title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2020-02 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Relative contribution of ecological and biological attributes in the fine-grain structure of ant-plant networks link: https://peerj.com/articles/8314 last-modified: 2020-02-28 description: BackgroundEcological communities of interacting species analyzed as complex networks have shown that species dependence on their counterparts is more complex than expected at random. As for other potentially mutualistic interactions, ant-plant networks mediated by extrafloral nectar show a nested (asymmetric) structure with a core of generalist species dominating the interaction pattern. Proposed factors structuring ecological networks include encounter probability (e.g., species abundances and habitat heterogeneity), behavior, phylogeny, and body size. While the importance of underlying factors that influence the structure of ant-plant networks have been separately explored, the simultaneous contribution of several biological and ecological attributes inherent to the species, guild or habitat level has not been addressed.MethodsFor a tropical seasonal site we recorded (in 48 censuses) the frequency of pairwise ant-plant interactions mediated by extrafloral nectaries (EFN) on different habitats and studied the resultant network structure. We addressed for the first time the role of mechanistic versus neutral determinants at the ‘fine-grain’ structure (pairwise interactions) of ant-plant networks. We explore the simultaneous contribution of several attributes of plant and ant species (i.e., EFN abundance and distribution, ant head length, behavioral dominance and invasive status), and habitat attributes (i.e., vegetation structure) in prevailing interactions as well as in overall network topology (community).ResultsOur studied network was highly-nested and non-modular, with core species having high species strengths (higher strength values for ants than plants) and low specialization. Plants had higher dependences on ants than vice versa. We found that habitat heterogeneity in vegetation structure (open vs. shaded habitats) was the main factor explaining network and fine-grain structure, with no evidence of neutral (abundance) effects.DiscussionCore ant species are relevant to most plants species at the network showing adaptations to nectar consumption and deterrent behavior. Thus larger ants interact with more plant species which, together with higher dependence of plants on ants, suggests potential biotic defense at a community scale. In our study site, heterogeneity in the ant-plant interactions among habitats is so prevalent that it emerges at community-level structural properties. High frequency of morphologically diverse and temporarily-active EFNs in all habitats suggests the relevance and seasonality of plant biotic defense provided by ants. The robust survey of ecological interactions and their biological/ecological correlates that we addressed provides insight of the interplay between adaptive-value traits and neutral effects in ecological networks. creator: Cecilia Díaz-Castelazo creator: Cristian A. Martínez-Adriano creator: Wesley Dáttilo creator: Victor Rico-Gray uri: https://doi.org/10.7717/peerj.8314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Díaz-Castelazo et al. title: Citizen science in the marine environment: estimating common dolphin densities in the north-east Atlantic link: https://peerj.com/articles/8335 last-modified: 2020-02-28 description: BackgroundCitizen science is increasingly popular and has the potential to collect extensive datasets at lower costs than traditional surveys conducted by professional scientists. Ferries have been used to collect data on cetacean populations for decades, providing long-term time series for monitoring of cetacean populations. One cetacean species of concern is the common dolphin, which has been found stranded around the north-east Atlantic in recent years, with high numbers on French coasts being attributed to fisheries bycatch. We estimate common dolphin densities in the north-east Atlantic and investigate the ability of citizen science data to identify changes in marine mammal densities and areas of importance.Materials and MethodsData were collected by citizen scientists on ferries between April and October in 2006–2017. Common dolphin sightings data from two ferry routes across three regions, Bay of Biscay (n = 569); south-west United Kingdom to the Isles of Scilly in the Celtic Sea (n = 260); and English Channel (n = 75), were used to estimate density across ferry routes. Two-stage Density Surface Models accounted for imperfect detection, and tested the influence of environmental (chlorophyll a, sea surface temperature, depth, and slope), spatial (latitude and longitude) and temporal terms (year and Julian day) on occurrence.ResultsOverall detection probability was highest in the areas sampled within the English Channel (0.384) and Bay of Biscay (0.348), and lowest on the Scilly’s route (0.158). Common dolphins were estimated to occur in higher densities on the Scilly’s route (0.400 per km2) and the Bay of Biscay (0.319 per km2), with low densities in the English Channel (0.025 per km2). Densities on the Scilly’s route appear to have been relatively stable since 2006 with a slight decrease in 2017. Densities peaked in the Bay of Biscay in 2013 with lower numbers since. Densities in the English Channel appear to have increased over time since 2009.DiscussionThis study highlights the effectiveness of citizen science data to investigate the distribution and density of cetaceans. The densities and temporal changes shown by this study are representative of those from wider-ranging robust estimates. We highlight the ability of citizen science to collect data over extensive periods of time which complements dedicated, designed surveys. Such long-term data are important to identify changes within a population; however, citizen science data may, in some situations, present challenges. We provide recommendations to ensure high-quality data which can be used to inform management and conservation of cetacean populations. creator: James R. Robbins creator: Lucy Babey creator: Clare B. Embling uri: https://doi.org/10.7717/peerj.8335 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Robbins et al. title: Correcting nuisance variation using Wasserstein distance link: https://peerj.com/articles/8594 last-modified: 2020-02-28 description: Profiling cellular phenotypes from microscopic imaging can provide meaningful biological information resulting from various factors affecting the cells. One motivating application is drug development: morphological cell features can be captured from images, from which similarities between different drug compounds applied at different doses can be quantified. The general approach is to find a function mapping the images to an embedding space of manageable dimensionality whose geometry captures relevant features of the input images. An important known issue for such methods is separating relevant biological signal from nuisance variation. For example, the embedding vectors tend to be more correlated for cells that were cultured and imaged during the same week than for those from different weeks, despite having identical drug compounds applied in both cases. In this case, the particular batch in which a set of experiments were conducted constitutes the domain of the data; an ideal set of image embeddings should contain only the relevant biological information (e.g., drug effects). We develop a general framework for adjusting the image embeddings in order to “forget” domain-specific information while preserving relevant biological information. To achieve this, we minimize a loss function based on distances between marginal distributions (such as the Wasserstein distance) of embeddings across domains for each replicated treatment. For the dataset we present results with, the only replicated treatment happens to be the negative control treatment, for which we do not expect any treatment-induced cell morphology changes. We find that for our transformed embeddings (i) the underlying geometric structure is not only preserved but the embeddings also carry improved biological signal; and (ii) less domain-specific information is present. creator: Gil Tabak creator: Minjie Fan creator: Samuel Yang creator: Stephan Hoyer creator: Geoffrey Davis uri: https://doi.org/10.7717/peerj.8594 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tabak et al. title: Screening and identification of critical biomarkers in erectile dysfunction: evidence from bioinformatic analysis link: https://peerj.com/articles/8653 last-modified: 2020-02-28 description: PurposeErectile dysfunction (ED) is one of the most common male-disease globally. Despite efforts to explain its pathogenesis, the molecular mechanisms of ED are still not well understood.MethodsThe microarray dataset GSE10804 was downloaded from the Gene Expression Omnibus (GEO) to find candidate genes in ED progression. After differentially expressed genes (DEGs) were identified, functional enrichment analysis was performed. In addition, a protein-protein interaction network (PPI) was established and module analysis was performed through the STRING and Cytoscape.Results and ConclusionsA total of 618 DEGs were identified in all, containing 430 downregulated genes and 188 upregulated genes. The enriched functions and pathways of the DEGs include transcription from RNA polymerase II promoter, cell adhesion, calcium ion binding, receptor binding, Akt signaling pathway, receptor interaction, protein digestion, and absorption. We picked out twenty-five hub genes, with biological process (BP) analyses revealing that the genes were principally associated with cellular responses to amino acid stimuli, extracellular matrix structural constituent, collagen trimer, protein digestion and absorption, ECM-receptor interaction and PI3K-Akt signaling pathway. To sum up, DEGs and hub genes distinguished in this study not only help us understand the molecular mechanisms behind the carcinogenesis and progression of ED, but also play a part in the diagnosis and treatment of ED by providing candidate targets. creator: Jialiang Hui creator: Ruiyu Liu creator: Haibo Zhang creator: Shuhua He creator: Anyang Wei uri: https://doi.org/10.7717/peerj.8653 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hui et al. title: Tensiomyographical responsiveness to peripheral fatigue in quadriceps femoris link: https://peerj.com/articles/8674 last-modified: 2020-02-28 description: BackgroundFatigue influences athletic performance and can also increase the risk of injury in sports, and most of the methods to evaluate it require an additional voluntary effort. Tensiomyography (TMG), which uses electrical stimulation and a displacement sensor to evaluate muscle contraction properties of one or more muscle bellies, has emerged as a technique that can assess the presence of peripheral and central fatigue without requiring additional voluntary efforts. However, the evaluation of the TMG’s ability to detect fatigue is limited, both at the level of muscle bellies and statistical methods. Thus, the aim of the present study was twofold: (i) to examine and compare the tensiomyographical responsiveness to quadriceps femoris (QF) fatigue by multiple statistical methods and (ii) to analyze sex differences in the variation produced by fatigue in TMG parameters.MethodsThirty-nine recreational athletes participated (19 males/20 females; aged 22 ± 2 years). TMG parameters of QF bellies and maximal voluntary isometric contraction (MVIC) were measured before and after a fatigue protocol. TMG parameters used were maximum radial deformation (Dm), contraction time between 10–90% of the Dm (Tc), contraction velocity between 10–90% (Vc) and of the first 10% (V10) of the Dm. Internal responsiveness of TMG to fatigue was analyzed by paired t-test and standardized response mean (SRM). External responsiveness was examined by correlations, regression models, and receiver operating characteristic (ROC) curves.ResultsAll TMG parameters, except for Tc of rectus femoris and vastus medialis, showed large internal responsiveness. In adjusted regression models by sex, only Dm and V10 of rectus femoris were statistically associated (p < 0.05) with b coefficients of 0.40 and 0.43, respectively. r2 explained the 22% of the total variance. In addition, these parameters could discriminate between QF with and without fatigue.ConclusionSince the QF is the main strength contributor during multiple physical activities, clinicians and trainers will be able to discriminate the presence of fatigue and the magnitude of changes in the QF strength by TMG evaluation. creator: Rodrigo Martín-San Agustín creator: Francesc Medina-Mirapeix creator: José Casaña-Granell creator: José A. García-Vidal creator: Carmen Lillo-Navarro creator: Josep C. Benítez-Martínez uri: https://doi.org/10.7717/peerj.8674 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Martín-San Agustín et al. title: Native bees of high Andes of Central Chile (Hymenoptera: Apoidea): biodiversity, phenology and the description of a new species of Xeromelissa Cockerell (Hymenoptera: Colletidae: Xeromelissinae) link: https://peerj.com/articles/8675 last-modified: 2020-02-28 description: High-altitude ecosystems are found in mountain chains and plateaus worldwide. These areas tend to be underrepresented in insect biodiversity assessments because of the challenges related to systematic survey at these elevations, such as extreme climatic and geographic conditions. Nonetheless, high-altitude ecosystems are of paramount importance because they have been seen to be species pumps for other geographic areas, such as adjacent locations, functioning as buffers for population declines. Moreover, these ecosystems and their biodiversity have been proposed to be fast-responding indicators of the impacts caused by global climate change. Bees have been highlighted among the insect groups that have been affected by these problems. This work used bees as a proxy to demonstrate and reinforce the importance of systematic surveys of high-altitude ecosystems. Here, field collections were undertaken and an updated review was conducted for the native bee biodiversity of the high-altitude ecosystem found at the Andes system of central Chile, including the phenological trends of these insects during the flowering season. Of the 58 species that have been described for this location, we were able to confirm the occurrence of 46 of these species as a result of our sampling. In addition, thanks to these recent collections, a new species of Xeromelissa Cockerell is described in the present work. These findings highlight the need for further high-altitude insect surveys of this biome, which include both temporal and spatial complexity in their design, to allow for accurate assessment of bee species diversity and compositional changes in these mountain regions. creator: Patricia Henríquez-Piskulich creator: Cristian A. Villagra creator: Alejandro Vera uri: https://doi.org/10.7717/peerj.8675 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Henríquez-Piskulich et al. title: Gene expression patterns of novel visual and non-visual opsin families in immature and mature Japanese eel males link: https://peerj.com/articles/8326 last-modified: 2020-02-27 description: This study was carried out to identify and estimate physiological function of a new type of opsin subfamily present in the retina and whole brain tissues of Japanese eel using RNA–Seq transcriptome method. A total of 18 opsin subfamilies were identified through RNA–seq. The visual opsin family included Rh2, SWS2, FWO, DSO, and Exo-Rhod. The non-visual opsin family included four types of melanopsin subfamily (Opn4x1, Opn4x2, Opn4m1, and Opn4m2), peropsin, two types of neuropsin subfamily (Opn5-like, Opn5), Opn3, three types of TMT opsin subfamily (TMT1, 2, 3), VA-opsin, and parapinopsin. In terms of changes in photoreceptor gene expression in the retina of sexually mature and immature male eels, DSO mRNA increased in the maturation group. Analysis of expression of opsin family gene in male eel brain before and after maturation revealed that DSO and SWS2 expression in terms of visual opsin mRNA increased in the sexually mature group. In terms of non-visual opsin mRNA, parapinopsin mRNA increased whereas that of TMT2 decreased in the fore-brain of the sexually mature group. The mRNA for parapinopsin increased in the mid-brain of the sexually mature group, whereas those of TMT1 and TMT3 increased in the hind-brain of the sexually mature group. DSO mRNA also increased in the retina after sexual maturation, and DSO and SWS2 mRNA increased in whole brain part, suggesting that DSO and SWS2 are closely related to sexual maturation. creator: Jun-Hwan Byun creator: Ji-Yeon Hyeon creator: Eun-Su Kim creator: Byeong-Hoon Kim creator: Hiroshi Miyanishi creator: Hirohiko Kagawa creator: Yuki Takeuchi creator: Se-Jae Kim creator: Akihiro Takemura creator: Sung-Pyo Hur uri: https://doi.org/10.7717/peerj.8326 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Byun et al. title: Evaluation of a new Argovit as an antiviral agent included in feed to protect the shrimp Litopenaeus vannamei against White Spot Syndrome Virus infection link: https://peerj.com/articles/8446 last-modified: 2020-02-27 description: In this study, four experimental assays were conducted to evaluate the use of a new silver nanoparticle formulation named Argovit-4, which was prepared with slight modifications to enhance its biological activity against white spot syndrome virus (WSSV) in shrimp culture. The goals of these assays were to (1) determine the protective effect of Argovit-4 against WSSV, (2) determine whether Argovit-4 supplemented in feed exhibits toxicity towards shrimp, (3) determine whether Argovit-4 as antiviral additive in feed can prevent or delay/reduce WSSV-induced shrimp mortality, and (4) determine whether Argovit-4 supplemented in feed alters the early stages of the shrimp immune response. In bioassay 1, several viral inocula calibrated at 7 SID50(shrimp infectious doses 50% endpoint) were exposed to 40, 100, 200 and 1,000 ng/SID50 of Ag+ and then intramuscularly injected into shrimp for 96 h. In bioassay 2, shrimp were fed Argovit-4 supplemented in feed at different concentrations (10, 100 and 1,000 µg per gram of feed) for 192 h. In bioassay 3, shrimp were treated with Argovit-4 supplemented in feed at different concentrations and then challenged against WSSV for 192 h. In bioassay 4, quantitative real-time RT-qPCR was performed to measure the transcriptional responses of five immune-relevant genes in haemocytes of experimental shrimp treated with Argovit-4 supplemented in feed at 0, 6, 12, 24 and 48 h. The intramuscularly injected Argovit-4 showed a dose-dependent effect (p < 0.05) on the cumulative shrimp mortality from 0–96 h post-infection. In the second bioassay, shrimp fed Argovit-4 supplemented in feed did not show signs of toxicity for the assayed doses over the 192-h experiment. The third and fourth bioassays showed that shrimp challenged with WSSV at 1,000 µg/g feed exhibited reduced mortality without altering the expression of some immune system-related genes according to the observed level of transcriptional. This study is the first show that the new Argovit-4 formulation has potential as an antiviral additive in feed against WSSV and demonstrates a practical therapeutic strategy to control WSSV and possibly other invertebrate pathogens in shrimp aquaculture. creator: Carlos R. Romo-Quiñonez creator: Ana R. Álvarez-Sánchez creator: Pindaro Álvarez-Ruiz creator: Maria C. Chávez-Sánchez creator: Nina Bogdanchikova creator: Alexey Pestryakov creator: Claudio H. Mejia-Ruiz uri: https://doi.org/10.7717/peerj.8446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Romo-Quiñonez et al. title: DISCo-microbe: design of an identifiable synthetic community of microbes link: https://peerj.com/articles/8534 last-modified: 2020-02-27 description: BackgroundMicrobiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains.ResultsTo address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members.ConclusionsDISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub (https://github.com/dlcarper/DISCo-microbe) and Python Package Index (PYPI). creator: Dana L. Carper creator: Travis J. Lawrence creator: Alyssa A. Carrell creator: Dale A. Pelletier creator: David J. Weston uri: https://doi.org/10.7717/peerj.8534 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Carper et al. title: Modelling the effective reproduction number of vector-borne diseases: the yellow fever outbreak in Luanda, Angola 2015–2016 as an example link: https://peerj.com/articles/8601 last-modified: 2020-02-27 description: The burden of vector-borne diseases (Dengue, Zika virus, yellow fever, etc.) gradually increased in the past decade across the globe. Mathematical modelling on infectious diseases helps to study the transmission dynamics of the pathogens. Theoretically, the diseases can be controlled and eventually eradicated by maintaining the effective reproduction number, (${\mathcal{R}}_{\mathrm{eff}}$Reff), strictly less than 1. We established a vector-host compartmental model, and derived (${\mathcal{R}}_{\mathrm{eff}}$Reff) for vector-borne diseases. The analytic form of the (${\mathcal{R}}_{\mathrm{eff}}$Reff) was found to be the product of the basic reproduction number and the geometric average of the susceptibilities of the host and vector populations. The (${\mathcal{R}}_{\mathrm{eff}}$Reff) formula was demonstrated to be consistent with the estimates of the 2015–2016 yellow fever outbreak in Luanda, and distinguished the second minor epidemic wave. For those using the compartmental model to study the vector-borne infectious disease epidemics, we further remark that it is important to be aware of whether one or two generations is considered for the transition “from host to vector to host” in reproduction number calculation. creator: Shi Zhao creator: Salihu S. Musa creator: Jay T. Hebert creator: Peihua Cao creator: Jinjun Ran creator: Jiayi Meng creator: Daihai He creator: Jing Qin uri: https://doi.org/10.7717/peerj.8601 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: Macrostylis metallicola spec. nov.—an isopod with geographically clustered genetic variability from a polymetallic-nodule area in the Clarion-Clipperton Fracture Zone link: https://peerj.com/articles/8621 last-modified: 2020-02-27 description: BackgroundThe Clarion-Clipperton Fracture Zone (CCFZ) in the Northeast Central Pacific Ocean is a region of heightened scientific and public interest because of its wealth in manganese nodules. Due to a poor ecological understanding at the abyssal seafloor and limited knowledge of the organisms inhabiting this area, huge efforts in alpha taxonomy are required. To predict and manage potential hazards associated with future mining, taxonomy is an essential first step to grasp fundamental ecosystem traits, such as biogeographic patterns, connectivity, and the potential for post-impact recolonization. Amongst samples from the Global Sea Mineral Resources NV exploration area (EA) in the CCFZ an undescribed species of the isopod crustacean family Macrostylidae was discovered. Previously, it has been reported from two other nearby regions, the Institut Français de Recherche pour l’Exploitation de la Mer and BGR EAs. There it was one of the more widely distributed and abundant species of the benthic macrofauna and exhibited geographically structured populations. It nevertheless remained taxonomically undescribed so far.MethodsThe new species is described by means of integrative taxonomy. Morphologically, macro photography, confocal microscopy, scanning electron microscopy and light microscopy were used to describe the species and to get first insights on its phylogenetic origin. Additionally, mitochondrial DNA markers were used to test the morphological allocation of the two dimorphic sexes and juvenile stages, to analyze geographic patterns of genetic differentiation, and to study intra-and inter-species relationships, also in light of previously published population genetics on this species.ResultsThe new species, Macrostylis metallicola spec. nov., is a typical representative of Macrostylidae as recognizable from the fossosoma, prognathous cephalothorax, and styliform uropods. It can be morphologically distinguished from congeners by a combination of character states which include the autapomorphic shape of the first pleopod of the copulatory male. A sexual dimorphism, as expressed by a peculiar sequence of article length-width ratios of the male antennula, indicates a relationship with M. marionaeKniesz, Brandt & Riehl (2018) and M. longipesHansen (1916) amongst other species sharing this dimorphism. Mitochondrial genetic markers point in a similar direction. M. metallicola appears to be amongst the more common and widely distributed components of the benthic macrofauna in this region which may suggest a resilience of this species to future mining activities because of its apparent potential for recolonization of impacted sites from adjacent areas of particular environmental interest. The genetic data, however, show geographic clustering of its genetic variability, pointing towards a limited potential for dispersal. Local extinction of populations could potentially not be compensated quickly and would mean a loss of genetic diversity of this species. creator: Torben Riehl creator: Bart De Smet uri: https://doi.org/10.7717/peerj.8621 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Riehl and De Smet title: Lactoferrin quantification in cattle faeces by ELISA link: https://peerj.com/articles/8631 last-modified: 2020-02-27 description: BackgroundPromoting and maintaining health is critical to ruminant welfare and productivity. Within human medicine, faecal lactoferrin is quantified for routine assessment of various gastrointestinal illnesses avoiding the need for blood sampling. This approach might also be adapted and applied for non-invasive health assessments in animals.MethodsIn this proof-of-concept study, a bovine lactoferrin enzyme-linked immunosorbent assays (ELISA), designed for serum and milk, was applied to a faecal supernatant to assess its potential for quantifying lactoferrin in the faeces of cattle. Faecal lactoferrin concentrations were compared to background levels to assess the viability of the technique. A comparison was then made against serum lactoferrin levels to determine if they were or were not reflective of one another.ResultsThe optical densities of faecal samples were significantly greater than background readings, supporting the hypothesis that the assay was effective in quantifying faecal lactoferrin (T13, 115 = 11.99, p < 0.0005). The mean faecal lactoferrin concentration was 0.269 µg mL−1 (S.E. 0.031) and the mean serum concentration 0.074 µg mL−1 (S.E. 0.005). Lactoferrin concentrations of faecal and serum samples, taken from the same animals on the same day, were significantly different (T21 = 2.20, p = 0.039) and did not correlate (r = 0.2699, p = 0.238).ConclusionResults support the hypothesis that lactoferrin can be quantified in cattle faeces by ELISA. Whilst further research is required to determine the physiological source of the lactoferrin, this highlights the potential of the method for non-invasive assessment of cattle immunology and pathology. creator: Andrew S. Cooke creator: Kathryn A. Watt creator: Greg F. Albery creator: Eric R. Morgan creator: Jennifer A.J. Dungait uri: https://doi.org/10.7717/peerj.8631 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cooke et al. title: Three-dimensional nephrometry scoring system: a precise scoring system to evaluate complexity of renal tumors suitable for partial nephrectomy link: https://peerj.com/articles/8637 last-modified: 2020-02-27 description: PurposeSeveral nephrometry scoring systems have been developed based on two-dimensional computerized tomography images to quantify anatomical features of renal tumors. We have developed an accurate three-dimensional nephrometry scoring system to respond to the urgent need for advanced systems based on three-dimensional images.Materials and MethodsWe retrospectively reviewed 135 patients who underwent partial nephrectomy in our institution. Stereoscopic models were reconstructed from preoperative computerized tomography images and three-dimensional scores were assigned directly on stereoscopic models. All tumors were analyzed for following features: tumor volume; endophytic tumor proportion; renal vascular variations; tumor’s relationships with urinary collecting system or renal sinus; longitudinal distance from tumor to equatorial plane. Correlation between three-dimensional score and warm ischemic time was calculated compared with existing classical nephrometry scoring systems. The value of nephrometry scoring systems predicting longer warm ischemic time was explored by receiver operating characteristic curves.ResultsMean tumor volume was 31.25 ml; endophytic volume was less than 50% in 42 cases, more than 50% in 79 cases, and 100% in 14 cases; mean longitudinal distance from tumor to equatorial plane was 1.41 cm; 30 patients (22.2%) presented renal vascular variations; 18 cases (13.3%) involved both urinary collecting system and sinus. Mean three-dimensional score was 8.3. Variance analysis and covariance analysis revealed warm ischemic time a significant association with all evaluated tumor features. Furthermore, three-dimensional scores most highly correlated with warm ischemic time (rs = 0.64, p < 0.001), followed by R.E.N.A.L. scores (rs = 0.21, p = 0.012), centrality index (rs = − 0.20, p = 0.019) and Preoperative Aspects and Dimensions Used for Anatomy score (rs = 0.20, p = 0.019). Area under curve of above nephrometry scoring systems was 0.91, 0.67, 0.68 and 0.67 respectively (p < 0.05).ConclusionsThe three-dimensional scoring system developed in this study was a highly-accurate system to quantify the anatomical features of renal tumors. It was identified to have a value in predicting duration of warm ischemic time. creator: Jingchao Liu creator: Jing Liu creator: Shuo Wang creator: Haifeng Zhao creator: Chuanxin Tian creator: Benkang Shi creator: Xianzhou Jiang uri: https://doi.org/10.7717/peerj.8637 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Antimicrobial resistance and genetic relationships of enterococci from siblings and non-siblings Heliconius erato phyllis caterpillars link: https://peerj.com/articles/8647 last-modified: 2020-02-27 description: BackgroundStudies evaluating bacteria in insects can provide information about host–microorganism–environment interactions. The gut microbial community has a profound effect on different physiological functions of insects. Enterococcus spp. are part of the gut community in humans and other animals, as well as in insects. The presence and antimicrobial resistance profile of enterococci are well studied in different animals; however, data for Heliconius erato phyllis (Lepidoptera: Nymphalidae) do not yet exist. Therefore, the aims of this study were to evaluate the distribution of enterococcal species, their antimicrobial resistance profile and virulence genes, and the genetic relationships between enterococci isolated from fecal samples from sibling and non-sibling H. erato phyllis caterpillars collected from different sites in South Brazil.MethodsThree H. erato phyllis females were captured (two from a forest fragment and one from an urban area), and kept individually in open-air insectaries. Eggs were collected and caterpillars (siblings and non-siblings) were fed daily with Passiflora suberosa leaves. Fecal samples (n = 12) were collected from fifth-instar caterpillars, inoculated in selective medium, and 15 bacterial colonies were randomly selected from each sample. Enterococci were identified by PCR and MALDI-TOF, analyzed by disk diffusion antimicrobial susceptibility tests, and screened for resistance and virulence genes by PCR. The genetic relationships between the strains were determined using pulsed-field gel electrophoresis (PFGE).ResultsA total of 178 enterococci strains were identified: E. casseliflavus (74.15%; n = 132), E. mundtii (21.34%; n = 38), E. faecalis (1.12%; n = 2) and Enterococcus sp. (3.37%; n = 6). High rates of resistance to rifampicin (56%) and erythromycin (31%) were observed; 120 (67.41%) of the isolates showed resistance to at least one antibiotic and six (3.37%) were multidrug-resistant.None of the erythromycin-resistant strains was positive for the erm(B) and msrC genes. The virulence genes esp, ace, and gelE were observed in 35%, 7%, and 1% of the strains, respectively. PFGE separated the enterococci into 22 patterns, four being composed of strains from sibling caterpillars.ConclusionEnterococcus casseliflavus was the dominant species in fecal samples of fifth-instar caterpillars. Resistant enterococci strains may be related to environmental pollution or the resistome. The PFGE analysis showed genetic relationships between some strains, suggesting that the enterococci isolated from fecal samples of the sibling caterpillars might have come from common sources, e.g., via diet (herbivory) and/or vertical transmission (through the egg surface). Further studies will be conducted to better understand the role of Enterococcus in the microbial community of the gastrointestinal tract of these insects, and the mechanisms involved in acquisition and maintenance of enterococci. creator: Rosana Huff creator: Rebeca Inhoque Pereira creator: Caroline Pissetti creator: Aldo Mellender de Araújo creator: Pedro Alves d’Azevedo creator: Jeverson Frazzon creator: Ana Paula GuedesFrazzon uri: https://doi.org/10.7717/peerj.8647 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huff et al. title: Comprehensive phenotyping and transcriptome profiling to study nanotoxicity in C. elegans link: https://peerj.com/articles/8684 last-modified: 2020-02-27 description: Engineered nanoparticles are used at an increasing rate in both industry and medicine without fully understanding their impact on health and environment. The nematode Caenorhabditis elegans is a suitable model to study the toxic effects of nanoparticles as it is amenable to comprehensive phenotyping, such as locomotion, growth, neurotoxicity and reproduction. In this study, we systematically evaluated the effects of silver (Ag) and five metal oxide nanoparticles: SiO2, CeO2, CuO, Al2O3 and TiO2. The results showed that Ag and SiO2 exposures had the most toxic effects on locomotion velocity, growth and reproduction, whereas CeO2, Al2O3 and CuO exposures were mostly neurotoxic. We further performed RNAseq to compare the gene expression profiles underlying Ag and SiO2toxicities. Gene set enrichment analyses revealed that exposures to Ag and SiO2consistently downregulated several biological processes (regulations in locomotion, reproductive process and cell growth) and pathways (neuroactive ligand-receptor interaction, wnt and MAPK signaling, etc.), with opposite effects on genes involved in innate immunity. Our results contribute to mechanistic insights into toxicity of Ag and SiO2 nanoparticles and demonstrated that C. elegans as a valuable model for nanotoxicity assessment. creator: Charles Viau creator: Orçun Haçariz creator: Farial Karimian creator: Jianguo Xia uri: https://doi.org/10.7717/peerj.8684 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Viau et al. title: Iroki: automatic customization and visualization of phylogenetic trees link: https://peerj.com/articles/8584 last-modified: 2020-02-26 description: Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki. creator: Ryan M. Moore creator: Amelia O. Harrison creator: Sean M. McAllister creator: Shawn W. Polson creator: K. Eric Wommack uri: https://doi.org/10.7717/peerj.8584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Moore et al. title: Sarcopenia in male patients with head and neck cancer receiving chemoradiotherapy: a longitudinal pilot study link: https://peerj.com/articles/8617 last-modified: 2020-02-26 description: IntroductionMuscle wasting conditions such as sarcopenia may be highly prevalent in advanced head and neck cancer (HNC) patients (16–71%), with these prevalence rates substantially greater in those who have received chemo-radiotherapy (CRT). According to the updated European Working Group on Sarcopenia in Older People consensus statement, sarcopenia is defined as the age-related loss of muscle strength, muscle mass and physical performance. The high prevalence of sarcopenia in HNC patients is concerning as it has been associated with substantially increased risk of CRT toxicity, respiratory complications and early mortality. With the high prevalence of HNC and sarcopenia in India and the strong link between sarcopenia and poor HNC patient outcomes, it is important to screen for the presence of sarcopenia in Indian patients receiving CRT for HNC.MethodsThis longitudinal pilot study aimed to routinely monitor 19 men receiving CRT for their HNC for a variety of sarcopenic-related outcomes over three time points during their 7 weeks of CRT. Participants were required to be male, with a minimum age of 30 years, with a Stage III, IVa or IVb diagnosis of HNC and be currently undergoing a 7 weeks course of CRT in an oncology department. Outcomes included probable sarcopenic diagnosis were estimated by the SARC-F, handgrip strength, skeletal muscle mass was estimated by bioelectrical impedance and physical performance was assessed by the Timed Up and Go. Repeated measures ANOVA and Bonferroni post-hoc tests were used to identify significant differences at the three time points with a p < 0.05.ResultsThe 19 participants in this trial at a mean age of 56.5 ± 10.2 years (range = 39–75 years), with most (n = 13, 68.4%) employed in laboring occupations. At baseline, 31.5% (n = 6) of the participants already had probable sarcopenia based on their total SARC-F score, with this increasing to 89.4% (n = 17) at the end of 7 weeks CRT. In addition, significant decreases in strength, skeletal muscle mass and Timed Up and Go performance were observed, with these declines significantly greater at 7 weeks than 3 weeks after commencing CRT.ConclusionsPatients with HNC undergoing 7 weeks of CRT showed clinically significant increases in the incidence of probable sarcopenia based on their total SARC-F score as well as clinically significant declines in handgrip strength, skeletal muscle mass and Timed Up and Go performance. Due to the relationship between sarcopenia and a host of adverse events related to CRT in HNC patients, these results suggest that oncologists and their allied health teams should routinely monitor these patients during CRT and provide the relevant exercise therapy and nutritional support to those patients in need. creator: Namrata S. Chauhan creator: Stephen Rajan Samuel creator: Niranjan Meenar creator: PU Prakash Saxena creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.8617 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chauhan et al. title: Identification and validation of potential key long noncoding RNAs in sorafenib-resistant hepatocellular carcinoma cells link: https://peerj.com/articles/8624 last-modified: 2020-02-26 description: As the first-line treatment, sorafenib has been used for advanced hepatocellular carcinoma (HCC), but the chemoresistance commonly restricts to the clinical efficiency. In this study, we intend to investigate the genome-wide expression pattern of long noncoding RNAs (lncRNAs) in sorafenib-resistant HCC. Herein, we identified thousands of differentially expressed lncRNAs in sorafenib-resistant HCC cells by high-throughput sequencing compared to the parental. Besides, based on GO (Gene Ontology) term enrichment analysis, these differentially expressed lncRNAs are mainly related to binding and catalytic activity and biological regulation of metabolic processes in both the sorafenib-resistant Huh7 cells (Huh7-S) and sorafenib-resistant HepG2 cells (HepG2-S) compared to the parental cells. Moreover, when analyzed by KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, the differentially expressed genes were significantly related to the tight junction. Among them, the expression of TCONS_00284048 and TCONS_00006019 was consistently up-regulated in sorafenib-resistant HCC cell lines, whereas when either was knocked down, the sensitivity of Huh7-S and HepG2-S cells to sorafenib was increased. Taken together, our data demonstrate that the lncRNA expression profile is significantly altered in sorafenib-resistant HCC cells as well as differentially expressed lncRNAs may play crucial functions on HCC sorafenib resistance and HCC progression. creator: Manya Wu creator: Xiaoyun Shen creator: Yanping Tang creator: Caifu Zhou creator: Haixia Li creator: Xiaoling Luo uri: https://doi.org/10.7717/peerj.8624 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wu et al. title: Tall Pinus luzmariae trees with genes from P. herrerae link: https://peerj.com/articles/8648 last-modified: 2020-02-26 description: ContextPinus herrerae and P. luzmariae are endemic to western Mexico, where they cover an area of more than 1 million hectares. Pinus herrerae is also cultivated in field trials in South Africa and South America, because of its considerable economic importance as a source of timber and resin. Seed quality, afforestation success and desirable traits may all be influenced by the presence of hybrid trees in seed stands.AimsWe aimed to determine the degree of hybridization between P. herrerae and P. luzmariae in seed stands of each species located in the Sierra Madre Occidental, Durango, Mexico.MethodsAFLP molecular markers from samples of 171 trees across five populations were analyzed with STRUCTURE and NewHybrids software to determine the degree of introgressive hybridization. The accuracy of STRUCTURE and NewHybrids in detecting hybrids was quantified using the software Hybridlab 1.0. Morphological analysis of 131 samples from two populations of P. herrerae and two populations of P. luzmariae was also conducted by Random Forest classification. The data were compared by Principal Coordinate Analysis (PCoA) in GenAlex 6.501.ResultsHybridization between Pinus herrerae and P. luzmariae was observed in all seed stands under study and resulted in enhancement of desirable silvicultural traits in the latter species. In P. luzmariae, only about 16% molecularly detected hybrids correspond to those identified on a morphological basis. However, the morphology of P. herrerae is not consistent with the molecularly identified hybrids from one population and is only consistent with 3.3 of those from the other population.ConclusionsThis is the first report of hybrid vigour (heterosis) in Mexican pines. Information about hybridization and introgression is essential for developing effective future breeding programs, successful establishment of plantations and management of natural forest stands. Understanding how natural hybridization may influence the evolution and adaptation of pines to climate change is a cornerstone to sustainable forest management including adaptive silviculture. creator: Christian Wehenkel creator: Samantha del Rocío Mariscal-Lucero creator: M. Socorro González-Elizondo creator: Víctor A. Aguirre-Galindo creator: Matthias Fladung creator: Carlos A. López-Sánchez uri: https://doi.org/10.7717/peerj.8648 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wehenkel et al. title: Element concentrations in pelagic Sargassum along the Mexican Caribbean coast in 2018-2019 link: https://peerj.com/articles/8667 last-modified: 2020-02-26 description: The massive influx of pelagic Sargassum spp. (sargasso) into the Mexican Caribbean Sea has caused major deterioration of the coastal environment and has affected the tourism industry as well as livelihoods since 2015. Species of Sargassum have high capacity to absorb metals; thus, leachates of sargasso may contribute to contamination by potentially toxic metals when they drain into the sea and into the groundwater when dumped in inadequate land deposits. Valorization of sargasso would contribute to sustainable management; therefore, knowledge on potentially toxic metal content is necessary to define possible uses of the algae. We present concentrations of 28 elements measured using a non-destructive X-ray fluorescence analyzer (XRF) in 63 samples of sargasso collected between August 2018 and June 2019 from eight localities along ∼370 km long coastline of the Mexican Caribbean Sea. The sargasso tissues contained detectable concentrations of Al, As, Ca, Cl, Cu, Fe, K, Mg, Mn, Mo, P, Pb, Rb, S, Si, Sr, Th, U, V, and Zn. The element concentration in sargasso varied on spatial and temporal scales, which likely depended on the previous trajectory of the pelagic masses, and whether these had (or had not) passed through contaminated areas. Total arsenic concentration varied between 24–172 ppm DW, exceeding the maximum limit for seaweed intended as animal fooder (40 ppm DW) in 86% of the samples. For valorization, we recommend analyses of metal contents as a mandatory practice or avoiding uses for nutritional purposes. The high arsenic content is also of concern for environmental contamination of the sea and aquifer. creator: Rosa E. Rodríguez-Martínez creator: Priyadarsi D. Roy creator: Nuria Torrescano-Valle creator: Nancy Cabanillas-Terán creator: Silvia Carrillo-Domínguez creator: Ligia Collado-Vides creator: Marta García-Sánchez creator: Brigitta I. van Tussenbroek uri: https://doi.org/10.7717/peerj.8667 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rodríguez-Martínez et al. title: Impact of examined lymph node count on long-term survival of T1-2N0M0 double primary NSCLC patients after surgery: a SEER study link: https://peerj.com/articles/8692 last-modified: 2020-02-26 description: PurposeThe relationship between examined lymph nodes (ELN) and survival has been confirmed in several single early-stage malignancies. We studied the association between the ELN count and the long-term survival of T1-2N0M0 double primary non-small cell lung cancer (DP-NSCLC) patients after surgery, based on the Surveillance, Epidemiology and End Results (SEER) database.MethodsA total of 948 patients were identified and their independent prognostic factors were analyzed. These factors included the ELN count, which related to overall survival (OS) and the cancer-specific survival (CSS) of synchronous (n = 426) and metachronous (n = 522) T1-2N0M0 DP-NSCLC patients after surgery.ResultsX-tile analysis indicated that the cutoff value for the sum of ELNs was 22 for both OS and CSS in the synchronous DP-NSCLC group. Patients with a sum of ELNs >22 were statistically more likely to survive than those with ≤22 ELNs. X-tile analysis revealed that the ELN count of the second lesion was related to both OS and CSS in the metachronous DP-NSCLC group. The optimal cutoff value was nine. These results were confirmed using univariate and multivariate Cox regression analyses.ConclusionOur findings indicate that ELN count was highly correlated with the long-term survival of T1-2N0M0 double primary NSCLC patients after surgery. creator: Kan Jiang creator: Xiaohui Zhi creator: Yue Shen creator: Yuanyuan Ma creator: Xinyu Su creator: Liqing Zhou uri: https://doi.org/10.7717/peerj.8692 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jiang et al. title: Holistic Environmental Approaches and Aichi Biodiversity Targets: accomplishments and perspectives for marine ecosystems link: https://peerj.com/articles/8171 last-modified: 2020-02-25 description: In order to help safeguard biodiversity from global changes, the Conference of the Parties developed a Strategic Plan for Biodiversity for the period 2011–2020 that included a list of twenty specific objectives known as the Aichi Biodiversity Targets. With the end of that timeframe in sight, and despite major advancements in biodiversity conservation, evidence suggests that the majority of the Targets are unlikely to be met. This article is part of a series of perspective pieces from the 4th World Conference on Marine Biodiversity (May 2018, Montréal, Canada) to identify next steps towards successful biodiversity conservation in marine environments. We specifically reviewed holistic environmental assessment studies (HEA) and their contribution to reaching the Targets. Our analysis was based on multiple environmental approaches which can be considered as holistic, and we discuss how HEA can contribute to the Aichi Biodiversity Targets in the near future. We found that only a few HEA articles considered a specific Biodiversity Target in their research, and that Target 11, which focuses on marine protected areas, was the most commonly cited. We propose five research priorities to enhance HEA for marine biodiversity conservation beyond 2020: (i) expand the use of holistic approaches in environmental assessments, (ii) standardize HEA vocabulary, (iii) enhance data collection, sharing and management, (iv) consider ecosystem spatio-temporal variability and (v) integrate ecosystem services in HEA. The consideration of these priorities will promote the value of HEA and will benefit the Strategic Plan for Biodiversity. creator: Elliot Dreujou creator: Charlotte Carrier-Belleau creator: Jesica Goldsmit creator: Dario Fiorentino creator: Radhouane Ben-Hamadou creator: Jose H. Muelbert creator: Jasmin A. Godbold creator: Rémi M. Daigle creator: David Beauchesne uri: https://doi.org/10.7717/peerj.8171 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dreujou et al. title: Transcriptome analysis and transcription factors responsive to drought stress in Hibiscus cannabinus link: https://peerj.com/articles/8470 last-modified: 2020-02-25 description: Kenaf is an annual bast fiber crop. Drought stress influences the growth of kenaf stems and causes a marked decrease in fiber yield and quality. Research on the drought resistance of kenaf is therefore important, but limited information is available on the response mechanism of kenaf to drought stress. In this study, a transcriptome analysis of genes associated with the drought stress response in kenaf was performed. About 264,244,210 bp high-quality reads were obtained after strict quality inspection and data cleaning. Compared with the control group, 4,281 genes were differentially expressed in plants treated with drought stress for 7 d (the drought stress group). Compared with the control group, 605 genes showed differential expression in plants subjected to drought stress for 6 d and then watered for 1 d (the rewatering group). Compared with the rewatering group, 5,004 genes were differentially expressed in the drought stress group. In the comparisons between the drought stress and control groups, and between the drought stress and rewatering groups, the pathway that showed the most highly significant enrichment was plant hormone signal transduction. In the comparison between the rewatering and control groups, the pathways that showed the most highly significant enrichment were starch and sucrose metabolism. Eight transcription factors belonging to the AP2/ERF, MYB, NAC, and WRKY families (two transcription factors per family) detected in the leaf transcriptome were associated with the drought stress response. The identified transcription factors provide a basis for further investigation of the response mechanism of kenaf to drought stress. creator: Xia An creator: Guanrong Jin creator: Xiahong Luo creator: Changli Chen creator: Wenlue Li creator: Guanlin Zhu uri: