp Oratosquilla oratoria. Herein, we applied nuclear microsatellite markers to examine patterns and causes of genetic differentiation in this morphotaxon. Population structure analyses revealed two genetically divergent and geographically structured clades in O. oratoria, one dominating the temperate zone of the Northwestern (NW) Pacific and the other occurring in the subtropical and tropical waters where are influenced by the Kuroshio Current. Two sympatric zones, one around the Changjiang Estuary in China coast and the other in the northern Japan Sea, were demonstrated to be hybrid zones where introgressive hybridization occurred asymmetrically. The interaction between historical climate shifts and contemporary factors (e.g., freshwater discharge, temperature gradient and isolation by distance) may contribute to the present-day genetic architecture in the Japanese mantis shrimp. Range shift induced by climate changes and oceanographic factors may promote hybridization and gene flow between the O. oratoria complex. Our results provide insights into the interacting mechanisms that give rise to diversification and speciation of coastal species in the NW Pacific. creator: Jiao Cheng creator: Nan Zhang creator: Zhongli Sha uri: https://doi.org/10.7717/peerj.10270 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cheng et al. title: Trait differences among discrete morphs of a color polymorphic lizard, Podarcis erhardii link: https://peerj.com/articles/10284 last-modified: 2020-11-05 description: Color polymorphism defies evolutionary expectations as striking phenotypic variation is maintained within a single species. Color and other traits mediate social interactions, and stable polymorphism within a population is hypothesized to be related to correlational selection of other phenotypic traits among color morphs. Here, we report on a previously unknown throat color polymorphism in the Aegean Wall Lizard (Podarcis erhardii) and examine morph-correlated differences in traits important to social behavior and communication: maximum bite force capacity and chemical signal profile. We find that both sexes of P. erhardii have three color morphs: orange, yellow, and white. Moreover, orange males are significantly larger and tend to bite harder than yellow and white males. Although the established color polymorphism only partially matches the observed intraspecific variation in chemical signal signatures, the chemical profile of the secretions of orange males is significantly divergent from that of white males. Our findings suggest that morph colors are related to differences in traits that are crucial for social interactions and competitive ability, illustrating the need to look beyond color when studying polymorphism evolution. creator: Kinsey M. Brock creator: Simon Baeckens creator: Colin M. Donihue creator: José Martín creator: Panayiotis Pafilis creator: Danielle L. Edwards uri: https://doi.org/10.7717/peerj.10284 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Brock et al. title: Robustness analysis in an inter-cities mobility network: modeling municipal, state and federal initiatives as failures and attacks toward SARS-CoV-2 containment link: https://peerj.com/articles/10287 last-modified: 2020-11-05 description: We present a robustness analysis of an inter-cities mobility complex network, motivated by the challenge of the COVID-19 pandemic and the seek for proper containment strategies. Brazilian data from 2016 are used to build a network with more than five thousand cities (nodes) and twenty-seven states with the edges representing the weekly flow of people between cities via terrestrial transports. Nodes are systematically isolated (removed from the network) either at random (failures) or guided by specific strategies (targeted attacks), and the impacts are assessed with three metrics: the number of components, the size of the giant component, and the total remaining flow of people. We propose strategies to identify which regions should be isolated first and their impact on people mobility. The results are compared with the so-called reactive strategy, which consists of isolating regions ordered by the date the first case of COVID-19 appeared. We assume that the nodes’ failures abstract individual municipal and state initiatives that are independent and possess a certain level of unpredictability. Differently, the targeted attacks are related to centralized strategies led by the federal government in agreement with municipalities and states. Removing a node means completely restricting the mobility of people between the referred city/state and the rest of the network. Results reveal that random failures do not cause a high impact on mobility restraint, but the coordinated isolation of specific cities with targeted attacks is crucial to detach entire network areas and thus prevent spreading. Moreover, the targeted attacks perform better than the reactive strategy for the three analyzed robustness metrics. creator: Vander L.S. Freitas creator: Gladston J.P. Moreira creator: Leonardo B.L. Santos uri: https://doi.org/10.7717/peerj.10287 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Freitas et al. title: Deep-learning convolutional neural networks with transfer learning accurately classify COVID-19 lung infection on portable chest radiographs link: https://peerj.com/articles/10309 last-modified: 2020-11-05 description: Portable chest X-ray (pCXR) has become an indispensable tool in the management of Coronavirus Disease 2019 (COVID-19) lung infection. This study employed deep-learning convolutional neural networks to classify COVID-19 lung infections on pCXR from normal and related lung infections to potentially enable more timely and accurate diagnosis. This retrospect study employed deep-learning convolutional neural network (CNN) with transfer learning to classify based on pCXRs COVID-19 pneumonia (N = 455) on pCXR from normal (N = 532), bacterial pneumonia (N = 492), and non-COVID viral pneumonia (N = 552). The data was randomly split into 75% training and 25% testing, randomly. A five-fold cross-validation was used for the testing set separately. Performance was evaluated using receiver-operating curve analysis. Comparison was made with CNN operated on the whole pCXR and segmented lungs. CNN accurately classified COVID-19 pCXR from those of normal, bacterial pneumonia, and non-COVID-19 viral pneumonia patients in a multiclass model. The overall sensitivity, specificity, accuracy, and AUC were 0.79, 0.93, and 0.79, 0.85 respectively (whole pCXR), and were 0.91, 0.93, 0.88, and 0.89 (CXR of segmented lung). The performance was generally better using segmented lungs. Heatmaps showed that CNN accurately localized areas of hazy appearance, ground glass opacity and/or consolidation on the pCXR. Deep-learning convolutional neural network with transfer learning accurately classifies COVID-19 on portable chest X-ray against normal, bacterial pneumonia or non-COVID viral pneumonia. This approach has the potential to help radiologists and frontline physicians by providing more timely and accurate diagnosis. creator: Shreeja Kikkisetti creator: Jocelyn Zhu creator: Beiyi Shen creator: Haifang Li creator: Tim Q. Duong uri: https://doi.org/10.7717/peerj.10309 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kikkisetti et al. title: An updated evolutionary study of the Notch family reveals a new ancient origin and novel invariable motifs as potential pharmacological targets link: https://peerj.com/articles/10334 last-modified: 2020-11-05 description: Notch family proteins play a key role in a variety of developmental processes by controlling cell fate decisions and operating in a great number of biological processes in several organ systems, such as hematopoiesis, somatogenesis, vasculogenesis, neurogenesis and homeostasis. The Notch signaling pathway is crucial for the majority of developmental programs and regulates multiple pathogenic processes. Notch family receptors’ activation has been largely related to its multiple effects in sustaining oncogenesis. The Notch signaling pathway constitutes an ancient and conserved mechanism for cell to cell communication. Much of what is known about Notch family proteins function comes from studies done in Caenorhabditis Elegans and Drosophila Melanogaster. Although, human Notch homologs had also been identified, the molecular mechanisms which modulate the Notch signaling pathway remained substantially unknown. In this study, an updated evolutionary analysis of the Notch family members among 603 different organisms of all kingdoms, from bacteria to humans, was performed in order to discover key regions that have been conserved throughout evolution and play a major role in the Notch signaling pathway. The major goal of this study is the presentation of a novel updated phylogenetic tree for the Notch family as a reliable phylogeny “map”, in order to correlate information of the closely related members and identify new possible pharmacological targets that can be used in pathogenic cases, including cancer. creator: Dimitrios Vlachakis creator: Louis Papageorgiou creator: Ariadne Papadaki creator: Maria Georga creator: Sofia Kossida creator: Elias Eliopoulos uri: https://doi.org/10.7717/peerj.10334 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Vlachakis et al. title: Geographic variation in the skull morphology of the lesser grison (Galictis cuja: Carnivora, Mustelidae) from two Brazilian ecoregions link: https://peerj.com/articles/9388 last-modified: 2020-11-04 description: BackgroundThe lesser grison (Galictis cuja) is one of the least known carnivores in the Neotropical region. Its wide geographical occurrence and range of habitats could lead to morphological variations along its distribution. So, this study aimed to investigate the variation in skull shape and size of this species, by testing the existence of ecotypes adapted to their respective environments (Uruguayan savanna and Atlantic Forest), as well as its relationship with selected abiotic variables.MethodsThe skulls of 52 museum specimens were photographed in the ventral, dorsal, and lateral views, and were analyzed using geometric morphometric techniques.ResultsWe found sexual size dimorphism, with males being larger than females. The shape variation between sexes, as well as between ecoregions, is mostly explained by the effect of allometry. The specimens from Uruguayan savanna are larger than the ones from the Atlantic Forest. Size variation was also significantly correlated to latitude, temperature and precipitation patterns. No correlation between skull shape with geographical distance was detected.DiscussionMorphometric measurements and diet data of lesser grison in regions from higher latitudes than our sampling show a tendency to heavier individuals, and the consumption of bigger prey compared to Uruguayan savanna. The results indicated the smaller specimens associated to low variability in annual temperature, congruent to Atlantic Forest region. An explanation for observed variation may be related to the “resource rule” but, due the minimal natural history information regards this species, we can just speculate about this. creator: Raissa Prior Migliorini creator: Rodrigo Fornel creator: Carlos Benhur Kasper uri: https://doi.org/10.7717/peerj.9388 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Migliorini et al. title: A new nurse frog (Anura: Allobates) from Brazilian Amazonia with a remarkably fast multi-noted advertisement call link: https://peerj.com/articles/9979 last-modified: 2020-11-04 description: Nurse frogs (Aromobatidae: Allobates) are probably the most extensively studied genus by taxonomists in Brazilian Amazonia. The southwestern portion of Amazonia is the most species-rich: as many as seven species may occur in sympatry at a single locality. In this study, we describe a new species of nurse frog from this region. The description integrates data from larval and adult morphology, advertisement calls and DNA sequences. Allobates velocicantus sp. nov. is distinguished from other Allobates mainly by the absence of hourglass-shaped dark marks on the dorsum and dark transverse bars on the thigh; a throat that is white centrally and yellow marginally; basal webbing on toes II and III; finger I longer than finger II; and an advertisement call composed of 66–138 pulsed notes with a note duration of 5–13 ms, inter-note intervals of 10–18 ms and a dominant frequency of 5,512–6,158 Hz. Tadpoles of the new species have 3–4 short, rounded papillae on the anterior labium, 16–23 papillae on the posterior labium, and a labial keratodont row formula 2(2)/3(1). This is the fifth species of Allobates described from the state of Acre, southwestern Brazilian Amazonia. creator: Jesus R.D. Souza creator: Miquéias Ferrão creator: James Hanken creator: Albertina P. Lima uri: https://doi.org/10.7717/peerj.9979 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Souza et al. title: Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism link: https://peerj.com/articles/10053 last-modified: 2020-11-04 description: BackgroundSilicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data.MethodsWe established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L−1 Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis.ResultsSi concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors.ConclusionPepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper. creator: Fernando Carlos Gómez-Merino creator: Libia Iris Trejo-Téllez creator: Atonaltzin García-Jiménez creator: Hugo Fernando Escobar-Sepúlveda creator: Sara Monzerrat Ramírez-Olvera uri: https://doi.org/10.7717/peerj.10053 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gómez-Merino et al. title: A model of k-mer surprisal to quantify local sequence information content surrounding splice regions link: https://peerj.com/articles/10063 last-modified: 2020-11-04 description: Molecular sequences carry information. Analysis of sequence conservation between homologous loci is a proven approach with which to explore the information content of molecular sequences. This is often done using multiple sequence alignments to support comparisons between homologous loci. These methods therefore rely on sufficient underlying sequence similarity with which to construct a representative alignment. Here we describe a method using a formal metric of information, surprisal, to analyse biological sub-sequences without alignment constraints. We applied our model to the genomes of five different species to reveal similar patterns across a panel of eukaryotes. As the surprisal of a sub-sequence is inversely proportional to its occurrence within the genome, the optimal size of the sub-sequences was selected for each species under consideration. With the model optimized, we found a strong correlation between surprisal and CG dinucleotide usage. The utility of our model was tested by examining the sequences of genes known to undergo splicing. We demonstrate that our model can identify biological features of interest such as known donor and acceptor sites. Analysis across all annotated coding exon junctions in Homo sapiens reveals the information content of coding exons to be greater than the surrounding intron regions, a consequence of increased suppression of the CG dinucleotide in intronic space. Sequences within coding regions proximal to exon junctions exhibited novel patterns within DNA and coding mRNA that are not a function of the encoded amino acid sequence. Our findings are consistent with the presence of secondary information encoding features such as DNA and RNA binding sites, multiplexed through the coding sequence and independent of the information required to define the corresponding amino-acid sequence. We conclude that surprisal provides a complementary methodology with which to locate regions of interest in the genome, particularly in situations that lack an appropriate multiple sequence alignment. creator: Sam Humphrey creator: Alastair Kerr creator: Magnus Rattray creator: Caroline Dive creator: Crispin J. Miller uri: https://doi.org/10.7717/peerj.10063 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Humphrey et al. title: Mortality of native and invasive ladybirds co-infected by ectoparasitic and entomopathogenic fungi link: https://peerj.com/articles/10110 last-modified: 2020-11-04 description: Harmonia axyridis is an invasive alien ladybird in North America and Europe. Studies show that multiple natural enemies are using Ha. axyridis as a new host. However, thus far, no research has been undertaken to study the effects of simultaneous infection by multiple natural enemies on Ha. axyridis. We hypothesized that high thallus densities of the ectoparasitic fungus Hesperomyces virescens on a ladybird weaken the host’s defenses, thereby making it more susceptible to infection by other natural enemies. We examined mortality of the North American-native Olla v-nigrum and Ha. axyridis co-infected with He. virescens and an entomopathogenic fungus—either Beauveria bassiana or Metarhizium brunneum. Laboratory assays revealed that He. virescens-infected O. v-nigrum individuals are more susceptible to entomopathogenic fungi, but Ha. axyridis does not suffer the same effects. This is in line with the enemy release hypothesis, which predicts that invasive alien species in new geographic areas experience reduced regulatory effects from natural enemies compared to native species. Considering our results, we can ask how He. virescens affects survival when confronted by other pathogens that previously had little impact on Ha. axyridis. creator: Danny Haelewaters creator: Thomas Hiller creator: Emily A. Kemp creator: Paul S. van Wielink creator: David I. Shapiro-Ilan creator: M. Catherine Aime creator: Oldřich Nedvěd creator: Donald H. Pfister creator: Ted E. Cottrell uri: https://doi.org/10.7717/peerj.10110 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Effects of food hydrocolloids on quality attributes of extruded red Jasmine rice noodle link: https://peerj.com/articles/10235 last-modified: 2020-11-04 description: The aim of this study was to examine the quality characteristics of extruded red Jasmine rice flour (RJF) noodle that had been prepared with hydrocolloids, namely guar gum (GG), carboxymethyl cellulose (CMC), and xanthan gum (XG) at the concentrations of 0.0 (control sample), 0.2, and 0.4% (w/w), respectively. The use of hydrocolloids had no effect on total phenolic contents, antioxidant properties (DPPH, ABTS, and FRAP), color, and X-ray diffraction patterns (p > 0.05). In contrast, the hydrocolloids tended to increase the expansion ration of the noodle. GG and CMC improved cooking, textural, and sensory properties. Ultimately, 0.2%-GG showed the lowest cooking loss (5.07%) when compared with others. Moreover, it also provided the noodle with better textural properties such as tensile strength, extensibility, hardness, cohesiveness, and chewiness (p < 0.05). For these reasons, the highest acceptability (6.75) for the noodle was achieved with GG02. XG resulted in lower overall acceptability (5.05), particularly the 0.4%-XG recipe (p < 0.05). Thus, usage of 0.2%-GG was the best option for improving the qualities of extruded RJF noodle. XG was deemed ineffective for improving the noodle. creator: Supaluck Kraithong creator: Saroat Rawdkuen uri: https://doi.org/10.7717/peerj.10235 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kraithong and Rawdkuen title: Prognostic model of invasive ductal carcinoma of the breast based on differentially expressed glycolysis-related genes link: https://peerj.com/articles/10249 last-modified: 2020-11-04 description: BackgroundInvasive ductal carcinoma (IDC) is a common pathological type of breast cancer that is characterized by high malignancy and rapid progression. Upregulation of glycolysis is a hallmark of tumor growth, and correlates with the progression of breast cancer. We aimed to establish a model to predict the prognosis of patients with breast IDC based on differentially expressed glycolysis-related genes (DEGRGs).MethodsTranscriptome data and clinical data of patients with breast IDC were from The Cancer Genome Atlas (TCGA). Glycolysis-related gene sets and pathways were from the Molecular Signatures Database (MSigDB). DEGRGs were identified by comparison of tumor tissues and adjacent normal tissues. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression were used to screen for DEGRGs with prognostic value. A risk-scoring model based on DEGRGs related to prognosis was constructed. Receiver operating characteristic (ROC) analysis and calculation of the area under the curve (AUC) were used to evaluate the performance of the model. The model was verified in different clinical subgroups using an external dataset (GSE131769). A nomogram that included clinical indicators and risk scores was established. Gene function enrichment analysis was performed, and a protein-protein interaction network was developed.ResultsWe analyzed data from 772 tumors and 88 adjacent normal tissues from the TCGA database and identified 286 glycolysis-related genes from the MSigDB. There were 185 DEGRGs. Univariate Cox regression and LASSO regression indicated that 13 of these genes were related to prognosis. A risk-scoring model based on these 13 DEGRGs allowed classification of patients as high-risk or low-risk according to median score. The duration of overall survival (OS) was longer in the low-risk group (P < 0.001), and the AUC was 0.755 for 3-year OS and 0.726 for 5-year OS. The results were similar when using the GEO data set for external validation (AUC for 3-year OS: 0.731, AUC for 5-year OS: 0.728). Subgroup analysis showed there were significant differences in OS among high-risk and low-risk patients in different subgroups (T1-2, T3-4, N0, N1-3, M0, TNBC, non-TNBC; all P < 0.01). The C-index was 0.824, and the AUC was 0.842 for 3-year OS and 0.808 for 5-year OS from the nomogram. Functional enrichment analysis demonstrated the DEGRGs were mainly involved in regulating biological functions.ConclusionsOur prognostic model, based on 13 DEGRGs, had excellent performance in predicting the survival of patients with IDC of the breast. These DEGRGs appear to have important biological functions in the progression of this cancer. creator: Xiaoping Li creator: Qihe Yu creator: Jishang Chen creator: Hui Huang creator: Zhuangsheng Liu creator: Chengxing Wang creator: Yaoming He creator: Xin Zhang creator: Weiwen Li creator: Chao Li creator: Jinglin Zhao creator: Wansheng