https://doi.org/10.7717/peerj.8470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 An et al. title: A comparative study of machine learning algorithms for predicting acute kidney injury after liver cancer resection link: https://peerj.com/articles/8583 last-modified: 2020-02-25 description: ObjectiveMachine learning methods may have better or comparable predictive ability than traditional analysis. We explore machine learning methods to predict the likelihood of acute kidney injury after liver cancer resection.MethodsThis is a secondary analysis cohort study. We reviewed data from patients who had undergone resection of primary hepatocellular carcinoma between January 2008 and October 2015.ResultsThe analysis included 1,173 hepatectomy patients, 77 (6.6%) of whom had AKI and 1,096 (93.4%) who did not. The importance matrix for the Gbdt algorithm model shows that age, cholesterol, tumor size, surgery duration and PLT were the five most important parameters. Figure 1 shows that Age, tumor size and surgery duration had weak positive correlations with AKI. Cholesterol and PLT also had weak negative correlations with AKI. The models constructed by the four machine learning algorithms in the training group were compared. Among the four machine learning algorithms, random forest and gbm had the highest accuracy, 0.989 and 0.970 respectively. The precision of four of the five algorithms was 1, random forest being the exception. Among the test group, gbm had the highest accuracy (0.932). Random forest and gbm had the highest precision, both being 0.333. The AUC values for the four algorithms were: Gbdt (0.772), gbm (0.725), forest (0.662) and DecisionTree (0.628).ConclusionsMachine learning technology can predict acute kidney injury after hepatectomy. Age, cholesterol, tumor size, surgery duration and PLT influence the likelihood and development of postoperative acute kidney injury. creator: Lei Lei creator: Ying Wang creator: Qiong Xue creator: Jianhua Tong creator: Cheng-Mao Zhou creator: Jian-Jun Yang uri: https://doi.org/10.7717/peerj.8583 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lei et al. title: The detection of trans gene fragments of hEPO in gene doping model mice by Taqman qPCR assay link: https://peerj.com/articles/8595 last-modified: 2020-02-25 description: BackgroundWith the rapid progress of genetic engineering and gene therapy methods, the World Anti-Doping Agency has raised concerns regarding gene doping, which is prohibited in sports. However, there is no standard method available for detecting transgenes delivered by injection of naked plasmids. Here, we developed a detection method for detecting transgenes delivered by injection of naked plasmids in a mouse model that mimics gene doping.MethodsWhole blood from the tail tip and one piece of stool were used as pre-samples of injection. Next, a plasmid vector containing the human erythropoietin (hEPO) gene was injected into mice through intravenous (IV), intraperitoneal (IP), or local muscular (IM) injection. At 1, 2, 3, 6, 12, 24, and 48 h after injection, approximately 50 µL whole blood was collected from the tail tip. One piece of stool was collected at 6, 12, 24, and 48 h. From each sample, total DNA was extracted and transgene fragments were analyzed by Taqman quantitative PCR (qPCR) and SYBR green qPCR.ResultsIn whole blood DNA samples evaluated by Taqman qPCR, the transgene fragments were detected at all time points in the IP sample and at 1, 2, 3, 6, and 12 h in the IV and IM samples. In the stool-DNA samples, the transgene fragments were detected at 6, 12, 24, and 48 h in the IV and IM samples by Taqman qPCR. In the analysis by SYBR green qPCR, the transgene fragments were detected at some time point in both specimens; however, many non-specific amplicons were detected.ConclusionsThese results indicate that transgene fragments evaluated after each injection method of naked plasmids were detected in whole-blood and stool DNA samples. These findings may facilitate the development of methods for detecting gene doping. creator: Kai Aoki creator: Takehito Sugasawa creator: Kouki Yanazawa creator: Koichi Watanabe creator: Tohru Takemasa creator: Yoshinori Takeuchi creator: Yuichi Aita creator: Naoya Yahagi creator: Yasuko Yoshida creator: Tomoaki Kuji creator: Nanami Sekine creator: Kaoru Takeuchi creator: Haruna Ueda creator: Yasushi Kawakami creator: Kazuhiro Takekoshi uri: https://doi.org/10.7717/peerj.8595 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Aoki et al. title: Forelimb musculoskeletal-tendinous growth in frogs link: https://peerj.com/articles/8618 last-modified: 2020-02-25 description: The tendons unite and transmit the strength of the muscles to the bones, allowing movement dexterity, the distribution of the strength of the limbs to the digits, and an improved muscle performance for a wide range of locomotor activities. Tissue differentiation and maturation of the structures involved in locomotion are completed during the juvenile stage; however, few studies have investigated the ontogenetic variation of the musculoskeletal-tendinous system. We ask whether all those integrated tissues and limb structures growth synchronically between them and along with body length. We examined the ontogenetic variation in selected muscles, tendons and bones of the forelimbs in seventy-seven specimens belonging to seven anuran species of different clades and of three age categories, and investigate the relative growth of the forelimb musculoskeletal-tendinous structures throughout ontogeny. Ten muscles and nine tendons and their respective large bones (humerus and radioulna) were removed intact, and their length was measured and analyzed through a multivariate approach of allometry. We obtained an allometry coefficient, which indicates how the coefficient departures from isometry as well as allometric trends. Our data suggest that along with the post-metamorphic ontogeny, muscles tend to elongate proportionally to bone length, with a positive allometric trend. On the contrary, tendons show a negative allometric growth trend. Only two species show different patterns: Rhinella granulosa and Physalaemus biligonigerus, with an isometric and positive growth of muscles and bones, and most tendons being isometric. creator: Mónica Soliz creator: María Jose Tulli creator: Virginia Abdala uri: https://doi.org/10.7717/peerj.8618 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Soliz et al. title: Taxonomic clarifications concerning the crocodyliform genus Isisfordia link: https://peerj.com/articles/8630 last-modified: 2020-02-25 description: BackgroundIn a recent paper, a new species of the crocodyliform genus Isisfordia was erected based on, in part, a specimen previously designated as the holotype of ‘Crocodylus (Bottosaurus)’ selaslophensis. This new species was given the name Isisfordia molnari. However, because the holotype of ‘Crocodylus (Bottosaurus)’ selaslophensis displays a unique combination of characters and does not overlap with the holotype of I. molnari, both names remain valid according to ICZN regulations.ResultsThe present work instates Isisfordia selaslophensis comb. nov., recognising the seniority of the original specific epithet given to the specimen. The specimen is also reaffirmed as the holotype of the species. Isisfordia molnari is rediagnosed based on non-overlapping material but is potentially referable to Isisfordia selaslophensis. All other analyses, descriptions, diagnoses and conclusions stated by the original study remain valid. creator: Lachlan J. Hart uri: https://doi.org/10.7717/peerj.8630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hart title: Campsites, forest fires, and entry point distance affect earthworm abundance in the Boundary Waters Canoe Area Wilderness link: https://peerj.com/articles/8656 last-modified: 2020-02-25 description: Factors controlling the spread of invasive earthworms in Minnesota’s Boundary Waters Canoe Area Wilderness are poorly known. Believed to have been introduced by anglers who use them as bait, invasive earthworms can alter the physical and chemical properties of soil and modify forest plant communities. To examine factors influencing earthworm distribution and abundance, we sampled 38 islands across five lakes to assess the effects of campsites, fire and entry point distance on earthworm density, biomass and species richness. We hypothesized that all three parameters would be greater on islands with campsites, lower on burned islands and would decrease with distance from the wilderness entry point. In addition to sampling earthworms, we collected soil cores to examine soil organic matter and recorded ground and vegetation cover. Campsite presence was the single most important factor affecting sampled earthworm communities; density, biomass and species richness were all higher on islands having campsites. Fire was associated with reduced earthworm density, but had no direct effects on earthworm biomass or species richness. Fire influenced earthworm biomass primarily through its negative relationship to groundcover and through an interaction with entry point distance. Entry point distance itself affected earthworm density and biomass. For islands with campsites, earthworm biomass increased with distance from the entry point. creator: Todd Wellnitz creator: Jenna L. Barlow creator: Cory M. Dick creator: Terrance R. Shaurette creator: Brian M. Johnson creator: Troy Wesley creator: Evan Weiher uri: https://doi.org/10.7717/peerj.8656 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wellnitz et al. title: Full-annual demography and seasonal cycles in a resident vertebrate link: https://peerj.com/articles/8658 last-modified: 2020-02-25 description: Wildlife demography is typically studied at a single point in time within a year when species, often during the reproductive season, are more active and therefore easier to find. However, this provides only a low-resolution glimpse into demographic temporal patterns over time and may hamper a more complete understanding of the population dynamics of a species over the full annual cycle. The full annual cycle is often influenced by environmental seasonality, which induces a cyclic behavior in many species. However, cycles have rarely been explicitly included in models for demographic parameters, and most information on full annual cycle demography is restricted to migratory species. Here we used a high-resolution capture-recapture study of a resident tropical lizard to assess the full intra-annual demography and within-year periodicity in survival, temporary emigration and recapture probabilities. We found important variation over the annual cycle and up to 92% of the total monthly variation explained by cycles. Fine-scale demographic studies and assessments on the importance of cycles within parameters may be a powerful way to achieve a better understanding of population persistence over time. creator: Murilo Guimarães creator: Decio T. Correa creator: Marília Palumbo Gaiarsa creator: Marc Kéry uri: https://doi.org/10.7717/peerj.8658 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guimarães et al. title: The body plan of Halszkaraptor escuilliei (Dinosauria, Theropoda) is not a transitional form along the evolution of dromaeosaurid hypercarnivory link: https://peerj.com/articles/8672 last-modified: 2020-02-25 description: The dromaeosaurid theropod Halszkaraptor escuilliei is characterized by several unusual features absent in other paravians, part of which has been interpreted as diagnostic of a novel lineage adapted to a semiaquatic ecology. Recently, these evolutionary and ecological interpretations have been challenged, and Halszkaraptor has been claimed to be a transitional form between non-dromaeosaurid maniraptoriforms and other dromaeosaurids: following that reevaluation, its peculiar body plan would represent the retention of several maniraptoran plesiomorphies, lost among other dromaeosaurids, and not an adaptation to a novel ecology. This alternative scenario is here carefully investigated and tested. It is shown that most statements supporting this scenario are based on misinterpretation of anatomical traits and bibliography. Once these statements have been corrected, character state transition optimization over a well-supported phylogenetic framework indicates that the large majority of the peculiar features of the Halszkaraptor lineage are derived novelties acquired by the latter after its divergence from the last ancestor shared with eudromaeosaurs, and thus are not maniraptoriform plesiomorphies. At least seven novelties of the Halszkaraptor lineage are convergently acquired with spinosaurids, and are integrated in semiaquatic adaptations: one of these is reported here for the first time. The amount of morphological divergence of Halszkaraptorinae from the ancestral dromaeosaurid condition is comparable to those of Microraptorinae and Velociraptorinae. Among extant taxa, the sawbills (Mergini, Anseriformes) show the closest ecomorphological similarity with the peculiar body plan inferred for Halszkaraptor. The halszkaraptorine bauplan is thus confirmed as a derived amphibious specialization, and does not represent a “transitional” stage along the evolution of dromaeosaurids. creator: Andrea Cau uri: https://doi.org/10.7717/peerj.8672 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cau title: Novel association between TGFA, TGFB1, IRF1, PTGS2 and IKBKB single-nucleotide polymorphisms and occurrence, severity and treatment response of major depressive disorder link: https://peerj.com/articles/8676 last-modified: 2020-02-25 description: BackgroundActivation of the immune system might affect the severity of depressive episodes as well as response to the antidepressant treatment. The purpose of this study was to investigate whether the occurrence of variant alleles of analyzed SNPs are involved in prevalence and progression of depression. Moreover, selected genes and SNPs have not been investigated in context of the disease severity and treatment. Therefore, six polymorphisms were selected: g.41354391A>G-TGFB1 (rs1800469), g.132484229C>A-IRF (rs2070729), g.186643058A>G-PTGS2 (rs5275), g.186640617C>T-PTGS2 (rs4648308), g.70677994G>A-TGFA (rs2166975) and g.42140549G>T–IKBKB (rs5029748).MethodsA total of 360 (180 patients and 180 controls) DNA samples were genotyped using TaqMan probes.ResultsWe observed that A/G of the rs2166975 TGFA, A/C of rs2070729 IRF1 and G/T of rs5029748 IKBKB were associated with an increased risk of depression development while the T/T of rs5029748 IKBKB, T/T of rs4648308 PTGS2 and G/G of rs2166975 TGFA reduced this risk. We also stratified the study group according to gender and found that genotype A/G and allele G of the rs2166975 TGFA, G/T of rs5029748 IKBKB as well as C allele of rs4648308 PTGS2, homozygote A/A and allele A of rs5275 PTGS2 were associated with increased risk of depression development in men while homozygote G/G of rs5275 PTGS2 decreased this risk. Moreover, C/T of rs4648308 PTGS2 and A/G of rs5275 PTGS2 was positively correlated with the risk of the disease occurrence in women. Furthermore, a gene–gene analysis revealed a link between studied polymorphisms and depression. In addition, A/A of rs1800469 TGFB1 was associated with earlier age of onset of the disease while G/G of this SNP increased severity of the depressive episode. Interestingly, A/C of rs2070729 IRF1 and T/T of rs5029748 IKBKB may modulate the effectiveness of selective serotonin reuptake inhibitors therapy. In conclusion, studied SNPs may modulate the risk of occurrence, age of onset, severity of the disease and response to the antidepressant treatment. creator: Katarzyna Bialek creator: Piotr Czarny creator: Cezary Watala creator: Paulina Wigner creator: Monika Talarowska creator: Piotr Galecki creator: Janusz Szemraj creator: Tomasz Sliwinski uri: https://doi.org/10.7717/peerj.8676 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bialek et al. title: Monitoring the training dose and acute fatigue response during elbow flexor resistance training using a custom-made resistance band link: https://peerj.com/articles/8689 last-modified: 2020-02-25 description: BackgroundHome-based resistance training offers an alternative to traditional, hospital-based or rehabilitation center-based resistance training and has attracted much attention recently. However, without the supervision of a therapist or the assistance of an exercise monitoring system, one of the biggest challenges of home-based resistance training is that the therapist may not know if the patient has performed the exercise as prescribed. A lack of objective measurements limits the ability of researchers to evaluate the outcome of exercise interventions and choose suitable training doses.ObjectiveTo create an automated and objective method for segmenting resistance force data into contraction phase-specific segments and calculate the repetition number and time-under-tension (TUT) during elbow flexor resistance training. A pilot study was conducted to evaluate the performance of the segmentation algorithm and to show the capability of the system in monitoring the compliance of patients to a prescribed training program in a practical resistance training setting.MethodsSix subjects (three male and three female) volunteered to participate in a fatigue and recovery experiment (5 min intermittent submaximal contraction (ISC); 1 min rest; 2 min ISC). A custom-made resistance band was used to help subjects perform biceps curl resistance exercises and the resistance was recorded through a load cell. The maximum and minimum values of the force-derivative were obtained as distinguishing features and a segmentation algorithm was proposed to divide the biceps curl cycle into concentric, eccentric and isometric contraction, and rest phases. Two assessors, who were unfamiliar with the study, were recruited to manually pick the visually observed cut-off point between two contraction phases and the TUT was calculated and compared to evaluate performance of the segmentation algorithm.ResultsThe segmentation algorithm was programmatically implemented and the repetition number and contraction-phase specific TUT were calculated. During isometric, the average TUT (3.75 ± 0.62 s) was longer than the prescribed 3 s, indicating that most subjects did not perform the exercise as prescribed. There was a good TUT agreement and contraction segment agreement between the proposed algorithm and the assessors.ConclusionThe good agreement in TUT between the proposed algorithm and the assessors indicates that the proposed algorithm can correctly segment the contraction into contraction phase-specific parts, thereby providing clinicians and researchers with an automated and objective method for quantifying home-based elbow flexor resistance training. The instrument is easy to use and cheap, and the segmentation algorithm is programmatically implemented, indicating good application prospect of the method in a practical setting. creator: Jingjing Yang creator: Hongbin Xu creator: Juke Liang creator: Jongyeob Jeong creator: Taojin Xu uri: https://doi.org/10.7717/peerj.8689 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Yang et al. title: SERPINA1 gene identified in RNA-Seq showed strong association with milk protein concentration in Chinese Holstein cows link: https://peerj.com/articles/8460 last-modified: 2020-02-24 description: The detection of candidate genes and mutations associated with phenotypic traits is important for livestock animals. A previous RNA-Seq study revealed that SERPINA1 gene was a functional candidate that may affect milk protein concentration in dairy cows. To further confirm the genetic effect of SERPINA1 on milk protein traits, genetic polymorphisms were identified and genotype-phenotype associations were performed in a large Chinese Holstein cattle population. The entire coding region and the 5′-regulatory region (5′-UTR) of SERPINA1 was sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed model with a population encompassing 1,027 Chinese Holstein cows. A total of four SNPs were identified in SERPINA1, among which rs210222822 and rs41257068 presented in exons, rs207601878 presented in an intron, and rs208607693 was in the 5′-UTR. Analyses of pairwise D′ measures of linkage disequilibrium (LD) showed strong linkage among these four SNPs (D′ = 0.99–1.00), and a 9 Kb haplotype block involving three main haplotypes with GTGT, CCCC and CCGT was inferred. An association study revealed that all four single SNPs and their haplotypes had significant genetic effects on milk protein percentage, milk protein yield and milk yield (P = 0.0458 −  < 0.0001). The phenotypic variance ratio for all 11 significant SNP-trait pairs ranged from 1.01% to 7.54%. The candidate gene of SERPINA1 revealed by our previous RNA-Seq study was confirmed to have pronounced effect on milk protein traits on a genome level. Two SNPs (rs208607693 and rs210222822) presented phenotypic variances of approximately 7% and may be used as key or potential markers to assist selection for new lines of cows with high protein concentration. creator: Cong Li creator: Wentao Cai creator: Shuli Liu creator: Chenghao Zhou creator: Hongwei Yin creator: Dongxiao Sun creator: Shengli Zhang uri: https://doi.org/10.7717/peerj.8460 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Sound production in the Meagre, Argyrosomus regius (Asso, 1801): intraspecific variability associated with size, sex and context link: https://peerj.com/articles/8559 last-modified: 2020-02-24 description: BackgroundMany fish taxa produce sound in voluntary and in disturbance contexts but information on the full acoustic repertoire is lacking for most species. Yet, this knowledge is critical to enable monitoring fish populations in nature through acoustic monitoring.MethodsIn this study we characterized the sounds emitted during disturbance and voluntary contexts by juvenile and adult meagre, Argyrosomus regius, in laboratory conditions. Breeding sounds produced by captive adults were also compared with meagre sounds registered in the Tagus estuary (Lisbon, Portugal) from unseen fish during the breeding season.ResultsThe present dataset demonstrates for the first time that in this species dominant frequency is inversely related to fish size, and that sounds vary according to sex, context and age. Sounds from captive breeding adults were similar to sounds recorded in the field.DiscussionOur findings indicate that A. regius sound features carry information about size, sex, age and motivation. This variability could potentially be used to identify meagre in the field and to infer about ontogenetic phase (i.e., juveniles vs. adults, and variation with size) and motivation (e.g., spawning). Future studies should confirm sex differences and ascertain the influence of water temperature on acoustic features. creator: Beatriz P. Pereira creator: Manuel Vieira creator: Pedro Pousão-Ferreira creator: Ana Candeias-Mendes creator: Marisa Barata creator: Paulo J. Fonseca creator: Maria Clara P. Amorim uri: https://doi.org/10.7717/peerj.8559 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pereira et al. title: lncRNA–mRNA competing endogenous RNA network in IR-hepG2 cells ameliorated by APBBR decreasing ROS levels: a systematic analysis link: https://peerj.com/articles/8604 last-modified: 2020-02-24 description: BackgroundRadix Astragali (Astragalus membranaceus var. mongholicus (Bunge)) and Coptis chinensis (Coptis chinensis var. angustiloba) are two commonly prescribed traditional Chinese herbs for diabetes. Astragalus Polysaccharide (AP) and Berberine (BBR) are active ingredients of these two herbs respectively and they are scientifically proved to have immunomodulatory and anti-inflammatory effects. They are also known for their antidiabetic potential by ameliorating insulin resistance (IR). AP and BBR have shown different advantages in treating diabetes according to previous reports. However, very few studies focus on the combined activities of the two potential antidiabetic ingredients. In this study, we discovered that reactive oxygen species (ROS) accumulated in IR-hepG2 cells and APBBR can decrease ROS level in model group significantly. We conjectured that APBBR can ameliorate IR in hepG2 cells by decreasing ROS level. In order to verify this hypothesis, we obtained phenotype and transcriptome information of IR-HepG2 cells and explore the underlying mechanism of the combination of AP and BBR(APBBR) activity on the relationship between ROS change in IR at whole-transcriptome level, so as to shed new light to efficacy and application of APBBR in treating diabetes.MethodsThe IR cell model was established with high-level insulin intervention. Glucose content, HepG2 cell viability as well as ROS level was detected to study the effect of IR-hepG2 cell phenotype. Unbiased genome-wide RNA sequencing was used to investigate alterations in experimental groups. Then, GO and KEGG functional enrichment was performed to explore the function and pathway of target genes. Venn analysis found out the differentially expressed lncRNAs that had close relationship with IR and ROS. Finally, we screened out candidate lncRNAs and these target genes to construct interaction network of differentiated lncRNA–miRNA–mRNA by according to the principle of competitive endogenous RNA (ceRNA).ResultsThe biochemical experiments showed that APBBR administration could improve the proliferation activity of IR-HepG2 cells and decrease ROS level in model cells. The GO and KEGG functional enrichment analyses demonstrated several mRNAs remarkably enriched in biological processes and signaling pathways related to ROS production and IR progression. Interaction network suggest that APBBR ameliorates IR in HepG2 cells by regulating the expression of multiple genes and activating relevant signaling pathway to decrease ROS level. Thus, we demonstrated that APBBR ameliorated IR in hepG2 cells via the ROS-dependent pathway. creator: Min Lin creator: Zhu-Jun Mao uri: https://doi.org/10.7717/peerj.8604 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lin and Mao title: Genome sequencing of Aspergillus glaucus ‘CCHA’ provides insights into salt-stress adaptation link: https://peerj.com/articles/8609 last-modified: 2020-02-24 description: Aspergillus, as a genus of filamentous fungi, has members that display a variety of different behavioural strategies, which are affected by various environmental factors. The decoded genomic sequences of many species vary greatly in their evolutionary similarities, encouraging studies on the functions and evolution of the Aspergillus genome in complex natural environments. Here, we present the 26 Mb de novo assembled high-quality reference genome of Aspergillus glaucus ‘China Changchun halophilic Aspergillus’ (CCHA), which was isolated from the surface of plants growing near a salt mine in Jilin, China, based on data from whole-genome shotgun sequencing using Illumina Solexa technology. The sequence, coupled with data from comprehensive transcriptomic survey analyses, indicated that the redox state and transmembrane transport might be critical molecular mechanisms for the adaptation of A. glaucus ‘CCHA’ to the high-salt environment of the saltern. The isolation of salt tolerance-related genes, such as CCHA-2114, and their overexpression in Escherichia coli demonstrated that A. glucus ‘CCHA’ is an excellent organism for the isolation and identification of salt tolerant-related genes. These data expand our understanding of the evolution and functions of fungal and microbial genomes, and offer multiple target genes for crop salt-tolerance improvement through genetic engineering. creator: Wenmin Qiu creator: Jingen Li creator: Yi Wei creator: Feiyu Fan creator: Jing Jiang creator: Mingying Liu creator: Xiaojiao Han creator: Chaoguang Tian creator: Shihong Zhang creator: Renying Zhuo uri: https://doi.org/10.7717/peerj.8609 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Qiu et al. title: Seasonal variability and vertical distribution of autotrophic and heterotrophic picoplankton in the Central Red Sea link: https://peerj.com/articles/8612 last-modified: 2020-02-24 description: The Red Sea is characterized by higher temperatures and salinities than other oligotrophic tropical regions. Here, we investigated the vertical and seasonal variations in the abundance and biomass of autotrophic and heterotrophic picoplankton. Using flow cytometry, we consistently observed five groups of autotrophs (Prochlorococcus, two populations of Synechococcus separated by their relative phycoerythrin fluorescence, low (LF-Syn) and high (HF-Syn), and two differently-sized groups of picoeukaryotes, small (Speuk) and large (Lpeuk)) and two groups of heterotrophic prokaryotes of low and high nucleic acid content (LNA and HNA, respectively). Samples were collected in 15 surveys conducted from 2015 to 2017 at a 700-m depth station in the central Red Sea. Surface temperature ranged from 24.6 to 32.6 °C with a constant value of 21.7 °C below 200 m. Integrated (0–100 m) chlorophyll a concentrations were low, with maximum values in fall (24.0 ± 2.7 mg m−2) and minima in spring and summer (16.1 ± 1.9 and 1.1 mg m−2, respectively). Picoplankton abundance was generally lower than in other tropical environments. Vertical distributions differed for each group, with Synechococcus and LNA prokaryotes more abundant at the surface while Prochlorococcus, picoeukaryotes and HNA prokaryotes peaked at the deep chlorophyll maximum, located between 40 and 76 m. Surface to 100 m depth-weighted abundances exhibited clear seasonal patterns for Prochlorococcus, with maxima in summer (7.83 × 104 cells mL−1, July 2015) and minima in winter (1.39 × 104 cells mL−1, January 2015). LF-Syn (0.32 – 2.70 × 104 cells mL−1 ), HF-Syn (1.11 – 3.20 × 104 cells mL−1) and Speuk (0.99 – 4.81 × 102 cells mL−1) showed an inverse pattern to Prochlorococcus, while Lpeuk (0.16 – 7.05 × 104 cells mL−1) peaked in fall. Synechococcus unexpectedly outnumbered Prochlorococcus in winter and at the end of fall. The seasonality of heterotrophic prokaryotes (2.29 – 4.21×105 cells mL−1 ) was less noticeable than autotrophic picoplankton. The contribution of HNA cells was generally low in the upper layers, ranging from 36% in late spring and early summer to ca. 50% in winter and fall. Autotrophs dominated integrated picoplankton biomass in the upper 100 m, with 1.4-fold higher values in summer than in winter (mean 387 and 272 mg C m–2, respectively). However, when the whole water column was considered, the biomass of heterotrophic prokaryotes exceeded that of autotrophic picoplankton with an average of 411 mg C m–2. Despite being located in tropical waters, our results show that the picoplankton community seasonal differences in the central Red Sea are not fundamentally different from higher latitude regions. creator: Najwa Al-Otaibi creator: Tamara M. Huete-Stauffer creator: Maria Ll. Calleja creator: Xabier Irigoien creator: Xosé Anxelu G. Morán uri: https://doi.org/10.7717/peerj.8612 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Al-Otaibi et al. title: Prevalence of and related risk factors in oral mucosa diseases among residents in the Baoshan District of Shanghai, China link: https://peerj.com/articles/8644 last-modified: 2020-02-24 description: BackgroundOral mucosal diseases (OMDs) encompass a variety of different types of diseases. Our aim was to evaluate the prevalence and related risk factors of OMDs among residents in the Baoshan District of Shanghai, China, and provide a scientific basis for prevention and control strategies.MethodsA sample of 653 residents aged 17 to 92 years from the Baoshan community was investigated in 2014. Each resident was surveyed by questionnaire to evaluate their oral mucosa and oral mucosa examinations were conducted. We followed up with 607 residents in 2018. All data were statistically analyzed using the SPSS 25.0 software package (Chicago, IL, USA) at the general population, gender and age levels. A X2 test was used to compare rates of risk factors and logistic regression analysis was used to detect the correlation between disease and risk factors.ResultsThe prevalence rate of OMDs was found to be 9.19%–9.56% (2014–2018). The most common OMDs were atrophic glossitis (1.84%), recurrent aphthous ulcer (RAU, 1.68%), burning mouth syndrome (BMS, 1.38%), oral lichen planus (OLP, 1.23%) and traumatic ulcers (1.23%). The prevalence of RAU and BMS in different age groups was significantly different. Tobacco and alcohol use and psychological factors in the OMDs group were higher than the no-OMDs group. Systemic diseases including diabetes mellitus (DM) was significantly relevant to OLP.ConclusionAge, tobacco and alcohol use, and psychological factor correlated strongly with the occurrence and development of OMDs, and they should be the focus of primary prevention. General epidemiological studies suggested that OLP was closely related to DM. creator: Shuyun Ge creator: Lin Liu creator: Qi Zhou creator: Binbin Lou creator: Zengtong Zhou creator: Jianing Lou creator: Yuan Fan uri: https://doi.org/10.7717/peerj.8644 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ge et al. title: Progress of research into circular RNAs in urinary neoplasms link: https://peerj.com/articles/8666 last-modified: 2020-02-24 description: Circular RNAs (circRNAs) are a large class of endogenous RNA that form a covalently closed continuous loop without 5′ or 3′ tails and are diffusely expressed in mammalian cells. Through the development of high-throughput sequencing, microarray, and bioinformatics analyses, recent studies have shown that the expression of circRNAs is dysregulated in human tumor tissues and cells, as well as in the blood of patients, and closely correlates with the development of tumors. circRNAs can regulate the progression of tumors through various mechanisms. An increasing number of studies have shown that circRNAs may play critical roles in the early diagnosis, targeted therapy, and prognostic prediction of cancer as biomarkers or therapeutic targets. This review briefly describes the definitions and functions of circRNAs, and the main content includes the most recent progress in research into their function, regulation, and clinical relevance to bladder, renal, and prostate cancers. We also provide some novel ideas regarding the treatment of these diseases. creator: Bangbei Wan creator: Bo Liu creator: Cai Lv uri: https://doi.org/10.7717/peerj.8666 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wan et al. title: Restored freshwater flow and estuarine benthic communities in the northern Gulf of Mexico: research trends and future needs link: https://peerj.com/articles/8587 last-modified: 2020-02-21 description: Restoring river connectivity to rebuild and sustain land is a promising restoration strategy in coastal areas experiencing rapid land loss, such as the Mississippi river delta. Results of these large-scale hydrologic changes are preliminary, and there exists limited empirical evidence regarding how benthic communities will respond, specifically in Barataria Bay and Breton Sound in southeast Louisiana. In this review, the body of existing research in this geographic region pertaining to the drivers of benthic community response that are related to restored freshwater flow and sediment deposition is examined. Overall trends include (1) potential displacement of some species down-estuary due to reduced salinities; (2) temporary lower diversity in areas closest to the inflow; (3) increased benthic production along the marsh edge, and in tidal bayous, as a result of nutrient loading; (4) more habitat coverage in the form of submerged aquatic vegetation; and (5) reduced predation pressure from large and/or salinity-restricted predators. These trends highlight opportunities for future research that should be conducted before large-scale hydrologic changes take place. creator: Jillian C. Tupitza creator: Cassandra N. Glaspie uri: https://doi.org/10.7717/peerj.8587 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tupitza and Glaspie title: Transcriptomic and proteomic profiles of II YOU 838 (Oryza sativa) provide insights into heat stress tolerance in hybrid rice link: https://peerj.com/articles/8306 last-modified: 2020-02-21 description: Heat stress is an increasing threat to rice production worldwide. To investigate the mechanisms of heat tolerance in hybrid rice and their contributions to rice heterosis, we compared the transcriptome of the hybrid rice II YOU 838 (II8) with the transcriptomes of its parents Fu Hui 838 (F8) and II-32A (II3) after heat stress at 42 °C for 0 h, 24 h, 72 h and 120 h. We also performed a proteomic analysis in II8 after heat stress at 42 °C for 24 h. The transcriptome data revealed time-dependent gene expression patterns under the heat stress conditions, and the heat stress response of II8 was greatly different from those of its parents. Gene ontology analysis of the differentially expressed genes that were clustered using k-means clustering showed that most of the up-regulated genes were involved in responses to stimuli, cell communication, and metabolic and transcription factor activities, whereas the down-regulated genes were enriched in photosynthesis and signal transduction. Moreover, 35 unique differentially abundant proteins, including a basic helix-loop-helix transcription factor (bHLH96), calmodulin-binding transcription activator, heat shock protein (Hsp70), and chaperonin 60 (CPN60), were detected in the proteomic analysis of II8 under heat stress. The co-regulatory analysis revealed novel genes and pathways involved in heat tolerance, namely, ferredoxin-NADP reductase, peroxidases, mitogen-activated protein kinase kinase kinase, and heat shock factor (HSF)–Hsp network. Members of the Hsp and HSF families had over-dominant expression patterns in the hybrid compared with its parents, to help maintain the higher photosynthesis and antioxidant defense systems in the hybrid. Our study suggests that the complex HSF–Hsp regulatory network contribute to the heat tolerance of the hybrid rice. creator: Yan Wang creator: Yang Yu creator: Min Huang creator: Peng Gao creator: Hao Chen creator: Mianxue Liu creator: Qian Chen creator: Zhirong Yang creator: Qun Sun uri: https://doi.org/10.7717/peerj.8306 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Molecular characterization of two recombinant isolates of telosma mosaic virus infecting Passiflora edulis from Fujian Province in China link: https://peerj.com/articles/8576 last-modified: 2020-02-21 description: Telosma mosaic virus (TeMV) is an important plant virus causing considerable economic losses to passion fruit (Passiflora edulis) production worldwide, including China. In this study, the complete genome sequence (excluding the poly (A) tail) of two TeMV isolates, Fuzhou and Wuyishan, were determined to be 10,050 and 10,057 nucleotides, respectively. Sequence analysis indicated that Fuzhou and Wuyishan isolates share 78–98% nucleotide and 83–99% amino acid sequence identities with two TeMV isolates of Hanoi and GX, and a proposed new potyvirus, tentatively named PasFru. Phylogenetic analysis indicated that these TeMV isolates and PasFru were clustered into a monophyletic clade with high confidences. This indicated that PasFru and the four TeMV isolates should be considered as one potyvirus species. Two recombination breakpoints were identified within the CI and NIb genes of the Fuzhou isolate, and also within the P1 gene of the Wuyishan isolate. To the best of our knowledge, this is the first report of TeMV recombinants worldwide. creator: Lixue Xie creator: Fangluan Gao creator: Jianguo Shen creator: Xiaoyan Zhang creator: Shan Zheng creator: Lijie Zhang creator: Tao Li uri: https://doi.org/10.7717/peerj.8576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xie et al. title: Long non-coding RNA polymorphisms on 8q24 are associated with the prognosis of gastric cancer in a Chinese population link: https://peerj.com/articles/8600 last-modified: 2020-02-21 description: BackgroundGastric cancer (GC) remains the third leading cause of cancer death in China. Although genome-wide association studies have identified the association between several single nucleotide polymorphisms (SNPs) on 8q24 and the risk of GC, the role of these SNPs in the prognosis of GC in Chinese populations has not yet been fully evaluated. Therefore, this study was conducted to explore the association between long non-coding RNA (lncRNA) polymorphisms on 8q24 and the prognosis of GC.MethodsWe genotyped 726 surgically resected GC patients to explore the association between eight SNPs in the lncRNAs CCAT1 (rs10087719, rs7816475), PCAT1 (rs1026411), PRNCR1 (rs12682421, rs13252298), and CASC8 (rs1562430, rs4871789, rs6983267) transcribed from the 8q24 locus and the prognosis of GC in a Chinese population.ResultsWe found that the patients carrying rs12682421 AA genotypes survived for a shorter time than those with the GG/GA genotype (HR = 1.39, 95% confidence interval (CI) [1.09–1.78]). Compared with the CC/CT genotype, the TT genotype of rs1562430 was associated with an increased risk of death (HR = 1.38, 95% CI [1.06–1.80]). Furthermore, the results also identified the rs1026411 SNP as an independent prognostic factor for poor survival in GC patients. Patients carrying AA/AG variant genotypes had a 36% increased risk of death compared to those carrying the GG genotype (HR = 1.36, 95% CI [1.06–1.74]). These findings suggested that the rs12682421, rs1026411 and rs1562430 SNPs may contribute to the survival of GC and be prognostic markers for GC. creator: Yangyu Zhang creator: Yanhua Wu creator: Zhifang Jia creator: Donghui Cao creator: Na Yang creator: Yueqi Wang creator: Xueyuan Cao creator: Jing Jiang uri: https://doi.org/10.7717/peerj.8600 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora link: https://peerj.com/articles/8603 last-modified: 2020-02-21 description: Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth’s most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes. creator: Özgül Doğan creator: Michael Schrödl creator: Zeyuan Chen uri: https://doi.org/10.7717/peerj.8603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Doğan et al. title: The practicality of different eGFR equations in centenarians and near-centenarians: which equation should we choose? link: https://peerj.com/articles/8636 last-modified: 2020-02-21 description: BackgroundNo studies have examined the practicality of the Modification of Diet in Renal Disease (MDRD), Chronic Kidney Disease Epidemiological Collaboration (CKD-EPI) and Berlin Initiative Study 1 (BIS1) equations for the estimated glomerular filtration rate (eGFR) in a large sample of centenarians. We aim to investigate the differences among the equations and suggest the most suitable equation for centenarians and near-centenarians.MethodsA total of 966 centenarians and 787 near-centenarians were enrolled, and the eGFR was calculated using the three equations mentioned above. Agreement among the equations was investigated with the κ statistic and Bland–Altman plots. Sources of discrepancy were investigated using a partial correlation analysis.ResultsThe three equations for assessing eGFR are not considered interchangeable in centenarians and near-centenarians. Δ(MDRD, CKD-EPI) and Δ(MDRD, BIS1) increased with age, but Δ(CKD-EPI, BIS1) was relatively stable with age. Δ(MDRD, CKD-EPI) and Δ(MDRD, BIS1) were considerable in subjects with Scr levels less than 0.7 mg/dL and decreased with the Scr level. A considerable difference between CKD-EPI and BIS1 was observed for participants with Scr levels ranging from 0.5 to 1.5 mg/dL. This difference increased with Scr levels ranging from 0.5 to 0.7 mg/dL, was relatively stable for Scr levels ranging from 0.7 to 0.9 mg/dL, and decreased with Scr levels ranging from 0.9 to 1.5 mg/dL. The differences in the three comparisons were all greater in women than in men (p < 0.05).ConclusionsWe tend to suggest the MDRD equation to calculate the glomerular filtration rate (GFR) in elderly individuals >95 years old who have no risk factors for cardiovascular disease; the BIS1 equation to calculate the eGFR for elderly individuals younger than 94 years old who have risk factors for cardiovascular disease; the CKD-EPI equation to calculate the eGFR of elderly individuals with Scr levels greater than 1.5 mg/dL; and the BIS1 equation to calculate the eGFR of older women with Scr levels less than 0.7 mg/dL. creator: Qiuxia Han creator: Dong Zhang creator: Yali Zhao creator: Liang Liu creator: Jing Li creator: Fu Zhang creator: Fuxin Luan creator: Jiayu Duan creator: Zhangsuo Liu creator: Guangyan Cai creator: Xiangmei Chen creator: Hanyu Zhu uri: https://doi.org/10.7717/peerj.8636 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Han et al. title: Retrospective study: clinicopathological features and prognosis of idiopathic membranous nephropathy with seronegative anti-phospholipase A2 receptor antibody link: https://peerj.com/articles/8650 last-modified: 2020-02-21 description: BackgroundTo discuss the clinicopathological features and prognosis of patients with idiopathic membranous nephropathy (IMN) who are serum-negative for the anti-PLA2R antibody.MethodOverall, 229 IMN patients were retrospectively collected in this study and classified into anti-PLA2R antibody-negative (PLA2R−, 59 cases) and antibody-positive (PLA2R+, 170 cases) groups. The clinical and pathological features of the PLA2R− group were analyzed; 162 patients in both groups were followed up, and the PLA2R antigen was detected in renal biopsies from the PLA2R− group. Kaplan-Meier and survival analyses were used to compare differences in prognosis.ResultsSerum albumin levels were higher and 24-hour urine protein, creatinine, and beta 2-microglobulin (BMG) levels were lower in the PLA2R− group than in the PLA2R+ group; the proportion of acute and chronic tubular lesions was also significantly lower in the PLA2R− group than in in the PLA2R+ group. After treatment, the remission rate was significantly higher in the negative group than in the positive group (93.02% vs 74.78%,), especially the rate of complete remission (51.16% vs 23.47%). Furthermore, the PLA2R antigen-positive staining rate of 43 patients in the PLA2R− group was 62.79%. Although not significant, the survival rate was higher in the PLA2R− group than in the PLA2R+ group. BMG, 24-hour urine protein and acute and chronic tubular lesions were risk factors for kidney death, and 24-hour urine protein was an independent risk factor for kidney death.ConclusionsCompared with the PLA2R+ group, the PLA2R− group had mild clinical manifestations and pathological damage and a higher clinical treatment remission rate. Renal tissue PLA2R antigen testing can be considered for patients with seronegative IMN to increase the diagnostic rate. creator: Wenkai Guo creator: Yan Zhang creator: Caifeng Gao creator: Jing Huang creator: Jiatong Li creator: Rong Wang creator: Bing Chen uri: https://doi.org/10.7717/peerj.8650 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: Transcriptome analysis of flavonoid biosynthesis in safflower flowers grown under different light intensities link: https://peerj.com/articles/8671 last-modified: 2020-02-21 description: BackgroundSafflower (Carthamus tinctorius L.) is a domesticated species with a long history of cultivation and widespread distribution across the globe, and light plays an important role in controlling its distribution boundary. Flowers from safflower have been widely used in traditional Chinese medicine because of their ability to improve cerebral blood flow. Flavonoids are the main active compounds in safflower and have many pharmacological effects. In this study, we aimed to explore the relationship between different light intensities and flavonoid biosynthesis in safflower flowers cultivated in greenhouse.MethodsThe transcriptome of safflower flowers grown under different light intensities were sequenced through BGISEQ-500 platform. After assembled and filtered, Unigenes were annotated by aligning with seven functional databases. Differential expression analysis of two samples was performed with the DEseq2 package. Differentially expressed genes (DEGs) related with flavonoids biosynthesis were analyzed by Real-time PCR (RT-PCR). Flavonoids accumulation in flowers were determined by high performance liquid chromatography and spectrophotometer.ResultsTranscriptome analysis of safflower flowers cultivated under different light intensities was performed. A total of 99.16 Gb data were obtained, and 78,179 Unigenes were annotated. Among the DEGs, 13 genes were related to flavonoid biosynthesis. The differential expressions of seven key genes were confirmed by RT-PCR. In addition, the levels of some flavonoids were measured in safflower flowers grown under different light intensities. CtHCT3 gene expression showed a significantly negative correlation with kaempferol content in safflower grown under different light intensities.ConclusionOur results strongly suggested that the reduction in light intensity in a suitable range promoted flavonoid biosynthesis in safflower flowers. We suggest that the expressions of HCT genes played an important role in flavonoid accumulation in safflower flowers. Our study lays a foundation for further research on the effects of light on flavonoid biosynthesis in safflower. creator: Chaoxiang Ren creator: Jie Wang creator: Bin Xian creator: Xiaohui Tang creator: Xuyun Liu creator: Xueli Hu creator: Zunhong Hu creator: Yiyun Wu creator: Cuiping Chen creator: Qinghua Wu creator: Jiang Chen creator: Jin Pei uri: https://doi.org/10.7717/peerj.8671 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ren et al. title: Recent update in diagnosis and treatment of human pythiosis link: https://peerj.com/articles/8555 last-modified: 2020-02-20 description: Human pythiosis is an infectious condition with high morbidity and mortality. The causative agent is the oomycete microorganism Pythium insidiosum. The pathogen inhabits ubiquitously in a wet environment, and direct exposure to the pathogen initiates the infection. Most patients with pythiosis require surgical removal of the affected organ, and many patients die from the disease. Awareness of pythiosis among healthcare personnel is increasing. In this review, we summarized and updated information on the diagnosis and treatment of human pythiosis. Vascular and ocular pythiosis are common clinical manifestations. Recognition of the typical clinical features of pythiosis is essential for early diagnosis. The definitive diagnosis of the disease requires laboratory testing, such as microbiological, serological, molecular, and proteomic assays. In vascular pythiosis, surgical intervention to achieve the organism-free margin of the affected tissue, in combination with the use of antifungal drugs and P. insidiosum immunotherapy, remains the recommended treatment. Ocular pythiosis is a serious condition and earliest therapeutic penetrating keratoplasty with wide surgical margin is the mainstay treatment. Thorough clinical assessment is essential in all patients to evaluate the treatment response and detect an early sign of the disease recurrence. In conclusion, early diagnosis and proper management are the keys to an optimal outcome of the patients with pythiosis. creator: Maria Nina Chitasombat creator: Passara Jongkhajornpong creator: Kaevalin Lekhanont creator: Theerapong Krajaejun uri: https://doi.org/10.7717/peerj.8555 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chitasombat et al. title: The effects of phylogeny, body size, and locomotor behavior on the three-dimensional shape of the pelvis in extant carnivorans link: https://peerj.com/articles/8574 last-modified: 2020-02-20 description: The mammalian pelvis is thought to exhibit adaptations to the functional demands of locomotor behaviors. Previous work in primates has identified form-function relationships between pelvic shape and locomotor behavior; few studies have documented such relationships in carnivorans, instead focusing on long bones. Most work on the functional morphology of the carnivoran pelvis, in particular, has used univariate measures, with only a few previous studies incorporating a three-dimensional (3D) analysis. Here we test the hypothesis that carnivoran taxa that are characterized by different locomotor modes also differ in 3D shape of the os coxae. Using 3D geometric morphometrics and phylogenetic comparative methods, we evaluate the phylogenetic, functional, and size-related effects on 3D pelvis shape in a sample of 33 species of carnivorans. Using surface models derived from laser scans, we collected a suite of landmarks (N = 24) and curve semilandmarks (N = 147). Principal component analysis on Procrustes coordinates demonstrates patterns of shape change in the ischiopubis and ilium likely related to allometry. Phylogenetic generalized least squares analysis on principal component scores demonstrates that phylogeny and body size have greater effects on pelvic shape than locomotor function. Our results corroborate recent research finding little evidence of locomotor specialization in the pelvis of carnivorans. More research on pelvic morphological integration and evolvability is necessary to understand the factors driving pelvic evolution in carnivorans. creator: Kristi L. Lewton creator: Ryan Brankovic creator: William A. Byrd creator: Daniela Cruz creator: Jocelyn Morales creator: Serin Shin uri: https://doi.org/10.7717/peerj.8574 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lewton et al. title: Effects of manganese and zinc on the growth process of Phytophthora nicotianae and the possible inhibitory mechanisms link: https://peerj.com/articles/8613 last-modified: 2020-02-20 description: BackgroundPhytophthora nicotianae is a fungal soil-borne pathogen that damages various plant species. Mancozeb and Zineb, fungicides containing manganese (Mn) and zinc (Zn) as the main components, are widely used to control the diseases caused by Phytophthora. However, the inhibition mechanism is still unclear. The purpose of this study was to examine the effects of Mn and Zn on P. nicotianae and to determine possible inhibitory mechanisms of Mn and Zn on sporangiogenesis of P. nicotianae.MethodsThe mycelial growth, sporangium generation, zoosporogenesis and zoospore germination of P. nicotianae were observed under Mn and Zn treatments. The gene (csn4 and csn7) expression levels of P. nicotianae in different growth stages were examined. Csn4 and csn7 gene expression, superoxide dismutase (SOD) activity, catalase (CAT) activity and malondialdehyde (MDA) content were tested at the stage of sporangiogenesis under different Mn and Zn concentrations.ResultsMycelial growth of P. nicotianae was significantly inhibited by Mn from ≥1 mg/L concentration and by Zn from ≥10 mg/L. The sporangia production, sporangia release, and zoospore germination of P. nicotianae were significantly reduced by Mn at all concentrations, while treatment with Zn from ≥0.5 mg/L concentration significantly inhibited the same processes. At the same concentration, the inhibition rate of Mn on the growth process of P. nicotianae was higher than that of Zn. The csn4 and csn7 gene transcription of P. nicotianae were significantly reduced by all treatments with Mn and Zn at the stage of sporangiogenesis. With the increase of Mn concentration, the activities of SOD and CAT increased to maxima and then decreased, and the content of MDA gradually increased during sporangiogenesis of P. nicotianae. The sporangia production of P. nicotianae was significantly positively correlated with the expression levels of the genes csn4 and csn7.ConclusionThe inhibitory effect of Mn on the growth process of P. nicotianae was stronger than that of Zn, especially on sporangiogenesis and zoosporogenesis. A possible mechanism of the inhibitory effect on sporangiogenesis of P. nicotianae was that Mn and Zn acted by inhibiting the expression levels of the genes csn4 and csn7 and by affecting antioxidant enzyme activity (further resulting in lipid peroxidation) in the sporangium of P. nicotianae. creator: Yifang Luo creator: Aimei Yao creator: Mouyi Tan creator: Zhenlun Li creator: Ling Qing creator: Shuiying Yang uri: https://doi.org/10.7717/peerj.8613 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Luo et al. title: Multidimensional evaluation of the TRMM 3B43V7 satellite-based precipitation product in mainland China from 1998–2016 link: https://peerj.com/articles/8615 last-modified: 2020-02-20 description: This study evaluates the applicability of the Tropical Rain Measurement Mission (TRMM) 3B43V7 product for use throughout mainland China. Four statistical metrics were used based on the observations made by rain gauges; these metrics were the correlation coefficient (R), the relative bias (RB), the root mean square error (RMSE) and Nash-Sutcliffe efficiency (NSE), and they were chosen to evaluate the performance of the 3B43V7 product at temporal and spatial scales. The results revealed that 3B43V7 performed satisfactorily on all timescales (R > 0.9 and NSE > 0.86); however, it overestimated the results when compared with the rain gauge observations in certain circumstances (RB = 9.7%). Monthly estimates from 3B43V7 were in agreement with rain gauge observations. 3B43V7 can effectively capture the seasonal patterns of precipitation characteristics over mainland China. However, 3B43V7 tends to register a greater overestimation of precipitation in the winter (RB = 14%) than in other seasons while showing greater consistency with the observations made by rain gauges during dry periods. The 3B43V7 product performs well in the eastern part of mainland China, while its performance is poor in the western part of mainland China. In terms of altitude, 3B43V7 performs satisfactorily in areas with moderate to low altitudes (when altitude < 3,500 m, R > 0.9, NSE > 0.8 and RB < 10.2%) but RB values increase with altitude. Overall, 3B43V7 had a favorable performance throughout mainland China. creator: Ziteng Zhou creator: Bin Guo creator: Youzhe Su creator: Zhongsheng Chen creator: Juan Wang uri: https://doi.org/10.7717/peerj.8615 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhou et al. title: Upregulated expression of pyruvate kinase M2 mRNA predicts poor prognosis in lung adenocarcinoma link: https://peerj.com/articles/8625 last-modified: 2020-02-20 description: BackgroundPyruvate kinase M2 (PKM2) is critical regulator contributing to Warburg effect. However, the expression pattern and prognostic value of PKM2 remain unknown in lung adenocarcinoma (LUAD). The aim of this study is to clarify the prognostic value of PKM2 via intergrated bioinformatics analysis.MethodsFirstly, mRNA expression levels of PKM2 in LUAD were systematically analyzed using the ONCOMINE and TCGA databases. Then, the association between PKM2 expression and clinical parameters was investigated by UALCAN. The Kaplan–Meier Plotter was used to assess the prognostic significance of PKM2. Finally, the relationship between PKM2 expression and its genetic and epigenetic changes was evaluated with MEXPRESS and MethHC database.ResultsPooled analysis showed that PKM2 is frequently upregulated expression in LUAD. Subsequently, PKM2 expression was identified to be positively associated with tumor stage and lymph node metastasis and also strongly correlated with worse OS (P = 2.80e−14), PPS (P = 0.022), FP (P = 1.30e−6) and RFS (P = 3.41e−8). Importantly, our results demonstrated that over-expressed PKM2 is associated with PKM2 hypomethylation and copy number variations (CNVs).ConclusionThis study confirms that over-expressed PKM2 in LUAD is associated with poor prognosis, suggesting that PKM2 might act as a promising prognostic biomarker and novel therapeutic target for LUAD. creator: Guiping Wang creator: Yingying Zhong creator: Jiecong Liang creator: Zhibin Li creator: Yun Ye uri: https://doi.org/10.7717/peerj.8625 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Single nucleotide polymorphism of MTHFR rs1801133 associated with elevated Hcy levels affects susceptibility to cerebral small vessel disease link: https://peerj.com/articles/8627 last-modified: 2020-02-20 description: BackgroundMethylenetetrahydrofolate reductase (MTHFR) is indispensable for the conversion of homocysteine (Hcy) to methionine. The single nucleotide polymorphism (SNP) of MTHFR gene (rs1801133, C667T) is correlated with decreased enzyme activity that eventually results in elevated plasma Hcy levels. Hyperhomocysteinemia has been confirmed to be involved in the pathogenesis of stroke, cerebral small vessel disease (CSVD), various metabolic disorders and so on. However, the relationship between the MTHFR gene polymorphisms, Hcy, and CSVD has not been investigated. In this study, the relationship between SNPs of MTHFR gene and CSVD was determined after adjusting for cardiovascular risk factors, and the potential mechanism based on Hcy levels was explored.MethodsA total of 163 consecutive CSVD patients were collected as the case group. In the corresponding period, 326 healthy people were selected as the control group, who were matched to these cases according to age (±2 years) and gender at a ratio of 2:1. SNPs of MTHFR rs1801133, rs1801131, rs2274976, rs4846048, rs4846049, rs13306561 and rs3737964, were genotyped with TaqMan Pre-Designed SNP Genotyping Assays. Plasma Hcy levels were detected using Hcy reagent through enzymatic cycling assay. Multivariate analysis was used to identify the SNPs associated with CSVD susceptibility. Plasma Hcy levels were compared between different genotypes.ResultsThe MTHFR rs1801133 TT and CT genotype had increased risk for CSVD, and the OR was higher in the TT genotype than in the CT genotype (2.307 vs 1.473). The plasma Hcy levels of different genotypes showed the tendency of the TT genotype > CT genotype > CC genotype (19.91 ± 8.73 pg/ml vs 17.04 ± 5.68 pg/ml vs 14.96 ± 4.85 pg/ml).ConclusionsThe SNP of MTHFR rs1801133 was correlated with CSVD, and the TT and CT genotypes had increased risk for CSVD compared to the CC genotype. The potential mechanism was associated with elevated Hcy levels. creator: Hongyu Yuan creator: Man Fu creator: Xianzhang Yang creator: Kun Huang creator: Xiaoyan Ren uri: https://doi.org/10.7717/peerj.8627 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yuan et al. title: Endoplasmic reticulum stress and the protein degradation system in ophthalmic diseases link: https://peerj.com/articles/8638 last-modified: 2020-02-20 description: ObjectiveEndoplasmic reticulum (ER) stress is involved in the pathogenesis of various ophthalmic diseases, and ER stress-mediated degradation systems play an important role in maintaining ER homeostasis during ER stress. The purpose of this review is to explore the potential relationship between them and to find their equilibrium sites.DesignThis review illustrates the important role of reasonable regulation of the protein degradation system in ER stress-mediated ophthalmic diseases. There were 128 articles chosen for review in this study, and the keywords used for article research are ER stress, autophagy, UPS, ophthalmic disease, and ocular.Data sourcesThe data are from Web of Science, PubMed, with no language restrictions from inception until 2019 Jul.ResultsThe ubiquitin proteasome system (UPS) and autophagy are important degradation systems in ER stress. They can restore ER homeostasis, but if ER stress cannot be relieved in time, cell death may occur. However, they are not independent of each other, and the relationship between them is complementary. Therefore, we propose that ER stability can be achieved by adjusting the balance between them.ConclusionThe degradation system of ER stress, UPS and autophagy are interrelated. Because an imbalance between the UPS and autophagy can cause cell death, regulating that balance may suppress ER stress and protect cells against pathological stress damage. creator: Jing-Yao Song creator: Xue-Guang Wang creator: Zi-Yuan Zhang creator: Lin Che creator: Bin Fan creator: Guang-Yu Li uri: https://doi.org/10.7717/peerj.8638 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Song et al. title: Engrailed-2 promotes a malignant phenotype of esophageal squamous cell carcinoma through upregulating the expression of pro-oncogenic genes link: https://peerj.com/articles/8662 last-modified: 2020-02-20 description: BackgroundA number of homeobox genes have been implicated in the development of various cancers. However, the role of engrailed 2 (EN2), a member of the homeobox gene superfamily, in esophageal squamous cell carcinoma (ESCC) remains unknown.MethodsThe expression of EN2 was examined using quantitative real-time PCR and immunohistochemistry. A stable cell line was established to express exogenous EN2 using a lentivirus system. The malignant phenotype was analyzed with proliferation, clonogenicity, wound-healing and invasion assays. The CRISPR/Cas9 system was adopted to deplete endogenous EN2. RNA profiling was performed using gene expression microarray. The ShRNA-mediated method was used to knock down the expression of SPARC. The structure-function relationship was determined using site-directed mutagenesis.ResultsEN2 is highly expressed in ESCC. The malignant phenotype of the ESCC cell line was amplified by an overexpression of EN2 but was attenuated by a disruption of EN2. RNA profiling analysis revealed that distinct sets of genes were modulated by the expression of EN2 in various ESCC cell lines and oncogenes were among these. EN2 greatly increased the expression of SPARC in Eca109. Site-directed mutagenesis revealed that the induction of SPARC was closely correlated with the protumor function of EN2. ShRNA-mediated knockdown of SPARC attenuated the malignant phenotype of EN2-infected cells. These data suggest that SPARC is crucial for mediating the protumor function of EN2.DiscussionEN2 has an oncogenic function in ESCC that is mediated by upregulating the expression of pro-oncogenic genes downstream. EN2 may potentially act as a diagnostic marker or therapeutic target for ESCC treatment in the future. creator: Yong Cao creator: Xiaoyan Wang creator: Li Tang creator: Yan Li creator: Xueqin Song creator: Xu Liu creator: Mingying Li creator: Feng Chen creator: Haisu Wan uri: https://doi.org/10.7717/peerj.8662 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cao et al. title: Reassessment of the Triassic archosauriform Scleromochlus taylori: neither runner nor biped, but hopper link: https://peerj.com/articles/8418 last-modified: 2020-02-19 description: The six known specimens of Scleromochlus taylori and casts made from their negative impressions were examined to reassess the osteological evidence that has been used to interpret Scleromochlus’s locomotion and phylogenetic relationships. It was found that the trunk was dorsoventrally compressed. The upper temporal fenestra was on the lateral surface of skull and two-thirds the size of the lower, the jaw joint posteriorly placed with short retroarticular process, and teeth short and subconical, but no evidence of external nares or antorbital fossae was found. The posterior trunk was covered with ~20 rows of closely spaced transversely elongate dorsal osteoderms. The coracoid was robust and elongate. The acetabulum was imperforate and the femoral head hemispherical and only weakly inturned such that the hip joint was unsuited to swinging in a parasagittal plane. The presence of four distal tarsals is confirmed. The marked disparity of tibial and fibular shaft diameters and of proximal tarsal dimensions indicates that the larger proximal tarsal is the astragalus and the significantly smaller tarsal is the calcaneum. The astragalus and calcaneum bear little resemblance to those of Lagosuchus, and the prominent calcaneal tuber confirms that the ankle was crurotarsal. There is no evidence that preserved body and limb postures are unnatural, and most specimens are preserved in what is interpreted as a typical sprawling resting pose. A principal component analysis of skeletal measurements of Scleromochlus and other vertebrates of known locomotor type found Scleromochlus to plot with frogs, and that finding combined with skeletal morphology suggests Scleromochlus was a sprawling quadrupedal hopper. Phylogenetic analyses found that Scleromochlus was not an ornithodiran, but was either within the Doswelliidae or outside the clade consisting of the most recent common ancestor of the Erythrosuchidae and Archosauria and all its descendants. creator: S. Christopher Bennett uri: https://doi.org/10.7717/peerj.8418 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bennett title: Mutant dlx3b disturbs normal tooth mineralization and bone formation in zebrafish link: https://peerj.com/articles/8515 last-modified: 2020-02-19 description: BackgroundTricho-dento-osseous (TDO) syndrome is an autosomal dominant disorder characterized by anomalies in hair, teeth and bone (OMIM190320). Various mutations of Distal-Less 3 (DLX3) gene are found to be responsible for human TDO. The aim of this study was to investigate effects of DLX3 on tooth and bone development using a zebrafish model.MethodsThe dlx3b mutant zebrafish lines were established using the gene targeting tool transcription activator-like effector nuclease (TALEN). Micro-computed tomography was used to render the three-dimensional skeletal structures of mutant fishes. The pharyngeal bone along with connected teeth was isolated and stained by Alizarine Red S, then observed under stereomicroscope. Scanning electron microscopy (SEM) and energy dispersive spectrometer (EDS) were used to examine the tooth surface morphology and mineral composition. Quantitative real-time PCR was used to analyze gene expression.ResultsA moderate curvature of the spine toward the dorsal side was found at the early larval stages, appearing in 86 out of 100 larvae in dlx3b-/- group as compared to 3 out of 99 in the dlx3b+/+ group. At the adult stage, three of the thirty dlx3b-/- homozygotes exhibited prominent abnormal curvature in the spine. SEM revealed morphological surface changes in pharyngeal teeth enameloid, accompanied by a decrease in the mineral content detected by EDS. Furthermore, specific secretory calcium-binding phosphoprotein (SCPP) genes, including odam, scpp9, spp1, scpp1, and scpp5 were significantly downregulated in dlx3b mutants.ConclusionThe findings of this study suggest that dlx3b is critical for enamel mineralization and bone formation in zebrafish. Moreover, the discovery of the downregulation of SCPP genes in dlx3b mutants sheds new light on the molecular mechanisms underlying TDO syndrome. creator: Liping Pang creator: Zhichun Zhang creator: Yan Shen creator: Zhenchao Cheng creator: Xuejun Gao creator: Bo Zhang creator: Xiaoyan Wang creator: Hua Tian uri: https://doi.org/10.7717/peerj.8515 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pang et al. title: Invasive vegetation affects amphibian skin microbiota and body condition link: https://peerj.com/articles/8549 last-modified: 2020-02-19 description: Invasive plants are major drivers of habitat modification and the scale of their impact is increasing globally as anthropogenic activities facilitate their spread. In California, an invasive plant genus of great concern is Eucalyptus. Eucalyptus leaves can alter soil chemistry and negatively affect underground macro- and microbial communities. Amphibians serve as excellent models to evaluate the effect of Eucalyptus invasion on ground-dwelling species as they predate on soil arthropods and incorporate soil microbes into their microbiotas. The skin microbiota is particularly important to amphibian health, suggesting that invasive plant species could ultimately affect amphibian populations. To investigate the potential for invasive vegetation to induce changes in microbial communities, we sampled microbial communities in the soil and on the skin of local amphibians. Specifically, we compared Batrachoseps attenuatus skin microbiomes in both Eucalyptus globulus (Myrtaceae) and native Quercus agriflolia (Fagaceae) dominated forests in the San Francisco Bay Area. We determined whether changes in microbial diversity and composition in both soil and Batrachoseps attenuatus skin were associated with dominant vegetation type. To evaluate animal health across vegetation types, we compared Batrachoseps attenuatus body condition and the presence/absence of the amphibian skin pathogen Batrachochytrium dendrobatidis. We found that Eucalyptus invasion had no measurable effect on soil microbial community diversity and a relatively small effect (compared to the effect of site identity) on community structure in the microhabitats sampled. In contrast, our results show that Batrachoseps attenuatus skin microbiota diversity was greater in Quercus dominated habitats. One amplicon sequence variant identified in the family Chlamydiaceae was observed in higher relative abundance among salamanders sampled in Eucalyptus dominated habitats. We also observed that Batrachoseps attenuatus body condition was higher in Quercus dominated habitats. Incidence of Batrachochytrium dendrobatidis across all individuals was very low (only one Batrachochytrium dendrobatidis positive individual). The effect on body condition demonstrates that although Eucalyptus may not always decrease amphibian abundance or diversity, it can potentially have cryptic negative effects. Our findings prompt further work to determine the mechanisms that lead to changes in the health and microbiome of native species post-plant invasion. creator: Obed Hernández-Gómez creator: Allison Q. Byrne creator: Alex R. Gunderson creator: Thomas S. Jenkinson creator: Clay F. Noss creator: Andrew P. Rothstein creator: Molly C. Womack creator: Erica B. Rosenblum uri: https://doi.org/10.7717/peerj.8549 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hernández-Gómez et al. title: The E2F family as potential biomarkers and therapeutic targets in colon cancer link: https://peerj.com/articles/8562 last-modified: 2020-02-19 description: BackgroundThe E2F family is a group of genes encoding a series of transcription factors in higher eukaryotes and participating in the regulation of cell cycle and DNA synthesis in mammals. This study was designed to investigate the role of E2F family in colon cancer.MethodsIn this study, the transcriptional levels of E2F1-8 in patients with colon cancer from GEPIA was examined. Meanwhile, the immunohistochemical data of the eight genes were also obtained in the The Human Protein Atlas website. Additionally, we re-identified the mRNA expression levels of these genes via real time PCR. Furthermore, the association between the levels of E2F family and stage plot as wells overall survival of patients with colon cancer were analyzed.ResultsWe found that the mRNA and protein levels of E2F1, E2F2, E3F3, E2F5, E2F7 and E2F8 were significantly higher in colon cancer tissues than in normal colon tissues while the expression levels of E2F4 and E2F6 displayed no significant difference between colon cancer tissues and normal tissues. Additionally, E2F3, E2F4, E2F7 and E2F8 were significantly associated with the stages of colon cancer. The Kaplan-Meier Plotter showed that the high levels of E2F3 conferred a worse overall survival and disease free survival of patients with colon cancer. Also, high levels of E2F4 resulted in a worse overall survival.ConclusionOur study implied that E2F3, E2F4, E2F7 and E2F8 are potential targets of precision therapy for patients with colon cancer while E2F1, E2F2, E3F3, E2F5, E2F7 and E2F8 are potential biomarkers for the diagnosis of colon cancer. creator: Haibo Yao creator: Fang Lu creator: Yanfei Shao uri: https://doi.org/10.7717/peerj.8562 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yao et al. title: Facilitating open-science with realistic fMRI simulation: validation and application link: https://peerj.com/articles/8564 last-modified: 2020-02-19 description: With advances in methods for collecting and analyzing fMRI data, there is a concurrent need to understand how to reliably evaluate and optimally use these methods. Simulations of fMRI data can aid in both the evaluation of complex designs and the analysis of data. We present fmrisim, a new Python package for standardized, realistic simulation of fMRI data. This package is part of BrainIAK: a recently released open-source Python toolbox for advanced neuroimaging analyses. We describe how to use fmrisim to extract noise properties from real fMRI data and then create a synthetic dataset with matched noise properties and a user-specified signal. We validate the noise generated by fmrisim to show that it can approximate the noise properties of real data. We further show how fmrisim can help researchers find the optimal design in terms of power. The fmrisim package holds promise for improving the design of fMRI experiments, which may facilitate both the pre-registration of such experiments as well as the analysis of fMRI data. creator: Cameron T. Ellis creator: Christopher Baldassano creator: Anna C. Schapiro creator: Ming Bo Cai creator: Jonathan D. Cohen uri: https://doi.org/10.7717/peerj.8564 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ellis et al. title: A high Mn(II)-tolerance strain, Bacillus thuringiensis HM7, isolated from manganese ore and its biosorption characteristics link: https://peerj.com/articles/8589 last-modified: 2020-02-19 description: Microorganisms play a significant part in detoxifying and immobilizing excessive metals. The present research isolated a strain (HM7) with high Mn(II) tolerance from Mn(II)-contaminated soil samples. The 16S rDNA sequence analysis showed that HM7 had a 99% similarity to Bacillus thuringiensis, which can survive under a high concentration 4,000 mg/L of Mn(II), and the highest removal rate was up to 95.04% at the concentration of 400 mg/L. The highest Mn(II) removal rate was detected at the contact time 72 h, temperature 30 °C, and pH 5.0, while the differences in strain growth and Mn(II) removal rate among different inoculation doses were insignificant. Scanning electron microscopy indicated B. thuringiensis HM7 cells appeared irregular and cracked under Mn(II) stress. Fourier transform infrared exhibited that functional groups like carboxyl, hydroxyl, amino, sulfhydryl groups, and amide bands might take part in the complexation of Mn(II). In addition, HM7 suggested the ability of indoleacetic acid production, siderophore production, and P’ solubilization potential. Therefore, HM7 might have a potential to promote metal absorption by changing the form of heavy metals, and the experiments supported the application of B. thuringiensis HM7 as a biological adsorbent in Mn(II) contaminated environment remediation. creator: Huimin Huang creator: Yunlin Zhao creator: Zhenggang Xu creator: Yi Ding creator: Xiaomei Zhou creator: Meng Dong uri: https://doi.org/10.7717/peerj.8589 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: SCelVis: exploratory single cell data analysis on the desktop and in the cloud link: https://peerj.com/articles/8607 last-modified: 2020-02-19 description: BackgroundSingle cell omics technologies present unique opportunities for biomedical and life sciences from lab to clinic, but the high dimensional nature of such data poses challenges for computational analysis and interpretation. Furthermore, FAIR data management as well as data privacy and security become crucial when working with clinical data, especially in cross-institutional and translational settings. Existing solutions are either bound to the desktop of one researcher or come with dependencies on vendor-specific technology for cloud storage or user authentication.ResultsTo facilitate analysis and interpretation of single-cell data by users without bioinformatics expertise, we present SCelVis, a flexible, interactive and user-friendly app for web-based visualization of pre-processed single-cell data. Users can survey multiple interactive visualizations of their single cell expression data and cell annotation, define cell groups by filtering or manual selection and perform differential gene expression, and download raw or processed data for further offline analysis. SCelVis can be run both on the desktop and cloud systems, accepts input from local and various remote sources using standard and open protocols, and allows for hosting data in the cloud and locally. We test and validate our visualization using publicly available scRNA-seq data.MethodsSCelVis is implemented in Python using Dash by Plotly. It is available as a standalone application as a Python package, via Conda/Bioconda and as a Docker image. All components are available as open source under the permissive MIT license and are based on open standards and interfaces, enabling further development and integration with third party pipelines and analysis components. The GitHub repository is https://github.com/bihealth/scelvis. creator: Benedikt Obermayer creator: Manuel Holtgrewe creator: Mikko Nieminen creator: Clemens Messerschmidt creator: Dieter Beule uri: https://doi.org/10.7717/peerj.8607 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Obermayer et al. title: ‘Remote’ behavioural ecology: do megaherbivores consume vegetation in proportion to its presence in the landscape? link: https://peerj.com/articles/8622 last-modified: 2020-02-19 description: Examination of the feeding habits of mammalian species such as the African elephant (Loxodonta africana) that range over large seasonally dynamic areas is exceptionally challenging using field-based methods alone. Although much is known of their feeding preferences from field studies, conclusions, especially in relation to differing habits in wet and dry seasons, are often contradictory. Here, two remote approaches, stable carbon isotope analysis and remote sensing, were combined to investigate dietary changes in relation to tree and grass abundances to better understand elephant dietary choice in the Kruger National Park, South Africa. A composited pair of Landsat Enhanced Thematic Mapper satellite images characterising flushed and senescent vegetation states, typical of wet and dry seasons respectively, were used to generate land-cover maps focusing on the forest to grassland gradient. Stable carbon isotope analysis of elephant faecal samples identified the proportion of C3 (typically browse)/C4 (typically grass) in elephant diets in the 1–2 days prior to faecal deposition. The proportion of surrounding C4 land-cover was extracted using concentric buffers centred on faecal sample locations, and related to the faecal %C4 content. Results indicate that elephants consume C4 vegetation in proportion to its availability in the surrounding area during the dry season, but during the rainy season there was less of a relationship between C4 intake and availability, as elephants targeted grasses in these periods. This study illustrates the utility of coupling isotope and cost-free remote sensing data to conduct complementary landscape analysis at highly-detailed, biologically meaningful resolutions, offering an improved ability to monitor animal behavioural patterns at broad geographical scales. This is increasingly important due to potential impacts of climate change and woody encroachment on broad-scale landscape habitat composition, allowing the tracking of shifts in species utilisation of these changing landscapes in a way impractical using field based methods alone. creator: Christopher G. Marston creator: David M. Wilkinson creator: Matt Sponheimer creator: Daryl Codron creator: Jacqui Codron creator: Hannah J. O’Regan uri: https://doi.org/10.7717/peerj.8622 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Marston et al. title: The expression of small RNAs in exosomes of follicular fluid altered in human polycystic ovarian syndrome link: https://peerj.com/articles/8640 last-modified: 2020-02-19 description: Polycystic ovary syndrome (PCOS) can cause reproductive disorders that may affect oocyte quality from punctured follicles in human follicular fluid (HFF). The non-coding RNA family includes micro RNA (miRNA), piwi-interacting RNA (piRNA) and transfer RNA (tRNA); these non-coding RNA transcripts play diverse functions and are implicated in a variety of diseases and health conditions, including infertility. In this study, to explore the role of HFF exosomes in PCOS, we extracted and sequenced RNA from HFF exosomes of PCOS patients and compared the analysis results with those of non-PCOS control group. The HFF exosomes were successfully isolated and characterized in a variety of ways. The sequencing results of the HFF exosomal RNA showed that about 6.6% of valid reads in the PCOS group and 8.6% in the non-PCOS group were successfully mapped to the human RNA database. Using a hierarchical clustering method, we found there were ten small RNA sequences whose expression was significantly different between the PCOS and non-PCOS groups. We chose six of them to predict target genes of interest for further GO analysis, and pathway analysis showed that the target genes are mainly involved in biosynthesis of amino acids, glycine, serine and glycosaminoglycan, as well as threonine metabolism. Therefore, the small RNA sequences contained in HFF EXs may play a key role in the mechanism that drives PCOS pathogenesis, and thereby can act as molecular biomarkers for PCOS diagnosis in the future. creator: Junhe Hu creator: Tao Tang creator: Zhi Zeng creator: Juan Wu creator: Xiansheng Tan creator: Jiao Yan uri: https://doi.org/10.7717/peerj.8640 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hu et al. title: The systematics of the Cervidae: a total evidence approach link: https://peerj.com/articles/8114 last-modified: 2020-02-18 description: Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervids. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging. creator: Nicola S. Heckeberg uri: https://doi.org/10.7717/peerj.8114 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Heckeberg title: Personality underground: evidence of behavioral types in the solitary subterranean rodent Ctenomys talarum link: https://peerj.com/articles/8490 last-modified: 2020-02-18 description: BackgroundAnimal personalities have been studied in a wide variety of taxa, but among rodents, available studies are relatively scarce and have focused mainly on social species. In this study, we evaluated the existence of personality in the solitary subterranean rodent Ctenomys talarum. Specifically, we aimed to test individual differences in behavior that are stable over time and context in males of C. talarum captured in the wild.MethodsOur experimental design included two series of three behavioral tests each, carried out with a 35 day time interval. Each series included an Open Field test, a Social Encounter test, and an Open Field test with a predator stimulus.ResultsOf the total recorded behaviors, 55.55% showed temporal consistency. Principal component analysis of consistent behaviors grouped them into four dimensions that explain inter individual behavioral variability, in order of importance: activity, socioaversion, boldness and exploration. Therefore, our results suggest that the concept of animal personality is applicable to C. talarum and the dimensions found are in accordance with the ecological and behavioral characteristics of this species. creator: María Sol Fanjul creator: Roxana R. Zenuto uri: https://doi.org/10.7717/peerj.8490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fanjul and Zenuto title: Greenhouse gas emissions from riparian zone cropland in a tributary bay of the Three Gorges Reservoir, China link: https://peerj.com/articles/8503 last-modified: 2020-02-18 description: BackgroundA huge reservoir was formed by the Three Gorges Dam in China, which also formed a riparian zone along the bank of the reservoir. In the period of low water-level, the riparian zone in tributary bays of the Three Gorges Reservoir (TGR) was always unordered cultivated, owing to its gentle slope and high soil fertility. This land-use practice creates high potential of generating greenhouse gas (GHG) emissions with periodic water level fluctuation.MethodsTo evaluate potential GHG emissions from the soil-air interface, the static opaque chamber method was adopted to evaluate the effect of elevations (180 m, 175 m, 170 m and 165 m) and land use types (dry lands, paddy fields and grass fields) from April to September in 2015 and 2016.ResultsThe results showed that carbon dioxide (CO2) was the main contributor of GHG emission in riparian zone most likely because of high organic carbon from residues. Furthermore, high soil water content in paddy fields resulted in significantly higher methane (CH4) flux than that in dry lands and grass fields. Compared to grass fields, anthropogenic activities in croplands were attributed with a decrease of soil total carbon and GHG emissions. However, inundation duration of different elevations was found to have no significant effect on CH4 and CO2 emissions in the riparian zone, and the mean nitrous oxide (N2O) flux from dry lands at an elevation of 165 m was significantly higher than that of other elevations likely because of tillage and manure application. The high N2O fluxes produced from tillage and fertilizer suggested that, in order to potentially mitigate GHG emissions from the riparian zone, more attention must be paid to the farming practices in dry lands at low elevations (below 165 m) in the riparian zone. Understanding factors that contribute to GHG emissions will help guide ecological restoration of riparian zones in the TGR. creator: XiaoXiao Wang creator: Ping Huang creator: Maohua Ma creator: Kun Shan creator: Zhaofei Wen creator: Shengjun Wu uri: https://doi.org/10.7717/peerj.8503 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Taxonomic revision of Dasydorylas Skevington, 2001 (Diptera, Pipunculidae) in the Middle East link: https://peerj.com/articles/8511 last-modified: 2020-02-18 description: Species of the distinctive and cosmopolitan genus Dasydorylas Skevington, 2001 in the Middle East are revised. Seven species are documented, and three new species, Dasydorylas dactylos sp. nov., D. forcipus sp. nov. and D. parazardouei sp. nov., are described, and one synonym, D. derafshani Motamedinia & Kehlmaier, 2017, syn. nov. is proposed, based on sequence information from the mitochondrial COI barcoding gene and morphological parameters. Diagnoses, illustrations and distributional data are provided for all studied species. Descriptions of new species as well as an identification key to all known species in the Middle East are also provided. creator: Behnam Motamedinia creator: Jeffrey H. Skevington creator: Scott Kelso uri: https://doi.org/10.7717/peerj.8511 license: http://www.nationalarchives.gov.uk/doc/open-government-licence/ rights: title: SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species link: https://peerj.com/articles/8544 last-modified: 2020-02-18 description: BackgroundQuantitative real-time PCR (qPCR) is a well-established method for detecting and quantifying bacteria, and it is progressively replacing culture-based diagnostic methods in food microbiology. High-throughput qPCR using microfluidics brings further advantages by providing faster results, decreasing the costs per sample and reducing errors due to automatic distribution of samples and reagents. In order to develop a high-throughput qPCR approach for the rapid and cost-efficient quantification of microbial species in complex systems such as fermented foods (for instance, cheese), the preliminary setup of qPCR assays working efficiently under identical PCR conditions is required. Identification of target-specific nucleotide sequences and design of specific primers are the most challenging steps in this process. To date, most available tools for primer design require either laborious manual manipulation or high-performance computing systems.ResultsWe developed the SpeciesPrimer pipeline for automated high-throughput screening of species-specific target regions and the design of dedicated primers. Using SpeciesPrimer, specific primers were designed for four bacterial species of importance in cheese quality control, namely Enterococcus faecium, Enterococcus faecalis, Pediococcus acidilactici and Pediococcus pentosaceus. Selected primers were first evaluated in silico and subsequently in vitro using DNA from pure cultures of a variety of strains found in dairy products. Specific qPCR assays were developed and validated, satisfying the criteria of inclusivity, exclusivity and amplification efficiencies.ConclusionIn this work, we present the SpeciesPrimer pipeline, a tool to design species-specific primers for the detection and quantification of bacterial species. We use SpeciesPrimer to design qPCR assays for four bacterial species and describe a workflow to evaluate the designed primers. SpeciesPrimer facilitates efficient primer design for species-specific quantification, paving the way for a fast and accurate quantitative investigation of microbial communities. creator: Matthias Dreier creator: Hélène Berthoud creator: Noam Shani creator: Daniel Wechsler creator: Pilar Junier uri: https://doi.org/10.7717/peerj.8544 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dreier et al. title: Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata link: https://peerj.com/articles/8550 last-modified: 2020-02-18 description: We examined genetic structure in the lobe coral Porites lobata among pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oahu and Maui, Hawaii. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVA FST = 0.04∼0.19, P < 0.001), but no significant isolation by distance between islands. Strikingly, corals from the two nearshore sites with higher levels of environmental stressors on different islands over 100 km apart with similar environmentally stressful conditions were genetically closer (FST = 0.0, P = 0.73) than those within a single location less than 2 km apart (FST = 0.04∼0.08, P < 0.01). In contrast, a third site with a less impacted nearshore site (i.e., less pronounced environmental gradient) showed no significant structure from the offshore comparison. Our results show much stronger support for environment than distance separating these populations. Our finding suggests that ecological boundaries from human impacts may play a role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow might be explained by selective pressure across contrasting habitats. creator: Kaho H. Tisthammer creator: Zac H. Forsman creator: Robert J. Toonen creator: Robert H. Richmond uri: https://doi.org/10.7717/peerj.8550 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tisthammer et al. title: Broad similarities in shoulder muscle architecture and organization across two amniotes: implications for reconstructing non-mammalian synapsids link: https://peerj.com/articles/8556 last-modified: 2020-02-18 description: The evolution of upright limb posture in mammals may have enabled modifications of the forelimb for diverse locomotor ecologies. A rich fossil record of non-mammalian synapsids holds the key to unraveling the transition from “sprawling” to “erect” limb function in the precursors to mammals, but a detailed understanding of muscle functional anatomy is a necessary prerequisite to reconstructing postural evolution in fossils. Here we characterize the gross morphology and internal architecture of muscles crossing the shoulder joint in two morphologically-conservative extant amniotes that form a phylogenetic and morpho-functional bracket for non-mammalian synapsids: the Argentine black and white tegu Salvator merianae and the Virginia opossum Didelphis virginiana. By combining traditional physical dissection of cadavers with nondestructive three-dimensional digital dissection, we find striking similarities in muscle organization and architectural parameters. Despite the wide phylogenetic gap between our study species, distal muscle attachments are notably similar, while differences in proximal muscle attachments are driven by modifications to the skeletal anatomy of the pectoral girdle that are well-documented in transitional synapsid fossils. Further, correlates for force production, physiological cross-sectional area (PCSA), muscle gearing (pennation), and working range (fascicle length) are statistically indistinguishable for an unexpected number of muscles. Functional tradeoffs between force production and working range reveal muscle specializations that may facilitate increased girdle mobility, weight support, and active stabilization of the shoulder in the opossum—a possible signal of postural transformation. Together, these results create a foundation for reconstructing the musculoskeletal anatomy of the non-mammalian synapsid pectoral girdle with greater confidence, as we demonstrate by inferring shoulder muscle PCSAs in the fossil non-mammalian cynodont Massetognathus pascuali. creator: Philip Fahn-Lai creator: Andrew A. Biewener creator: Stephanie E. Pierce uri: https://doi.org/10.7717/peerj.8556 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fahn-Lai et al. title: Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences link: https://peerj.com/articles/8569 last-modified: 2020-02-18 description: BackgroundThe concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings.MethodsThe tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer.ResultsAlthough the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound sequences. A set of oligonucleotides containing sites of possible GQs were designed and ordered. Three of them represented the minus strand of the CT-repeat. Two were derived from sequences of two clones of nitrocellulose retained fraction from leaves and contained GC-rich motifs different from the CT motif. Circular dichroism spectroscopy revealed profound changes in spectra when oligonucleotides were incubated with 100 mM KCl. There was either an increase of positive band in the area of 260 nm or the formation of a positive band at 290 nm. In the former case, changes are typical for parallel G-quadruplexes and, in the latter, 3 + 1 structures. DiscussionThe G-quadruplexes anchor proteins are probably involved in the maintenance of the topologically associated domain structure. creator: Tatjana Sjakste creator: Elina Leonova creator: Rudolfs Petrovs creator: Ilva Trapina creator: Marion S. Röder creator: Nikolajs Sjakste uri: https://doi.org/10.7717/peerj.8569 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sjakste et al. title: Nomograms predict survival outcome of Klatskin tumors patients link: https://peerj.com/articles/8570 last-modified: 2020-02-18 description: ObjectiveKlatskin tumors are rare, malignant tumors of the biliary system with a poor prognosis for patient survival. The current understanding of these tumors is limited to a small number of case reports or case series; therefore, we examined prognostic factors of this disease.MethodsA population cohort study was conducted in patients selected from the Surveillance, Epidemiology, and End Results (SEER) database with a Klatskin tumor that was histologically diagnosed between 2004 to 2014. Propensity-matching (PSM) analysis was performed to determine the overall survival (OS) among those with a Klatskin tumor (KCC), intrahepatic cholangiocarcinoma (ICCA), or hepatocellular carcinoma (HCC). The nomogram was based on 317 eligible Klatskin tumor patients and its predictive accuracy and discriminatory ability were determined using the concordance index (C-index).ResultsKaplan-Meier analysis showed that patients with Klatskin tumors had significantly worse overall survival rates (1-year OS = 26.2%, 2-year OS = 10.7%, 3-year OS = 3.4%) than those with intrahepatic cholangiocarcinoma (1-year OS = 62.2%, 2-year OS = 36.4%, 3-year OS = 19.1%, p < 0.001) or hepatocellular carcinoma (1-year OS = 72.4% , 2-year OS = 48.5%, 3-year OS = 36.2%, p < 0.001). A poor prognosis was also significantly associated with older age, higher grade, SEER historic stage, and lymph node metastasis. Local destruction of the tumor (HR = 0.635, 95% CI [0.421–0.956], p = 0.03) and surgery (HR = 0.434, 95% [CI 0.328–0.574], p < 0.001) were independent protective factors. Multivariate Cox analysis showed that older age, SEER historic stage, and lymph node metastases (HR = 1.468, 95% CI [1.008–2.139], p = 0.046) were independent prognostic factors of poor survival rates in Klatskin tumor patients, while cancer-directed surgery was an independent protective factor (HR = 0.555, 95% CI [0.316–0.977], p = 0.041). The prognostic and protective factors were included in the nomogram (C-index for survival = 0.651; 95% CI [0.607–0.695]).ConclusionsThe Klatskin tumor group had poorer rates of OS and cancer-specific survival than the ICCA and HCC groups. Early detection and diagnosis were associated with a higher rate of OS in Klatskin tumor patients. creator: Feng Qi creator: Bin Zhou creator: Jinglin Xia uri: https://doi.org/10.7717/peerj.8570 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Qi et al. title: No island-effect on glucocorticoid levels for a rodent from a near-shore archipelago link: https://peerj.com/articles/8590 last-modified: 2020-02-18 description: Island rodents are often larger and live at higher population densities than their mainland counterparts, characteristics that have been referred to as “island syndrome”. Island syndrome has been well studied, but few studies have tested for island-mainland differences in stress physiology. We evaluated island syndrome within the context of stress physiology of white-footed mice (Peromyscus leucopus) captured from 11 islands and five mainland sites in Thousand Islands National Park, Ontario, Canada. Stress physiology was evaluated by quantifying corticosterone (a stress biomarker), the primary glucocorticoid in mice, from hair and its related metabolites from fecal samples. White-footed mice captured in this near-shore archipelago did not display characteristics of island syndrome, nor differences in levels of hair corticosterone or fecal corticosterone metabolites compared with mainland mice. We suggest that island white-footed mice experience similar degrees of stress in the Thousand Islands compared with the mainland. Although we did not find evidence of island syndrome or differences in glucocorticoid levels, we identified relationships between internal (sex, body mass) and external (season) factors and our hormonal indices of stress in white-footed mice. creator: Nathan D. Stewart creator: Gabriela F. Mastromonaco creator: Gary Burness uri: https://doi.org/10.7717/peerj.8590 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Stewart et al. title: Effectiveness of slightly acidic electrolyzed water on bacteria reduction: in vitro and spray evaluation link: https://peerj.com/articles/8593 last-modified: 2020-02-18 description: Bacterial inactivation is a crucial aspect of sanitation and hygiene. The effectiveness of slightly acidic electrolyzed water (SAEW) for reduction or removal of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus epidermidis was evaluated. The bactericidal activity of SAEW and sodium hypochlorite (NaOCl) against E. coli and P. aeruginosa were compared through in vitro experiments. The effectiveness of SAEW spray was tested against S. epidermidis. Results showed