Long uri: https://doi.org/10.7717/peerj.10249 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Identifying myocardial injuries in “normal-appearing” myocardium in pediatric patients with clinically suspected myocarditis using mapping techniques link: https://peerj.com/articles/10252 last-modified: 2020-11-04 description: BackgroundMapping techniques using cardiac magnetic resonance imaging have significantly improved the diagnostic accuracy for myocarditis with focal myocardial injuries. The aim of our study was to determine whether T1 and T2 mapping techniques could identify diffuse myocardial injuries in “normal-appearing” myocardium in pediatric patients with clinically suspected myocarditis and to evaluate the associations between diffuse myocardial injuries and cardiac function parameters.MethodsForty-six subjects were included in this study: 20 acute myocarditis patients, 11 subacute/chronic myocarditis patients and 15 control children. T2 values, native T1 values and the extracellular volume (ECV) of “normal-appearing” myocardium were compared among the three groups of patients. Associations between diffuse myocardial injuries and cardiac function parameters were also evaluated.ResultsThe ECV of “normal-appearing” myocardium was significantly higher in the subacute/chronic myocarditis group than in the control group (30.1 ± 0.9 vs 27.0 ± 0.6, P =0.004). No significant differences in T1 and T2 values between the acute myocarditis and control groups were found. In the subacute/chronic myocarditis group, a significant association between ECV and left ventricle ejection fraction was found (P=0.03).ConclusionsDiffuse myocardial injuries are likely to occur in subacute/chronic myocarditis patients with prolonged inflammatory responses. Mapping techniques have great value for the diagnosis and monitoring of myocarditis. creator: Haipeng Wang creator: Bin Zhao creator: Huan Yang creator: Tianyi Qian creator: Bo Han creator: Haipeng Jia creator: Jing An creator: Junyu Zhao creator: Ximing Wang creator: Cuiyan Wang uri: https://doi.org/10.7717/peerj.10252 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Tnni1b-ECR183-d2, an 87 bp cardiac enhancer of zebrafish link: https://peerj.com/articles/10289 last-modified: 2020-11-04 description: BackgroundSeveral heart malformations are associated with mutations in the regulatory regions of cardiac genes. Troponin I type 1b (tnni1b) is important for the formation of the atrioventricular canal in zebrafish hearts; however, the regulation of tnni1b is poorly understand. We aimed to identify a small but functional enhancer that is distal to tnni1b.MethodsEvolutionary Conserved Region (ECR) Browser was used to analyze the 219 kb zebrafish and human genomes covering the tnni1b gene as well as the 100 kb regions upstream and downstream of tnni1b. Putative transcription factor binding sites (TFBSs) were analyzed using JASPAR and PROMO, and the enhancer activity was identified using zebrafish embryos and the luciferase reporter assay. A correlation analysis between the enhancer and transcription factors (TFs) was performed via TF overexpression and TFBS mutation experiments and the electrophoretic mobility shift assay (EMSA). To analyze the conservation between zebrafish and human enhancers, human DNA fragments were functionally verified. Images were captured and analyzed by fluorescence microscopy or confocal microscopy.ResultsCombined with comparative analysis and functional validation, we identified a 183 bp ECR (termed tnni1b-ECR183) that was located approximately 84 kb upstream of tnni1b that had the heart-specific enhancer activity in zebrafish. TFBS analysis and the enhancer activity detection assay data showed that the 87 bp core region (termed tnni1b-ECR183-d2) was capable of driving specific GFP expression near the atrioventricular junction and increased luciferase expression in HEK293 and HL1 cell lines. The GFP pattern in zebrafish embryos was similar to the expression profiles of tnni1b. A correlation analysis showed that the enhancer activity of tnni1b-ECR183-d2 was increased when NKX2.5 (p = 0.0006) or JUN (p < 0.0001) was overexpressed and was decreased when the TFBSs of NKX2.5 (p < 0.0001) or JUN (p = 0.0018) were mutated. In addition, DNA-protein interactions were not observed between these TFs and tnni1b-ECR183-d2 in the EMSA experiment. The conservation analysis showed that tnni1b-ECR183-h179 (aligned from tnni1b-ECR183) drove GFP expression in the heart and skeletal muscles and increased the luciferase expression after NKX2.5 (p < 0.0001), JUN (p < 0.0001) or ETS1 (p < 0.0001) was overexpressed. Interestingly, the truncated fragment tnni1b-ECR183-h84 mainly drove GFP expression in the skeletal muscles of zebrafish and the enhancer activity decreased when NKX2.5 (p = 0.0028), ETS1 (p = 0.0001) or GATA4 (p < 0.0001) was overexpressed.ConclusionsAn 87 bp cardiac-specific enhancer located 84 kb upstream of tnni1b in zebrafish was positively correlated with NKX2.5 or JUN. The zebrafish and human enhancers in this study target different tissues. The GFP expression mediated by tnni1b-ECR183-d2 is a valuable tool for marking the domain around the atrioventricular junction. creator: Yawen Zhang creator: Feng Wang creator: Fang Wu creator: Youhua Wang creator: Xu Wang creator: Yonghao Gui creator: Qiang Li uri: https://doi.org/10.7717/peerj.10289 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Identification of the miRNA-mRNA regulatory pathways and a miR-21-5p based nomogram model in clear cell renal cell carcinoma link: https://peerj.com/articles/10292 last-modified: 2020-11-04 description: BackgroundThe purpose of this study was to determine the key microRNAs (miRNAs) and their regulatory networks in clear cell renal cell carcinoma (ccRCC).MethodsFive mRNA and three microRNA microarray datasets were downloaded from the Gene Expression Omnibus database and used to screen the differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs). Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed with Metascape. A miRNA-mRNA network was mapped with the Cytoscape tool. The results were validated with data from The Cancer Genome Atlas (TCGA) and qRT-PCR. A nomogram model based on independent prognostic key DEMs, stage and grade was constructed for further investigation.ResultsA total of 26 key DEMs and 307 DEGs were identified. Dysregulation of four key DEMs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) was identified to correlate with overall survival. The results were validated with TCGA data and qRT-PCR. The nomogram model showed high accuracy in predicting the prognosis of patients with ccRCC.ConclusionWe identified 26 DEMs that may play vital roles in the regulatory networks of ccRCC. Four miRNAs (miR-21-5p, miR-142-3p, miR-155-5p and miR-342-5p) were considered as potential biomarkers in the prognosis of ccRCC, among which only miR-21-5p was found to be an independent prognostic factor. A nomogram model was then created on the basis of independent factors for better prediction of prognosis for patients with ccRCC. Our results suggest a need for further experimental validation studies. creator: Yiqiao Zhao creator: Zijia Tao creator: Xiaonan Chen uri: https://doi.org/10.7717/peerj.10292 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: Biomechanics of lower limb in badminton lunge: a systematic scoping review link: https://peerj.com/articles/10300 last-modified: 2020-11-04 description: BackgroundBadminton is a popular sport activity in both recreational and elite levels. A lot of biomechanical studies have investigated badminton lunge, since good lunge performance may increase the chances to win the game. This review summarized the current trends, research methods, and parameters-of-interest concerning lower-extremity biomechanics in badminton lunges.MethodologyDatabases including Web of Science, Cochrane Library, Scopus, and PubMed were searched from the oldest available date to September 2020. Two independent authors screened all the articles and 20 articles were eligible for further review. The reviewed articles compared the differences among playing levels, footwear designs, and lunge directions/variations, using parameters including ground reaction forces, plantar pressure distribution, kinematics, and kinetics.ResultsElite badminton players demonstrated higher impact attenuation capability, more aggressive knee and ankle strategy (higher mechanical moment), and higher medial plantar load than amateur players. Footwear modifications can influence comfort perception and movement mechanics, but it remains inconclusive regarding how these may link with lunging performance. Contradicting findings in kinematics is possibly due to the variations in lunge and instructions.ConclusionsPlaying levels and shoe designs have significant effects on biomechanics in badminton lunges. Future studies can consider to use an unanticipated testing protocol and realistic movement intensity. They can study the inter-limb coordination as well as the contributions and interactions of intrinsic and extrinsic factors to injury risk. Furthermore, current findings can stimulate further research studying whether some specific footwear materials with structural design could potentially compromise impact attenuation, proprioception, and performance. creator: Wing-Kai Lam creator: Duo Wai-Chi Wong creator: Winson Chiu-Chun Lee uri: https://doi.org/10.7717/peerj.10300 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lam et al. title: Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields link: https://peerj.com/articles/10302 last-modified: 2020-11-04 description: Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium. creator: Li Song creator: Zhenzhi Pan creator: Yi Dai creator: Lin Chen creator: Li Zhang creator: Qilin Liao creator: Xiezhi Yu creator: Hongyan Guo creator: Guisheng Zhou uri: https://doi.org/10.7717/peerj.10302 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Song et al. title: Duration of hemodialysis associated with cardio-respiratory dysfunction and breathlessness: a multicenter study link: https://peerj.com/articles/10333 last-modified: 2020-11-04 description: BackgroundPatients with hemodialysis suffer with protein-energy wasting and uremic myopathy lead to lack of physical activity and poor functional performance. However, ventilation abnormality in patients undergone hemodialysis remains controversial regarding the respiratory impairment. Therefore, the study aimed to determine the effect of duration of dialysis on respiratory function.MethodsA multicenter study with cross-sectional study was designed in four hemodialysis outpatient clinics. Respiratory muscle strength (i.e., maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP)) pulmonary function test (i.e., forced vital capacity (FVC), forced expiratory volume in one second (FEV1) and FEV1/FVC ratio), functional capacity (6-minute walk test) and sensation of breathlessness were assessed prior to dialysis.ResultsA total of 100 hemodialysis patients were recruited with 38 females and 62 males. An average of duration of hemodialysis was 5.93± 4.96 years. Decreased MIP values, FEV1 values, FVC values, %FEV1 and %FVC were noted in patients with long duration of dialysis (defined as ≥ 5 years of