that SAEW had a more powerful bactericidal activity than NaOCl at the same available chlorine concentrations. For E. coli, SAEW decreased the bacterial counts from 8.4 log10 CFU/mL to less than 3.9 log10 CFU/mL; NaOCl with the same available chlorine of 0.5 mg/L, caused a decrease from 8.4 log10 CFU/mL to 7.1 log10 CFU/mL. For P. aeruginosa, SAEW caused bacterial counts to decrease from 8.5 log10 CFU/mL to less than 4.1 log10 CFU/mL against 8.5 log10 CFU/mL to 6.2 log10 CFU/mL for NaOCl with the same available chlorine of 0.5 mg/L. Spray experiments showed that 10 mg/L of SAEW spray decreased the bacterial counts of S. epidermidis from 3.7 log10 CFU/m3 to 2.8 log10 CFU/m3, with 20 mg/L causing a reduction from 3.8 log10 CFU/m3 to 0 CFU/m3. The overall findings of this study indicate that SAEW may be a promising disinfectant agent either as a solution or spray. creator: Angelica Naka creator: Masaya Yakubo creator: Kenji Nakamura creator: Midori Kurahashi uri: https://doi.org/10.7717/peerj.8593 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Naka et al. title: Fasciola gigantica, F. hepatica and Fasciola intermediate forms: geometric morphometrics and an artificial neural network to help morphological identification link: https://peerj.com/articles/8597 last-modified: 2020-02-18 description: BackgroundFasciola hepatica and F. gigantica cause fascioliasis in both humans and livestock. Some adult specimens of Fasciola sp. referred to as “intermediate forms” based on their genetic traits, are also frequently reported. Simple morphological criteria are unreliable for their specific identification. In previous studies, promising phenotypic identification scores were obtained using morphometrics based on linear measurements (distances, angles, curves) between anatomical features. Such an approach is commonly termed “traditional” morphometrics, as opposed to “modern” morphometrics, which is based on the coordinates of anatomical points.MethodsHere, we explored the possible improvements that modern methods of morphometrics, including landmark-based and outline-based approaches, could bring to solving the problem of the non-molecular identification of these parasites. F. gigantica and Fasciola intermediate forms suitable for morphometric characterization were selected from Thai strains following their molecular identification. Specimens of F. hepatica were obtained from the Liverpool School of Tropical Medicine (UK). Using these three taxa, we tested the taxonomic signal embedded in traditional linear measurements versus the coordinates of anatomical points (landmark- and outline-based approaches). Various statistical techniques of validated reclassification were used, based on either the shortest Mahalanobis distance, the maximum likelihood, or the artificial neural network method.ResultsOur results revealed that both traditional and modern morphometric approaches can help in the morphological identification of Fasciola sp. We showed that the accuracy of the traditional approach could be improved by selecting a subset of characters among the most contributive ones. The influence of size on discrimination by shape was much more important in traditional than in modern analyses. In our study, the modern approach provided different results according to the type of data: satisfactory when using pseudolandmarks (outlines), less satisfactory when using landmarks. The different reclassification methods provided approximately similar scores, with a special mention to the neural network, which allowed improvements in accuracy by combining data from both morphometric approaches.ConclusionWe conclude that morphometrics, whether traditional or modern, represent a valuable tool to assist in Fasciola species recognition. The general level of accuracy is comparable among the various methods, but their demands on skills and time differ. Based on the outline method, our study could provide the first description of the shape differences between species, highlighting the more globular contours of the intermediate forms. creator: Suchada Sumruayphol creator: Praphaiphat Siribat creator: Jean-Pierre Dujardin creator: Sébastien Dujardin creator: Chalit Komalamisra creator: Urusa Thaenkham uri: https://doi.org/10.7717/peerj.8597 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sumruayphol et al. title: Injuries among adolescents in Greenland: behavioural and socio-economic correlates among a nationally representative sample link: https://peerj.com/articles/8605 last-modified: 2020-02-18 description: BackgroundInjuries are among the most important threats to adolescent health, making examination of the patterns and risk factors a critical area of research. There exists a paucity of information on the health and injury experience of school-attending adolescents in Greenland. Consenting Greenlandic schoolchildren (n = 2,254) aged 9–19 years were included in the Health Behavior in School-Aged Children study 2005/2006. The aim of this study was to examine the socio-economic and behavioural correlates that were associated with injury occurrence among school-attending Greenlandic adolescents.MethodsThis study made use of two multinomial regression models to examine injury occurrence regarding potential influencing factors such as physical activity, risk behaviours, bullying and family socio-economic status (SES).ResultsThose self-reporting 1–2 injuries within the recall period were more likely to be male (OR = 1.70; CI [1.39–2.09]), involved in physical fighting (OR = 1.82; CI [1.33–2.47]), bullied (OR = 1.81; CI [1.47–2.24]) and participated in bullying others (OR = 1.53; CI [1.25–1.89]). Those reporting three or more injuries were again mostly male (OR = 2.13; CI [1.44–3.14]), involved in physical fighting at higher rates (OR = 4.47; CI [2.86–7.01]), bullied more often (OR = 2.43; CI [1.65–3.57]) and were more likely to bully others (OR = 1.67; CI [1.13–2.45]). Living without a mother proved to be significantly correlated with suffering 3 or more injuries during the recall period (OR = 1.63; CI [1.05–2.52]). The study results support the idea that factors that were found to be associated with injury occurrence, such as bullying and aggressive behaviour, should be taken into account when conducting future research on the nature of injuries among Greenlandic adolescents. More research on this topic is needed to identify factors that might modify the associations between injuries and adolescent behaviour and SES. creator: Louis Jansen creator: Till Bärnighausen creator: Michael Lowery Wilson uri: https://doi.org/10.7717/peerj.8605 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jansen et al. title: Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis link: https://peerj.com/articles/8611 last-modified: 2020-02-18 description: BackgroundJuvenile dermatomyositis (JDM) is an immune-mediated disease characterized by chronic organ inflammation. The pathogenic mechanisms remain ill-defined.MethodsRaw microarray data of JDM were obtained from the gene expression omnibus (GEO) database. Based on the GSE3307 dataset with 39 samples, weighted correlation network analysis (WGCNA) was performed to identify key modules associated with pathological state. Functional enrichment analyses were conducted to identify potential mechanisms. Based on the criteria of high connectivity and module membership, candidate hub genes were selected. A protein-protein interaction network was constructed to identify hub genes. Another dataset (GSE11971) was used for the validation of real hub genes. Finally, the real hub genes were used to screen out small-molecule compounds via the Connectivity map database.ResultsThree modules were considered as key modules for the pathological state of JDM. Functional enrichment analysis indicated that responses to interferon and metabolism were dysregulated. A total of 45 candidate hub genes were selected according to the pre-established criteria, and 20 genes could differentiate JDM from normal controls by validation of another external dataset (GSE11971). These real hub genes suggested the pivotal role of mitochondrial dysfunction and interferon signature in JDM. Furthermore, drug repositioning highlighted the importance of acacetin, helveticoside, lanatoside C, deferoxamine, LY-294002, tanespimycin and L01AD from downregulated genes with the potential to perturb the development of JDM, while betonicine, felodipine, valproic acid, trichostatin A and sirolimus from upregulated genes provided potentially therapeutic goals for JDM.ConclusionsThere are 20 real hub genes associated with the pathological state of JDM, suggesting the pivotal role of mitochondrial dysfunction and interferon signature in JDM. This analysis predicted several kinds of small-molecule compounds to treat JDM. creator: Danli Zhong creator: Chanyuan Wu creator: Jingjing Bai creator: Dong Xu creator: Xiaofeng Zeng creator: Qian Wang uri: https://doi.org/10.7717/peerj.8611 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhong et al. title: Association between 9-minute walk/run test and obesity among children and adolescents: evidence for criterion-referenced cut-points link: https://peerj.com/articles/8651 last-modified: 2020-02-18 description: BackgroundCriterion-referenced cut-points for field-based aerobic fitness for children and adolescents are lacking. This study aimed to determine the associations between aerobic fitness and obesity to propose criterion-referenced cut-points for boys and girls (6–17 years).MethodsA total of 61,465 children and adolescents aged 11.2 ± 2.0 years were recruited from 27 sites (all 26 states and Federal District) across Brazil. Aerobic fitness was assessed using 9-min walk/run test reported as distance attained during the test. Body mass index was calculated from measured height and weight and was used to identify obesity.ResultsThe distance covered in the 9-min walk/run test (area under curve > 0.65) had satisfactory predictive ability for obesity. Sensitivity and specificity were moderate (>60%) to strong (>70%) for all age- and sex-specific cut-points. For boys, the optimal physical performance cut-points were, approximately, 1,200 m from 6 to 8 years, 1,300 m from 9 to 11 years, 1,380 m from 12 to 14 years, 1,520 m from 15 to 17 years. For girls, the best cut-points were, approximately, 1,070 m from 6 to 8 years, 1,160 m from 9 to 11 years and 1,200 m from 12 to 17 years.ConclusionsThe 9-min walk/run test had satisfactory predictive ability for obesity in children and adolescents. The physical fitness cut-points proposed in the present study varied according to age and sex and could be useful and practical tools to identify low levels of physical fitness in children and adolescents in Brazil. creator: Diego Augusto Santos Silva creator: Justin J. Lang creator: Edio L. Petroski creator: Júlio B. Mello creator: Adroaldo C.A. Gaya creator: Mark S. Tremblay uri: https://doi.org/10.7717/peerj.8651 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Silva et al. title: Molecular phylogeny and intraspecific differentiation of the Trapelus agilis species complex in Iran (Squamata: Agamidae) inferred from mitochondrial DNA sequences link: https://peerj.com/articles/8295 last-modified: 2020-02-17 description: Background Trapelus agilis consists of different morphotypes with restricted distributions in the Iranian Plateau. The phylogeny of the species complex has not been resolved so far, but recently Trapelus sanguinolentus were elevated from this complex into a full species. Other populations of the species complex need to be evaluated taxonomically.MethodsIn the present study, several populations of this species complex along with specimens of its closely related taxa in Iran, T. sanguinolentus, T. ruderatus and T. persicus, were examined using partial nucleotide sequences of two mitochondrial genes (cytb and ND2) (total length 1,322 bp).ResultPopulations of T. sanguinolentus clustered within the T. agilis species complex, thus indicating its paraphyly, but T. sanguinolentus was previously determined to be a species based on morphological features. The T. agilis species complex forms two distinct major clades, each of which is represented by several local populations on the Iranian Plateau. At least five distinct taxa can be identified within this traditional group. Our biogeographic evaluation of the molecular dataset suggested that the Trapelus complex originated in the Late Oligocene (30 mya) and subsequently diversified during the early to middle Miocene (22–13 mya). At first, the predominantly western clade of Trapelus ruderatus diverged from the other clades (22 mya). Afterward, Trapelus persicus diverged around 18 mya ago. The broader T. agilis complex started to diverge about 16 mya, forming several clades on the Iranian Plateau and in Central Asia. The different lineages within this species complex appear to be the result of vicariance events and dispersal waives. The corresponding vicariance events are the formation of the Zagros and Kopet Dagh basins (16–14 mya), and consequently, the aridification of the Iranian Plateau in the late Miocene (11–6 Mya). creator: Ali-Asghar Shahamat creator: Eskandar Rastegarpouyani creator: Nasrullah Rastegar-Pouyani creator: Seyyed Saeed Hosseinian Yousefkhani creator: Michael Wink uri: https://doi.org/10.7717/peerj.8295 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shahamat et al. title: Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon link: https://peerj.com/articles/8358 last-modified: 2020-02-17 description: The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon–intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon. creator: Yong Zhou creator: Yuan Cheng creator: Chunpeng Wan creator: Jingwen Li creator: Youxin Yang creator: Jinyin Chen uri: https://doi.org/10.7717/peerj.8358 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhou et al. title: The R2R3-MYB transcription factor family in Taxus chinensis: identification, characterization, expression profiling and posttranscriptional regulation analysis link: https://peerj.com/articles/8473 last-modified: 2020-02-17 description: The MYB transcription factor family is one of the largest gene families playing regulatory roles in plant growth and development. The MYB family has been studied in a variety of plant species but has not been reported in Taxus chinensis. Here we identified 72 putative R2R3-MYB genes in T. chinensis using a comprehensive analysis. Sequence features, conversed domains and motifs were characterized. The phylogenetic analysis showed TcMYBs and AtMYBs were clustered into 36 subgroups, of which 24 subgroups included members from T. chinensis and Arabidopsis thaliana, while 12 subgroups were specific to one species. This suggests the conservation and specificity in structure and function of plant R2R3-MYBs. The expression of TcMYBs in various tissues and different ages of xylem were investigated. Additionally, miRNA-mediated posttranscriptional regulation analysis revealed that TcMYBs were the targets of miR858, miR159 and miR828, suggesting the posttranscriptional regulation of MYBs is highly conserved in plants. The results provide a basis for further study the role of TcMYBs in the regulation of secondary metabolites of T. chinensis. creator: Xinling Hu creator: Lisha Zhang creator: Iain Wilson creator: Fenjuan Shao creator: Deyou Qiu uri: https://doi.org/10.7717/peerj.8473 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hu et al. title: Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based sequencing of bioaerosols link: https://peerj.com/articles/8523 last-modified: 2020-02-17 description: This paper presents the performance of two eukaryotic genomic ribosomal regions, ITS1 and ITS2, in describing fungal diversity in aerosol samples using amplicon-based High-Throughput Sequencing (HTS). Composting sites, biomethanization facilities, and dairy farms, all affected by the presence of fungi, were visited to collect air samples. The amplicon-based HTS approach is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of amplification. For this reason, the authors of this paper used a shotgun metagenomic approach to compare its outcome with the amplicon-based method. Indeed, shotgun metagenomic does not rely on any amplification prior to sequencing, because all genes are sequenced without a specific target. In addition, culture methods were added to the analyses in biomethanization and dairy farms samples to validate their contribution to fungal diversity of aerosols. The results obtained are unequivocal towards ITS1 outperformance to ITS2 in terms of richness, and taxonomic coverage. The differential abundance analysis did demonstrate that some taxa were exclusively detected only by ITS2, and vice-versa for ITS1. However, the shotgun metagenomic approach showed a taxonomic profile more resembling to ITS1 than ITS2. Based on these results, neither of the barcodes evaluated is perfect in terms of distinguishing all species. Using both barcodes offers a broader view of the fungal aerosol population. However, with the actual knowledge, the authors strongly recommend using ITS1 as a universal fungal barcode for quick general analyses of diversity and when limited financial resources are available, primarily due its ability to capture taxonomic profiles similar to those obtained using the shotgun metagenomic. The culture comparison with amplicon-based sequencing showed the complementarity of both approaches in describing the most abundant taxa. creator: Hamza Mbareche creator: Marc Veillette creator: Guillaume Bilodeau creator: Caroline Duchaine uri: https://doi.org/10.7717/peerj.8523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mbareche et al. title: AIF1 was identified as an up-regulated gene contributing to CSFV Shimen infection in porcine alveolar macrophage 3D4/21 cells link: https://peerj.com/articles/8543 last-modified: 2020-02-17 description: Classical swine fever (CSF) is a disease that is characterized by diffuse hemorrhaging, high fever, and high mortality rates. The pro-inflammatory characteristics of allograft inflammatory factor 1 (AIF1) have been well documented; however, insufficient attention has been given to porcine AIF1. In the present study, AIF1 was identified as a key player contributing to CSFV Shimen infection in porcine alveolar macrophage (PAM) 3D4/21 cell line. Our evaluation showed that AIF1 mRNA and protein are expressed at a time-dependent high level in CSFV Shimen-infected PAM 3D4/21 cells. The transcription and translation of IL6 were also significantly upregulated in infected PAM 3D4/21 cells. By utilizing overexpression RNAs approach, we showed that the cellular AIF1 induced an increased IL6 in PAM 3D4/21 cells. Furthermore, silencing of AIF1 suppressed CSFV Shimen-induced IL6 production in PAM 3D4/21 cells and also inhibited CSFV replication, whereas overexpression of recombinant AIF1 was beneficial for the replication of CSFV Shimen and promoting IL6 production in CSFV Shimen-infected PAM 3D4/21 cells. It is suggested CSFV Shimen induced IL6 in PAM 3D4/21 cells via AIF1 activation, which help clarify the AIF1-related inflammatory processes that occur on CSFV Shimen infected macrophages. creator: Xiaocheng Gong creator: Xuepeng Li creator: Xin You creator: Aoxue Hu creator: Min Liu creator: Huimin Yao creator: Jun He creator: Xianghan Zhang creator: Pengbo Ning uri: https://doi.org/10.7717/peerj.8543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gong et al. title: Crocodylus acutus (American crocodile) bite marks on a nest data logger link: https://peerj.com/articles/8577 last-modified: 2020-02-17 description: Several data loggers deployed to monitor temperature and humidity of Crocodylus acutus (American crocodile) nests in South Florida could not be located after hatching. One badly damaged data logger was retrieved, providing insight into the possible fate of the others. Using a taphonomic approach, we identified numerous indentations, consistent with crocodylian bite marks, and inconsistent with potential mammalian or squamate bites. It seems most likely that the data logger was damaged by the nesting C. acutus rather than during attempted nest predation. Estimated bite forces for reproductive age, female C. acutus exceed the predicted material properties of the data logger’s housing, suggesting that the bites were exploratory in nature. We suggest that data loggers be removed prior to hatching or permit remote data storage. creator: Stephanie K. Drumheller creator: Jennifer H. Nestler creator: Caitlin E. Hackett Farris creator: Seth C. Farris creator: Frank J. Mazzotti uri: https://doi.org/10.7717/peerj.8577 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Drumheller et al. title: DISNET: a framework for extracting phenotypic disease information from public sources link: https://peerj.com/articles/8580 last-modified: 2020-02-17 description: BackgroundWithin the global endeavour of improving population health, one major challenge is the identification and integration of medical knowledge spread through several information sources. The creation of a comprehensive dataset of diseases and their clinical manifestations based on information from public sources is an interesting approach that allows one not only to complement and merge medical knowledge but also to increase it and thereby to interconnect existing data and analyse and relate diseases to each other. In this paper, we present DISNET (http://disnet.ctb.upm.es/), a web-based system designed to periodically extract the knowledge from signs and symptoms retrieved from medical databases, and to enable the creation of customisable disease networks.MethodsWe here present the main features of the DISNET system. We describe how information on diseases and their phenotypic manifestations is extracted from Wikipedia and PubMed websites; specifically, texts from these sources are processed through a combination of text mining and natural language processing techniques.ResultsWe further present the validation of our system on Wikipedia and PubMed texts, obtaining the relevant accuracy. The final output includes the creation of a comprehensive symptoms-disease dataset, shared (free access) through the system’s API. We finally describe, with some simple use cases, how a user can interact with it and extract information that could be used for subsequent analyses.DiscussionDISNET allows retrieving knowledge about the signs, symptoms and diagnostic tests associated with a disease. It is not limited to a specific category (all the categories that the selected sources of information offer us) and clinical diagnosis terms. It further allows to track the evolution of those terms through time, being thus an opportunity to analyse and observe the progress of human knowledge on diseases. We further discussed the validation of the system, suggesting that it is good enough to be used to extract diseases and diagnostically-relevant terms. At the same time, the evaluation also revealed that improvements could be introduced to enhance the system’s reliability. creator: Gerardo Lagunes-García creator: Alejandro Rodríguez-González creator: Lucía Prieto-Santamaría creator: Eduardo P. García del Valle creator: Massimiliano Zanin creator: Ernestina Menasalvas-Ruiz uri: https://doi.org/10.7717/peerj.8580 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lagunes-García et al. title: Increased absorption in autonomous sensory meridian response link: https://peerj.com/articles/8588 last-modified: 2020-02-17 description: BackgroundAutonomous sensory meridian response (ASMR) is a cross-sensory phenomenon characterised by a static-like sensation which typically originates on the scalp and spreads throughout the body leading to a state of deep relaxation. It can be triggered by visual and auditory stimuli in real life, incidentally by various media and via intentionally created ASMR videos. Previously ASMR has been linked to a specific personality profile and this study aimed to further elucidate individual differences associated with this phenomenon.MethodsTo this effect ASMR-Experiencers and age and gender matched controls were compared on measures of flow, absorption and mindfulness.ResultsThis revealed that ASMR was associated with elevated absorption but no group differences were found with respect to the other constructs, suggesting that the ability to get deeply immersed with the current experience accompanied by loss of reflective awareness may be an important factor contributing to the experience of ASMR. creator: Agnieszka B. Janik McErlean creator: Eleanor J. Osborne-Ford uri: https://doi.org/10.7717/peerj.8588 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Janik McErlean and Osborne-Ford title: Investigating the potential use of Sentinel-1 data for monitoring wetland water level changes in China’s Momoge National Nature Reserve link: https://peerj.com/articles/8616 last-modified: 2020-02-17 description: BackgroundInterferometric Synthetic Aperture Radar (InSAR) has become a promising technique for monitoring wetland water levels. However, its capability in monitoring wetland water level changes with Sentine-1 data has not yet been thoroughly investigated.MethodsIn this study, we produced a multitemporal Sentinel-1 C-band VV-polarized SAR backscatter images and generated a total of 28 interferometric coherence maps for marsh wetlands of China’s Momoge National Nature Reserve to investigate the interferometric coherence level of Sentinel-1 C-VV data as a function of perpendicular and temporal baseline, water depth, and SAR backscattering intensity. We also selected six interferogram pairs acquired within 24 days for quantitative analysis of the accuracy of water level changes monitored by Sentinel-1 InSAR. The accuracy of water level changes determined through the Sentinel-1 InSAR technique was calibrated by the values of six field water level loggers.ResultsOur study showed that (1) the coherence was mainly dependent on the temporal baseline and was little affected by the perpendicular baseline for Sentinel-1 C-VV data in marsh wetlands; (2) in the early stage of a growing season, a clear negative correlation was found between Sentinel-1 coherence and water depth; (3) there was an almost linear negative correlation between Sentinel-1 C-VV coherence and backscatter for the marsh wetlands; (4) once the coherence exceeds a threshold of 0.3, the stage during the growing season, rather than the coherence, appeared to be the primary factor determining the quality of the interferogram for the marsh wetlands, even though the quality of the interferogram largely depends on the coherence; (5) the results of water level changes from InSAR processing show no agreement with in-situ measurements during most growth stages. Based on the findings, we can conclude that although the interferometric coherence of the Sentinel-1 C-VV data is high enough, the data is generally unsuitable for monitoring water level changes in marsh wetlands of China’s Momoge National Nature Reserve. creator: Yueqing Chen creator: Sijia Qiao creator: Guangxin Zhang creator: Y. Jun Xu creator: Liwen Chen creator: Lili Wu uri: https://doi.org/10.7717/peerj.8616 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: Molecular cloning and expression analysis of tyrosinases (tyr) in four shell-color strains of Manila clam Ruditapes philippinarum link: https://peerj.com/articles/8641 last-modified: 2020-02-17 description: The Manila clam (Ruditapes philippinarum) is an economically important molluscan bivalve with variation in pigmentation frequently observed in the shell. In nature, tyrosinase is widely distributed in invertebrates and vertebrates, and plays a crucial role in a variety of physiological activities. In this study, a tyrosinase gene (tyr 9) was cloned and the expression level of tyr genes (tyr 6, tyr 9, tyr 10, and tyr 11) were investigated in different shell colors. Quantitative real-time PCR showed that tyr genes were significantly expressed in the mantle, a shell formation and pigmentation-related tissue. Moreover, the expression pattern of the tyr genes in the mantle of different shell-color strains was different, suggesting that tyrosinases might be involved in different shell-color formation. In addition, the expression profile of tyr 6, tyr 9, tyr 10, and tyr 11 genes were detected at different early developmental stages and the expression level varied with embryonic and larval growth. RNA interference (RNAi) results showed that the expression level of tyr 9 in the RNAi group was significantly down-regulated compared to control and negative control groups, indicating that Rptyr 9 might participate in shell-color formation. Our results indicated that tyr genes were likely to play vital roles in the formation of shell and shell-color in R. philippinarum. creator: Kunyin Jiang creator: Liwen Jiang creator: Hongtao Nie creator: Zhongming Huo creator: Xiwu Yan uri: https://doi.org/10.7717/peerj.8641 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jiang et al. title: Modelling the prognostic effect of glucose and lipid profiles on stroke recurrence in Malaysia: an event-history analysis link: https://peerj.com/articles/8378 last-modified: 2020-02-14 description: BackgroundDiabetes and dyslipidemia are significantly associated with stroke recurrence, yet the evidence for this relationship is conflicting. Consequently, the parameters in the glucose and lipid profiles may inform us regarding their relationship with stroke recurrence, thus enhancing the physicians’ clinical decision-making.AimThis study sought to investigate whether glucose and lipid profiles could prognosticate stroke recurrence in Malaysia.MethodsWe conducted a retrospective hospital-based study where we analyzed the first-ever stroke cases regarding about which the Malaysia National Stroke Registry was informed between 2009 and 2017, that fulfilled this study’s criteria, and that were followed for stroke recurrence. Using the Cox proportional hazard regression analysis, we estimated the adjusted hazard ratios (HRs), which reflected the prognostic effect of the primary variables (i.e., glucose and lipid profiles on the first-stroke admission) on stroke recurrence.ResultsAmong the 8,576 first-ever stroke patients, 394 (4.6%) experienced a subsequent first stroke recurrence event. The prognostic effect measured by univariable Cox regression showed that, when unadjusted, ten variables have prognostic value with regards to stroke recurrence. A multivariable regression analysis revealed that glucose was not a significant prognostic factor (adjusted HR 1.28; 95% CI [1.00–1.65]), while triglyceride level was the only parameter in the lipid profile found to have an independent prognostication concerning stroke recurrence (adjusted HR: 1.28 to 1.36).ConclusionsTriglyceride could independently prognosticate stroke recurrence, which suggests the role of physicians in intervening hypertriglyceridemia. In line with previous recommendations, we call for further investigations in first-ever stroke patients with impaired glucose and lipid profiles and suggest a need for interventions in these patients. creator: Xin Wee Chen creator: Mohd Nazri Shafei creator: Zariah Abdul Aziz creator: Norsima Nazifah Sidek creator: Kamarul Imran Musa uri: https://doi.org/10.7717/peerj.8378 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: The endoplasmic reticulum-associated mRNA-binding proteins ERBP1 and ERBP2 interact in bloodstream-form Trypanosoma brucei link: https://peerj.com/articles/8388 last-modified: 2020-02-14 description: Kinetoplastids rely heavily on post-transcriptional mechanisms for control of gene expression, and on RNA-binding proteins that regulate mRNA splicing, translation and decay. Trypanosoma brucei ERBP1 (Tb927.10.14150) and ERBP2 (Tb927.9.9550) were previously identified as mRNA binding proteins that lack canonical RNA-binding domains. We show here that ERBP1 is associated with the endoplasmic reticulum, like ERBP2, and that the two proteins interact in vivo. Loss of ERBP1 from bloodstream-form T. brucei initially resulted in a growth defect but proliferation was restored after more prolonged cultivation. Pull-down analysis of tagged ERBP1 suggests that it preferentially binds to ribosomal protein mRNAs. The ERBP1 sequence resembles that of Saccharomyces cerevisiae Bfr1, which also localises to the endoplasmic reticulum and binds to ribosomal protein mRNAs. However, unlike Bfr1, ERBP1 does not bind to mRNAs encoding secreted proteins, and it is also not recruited to stress granules after starvation. creator: Kathrin Bajak creator: Kevin Leiss creator: Christine E. Clayton creator: Esteban Erben uri: https://doi.org/10.7717/peerj.8388 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bajak et al. title: Aerosols chemical composition, light extinction, and source apportionment near a desert margin city, Yulin, China link: https://peerj.com/articles/8447 last-modified: 2020-02-14 description: Daily PM10and PM2.5 sampling was conducted during four seasons from December 2013 to October 2014 at three monitoring sites over Yulin, a desert margin city. PM10 and PM2.5 levels, water soluble ions, organic carbon (OC), and elemental carbon (EC) were also analyzed to characterize their chemical profiles. bext (light extinction coefficient) was calculated, which showed the highest in winter with an average of 232.95 ± 154.88 Mm−1, followed by autumn, summer, spring. Light extinction source apportionment results investigated (NH4)2SO4 and NH4NO3 played key roles in the light extinction under high RH conditions during summer and winter. Sulfate, nitrate and Ca2 + dominated in PM10/PM2.5 ions. Ion balance results illustrated that PM samples were alkaline, and PM10 samples were more alkaline than PM2.5. High SO42−/K+ and Cl−/K+ ratio indicated the important contribution of coal combustion, which was consistent with the OC/EC regression equation intercepts results. Principal component analysis (PCA) analyses results showed that the fugitive dust was the most major source of PM, followed by coal combustion & gasoline vehicle emissions, secondary formation and diesel vehicle emissions. Potential contribution source function (PSCF) results suggested that local emissions, as well as certain regional transport from northwesterly and southerly areas contributed to PM2.5 loadings during the whole year. Local government should take some measures to reduce the PM levels. creator: Yali Lei creator: Zhenxing Shen creator: Zhuoyue Tang creator: Qian Zhang creator: Jian Sun creator: Yongjing Ma creator: Xiaoyan Wu creator: Yiming Qin creator: Hongmei Xu creator: Renjian Zhang uri: https://doi.org/10.7717/peerj.8447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lei et al. title: Mediterranean nekton traits: distribution, relationships and significance for marine ecology monitoring and management link: https://peerj.com/articles/8494 last-modified: 2020-02-14 description: Biological traits are increasingly used in order to study aspects of ecology as they are related to the organisms’ fitness. Here we analyze a dataset of 23 traits regarding the life cycle, distribution, ecology and behavior of 235 nektonic species of the Mediterranean Sea in order to evaluate the distribution of traits, identify rare ones, detect relationships between trait pairs and identify species functional groups. Trait relationships were tested using correlation and non-linear regression for continuous traits, parametric and non-parametric inference tests for pairs of continuous-categorical traits and cooccurrence testing for categorical traits. The findings have significant implications concerning the potential effects of climate change (e.g., through the relationships of the trait of optimal temperature), fisheries or habitat loss (from the relationships of traits related to tolerance ranges). Furthermore, some unexpected relationships are documented, like the inversely proportional relationship between longevity and age at maturity as a percentage of life span. Associations between functional traits show affinities derived from phylogenetic constraints or life strategies; however, relationships among functional and ecological traits can indicate the potential environmental filtering that acts on functional traits. In total, 18 functional groups were identified by Hill-Smith ordination and hierarchical clustering and were characterized by their dominant traits. For the assessment of the results, we first evaluate the importance of each trait at the level of population, community, ecosystem and landscape and then propose the traits that should be monitored for the regulation and resilience of ecosystem functioning and the management of the marine ecosystems. creator: Evangelos Tzanatos creator: Catherine Moukas creator: Martha Koutsidi uri: https://doi.org/10.7717/peerj.8494 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tzanatos et al. title: A transcriptional co-expression network-based approach to identify prognostic biomarkers in gastric carcinoma link: https://peerj.com/articles/8504 last-modified: 2020-02-14 description: BackgroundGastric carcinoma is a very diverse disease. The progression of gastric carcinoma is influenced by complicated gene networks. This study aims to investigate the actual and potential prognostic biomarkers related to survival in gastric carcinoma patients to further our understanding of tumor biology.MethodsA weighted gene co-expression network analysis was performed with a transcriptome dataset to identify networks and hub genes relevant to gastric carcinoma prognosis. Data was obtained from 300 primary gastric carcinomas (GSE62254). A validation dataset (GSE34942 and GSE15459) and TCGA dataset confirmed the results. Gene ontology, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene set enrichment analysis (GSEA) were performed to identify the clusters responsible for the biological processes and pathways of this disease.ResultsA brown transcriptional module enriched in the organizational process of the extracellular matrix was significantly correlated with overall survival (HR = 1.586, p = 0.005, 95% CI [1.149–2.189]) and disease-free survival (HR = 1.544, p = 0.008, 95% CI [1.119–2.131]). These observations were confirmed in the validation dataset (HR = 1.664, p = 0.006, 95% CI [1.155–2.398] in overall survival). Ten hub genes were identified and confirmed in the validation dataset from this brown module; five key biomarkers (COL8A1, FRMD6, TIMP2, CNRIP1 and GPR124 (ADGRA2)) were identified for further research in microsatellite instability (MSI) and epithelial-tomesenchymal transition (MSS/EMT) gastric carcinoma molecular subtypes. A high expression of these genes indicated a poor prognosis.ConclusionA transcriptional co-expression network-based approach was used to identify prognostic biomarkers in gastric carcinoma. This method may have potential for use in personalized therapies, however, large-scale randomized controlled clinical trials and replication experiments are needed before these key biomarkers can be applied clinically. creator: Danqi Liu creator: Boting Zhou creator: Rangru Liu uri: https://doi.org/10.7717/peerj.8504 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Characterization of a Mn-SOD from the desert beetle Microdera punctipennis and its increased resistance to cold stress in E. coli cells link: https://peerj.com/articles/8507 last-modified: 2020-02-14 description: Insects have developed a complex network of enzymatic antioxidant systems for handling reactive oxygen species (ROS) generated during stress. Superoxide dismutases (SODs) play a determinant role in balancing ROS in insect. However, studies devoted to SODs functions in insects under cold stress are limited. In the present study, we attempted to identify and characterize a mitochondrial manganese SOD (mMn-SOD) from the desert beetle Micordera punctipennis (denoted as MpmMn-SOD) and explore its protective effects on bacteria cells under cold stress. MpmMn-SOD is composed of 202 amino acids with conserved domains required for metal ions binding and enzyme activity. RT-qPCR experiments revealed that the expression of MpmMn-SOD was ubiquitous but tissue-specific and was induced by cold stress. An E. coli (BL21) system was applied to study the function of MpmMn-SOD. The MpmMn-SOD gene was cloned into the prokaryotic expression vector pET-32a to generate a recombinant plasmid pET-32a(MpmMn-SOD). After transformation of the plasmid into E. coli BL21, the fusion protein Trx-His-MpmMn-SOD was overexpressed and identified by SDS-PAGE and Western blotting. Antioxidant activity assay showed that the death zones of the transformed bacteria BL21 (pET32a-mMn-SOD) were smaller in diameter than the control bacteria BL21 (pET32a). Survival curves under −4 °C showed that BL21 (pET32a-mMn-SOD) had significant enhanced cold resistance compared to BL21 (pET32a). Its SOD activity under −4 °C had a significant negative correlation (r = − 0.995) with superoxide anion O2•− content. Accordingly, under cold stress BL21 (pET32a-mMn-SOD) had lower electric conductivity and malondialdehyde (MDA) content than BL21 (pET32a). Taken together, our results showed that cold stress stimulated the expression of MpmMn-SOD in M. punctipennis. The E. coli cells that overexpress MpmMn-SOD increase their resistance to cold stress by scavenging ROS, and mitigate potential cell damage caused by ROS under cold conditions. creator: Zilajiguli Xikeranmu creator: Ji Ma creator: Xiaoning Liu uri: https://doi.org/10.7717/peerj.8507 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xikeranmu et al. title: Association between the levels of physical activity and plantar pressure in 6-14-year-old children link: https://peerj.com/articles/8551 last-modified: 2020-02-14 description: BackgroundThe main purpose of the study was to determine whether lower levels of physical activity were associated with higher plantar pressure generated under each foot.MethodsIn this cross-sectional study, we recruited 641 children aged 6–14 years (agemean ± SD = 9.7  ± 2.4 years; heightmean ± SD = 143.6  ± 15.3 cm, weightmean ± SD = 37.6  ± 13.4 kg; body-mass indexmean ± SD = 17.6  ± 3.2 kg/m2; 44.2% girls). We used EMED –XL pressure platform to measure force time integral, pressure-time integral, contact-time and contact area, peak plantar pressure and mean plantar pressure of the right and the left foot during the gait analysis. The level of physical activity was measured by using The Physical Activity Questionnaire for Older Children (PAQ–C). The associations were calculated by using generalized estimating equations with linear regression models.ResultsLower levels of physical activity were associated with higher force- and pressure-time integrals, longer contact time and higher peak and mean plantar pressures in both feet.ConclusionOur study shows that the level of physical activity is strongly and inversely associated with plantar pressure in a sample of 6–14 year olds. creator: Lovro Štefan creator: Mario Kasović creator: Martin Zvonar uri: https://doi.org/10.7717/peerj.8551 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Stefan et al. title: Implicit motor imagery performance is impaired in people with chronic, but not acute, neck pain link: https://peerj.com/articles/8553 last-modified: 2020-02-14 description: BackgroundPeople with chronic neck pain have impaired proprioception (i.e., sense of neck position). It is unclear whether this impairment involves disruptions to the proprioceptive representation in the brain, peripheral factors, or both. Implicit motor imagery tasks, namely left/right judgements of body parts, assess the integrity of the proprioceptive represention. Previous studies evaluating left/right neck judgements in people with neck pain are conflicting. We conducted a large online study to comprehensively address whether people with neck pain have altered implicit motor imagery performance.MethodsPeople with and without neck pain completed online left/right neck judgement tasks followed by a left/right hand judgement task (control). Participants judged whether the person in the image had their head rotated to their left or right side (neck task) or whether the image was of a left hand or a right hand (hand task). Participants were grouped on neck pain status (no pain; <3 months—acute; ≥3 months—chronic) and pain location (none, left-sided, right-sided, bilateral). Outcomes included accuracy (primary) and response time (RT; secondary). Our hypotheses—that (i) chronic neck pain is associated with disrupted performance for neck images and (ii) the disruption is dependent on the side of usual pain, were tested with separate ANOVAs.ResultsA total of 1,404 participants were recruited: 105 reported acute neck pain and 161 reported chronic neck pain. When grouped on neck pain status, people with chronic neck pain were less accurate than people without neck pain (p = 0.001) for left/right neck judgements, but those with acute neck pain did not differ from those without neck pain (p = 0.14) or with chronic neck pain (p = 0.28). Accuracy of left/right hand judgements did not differ between groups (p = 0.58). RTs did not differ between groups for any comparison. When grouped on neck pain location, people were faster and more accurate at identifying right-turning neck images than left-turning neck images, regardless of history or location of pain (p < 0.001 for both); people with no pain were more accurate and faster than people with bilateral neck pain (p = 0.001, p = 0.015) and were faster than those with left-sided neck pain (p = 0.021); people with right-sided neck pain were more accurate than people with bilateral neck pain (p = 0.018). Lastly, there was a significant interaction between neck image and side of neck pain: people with right-sided neck pain were more accurate at identifying right-sided neck turning images than people with left-sided neck pain (p = 0.008), but no different for left-sided neck turning images (p = 0.62).ConclusionsThere is evidence of impaired implicit motor imagery performance in people with chronic neck pain, which may suggest disruptions to proprioceptive representation of the neck. These disruptions seem specific to the neck (performance on hand images intact) but non-specific to the exact location of neck pain. creator: Sarah B. Wallwork creator: Hayley B. Leake creator: Aimie L. Peek creator: G. Lorimer Moseley creator: Tasha R. Stanton uri: https://doi.org/10.7717/peerj.8553 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wallwork et al. title: Towards a taxonomic revision of the genus Cyrtochilum (Orchidaceae) in Northwestern South America (Northern Peru, Ecuador, Colombia, Venezuela) link: https://peerj.com/articles/8566 last-modified: 2020-02-14 description: This article is a presentation of taxonomic diversity of the orchid genus Cyrtochilum in Northwestern South America. The morphological characteristics of over 90 species occurring in northern Peru, Ecuador, Colombia and Venezuela are presented together with illustrations of their floral segments. Information about the distribution of each taxon is provided. Ten morphologically consistent groups have been delineated to facilitate identification of Cyrtochilum representatives in the studied area. Keys for determination of species within each group are provided. Seven new species of Cyrtochilum are described and one new combination is proposed. creator: Dariusz L. Szlachetko creator: Marta Kolanowska uri: https://doi.org/10.7717/peerj.8566 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Szlachetko and Kolanowska title: Phylogeny of Libellulidae (Odonata: Anisoptera): comparison of molecular and morphology-based phylogenies based on wing morphology and migration link: https://peerj.com/articles/8567 last-modified: 2020-02-14 description: BackgroundEstablishing the species limits and resolving phylogenetic relationships are primary goals of taxonomists and evolutionary biologists. At present, a controversial question is about interspecific phylogenetic information in morphological features. Are the interspecific relationships established based on genetic information consistent with the traditional classification system? To address these problems, this study analyzed the wing shape structure of 10 species of Libellulidae, explored the relationship between wing shape and dragonfly behavior and living habits, and established an interspecific morphological relationship tree based on wing shape data. By analyzing the sequences of mitochondrial COI gene and the nuclear genes 18S, 28S rRNA and ITS in 10 species of dragonflies, the interspecific relationship was established.MethodThe wing shape information of the male forewings and hindwings was obtained by the geometric morphometrics method. The inter-species wing shape relationship was obtained by principal component analysis (PCA) in MorphoJ1.06 software. The inter-species wing shape relationship tree was obtained by cluster analysis (UPGMA) using Mesquite 3.2 software. The COI, 18S, ITS and 28S genes of 10 species dragonfly were blasted and processed by BioEdit v6 software. The Maximum Likelihood(ML) tree was established by raxmlGUI1.5b2 software. The Bayes inference (BI) tree was established by MrBayes 3.2.6 in Geneious software.ResultsThe main difference in forewings among the 10 species of dragonfly was the apical, radial and discoidal regions dominated by the wing nodus. In contrast, the main difference among the hindwings was the apical and anal regions dominated by the wing nodus. The change in wing shape was closely related to the ability of dragonfly to migrate. The interspecific relationship based on molecular data showed that the species of Orthetrum genus branched independently of the other species. Compared to the molecular tree of 10 species, the wing shape clustering showed some phylogenetic information on the forewing shape (with large differences on the forewing shape tree vs. molecular tree), and there was no interspecific phylogenetic information of the hindwing shape tree vs. molecular tree.ConclusionThe dragonfly wing shape characteristics are closely related to its migration ability. Species with strong ability to migrate have the forewing shape that is longer and narrower, and have larger anal region, whereas the species that prefer short-distance hovering or standing still for a long time have forewing that are wider and shorter, and the anal region is smaller. Integrating morphological and molecular data to evaluate the relationship among dragonfly species shows there is some interspecific phylogenetic information in the forewing shape and none in the hindwing shape. The forewing and hindwing of dragonflies exhibit an inconsistent pattern of morphological changes in different species. creator: Shu-Ting Huang creator: Hai-Rui Wang creator: Wan-Qin Yang creator: Ya-Chu Si creator: Yu-Tian Wang creator: Meng-Lian Sun creator: Xin Qi creator: Yi Bai uri: https://doi.org/10.7717/peerj.8567 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Gynodioecy in the common spindle tree (Euonymus europaeus L.) involves differences in the asymmetry of corolla shapes between sexually differentiated flowers link: https://peerj.com/articles/8571 last-modified: 2020-02-14 description: Gynodioecy is typically associated with a smaller perianth size in purely pistillate flowers than in hermaphrodite flowers. However, it is unclear whether this size differentiation is associated with any differences in flower shape between the two sexual groups. A geometric morphometric analysis of the symmetry of tetrameric corolla shapes was used in the study of Euonymus europaeus L., Darwin’s classical system of floral sexual differentiation. I investigated whether there are any shape differences between the female and bisexual flowers, with respect to both purely symmetric variation involving coordinated shape changes of the four petals and asymmetry among petals within flowers. The corolla shapes of the female and bisexual flowers and the variability among flowers within each sexual group were very similar in the purely symmetric components of shape variation. However, the female flowers were significantly more asymmetric with respect to both the lateral and transversal asymmetry of their corolla shapes. This is the first study to apply geometric morphometrics in the analysis of morphological patterns in a sexually differentiated gynodioecious plant system. The results showed that subtle shape differences in corolla asymmetry differ between the sexual groups and indicate diverging developmental or selection signals between the sexes. creator: Jiri Neustupa uri: https://doi.org/10.7717/peerj.8571 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Neustupa title: Intracranial aneurysm’s association with genetic variants, transcription abnormality, and methylation changes in ADAMTS genes link: https://peerj.com/articles/8596 last-modified: 2020-02-14 description: PurposeThe development of intracranial aneurysm (IA) has been linked to genetic factors. The current study examines the potential role of genes encoding disintegrin and metalloproteinase using thrombospondin motifs (ADAMTS) in IA development.Material and MethodsHigh-throughput whole-genome and whole-exome sequencing were used when screening for deleterious single-nucleotide variants (SNVs) in ADAMTS genes using samples from 20 Han Chinese patients: 19 with familial IA and one patient with sporadic IA. The variant frequencies in these subjects were compared to those in control individuals found in the Genome Aggregation Database. Transcriptome sequencing and methylation sequencing data were retrieved from the Gene Expression Omnibus (GEO) database to identify differentially expressed ADAMTS genes and their methylation sites. We predicted the network of interactions among proteins encoded by the overlapping set of ADAMTS genes showing deleterious variants and both differential expression and abnormal methylation in IA. Possible candidate proteins linked to IA were validated using Western blot analysis. The associations between IA and SNVs rs11750568 in ADAMTS2, as well as rs2301612 and rs2285489 in ADAMTS13, were verified using the Sequenom MassArray system on a separate sample set of 595 Han Chinese patients with sporadic IA and 600 control individuals.ResultsA total of 16 deleterious variants in 13 ADAMTS genes were identified in our patients, and seven of these genes overlapped with the genes found to be differentially expressed and differentially methylated in the GEO database. Protein–protein interaction analysis predicted that ADAMTSL1 was at the center of the seven genes. ADAMTSL1 protein was lower expressed in IA tissue than in the control cerebral artery. Frequencies of the IA-related SNVs rs11750568 in ADAMTS2 and rs2301612 and rs2285489 in ADAMTS13 were not significantly different between sporadic IA patients and controls.ConclusionIA is associated with genetic variants, differential expression, and abnormal methylation in ADAMTS genes, ADAMTSL1 in particular. creator: Shi Chen creator: Mengqi Li creator: Wenqiang Xin creator: Shengze Liu creator: Linfei Zheng creator: Yan Li creator: Mengyao Li creator: Mengxiong Zhan creator: Xinyu Yang uri: https://doi.org/10.7717/peerj.8596 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chen et al. title: A convenient diagnostic tool for discriminating adult-onset glutamic acid decarboxylase antibody-positive autoimmune diabetes from type 2 diabetes: a retrospective study link: https://peerj.com/articles/8610 last-modified: 2020-02-14 description: BackgroundThe glutamic acid decarboxylase antibody (GADA) test, commonly used to diagnose autoimmune diabetes, is not cost-effective in areas of low prevalence. The aim of this study was to develop a convenient tool to discriminate adult-onset GADA-positive autoimmune diabetes from type 2 diabetes (T2DM) in patients with newly diagnosed diabetes.MethodsThis retrospective cross-sectional study, conducted at Changhua Christian Hospital in Taiwan, collected electronic medical record data from January 2009 to December 2018. Patients were divided into a case group (GADA+, n = 152) and a reference group (T2DM, n = 358). Variables that differed significantly between the groups were subjected to receiver operator characteristic analysis to establish cutoff values. Discriminant function analysis was then employed to discriminate the two groups.ResultsAt the onset of diabetes, the GADA+ group was younger, with lower body mass index (BMI), higher hemoglobin A1c (HbA1c), higher high-density lipoprotein cholesterol (HDL-C), and lower total cholesterol and triglycerides (TG). Five major factors were identified to form the linear discriminant functions: BMI, age at onset, TG, HDL-C, and HbA1c. BMI < 23 kg/m2 was the most important factor, followed by TG < 98 mg/dL, HDL-C ≥ 46 mg/dL, age at onset < 30 years, and HbA1c ≥ 8.6%. The overall accuracy of the linear discriminant functions was 87.1%, with 84.2% sensitivity and 88.3% specificity.ConclusionsRoutine tests in diabetes care were used to establish a convenient, low-cost tool that may assist in the early identification of adult-onset GAD+ autoimmune diabetes in clinical practice. creator: Hon-Ke Sia creator: Shih-Te Tu creator: Pei-Yung Liao creator: Kuan-Han Lin creator: Chew-Teng Kor creator: Ling-Ling Yeh uri: https://doi.org/10.7717/peerj.8610 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sia et al. title: Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites link: https://peerj.com/articles/8614 last-modified: 2020-02-13 description: “Higher” termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the genus level. We recovered MAGs from most of the termite-specific clusters in the radiation of, for example, Planctomycetes, Fibrobacteres, Bacteroidetes, Euryarchaeota, Bathyarchaeota, Spirochaetes, Saccharibacteria, and Firmicutes, which to date contained only few or no representative genomes. Moreover, the MAGs included abundant members of the termite gut microbiota. This dataset represents the largest genomic resource for arthropod-associated microorganisms available to date and contributes substantially to populating the tree of life. More importantly, it provides a backbone for studying the metabolic potential of the termite gut microbiota, including the key members involved in carbon and nitrogen biogeochemical cycles, and important clues that may help cultivating representatives of these understudied clades. creator: Vincent Hervé creator: Pengfei Liu creator: Carsten Dietrich creator: David Sillam-Dussès creator: Petr Stiblik creator: Jan Šobotník creator: Andreas Brune uri: https://doi.org/10.7717/peerj.8614 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Hervé et al. title: Improving sustainable use of genetic resources in biodiversity archives link: https://peerj.com/articles/8369 last-modified: 2020-02-13 description: Tissue sample databases housed in biodiversity archives represent a vast trove of genetic resources, and these tissues are often destructively subsampled and provided to researchers for DNA extractions and subsequent sequencing. While obtaining a sufficient quantity of DNA for downstream applications is vital for these researchers, it is also important to preserve tissue resources for future use given that the original material is destructively and consumptively sampled with each use. It is therefore necessary to develop standardized tissue subsampling and loaning procedures to ensure that tissues are being used efficiently. In this study, we specifically focus on the efficiency of DNA extraction methods by using anuran liver and muscle tissues maintained at a biodiversity archive. We conducted a series of experiments to test whether current practices involving coarse visual assessments of tissue size are effective, how tissue mass correlates with DNA yield and concentration, and whether the amount of DNA recovered is correlated with sample age. We found that tissue samples between 2 and 8 mg resulted in the most efficient extractions, with tissues at the lower end of this range providing more DNA per unit mass and tissues at the higher end of this range providing more total DNA. Additionally, we found no correlation between tissue age and DNA yield. Because we find that even very small tissue subsamples tend to yield far more DNA than is required by researchers for modern sequencing applications (including whole genome shotgun sequencing), we recommend that biodiversity archives consider dramatically improving sustainable use of their archived material by providing researchers with set quantities of extracted DNA rather than with the subsampled tissues themselves. creator: E. J. Tuschhoff creator: Carl R. Hutter creator: Richard E. Glor uri: https://doi.org/10.7717/peerj.8369 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tuschhoff et al. title: Upregulation of desmoglein 2 and its clinical value in lung adenocarcinoma: a comprehensive analysis by multiple bioinformatics methods link: https://peerj.com/articles/8420 last-modified: 2020-02-13 description: BackgroundDesmoglein-2 (DSG2), a desmosomal adhesion molecule, is found to be closely related to tumorigenesis in recent years. However, the clinical value of DSG2 in lung adenocarcinoma remains unclear.MethodsReal-time reverse transcription-quantitative polymerase chain reaction (qRT-PCR) was utilized to detect the expression of DSG2 in 40 paired lung adenocarcinoma tissues and corresponding non-cancerous tissues. Data from The Cancer Genome Atlas (TCGA) and Oncomine datasets were also downloaded and analyzed. The correlation between DSG2 and clinicopathological features was investigated. The expression of DSG2 protein by immunohistochemical was also detected from tissue microarray and the Human Protein Atlas database. Integrated meta-analysis combining the three sources (qRT-PCR data, TCGA data and Oncomine datasets) was performed to evaluate the clinical value of DSG2. Univariate and multivariate Cox regression analyses were used to explore the prognostic value of DSG2. Then, co-expressed genes were calculated by Pearson correlation analysis. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to investigate the underlying molecular mechanism. The expression level in lung adenocarcinoma and prognostic significance of the top ten co-expressed genes were searched from Gene Expression Profiling Interactive Analysis (GEPIA) online database.ResultsDSG2 was highly expressed in lung adenocarcinoma tissues based on qRT-PCR, TCGA and Oncomine datasets. The protein expression of DSG2 was also higher in lung adenocarcinoma. According to qRT-PCR and TCGA, high DSG2 expression was positively associated with tumor size (p = 0.027, p = 0.001), lymph node metastasis (p = 0.014, p < 0.001) and TNM stage (p = 0.023, p < 0.001). The combined standard mean difference values of DSG2 expression based on the three sources were 1.30 (95% confidence interval (CI): 1.08–1.52) using random effect model. The sensitivity and specificity were 0.73 (95% CI [0.69–0.76]) and 0.96 (95% CI [0.89–0.98]). The area under the curve based on summarized receiver operating characteristic (SROC) curve was 0.79 (95% CI [0.75–0.82]). Survival analysis revealed that high DSG2 expression was associated with a short overall survival (hazard ratio [HR] = 1.638; 95% CI [1.214–2.209], p = 0.001) and poor progression-free survival (HR = 1.475; 95% CI [1.102–1.974], p < 0.001). A total of 215 co-expressed genes were identified. According to GO and KEGG analyses, these co-expressed genes may be involved in “cell division”, “cytosol”, “ATP binding” and “cell cycle”. Based on GEPIA database, seven of the top ten co-expressed genes were highly expressed in lung adenocarcinoma (DSC2, SLC2A1, ARNTL2, ERO1L, ECT2, ANLN and LAMC2). High expression of these genes had shorter overall survival.ConclusionsThe expression of DSG2 is related to the tumor size, lymph node metastasis and TNM stage. Also, DSG2 predicts poor prognosis in lung adenocarcinoma. creator: Ruiying Sun creator: Chao Ma creator: Wei Wang creator: Shuanying Yang uri: https://doi.org/10.7717/peerj.8420 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: Homeoprotein OTX1 and OTX2 involvement in rat myenteric neuron adaptation after DNBS-induced colitis link: https://peerj.com/articles/8442 last-modified: 2020-02-13 description: BackgroundInflammatory bowel diseases are associated with remodeling of neuronal circuitries within the enteric nervous system, occurring also at sites distant from the acute site of inflammation and underlying disturbed intestinal functions. Homeoproteins orthodenticle OTX1 and OTX2 are neuronal transcription factors participating to adaptation during inflammation and underlying tumor growth both in the central nervous system and in the periphery. In this study, we evaluated OTX1 and OTX2 expression in the rat small intestine and distal colon myenteric plexus after intrarectal dinitro-benzene sulfonic (DNBS) acid-induced colitis.MethodsOTX1 and OTX2 distribution was immunohistochemically investigated in longitudinal muscle myenteric plexus (LMMP)-whole mount preparations. mRNAs and protein levels of both OTX1 and OTX2 were evaluated by qRT-PCR and Western blotting in LMMPs.ResultsDNBS-treatment induced major gross morphology and histological alterations in the distal colon, while the number of myenteric neurons was significantly reduced both in the small intestine and colon. mRNA levels of the inflammatory markers, TNFα, pro-IL1β, IL6, HIF1α and VEGFα and myeloperoxidase activity raised in both regions. In both small intestine and colon, an anti-OTX1 antibody labeled a small percentage of myenteric neurons, and prevalently enteric glial cells, as evidenced by co-staining with the glial marker S100β. OTX2 immunoreactivity was present only in myenteric neurons and was highly co-localized with neuronal nitric oxide synthase. Both in the small intestine and distal colon, the number of OTX1- and OTX2-immunoreactive myenteric neurons significantly increased after DNBS treatment. In these conditions, OTX1 immunostaining was highly superimposable with inducible nitric oxide synthase in both regions. OTX1 and OTX2 mRNA and protein levels significantly enhanced in LMMP preparations of both regions after DNBS treatment.ConclusionsThese data suggest that colitis up-regulates OTX1 and OTX2 in myenteric plexus both on site and distantly from the injury, potentially participating to inflammatory-related myenteric ganglia remodeling processes involving nitrergic transmission. creator: Michela Bistoletti creator: Giovanni Micheloni creator: Nicolò Baranzini creator: Annalisa Bosi creator: Andrea Conti creator: Viviana Filpa creator: Cristina Pirrone creator: Giorgia Millefanti creator: Elisabetta Moro creator: Annalisa Grimaldi creator: Roberto Valli creator: Andreina Baj creator: Francesca Crema creator: Cristina Giaroni creator: Giovanni Porta uri: https://doi.org/10.7717/peerj.8442 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bistoletti et al. title: Get a grip—evolution of claw shape in relation to microhabitat use in intertidal arthropods (Acari, Oribatida) link: https://peerj.com/articles/8488 last-modified: 2020-02-13 description: Claws may be the most common biological attachment devices in animals but relatively few studies have examined the ecological and evolutionary significance of their morphology. We performed the first geometric morphometric investigation of arthropod claws using 15 intertidal oribatid mite species from two different families living in three different habitat types to determine if claw shape is correlated with ecology. Our results show that species living on rocky shores show remarkably high and strongly curved claws while species from mangrove habitats show significantly lower and less curved claws. Euryoecious species are able to dwell in a wide range of habitats and show an intermediate claw type. These results indicate a strong relationship between claw shape and microhabitat and the best predictors of microhabitat use seem to be claw height and curvature. Claw length varied to some degree among the species but without any noticeable ecological pattern. A comparison with terrestrial and freshwater aquatic oribatid mite species, on the other hand, confirms that their claws are only half as long as that of intertidal mites and it is suggested that tidal flooding and wave action strongly selects for long claws. In this microarthropod group which occupies a vast array of microhabitats, claw morphology may play an important role in niche separation and hence demonstrate the importance of ecomorphological studies. creator: Tobias Pfingstl creator: Michaela Kerschbaumer creator: Satoshi Shimano uri: https://doi.org/10.7717/peerj.8488 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pfingstl et al. title: The history of mesowear: a review link: https://peerj.com/articles/8519 last-modified: 2020-02-13 description: Published mesowear data was reviewed from the year 2000 to November 2019 (211 publications, 707 species, 1,396 data points). Mesowear is a widely applied tooth wear technique that can be used to infer a herbivore’s diet by scoring the height and sharpness of molar tooth cusps with the naked eye. Established as a fast and efficient tool for paleodiet reconstruction, the technique has seen multiple adaptations, simplifications, and extensions since its establishment, which have become complex to follow. The present study reviews all successive changes and adaptations to the mesowear technique in detail, providing a template for the application of each technique to the research question at hand. In addition, the array of species to which mesowear has been applied, along with the equivalent recorded diets have been compiled here in a large dataset. This review provides an insight into the metrics related to mesowear publication since its establishment. The large dataset overviews whether the species to which the various techniques of mesowear are applied are extant or extinct, their phylogenetic classification, their assigned diets and diet stability between studies, as a resource for future research on the topic. creator: Nicole L. Ackermans uri: https://doi.org/10.7717/peerj.8519 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ackermans title: The effects of single versus multiple training sessions on the motor learning of two Krav Maga strike techniques, in women link: https://peerj.com/articles/8525 last-modified: 2020-02-13 description: BackgroundExperts of the Krav Maga (KM) self-defense system propose that KM techniques are based on simple body movements which are suggested to be learned rapidly and retained. This study investigated the acquisition, retention, and further improvement with additional training of two KM strike techniques among novice female practitioners: straight punch and defensive kick.MethodsSixteen healthy females (age: 23 ± 3.7 years) without any previous martial arts/self-defense experience volunteered to participate. All participants received an initial 30-min instruction session (AQ), taught by a certified KM instructor, where each technique was deconstructed into three checkpoints (defined as a component of the entire movement) for learning. Participants were divided into two groups, one of which received additional training. Several kinematic and kinetic measures were recorded at four timepoints: immediately before AQ, immediately after AQ, 5 days after AQ, and 12 days after AQ.ResultsResults suggest that both techniques were learned rapidly, as checkpoint performance was significantly improved after AQ. Kick velocity and impact force also increased significantly after AQ; however, these measures did not change after AQ for the punch technique. Additional training did not improve either punch or kick performance beyond that learned during AQ.ConclusionThe findings from this study suggest that a single training session may be sufficient to learn and retain KM strike techniques relatively permanently; and the acquisition of the kick technique may lead to concomitant improvements in kick velocity and impact force. creator: Vincenzo E. Di Bacco creator: Mehran Taherzadeh creator: Olivier Birot creator: William H. Gage uri: https://doi.org/10.7717/peerj.8525 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Di Bacco et al. title: Proteomic similarity of the Littorinid snails in the evolutionary context link: https://peerj.com/articles/8546 last-modified: 2020-02-13 description: BackgroundThe introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions.MethodsHere we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering—using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson–Foulds distance, the Fowlkes–Mallows index and cophenetic correlation.ResultsOverall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups (“saxatilis” and “obtusata” groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species. creator: Arina L. Maltseva creator: Marina A. Varfolomeeva creator: Arseniy A. Lobov creator: Polina Tikanova creator: Marina Panova creator: Natalia A. Mikhailova creator: Andrei I. Granovitch uri: https://doi.org/10.7717/peerj.8546 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Maltseva et al. title: LINC00958 and HOXC13-AS as key candidate biomarkers in head and neck squamous cell carcinoma by integrated bioinformatics analysis link: https://peerj.com/articles/8557 last-modified: 2020-02-13 description: BackgroundHead and neck squamous cell carcinoma (HNSCC) is a malignant tumor with a strong tendency for metastasis and recurrence. Finding effective biomarkers for the early diagnosis of HNSCC is critical for the early treatment and prognosis of patients.MethodsRNA sequencing data including long non-coding RNAs (lncRNAs), messenger RNA (mRNAs) and microRNAs (miRNAs) of 141 HNSCC and 44 adjacent normal tissues were obtained from the TCGA. Differentially expressed genes were analyzed using the R package DESeq. GO terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. A competing endogenous RNAs (ceRNA) network was constructed. The most differentially expressed genes in the main ceRNA network were chosen for nasopharyngeal carcinoma (NPC) cell lines and NPEC2 Bmi-1 cell line verification. A receiver operating characteristic (ROC) curve was constructed for 141 specimens of HNSCC tissues from 44 control samples.ResultsIn our study, 79 HNSCC-associated abnormally expressed lncRNAs , 86 abnormally expressed miRNAs and 324 abnormally expressed mRNAs were identified. The public microarray results showed that LINC00958 and HOXC13-AS expression levels were upregulated in HNSCC tissues compared with the adjacent normal tissues in this study (p < 0.0001). LINC00958 and HOXC13-AS expression levels in NPC cell lines were higher than those in the NPEC2 Bmi-1 cell line (p < 0.05). The results showed that the area under the ROC curve (AUC) of LINC00958 reached up to 0.906 at a cutoff value of 7.96, with a sensitivity and specificity of 80.85% and 90.91%, respectively. The AUC of HOXC13-AS reached up to 0.898 at a cutoff value of 0.695, with sensitivity and specificity values of 86.23% and 83.78%, respectively.ConclusionThe current study indicates that LINC00958 and HOXC13-AS are new candidate diagnostic biomarkers for HNSCC patients. creator: Dan Xiong creator: Wei Wu creator: Lijuan Kan creator: Dayang Chen creator: Xiaowen Dou creator: Xiang Ji creator: Mengmeng Wang creator: Zengyan Zong creator: Jian Li creator: Xiuming Zhang uri: https://doi.org/10.7717/peerj.8557 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xiong et al. title: The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions link: https://peerj.com/articles/8573 last-modified: 2020-02-13 description: BackgroundOlive (Olea europaea L.) is an important oil and fruit crop worldwide, owning a rich germplasm with a large number of cultivars. Simple sequence repeats (SSRs) are excellent markers and have been used for the identification of olive cultivars. However, the limited number of SSR markers and the occurrence of confusion on the names of cultivars, as well as the possible appearance of clonal variation make it difficult to identify cultivars and interpret relationships among olive cultivars.MethodSSR markers were designed based on trinucleotide repeat sequences by screening the whole genome of olive, and the polymorphic SSR markers were developed that were applied to the identification of 53 olive accessions. The genetic characteristics and relationships of these olive accessions were evaluated based on the developed SSR markers.ResultsTwenty-one highly polymorphic genomic-SSR markers were developed, covering most chromosomes of olive. These SSR markers could well distinguish all 53 olive accessions, confirming their effectiveness. DNA fingerprints of the 53 olive accessions were constructed based on the 21 SSR markers. The dendrogram clearly divided the tested accessions into two main groups, which was also supported by the results of principal coordinate analysis. A total of 31 private alleles were detected in 15 olive accessions, which reflected the genetic diversity within 53 olive accessions to some extent. Six homonymy cases were also clarified by genetic analysis. These results suggest that the newly developed olive SSR markers are informative for the exploitation, preservation and breeding of olive. creator: Danyang Li creator: Cui Long creator: Xiaoming Pang creator: Delu Ning creator: Tao Wu creator: Mingliang Dong creator: Xiaoning Han creator: Huihong Guo uri: https://doi.org/10.7717/peerj.8573 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Optimization of aeration enhanced surfactant soil washing for remediation of diesel-contaminated soils using response surface methodology link: https://peerj.com/articles/8578 last-modified: 2020-02-13 description: Surfactant-enhanced soil washing has been used for remediation of organic pollutants for an extended period, but its effectiveness and wide application was limited by the high concentration of surfactants utilized. In this work, the efficiency of conventional soil washing performance was enhanced by 12–25% through the incorporation of air bubbles into the low concentration surfactant soil washing system. Surfactant selection pre-experiment using aerated and conventional soil washing reveals Brij 35 > TX100 > Tween 80 > Saponin in diesel oil removal. Optimization of the effect of time, surfactant concentration, pH, agitation speed, and airflow rate in five levels were undertaken using Response Surface Methodology and Central composite design. The optimum degree of variables achieved was 90 min of washing time, 370 mg/l of concentration, washing pH of 10,535 rpm of agitation speed and 7.2 l/min of airflow rate with 79.5% diesel removal. The high predicted R2 value of 0.9517 showed that the model could efficiently be used to predict diesel removal efficiency. The variation in efficiency of aeration assisted and conventional soil washing was variable depending on the type of surfactant, organic matter content of the soil, particle size distribution and level of pollutant weathering. The difference in removal efficiency of the two methods increases when the level of organic matter increases and when the particle size and age of contamination decreases. creator: Befkadu Abayneh Ayele creator: Jun Lu creator: Quanyuan Chen uri: https://doi.org/10.7717/peerj.8578 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ayele et al. title: Lack of recovery of the long-spined sea urchin Diadema antillarum Philippi in Puerto Rico 30 years after the Caribbean-wide mass mortality link: https://peerj.com/articles/8428 last-modified: 2020-02-12 description: Caribbean populations of the long-spined black sea urchin Diadema antillarum Philippi were decimated by a disease-induced mass mortality in the early 1980’s. The present study provides an updated status of the D. antillarum recovery and population characteristics in La Parguera Natural Reserve, Puerto Rico. The last detailed study to assess population recovery in 2001, indicated a slow, and modest recovery, albeit densities remained far below pre-mass mortality levels. Population densities were assessed along three depth intervals in six reef localities and one depth in three lagoonal sea-grass mounds using ten 20 m2 (10 × 2 m) belt-transects at each depth interval. Most of these were previously surveyed in 2001. All individuals encountered along the belt transects were sized in situ with calipers and rulers to characterize the size (age) structure of each population and get insight into the urchin’s population dynamics and differences across localities in the area. Habitat complexity (rugosity) was assessed in all depth intervals. No significant differences in population densities between reef zones (inner shelf and mid-shelf) were observed, but significantly higher densities were found on shallow habitats (<5 m depth; 2.56 ± 1.6 ind/m2) compared to intermediate (7–12 m; 0.47 ± 0.8 ind/m2) and deep (>12 m; 0.04 ± 0.08 ind/m2) reef habitats in almost all sites surveyed. Habitat complexity had the greatest effect on population densities at all levels (site, zone and depth) with more rugose environments containing significantly higher densities and wider size structures. Comparison between survey years revealed that D. antillarum populations have not increased since 2001, and urchins seem to prefer shallower, more complex and productive areas of the reef. Populations were dominated by medium to large (5–9 cm in test diameter) individuals and size-frequency distributions indicated that smaller juveniles were virtually absent compared to 2001, which could reflect a recruitment-limited population and explain in part, the lack of increase in population densities. The limited temporal scale of this study, high horizontal movement of individuals along the complex, shallower reef and inshore habitats could also explain the general decline in mean densities. Other extrinsic factors affecting reproductive output and/or succesful recruitment and survival of juveniles likely contribute to the high variablility in population densities observed over time. creator: Evan Tuohy creator: Christina Wade creator: Ernesto Weil uri: https://doi.org/10.7717/peerj.8428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tuohy et al. title: An effective survey method for studying volant species activity and behavior at tall structures link: https://peerj.com/articles/8438 last-modified: 2020-02-12 description: The effects of anthropogenic modification of air space on wildlife, particularly volant species, is not fully understood. Thus, it is essential to understand wildlife-interactions with tall structures to implement effective mitigation strategies. Yet, we are currently lacking standard protocols for visual surveys of wildlife behavior at such heights. Our study sought to determine an effective, repeatable method using readily available night vision and thermal technology to survey wildlife at tall structures. Using bats as the taxonomic group of interest, we (1) created a key to identify bats and their behavior, (2) compared the effectiveness of 2 different technologies, and (3) assessed optimal equipment placement to visually capture bat activity and behavior in proximity to wind turbine towers. For the latter, we tested thermal cameras at four distances from the base of the tower. The results of our study revealed that thermal cameras captured ∼34% more flying animals than night vision at a 2 m distance. However, due to the heat signature of the turbine towers themselves, it was challenging to identify behaviors and interactions that occurred in close proximity to the towers. In contrast, it was difficult to identify bats approaching the towers using night vision, yet we were able to clearly observe interactions with the towers themselves. With regards to equipment placement, we visually captured more bats with the thermal cameras placed 2 m from the tower base compared to farther distances. From our findings, we recommend that when using either thermal or night vision technology at tall structures, they be placed 2 m from the base to effectively observe interactions along the length of these structures. In addition, we further recommend that consideration be given to the use of these two technology types together to effectively conduct such surveys. If these survey techniques are incorporated into standard protocols, future surveys at a variety of tall structures are likely to become comparable and repeatable, thereby more effectively informing any mitigation strategies that may be required. creator: Brynn E. Huzzen creator: Amanda M. Hale creator: Victoria J. Bennett uri: https://doi.org/10.7717/peerj.8438 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huzzen et al. title: A field-based investigation of behavioural interactions between invasive green crab (Carcinus maenas), rock crab (Cancer irroratus), and American lobster (Homarus americanus) in southern Newfoundland link: https://peerj.com/articles/8444 last-modified: 2020-02-12 description: Marine species invasions pose a global threat to native biodiversity and commercial fisheries. The European green crab (Carcinus maenas) is one of the most successful marine invaders worldwide and has, in the last decade, invaded the southern and western coastal waters of the island of Newfoundland, Newfoundland and Labrador (NL), Canada. Impacts of green crab on the American lobster (Homarus americanus), which are native to Newfoundland, are not well understood, particularly for interactions around deployed fishing gear. Declines in lobster catch rates in invaded systems (i.e., Placentia Bay, NL), have prompted concerns among lobster fishers that green crab are interfering with lobster catch. Here, we conducted a field experiment in a recently-invaded bay (2013) in which we deployed lobster traps pre-stocked with green crab, native rock crab (Cancer irroratus) (a procedural control), or empty (control). We compared catch per unit effort across each category, and used underwater cameras to directly observe trap performance in situ. In addition, we used SCUBA surveys to determine the correlation between ambient density of lobster and green crab in the ecosystem and the catch processes of lobster in traps. We found: (1) Regardless of the species of crab stocked, crab presence reduced the total number of lobster that attempted to enter the trap, and also reduced entry success rate, (2) lobster consumed green crab, rock crab and other lobster inside traps and (3) there was a positive association between lobster catch and ambient lobster density. Our results suggest that while there was a relationship between in-trap crab density and trap catch rates, it was not linked to the non-native/native status of the crab species. creator: Nicola Zargarpour creator: Cynthia H. McKenzie creator: Brett Favaro uri: https://doi.org/10.7717/peerj.8444 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zargarpour et al. title: Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells link: https://peerj.com/articles/8522 last-modified: 2020-02-12 description: BackgroundMicroRNAs (miRNAs) play an essential role in gene regulators in many biological and molecular phenomena. Unraveling the involvement of miRNA as a key cellular factor during in vitro canine parvovirus (CPV) infection may facilitate the discovery of potential intervention candidates. However, the examination of miRNA expression profiles in CPV in tissue culture systems has not been fully elucidated.MethodIn the present study, we utilized high-throughput small RNA-seq (sRNA-seq) technology to investigate the altered miRNA profiling in miRNA libraries from uninfected (Control) and CPV-2c infected Crandell Reese Feline Kidney cells.ResultsWe identified five of known miRNAs (miR-222-5p, miR-365-2-5p, miR-1247-3p, miR-322-5p and miR-361-3p) and three novel miRNAs (Novel 137, Novel 141 and Novel 102) by sRNA-seq with differentially expressed genes in the miRNA repertoire of CPV-infected cells over control. We further predicted the potential target genes of the aforementioned miRNAs using sequence homology algorithms. Notably, the targets of miR-1247-3p exhibited a potential function associated with cellular defense and humoral response to CPV. To extend the probing scheme for gene targets of miR-1247-3p, we explored and performed Gene Ontology (GO) enrichment analysis of its target genes. We discovered 229 putative targets from a total of 38 enriched GO terms. The top over-represented GO enrichment in biological process were lymphocyte activation and differentiation, marginal zone B cell differentiation, negative regulation of cytokine production, negative regulation of programed cell death, and negative regulation of signaling. We next constructed a GO biological process network composed of 28 target genes of miR-1247-3p, of which, some genes, namely BCL6, DLL1, GATA3, IL6, LEF1, LFNG and WNT1 were among the genes with obviously intersected in multiple GO terms.ConclusionThe miRNA-1247-3p and its cognate target genes suggested their great potential as novel therapeutic targets or diagnostic biomarkers of CPV or other related viruses. creator: Phongsakorn Chuammitri creator: Soulasack Vannamahaxay creator: Benjaporn Sornpet creator: Kidsadagon Pringproa creator: Prapas Patchanee uri: https://doi.org/10.7717/peerj.8522 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chuammitri et al. title: The N-terminal domain of rhamnosyltransferase EpsF influences exopolysaccharide chain length determination in Streptococcus thermophilus 05-34 link: https://peerj.com/articles/8524 last-modified: 2020-02-12 description: Glycosyltransferases are key enzymes involved in the assembly of repeating units of exopolysaccharides (EPS). A glycosyltransferase generally consists of the N-terminal and the C-terminal domain, however, the functional role of these domains in EPS biosynthesis remains largely unknown. In this study, homologous overexpression was employed to investigate the effects of EpsFN, a truncated form of rhamnosyltransferase EpsF with only the N-terminal domain, on EPS biosynthesis in Streptococcus thermophilus 05-34. Reverse transcription qPCR and Western blotting analysis confirmed the successful expression of epsFN in 05-34 at the transcription and translation level, respectively. Further analysis showed that the monosaccharide composition and yield of EPS were not affected by the overexpression of epsFN, whereas the molecular mass decreased by 5-fold. Accordingly, the transcription levels of genes involved in EPS biosynthesis, including chain-length determination gene epsC, were down-regulated by 5- to 6-fold. These results indicated that the N-terminal domain of EpsF alone could influence the molecular mass of EPS, probably via lowering the concentration of sugar precursors, which may lead to decreased expression of genes responsible for chain-length determination. creator: Guohong Wang creator: Jiaxi Li creator: Shuxin Xie creator: Zhengyuan Zhai creator: Yanling Hao uri: https://doi.org/10.7717/peerj.8524 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: The community composition variation of Russulaceae associated with the Quercus mongolica forest during the growing season at Wudalianchi City, China link: https://peerj.com/articles/8527 last-modified: 2020-02-12 description: BackgroundMost species of the Russulaceae are ectomycorrhizal (ECM) fungi, which are widely distributed in different types of forest ecology and drive important ecological and economic functions. Little is known about the composition variation of the Russulaceae fungal community aboveground and in the root and soil during the growing season (June–October) from a Quercus mongolica forest. In this study, we investigated the changes in the composition of the Russulaceae during the growing season of this type of forest in Wudalianchi City, China.MethodsTo achieve this, the Sanger sequencing method was used to identify the Russulaceae aboveground, and the high-throughput sequencing method was used to analyze the species composition of the Russulaceae in the root and soil. Moreover, we used the Pearson correlation analysis, the redundancy analysis and the multivariate linear regression analysis to analyze which factors significantly affected the composition and distribution of the Russulaceae fungal community.ResultsA total of 56 species of Russulaceae were detected in the Q. mongolica forest, which included 48 species of Russula, seven species of Lactarius, and one species of Lactifluus. Russula was the dominant group. During the growing season, the sporocarps of Russula appeared earlier than those of Lactarius. The number of species aboveground exhibited a decrease after the increase and were significantly affected by the average monthly air temperature (r = −0.822, p = 0.045), average monthly relative humidity (r = −0.826, p = 0.043), monthly rainfall (r = 0.850, p = 0.032), soil moisture (r = 0.841, p = 0.036) and soil organic matter (r = 0.911, p = 0.012). In the roots and soils under the Q. mongolica forest, the number of species did not show an apparent trend. The number of species from the roots was the largest in September and the lowest in August, while those from the soils were the largest in October and the lowest in June. Both were significantly affected by the average monthly air temperature (r2 = 0.6083, p = 0.040) and monthly rainfall (r2 = 0.6354, p = 0.039). Moreover, the relative abundance of Russula and Lactarius in the roots and soils showed a linear correlation with the relative abundance of the other fungal genera. creator: Pengjie Xing creator: Yang Xu creator: Tingting Gao creator: Guanlin Li creator: Jijiang Zhou creator: Mengle Xie creator: Ruiqing Ji uri: https://doi.org/10.7717/peerj.8527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xing et al. title: In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses link: https://peerj.com/articles/8539 last-modified: 2020-02-12 description: Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. However, systematic analysis of HDAC gene family and gene expression in response to abiotic and biotic stresses has not yet been reported. In this study, a systematic analysis of the HDAC gene family in maize was performed and 18 ZmHDACs distributed on nine chromosomes were identified. Phylogenetic analysis of ZmHDACs showed that this gene family could be divided into RPD3/HDA1, SIR2, and HD2 groups. Tissue-specific expression results revealed that ZmHDACs exhibited diverse expression patterns in different tissues, indicating that these genes might have diversified functions in growth and development. Expression pattern of ZmHDACs in hormone treatment and inoculation experiment suggested that several ZmHDACs might be involved in jasmonic acid or salicylic acid signaling pathway and defense response. Interestingly, HDAC genes were downregulated under heat stress, and immunoblotting results demonstrated that histones H3K9ac and H4K5ac levels were increased under heat stress. These results provide insights into ZmHDACs, which could help to reveal their functions in controlling maize development and responses to abiotic or biotic stresses. creator: Kang Zhang creator: Lu Yu creator: Xi Pang creator: Hongzhe Cao creator: Helong Si creator: Jinping Zang creator: Jihong Xing creator: Jingao Dong uri: https://doi.org/10.7717/peerj.8539 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Elevated CO2 not increased temperature has specific effects on soil nematode community either with planting of transgenic Bt rice or non-Bt rice link: https://peerj.com/articles/8547 last-modified: 2020-02-12 description: BackgroundTransgenic Bt rice has not been approved for commercial cultivation because of the fierce public debate on food safety, biosafety regulation and ecological risk. Meanwhile, the concentration of CO2 and temperature in the atmosphere, as important environmental factors affecting the persistence of exogenous Bt protein, have increased. Elevated CO2, increased temperature, the planting of transgenic Bt rice and their interactions may further influence the structure and complexity of soil food web. However, the effects of transgenic Bt rice planting on soil organism remain largely unexplored before its commercial production especially under global climate change.MethodsHere, we assessed the influences of transgenic Bt rice (cv. HH with fused Cry1Ab/Cry1Ac in contrast to its parental line of non-Bt rice cv. MH63) on soil nematode communities under the conditions of elevated CO2 concentration and increased temperature for 2 years of 2016 and 2017 in open-top chambers located in Ningjin County, Shandong Province of China.ResultsElevated CO2 concentration remarkably increased the abundance of fungivores and significantly decreased their nematode channel ratio (NCR) and enrichment index (EI) irrespective of rice variety (transgenic Bt rice or non-Bt rice) or temperature (normal temperature or increased temperature). Additionally, rice variety and temperature did not significantly change soil nematode composition, abundance and ecological indices (including total maturity index (∑MI), Shannon diversity (H′), structure index (SI), NCR and EI). However, apparent seasonal changes were observed in theses aforementioned variables.DiscussionThese results suggested that atmospheric CO2 concentration but not temperature or rice variety has great impacts on soil nematode community, especially fungivores. creator: Yingying Song creator: Jiawen Liu creator: Fajun Chen uri: https://doi.org/10.7717/peerj.8547 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Song et al. title: Comprehensive analysis of long non-coding RNAs and mRNAs in skeletal muscle of diabetic Goto-Kakizaki rats during the early stage of type 2 diabetes link: https://peerj.com/articles/8548 last-modified: 2020-02-12 description: Skeletal muscle long non-coding RNAs (lncRNAs) were reported to be involved in the development of type 2 diabetes (T2D). However, little is known about the mechanism of skeletal muscle lncRNAs on hyperglycemia of diabetic Goto-Kakizaki (GK) rats at the age of 3 and 4 weeks. To elucidate this, we used RNA-sequencing to profile the skeletal muscle transcriptomes including lncRNAs and mRNAs, in diabetic GK and control Wistar rats at the age of 3 and 4 weeks. In total, there were 438 differentially expressed mRNAs (DEGs) and 401 differentially expressed lncRNAs (DELs) in skeletal muscle of 3-week-old GK rats compared with age-matched Wistar rats, and 1000 DEGs and 726 DELs between GK rats and Wistar rats at 4 weeks of age. The protein–protein interaction analysis of overlapping DEGs between 3 and 4 weeks, the correlation analysis of DELs and DEGs, as well as the prediction of target DEGs of DELs showed that these DEGs (Pdk4, Stc2, Il15, Fbxw7 and Ucp3) might play key roles in hyperglycemia, glucose intolerance, and increased fatty acid oxidation. Considering the corresponding co-expressed DELs with high correlation coefficients or targeted DELs of these DEGs, our study indicated that these dysregulated lncRNA-mRNA pairs (NONRATG017315.2-Pdk4, NONRATG003318.2-Stc2, NONRATG011882.2-Il15, NONRATG013497.2-Fbxw7, MSTRG.1662-Ucp3) might be related to above biological processes in GK rats at the age of 3 and 4 weeks. Our study could provide more comprehensive knowledge of mRNAs and lncRNAs in skeletal muscle of GK rats at 3 and 4 weeks of age. And our study may provide deeper understanding of the underlying mechanism in T2D of GK rats at the age of 3 and 4 weeks. creator: Wenlu Zhang creator: Yunmeng Bai creator: Zixi Chen creator: Xingsong Li creator: Shuying Fu creator: Lizhen Huang creator: Shudai Lin creator: Hongli Du uri: https://doi.org/10.7717/peerj.8548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: People in early stages of Parkinson’s disease are able to intentionally reweight the use of visual information for postural control link: https://peerj.com/articles/8552 last-modified: 2020-02-12 description: BackgroundParkinson’s disease (PD) leads to several changes in motor control, many of them related to informational or cognitive overload. The aim of this study was to investigate the influence of knowledge and intention on the postural control performance and on the coupling between visual information and body sway in people with and without PD standing upright.MethodsParticipants were 21 people with PD (62.1 ± 7.2 years), stages 1 and 2 (Hoehn & Yahr scale), under dopaminergic medication, and 21 people in the control group (62.3 ± 7.1 years). Participants stood upright inside a moving room, performing seven trials of 60 s. In the first trial, the room remained motionless. In the others, the room oscillated at 0.2 Hz in the anterior-posterior direction: in the first block of three trials, the participants were not informed about the visual manipulation; in the second block of three trials, participants were informed about the room movement and asked to resist the visual influence. An OPTOTRAK system recorded the moving room displacement and the participants’ sway. The variables mean sway amplitude (MSA), coherence and gain were calculated.ResultsWith no visual manipulation, no difference occurred between groups for MSA. Under visual manipulation conditions, people with PD presented higher MSA than control, and both groups reduced the sway magnitude in the resisting condition. Control group reduced sway magnitude by 6.1%, while PD group reduced by 11.5%. No difference was found between groups and between conditions for the coupling strength (coherence). For the coupling structure (gain), there was no group difference, but both groups showed reduced gain in the resisting condition. Control group reduced gain by 12.0%, while PD group reduced by 9.3%.ConclusionsPeople with PD, under visual manipulation, were more influenced than controls, but they presented the same coupling structure between visual information and body sway as controls. People in early stages of PD are able to intentionally alter the influence of visual information. creator: Caio F. Cruz creator: Giovanna G. Genoves creator: Flávia Doná creator: Henrique B. Ferraz creator: José A. Barela uri: https://doi.org/10.7717/peerj.8552 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cruz et al. title: The effect of hepatopancreas homogenate of the Red king crab on HA-based filler link: https://peerj.com/articles/8579 last-modified: 2020-02-12 description: In this study, several methods were used to analyze the hydrolysis of hyaluronic acid (HA)-based cosmetic fillers by the hepatopancreas homogenate of the Red king crab. The results show that the homogenate and commercially available hyaluronidases have similar hydrolysis activities on the fillers. Atomic force microscopy images reveal that the HA fillers consist mainly of spherical-like particles, which are converted into filamentous structures as a result of hydrolysis by the Red king crab hepatopancreas homogenate. Turbidimetric analysis of the hydrolysis process shows that HA aggregation with acidic albumin exhibits a bell-shaped dependence on reaction time. Analysis of the hydrolysis process by nuclear magnetic resonance shows that HA degradation lasts several days. The maximum rate of the reaction is detected in the 1st h of incubation. The data confirm that the purified homogenate of the Red king crab hepatopancreas exerts hyaluronidase