dialysis) compared to those with short duration of dialysis (ps < .05). In addition, increased sensation of breathlessness was observed in patients with long duration of dialysis (p < .05). Furthermore, participants with long duration of dialysis had an increased risk of ventilatory restriction (OR 6.093, p = .007). creator: Kornanong Yuenyongchaiwat creator: Phatsara Vasinsarunkul creator: Phoomipat Phongsukree creator: Kodchaphan Chaturattanachaiyaporn creator: Opas Tritanon uri: https://doi.org/10.7717/peerj.10333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yuenyongchaiwat et al. title: Gut microbiota in hospitalized children with acute infective gastroenteritis caused by virus or bacteria in a regional Peruvian hospital link: https://peerj.com/articles/9964 last-modified: 2020-11-03 description: BackgroundAcute infective gastroenteritis (AIG) is a leading cause of mortality in children worldwide. In Peru, more than 40% of cases of AIG occurring in children under 5 years old. The disruption of the gut microbiota can increase risk for several health complications especially in patients with gastric infections caused by viruses or bacteria.ObjectiveThe main objective of this study was to describe the prevalence of 13 representative bacteria from the gut microbiota (GM) in stools samples from children under 5 years of age with acute infective gastroenteritis.ResultsThe most commonly isolated bacteria from the GM were Firmicutes (63.2% 74/117) Bacteriodetes (62.4%; 73/117), Lactobacillus (59.8%; 70/117), Prevotella (57.2%; 67/117), Proteobacterium (53.8%; 63/117), regardless of the etiological agent responsible for the AIG. Interestingly, despite the high prevalence of Firmicutes, Bacteroidetes, Lactobacillus and Prevotella across all samples, a visible reduction of these agents was observed especially among patients with a single bacterial infection or even bacteria–bacteria coinfections when compared to viral etiologies. Patients with exclusive or mixed breastfeeding registered the highest amount of gut microbiota bacteria, in contrast to infants who received formula or were not breastfed. creator: Andre Alonso Taco-Masias creator: Augusto R. Fernandez-Aristi creator: Angela Cornejo-Tapia creator: Miguel Angel Aguilar-Luis creator: Luis J. del Valle creator: Wilmer Silva-Caso creator: Victor Zavaleta-Gavidia creator: Pablo Weilg creator: Hernán Cornejo-Pacherres creator: Jorge Bazán-Mayra creator: Zully M. Puyen creator: Juana del Valle-Mendoza uri: https://doi.org/10.7717/peerj.9964 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Taco-Masias et al. title: Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics link: https://peerj.com/articles/9971 last-modified: 2020-11-03 description: BackgroundAlthough asthma is one of the most common chronic, noncommunicable diseases worldwide, the pathogenesis of childhood asthma is not yet clear. Genetic factors and environmental factors may lead to airway immune-inflammation responses and an imbalance of airway nerve regulation. The aim of the present study was to determine which serum proteins are differentially expressed between children with or without asthma and to ascertain the potential roles that these differentially expressed proteins (DEPs) may play in the pathogenesis of childhood asthma.MethodsSerum samples derived from four children with asthma and four children without asthma were collected. The DEPs were identified by using isobaric tags for relative and absolute quantitation (iTRAQ) combined with liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses. Using biological information technology, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Cluster of Orthologous Groups of Proteins (COG) databases and analyses, we determined the biological processes associated with these DEPs. Key protein glucose-6-phosphate dehydrogenase (G6PD) was verified by enzyme linked immunosorbent assay (ELISA).ResultsWe found 46 DEPs in serum samples of children with asthma vs. children without asthma. Among these DEPs, 12 proteins were significantly (>1.5 fold change) upregulated and 34 proteins were downregulated. The results of GO analyses showed that the DEPs were mainly involved in binding, the immune system, or responding to stimuli or were part of a cellular anatomical entity. In the KEGG signaling pathway analysis, most of the downregulated DEPs were associated with cardiomyopathy, phagosomes, viral infections, and regulation of the actin cytoskeleton. The results of a COG analysis showed that the DEPs were primarily involved in signal transduction mechanisms and posttranslational modifications. These DEPs were associated with and may play important roles in the immune response, the inflammatory response, extracellular matrix degradation, and the nervous system. The downregulated of G6PD in the asthma group was confirmed using ELISA experiment.ConclusionAfter bioinformatics analyses, we found numerous DEPs that may play important roles in the pathogenesis of childhood asthma. Those proteins may be novel biomarkers of childhood asthma and may provide new clues for the early clinical diagnosis and treatment of childhood asthma. creator: Ming Li creator: Mingzhu Wu creator: Ying Qin creator: Huaqing Liu creator: Chengcheng Tu creator: Bing Shen creator: Xiaohong Xu creator: Hongbo Chen uri: https://doi.org/10.7717/peerj.9971 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Cryptosporidium spp. and Giardia duodenalis emissions from humans and animals in the Three Gorges Reservoir in Chongqing, China link: https://peerj.com/articles/9985 last-modified: 2020-11-03 description: Cryptosporidium spp. and Giardia duodenalis are two waterborne protozoan parasites that can cause diarrhea. Human and animal feces in surface water are a major source of these pathogens. This paper presents a GloWPa-TGR-Crypto model that estimates Cryptosporidium and G. duodenalis emissions from human and animal feces in the Three Gorges Reservoir (TGR), and uses scenario analysis to predict the effects of sanitation, urbanization, and population growth on oocyst and cyst emissions for 2050. Our model estimated annual emissions of 1.6 × 1015 oocysts and 2.1 × 1015 cysts from human and animal feces, respectively. Humans were the largest contributors of oocysts and cysts, followed by pigs and poultry. Cities were hot-spots for human emissions, while districts with high livestock populations accounted for the highest animal emissions. Our model was the most sensitive to oocyst excretion rates. The results indicated that 74% and 87% of total emissions came from urban areas and humans, respectively, and 86% of total human emissions were produced by the urban population. The scenario analysis showed a potential decrease in oocyst and cyst emissions with improvements in urbanization, sanitation, wastewater treatment, and manure management, regardless of population increase. Our model can further contribute to the understanding of environmental pathways, the risk assessment of Cryptosporidium and Giardia pollution, and effective prevention and control strategies that can reduce the outbreak of waterborne diseases in the TGR and other similar watersheds. creator: Qian Huang creator: Ling Yang creator: Bo Li creator: Huihui Du creator: Feng Zhao creator: Lin Han creator: Qilong Wang creator: Yunjia Deng creator: Guosheng Xiao creator: Dayong Wang uri: https://doi.org/10.7717/peerj.9985 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Exosomal cargoes in OSCC: current findings and potential functions link: https://peerj.com/articles/10062 last-modified: 2020-11-03 description: Oral squamous cell carcinoma (OSCC) is the most prevalent malignancy in head and neck cancer, with high recurrence and mortality. Early diagnosis and efficient therapeutic strategies are vital for the treatment of OSCC patients. Exosomes can be isolated from a broad range of different cell types, implicating them as important factors in the regulation of human physiological and pathological processes. Due to their abundant cargo including proteins, lipids, and nucleic acids, exosomes have played a valuable diagnostic and therapeutic role across multiple diseases, including cancer. In this review, we summarize recent findings concerning the content within and participation of exosomes relating to OSCC and their roles in tumorigenesis, proliferation, migration, invasion, metastasis, and chemoresistance. We conclude this review by looking ahead to their potential utility in providing new methods for treating OSCC to inspire further research in this field. creator: Chengzhi Zhao creator: Geru Zhang creator: Jialing Liu creator: Chenghao Zhang creator: Yang Yao creator: Wen Liao uri: https://doi.org/10.7717/peerj.10062 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: Serum uric acid level is correlated with the clinical, pathological progression and prognosis of IgA nephropathy: an observational retrospective pilot-study link: https://peerj.com/articles/10130 last-modified: 2020-11-03 description: ObjectivesThis study was aimed to assess the relationship between serum uric acid (SUA) level and the clinical, pathological phenotype of IgA nephropathy (IgAN), and to determine the role of SUA level in the progression and prognosis of IgAN.MethodsA total of 208 patients with IgAN were included in this study, and were classified into the normo-uricemia group and hyperuricemia group according to the SUA level. The clinical data at baseline, IgAN Oxford classification scores (MEST-C scoring system), and other pathological features were collected and further analyzed. All patients were followed up and the prognosis was assessed using Kaplan-Meier survival curves. GraphPad Prism 7.0 and SPSS 23.0 were used for statistical analyses.ResultsIn clinical indicators, patients with hyperuricemia had the significantly higher proportion of males to females, mean arterial pressure, the levels of total cholesterol, triglyceride, Scr, BUN, 24 hour-urine protein, C3, and C4, the lower levels of high-density lipoprotein cholesterol and eGFR than those without (p < 0.05). In terms of pathological characteristics, the tubular atrophy/interstitial fibrosis scores, vascular injury scores, and glomerular sclerosis percentage were significantly higher in patients with hyperuricemia compared with those without (p < 0.01). There was no significant difference in the scores of mesangial hypercellularity, endocapillary hypercellularity, focal segmental glomerulosclerosis, as well as crescents between the two groups (p > 0.05). As for the depositions of immune complexes deposition in IgAN, the hyperuricemia group had less deposition of immunoglobulin G and FRA than the normo-uricemia group (p < 0.05), while the deposition of immunoglobulin A, immunoglobulin M, and complement C3 in the two groups showed no statistical difference. The survival curve suggested that patients in the hyperuricemia group have significantly poorer renal outcome than those in the normo-uricemia group (p = 0.0147). Results also revealed that the SUA level is a valuable predictor of renal outcome in patients with IgAN. The optimal cutoff value was 361.1 µmol/L (AUC = 0.76 ± 0.08167) and 614 µmol/L (AUC = 0.5728 ± 0.2029) for female and male, respectively.ConclusionsThe level of SUA is associated with renal function level and pathological severity of IgAN, and maybe a prognostic indicator of IgAN. creator: Pingfan Lu creator: Xiaoqing Li creator: Na Zhu creator: Yuanjun Deng creator: Yang Cai creator: Tianjing Zhang creator: Lele Liu creator: Xueping Lin creator: Yiyan Guo creator: Min Han uri: https://doi.org/10.7717/peerj.10130 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lu et al. title: In silico structural homology modeling and characterization of multiple N-terminal domains of selected bacterial Tcps link: https://peerj.com/articles/10143 last-modified: 2020-11-03 description: Several bacterial pathogens produce Toll/interleukin-1 receptor (TIR) domain-containing protein homologs that are important for subverting the Toll-like receptor (TLR) signaling cascades in hosts. Consequently, promoting the persistence and survival of the bacterial pathogens. However, the exact molecular mechanisms elucidating the functional characteristics of these bacterial proteins are not clear. Physicochemical and homology modeling characterization studies have been conducted to predict the conditions suitable for the stability and purification of these proteins and to predict their structural properties. The outcomes of these studies have provided important preliminary data for the drug discovery pipeline projects. Here, using in silico physicochemical and homology modeling tools, we have reported the primary, secondary and tertiary structural characteristics of multiple N-terminal domains of selected bacterial TIR domain-containing proteins (Tcps). The results show variations between the primary amino acid sequences, secondary structural components and three-dimensional models of the proteins, suggesting the role of different molecular mechanisms in the functioning of these proteins in subverting the host immune system. This study could form the basis of future experimental studies advancing our understanding of the molecular basis of the inhibition of the host immune response by the bacterial Tcps. creator: Mohammed Alaidarous uri: https://doi.org/10.7717/peerj.10143 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Alaidarous title: A 22-amino-acid peptide regulates tight junctions through occludin and cell apoptosis link: https://peerj.com/articles/10147 last-modified: 2020-11-03 description: Occludin is a structural protein of tight junctions (TJ) in the blood–testis barrier (BTB). A 22-amino-acid peptide (22AA) in the second extracellular loop can reversibly regulate TJ, but its regulatory mechanism is unknown. In this study, a 22AA-induced TJ destruction animal model was constructed to investigate the effect of 22AA on Sertoli cells (SCs) and spermatid counts and cell apoptosis at different time points using a multiplex immunofluorescence technique. The effect of 22AA on the location and distribution of occludin was analyzed via dual confocal fluorescence microscope. Western blotting was used to analyze dynamic changes in occludin expression. Real-time RT-PCR was used to analyze miR-122-5p expression changes. Sperm density counts and mating methods were used to analyze the effect of 22AA on fertility in mice. The results showed that 22AA promoted SC and spermatid apoptosis, downregulated occludin, upregulated miR-122-5p, and decreased sperm density and litter size before 27 days (27D). After 27D, the expression of occludin increased again, miR-122-5p expression decreased again, both sperm density and litter size returned to normal, apoptosis stopped, and spermatogenesis began to recover. Therefore, it can be concluded that 22AA can destroy TJ by downregulating occludin and inducing cell apoptosis. After 27D, TJ and spermatogenesis functions return to normal. creator: Maoying Zhu creator: Juan Lu creator: Jianyun Shen creator: Lumin Fei creator: Deyu Chen uri: https://doi.org/10.7717/peerj.10147 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhu et al. title: Habitat preference, movements and growth of giant mottled eels, Anguilla marmorata, in a small subtropical Amami-Oshima Island river link: https://peerj.com/articles/10187 last-modified: 2020-11-03 description: Although anguillid eel populations have decreased remarkably in recent decades, few detailed ecological studies have been conducted on tropical eels such as the giant mottled eel whose range extends across the whole Indo-Pacific. This species was studied throughout the entire 0.5 km mainstem reaches of Oganeku River on the subtropical Amami-Oshima Island of Japan over a two-year period using four sampling periods to understand its habitat preference, early life-stage dispersal process, movements, and annual growth using a mark-recapture experiment conducted with quantitative electrofishing. A total of 396 juvenile growth-phase A. marmorata eels were caught and tagged, with 48 individuals being recaptured at least once. Their density irrespective of size of eels was most strongly determined by distance from the river mouth, followed by riverbank type according to random forest models. Eel density decreased with increasing distance from the freshwater tidal limit located about 100–150 m from the river mouth. Eels preferred vegetated riverbanks, while they avoided those of concrete and sand. The density of small eels (total length: TL < 240 mm) was also associated with depth and velocity, with small eels tending to prefer riffle or run habitats. In contrast, large eels (TL ≥ 240 mm) were found in habitats of any depth and velocity. The TL of eels had a minimum peak at around the tidal limit, and it increased with increasing distance from the tidal limit. The observed density and size gradients of eels in relation to the distance from the river mouth suggested that A. marmorata initially recruited to freshwater tidal limit areas and then dispersed in both downstream and upstream directions. The growth rate of eels varied greatly among individuals that were at large for various periods of time and ranged from 0 to 163.2 mm/year (mean ± SD of 31.8 ± 31.0 mm/year). Of the recaptured eels, 52.1% were recaptured in a section that was different from the original capture section, and their mean ± SD distance travelled was 46.5 ± 72.5 m (median = 20 m). 47.9% of the eels were recaptured from the original section of capture (i.e., <10 m distances travelled), suggesting that they had strong fidelity to specific habitats with limited movements. The distance travelled of eels that had moved was greater for small eels (range = 10–380 m; mean ± SD = 84.4 ± 121.9 m) than large individuals (range = 10–120 m; mean ± SD = 30.9 ± 31.0 m), which indicates that the mobility of the eels declines as they grow. This is the first clear detailed documentation of the spatial distribution, growth, and movements of tropical eels in a small river system in relation to environmental conditions that provides an example of how future studies can be conducted in other areas to understand how conservation efforts can be most efficiently targeted for maximum success. creator: Hikaru Itakura creator: Ryoshiro Wakiya uri: https://doi.org/10.7717/peerj.10187 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Itakura and Wakiya title: A model of population dynamics with complex household structure and mobility: implications for transmission and control of communicable diseases link: https://peerj.com/articles/10203 last-modified: 2020-11-03 description: Households are known to be high-risk locations for the transmission of communicable diseases. Numerous modelling studies have demonstrated the important role of households in sustaining both communicable diseases outbreaks and endemic transmission, and as the focus for control efforts. However, these studies typically assume that households are associated with a single dwelling and have static membership. This assumption does not appropriately reflect households in some populations, such as those in remote Australian Aboriginal and Torres Strait Islander communities, which can be distributed across more than one physical dwelling, leading to the occupancy of individual dwellings changing rapidly over time. In this study, we developed an individual-based model of an infectious disease outbreak in communities with demographic and household structure reflective of a remote Australian Aboriginal community. We used the model to compare the dynamics of unmitigated outbreaks, and outbreaks constrained by a household-focused prophylaxis intervention, in communities exhibiting fluid vs. stable dwelling occupancy. We found that fluid dwelling occupancy can lead to larger and faster outbreaks in modelled scenarios, and may interfere with the effectiveness of household-focused interventions. Our findings suggest that while short-term restrictions on movement between dwellings may be beneficial during outbreaks, in the longer-term, strategies focused on reducing household crowding may be a more effective way to reduce the risk of severe outbreaks occurring in populations with fluid dwelling occupancy. creator: Rebecca H. Chisholm creator: Bradley Crammond creator: Yue Wu creator: Asha C. Bowen creator: Patricia T. Campbell creator: Steven Y.C. Tong creator: Jodie McVernon creator: Nicholas Geard uri: https://doi.org/10.7717/peerj.10203 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chisholm et al. title: Neurocognitive effects of six ketamine infusions and the association with antidepressant effects in treatment-resistant bipolar depression: a preliminary study link: https://peerj.com/articles/10208 last-modified: 2020-11-03 description: ObjectiveThe N-methyl-D-aspartate subtype glutamate receptor antagonist ketamine has rapid antidepressant and antisuicidal effects in treating treatment-resistant bipolar depression (TRBD). The neurocognitive effects of repeated ketamine infusions in TRBD are not known.MethodsSix intravenous infusions of ketamine (0.5 mg/kg over 40 min) were administered on a Monday–Wednesday–Friday schedule during a 12-day period on 16 patients with TRBD followed by a 2-week observational period. The assessment of neurocognitive function was conducted using the MATRICS Consensus Cognitive Battery at baseline, 13 and 26 days. Tasks were designed to test speed of processing, working memory, visual learning and verbal learning.ResultsA significant improvement was found only in scores of speed of processing (F = 9.9, p = 0.001) after a 2-week observational period, which was accounted for by the improvement of depression symptoms. There were no significant changes over time in terms of working memory, visual learning and verbal learning. Pearson correlation analysis showed that the improvement of depression symptoms through six ketamine infusions was greater among TRBD patients with lower working memory at baseline (r = 0.54, p = 0.03). In multiple regression analysis, the significant correlation was still maintained (beta = 0.67, t = 2.2, p = 0.04).ConclusionThis preliminary study indicated that six ketamine infusions were not harmful but were slightly beneficial for speed of processing in TRBD. However, this change was mainly accounted for the improvement of depression symptoms over time. Lower baseline working memory appears to be associated with greater antidepressant response after completion of six ketamine infusions in patients with TRBD. creator: Wei Zheng creator: Yan-Ling Zhou creator: Cheng-Yu Wang creator: Xiao-Feng Lan creator: Bin Zhang creator: Ming-Zhe Yang creator: Sha Nie creator: Yu-Ping Ning uri: https://doi.org/10.7717/peerj.10208 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zheng et al. title: Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management link: https://peerj.com/articles/10258 last-modified: 2020-11-03 description: The persistence of antimicrobial resistant (AMR) genes in the soil-environment is a concern, yet practices that mitigate AMR are poorly understood, especially in grasslands. Animal manures are widely deposited on grasslands, which are the largest agricultural land-use in the United States. These nutrient-rich manures may contain AMR genes. The aim of this study was to enumerate AMR genes in grassland soils following 14-years of poultry litter and cattle manure deposition and evaluate if best management practices (rotationally grazed with a riparian (RBR) area and a fenced riparian buffer strip (RBS), which excluded cattle grazing and poultry litter applications) relative to standard pasture management (continuously grazed (CG) and hayed (H)) minimize the presence and amount of AMR genes. Quantitative PCR (Q-PCR) was performed to enumerate four AMR genes (ermB, sulI, intlI, and blactx-m-32) in soil, cattle manure, and poultry litter environments. Six soil samples were additionally subjected to metagenomic sequencing and resistance genes were identified from assembled sequences. Following 14-years of continuous management, ermB, sulI, and intlI genes in soil were greatest (P < 0.05) in samples collected under long-term continuous grazing (relative to conservation best management practices), under suggesting overgrazing and continuous cattle manure deposition may increase AMR gene presence. In general, AMR gene prevalence increased downslope, suggesting potential lateral movement and accumulation based on landscape position. Poultry litter had lower abundance of AMR genes (ermB, sulI, and intlI) relative to cattle manure. Long-term applications of poultry litter increased the abundance of sulI and intlI genes in soil (P < 0.05). Similarly, metagenomic shotgun sequencing revealed a greater total number of AMR genes under long-term CG, while fewer AMR genes were found in H (no cattle manure) and RBS (no animal manure or poultry litter). Results indicate long-term conservation pasture management practices (e.g., RBS and RBR) and select animal manure (poultry litter inputs) may minimize the presence and abundance of AMR genes in grassland soils. creator: Yichao Yang creator: Amanda J. Ashworth creator: Jennifer M. DeBruyn creator: Lisa M. Durso creator: Mary Savin creator: Kim Cook creator: Philip A. Moore Jr. creator: Phillip R. Owens uri: https://doi.org/10.7717/peerj.10258 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2020 Yang et al. title: Increased expression of POLR3G predicts poor prognosis in transitional cell carcinoma link: https://peerj.com/articles/10281 last-modified: 2020-11-03 description: BackgroundPrevious studies have shown that RNA Polymerase III Subunit G (POLR3G) has oncogenic effects in cultured cells and mice. However, the role of POLR3G in transitional cell carcinoma (TCC) has not been reported. This study explores the potential of POLR3G as a novel molecular marker for TCC.MethodsThe RNA sequencing data and clinical information of patients with TCC were downloaded from The Cancer Genome Atlas official website. Transcriptome analysis was performed as implemented in the edgeR package to explore whether POLR3G was up-regulated in TCC tissues compared to normal bladder tissues. The expression of POLR3G in bladder cancer cell line T24 and human uroepithelial cell line SV-HUC-1 were detected via quantitative real time polymerase chain reaction (qRT-PCR). Correlations between POLR3G expression and clinicopathological characteristics were analyzed using Mann-Whitney U test or Kruskal-Wallis H test. Clinicopathological characteristics associated with overall survival were explored using the Kaplan-Meier method and Cox regression analyses. Gene set enrichment analysis (GSEA) was performed to explore the associated gene sets enriched in different POLR3G expression phenotypes and the online tool Tumor IMmune Estimation Resource (TIMER) was used to explore the correlation between POLR3G expression and tumor immune infiltration in TCC.ResultsTranscriptome analysis showed that POLR3G was significantly up-regulated in TCC tissues compared to normal bladder tissues. Furthermore, qRT-PCR revealed high expression of POLR3G in T24 cells compared to SV-HUC-1 cells. Overall, POLR3G expression was associated with race, tumor status, tumor subtype, T classification, and pathological stage. Kaplan-Meier survival analysis revealed that higher POLR3G expression was associated with lower overall survival. The univariate Cox regression model revealed that age at diagnosis, pathological stage, and POLR3G expression were associated with prognosis of TCC patients. Further multivariate analyses identified these three clinicopathological characteristics as independent prognostic factors for overall survival. GSEA analysis showed that several gene sets associated with tumor development and metastasis, including TGF-β signaling, PI3K-AKT-mTOR signaling, and IL6-JAK-STAT3 signaling, were significantly enriched in POLR3G high expression phenotype. Immune infiltration analysis revealed that the expression of POLR3G was significantly correlated with infiltrating levels of immune cells, including CD8+ T cells, neutrophils, and dendritic cells; and the expression of POLR3G was also significantly correlated with the expression of immune checkpoint molecules, such as PD1, PD-L1, PD-L2, CTLA4, LAG3, HAVCR2, and TIGIT.ConclusionsPOLR3G was up-regulated in TCC and high POLR3G expression correlated with poor prognosis. POLR3G can potentially be used as a prognostic marker for TCC and might be of great value in predicting the response to immunotherapy. creator: Xianhui Liu creator: Weiyu Zhang creator: Huanrui Wang creator: Chin-Hui Lai creator: Kexin Xu creator: Hao Hu uri: https://doi.org/10.7717/peerj.10281 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Clonal versus non-clonal milkweeds (Asclepias spp.) respond differently to stem damage, affecting oviposition by monarch butterflies link: https://peerj.com/articles/10296 last-modified: 2020-11-03 description: BackgroundOviposition decisions are critical to the fitness of herbivorous insects and are often impacted by the availability and condition of host plants. Monarch butterflies (Danaus plexippus) rely on milkweeds (Asclepias spp.) for egg-laying and as food for larvae. Previous work has shown that monarchs prefer to oviposit on recently regrown plant tissues (after removal of above-ground biomass) while larvae grow poorly on plants previously damaged by insects. We hypothesized that these effects may depend on the life-history strategy of plants, as clonal and non-clonal milkweed species differ in resource allocation and defense strategies.Methodology/Principal FindingsWe first confirmed butterfly preference for regrown tissue in a field survey of paired mowed and unmowed plots of the common milkweed A. syriaca. We then experimentally studied the effects of plant damage (comparing undamaged controls to plants clipped and regrown, or damaged by insects) on oviposition choice, larval performance, and leaf quality of two closely related clonal and non-clonal species pairs: (1) A. syriaca and A. tuberosa, and (2) A. verticillata and A. incarnata. Clonal and non-clonal species displayed different responses to plant damage, impacting the proportions of eggs laid on plants. Clonal species had similar mean proportions of eggs on regrown and control plants (≈35–40% each), but fewer on insect-damaged plants (≈20%). Meanwhile non-clonal species had similar oviposition on insect-damaged and control plants (20–30% each) but more eggs on regrown plants (40–60%). Trait analyses showed reduced defenses in regrown plants and we found some evidence, although variable, for negative effects of insect damage on subsequent larval performance.Conclusions/SignificanceOverall, non-clonal species are more susceptible and preferred by monarch butterflies following clipping, while clonal species show tolerance to clipping and induced defense to insect herbivory. These results have implications for monarch conservation strategies that involve milkweed habitat management by mowing. More generally, plant life-history may mediate growth and defense strategies, explaining species-level variation in responses to different types of damage. creator: Elise He creator: Anurag A. Agrawal uri: https://doi.org/10.7717/peerj.10296 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 He and Agrawal title: A case against default effect sizes in sport and exercise science link: https://peerj.com/articles/10314 last-modified: 2020-11-03 description: Recent discussions in the sport and exercise science community have focused on the appropriate use and reporting of effect sizes. Sport and exercise scientists often analyze repeated-measures data, from which mean differences are reported. To aid the interpretation of these data, standardized mean differences (SMD) are commonly reported as a description of effect size. In this manuscript, we hope to alleviate some confusion. First, we provide a philosophical framework for conceptualizing SMDs; that is, by dichotomizing them into two groups: magnitude-based and signal-to-noise SMDs. Second, we describe the statistical properties of SMDs and their implications. Finally, we provide high-level recommendations for how sport and exercise scientists can thoughtfully report raw effect sizes, SMDs, or other effect sizes for their own studies. This conceptual framework provides sport and exercise scientists with the background necessary to make and justify their choice of an SMD. creator: Aaron Caldwell creator: Andrew D. Vigotsky uri: https://doi.org/10.7717/peerj.10314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Caldwell and Vigotsky title: Projection of premature mortality from noncommunicable diseases for 2025: a model based study from Hunan Province, China, 1990–2016 link: https://peerj.com/articles/10298 last-modified: 2020-11-03 description: BackgroundIn 2011, the United Nations set a target to reduce premature mortality from non-communicable diseases (NCDs) by 25% by 2025. While studies have reported the target in some countries, no studies have been done in China. This study aims to project the ability to reach the target in Hunan Province, China, and establish the priority for future interventions.MethodsWe conducted the study during 2019–2020. From the Global Burden of Disease Study 2016, we extracted death data for Hunan during 1990–2016 for four main NCDs, namely cancer, cardiovascular disease (CVD), chronic respiratory diseases, and diabetes. We generated estimates for 2025 by fitting a linear regression to the premature mortality over the most recent trend identified by a joinpoint regression model. We also estimated excess premature mortality attributable to unfavorable changes over time.ResultsThe rate of premature mortality from all NCDs in Hunan will be 19.5% (95% CI [19.0%–20.1%]) by 2025, with the main contributions being from CVD (8.2%, 95% CI [7.9%–8.5%]) and cancer (7.9%, 95% CI [7.8%–8.1%]). Overall, it will be impossible to achieve the target, with a relative reduction of 16.4%. Women may be able to meet the target except with respect to cancer, and men will not except with respect to chronic respiratory diseases. Most of the unfavorable changes have occurred since 2008–2009.DiscussionMore urgent efforts, especially for men, should be exerted in Hunan by integrating population-wide interventions into a stronger health-care system. In the post lock-down COVID-19 era in China, reducing the NCD risk factors can also lower the risk of death from COVID-19. creator: Qiaohua Xu creator: Maigeng Zhou creator: Donghui Jin creator: Xinying Zeng creator: Jinlei Qi creator: Li Yin creator: Yuan Liu creator: Lei Yin creator: Yuelong Huang uri: https://doi.org/10.7717/peerj.10298 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xu et al. title: Identification and functional characterization of SlDronc in Spodoptera littoralis link: https://peerj.com/articles/10329 last-modified: 2020-11-03 description: BackgroundApoptosis is responsible for eliminating damaged and virus-infected cells, regulating normal cell turnover, and maintaining the immune system’s development and function. Caspases play a vital role in both mammal and invertebrate apoptosis. Spodoptera littoralis is a generalist insect herbivore that is one of the most destructive pests in tropical and subtropical areas and attacks a wide range of commercially important crops. Although S. littoralis is a model organism in the study of baculovirus infection, its apoptotic pathway has not been explored.MethodsWe cloned a new caspase gene named sldronc in S. littoralis using Rapid Amplification of cDNA Ends (RACE). We then measured caspase activity on synthetic caspase substrates and S. littoralis’ effector caspase. SlDronc’s function in the apoptotic pathway and its interaction with caspase inhibitors were also tested in SL2 cells.ResultsWe found that the initiator caspase SlDronc cleaved and activated effector caspase in S. littoralis. SlDronc overexpression induced apoptosis in SL2 cells, and Sldronc knockdown decreased apoptosis induced by UV irradiation in SL2 cells. Our results indicate that SlDronc acts as an apoptotic initiator caspase in S. littoralis. Additionally, we found that processed forms of SlDronc increased in the presence of N-terminally truncated S. littoralis inhibitors of apoptosis (SlIAP) and that SlDronc was inhibited by P49. This study contributes to the further understanding of S. littoralis’ apoptotic pathway and may facilitate future studies on baculovirus infection-induced apoptosis. creator: Hao Liu creator: Ke Zhou creator: Zhouning Yang uri: https://doi.org/10.7717/peerj.10329 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Genome-wide discovery and characterization of long noncoding RNAs in African oil palm (Elaeis guineensis Jacq.) link: https://peerj.com/articles/9585 last-modified: 2020-11-02 description: Long noncoding RNAs (lncRNAs) are an important class of genes and play important roles in a range of biological processes. However, few reports have described the identification of lncRNAs in oil palm. In this study, we applied strand specific RNA-seq with rRNA removal to identify 1,363 lncRNAs from the equally mixed tissues of oil palm spear leaf and six different developmental stages of mesocarp (8–24 weeks). Based on strand specific RNA-seq data and 18 released oil palm transcriptomes, we systematically characterized the expression patterns of lncRNA loci and their target genes. A total of 875 uniq target genes for natural antisense lncRNAs (NAT-lncRNA, 712), long intergenic noncoding RNAs (lincRNAs, 92), intronic-lncRNAs (33), and sense-lncRNAs (52) were predicted. A majority of lncRNA loci (77.8%–89.6%) had low expression in 18 transcriptomes, while only 89 lncRNA loci had medium to high expression in at least one transcriptome. Coexpression analysis between lncRNAs and their target genes indicated that 6% of lncRNAs had expression patterns positively correlated with those of target genes. Based on single nucleotide polymorphism (SNP) markers derived from our previous research, 6,882 SNPs were detected for lncRNAs and 28 SNPs belonging to 21 lncRNAs were associated with the variation of fatty acid contents. Moreover, seven lncRNAs showed expression patterns positively correlated expression pattern with those of genes in de novo fatty acid synthesis pathways. Our study identified a collection of lncRNAs for oil palm and provided clues for further research into lncRNAs that may regulate mesocarp development and lipid metabolism. creator: Wei Xia creator: Yajing Dou creator: Rui Liu creator: Shufang Gong creator: Dongyi Huang creator: Haikuo Fan creator: Yong Xiao uri: https://doi.org/10.7717/peerj.9585 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xia et al. title: Static and dynamic alterations in the amplitude of low-frequency fluctuation in patients with amyotrophic lateral sclerosis link: https://peerj.com/articles/10052 last-modified: 2020-11-02 description: BackgroundStatic changes in local brain activity in patients suffering from amyotrophic lateral sclerosis (ALS) have been studied. However, the dynamic characteristics of local brain activity are poorly understood. Whether dynamic alterations could differentiate patients with ALS from healthy controls (HCs) remains unclear.MethodsA total of 54 patients with ALS (mean age = 48.71 years, male/female = 36/18) and 54 (mean age = 48.30 years, male/female = 36/18) HCs underwent magnetic resonance imaging scans. To depict static alterations in cortical activity, amplitude of low-frequency fluctuations (ALFF) which measures the total power of regional activity was computed. Dynamic ALFF (d-ALFF) from all subjects was calculated using a sliding-window approach. Statistical differences in ALFF and d-ALFF between both groups were used as features to explore whether they could differentiate ALS from HC through support vector machine method.ResultsIn contrast with HCs, patients with ALS displayed increased ALFF in the right inferior temporal gyrus and bilateral frontal gyrus and decreased ALFF in the left middle occipital gyrus and left precentral gyrus. Furthermore, patients with ALS demonstrated lower d-ALFF in widespread regions, including the right lingual gyrus, left superior temporal gyrus, bilateral precentral gyrus, and left paracentral lobule by comparison with HCs. In addition, the ALFF in the left superior orbitofrontal gyrus had a tendency of correlation with ALSFRS-R score and disease progression rate. The classification performance in distinguishing ALS was higher with both features of ALFF and d-ALFF than that with a single approach.ConclusionsDecreased dynamic brain activity in the precentral gyrus, paracentral gyrus, lingual gyrus, and temporal regions was found in the ALS group. The combined ALFF and d-ALFF could distinguish ALS from HCs with a higher accuracy than ALFF and d-ALFF alone. These findings may provide important evidence for understanding the neuropathology underlying ALS. creator: Xujing Ma creator: Fengmei Lu creator: Heng Chen creator: Caihong Hu creator: Jiao Wang creator: Sheng Zhang creator: Shuqin Zhang creator: Guiran Yang creator: Jiuquan Zhang uri: https://doi.org/10.7717/peerj.10052 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ma et al. title: In vitro anti-diabetic effects and phytochemical profiling of novel varieties of Cinnamomum zeylanicum (L.) extracts link: https://peerj.com/articles/10070 last-modified: 2020-11-02 description: BackgroundDiabetes mellitus type 2 (DMT2) is a leading metabolic disorder in the world. Anti-diabetic actions of phytochemicals from various medicinal herbs have been explored as an alternative therapy in the management of DMT2 due to adverse effects of synthetic drugs used in allopathic medicine. α-amylase and α-glucosidase inhibitory potential and phytochemical profiling were investigated in aqueous extracts of two new Cinnamomum zeylanicum accessions, namely C. zeylanicum Sri Wijaya (SW), C. zeylanicum Sri Gemunu (SG) and commercially available C. zeylanicum (CC).MethodsMicrowave Digestion (MD), Pressurized Water Extraction (PWE), Steam Distillation (SD), Solvent Extraction (SE), Decoction Water Extraction (DWE) and Infusion Water Extraction (IWE) methods were used to prepare Cinnamon quill extracts. Total phenolic content (TPC, Folin-Ciocalteu method) and Proanthocyanidin content (PC, vanillin assay), α-amylase and α-glucosidase inhibition of Cinnamon extracts were determined spectrophotometrically. The α-amylase and α-glucosidase inhibition were reported in terms of IC50 value. The phytochemical profiling was accomplished by GC-MS technique.Results and DiscussionLowest IC50 values were observed in PWE and DWE of SW. The highest PC and TPC were also observed in PWE and DWE of SW. Pressured water and decoctions are promising methods for the extraction of antidiabetic constituents from cinnamon. Benzoic acid, cinnamyl alcohol, benzyl alcohol, and 4-Allyl-2,6-dimethoxyphenol were identified as major compounds in SW extracts. These compounds are believed to be responsible for strong enzyme inhibitory activity of the extracts.ConclusionsThis is the first study to explore the use of pressured and decoctions water to extract anti-diabetic phytochemicals from cinnamon. The extensive metabolite profiling of novel SW and SG extracts and comparison of that with commercially available CC are reported for the first time in this study. The C. zeylanicum, SW accession holds some promise in the management of diabetes. creator: W.A. Niroshani M. Wariyapperuma creator: Sagarika Kannangara creator: Yasanandana S. Wijayasinghe creator: Sri Subramanium creator: Bimali Jayawardena uri: https://doi.org/10.7717/peerj.10070 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wariyapperuma et al. title: Assessment of autonomous nerve system through non-linear heart rate variability outcomes in sedentary healthy adults link: https://peerj.com/articles/10178 last-modified: 2020-11-02 description: BackgroundHeart rate variability (HRV) is a psycho-physiological phenomenon with broad health implications. Different data analysis methods have been used to assess the autonomic nervous system activity, but the validation of new indexes that accurately describe its balance through non-invasive methods (i.e., HRV analysis) is of clinical interest. This study aimed: (i) to evaluate the association of the Stress Score (SS) and the Sympathetic/Parasympathetic Ratio (S/PS) with time domain and frequency domain analysis of HRV, and (ii) to set reference values of SS and S/PS in sedentary healthy adults.MethodsA total of 156 sedentary healthy adults (38.4 ± 15.57 years old, 81 women), aged were involved in this study. HRV was measured for 15 min in a supine position at rest. SS and S/PS were calculated from the non-linear HRV analyses based on Poincare Plot.ResultsStress Score showed a non-linear negative power-law relationship with SDNN (β = −0.969; R2 = 0.963; P < 0.001), RMSSD (β = −0.867; R2 = 0.722; P < 0.001), high frequency (β = −0.834; R2 = 0.752; P =< 0.001), low frequency (β = −0.627; R2 = 