activity on HA-based cosmetic fillers; therefore, it may be considered as a potential therapeutic agent for treating filler complications. creator: Tatyana Ponomareva creator: Dmitrii Sliadovskii creator: Maria Timchenko creator: Maxim Molchanov creator: Alexander Timchenko creator: Evgeny Sogorin uri: https://doi.org/10.7717/peerj.8579 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ponomareva et al. title: HER2 and BRAF mutation in colorectal cancer patients: a retrospective study in Eastern China link: https://peerj.com/articles/8602 last-modified: 2020-02-12 description: ObjectiveTo investigate the frequency and prognostic role of the human epidermal growth factor receptor 2 gene (HER2) and BRAF V600E gene mutation in Chinese patients with colorectal cancer (CRC).MethodsClinicopathological and survival information from 480 patients with stage I–III CRC were reviewed and recorded. HER2 amplification was analyzed by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), BRAF V600E mutation was tested by IHC and Sanger sequencing. The relationship between HER2 and BRAF V600E mutation status and clinicopathological characteristics and outcomes were determined.ResultsThe amplification of HER2 and BRAF V600E mutation were identified in 27 of 480 (5.63%) and 19 of 480 (3.96%) CRC patients, respectively. HER2 amplification significantly correlated with greater bowel wall invasion (P = 0.041) and more advanced TNM stage (I vs. II vs. III; 0 vs 5.78% vs. 7.41%, P = 0.013). Patients suffering from tumors with poor differentiation had a higher incidence rate of BRAF V600E mutation than those with moderate/well differentiation (7.77% vs 2.92%, P = 0.04). HER2 amplification was an independent prognostic factor for worse disease-free survival (DFS) (HR = 2.53, 95% CI: 1.21–5.30, P = 0.014).ConclusionThe prevalence of HER2 amplification and BRAF V600E mutation in stage I–III CRC patients in Chinese was 6% and 4%, respectively, and HER2 amplification appeared to be associated with a worse DFS. More comprehensive molecular classification and survival analysis are needed to validate our findings. creator: Xiangyan Zhang creator: Jie Wu creator: Lili Wang creator: Han Zhao creator: Hong Li creator: Yuhe Duan creator: Yujun Li creator: Ping Xu creator: Wenwen Ran creator: Xiaoming Xing uri: https://doi.org/10.7717/peerj.8602 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Proximate composition determination in goat cheese whey by near infrared spectroscopy (NIRS) link: https://peerj.com/articles/8619 last-modified: 2020-02-12 description: BackgroundIn Brazil, over the last few years there has been an increase in the production and consumption of goat cheeses. In addition, there was also a demand to create options to use the whey extracted during the production of cheeses. Whey can be used as an ingredient in the development of many products. Therefore, knowing its composition is a matter of utmost importance, considering that the reference methods of food analysis require time, trained labor and expensive reagents for its execution.MethodsGoat whey samples produced in winter and summer were submitted to proximate composition analysis (moisture, total solids, ashes, proteins, fat and carbohydrates by difference) using reference methods and near infrared spectroscopy (NIRS). The spectral data was preprocessed by baseline correction and the Savitzky–Golay derivative. The models were built using Partial Least Square Regression (PLSR) with raw and preprocessed data for each dependent variable (proximate composition parameter).ResultsThe average whey composition values obtained using the referenced methods were in accordance with the consulted literature. The composition did not differ significantly (p > 0.05) between the summer and winter whey samples. The PLSR models were made available using the following figures of merit: coefficients of determination of the calibration and prediction models (R2cal and R2pred, respectively) and the Root Mean Squared Error Calibration and Prediction (RMSEC and RMSEP, respectively). The best models used raw data for fat and protein determinations and the values obtained by NIRS for both parameters were consistent with their referenced methods. Consequently, NIRS can be used to determine fat and protein in goat whey. creator: Isadora Kaline Camelo Pires de Oliveira Galdino creator: Hévila Oliveira Salles creator: Karina Maria Olbrich dos Santos creator: Germano Veras creator: Flávia Carolina Alonso Buriti uri: https://doi.org/10.7717/peerj.8619 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Galdino et al. title: Identification of prognostic splicing factors and exploration of their potential regulatory mechanisms in pancreatic adenocarcinoma link: https://peerj.com/articles/8380 last-modified: 2020-02-11 description: Pancreatic adenocarcinoma (PAAD), the most common subtype of pancreatic cancer, is a highly lethal disease. In this study, we integrated the expression profiles of splicing factors (SFs) of PAAD from RNA-sequencing data to provide a comprehensive view of the clinical significance of SFs. A prognostic index (PI) based on SFs was developed using the least absolute shrinkage and selection operator (LASSO) COX analysis. The PI exhibited excellent performance in predicting the status of overall survival of PAAD patients. We also used the percent spliced in (PSI) value obtained from SpliceSeq software to quantify different types of alternative splicing (AS). The prognostic value of AS events was explored using univariate COX and LASSO COX analyses; AS-based PIs were also proposed. The integration of prognosis-associated SFs and AS events suggested the potential regulatory mechanisms of splicing processes in PAAD. This study defined the markedly clinical significance of SFs and provided novel insight into their potential regulatory mechanisms. creator: Min-hua Rong creator: Zhan-hui Zhu creator: Ying Guan creator: Mei-wei Li creator: Jia-shuo Zheng creator: Yue-qi Huang creator: Dan-ming Wei creator: Ying-mei Li creator: Xiao-ju Wu creator: Hui-ping Bu creator: Hui-liu Peng creator: Xiao-lin Wei creator: Guo-sheng Li creator: Ming-xuan Li creator: Ming-hui Chen creator: Su-ning Huang uri: https://doi.org/10.7717/peerj.8380 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rong et al. title: Glycerophosphodiester phosphodiesterase 1 (GDE1) acts as a potential tumor suppressor and is a novel therapeutic target for non-mucin-producing colon adenocarcinoma link: https://peerj.com/articles/8421 last-modified: 2020-02-11 description: Colon adenocarcinoma (COAD) represents a major public health issue due to its high incidence and mortality. As different histological subtypes of COAD are related to various survival outcomes and different therapies, finding specific targets and treatments for different subtypes is one of the major demands of individual disease therapy. Interestingly, as these different subtypes show distinct metabolic profiles, it may be possible to find specific targets related to histological typing by targeting COAD metabolism. In this study, the differential expression patterns of metabolism-related genes between COAD (n = 289) and adjacent normal tissue (n = 41) were analyzed by one-way ANOVA. We then used weighted gene co-expression network analysis (WGCNA) to further identify metabolism-related gene connections. To determine the critical genes related to COAD metabolism, we obtained 2,114 significantly differentially expressed genes (DEGs) and 12 modules. Among them, we found the hub module to be significantly associated with histological typing, including non-mucin-producing colon adenocarcinoma and mucin-producing colon adenocarcinoma. Combining survival analysis, we identified glycerophosphodiester phosphodiesterase 1 (GDE1) as the most significant gene associated with histological typing and prognosis. This gene displayed significantly lower expression in COAD compared with normal tissues and was significantly correlated with the prognosis of non-mucin-producing colon adenocarcinoma (p = 0.0017). Taken together, our study showed that GDE1 exhibits considerable potential as a novel therapeutic target for non-mucin-producing colon adenocarcinoma. creator: Qiu Shen creator: Chao Lu creator: Hua Yang creator: Ming-Xia Ge creator: Wang-Xiao Xia creator: Qing-Peng Kong creator: Gong-Hua Li creator: Yan-Hong Gu uri: https://doi.org/10.7717/peerj.8421 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shen et al. title: Growth dynamics in Acropora cervicornis and A. prolifera in southwest Puerto Rico link: https://peerj.com/articles/8435 last-modified: 2020-02-11 description: Natural population recovery of Acropora palmata, A. cervicornis and their hybrid, Acropora prolifera, have fluctuated significantly after their Caribbean-wide, disease-induced mass mortality in the early 1980s. Even though significant recovery has been observed in a few localities, recurrent disease outbreaks, bleaching, storm damage, local environmental deterioration, algae smothering, predation, low sexual recruitment and low survivorship have affected the expected, quick recovery of these weedy species. In this study, the status of three recovering populations of A. cervicornis and two of A. prolifera were assessed over one year using coral growth and mortality metrics, and changes in their associated algae and fish/invertebrate communities in three localities in the La Parguera Natural Reserve (LPNR), southwest coast of Puerto Rico. Five branches were tagged in each of 29, medium size (1–2 m in diameter) A. cervicornis and 18 A. prolifera colonies in the Media Luna, Mario and San Cristobal reefs off LPNR. Branches were measured monthly, together with observations to evaluate associated disease(s), algae accumulation and predation. A. cervicornis grew faster [3.1 ± 0.44 cm/month (= 37.2 cm/y)] compared to A. prolifera [2.6 ± 0.41 cm/month (= 31.2 cm/y)], and growth was significantly higher during Winter-Spring compared to Summer-Fall for both taxa (3.5 ± 0.58 vs. 0.53 ± 0.15 cm/month in A. cervicornis, and 2.43 ± 0.71 vs. 0.27 ± 0.20 cm/month in A. prolifera, respectively). Algal accumulation was only observed in A. cervicornis, and was higher during Spring-Summer compared to Fall-Winter (6.1 ± 0.91 cm/month and 3.8 ± 0.29 cm/month, respectively, (PERMANOVA, df = 2, MS = 10.2, p = 0.37)). Mortality associated with white band disease, algae smothering and fish/invertebrate predation was also higher in A. cervicornis and varied among colonies within sites, across sites and across season. The balance between tissue grow and mortality determines if colonies survive. This balance seems to be pushed to the high mortality side often by increasing frequency of high thermal anomalies, inducing bleaching and disease outbreaks and other factors, which have historically impacted the natural recovery of these taxa in the La Parguera Natural Reserve in Puerto Rico and possibly other areas in the region. Overall, results indicate variability in both growth and mortality rates in both taxa across localities and seasons, with A. cervicornis showing overall higher mortalities compared to A. prolifera. creator: Ernesto Weil creator: Nicholas M. Hammerman creator: Rebecca L. Becicka creator: Juan Jose Cruz-Motta uri: https://doi.org/10.7717/peerj.8435 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Weil et al. title: Using approximate Bayesian inference for a “steps and turns” continuous-time random walk observed at regular time intervals link: https://peerj.com/articles/8452 last-modified: 2020-02-11 description: The study of animal movement is challenging because movement is a process modulated by many factors acting at different spatial and temporal scales. In order to describe and analyse animal movement, several models have been proposed which differ primarily in the temporal conceptualization, namely continuous and discrete time formulations. Naturally, animal movement occurs in continuous time but we tend to observe it at fixed time intervals. To account for the temporal mismatch between observations and movement decisions, we used a state-space model where movement decisions (steps and turns) are made in continuous time. That is, at any time there is a non-zero probability of making a change in movement direction. The movement process is then observed at regular time intervals. As the likelihood function of this state-space model turned out to be intractable yet simulating data is straightforward, we conduct inference using different variations of Approximate Bayesian Computation (ABC). We explore the applicability of this approach as a function of the discrepancy between the temporal scale of the observations and that of the movement process in a simulation study. Simulation results suggest that the model parameters can be recovered if the observation time scale is moderately close to the average time between changes in movement direction. Good estimates were obtained when the scale of observation was up to five times that of the scale of changes in direction. We demonstrate the application of this model to a trajectory of a sheep that was reconstructed in high resolution using information from magnetometer and GPS devices. The state-space model used here allowed us to connect the scales of the observations and movement decisions in an intuitive and easy to interpret way. Our findings underscore the idea that the time scale at which animal movement decisions are made needs to be considered when designing data collection protocols. In principle, ABC methods allow to make inferences about movement processes defined in continuous time but in terms of easily interpreted steps and turns. creator: Sofia Ruiz-Suarez creator: Vianey Leos-Barajas creator: Ignacio Alvarez-Castro creator: Juan Manuel Morales uri: https://doi.org/10.7717/peerj.8452 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ruiz-Suarez et al. title: Phosphorylation systems in symbiotic nitrogen-fixing bacteria and their role in bacterial adaptation to various environmental stresses link: https://peerj.com/articles/8466 last-modified: 2020-02-11 description: Symbiotic bacteria, commonly called rhizobia, lead a saprophytic lifestyle in the soil and form nitrogen-fixing nodules on legume roots. During their lifecycle, rhizobia have to adapt to different conditions prevailing in the soils and within host plants. To survive under these conditions, rhizobia fine-tune the regulatory machinery to respond rapidly and adequately to environmental changes. Symbiotic bacteria play an essential role in the soil environment from both ecological and economical point of view, since these bacteria provide Fabaceae plants (legumes) with large amounts of accessible nitrogen as a result of symbiotic interactions (i.e., rhizobia present within the nodule reduce atmospheric dinitrogen (N2) to ammonia, which can be utilized by plants). Because of its restricted availability in the soil, nitrogen is one of the most limiting factors for plant growth. In spite of its high content in the atmosphere, plants are not able to assimilate it directly in the N2 form. During symbiosis, rhizobia infect host root and trigger the development of specific plant organ, the nodule. The aim of root nodule formation is to ensure a microaerobic environment, which is essential for proper activity of nitrogenase, i.e., a key enzyme facilitating N2 fixation. To adapt to various lifestyles and environmental stresses, rhizobia have developed several regulatory mechanisms, e.g., reversible phosphorylation. This key mechanism regulates many processes in both prokaryotic and eukaryotic cells. In microorganisms, signal transduction includes two-component systems (TCSs), which involve membrane sensor histidine kinases (HKs) and cognate DNA-binding response regulators (RRs). Furthermore, regulatory mechanisms based on phosphoenolopyruvate-dependent phosphotranspherase systems (PTSs), as well as alternative regulatory pathways controlled by Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases (STPs) play an important role in regulation of many cellular processes in both free-living bacteria and during symbiosis with the host plant (e.g., growth and cell division, envelope biogenesis, biofilm formation, response to stress conditions, and regulation of metabolism). In this review, we summarize the current knowledge of phosphorylation systems in symbiotic nitrogen-fixing bacteria, and their role in the physiology of rhizobial cells and adaptation to various environmental conditions. creator: Paulina Lipa creator: Monika Janczarek uri: https://doi.org/10.7717/peerj.8466 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lipa and Janczarek title: Comprehensive transcriptome analysis of reference genes for fruit development of Euscaphis konishii link: https://peerj.com/articles/8474 last-modified: 2020-02-11 description: BackgroundQuantitativereal-time reverse transcriptase polymerase chain reaction is the common method to quantify relative gene expression. Normalizating using reliable genes is critical in correctly interpreting expression data from qRT-PCR. Euscaphis konishii is a medicinal plant with a long history in China, which has various chemical compounds in fruit. However, there is no report describing the selection of reference genes in fruit development of Euscaphis konishii.MethodsWe selected eight candidate reference genes based on RNA-seq database analysis, and ranked expression stability using statistical algorithms GeNorm, NormFinder, BestKeeper and ReFinder. Finally, The nine genes related to the anthocyanin synthesis pathway of Euscaphis konishii were used to verify the suitability of reference gene.ResultsThe results showed that the stability of EkUBC23, EkCYP38 and EkGAPDH2 was better, and the low expression reference genes (EkUBC23 and EkCYP38) were favourable for quantifying low expression target genes, while the high expression reference gene (EkGAPDH2) was beneficial for quantifying high expression genes. In this study, we present the suitable reference genes for fruit development of Euscaphis konishii based on transcriptome data, our study will contribute to further studies in molecular biology and gene function on Euscaphis konishii and other closely related species. creator: Cheng-Long Yang creator: Xue-Yan Yuan creator: Jie Zhang creator: Wei-Hong Sun creator: Zhong-Jian Liu creator: Shuang-Quan Zou uri: https://doi.org/10.7717/peerj.8474 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Patterns of biodiversity response along a gradient of forest use in Eastern Amazonia, Brazil link: https://peerj.com/articles/8486 last-modified: 2020-02-11 description: The preservation of tropical forests is increasingly at risk, including forests located within human-modified landscapes that retain high conservation value. People modify and interact with these landscapes through a wide range of uses. However, our knowledge of how different forest uses affect biodiversity is limited. Here, we analyse the responses of different taxa to four distinct categories of forest management, namely old-growth forest, Brazil nut extraction areas, reduced impact logging areas, and eucalyptus plantations. Within six independent replicates of each category, we sampled three taxa (fruit-feeding butterflies, dung beetles, and trees) in eastern Amazonia. Forests under moderate use (Brazil nut extraction and reduced-impact logging) had similar, albeit slightly lower, diversity levels relative to old-growth forests, while communities in plantations were significantly less diverse. Only 4%, 20%, and 17%, of the sampled butterfly, dung beetle, and tree species, respectively, were restricted to old-growth forests. This study provides further empirical evidence of the importance of old-growth forest conservation in the context of human-modified landscapes. It also suggests that landscape matrices integrating forest uses at varying intensities are well positioned to reconcile biodiversity conservation with the production of goods that support local livelihoods. creator: Sérgio G. Milheiras creator: Marcelino Guedes creator: Fernando Augusto Barbosa Silva creator: Perseu Aparício creator: Georgina M. Mace uri: https://doi.org/10.7717/peerj.8486 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Milheiras et al. title: DNA barcoding reveals incorrect labelling of insects sold as food in the UK link: https://peerj.com/articles/8496 last-modified: 2020-02-11 description: BackgroundInsects form an established part of the diet in many parts of the world and insect food products are emerging into the European and North American marketplaces. Consumer confidence in product is key in developing this market, and accurate labelling of content identity is an important component of this. We used DNA barcoding to assess the accuracy of insect food products sold in the UK.MethodsWe purchased insects sold for human consumption from online retailers in the UK and compared the identity of the material ascertained from DNA barcoding to that stated on the product packaging. To this end, the COI sequence of mitochondrial DNA was amplified and sequenced, and compared the sequences produced to reference sequences in NCBI and the Barcode of Life Data System (BOLD).ResultsThe barcode identity of all insects that were farmed was consistent with the packaging label. In contrast, disparity between barcode identity and package contents was revealed in two cases of foraged material (mopane worm and winged termites). One case of very broad family-level description was also highlighted, where material described as grasshopper was identified as Locusta migratoria from DNA barcode.ConclusionOverall these data indicate the need to establish tight protocols to validate product identity in this developing market. Maintaining biosafety and consumer confidence rely on accurate and consistent product labelling that provides a clear chain of information from producer to consumer. creator: Stefanos Siozios creator: Annie Massa creator: Catherine L. Parr creator: Rudi L. Verspoor creator: Gregory D.D. Hurst uri: https://doi.org/10.7717/peerj.8496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Siozios et al. title: Development and validation of a predictive model for end-stage renal disease risk in patients with diabetic nephropathy confirmed by renal biopsy link: https://peerj.com/articles/8499 last-modified: 2020-02-11 description: This study was performed to develop and validate a predictive model for the risk of end-stage renal disease (ESRD) inpatients with diabetic nephropathy (DN) confirmed by renal biopsy. We conducted a retrospective study with 968 patients with T2DM who underwentrenal biopsy for the pathological confirmation of DNat the First Affiliated Hospital of Zhengzhou University from February 2012 to January 2015; the patients were followed until December 2018. The outcome was defined as a fatal or nonfatal ESRD event (peritoneal dialysis or hemodialysis for ESRD, renal transplantation, or death due to chronic renal failure or ESRD). The dataset was randomly split into development (75%) and validation (25%) cohorts. We used stepwise multivariablelogistic regression to identify baseline predictors for model development. The model’s performance in the two cohorts, including discrimination and calibration, was evaluated by the C-statistic and the P value of the Hosmer-Lemeshow test. During the 3-year follow-up period, there were 225 outcome events (47.1%) during follow-up. Outcomes occurred in 187 patients (52.2%) in the derivation cohort and 38 patients (31.7%) in the validation cohort. The variables selected in the final multivariable logistic regression after backward selection were pathological grade, Log Urinary Albumin-to-creatinine ratio (Log ACR), cystatin C, estimated glomerular filtration rate (eGFR) and B-type natriuretic peptide (BNP). 4 prediction models were created in a derivation cohort of 478 patients: a clinical model that included cystatin C, eGFR, BNP, Log ACR; a clinical-pathological model and a clinical-medication model, respectively, also contained pathological grade and renin-angiotensin system blocker (RASB) use; and a full model that also contained the pathological grade, RASB use and age. Compared with the clinical model, the clinical-pathological model and the full model had better C statistics (0.865 and 0.866, respectively, vs. 0.864) in the derivation cohort and better C statistics (0.876 and 0.875, respectively, vs. 0.870) in the validation cohort. Among the four models, the clinical-pathological model had the lowest AIC of 332.53 and the best P value of 0.909 of the Hosmer-Lemeshow test. We constructed a nomogram which was a simple calculator to predict the risk ratio of progression to ESRD for patients with DN within 3 years. The clinical-pathological model using routinely available clinical measurements was shown to be accurate and validated method for predicting disease progression in patients with DN. The risk model can be used in clinical practice to improve the quality of risk management and early intervention. creator: Lulu Sun creator: Jin Shang creator: Jing Xiao creator: Zhanzheng Zhao uri: https://doi.org/10.7717/peerj.8499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: A Bayesian approach to construct confidence intervals for comparing the rainfall dispersion in Thailand link: https://peerj.com/articles/8502 last-modified: 2020-02-11 description: Natural disasters such as drought and flooding are the consequence of severe rainfall fluctuation, and rainfall amount data often contain both zero and positive observations, thus making them fit a delta-lognormal distribution. By way of comparison, rainfall dispersion may not be similar in enclosed regions if the topography and the drainage basin are different, so it can be evaluated by the ratio of variances. To estimate this, credible intervals using the highest posterior density based on the normal-gamma prior (HPD-NG) and the method of variance estimates recovery (MOVER) for the ratio of delta-lognormal variances are proposed. Monte Carlo simulation was used to assess the performance of the proposed methods in terms of coverage probability and relative average length. The results of the study reveal that HPD-NG performed very well and was able to meet the requirements in various situations, even with a large difference between the proportions of zeros. However, MOVER is the recommended method for equal small sample sizes. Natural rainfall datasets for the northern and northeastern regions of Thailand are used to illustrate the practical use of the proposed credible intervals. creator: Patcharee Maneerat creator: Sa-aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.8502 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Maneerat et al. title: Ecosystem antifragility: beyond integrity and resilience link: https://peerj.com/articles/8533 last-modified: 2020-02-11 description: We review the concept of ecosystem resilience in its relation to ecosystem integrity from an information theory approach. We summarize the literature on the subject identifying three main narratives: ecosystem properties that enable them to be more resilient; ecosystem response to perturbations; and complexity. We also include original ideas with theoretical and quantitative developments with application examples. The main contribution is a new way to rethink resilience, that is mathematically formal and easy to evaluate heuristically in real-world applications: ecosystem antifragility. An ecosystem is antifragile if it benefits from environmental variability. Antifragility therefore goes beyond robustness or resilience because while resilient/robust systems are merely perturbation-resistant, antifragile structures not only withstand stress but also benefit from it. creator: Miguel Equihua creator: Mariana Espinosa Aldama creator: Carlos Gershenson creator: Oliver López-Corona creator: Mariana Munguía creator: Octavio Pérez-Maqueo creator: Elvia Ramírez-Carrillo uri: https://doi.org/10.7717/peerj.8533 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Equihua et al. title: Short-term effects of thinning on the development and communities of understory vegetation of Chinese fir plantations in Southeastern China link: https://peerj.com/articles/8536 last-modified: 2020-02-11 description: BackgroundHigh-density conditions are global issues that threaten the sustainable management of plantations throughout the world. Monocultures and untimely management practices have identically resulted in the simplex of community structures, decreases in biodiversity, and long-term productivity losses in plantations China. The most popular measure which is commonly used to address these issues is thinning, which potentially results in increases in the development of understory plants in plantations. However, there is limited information currently available regarding the community composition of understory vegetation and the associated environmental factors, which has limited the sustainable management of China’s fir plantation ecosystems.MethodIn the present study, a thinning experiment was implemented which included a control check (CK: no thinning), as well as low intensity thinning (LIT: 20%), moderate intensity thinning (MIT: 33%), and high intensity thinning (HIT: 50%) in Chinese fir plantations located in the Southeastern China. During the investigation process, the understory vegetation examined three years after thinning measures were completed, in order to analyze the impacts of different thinning intensities on the growth and community composition of the understory plants. At the same time, the associated environmental factors in the fir plantations were also investigated.ResultsThe species richness, total coverage, and biomass of the understory vegetation were observed to be apparently increased with increasing thinning intensity. In addition, it was found that the thinning measures had prominently influenced the soil nutrients. The community compositions of the understory vegetation were significantly different among the four thinning intensity levels, especially between the CK and the HIT. Furthermore, the development of the understory vegetation was found to be significantly correlated with the soil nutrient contents, and the community compositions of the understory vegetation were prominently driven by the tree densities, slope positions, and soil nutrient contents. creator: Xuelei Xu creator: Xinjie Wang creator: Yang Hu creator: Ping Wang creator: Sajjad Saeed creator: Yujun Sun uri: https://doi.org/10.7717/peerj.8536 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xu et al. title: Proteogenomic analysis of pitaya reveals cold stress-related molecular signature link: https://peerj.com/articles/8540 last-modified: 2020-02-11 description: Pitayas (Hylocereus spp.) is an attractive, highly nutritious and commercially valuable tropical fruit. However, low-temperature damage limits crop production. Genome of pitaya has not been sequenced yet. In this study, we sequenced the transcriptome of pitaya as the reference and further investigated the proteome under low temperature. By RNAseq technique, approximately 25.3 million reads were obtained, and further trimmed and assembled into 81,252 unigene sequences. The unigenes were searched against UniProt, NR and COGs at NCBI, Pfam, InterPro and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and 57,905 unigenes were retrieved annotations. Among them, 44,337 coding sequences were predicted by Trandecoder (v2.0.1), which served as the reference database for label-free proteomic analysis study of pitaya. Here, we identified 116 Differentially Abundant Proteins (DAPs) associated with the cold stress in pitaya, of which 18 proteins were up-regulated and 98 proteins were down-regulated. KEGG analysis and other results showed that these DAPs mainly related to chloroplasts and mitochondria metabolism. In summary, chloroplasts and mitochondria metabolism-related proteins may play an important role in response to cold stress in pitayas. creator: Junliang Zhou creator: Zhuang Wang creator: Yongya Mao creator: Lijuan Wang creator: Tujian Xiao creator: Yang Hu creator: Yang Zhang creator: Yuhua Ma uri: https://doi.org/10.7717/peerj.8540 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhou et al. title: A reevaluation of the basal turtle Indochelys spatulata from the Early–Middle Jurassic (Toarcian–Aalenian) of India, with descriptions of new material link: https://peerj.com/articles/8542 last-modified: 2020-02-11 description: BackgroundIndochelys spatulata is an extinct turtle from the Early to Middle Jurassic Kota Formation of the Pranhita–Godavari Gondwana basin, India. The holotype and previously only known specimen is a partially eroded shell that had been collected near Kota village, north of Sironcha, in Maharashtra State. Phylogenetic analyses have consistently suggested placement at the base of the clade Mesochelydia.MethodsWe here figure and describe the holotype of Indochelys spatulata and two new specimens, which were collected from the Kota Formation near Kistapur village, Telengana State, about 60 km NW from the type locality. We furthermore explore the relationships of this fossil turtle by updating its scoring based on all available material in the most recent analysis of basal turtle relationships.ResultsThe revision of the holotype of Indochelys spatulata provides minor adjustments to the morphology of this specimen, in particular recognition of a transverse break across the carapace, presence of only eight neurals, of which the eight is octagonal, and presence of a pathological element located between neurals VII and VIII. The new material provides new anatomical insights, in particular presence of a broad cervical, a vertebral V that inserts deeply into vertebral IV, narrow pleurals within increasingly short posteromedial contacts with the vertebrals towards the posterior, at least three pairs of musk duct foramina, and numerous insights into the morphology of the girdles and stylopodium. In combination, all material allows affirming the validity of Indochelys spatulata with confidence. The phylogenetic analysis affirms the placement of Indochelys spatulata as a basal mesochelydian, but cannot resolve its relationships relative to the roughly coeval Condorchelys antiqua and Kayentachelys aprix. creator: Walter G. Joyce creator: Saswati Bandyopadhyay uri: https://doi.org/10.7717/peerj.8542 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Joyce and Bandyopadhyay title: Repertoire of morphable proteins in an organism link: https://peerj.com/articles/8606 last-modified: 2020-02-11 description: All living organisms have evolved to contain a set of proteins with variable physical and chemical properties. Efforts in the field of structural biology have contributed to uncovering the shape and the variability of each component. However, quantification of the variability has been performed mostly by multiple pair-wise comparisons. A set of experimental coordinates for a given protein can be used to define the “morphness/unmorphness”. To understand the evolved repertoire in an organism, here we show the results of global analysis of more than a thousand Escherichia coli proteins, by the recently introduced method, distance scoring analysis (DSA). By collecting a new index “UnMorphness Factor” (UMF), proposed in this study and determined from DSA for each of the proteins, the lowest and the highest boundaries of the experimentally observable structural variation are comprehensibly defined. The distribution plot of UMFs obtained for E. coli represents the first view of a substantial fraction of non-redundant proteome set of an organism, demonstrating how rigid and flexible components are balanced. The present analysis extends to evaluate the growing data from single particle cryo-electron microscopy, providing valuable information on effective interpretation to structural changes of proteins and the supramolecular complexes. creator: Keisuke Izumi creator: Eitaro Saho creator: Ayuka Kutomi creator: Fumiaki Tomoike creator: Tetsuji Okada uri: https://doi.org/10.7717/peerj.8606 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Izumi et al. title: Life history stage explains behavior in a social network before and during the early breeding season in a cooperatively breeding bird link: https://peerj.com/articles/8302 last-modified: 2020-02-10 description: In species with stage-structured populations selection pressures may vary between different life history stages and result in stage-specific behaviors. We use life history stage to explain variation in the pre and early breeding season social behavior of a cooperatively breeding bird, the Florida scrub-jay (Aphelocoma coerulescens) using social network analysis. Life history stage explains much of the variation we observed in social network position. These differences are consistent with nearly 50 years of natural history observations and generally conform to a priori predictions about how individuals in different stages should behave to maximize their individual fitness. Where the results from the social network analysis differ from the a priori predictions suggest that social interactions between members of different groups are more important for breeders than previously thought. Our results emphasize the importance of accounting for life history stage in studies of individual social behavior. creator: Angela Tringali creator: David L. Sherer creator: Jillian Cosgrove creator: Reed Bowman uri: https://doi.org/10.7717/peerj.8302 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tringali et al. title: Genome-wide analysis of lncRNAs, miRNAs, and mRNAs forming a prognostic scoring system in esophageal squamous cell carcinoma link: https://peerj.com/articles/8368 last-modified: 2020-02-10 description: BackgroundEsophageal squamous cell carcinoma (ESCC) is the main subtype of esophageal carcinoma. Protein coding genes and non-coding RNAs can be powerful prognostic factors in multiple cancers, including ESCC. However, there is currently no model that integrates multiple types of RNA expression signatures to predict clinical outcomes.MethodsThe sequencing data (RNA-sequencing and miRNA-sequencing) and clinical data of ESCC patients were obtained from The Cancer Genome Atlas (TCGA) database, and Differential gene expression analysis, Cox regression analysis and Spearman correlation analysis were used to construct prognosis-related lncRNA-mRNA co-expression network and scoring system with multiple types of RNA. The potential molecular mechanisms of prognostic mRNAs were explored by functional enrichment analysis.ResultsA total of 62 prognostic lncRNAs, eight prognostic miRNAs and 66 prognostic mRNAs were identified in ESCC (P-value < 0.05) and a prognosis-related lncRNA-mRNA co-expression network was created. Five prognosis-related hub RNAs (CDCA2, MTBP, CENPE, PBK, AL033384.1) were identified. Biological process analysis revealed that mRNAs in prognosis-related co-expression RNA network were mainly enriched in cell cycle, mitotic cell cycle and nuclear division. Additionally, we constructed a prognostic scoring system for ESCC using ten signature RNAs (MLIP, TNFSF10, SIK2, LINC01068, LINC00601, TTTY14, AC084262.1, LINC01415, miR-5699-3p, miR-552-5p). Using this system, patients in the low-risk group had better long-term survival than those in the high-risk group (log-rank, P-value < 0.0001). The area under the ROC curve (AUCs) revealed that the accuracy of the prediction model was higher than the accuracy of single type of RNA prediction model.ConclusionIn brief, we constructed a prognostic scoring system based on multiple types of RNA for ESCC that showed high predicting prognosis performance, and deeply understood the regulatory mechanism of prognosis-related lncRNA-mRNA co-expression network. creator: Xiaobo Shi creator: You Li creator: Yuchen Sun creator: Xu Zhao creator: Xuanzi Sun creator: Tuotuo Gong creator: Zhinan Liang creator: Yuan Ma creator: Xiaozhi Zhang uri: https://doi.org/10.7717/peerj.8368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shi et al. title: The role of rarity as a surrogate of marine fish species representation link: https://peerj.com/articles/8373 last-modified: 2020-02-10 description: Because the distribution of most of the species is poorly known, conservationists use surrogates to help maximize the representation level of all species. Historically, species richness has been used to calculate the importance of priority areas for conservation, but several studies revealed sites with high species richness often fail to determine the smallest number of sites that will protect the highest number of species. Rarity, however, has played a prominent role in safeguarding planning units. While the performance of rarity has been previously assessed in terrestrial systems, we tested the hypothesis that rarity of a site can be used as a measure of the importance of a site to a conservation network in marine ecosystems. We used the presence data (at a 1-degree resolution) to calculate five rarity indices of fish diversity at a global extent and compared the results to those obtained by using species richness and site complementarity. Our objectives were to: (1) determine if rarity indices can be used as surrogates of fish biodiversity by representing the highest number of species in the smallest number of sites; and (2) determine if the effectiveness of these indices to represent fish biodiversity is impacted by the metric used to define rarity. Results indicate that rarity could be an effective surrogate for marine fishes, as most results showed a mean of 100% effectiveness. In the context of marine biodiversity conservation, results show that rarity indices could be considered affordable and feasible surrogates of species representation, with the most significant benefit to those areas of the world that are in most need to access alternative tools. Results also open a new area of collaboration between biogeography and marine conservation biology since planners can use biogeographical patterns of rarity to enhance the performance of the current protected area network. creator: Fabio Albuquerque creator: Yaiyr Astudillo-Scalia uri: https://doi.org/10.7717/peerj.8373 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Albuquerque and Astudillo-Scalia title: Fluid resuscitation-related coagulation impairment in a porcine hemorrhagic shock model link: https://peerj.com/articles/8399 last-modified: 2020-02-10 description: BackgroundFast and effective treatment of hemorrhagic shock is one of the most important preclinical trauma care tasks e.g., in combat casualties in avoiding severe end-organ damage or death. In scenarios without immediate availability of blood products, alternate regimens of fluid resuscitation represent the only possibility of maintaining sufficient circulation and regaining adequate end-organ oxygen supply. However, the fluid choice alone may affect the extent of the bleeding by interfering with coagulation pathways. This study investigates the impact of hydroxyethyl starch (HES), gelatine-polysuccinate (GP) and balanced electrolyte solution (BES) as commonly used agents for fluid resuscitation on coagulation using a porcine hemorrhagic shock model.MethodsFollowing approval by the State and Institutional Animal Care Committee, life-threatening hemorrhagic shock was induced via arterial blood withdrawal in 24 anesthetized pigs. Isovolumetric fluid resuscitation with either HES, GP or BES (n = 3 × 8) was performed to compensate for the blood loss. Over four hours, hemodynamics, laboratory parameters and rotational thromboelastometry-derived coagulation were analyzed. As secondary endpoint the porcine values were compared to human blood.ResultsAll the agents used for fluid resuscitation significantly affected coagulation. We measured a restriction of laboratory parameters, clot development and clot firmness, particularly in HES- and GP-treated animals. Hemoglobin content dropped in all groups but showed a more pronounced decline in colloid-treated pigs. This effect was not maintained over the four-hour monitoring period.ConclusionHES, GP, and BEL sufficiently stabilized the macrocirculation, but significantly affected coagulation. These effects were most pronounced after colloid and particularly HES administration. Despite suitability for rapid hemodynamic stabilization, colloids have to be chosen with caution, because their molecular properties may affect coagulation directly and as a consequence of pronounced hemodilution. Our comparison of porcine and human coagulation showed increased coagulation activity in pig blood. creator: Alexander Ziebart creator: Robert Ruemmler creator: Christian Möllmann creator: Jens Kamuf creator: Andreas Garcia-Bardon creator: Serge C. Thal creator: Erik K. Hartmann uri: https://doi.org/10.7717/peerj.8399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ziebart et al. title: Downregulation of miR-193a-3p is involved in the pathogenesis of hepatocellular carcinoma by targeting CCND1 link: https://peerj.com/articles/8409 last-modified: 2020-02-10 description: BackgroundHepatocellular carcinoma (HCC) is the second-highest cause of malignancy-related death worldwide, and many physiological and pathological processes, including cancer, are regulated by microRNAs (miRNAs). miR-193a-3p is an anti-oncogene that plays an important part in health and disease biology by interacting with specific targets and signals.MethodsIn vitro assays were performed to explore the influences of miR-193a-3p on the propagation and apoptosis of HCC cells. The sequencing data for HCC were obtained from The Cancer Genome Atlas (TCGA), and the expression levels of miR-193a-3p in HCC and non-HCC tissues were calculated. The differential expression of miR-193a-3p in HCC was presented as standardized mean difference (SMD) with 95% confidence intervals (CIs) in Stata SE. The impact of miR-193a-3p on the prognoses of HCC patients was determined by survival analysis. The potential targets of miR-193a-3p were then predicted using miRWalk 2.0 and subjected to enrichment analyses, including Gene Ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Protein-Protein Interaction (PPI) network analysis. The interaction between miR-193a-3p and one predicted target, Cyclin D1 (CCND1), was verified by dual luciferase reporter assays and Pearson correlation analysis.ResultsMiR-193a-3p inhibited the propagation and facilitated the apoptosis of HCC cells in vitro. The pooled SMD indicated that miR-193a-3p had a low level of expression in HCC (SMD: −0.88, 95% CI [−2.36 −0.59]). Also, HCC patients with a higher level of miR-193a-3p expression tended to have a favorable overall survival (OS: HR = 0.7, 95% CI [0.43–1.13], P = 0.14). For the KEGG pathway analysis, the most related pathway was “proteoglycans in cancer”, while the most enriched GO term was “protein binding”. The dual luciferase reporter assays demonstrated the direct interaction between miR-193a-3p and CCND1, and the Pearson correlation analysis suggested that miR-193a-3p was negatively correlated with CCND1 in HCC tissues (R =  − 0.154, P = 0.002).ConclusionmiR-193a-3p could suppress proliferation and promote apoptosis by targeting CCND1 in HCC cells. Further, miR-193a-3p can be used as a promising biomarker for the diagnosis and treatment of HCC in the future. creator: Shi-shuo Wang creator: Zhi-guang Huang creator: Hua-yu Wu creator: Rong-quan He creator: Li-hua Yang creator: Zhen-bo Feng creator: Yi-wu Dang creator: Hui-ping Lu creator: Ye-ying Fang creator: Gang Chen uri: https://doi.org/10.7717/peerj.8409 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Prognostic analysis of very early onset pancreatic cancer: a population-based analysis link: https://peerj.com/articles/8412 last-modified: 2020-02-10 description: BackgroundWe aimed to use competing risk model to assess whether very early onset pancreatic cancer (VEOPC ) (<45 years) had a worse prognosis than older pancreatic cancer (PC) patients, and to build a competing risk nomogram for predicting the risk of death of VEOPC.MethodsWe selected pancreatic adenocarcinoma (PDAC) patients as our cohort from the Surveillance, Epidemiology, and End Results (SEER) database. The impact of cancer specific death was estimated by competing risk analysis. Multivariate Fine-Gray regression for proportional hazards modeling of the subdistribution hazard (SH) model based nomogram was constructed, which was internally validated by discrimination and calibration with 1,000 bootstraps.ResultsOur cohort included 1,386 VEOPC patients and 53,940 older patients. We observed that in unresectablePDAC patients, VEOPC had better cancer specific survival (CSS) than each older group (45–59 years, 60–69 years, 70–79 years and >79 years). There was no significant prognostic difference between VEOPC and each older group in resectablePDAC. Our competing nomogram showed well discrimination and calibration by internal validation.ConclusionFor unresectable PDAC patients, VEOPC had better CSS than older patients. Our competing risk nomogram might be an easy-to-use tool for the specific death prediction of VEOPC patients with PDAC. creator: Dongjun Dai creator: Yanmei Wang creator: Xinyang Hu creator: Hongchuan Jin creator: Xian Wang uri: https://doi.org/10.7717/peerj.8412 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dai et al. title: Early changes in the urine proteome in a rat liver tumour model link: https://peerj.com/articles/8462 last-modified: 2020-02-10 description: BackgroundUrine, as a potential biomarker source among body fluids, can accumulate many early changes in the body due to the lack of mechanisms to maintain a homeostatic state. This study aims to detect early changes in the urinary proteome in a rat liver tumour model.MethodsThe tumour model was established with the Walker-256 carcinosarcoma cell line (W256). Urinary proteins at days 3, 5, 7 and 11 were profiled by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Compared with controls, differential proteins were selected. Associations of differential proteins with cancer were retrieved.ResultsAt days 3, 5, 7 and 11, five, fifteen, eleven and twelve differential proteins were identified, respectively. Some of the differential proteins were reported to be associated with liver cancer. This differential urinary protein pattern was different from the patterns in W256 subcutaneous, lung metastasis and intracerebral tumour models.ConclusionsThis study demonstrates that (1) early changes in urinary proteins can be found in the rat liver tumour model; (2) urinary proteins can be used to differentiate the same tumour cells grown in different organs. creator: Yameng Zhang creator: Yufei Gao creator: Youhe Gao uri: https://doi.org/10.7717/peerj.8462 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Coupled influence of precipitation regimes and seedling emergence time on the reproductive strategy in Chloris virgata link: https://peerj.com/articles/8476 last-modified: 2020-02-10 description: Precipitation regime and seedling emergence time both influence plant growth and reproduction. However, little attention has been given to the effects of these combined factors on the reproductive strategy of Chloris virgata, which is a vital species in Songnen grassland. Here, we simulated the changes in the precipitation regime and seedling emergence time to evaluate tiller traits and seed production. The results showed that tiller number behaved similarly among three precipitation regimes when sowed on 15 May (T1), while it increased significantly with precipitation regimes when sowed on 15 June (T2) and 15 July (T3). Tiller number decreased significantly with the seedling emergence time under the same water supply treatment. The proportional allocation of reproductive tiller number to total tiller number was significantly higher at T3 than at T1 and T2. Seed number remained similar under different precipitation regimes at T2 and T3, whereas it was significantly lower under low precipitation than under other water levels at T1. Seed number reached the maximum values at T2 under the same level of precipitation treatment. Seed size was significantly lower under low precipitation compared to other water supply treatments and the lowest values in seed size, about 0.5 mg, occurred at T2 under all the precipitation regimes. The lowest values in spike number were under low precipitation at all seedling emergence times. Seed yield exhibited similar trends with seed size under different precipitation regimes, while the greatest gains in these values were at T1 under all the precipitation regimes. Our findings showed that simulated precipitation regimes and seedling emergence time affected the reproductive strategy of C. virgata. Typical and high precipitation, as well as early seedling emergence, will improve the seed yield and seed quality in this species. creator: Ying Wang creator: Jiawei Chen creator: Yige Huang creator: Zhongsheng Mu creator: Changfu Wang uri: https://doi.org/10.7717/peerj.8476 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Evaluating the effects of red imported fire ants (Solenopsis invicta) on juvenile Houston Toads (Bufo [=Anaxyrus] houstonensis) in Colorado County, TX link: https://peerj.com/articles/8480 last-modified: 2020-02-10 description: The spread of invasive species is considered a major threat to biodiversity, second only to habitat loss. Red Imported Fire Ants (Solenopsis invicta) are a globally invasive species with negative impacts reported on native invertebrate and vertebrate species. Federally endangered Houston Toads (Bufo [=Anaxyrus] houstonensis), endemic to Texas, are among the vertebrates reportedly negatively impacted by Red Imported Fire Ants (RIFA). Threats posed by RIFA to Houston Toads needed to be explicitly characterized. Large-scale chemical treatments to suppress RIFA and facilitate brood survival in Attwater’s prairie-chickens (Tympanuchus cupido attwateri) at the Attwater Prairie Chicken National Wildlife Refuge (APCNWR) afforded us an opportunity to experimentally examine the influence of RIFA abundance on juvenile Houston Toad growth and survival. We also sought to examine whether juvenile Houston Toads could grow and survive in a vegetation type similar to a historic species locality. We conducted a terrestrial mesocosm experiment to test whether the application of bait-driven suppressant decreased counts of RIFA relative to untreated sites. We examined whether counts of native ant and non-ant native invertebrates were higher in response to potential decreases in RIFA. We compared growth and survival rates in juvenile Houston Toads among treated and untreated sites, expecting juvenile growth and survival to be higher in response to potentially decreased RIFA counts and increased native invertebrate counts. We saw lower counts of RIFA in treated prairies, but we also observed a decrease in native ant counts possibly due to chemical treatment. Therefore, the application of bait-driven suppressant may not affect RIFA alone. We saw no difference in counts of non-ant invertebrates among treated and untreated sites. Juvenile Houston Toads did not differ in growth and survival among treated and untreated sites. We recognize that the lack of a relationship between juvenile growth and survival with a treatment effect, and therefore RIFA abundance, may be limited to APCNWR. We encourage additional experimental studies to elucidate RIFA impacts at other sites. We extrapolated apparent survival estimates from our study to one year. These appear comparable to juvenile survivorship required in simulations for Houston Toad population persistence and on this basis, we recommend that APCNWR be re-evaluated as a reintroduction site for Houston Toads. We also recommend further studies to potentially broaden the regulatory definition of Houston Toad habitat beyond the current restrictive view of canopied forest alone. Such studies would need to examine the utility of native grasslands as dispersal corridors/upland habitat for juvenile Houston Toads. Our findings emphasize the utility of experimental studies in directly examining the influence of perceived threats to imperiled species and the role of such clarifications in adapting recovery efforts. creator: Shashwat Sirsi creator: Madeleine J. Marsh creator: Michael R.J. Forstner uri: https://doi.org/10.7717/peerj.8480 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sirsi et al. title: Comparison of lipid accumulation product and body mass index as indicators of diabetes diagnosis among 215,651 Chinese adults link: https://peerj.com/articles/8483 last-modified: 2020-02-10 description: PurposeWe aimed to assess if lipid accumulation product (LAP) could outperform body mass index (BMI) as a marker for diabetes diagnosis.MethodsWe analyzed the results of a national physical examination project in Urumqi, China. This project was conducted in 442 community clinics in Urumqi from October 2016 to February 2017.ResultsLAP was highly correlated with diabetes. The subjects with higher amounts of LAP had a higher risk of diabetes, and the prevalence of diabetes in the fourth quartile of LAP was dramatically higher than in the first quartile (5.72% vs. 21.76%). The adjusted odds ratios (AOR) associated with diabetes in the fourth quartile of LAP was significantly higher than the AOR associated with diabetes in the first quartile, and when BMI ≥ 28 kg/m2 was compared with BMI < 28 kg/m2 (3.24 (3.11, 3.37) vs. 1.65 (1.60, 1.70)). The LAP’s area under the curve (AUC) was significantly higher than the BMI’s AUC when based on diabetes (0.655 vs. 0.604). In the normal BMI group, 34% of participants had a LAP value higher than the cutoff point found during ROC analysis. In this subgroup, we observed a significantly higher prevalence of diabetes that was similar to that of the subgroup with a BMI ≥ 28 kg/m2, and both of their LAP values were higher than the cutoff point.ConclusionWhen use as a tool for diabetes diagnosis, LAP performed better than BMI, implying that LAP could be a preferable anthropometry assessment. creator: Tian Tian creator: Hualian Pei creator: Zhen Chen creator: Gulisiya Hailili creator: Shuxia Wang creator: Yong Sun creator: Hua Yao creator: Dai Jianghong uri: https://doi.org/10.7717/peerj.8483 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tian et al. title: Gene flow between subpopulations of gray snapper (Lutjanus griseus) from the Caribbean and Gulf of Mexico link: https://peerj.com/articles/8485 last-modified: 2020-02-10 description: BackgroundThe gray snapper (Lutjanus griseus) has a tropical and subtropical distribution. In much of its range this species represents one of the most important fishery resources because of its high quality meat and market value. Due to this, this species is vulnerable to overfishing, and population declines have been observed in parts of its range. In recent decades, it has been established that knowing the level of genetic connectivity is useful for establishing appropriate management and conservation strategies given that genetic isolation can drive towards genetic loss. Presently the level of genetic connectivity between subpopulations of L. griseus of the southern region of the Gulf of Mexico and the Caribbean Sea remains unknown.MethodsIn the present study we analyze genetic structure and diversity for seven subpopulations in the southern Gulf of Mexico and the Mexican Caribbean Sea. Eight microsatellite primers of phylogenetically closely related species to L. griseus were selected.ResultsTotal heterozygosity was 0.628 and 0.647 in the southern Gulf of Mexico and the Mexican Caribbean Sea, however, results obtained from AMOVA and RST indicated a lack of genetic difference between the major basins. We also found no association between genetic difference and geographic distance, and moderately high migration rates (Nm = > 4.1) suggesting ongoing gene flow among the subpopulations. Gene flow within the southern Gulf of Mexico appears to be stronger going from east-to-west.ConclusionsMigration rates tended to be higher between subpopulations within the same basin compared to those across basins indicating some regionalization. High levels of genetic diversity and genetic flow suggest that the population is quite large; apparently, the fishing pressure has not caused a bottleneck effect. creator: Oscar de Jesús Rosado-Nic creator: J. Derek Hogan creator: José Héctor Lara-Arenas creator: Rigoberto Rosas-Luis creator: Laura Carrillo creator: Carmen Amelia Villegas-Sánchez uri: https://doi.org/10.7717/peerj.8485 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Rosado-Nic et al. title: A new species of the genus Sarsamphiascus Huys, 2009 (Copepoda: Harpacticoida: Miraciidae) from a sublittoral zone of Hawaii link: https://peerj.com/articles/8506 last-modified: 2020-02-10 description: A new species of SarsamphiascusHuys, 2009 was collected from sandy sediments of Hawaii at 12 –18 m depth. While the new species, Sarsamphiascus hawaiiensis sp. nov., is morphologically most closely related to S. kawamurai (Ueda & Nagai, 2005), the two species can be distinguished by the combination of the following morphological characteristics: elongated segments of the antennule in the new species, type of outer setae of the P5 exopod (bare in S. kawamurai), position of the inner seta of the P5 exopod in both sexes (more proximal in S. kawamurai), length and type of the setae of female P6 (shorter and bare in S. kawamurai). This is the first species of Sarsamphiascus from Hawaii to be discovered. Molecular analyses of mitochondrial cytochrome c oxidase subunit I (mtCOI) and nuclear 18S ribosomal RNA (18S rRNA) genes confirmed that S. hawaiiensis and S. kawamurai are distinct species. creator: Jisu Yeom creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.8506 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yeom and Lee title: HPV vaccination and sexual behaviour in healthcare seeking young women in Luxembourg link: https://peerj.com/articles/8516 last-modified: 2020-02-10 description: IntroductionHuman papillomavirus (HPV) is the most common sexually transmitted infection (STI) worldwide. Despite recommendations for HPV vaccination of young women from health authorities, parental concerns were raised whether vaccination could induce unsafe sexual behaviour in young women. Therefore, the primary aim of this study was to investigate if HPV vaccination in healthcare seeking adult women in Luxembourg was associated with unsafe sexual behaviour.MethodsSeven hundred twenty-nine women (mean age = 22.5; range 18–43 years) were recruited either at Luxembourg family planning centres or at private gynaecology practices. All participants completed a questionnaire on vaccination status and sexual behaviour. Poisson and logistic regressions were used to study the association between sexual behaviour and vaccination status (N = 538). Both models were restricted to women younger than 26 years, since the first cohort being vaccinated would be 25 years old at the time of sampling. Assortativity of sexual mixing by age was also assessed for further transmission modelling for women <30 years reporting age of last/current sexual partner (N = 649). Women older than 29 years were excluded from the assortativity analysis due to restricted sample size.ResultsIn total, 386/538 (71.8%) of participants reported receiving HPV vaccine. Vaccination uptake significantly varied by nationality and was higher in Portuguese 112/142 (78.9%) and in Luxembourgish 224/313(71.6%) residents, and lower in residents of other nationalities 50/83 (60.2%) (p = 0.011). HPV vaccination was not associated with unsafe sexual behaviour such as shorter relationship duration with current or last sexual partner (odds ratio (OR) = 1.05, 95% CI [0.94–1.16]), younger age of sexual debut (OR = 1.00, 95% CI [0.88–1.14]), increased number of lifetime sexual partners (OR = 0.95, 95% CI [0.87–1.03), higher age difference with sexual partner (OR = 1.01, 95% CI [0.95–1.08]), condom use (OR = 0.97, 95% CI [0.60–1.56]), nor with other factors like smoking (OR = 0.73, 95% CI [0.47–1.15]) and nationality. HPV vaccination was only associated with younger age (OR = 0.84, 95% CI [0.75–0.94]). Relationship duration, age of sexual debut, age difference with sexual partner, smoking, age and non-Portuguese foreign nationality were predictors of number of lifetime sexual partners. Assortativity analysis revealed that young women chose sexual partners who were 2.3 years older on average.ConclusionsOur study found no association between unsafe sexual behaviour and HPV vaccination. creator: Camille Soudeyns creator: Niko Speybroeck creator: Marc Brisson creator: Joël Mossong creator: Ardashel Latsuzbaia uri: https://doi.org/10.7717/peerj.8516 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Soudeyns et al. title: Uncertainty in gap filling and estimating the annual sum of carbon dioxide exchange for the desert Tugai forest, Ebinur Lake Basin, Northwest China link: https://peerj.com/articles/8530 last-modified: 2020-02-10 description: In most eddy covariance (EC) studies, carbon flux measurements have a high defect rate for a variety of reasons. Obtaining the annual sum of carbon dioxide exchange requires imputation of data gaps with high precision and accuracy. This study used five methods to fill the gaps in carbon flux data and estimate the total annual carbon dioxide exchange of the Tugai forest in the arid desert ecosystem of Ebinur Lake Basin, Northwest China. The Monte Carlo method was used to estimate the random error and bias caused by gap filling. The results revealed that (1) there was a seasonal difference in the friction velocity threshold of nighttime flux, with values in the growing season and non-growing season of 0.12 and 0.10 m/s, respectively; (2) the five gap-filling methods explained 77–84% of the data variability in the fluxes, and the random errors estimated by these methods were characterized by non-normality and leptokurtic heavy tail features, following the Laplacian (or double-exponential) distribution; (3) estimates of the annual sum of carbon dioxide exchange using the five methods at the study site in 2015 ranged from −178.25 to −155.21 g C m−2 year−1, indicating that the Tugai forest in the Ebinur Lake Basin is a net carbon sink. The standard deviation of the total annual carbon dioxide exchange sums estimated by the five different methods ranged from 3.15 to 19.08 g C m−2 year−1, with bias errors ranging from −13.69 to 14.05 g C m−2 year−1. This study provides a theoretical basis for the carbon dioxide exchange and carbon source/sink assessment of the Tugai forest in an arid desert ecosystem. In order to explore the functioning of the Tugai forest at this site, a greater understanding of the underlying ecological mechanisms is necessary. creator: Dexiong Teng creator: Xuemin He creator: Jingzhe Wang creator: Jinlong Wang creator: Guanghui Lv uri: https://doi.org/10.7717/peerj.8530 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Teng et al. title: A retrospective study comparing super-mini percutaneous nephrolithotomy and flexible ureteroscopy for the treatment of 20–30 mm renal stones in obese patients link: https://peerj.com/articles/8532 last-modified: 2020-02-10 description: ObjectiveThis study aimed to compare the efficacy and safety of Super-mini percutaneous nephrolithotomy (SMP) and flexible ureteroscopy (F-URS) in the treatment of 20–30 mm renal stones in obese patients.MethodsWe conducted a retrospective analysis of outcomes of patients who underwent SMP and F-URS to treat 20–30 mm renal stones from August 2017 to September 2018. Patients with BMI >30 kg/m2 were enrolled into this study. Forty-eight patients underwent SMP, while 104 patients underwent F-URS by the same surgeon. The patients’ demographic data, stone characteristics, perioperative parameters and outcomes, complications, stone-free rate (SFR) and overall costs were retrospectively assessed.ResultsNo significant differences were found between the two groups in terms of age, gender, BMI, operation side, stone size, number, locations, stone compositions and CT value. The mean operation time was significantly shorter in the SMP group (p < 0.001), while the F-URS group had significantly shorter postoperative stays (p < 0.001) and lower complication rates (p < 0.001). Both groups had similar SFR at a 3-month follow-up (p = 0.190), while the SMP group achieved significant higher SFR 3 days after the operation (p < 0.001). The SMP group had a significantly lower overall cost and fewer stage-2 procedures than the F-URS group.ConclusionSMP and F-URS are equally effective in obese patients with 20–30 mm renal stones. However, F-URS offers the advantage of a lower complication rate, while SMP performed better in terms of operation time, tubeless rate, stage-2 procedures and overall costs. creator: Chen Xu creator: Rijin Song creator: Pei Lu creator: Minjun Jiang creator: Guohua Zeng creator: Wei Zhang uri: https://doi.org/10.7717/peerj.8532 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Xu et al. title: Rural children remain more at risk of acute malnutrition following exit from community based management of acute malnutrition program in South Gondar Zone, Amhara Region, Ethiopia: a comparative cross-sectional study link: https://peerj.com/articles/8419 last-modified: 2020-02-07 description: BackgroundCommunity-based management of acute malnutrition has been reported effective in terms of recovery rate, but recovered children may be at increased risk of developing acute malnutrition after returning to the same household (HH) environment.ObjectiveCompare the magnitude and factors associated with acute malnutrition among recovered and never treated children in South Gondar Zone, Amhara Region, Ethiopia.MethodA comparative cross-sectional study was conducted in three districts of South Gondar Zone by tracing 720 recovered and an equal number of age matched children who were never treated for acute malnutrition. Parents were asked to bring children to health post for survey data collection, anthropometric measurements, and edema assessment. Data were collected using a survey questionnaire, entered in to EpiData and analyzed using SPSS v20. Anthropometric indices were generated according to the WHO’s 2006 Child Growth Standards using WHO Anthro software version 3.2.2. Bivariate and multivariable logistic regression was utilized. Values with P < 0.05 were considered statistically significant and Odds Ratio with 95% CI was used to measure strength of association.ResultA total of 1,440 parents were invited, of which 1,414 participated (98.2% response rate). Mean age in months of children (±SD) was 23.7 (±10.4) for recovered and 23.3 (±10.8) for comparison group. About 49% of recovered and 46% of comparison children were females. A significant difference was observed on magnitude of acute malnutrition between recovered (34.2% (95% CI [30.9–38.0]) and comparison groups (26.7% (95% CI [23.5–30.2]), P = 0.002. Factors associated with acute malnutrition among recovered were district of Ebnat (AOR = 3.7; 95% CI [1.9–7.2]), Tach-Gayint (AOR = 2.4; 95% CI [1.2–4.7]); male child (AOR = 1.4; 95% CI [1.0–2.0]); prelactal feeding (AOR = 2.6; 95% CI [1.3 –5.1]); not feeding colostrum (AOR = 1.5; 95% CI [1.1–2.3]); not consuming additional food during pregnancy/lactation (AOR = 1.6; 95% CI [1.1–2.3]); not given Vitamin A supplement (AOR = 2.1; 95% CI [1.4–3.2]); and safe child feces disposal practice (AOR = 1.7; 95% CI [1.2–2.5]) while district of Tach-Gayint (AOR = 2.5; 95% CI [1.3–4.8]); male child (AOR = 1.5; 95% CI [1.1–2.1]), not feeding colostrum (AOR = 1.7; 95% CI [1.2–2.5]), poor hand washing practice (AOR = 1.6; 95% CI [1.1–2.2]); food insecure HH (AOR = 1.6; 95% CI [1.1–2.4]), birth interval <24 months (AOR = 1.9; 95% CI [1.2–3.2]), and poor access to health facility (AOR = 1.7; 95% CI [1.2–2.4]) were factors associated with acute malnutrition among comparison group.ConclusionRecovered children were more at risk of acute malnutrition than the comparison group. Nutrition programs should invest in improving nutrition counseling and education; as well as the hygienic practices to protect children against post-discharge relapse of acute malnutrition. creator: Dereje B. Abitew creator: Alemayehu Worku creator: Afework Mulugeta creator: Alessandra N. Bazzano uri: https://doi.org/10.7717/peerj.8419 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Abitew et al. title: Cavity treatment in primary molars and malocclusion: quasi-randomised clinical trial link: https://peerj.com/articles/8439 last-modified: 2020-02-07 description: BackgroundAn innovative caries treatment protocol for primary teeth, termed Ultra-Conservative Treatment (UCT), restores small cavities through the Atraumatic Restorative Treatment (ART) protocol and cleans medium to large open cavities with toothbrush and fluoride toothpaste. However, UCT-treated primary molars were found to exfoliate earlier than amalgam (CRT) and ART-restored cavities, which may lead to unacceptable loss of space for normal eruption of permanent successors. The null-hypothesis tested was that there is no difference between the three treatment protocols and the intra-arch distances, and index of orthodontic treatment need (IOTN) after 4 years.MethodsDental casts were taken at baseline (T0) and four (T4) years. The space of the premolars (D + E space), arch perimeter, anterior and total arch depth were measured using a morphometric computer programme. The presence and level of malocclusion were assessed according to the IOTN index. Dependent variables were all intra-arch distances and the IOTN while the independent variable was treatment protocol (CRT, ART and UCT). Data were analysed using linear and logistic regression.ResultsThe sample consisted of 867 pairs of casts of 272 initial 6–7-year-olds. No difference was observed between the UCT protocol and the two restorative protocols for the intra-arch variables in both maxilla and mandible over the 4 year period. There was no difference between the UCT and the CRT and ART protocols regarding the occurrence of orthodontic treatment need (malocclusion). In conclusion, the UCT treatment protocol does not differ significantly from the traditional amalgam (CRT) and ART restorative protocols with respect to intra-arch distances and malocclusion. The earlier exfoliation of UCT-treated primary molars does not lead to a worsening of the eruption pattern of permanent successors. creator: Rafael T. Gomide creator: Jo E. Frencken creator: Jorge Faber creator: Anne Marie Kuijpers-Jagtman creator: Soraya C. Leal uri: https://doi.org/10.7717/peerj.8439 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gomide et al. title: Survival of side grafts with scions from pure species Pinus engelmannii Carr. and the P. engelmannii × P. arizonica Engelm. var. arizonica hybrid link: https://peerj.com/articles/8468 last-modified: 2020-02-07 description: Grafting is one of the most widely used methods for vegetative propagation, particularly for multiplying trees considered important, but there has been little research done on the effect of hybridization on grafts from the genus Pinus. Sometimes hybrids show the ability to reproduce and adapt efficiently to the environment. However, they reduce the genetic gain of seed orchards. The objective in this research was to evaluate the effect of scion grafts from pure species donor Pinus engelmannii Carr. and from putative hybrid trees P. engelmannii × P. arizonica Engelm., grafted on rootstocks of pure species P. engelmannii, along with the effect of the position of the scion in the donor tree crown (upper third and middle third). The scions were collected from three trees of the pure species and three hybrids. In each tree, 20 scions were collected from each third of the crown evaluated. 120 side-veneer grafts were made at the beginning of spring (March) 2018. Variance analyses were performed to evaluate the treatments and adjustments of the Logit and Weibull models to obtain the probability of graft survival. Significant differences were found between the origins of scions (p < 0.0083, after Bonferroni correction), showing grafts with hybrid tree scions taking hold better. In addition, the probability of survival at 5 months after grafting with hybrid tree scions was greater (p < 0.0001) than in grafts with scions from trees of the pure species (Logit model), which coincides with the results of the Weibull model, which indicated that the probability of graft death with pure species donor tree scions is greater than for grafts with hybrid scions. There were no significant differences regarding the position of the scion in the donor tree crown. creator: Alberto Pérez-Luna creator: Christian Wehenkel creator: José Ángel Prieto-Ruíz creator: Javier López-Upton creator: José Ciro Hernández-Díaz uri: https://doi.org/10.7717/peerj.8468 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Pérez-Luna et al. title: Reforming teaching methods by integrating dental theory with clinical practice for dental students link: https://peerj.com/articles/8477 last-modified: 2020-02-07 description: BackgroundTransitioning from theoretical medicine to clinical practice is both an important and difficult process in dental education. Thus, there is an urgent need for teaching methods that can improve the ability of dental students to integrate dental theory with clinical practice.MethodsFirst, we conducted training for problem-based learning based on real clinical cases for dental students. The students were then assigned to dentist/patient roles to rehearse and perform simulated clinical scenarios. Finally, questionnaires, clinical patient care scores, and performance assessments were utilized to evaluate and compare the effectiveness of this training with that of traditional teaching methods.ResultsStudents’ abilities to treat and communicate with patients markedly improved after using this reformed teaching method. Among the 30 enrolled students, 29 liked the method, found it time-efficient, and believed that it could help enhance their problem-solving confidence and interest in prosthodontics. They also believed that this teaching method could help them gain a good understanding of related theoretical material, generally thought that the reformed teaching method was more valuable than the traditional approach, and would like to introduce it to others.ConclusionAfter the reformed teaching method was implemented, the students not only achieved better scholastically, but also demonstrated greater accuracy in diagnosing the conditions of patients and formulating treatment plans. They were also more frequently acknowledged by patients, indicating that this method is effective for dental students. creator: Wei Wang creator: Xuewei Bi creator: Yuhe Zhu creator: Xiaoming Li uri: https://doi.org/10.7717/peerj.8477 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Notes on the cheek region of the Late Jurassic theropod dinosaur Allosaurus link: https://peerj.com/articles/8493 last-modified: 2020-02-07 description: Allosaurus, from the Late Jurassic of North America and Europe, is a model taxon for Jurassic basal tetanuran theropod dinosaurs. It has achieved an almost iconic status due to its early discovery in the late, 19th century, and due to the abundance of material from the Morrison Formation of the western U.S.A., making Allosaurus one of the best-known theropod taxa. Despite this, various aspects of the cranial anatomy of Allosaurus are surprisingly poorly understood. Here, we discuss the osteology of the cheek region, comprised by the jugal, maxilla, and lacrimal. This region of the skull is of importance for Allosaurus taxonomy and phylogeny, particularly because Allosaurus has traditionally been reconstructed with an unusual cheek configuration, and because the European species Allosaurus europaeus has been said to be different from North American material in the configuration of these bones. Based on re-examination of articulated and disarticulated material from a number of repositories, we show that the jugal participates in the antorbital fenestra, contradicting the common interpretation. The jugal laterally overlies the lacrimal, and forms an extended antorbital fossa with this bone. Furthermore, we document previously unrecorded pneumatic features of the jugal of Allosaurus. creator: Serjoscha W. Evers creator: Christian Foth creator: Oliver W.M. Rauhut uri: https://doi.org/10.7717/peerj.8493 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Evers et al. title: Microbial communities on fish eggs from Acanthopagrus schlegelii and Halichoeres nigrescens at the XuWen coral reef in the Gulf of Tonkin link: https://peerj.com/articles/8517 last-modified: 2020-02-07 description: Coral reefs are an important part of the ocean ecosystem and are a vital spawning ground for marine fish. Microorganisms are abundant in this environment and play a key role in the growth and development of host species. Many studies have investigated the microbial communities of fish with a focus on the intestinal microbiome of laboratory-reared adult fish. Little is known about the relationship between fish eggs and their microorganisms, especially as microbial communities relate to wild fish eggs in coral reefs. In this study, we analyzed the microbial communities of two species of coral fish eggs, Acanthopagrus schlegelii and Halichoeres nigrescens, using 16S rRNA gene amplicon sequencing technology. Pseudomonas, Archromobacter, and Serratia were the main bacterial genera associated with these fish eggs and are known to be bacteria with potentially pathogenic and spoilage effects. The microbial community structures of Acanthopagrus schlegelii and Halichoeres nigrescens eggs were separated based on the 30 most abundant operational taxonomic units (OTUs). Principal coordinate analysis (PCoA) and non-metric multidimensional scaling analysis (NMDS) further confirmed that the microbial communities of coral fish eggs differ by species, which may be due to host selection. A functional prediction of the microbial communities indicated that most of the microbial communities were chemoheterotrophic and involved in nitrogen cycling. Our results showed that the microbial communities of coral fish eggs were distinct by species and that key microorganisms were potentially pathogenic, leading to the spoilage of fish eggs, high mortality, and low incubation rates. This study provided new insights for understanding the relationship between microorganisms and wild fish eggs. creator: Shijie Bai creator: Gang Hou uri: https://doi.org/10.7717/peerj.8517 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bai and Hou title: Comparison of routine hematological indicators of liver and kidney function, blood count and lipid profile in healthy people and stroke patients link: https://peerj.com/articles/8545 last-modified: 2020-02-07 description: Background and methodsStroke has become a major public health problem worldwide. In this article, we carried out statistical analysis, correlation analysis and principal component analysis (PCA) to evaluate the clinical value of routine hematological indicators in early diagnosis of ischemic stroke using R language.ResultsFor the full blood count comparisons, stroke patients had obvious differences in the distribution width of red blood cells (RDW-CV), average distribution width of red blood cells (RDW-SD), mean hemoglobin concentrations, platelet large cell ratio, mean platelet volume and lymphocytes. Patients with ischemic stroke also exhibited different degrees of abnormalities in liver function test. With respect to renal function, stroke patients had obvious changes in uric acid and urea levels. Finally, when comparing the lipid profile, triglyceride concentrations were increased and high-density lipoprotein cholesterol concentrations were reduced in stroke patients. In addition, correlation analysis among these clinical indicators indicated that there were both common characteristics and differences between patients and health controls. Furthermore, the results of PCA indicated that these clinical indicators could distinguish patients from the healthy controls.ConclusionConventional hematological clinical indicators, such as liver function, renal function, full blood count and lipid concentration profiles highly correlated with the occurrence of ischemic stroke. Therefore, the detection and analyzation of these clinical indicators are of great significance for the prediction of ischemic stroke. creator: Xiaofang Cui creator: Wei Wei creator: Xiao Qin creator: Fei Hou creator: Jin Zhu creator: Weiyang Li uri: https://doi.org/10.7717/peerj.8545 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Cui et al. title: Postoperative hyperlactatemia and serum lactate level trends among heart transplant recipients link: https://peerj.com/articles/8334 last-modified: 2020-02-06 description: BackgroundAdvanced heart failure (HF), that affects 10% of the HF population, is associated with high mortality rate, meeting 50% at 1-year from diagnosis. For these individuals, heart transplantation (HTX) remains the ultimate and the gold-standard treatment option. Serum lactate level measurements has been proven useful for determining the outcome following other cardiac surgeries and among critically ill patients. Increased serum lactate levels are expected following HTX; however, no detailed analysis has been yet performed in this population. The research aims to estimate the prevalence of hyperlactatemia and describe early postoperative serum lactate level trends among heart transplant recipients.Materials and MethodsForty-six consecutive patients, who underwent HTX between 2010 and 2015, were enrolled into the retrospective analysis. Serum lactate level measurements within first 48 hours post-HTX were obtained every 6 hours from routinely conducted arterial blood gas analyses. The threshold for hyperlactatemia was considered at >1.6 mmol/L, according to upper limit of normal, based on internal laboratory standardization. The highest observed measurement within the observation, regardless of the time point of observation was determined for each patient individually and was appointed as Peak Value.ResultsConsecutively measured serum lactate levels differed in time (p = 0.000), with the initial increase and subsequent decrease of the values (4.3 vs. 1.9 mmol/l; p = 0.000). The increase from the baseline level to the Peak Value was statistically significant (4.3 vs. 7.0 mmol/l; p = 0.000). Various serum lactate level trends were identified, with one or more hyperlactatemia episodes. Eventually, 50% of the individuals had normal serum lactate levels at the end of the study, and hyperlactatemia was observed in the other half.ConclusionsThroughout the observation, all of the patients experienced at least one episode of hyperlactatemia, with the median Peak Value of 7.0 (4.5–8.4) mmol/L. Various serum lactate level trends can be identified in post-HTX patients. Further research is required to determine the clinical usefulness of newly reported serum lactate level trends among heart transplant recipients. creator: Anna Kędziora creator: Karol Wierzbicki creator: Jacek Piątek creator: Hubert Hymczak creator: Izabela Górkiewicz-Kot creator: Irena Milaniak creator: Paulina Tomsia creator: Dorota Sobczyk creator: Rafal Drwila creator: Boguslaw Kapelak uri: https://doi.org/10.7717/peerj.8334 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kędziora et al. title: Seasonal contributions of nutrients from small urban and agricultural watersheds in northern Poland link: https://peerj.com/articles/8381 last-modified: 2020-02-06 description: Diffuse sources of pollution like agricultural or urban runoff are important factors in determining the quality of surface waters, although they are more difficult to monitor than point sources. The objective of our study was to verify assumptions that the inflow from agricultural nutrient sources is higher than from urbanized ones. It has been done by comparing the nutrients and organic matter concentrations and loads for three small streams in northern Poland (Pomerania Region). Two streams flowing through agricultural catchments and an urban stream flowing through the city of Gdansk were analysed. Concentrations of nutrients: N-NO${}_{3}^{-}$3− N-NH${}_{4}^{+}$4+, P-PO${}_{4}^{3-}$43−, total phosphorus, total nitrogen and COD were measured 1–3 times per month in the period from July 2017 to December 2018 in agricultural watersheds and from October 2016 to March 2018 for an urban stream. Seasonal changes in concentrations were analysed with descriptive statistics tools. Principal Component Analysis (PCA) was used to point out the most significant factors determining variations in nutrients and organic matter concentrations with respect to different seasons. The factors included a number of characteristics regarding the catchment and streams: total catchment area, stream length, watershed form ratio, stream slope, flow rate and land use with respect to paved areas, agricultural areas and green areas (parks, forests, meadows and pastures). Although concentrations of nitrogen compounds were higher in streams flowing through agricultural areas, our study showed that total concentrations of phosphorus were higher in the urban stream, especially in summer. In agricultural areas the summer concentrations of nutrients were not high, which was probably due to dense vegetation. The correlation between P-PO${}_{4}^{3-}$43− concentration and size of agricultural area in the catchment was observed in winter when no vegetation field cover exists. Our study shows an urgent need to monitor the nutrient loads carried with urban streams especially if discharged into receivers prone to eutrophication. creator: Karolina Matej-Lukowicz creator: Ewa Wojciechowska creator: Nicole Nawrot creator: Lidia Anita Dzierzbicka-Głowacka uri: https://doi.org/10.7717/peerj.8381 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Matej-Lukowicz et al. title: Effects of personality and rearing-history on the welfare of captive Asiatic lions (Panthera leo persica) link: https://peerj.com/articles/8425 last-modified: 2020-02-06 description: BackgroundThe long-term success of ex-situ conservation programmes depends on species-appropriate husbandry and enrichment practices complemented by an accurate welfare assessment protocol. Zoos and conservation breeding programmes should employ a bottom-up approach to account for intraspecific variations in measures of animal welfare. We studied 35 (14:21) captive Asiatic lions in Sakkarbaug Zoological Garden, Junagadh, India to understand the implications of individual variations on welfare measures. We categorized the subjects based on personality traits (bold or shy), rearing history (wild-rescued or captive-raised), sex, and social-grouping. We explored the association of these categorical variables on welfare indices such as behavioural diversity, latency to approach novel objects, enclosure usage and aberrant repetitive behaviours. Further, we assessed the inter-relationships between different behavioural measures of welfare.ResultsOur results show that intraspecific variations based on rearing-history and personality traits are significantly associated with the welfare states of captive Asiatic lions. Asiatic lions with bold personality traits (M = 0.50, SD = 0.12, N = 21) and those raised in captivity (M = 0.47, SD = 0.12, N = 16) used enclosure space more homogenously compared to shy (M = 0.71, SD = 0.15, N = 14) and wild-rescued (M = 0.67, SD = 0.15, N = 19) animals. Behaviour diversity was significantly higher in captive-raised (M = 1.26, SD = 0.3, N = 16) and bold (M = 1.23, SD = 0.26, N = 21) subjects compared to wild-rescued (M = 0.83, SD = 0.35, N = 19) and shy (M = 0.73, SD = 0.34, N = 14) individuals. Aberrant repetitive behaviours (stereotypy) were significantly lower in bold (M = 7.01, SD = 4, N = 21) and captive-raised (M = 7.74, SD = 5.3) individuals compared to wild-rescued (M = 13.12, SD = 6.25, N = 19) and shy (M = 16.13, SD = 5.4, N = 16) lions. Sex and social-grouping of subjects did not show significant associations with behavioural welfare indices. Interestingly, behaviour diversity was reliably predicted by the enclosure usage patterns and aberrant repetitive behaviours displayed by subjects.DiscussionOur findings underline the importance of individual-centric, behaviour-based, and multi-dimensional welfare assessment approaches in ex-situ conservation programmes. The results suggest that behavioural welfare indices complemented with individual variations can explain inter-individual differences in behavioural welfare measure outcomes of Asiatic lions. These findings also provide zoo managers with a non-invasive tool to reliably assess and improve husbandry practices for Asiatic lions. Understanding the unique welfare requirement of individuals in captivity will be crucial for the survival of the species. creator: Sitendu Goswami creator: Praveen C. Tyagi creator: Pradeep K. Malik creator: Shwetank J. Pandit creator: Riyazahmed F. Kadivar creator: Malcolm Fitzpatrick creator: Samrat Mondol uri: https://doi.org/10.7717/peerj.8425 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Goswami et al. title: Late Jurassic theropod dinosaur bones from the Langenberg Quarry (Lower Saxony, Germany) provide evidence for several theropod lineages in the central European archipelago link: https://peerj.com/articles/8437 last-modified: 2020-02-06 description: Marine limestones and marls in the Langenberg Quarry provide unique insights into a Late Jurassic island ecosystem in central Europe. The beds yield a varied assemblage of terrestrial vertebrates including extremely rare bones of theropod from theropod dinosaurs, which we describe here for the first time. All of the theropod bones belong to relatively small individuals but represent a wide taxonomic range. The material comprises an allosauroid small pedal ungual and pedal phalanx, a ceratosaurian anterior chevron, a left fibula of a megalosauroid, and a distal caudal vertebra of a tetanuran. Additionally, a small pedal phalanx III-1 and the proximal part of a small right fibula can be assigned to indeterminate theropods. The ontogenetic stages of the material are currently unknown, although the assignment of some of the bones to juvenile individuals is plausible. The finds confirm the presence of several taxa of theropod dinosaurs in the archipelago and add to our growing understanding of theropod diversity and evolution during the Late Jurassic of Europe. creator: Serjoscha W. Evers creator: Oliver Wings uri: https://doi.org/10.7717/peerj.8437 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Evers and Wings title: Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution link: https://peerj.com/articles/8450 last-modified: 2020-02-06 description: The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species. creator: Sunan Huang creator: Xuejun Ge creator: Asunción Cano creator: Betty Gaby Millán Salazar creator: Yunfei Deng uri: https://doi.org/10.7717/peerj.8450 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Unexpectedly high genetic diversity in a rare and endangered seabird in the Hawaiian Archipelago link: https://peerj.com/articles/8463 last-modified: 2020-02-06 description: Seabirds in the order of Procellariiformes have one of the highest proportions of threatened species of any avian order. Species undergoing recovery may be predicted to have a genetic signature of a bottleneck, low genetic diversity, or higher rates of inbreeding. The Hawaiian Band-rumped Storm Petrel (‘Akē‘akē; Hydrobates castro), a long-lived philopatric seabird, suffered massive population declines resulting in its listing under the Endangered Species Act in 2016 as federally Endangered. We used high-throughput sequencing to assess patterns of genetic diversity and potential for inbreeding in remaining populations in the Hawaiian Islands. We compared a total of 24 individuals, including both historical and modern samples, collected from breeding colonies or downed individuals found on the islands of Kaua‘i, O‘ahu, Maui, and the Big Island of Hawai‘i. Genetic analyses revealed little differentiation between breeding colonies on Kaua‘i and the Big Island colonies. Although small sample sizes limit inferences regarding other island colonies, downed individuals from O‘ahu and Maui did not assign to known breeding colonies, suggesting the existence of an additional distinct breeding population. The maintenance of genetic diversity in future generations is an important consideration for conservation management. This study provides a baseline of population structure for the remaining nesting colonies that could inform potential translocations of the Endangered H. castro. creator: Carmen C. Antaky creator: Emily E. Conklin creator: Robert J. Toonen creator: Ingrid S.S. Knapp creator: Melissa R. Price uri: https://doi.org/10.7717/peerj.8463 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Antaky et al. title: The nutritional status of children living within institutionalized care: a systematic review link: https://peerj.com/articles/8484 last-modified: 2020-02-06 description: BackgroundThere are an estimated 2.7 million children living within institutionalized care worldwide. This review aimed to evaluate currently available data on the nutrition status of children living within institutionalized care.MethodsWe searched four databases (Pubmed/Medline, CINHAL Plus, Embase and Global Health Database) for relevant articles published from January 1990 to January 2019. Studies that included information on anthropometry or micronutrient status of children living within institutionalized care were eligible for inclusion. The review is registered on PROSPERO: CRD42019117103.ResultsFrom 3,602 titles screened, we reviewed 98 full texts, of which 25 papers were eligible. Two (8%) studies reported data from multiple countries, nine (36%) were from Asia, four (16%) from Africa, three (12%) from Eastern Europe, four (16%) from the European Union and one (4%) from each of the remaining regions (Middle East, South America and the Caribbean). Twenty-two (88%) were cross sectional. Ten (40%) of the studies focused on children >5 years, seven (28%) on children <5 years, seven (28%) covered a wide age range and one did not include ages. Low birth weight prevalence ranged from 25–39%. Only five (20%) included information on children with disabilities and reported prevalence from 8–75%. Prevalence of undernutrition varied between ages, sites and countries: stunting ranged from 9–72%; wasting from 0–27%; underweight from 7–79%; low BMI from 5–27%. Overweight/obesity ranged from 10–32% and small head circumference from 17–41%. The prevalence of HIV was from 2–23% and anemia from 3–90%. Skin conditions or infections ranged from 10–31% and parasites from 6–76%. Half the studies with dietary information found inadequate intake or diet diversity. Younger children were typically more malnourished than older children, with a few exceptions. Children living within institutions were more malnourished than community peers, although children living in communities were also often below growth standards. High risk of bias was found.ConclusionsThis study highlights the limited amount of evidence-based data available on the nutritional status of children in institutions. Of the studies reviewed, children living within institutionalized care were commonly malnourished, with undernutrition affecting young children particularly. Micronutrient deficiencies and obesity were also prevalent. Data quality was often poor: as well as suboptimal reporting of anthropometry, few looked for or described disabilities, despite disability being common in this population and having a large potential impact on nutrition status. Taken together, these findings suggest a need for greater focus on improving nutrition for younger children in institutions, especially those with disabilities. More information is needed about the nutritional status of the millions of children living within institutionalized care to fully address their right and need for healthy development. creator: Emily DeLacey creator: Cally Tann creator: Nora Groce creator: Maria Kett creator: Michael Quiring creator: Ethan Bergman creator: Caryl Garcia creator: Marko Kerac uri: https://doi.org/10.7717/peerj.8484 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 DeLacey et al. title: Integrated analysis of the roles and prognostic value of RNA binding proteins in lung adenocarcinoma link: https://peerj.com/articles/8509 last-modified: 2020-02-06 description: Lung cancer is the top cause of carcinoma-associated deaths worldwide. RNA binding proteins (RBPs) dysregulation has been reported in various malignant tumors, and that dysregulation is closely associated with tumorigenesis and tumor progression. However, little is known about the roles of RBPs in lung adenocarcinoma (LUAD). In this study, we downloaded the RNA sequencing data of LUAD from The Cancer Genome Atlas (TCGA) database and determined the differently expressed RBPs between normal and cancer tissues. We then performed an integrative analysis to explore the expression and prognostic significance of these RBPs. A total of 164 differently expressed RBPs were identified, including 40 down-regulated and 124 up-regulated RBPs. Pathway and Gene ontology (GO) analysis indicated that the differently expressed RBPs were mainly related to RNA processing, RNA metabolic process, RNA degradation, RNA transport, splicing, localization, regulation of translation, RNA binding, TGF-beta signaling pathway, mRNA surveillance pathway, and aminoacyl-tRNA biosynthesis. Survival analysis revealed that the high expression of BOP1 or GNL3 or WDR12 or DCAF13 or IGF2BP3 or IGF2BP1 were associated with poor overall survival (OS). Conversely, overexpression of KHDRBS2/SMAD predicted high OS in these patients. ROC curve analysis showed that the eight hub genes with a better diagnostic accuracy to distinguish lung adenocarcinoma. The results provided novel insights into the pathogenesis of LUAD and the development of treatment targets and prognostic molecular markers. creator: Wei Li creator: Na Li creator: Lina Gao creator: Chongge You uri: https://doi.org/10.7717/peerj.8509 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Assessment of the vulnerability of alpine grasslands on the Qinghai-Tibetan Plateau link: https://peerj.com/articles/8513 last-modified: 2020-02-06 description: Assessing ecosystem vulnerability to climate change is critical for sustainable and adaptive ecosystem management. Alpine grasslands on the Qinghai-Tibetan Plateau are considered to be vulnerable to climate change, yet the ecosystem tends to maintain stability by increasing resilience and decreasing sensitivity. To date, the spatial pattern of grassland vulnerability to climate change and the mechanisms that vegetation applies to mitigate the impacts of climate change on grasslands by altering relevant ecosystem characteristics, especially sensitivity and resilience, remain unknown. In this study, we first assessed the spatial pattern of grassland vulnerability to climate change by integrating exposure, sensitivity, and resilience simultaneously, and