0.330; P < 0.001), SD1 (β = −0.867; R2 = 0.722; P < 0.001) and SD2 (β = −1.000; R2 > 0.999; P < 0.001). There was observed a negative cubic relationship between SS with PNN50 (β = −1.972; R2 = 0.644; P < 0.001). A linear regression model was conducted between SS with Ratio Low/High Frequency (β = 0.026; R2 < 0.001; P = 0.750). Non-linear power-law regression models were built between S/PS and SDNN (β = −0.990; R2 = 0.981; P < 0.001), RMSSD (β = −0.973; R2 = 0.939; P < 0.001), high frequency (β = −0.928; R2 = 0.970; P < 0.001), low frequency (β = −2.344; R2 = 0.557; P < 0.001), SD1 (β = −0.973; R2 = 0.939; P < 0.001) and SD2 (β = −0.611; R2 = 0.908; P < 0.001). A non-linear negative regression model was built between S/PS and PNN50 (β = −3.412; R2 = 0.868; P < 0.001). A linear regression model was conducted between S/PS and SD2/SD1 (β = 0.075; R2 = 0.006; P < 0.001).ConclusionOur results support the use of SS as a sympathetic activity marker, and S/PS as an indicator of the sympathetic and parasympathetic activity of the autonomic nervous system in sedentary healthy adults. creator: Gines Navarro-Lomas creator: Alejandro De-la-O creator: Lucas Jurado-Fasoli creator: Manuel J. Castillo creator: Pedro Femia creator: Francisco J. Amaro-Gahete uri: https://doi.org/10.7717/peerj.10178 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Navarro-Lomas et al. title: Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages link: https://peerj.com/articles/10223 last-modified: 2020-11-02 description: BackgroundRed palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control.MethodsIn this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest.ResultsSequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus. creator: Hongjun Yang creator: Danping Xu creator: Zhihang Zhuo creator: Jiameng Hu creator: Baoqian Lu uri: https://doi.org/10.7717/peerj.10223 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections link: https://peerj.com/articles/10246 last-modified: 2020-11-02 description: BackgroundIn December 2019, an ongoing outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/ 2019-nCoV) infection was initially reported in Wuhan, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be a Public Health Emergency of International Concern (PHEIC). Cellular co-infection is a critical determinant of viral fitness and infection outcomes and plays a crucial role in shaping the host immune response to infections.MethodsIn this study, 68 public next-generation sequencing data from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Data screening was performed using an alignment-free method based on k-mer mapping and extension, fastv. Taxonomic classification was performed using Kraken 2 on all reads containing one or more virus sequences other than SARS-CoV-2.ResultsSARS-CoV-2 was identified in all except three patients. Influenza type A (H7N9) virus, human immunodeficiency virus, rhabdovirus, human metapneumovirus, Human adenovirus, Human herpesvirus 1, coronavirus NL63, parvovirus, simian virus 40, and hepatitis virus genomes sequences were detected in SARS-CoV-2 infected patients. Besides, a very diverse group of bacterial populations were observed in the samples. creator: Mohamed A. Abouelkhair uri: https://doi.org/10.7717/peerj.10246 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Abouelkhair title: Optimizing and purifying extracellular amylase from soil bacteria to inhibit clinical biofilm-forming bacteria link: https://peerj.com/articles/10288 last-modified: 2020-11-02 description: BackgroundBacterial biofilms have become a major threat to human health. The objective of this study was to isolate amylase-producing bacteria from soil to determine the overall inhibition of certain pathogenic bacterial biofilms.MethodsWe used serial dilution and the streaking method to obtain a total of 75 positive amylase isolates. The starch-agar plate method was used to screen the amylolytic activities of these isolates, and we used morphological and biochemical methods to characterize the isolates. Optimal conditions for amylase production and purification using Sephadex G-200 and SDS-PAGE were monitored. We screened these isolates’ antagonistic activities and the purified amylase against pathogenic and multi-drug-resistant human bacteria using the agar disk diffusion method. Some standard antibiotics were controlled according to their degree of sensitivity. Finally, we used spectrophotometric methods to screen the antibiofilm 24 and 48 h after application of filtering and purifying enzymes in order to determine its efficacy at human pathogenic bacteria.ResultsThe isolated Bacillus species were Bacillus megaterium (26.7%), Bacillus subtilis (16%), Bacillus cereus (13.3%), Bacillus thuringiesis (10.7%), Bacillus lentus (10.7%), Bacillus mycoides (5.3%), Bacillus alvei (5.3%), Bacillus polymyxa (4%), Bacillus circulans (4%), and Micrococcus roseus (4%). Interestingly, all isolates showed a high antagonism to target pathogens. B. alevi had the highest recorded activity (48 mm) and B. polymyxa had the lowest recorded activity (12 mm) against Staphylococcus aureus (MRSA) and Escherichia coli, respectively. On the other hand, we detected no antibacterial activity for purified amylase. The supernatant of the isolated amylase-producing bacteria and its purified amylase showed significant inhibition for biofilm: 93.7% and 78.8%, respectively. This suggests that supernatant and purified amylase may be effective for clinical and environmental biofilm control.DiscussionOur results showed that soil bacterial isolates such as Bacillus sp. supernatant and its purified amylase are good antibiofilm tools that can inhibit multidrug-resistant former strains. They could be beneficial for pharmaceutical use. While purified amylase was effective as an antibiofilm, the isolated supernatant showed better results. creator: Rokaia Elamary creator: Wesam M. Salem uri: https://doi.org/10.7717/peerj.10288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Elamary and Salem title: The current knowledge gap on metallothionein mediated metal-detoxification in Elasmobranchs link: https://peerj.com/articles/10293 last-modified: 2020-11-02 description: Elasmobranchs are particularly vulnerable to environmental contamination, especially pollutants that may bioaccumulate and biomagnify, throughout the trophic web, such as metals. However, Elasmobranch management and conservation plans are challenging, and this group is often neglected regarding ecotoxicological analyses, particularly concerning metal detoxification mechanisms. This article discusses metallothionein (MT) mediated metal detoxification in Elasmobranchs and reflects on the current knowledge gap in this regard. creator: Rachel Ann Hauser-Davis uri: https://doi.org/10.7717/peerj.10293 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hauser-Davis title: Changing health compliance through message repetition based on the extended parallel process model in the COVID-19 pandemic link: https://peerj.com/articles/10318 last-modified: 2020-11-02 description: When people are confronted with health proposals during the coronavirus disease 2019 (COVID-19) pandemic, it has been suggested that fear of COVID-19 can serve protective functions and ensure public health compliance. However, health proposal repetition and its perceived efficacy also influence the behavior intention toward the proposal, which has not yet been confirmed in the COVID-19 context. The present study aims to examine whether the extended parallel process model (EPPM) can be generalized to a naturalistic context like the COVID-19 pandemic. Additionally, we will explore how repetition of a health proposal is involved with the EPPM. In this study, two groups of participants are exposed to the same health proposal related to COVID-19, where one group is exposed once and another group twice. They then fill out a questionnaire consisting of items concerning behavior intention and adapted from the Risk Behavior Diagnosis Scale. Structural equation modeling will be used to determine the multivariate associations between the variables. We predict that repetition of the health proposal will associate with response efficacy (i.e., a belief about the effectiveness of the health proposal in deterring the threat) and perceived susceptibility (i.e., a belief about the risk of experiencing the threat). It is also predicted that following the EPPM, behavior intention will associate with both perceived efficacy of the health proposal, which will underlie response efficacy, and perceived threat of COVID-19, which will underlie perceived susceptibility. We will discuss the process, based on the model, where health message repetition affects behavior intention during the COVID-19 pandemic. creator: Jingwen Yang creator: Xue Wu creator: Kyoshiro Sasaki creator: Yuki Yamada uri: https://doi.org/10.7717/peerj.10318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: The efficacy of IL-6 inhibitor Tocilizumab in reducing severe COVID-19 mortality: a systematic review link: https://peerj.com/articles/10322 last-modified: 2020-11-02 description: BackgroundIn the absence of highly effective antiviral therapies against SARS-CoV-2, it is crucial to counter the known pathophysiological causes of severe COVID-19. Evaluating the efficacy existing drugs may expedite the development of such therapeutics. Severe COVID-19 is largely the result of a dysregulated immune response characterized by lymphocytopenia, neutrophilia and critical hypercytokinemia, or “cytokine storm,” which is largely mediated by the cytokine interleukin-6 (IL-6). The IL-6 inhibitor tocilizumab (TCZ) could potentially suppress the effects of the pro-inflammatory cytokine and thereby lower mortality from the disease. This systematic analysis aimed to investigate and synthesize existing evidence for the efficacy of TCZ in reducing COVID-19 mortality.MethodologyPubMed and SearchWorks searches were performed to locate clinical studies with primary data on TCZ treatment for severe COVID-19. Sixteen case-control studies comparing mortality between TCZ and standard of care (SOC) were identified for quantitative synthesis. The systematic analysis was pre-approved through PROSPERO (CRD42020193479).ResultsCombined mortality for the TCZ-treated and SOC groups were 26.0% and 43.4% respectively. In all but one of the studies, the odds ratio of mortality from COVID-19 pointed towards lower fatality with TCZ vs the SOC. A combined random effects odds ratio calculation yielded an odds ratio of 0.453 (95% CI [0.376–0.547], p < 0.001). Additionally, 18 uncontrolled trials were identified for qualitative analysis producing a raw combined mortality rate of 16.0%.ConclusionsImportant caveats to this research include the lack of prospective randomized control trials and the absence of data from the large COVATA study from the published literature. However, results from this systematic analysis of published research provide positive evidence for the potential efficacy of TCZ to treat severe COVID-19, validating the ethical basis and merit of ongoing randomized controlled clinical trials. creator: Avi Gurion Kaye creator: Robert Siegel uri: https://doi.org/10.7717/peerj.10322 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kaye and Siegel