then identified its driving forces. The results show that grasslands with high vulnerability were mainly located on the edges of the plateau, whereas alpine grasslands in the hinterlands of the plateau showed a low vulnerability. This spatial pattern of alpine grassland vulnerability was controlled by climatic exposure, and grassland sensitivity and resilience to climate change might also exacerbate or alleviate the degree of vulnerability. Climate change had variable impacts on different grassland types. Desert steppes were more vulnerable to climate change than alpine meadows and alpine steppes because of the high variability in environmental factors and their low ability to recover from perturbations. Our findings also confirm that grazing intensity, a quantitative index of the most important human disturbance on alpine grasslands in this plateau, was significantly correlated with ecosystem vulnerability. Moderate grazing intensity was of benefit for increasing grassland resilience and then subsequently reducing grassland vulnerability. Thus, this study suggests that future assessments of ecosystem vulnerability should not ignore anthropogenic disturbances, which might benefit environmental protection and sustainable management of grasslands on the Qinghai-Tibetan Plateau. creator: Meng Li creator: Xianzhou Zhang creator: Yongtao He creator: Ben Niu creator: Jianshuang Wu uri: https://doi.org/10.7717/peerj.8513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Obama chez moi! The invasion of metropolitan France by the land planarian Obama nungara (Platyhelminthes, Geoplanidae) link: https://peerj.com/articles/8385 last-modified: 2020-02-06 description: BackgroundObama nungara is a species of land flatworm originating from South America; the species was recently described and distinguished from a similar species, Obama marmorata. Obama nungara has invaded several countries of Europe, but the extent of the invasion has not been thoroughly mapped.MethodsIn this article, based on a five and a half-year survey undertaken by citizen science, which yielded 530 records from 2013 to 2018, we analysed information about the invasion of Metropolitan France by O. nungara. We also investigated the variability of newly obtained cytochrome c oxidase 1 (COI) sequences of specimens from France, Italy and Switzerland.ResultsObama nungara was recorded from 72 of the 96 Departments of Metropolitan France. The species is especially abundant along the Atlantic coast, from the Spanish border to Brittany, and along the Mediterranean coast, from the Spanish border to the Italian border. More than half of the records were from an altitude below 50 m, and no record was from above 500 m; mountainous regions such as the Alps, Pyrenees and Massif Central are not invaded. Local abundance can be impressive, with 100 of specimens found in a small garden. An analysis of our new COI sequences, combined with published sequences of specimens from several countries, confirmed that three clades comprise the species. The first clade, ‘Brazil’, is currently confined to this country in South America; the second clade, ‘Argentina 2’, was found in Argentina and in Europe, only in Spain; and the third, ‘Argentina 1’, was found in Argentina and in Europe, in Spain, Portugal, France, UK, Italy, Belgium, and Switzerland. This suggests that two clades of O. nungara from Argentina have invaded Europe, with one widely spread.DiscussionThe present findings strongly suggest that O. nungara is a highly invasive species and that the population which has invaded several countries in Europe comes from Argentina. The wide dispersion of the species and its reported local abundance, combined with the predatory character of the species, make O. nungara a potential threat to the biodiversity and ecology of the native soil fauna in Europe, and probably the most threatening species of all invasive land planarians present in Europe. creator: Jean-Lou Justine creator: Leigh Winsor creator: Delphine Gey creator: Pierre Gros creator: Jessica Thévenot uri: https://doi.org/10.7717/peerj.8385 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Justine et al. title: Genetic recombination and diversity of sapovirus in pediatric patients with acute gastroenteritis in Thailand, 2010–2018 link: https://peerj.com/articles/8520 last-modified: 2020-02-06 description: BackgroundHuman sapovirus (SaV) is an etiologic agent of acute gastroenteritis (AGE) in all age groups worldwide. Genetic recombination of SaV has been reported from many countries. So far, none of SaV recombinant strain has been reported from Thailand. This study examined the genetic recombination and genotype diversity of SaV in children hospitalized with AGE in Chiang Mai, Thailand.MethodsStool samples were collected from children suffering from diarrhea who admitted to the hospitals in Chiang Mai, Thailand between 2010 and 2018. SaV was detected by RT-PCR and the polymerase and capsid gene sequences were analysed.ResultsFrom a total of 3,057 samples tested, 50 (1.6%) were positive for SaV. Among positive samples, SaV genotype GI.1 was the most predominant genotype (40%; 20/50), followed by GII.1 and GII.5 (each of 16%; 8/50), GI.2 (14%; 7/50), GIV.1 (4%; 2/50), and GI.5 (2%; 1/50). In addition, 4 SaV recombinant strains of GII.1/GII.4 were identified in this study (8%; 4/50).ConclusionsThe data revealed the genetic diversity of SaV circulating in children with AGE in Chiang Mai, Thailand during 2010 to 2018 and the intragenogroup SaV recombinant strains were reported for the first time in Thailand. creator: Kattareeya Kumthip creator: Pattara Khamrin creator: Hiroshi Ushijima creator: Limin Chen creator: Shilin Li creator: Niwat Maneekarn uri: https://doi.org/10.7717/peerj.8520 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kumthip et al. title: RNA-sequencing analysis of the effect of luteolin on methamphetamine-induced hepatotoxicity in rats: a preliminary study link: https://peerj.com/articles/8529 last-modified: 2020-02-06 description: In this study, RNA-sequencing (RNA-seq) was utilized to investigate the effects of luteolin on hepatotoxicity caused by methamphetamine (METH). The rats in METH group were administrated with METH (15 mg/kg, two times per day) via intraperitoneal (i.p.) injections for four consecutive days. The rats in luteolin + METH group were firstly administrated with luteolin (100 mg/kg, once a day) by oral gavage for 3 days before METH treatment. Lueolin attenuated the hepatotoxicity induced by METH via histopathological and biochemical analysis. The results of RNA-seq showed that luteolin could regulate 497 differentially expressed genes (DEGs), and the selected DEGs were mainly enriched in eight pathways, according to KEGG analysis. Furthermore, qRT-PCR was utilized to verify the results of RNA-seq. Six genes were selected as follows: liver enriched antimicrobial peptide 2 (Leap2), fatty acid synthase (Fasn), fatty acid binding protein 5 (Fabp5), patatin like phospholipase domain containing 3 (Pnpla3), myelin basic protein (Mbp) and calmodulin 3 (Calm3). Though because of the design flaws, the luteolin group has not been included, this study demonstrated that luteolin might exert hepato-protective effects from METH via modulation of oxidative phosphorylation, cytochrome P450 and certain signaling pathways. creator: Dong Qu creator: Kaikai Zhang creator: Lijian Chen creator: Qi Wang creator: Huijun Wang uri: https://doi.org/10.7717/peerj.8529 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Qu et al. title: Genome-wide identification and characterization of the soybean SOD family during alkaline stress link: https://peerj.com/articles/8457 last-modified: 2020-02-05 description: BackgroundSuperoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported.MethodsWe identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR.ResultsIn this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1–2), FeSODs (GmFSD1–5) and Cu/ZnSODs (GmCSD1–6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future. creator: Wenxiu Lu creator: Huizi Duanmu creator: Yanhua Qiao creator: Xiaoxia Jin creator: Yang Yu creator: Lijie Yu creator: Chao Chen uri: https://doi.org/10.7717/peerj.8457 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lu et al. title: Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.) link: https://peerj.com/articles/8467 last-modified: 2020-02-05 description: The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function. creator: Lin Zhang creator: Wei Chen creator: Ben Shi uri: https://doi.org/10.7717/peerj.8467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Isolation and characterization of vaginal Lactobacillus spp. in dromedary camels (Camelus dromedarius): in vitro evaluation of probiotic potential of selected isolates link: https://peerj.com/articles/8500 last-modified: 2020-02-05 description: Lactobacillus spp. is one of the beneficial lactic acid producing microbiota in the vagina, which is important for a healthy vaginal environment. However, little is known about vaginal Lactobacillus in dromedary camels (Camelus dromedarius). Therefore, this study aimed to isolate vaginal lactic acid bacteria (LAB) in dromedary camels and to study the probiotic potential of selected isolates. A total of 75 vaginal swabs were collected from pluriparous, non-pregnant, non-lactating dromedary camels. The LAB were isolated using deMan, Rogosa and Sharpe broth and agar media. Suspected LAB isolates were subjected to catalase testing and Gram staining and examined for indole production, nitrate reduction, hemolytic activity, cell surface hydrophobicity, auto- and coaggregation, antibacterial activity and characterized by 16S rRNA amplification and sequencing. Eighteen LABs were isolated from the 75 vaginal swabs. Among the 18 LAB isolates, six were Lactobacillus plantarum, eight were Lactobacillus fermentum, and four were Lactobacillus rhamnosus. None of the LAB isolates was hemolytic and only four LAB were H2O2 producing. The percentage of hydrophobicity ranged from 0% to 49.6%, 0% to 44.3% and 0% to 41.6% for hexadecane, xylene and toluene, respectively. All isolates showed higher (P < 0.05) autoaggregation after 24 h of incubation compared to 4 h. Furthermore, all LAB showed higher coaggregation (P < 0.05) and antimicrobial activity toward Staphylococcus aureus than to Escherichia coli. All LAB isolates were vancomycin resistant and sensitive to streptomycin, erythromycin, kanamycin and chloramphenicol. Only, three LAB isolates were resistant to tetracycline. The dromedary camel vaginal LAB isolates exhibited varying degrees of in vitro probiotic properties tested in this study and showed promising activity against the most common bacterial causes of endometritis in dromedary camels. Further investigation of the in vivo effect of these isolates is warranted. creator: Wael M. El-Deeb creator: Mahmoud Fayez creator: Ibrahim Elsohaby creator: Ibrahim Ghoneim creator: Theeb Al-Marri creator: Mahmoud Kandeel creator: Magdy ElGioushy uri: https://doi.org/10.7717/peerj.8500 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 El-Deeb et al. title: Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing link: https://peerj.com/articles/8501 last-modified: 2020-02-05 description: During the early-life period, the hatchlings of red-eared slider turtles (Trachemys scripta elegans) rely on their own post-hatching internal yolk for several days before beginning to feed. The gut microbiome is critical for the adaptation of organisms to new environments, but, to date, how the microbiome taxa are assembled during early life of the turtle is unknown. In this study, the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0 d, 10 d, 20 d, 30 d) by a high-throughput sequencing approach. Results showed that the dominant phyla were Firmicutes (58.23%) and Proteobacteria (41.42%) at 0-day, Firmicutes (92.94%) at 10-day, Firmicutes (67.08%) and Bacteroidetes (27.17%) at 20-day, and Firmicutes (56.46%), Bacteroidetes (22.55%) and Proteobacteria (20.66%) at 30-day post-hatching. Members of the Bacteroidaceae family were absent in 0-day and 10-day turtles, but dominated in 20-day and 30-day turtles. The abundance of Clostridium also showed the highest value in 10-day turtles. The richness of the intestinal microbiomes was lower at 0-day and 30-day than that at 10-day and 20-day, while the diversity was higher at 10-day and 30-day than that at 0-day and 20-day. The results endowed the turtles with an ability to enhance their tolerance to the environment. creator: Qin Peng creator: Yahui Chen creator: Li Ding creator: Zimiao Zhao creator: Peiyu Yan creator: Kenneth B. Storey creator: Haitao Shi creator: Meiling Hong uri: https://doi.org/10.7717/peerj.8501 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Peng et al. title: Postharvest biochemical characteristics and ultrastructure of Coprinus comatus link: https://peerj.com/articles/8508 last-modified: 2020-02-05 description: BackgroundCoprinus comatus is a novel cultivated edible fungus, hailed as a new preeminent breed of mushroom. However, C. comatus is difficult to keep fresh at room temperature after harvest due to high respiration, browning, self-dissolve and lack of physical protection.MethodsIn order to extend the shelf life of C. comatus and reduce its loss in storage, changes in quality, biochemical content, cell wall metabolism and ultrastructure of C. comatus (C.c77) under 4 °C and 90% RH storage regimes were investigated in this study.ResultsThe results showed that: (1) After 10 days of storage, mushrooms appeared acutely browning, cap opening and flowing black juice, rendering the mushrooms commercially unacceptable. (2) The activity of SOD, CAT, POD gradually increased, peaked at the day 10, up to 31.62 U g−1 FW, 16.51 U g−1 FW, 0.33 U g−1 FW, respectively. High SOD, CAT, POD activity could be beneficial in protecting cells from ROS-induced injuries, alleviating lipid peroxidation and stabilizing membrane integrity. (3) The activities of chitinase, β-1,3-glucanase were significantly increased. Higher degrees of cell wall degradation observed during storage might be due to those enzymes’ high activities. (4) The fresh C. comatus had dense tissue and every single cell had the number of intracellular organelles which structure can be observed clearly. After 10 d storage, the number of intracellular organelles was declined and the structure was fuzzy, the nucleus disappeared. After 20 d storage, C. comatus’s organization was completely lost, many cells were stacked together and the cell wall was badly damaged. creator: Yi Peng creator: Tongling Li creator: Huaming Jiang creator: Yunfu Gu creator: Qiang Chen creator: Cairong Yang creator: Wei liang Qi creator: Song-qing Liu creator: Xiaoping Zhang uri: https://doi.org/10.7717/peerj.8508 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Peng et al. title: Niche differentiation in the rhizosphere and endosphere fungal microbiome of wild Paris polyphylla Sm. link: https://peerj.com/articles/8510 last-modified: 2020-02-05 description: BackgroundThe plant microbiome is one of the key determinants of plant health and metabolite production. The plant microbiome affects the plant’s absorption of nutrient elements, improves plant tolerance to negative environmental factors, increases the accumulation of active components, and alters tissue texture. The microbial community is also important for the accumulation of secondary metabolites by plants. However, there are few studies on the niche differentiation of endophytic microorganisms of plants, especially at different elevations.MethodsWe investigated the effects of altitude on the community composition of endophytic fungal communities and the differentiation of endophytic microorganisms among different niches in Paris polyphylla Sm. The rhizosphere soil, roots, rhizomes and leaves of wild-type P. polyphylla Sm. at different altitudes were sampled, and the fungal communities of all samples were analyzed by internal transcribed spacer one amplification sequencing.ResultsThe results showed that in rhizosphere soil, the number of operational taxonomic units (OTUs) that could be classified or identified decreased significantly with increasing altitude, whereas in the endosphere of plants, the total number of OTUs was higher at intermediate altitudes than other altitudes. Furthermore, the structural variability in the rhizosphere fungal community was significantly lower than that in the endophytic communities. In addition, our results confirmed the presence of niche differentiation among members of the endophytic microbial community. Finally, we also determined that the predominant genus of mycobiota in the rhizome was Cadophora. This study provides insight into the relationships between the endosphere microbiome and plants and can guide the artificial cultivation of this plant. creator: Yan Wang creator: Hanping Wang creator: HuYin Cheng creator: Fan Chang creator: Yi Wan creator: Xiaoping She uri: https://doi.org/10.7717/peerj.8510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Association of the CACNA2D2 gene with schizophrenia in Chinese Han population link: https://peerj.com/articles/8521 last-modified: 2020-02-05 description: BackgroundSchizophrenia (SCZ) is a severely complex psychiatric disorder in which ~80% can be explained by genetic factors. Single nucleotide polymorphisms (SNPs) in calcium channel genes are potential genetic risk factors for a spectrum of psychiatric disorders including SCZ. This study evaluated the association between SNPs in the voltage-gated calcium channel auxiliary subunit alpha2delta 2 gene (CACNA2D2) and SCZ in the Han Chinese population of Northeast China.MethodsA total of 761 SCZ patients and 775 healthy controls were involved in this case-control study. Three SNPs (rs3806706, rs45536634 and rs12496815) of CACNA2D2 were genotyped by the MALDI-TOF-MS technology. Genotype distribution and allele frequency differences between cases and controls were tested by Chi-square (χ2) in males and females respectively using SPSS 24.0 software. Linkage disequilibrium and haplotype analyses were conducted using Haploview4.2. The false discovery rate correction was utilized to control for Type I error by R3.2.3.ResultsThere was a significant difference in allele frequencies (χ2 = 9.545, Padj = 0.006) and genotype distributions (χ2 = 9.275, Padj = 0.006) of rs45536634 between female SCZ patients and female healthy controls after adjusting for multiple comparisons. Minor allele A (OR = 1.871, 95% CI [1.251–2.798]) and genotype GA + AA (OR = 1.931, 95% CI [1.259–2.963]) were associated with an increased risk of SCZ. Subjects with haplotype AG consisting of rs45536634 and rs12496815 alleles had a higher risk of SCZ (OR = 1.91, 95% CI [1.26–2.90]) compared those with other haplotypes.ConclusionsThis study provides evidence that CACNA2D2 polymorphisms may influence the susceptibility to SCZ in Han Chinese women. creator: Yingli Fu creator: Na Zhou creator: Wei Bai creator: Yaoyao Sun creator: Xin Chen creator: Yueying Wang creator: Mingyuan Zhang creator: Changgui Kou creator: Yaqin Yu creator: Qiong Yu uri: https://doi.org/10.7717/peerj.8521 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Fu et al. title: Prioritizing riparian corridors for ecosystem restoration in urbanizing watersheds link: https://peerj.com/articles/8174 last-modified: 2020-02-04 description: BackgroundRiparian corridors can affect nutrient, organic matter, and sediment transport, all of which shape water quality in streams and connected downstream waters. When functioning riparian corridors remain intact, they provide highly valued water quality ecosystem services. However, in rapidly urbanizing watersheds, riparian corridors are susceptible to development modifications that adversely affect those ecosystem services. Protecting high quality riparian corridors or restoring low quality corridors are widely advocated as watershed level water quality management options for protecting those ecosystem services. The two approaches, protection or restoration, should be viewed as complementary by watershed managers and provide a foundation for targeting highly functioning riparian corridors for protection or for identifying poorly functioning corridors for restoration. Ascertaining which strategy to use is often motivated by a specific ecosystem service, for example water quality, upon which watershed management is focused. We have previously reported on a spatially explicit model that focused on identifying riparian corridors that have specific characteristics that make them well suited for purposes of preservation and protection focused on water quality. Here we hypothesize that focusing on restoration, rather than protection, can be the basis for developing a watershed level strategy for improving water quality in urbanizing watersheds.MethodsThe model described here represents a geographic information system (GIS) based approach that utilizes riparian characteristics extracted from 40-meter wide corridors centered on streams and rivers. The model focuses on drinking water reservoir watersheds that can be analyzed at the sub-watershed level. Sub-watershed riparian data (vegetation, soil erodibility and surface slope) are scaled and weighted based on watershed management theories for water quality, and riparian restoration scores are assigned. Those scores are used to rank order riparian zones –the lower the score the higher the priority for riparian restoration.ResultsThe model was applied to 90 sub-watersheds in the watershed of an important drinking water reservoir in north central Texas, USA. Results from this study area suggest that corridor scores were found to be most correlated to the amount of: forested vegetation, residential land use, soils in the highest erodibility class, and highest surface slope (r2 = 0.92, p < 0.0001). Scores allow watershed managers to rapidly focus on riparian corridors most in need of restoration. A beneficial feature of the model is that it also allows investigation of multiple scenarios of restoration strategies (e.g.,  revegetation, soil stabilization, flood plain leveling), giving watershed managers a tool to compare and contrast watershed level management plans. creator: Samuel F. Atkinson creator: Matthew C. Lake uri: https://doi.org/10.7717/peerj.8174 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Atkinson and Lake title: A novel transcript of MEF2D promotes myoblast differentiation and its variations associated with growth traits in chicken link: https://peerj.com/articles/8351 last-modified: 2020-02-04 description: BackgroundDevelopment of skeletal muscle is closely related to broiler production traits. The myocyte-specific enhancer binding factor (MEF) 2D gene (MEF2D) and its variant transcripts play important parts in myogenesis.MethodsTo identify the transcript variants of chicken MEF2D gene and their function, this study cloned chicken MEF2D gene and identified its transcript variants from different tissue samples. The expression levels of different transcripts of MEF2D gene in different tissues and different periods were measured, and their effects on myoblast proliferation and differentiation were investigated. Variations in MEF2D were identified and association analysis with chicken production traits carried out.ResultsFour novel transcript variants of MEF2D were obtained, all of which contained highly conserved sequences, including MADS-Box and MEF2-Domain functional regions. Transcript MEF2D-V4 was expressed specifically in muscle, and its expression was increased during embryonic muscle development. The MEF2D-V4 could promote differentiation of chicken myoblasts and its expression was regulated by RBFOX2. The single nucleotide polymorphism g.36186C > T generated a TAG stop codon, caused MEF2D-V4 to terminate translation early, and was associated with several growth traits, especially on early body weight.ConclusionWe cloned the muscle-specific transcript of MEF2D and preliminarily revealed its role in embryonic muscle development. creator: Hongjia Ouyang creator: Jiao Yu creator: Xiaolan Chen creator: Zhijun Wang creator: Qinghua Nie uri: https://doi.org/10.7717/peerj.8351 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ouyang et al. title: Sea whip coral Leptogorgia virgulata in the Mid-Atlantic Bight: Colony complexity, age, and growth link: https://peerj.com/articles/8372 last-modified: 2020-02-04 description: Sea whip coral Leptogorgia virgulata are a common structural component of both natural and artificial hard-bottom reef habitats in the mid-Atlantic region and may serve as essential habitat for commercially valuable species. However, they are slow-growing, easily damaged, and especially vulnerable to damage by passive fishing gear such as pots and traps. Despite their potential importance, until recently, sea whips have been generally understudied in this region. We examined the colony complexity, length, age, and growth of sea whips from four artificial reef sites in the mid-Atlantic region to gain a better understanding of their biology in the area. There were no significant differences in the bifurcation (Rb) and tributary to source (T/S) ratios between sites, with the Rb ≈3 for all sites, indicating similar complexity between sites. The total length distribution was 8.3 cm to 85.3 cm, and 50% of corals in the range of 34.2–56.4 cm. Age, estimated from annual growth ring counts, ranged from 2 to 15 y, with 50% of corals in the range of 6 to 8 y. The large proportion of middle-sized and middle-aged corals suggests episodic recruitment. Age-length keys showed the trend of age increasing with total coral length, and a von Bertalanffy growth model demonstrated size-dependent growth following the equation: E[L—t] (cm) = 86.1(1−e−0.14(t−1.44)). This is the first study providing such data for sea whips in the coastal mid-Atlantic region, and the baseline created will be a useful reference to study changes over time. creator: Rebecca P. Wenker creator: Bradley G. Stevens uri: https://doi.org/10.7717/peerj.8372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wenker and Stevens title: Development and validation of statistical shape models of the primary functional bone segments of the foot link: https://peerj.com/articles/8397 last-modified: 2020-02-04 description: IntroductionMusculoskeletal models are important tools for studying movement patterns, tissue loading, and neuromechanics. Personalising bone anatomy within models improves analysis accuracy. Few studies have focused on personalising foot bone anatomy, potentially incorrectly estimating the foot’s contribution to locomotion. Statistical shape models have been created for a subset of foot-ankle bones, but have not been validated. This study aimed to develop and validate statistical shape models of the functional segments in the foot: first metatarsal, midfoot (second-to-fifth metatarsals, cuneiforms, cuboid, and navicular), calcaneus, and talus; then, to assess reconstruction accuracy of these shape models using sparse anatomical data.MethodsMagnetic resonance images of 24 individuals feet (age = 28 ± 6 years, 52% female, height = 1.73 ± 0.8 m, mass = 66.6 ± 13.8 kg) were manually segmented to generate three-dimensional point clouds. Point clouds were registered and analysed using principal component analysis. For each bone segment, a statistical shape model and principal components were created, describing population shape variation. Statistical shape models were validated by assessing reconstruction accuracy in a leave-one-out cross validation. Statistical shape models were created by excluding a participant’s bone segment and used to reconstruct that same excluded bone using full segmentations and sparse anatomical data (i.e. three discrete points on each segment), for all combinations in the dataset. Tali were not reconstructed using sparse anatomical data due to a lack of externally accessible landmarks. Reconstruction accuracy was assessed using Jaccard index, root mean square error (mm), and Hausdorff distance (mm).ResultsReconstructions generated using full segmentations had mean Jaccard indices between 0.77 ± 0.04 and 0.89 ± 0.02, mean root mean square errors between 0.88 ± 0.19 and 1.17 ± 0.18 mm, and mean Hausdorff distances between 2.99 ± 0.98 mm and 6.63 ± 3.68 mm. Reconstructions generated using sparse anatomical data had mean Jaccard indices between 0.67 ± 0.06 and 0.83 ± 0.05, mean root mean square error between 1.21 ± 0.54 mm and 1.66 ± 0.41 mm, and mean Hausdorff distances between 3.21 ± 0.94 mm and 7.19 ± 3.54 mm. Jaccard index was higher (P < 0.01) and root mean square error was lower (P < 0.01) in reconstructions from full segmentations compared to sparse anatomical data. Hausdorff distance was lower (P < 0.01) for midfoot and calcaneus reconstructions using full segmentations compared to sparse anatomical data.ConclusionFor the first time, statistical shape models of the primary functional segments of the foot were developed and validated. Foot segments can be reconstructed with minimal error using full segmentations and sparse anatomical landmarks. In future, larger training datasets could increase statistical shape model robustness, extending use to paediatric or pathological populations. creator: Tamara M. Grant creator: Laura E. Diamond creator: Claudio Pizzolato creator: Bryce A. Killen creator: Daniel Devaprakash creator: Luke Kelly creator: Jayishni N. Maharaj creator: David J. Saxby uri: https://doi.org/10.7717/peerj.8397 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Grant et al. title: High-throughput sequencing analysis identified microRNAs associated with egg production in ducks ovaries link: https://peerj.com/articles/8440 last-modified: 2020-02-04 description: BackgroundMicroRNAs (miRNAs) exist widely and are involved in multiple biological processes in ducks, whereas the regulatory mechanism of miRNAs in egg laying of ducks has remained unclear. This study aims to reveal key miRNAs involved in the regulation of egg production in duck ovaries.MethodsHigh-throughput sequencing was performed on four egg-type duck ovaries and four egg-meat-type duck ovaries at the start of the egg-laying stage. Quantitative reverse transcription PCR (qRT-PCR) validation was performed on differentially expressed miRNAs (DE miRNAs). Gene network of DEmiRNA-mRNA-pathway was constructed by Cytoscape.ResultsA total of 251 know miRNAs and 1,972 novel miRNAs were obtained from whole clean reads. Among the known miRNAs, we identified 21 DEmiRNAs, including eight down-regulated and 13 up-regulated miRNAs in egg-type ducks compared with egg-meat-type ducks. Among the novel miRNAs, we identified 70 DEmiRNAs, including 58 down-regulated and 12 up-regulated in egg-type ducks compared with egg-meat-type ducks. The expression patterns of four miRNAs were verified by qRT-PCR. The DEmiRNAs were involved in the function of response to folic acid and the pathway of valine, leucine and isoleucine degradation. Specific target genes of DEmiRNAs enrichment was found in some egg-laying regulation pathways, such as dopaminergic synapse, ovarian steroidogenesis and oocyte meiosis. The DEmiRNA-mRNA-pathway network including three DEmiRNAs, nine mRNAs and 11 pathways. apl-miR-194-5p and apl-miR-215-5p may be potential key miRNAs in regulating egg laying.ConclusionsThis study provided miRNAs profiles in ducks about egg laying and establish a theoretical basis for subsequent selection or modification of duck phenotypes at the molecular level. creator: Mohan Qiu creator: Zengrong Zhang creator: Xia Xiong creator: Huarui Du creator: Qingyun Li creator: Chunlin Yu creator: Wu Gan creator: Hehe Liu creator: Han Peng creator: Bo Xia creator: Jialei Chen creator: Chenming Hu creator: Xiaoyan Song creator: Li Yang creator: Xiaosong Jiang creator: Chaowu Yang uri: https://doi.org/10.7717/peerj.8440 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Qiu et al. title: Genome-wide identification and expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula link: https://peerj.com/articles/8471 last-modified: 2020-02-04 description: Valine-glutamine (VQ) proteins are plant-specific proteins that play crucial roles in plant development as well as biotic and abiotic stress responses. VQ genes have been identified in various plants; however, there are no systematic reports in Cicer arietinum or Medicago truncatula. Herein, we identified 19 and 32 VQ genes in C. arietinum and M. truncatula, respectively. A total of these VQ genes were divided into eight groups (I–VIII) based on phylogenetic analysis. Gene structure analyses and motif patterns revealed that these VQ genes might have originated from a common ancestor. In silico analyses demonstrated that these VQ genes were expressed in different tissues. qRT-PCR analysis indicated that the VQ genes were differentially regulated during multiple abiotic stresses. This report presents the first systematic analysis of VQ genes from C. arietinum and M. truncatula and provides a solid foundation for further research of the specific functions of VQ proteins. creator: Lei Ling creator: Yue Qu creator: Jintao Zhu creator: Dan Wang creator: Changhong Guo uri: https://doi.org/10.7717/peerj.8471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ling et al. title: Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across the Indian subcontinent link: https://peerj.com/articles/8482 last-modified: 2020-02-04 description: BackgroundLarge carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline.MethodsWe collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities.ResultsOur genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75–90% population decline between ∼120–200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India.ConclusionsOur results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard. creator: Supriya Bhatt creator: Suvankar Biswas creator: Krithi Karanth creator: Bivash Pandav creator: Samrat Mondol uri: https://doi.org/10.7717/peerj.8482 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bhatt et al. title: Influence of host phylogeny, geographical location and seed harvesting diet on the bacterial community of globally distributed Pheidole ants link: https://peerj.com/articles/8492 last-modified: 2020-02-04 description: The presence of symbiotic relationships between organisms is a common phenomenon found across the tree of life. In particular, the association of bacterial symbionts with ants is an active area of study. This close relationship between ants and microbes can significantly impact host biology and is also considered one of the driving forces in ant evolution and diversification. Diet flexibility of ants may explain the evolutionary success of the group, which may be achieved by the presence of endosymbionts that aid in nutrition acquisition from a variety of food sources. With more than 1,140 species, ants from the genus Pheidole have a worldwide distribution and an important role in harvesting seeds; this behavior is believed to be a possible key innovation leading to the diversification of this group. This is the first study to investigate the bacterial community associated with Pheidole using next generation sequencing (NGS) to explore the influences of host phylogeny, geographic location and food preference in shaping the microbial community. In addition, we explore if there are any microbiota signatures related to granivory. We identified Proteobacteria and Firmicutes as the major phyla associated with these ants. The core microbiome in Pheidole (those found in >50% of all samples) was composed of 14 ASVs and the most prevalent are family Burkholderiaceae and the genera Acinetobacter, Streptococcus, Staphylococcus, Cloacibacterium and Ralstonia. We found that geographical location and food resource may influence the bacterial community of Pheidole ants. These results demonstrate that Pheidole has a relatively stable microbiota across species, which suggests the bacterial community may serve a generalized function in this group. creator: Cíntia Martins creator: Corrie S. Moreau uri: https://doi.org/10.7717/peerj.8492 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Martins and Moreau title: Development of a prognostic scoring model for predicting the survival of elderly patients with hepatocellular carcinoma link: https://peerj.com/articles/8497 last-modified: 2020-02-04 description: BackgroundThe number of elderly hepatocellular carcinoma (HCC) patients is increasing, and precisely assessing of the prognosis of these patients is necessary. We developed a prognostic scoring model to predict survival in elderly HCC patients.MethodsWe extracted data from 4,076 patients ≥65 years old from the Surveillance, Epidemiology, and End Results (SEER) database and randomly divided them into training and validation groups. Cox regression analysis was used to screen for meaningful independent prognostic factors. The receiver operating characteristic curve reflected the model’s discrimination power.ResultsAge, race, American Joint Committee on Cancer stage, degree of tumour differentiation, tumour size, alpha-fetoprotein and tumour therapy were independent prognostic factors for survival in elderly HCC patients. We developed a prognostic scoring model based on the seven meaningful variables to predict survival in elderly HCC patients. The AUCs of the model were 0.805 (95% CI [0.788–0.821]) and 0.788 (95% CI [0.759–0.816]) in the training and validation groups, respectively. We divided the patients into low-risk groups and high-risk groups according to the optimal cut-off value. The Kaplan–Meier survival curve showed that in the training and validation groups, the survival rate of the low-risk group was significantly higher than that of the high-risk group (P < 0.001).ConclusionBased on a large population, we constructed a prognostic scoring model for predicting survival in elderly HCC patients. The model may provide a reference for clinicians for preoperative and postoperative evaluations of elderly HCC patients. creator: Sizhe Wan creator: Yuan Nie creator: Xuan Zhu uri: https://doi.org/10.7717/peerj.8497 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wan et al. title: Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis link: https://peerj.com/articles/8505 last-modified: 2020-02-04 description: BackgroundOral squamous cell carcinoma (OSCC) is a major lethal malignant cancer of the head and neck region, yet its molecular mechanisms of tumourigenesis are still unclear.Patients and methodsWe performed weighted gene co-expression network analysis (WGCNA) on RNA-sequencing data with clinical information obtained from The Cancer Genome Atlas (TCGA) database. The relationship between co-expression modules and clinical traits was investigated by Pearson correlation analysis. Furthermore, the prognostic value and expression level of the hub genes of these modules were validated based on data from the TCGA database and other independent datasets from the Gene Expression Omnibus (GEO) database and the Human Protein Atlas database. The significant modules and hub genes were also assessed by functional analysis and gene set enrichment analysis (GSEA).ResultsWe found that the turquoise module was strongly correlated with pathologic T stage and significantly enriched in critical functions and pathways related to tumourigenesis. PPP1R12B, CFD, CRYAB, FAM189A2 and ANGPTL1 were identified and statistically validated as hub genes in the turquoise module and were closely implicated in the prognosis of OSCC. GSEA indicated that five hub genes were significantly involved in many well-known cancer-related biological functions and signaling pathways.ConclusionIn brief, we systematically discovered a co-expressed turquoise module and five hub genes associated with the pathologic T stage for the first time, which provided further insight that WGCNA may reveal the molecular regulatory mechanism involved in the carcinogenesis and progression of OSCC. In addition, the five hub genes may be considered candidate prognostic biomarkers and potential therapeutic targets for the precise early diagnosis, clinical treatment and prognosis of OSCC in the future. creator: Xuegang Hu creator: Guanwen Sun creator: Zhiqiang Shi creator: Hui Ni creator: Shan Jiang uri: https://doi.org/10.7717/peerj.8505 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hu et al. title: Bovine tuberculosis breakdown duration in cattle herds: an investigation of herd, host, pathogen and wildlife risk factors link: https://peerj.com/articles/8319 last-modified: 2020-02-03 description: BackgroundDespite rigorous controls placed on herds which disclose ante-mortem test positive cattle to bovine tuberculosis, caused by the infection of Mycobacterium bovis, many herds in Northern Ireland (NI) experience prolonged breakdowns. These herds represent a considerable administrative and financial burden to the State and farming community.MethodsA retrospective observational study was conducted to better understand the factors associated with breakdown duration, which was modelled using both negative binomial and ordinal regression approaches.ResultsSix explanatory variables were important predictors of breakdown length in both models; herd size, the number of reactors testing positive in the initial SICCT test, the presence of a lesioned animal at routine slaughter (LRS), the count of M. bovis genotypes during the breakdown (MLVA richness), the local herd-level bTB prevalence, and the presence of herds linked via management factors (associated herds). We report that between 2008 and 2014, mean breakdown duration in NI was 226 days (approx. seven months; median: 188 days). In the same period, however, more than 6% of herds in the region remained under movement restriction for more than 420 days (13 months); almost twice as long as the mean. The MLVA richness variable was a particularly important predictor of breakdown duration. We contend that this variable primarily represents a proxy for beef fattening herds, which can operate by purchasing cattle and selling animals straight to slaughter, despite prolonged trading restrictions. For other herd types, the model supports the hypothesis that prolonged breakdowns are a function of both residual infection within the herd, and infection from the environment (e.g. infected wildlife, contiguous herds and/or a contaminated environment). The impact of badger density on breakdown duration was assessed by including data on main sett (burrow) density. Whilst a positive association was observed in the univariate analysis, confounding with other variables means that the contribution of badgers to prolonged breakdowns was not clear from our study. We do not fully reject the hypothesis that badgers are implicated in prolonging bTB breakdowns via spillback infection, but given our results, we posit that increased disease risk from badgers is unlikely to simply be a function of increasing badger density measured using sett metrics. creator: Georgina Milne creator: Adrian Allen creator: Jordon Graham creator: Angela Lahuerta-Marin creator: Carl McCormick creator: Eleanor Presho creator: Neil Reid creator: Robin Skuce creator: Andrew W. Byrne uri: https://doi.org/10.7717/peerj.8319 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Milne et al. title: ViSiElse: an innovative R-package to visualize raw behavioral data over time link: https://peerj.com/articles/8341 last-modified: 2020-02-03 description: The scientific community encourages the use of raw data graphs to improve the reliability and transparency of the results presented in articles. However, the current methods used to visualize raw data are limited to one or two numerical variables per graph and/or small sample sizes. In the behavioral sciences, numerous variables must be plotted together in order to gain insight into the behavior in question. In this article, we present ViSiElse, an R-package offering a new approach in the visualization of raw data. ViSiElse was developed with the open-source software R to visualize behavioral observations over time based on raw time data extracted from visually recorded sessions of experimental observations. ViSiElse gives a global overview of a process by creating a visualization of the timestamps for multiple actions and all participants into a single graph; individual or group behavior can then be easily assessed. Additional features allow users to further inspect their data by including summary statistics and time constraints. creator: Elodie M. Garnier creator: Nastasia Fouret creator: Médéric Descoins uri: https://doi.org/10.7717/peerj.8341 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Garnier et al. title: Identification of key genes associated with multiple sclerosis based on gene expression data from peripheral blood mononuclear cells link: https://peerj.com/articles/8357 last-modified: 2020-02-03 description: The aim of this study was to identify the potential key candidate genes of multiple sclerosis (MS) and uncover mechanisms in MS. We combined data from the microarray expression profile of three MS stages and performed bioinformatics analysis. Differentially expressed genes (DEGs) were identified among the distinct stages of MS and healthy controls, and a total of 349 shared DEGs were identified. Gene ontology (GO) and pathway enrichment analyses showed that the DEGs were significantly enriched in the biological processes (BPs) of purine-related metabolic processes and signaling, especially the common DEGs, which were enriched in some immunological processes. Most of the DEGs were enriched in signaling pathways associated with the immune system, some immune diseases and infectious disease pathways. Through a protein–protein interaction (PPI) network analysis and a gene expression regulatory network constructed with MS-related miRNAs, we confirmed FOS, TP53, VEGFA, JUN, HIF1A, RB1, PTGS2, CXCL8, OAS2, NFKBIA and OAS1 as candidate genes of MS. Furthermore , we explored the potential SNPs associated with MS by database mining. In conclusion, this study provides the identified genes, SNPs, biological processes, and cellular pathways associated with MS. The uncovered candidate genes may be potential biomarkers involved in the diagnosis and therapy of MS. creator: Zhenwei Shang creator: Wenjing Sun creator: Mingming Zhang creator: Lidan Xu creator: Xueyuan Jia creator: Ruijie Zhang creator: Songbin Fu uri: https://doi.org/10.7717/peerj.8357 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shang et al. title: Cross-cultural adaptation and validation of the Romanian International Knee Documentation Committee—subjective knee form link: https://peerj.com/articles/8448 last-modified: 2020-02-03 description: AimWe aimed to translate and cross-culturally adapt the International Knee Documentation Committee—subjective knee form (IKDC) in Romanian.MethodThe original (US) IKDC—subjective knee form was translated according to recommended guidelines. Validity was tested using Spearmans’s correlation coefficient between score sand test-retest reproducibility. Reliability and internal consistency were determined using Cronbach’s alpha coefficient and intraclass correlation coefficient (ICC).ResultsA total of 106 data sets were available for processing. The average age was 52 years and the male to female ratio was 40:66. Fifty-five subjects repeated the form after an average of 4 days. There were no floor or ceiling effects (range 3.4–74.7). There was a strong correlation between the first and repeated administration of the IKDC—subjective knee form (r = 0.816, n = 50) and moderate compared to Tegner-Lysholm knee rating scale (r = 0.506, n = 102), KOOSJR (Knee disability and Osteoarthritis Outcome Score for Joint Replacement, r =  − 0.622, n = 96), EuroqolEQ-5D-5L Index (r = 0.633, n = 100) and visual analogue scale VAS (r = 0.484, n = 99). Internal consistency was moderate with Cronbach’s alpha 0.611 (n = 102) and ICC 0.611 for average measures (95% CI 0.493–0.713).ConclusionThe Romanian translation of the IKDC—subjective knee form is a valid, consistent and reproducible outcome measure in patients with knee pain and dysfunction. creator: Adrian Todor creator: Dinu Vermesan creator: Horia Haragus creator: Jenel M. Patrascu Jr creator: Bogdan Timar creator: Dan I. Cosma uri: https://doi.org/10.7717/peerj.8448 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Todor et al. title: Comparison of Symbiodiniaceae diversities in different members of a Palythoa species complex (Cnidaria: Anthozoa: Zoantharia)—implications for ecological adaptations to different microhabitats link: https://peerj.com/articles/8449 last-modified: 2020-02-03 description: In this study we compared genotypes of zoantharian host-associating algal symbionts among Palythoa species, which are among the dominant benthic reef organisms in the Ryukyu Archipelago, Japan, and evaluated Symbiodiniaceae diversities of closely related congeneric Palythoa species. We targeted a species complex of the zoantharian genus Palythoa (P. tuberculosa, P. sp. yoron, P. mutuki) living among different microhabitats in a narrow reef area of Tokunoshima Island. For phylogenetic analyses, we used two DNA marker regions; nuclear internal transcribed spacer (ITS) and plastid mini-circle non-coding region (psbAncr), both of which have previously been used to determine Symbiodiniaceae genotypes of zoantharian species. Our results showed that all Palythoa species hosted symbionts of the genus Cladocopium, with genotypic compositions of this genus showing some variations among the three different Palythoa species. Additionally, we found that the Cladocopium genotypic composition was statistically different among Palythoa species, and among P. tuberculosa specimens in different microhabitats. Our results suggest that ecological divergence among these three Palythoa species may be related to differing Symbiodiniaceae diversities that may in turn contribute to eco-physiological adaptation into different microhabitats on coral reefs. creator: Masaru Mizuyama creator: Akira Iguchi creator: Mariko Iijima creator: Kodai Gibu creator: James Davis Reimer uri: https://doi.org/10.7717/peerj.8449 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Mizuyama et al. title: Exploring abnormal Cambrian-aged trilobites in the Smithsonian collection link: https://peerj.com/articles/8453 last-modified: 2020-02-03 description: Biomineralised trilobite exoskeletons provide a 250 million year record of abnormalities in one of the most diverse arthropod groups in history. One type of abnormality—repaired injuries—have allowed palaeobiologists to document records of Paleozoic predation, accidental damage, and complications in moulting experienced by the group. Although Cambrian trilobite injuries are fairly well documented, the illustration of new injured specimens will produce a more complete understanding of Cambrian prey items. To align with this perspective, nine new abnormal specimens displaying healed injuries from the Smithsonian National Museum of Natural History collection are documented. The injury pattern conforms to the suggestion of lateralised prey defence or predator preference, but it is highlighted that the root cause for such patterns is obscured by the lumping of data across different palaeoecological and environmental conditions. Further studies of Cambrian trilobites with injuries represent a key direction for uncovering evidence for the Cambrian escalation event. creator: Russell D.C. Bicknell creator: Stephen Pates uri: https://doi.org/10.7717/peerj.8453 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bicknell and Pates title: Key genes and co-expression modules involved in asthma pathogenesis link: https://peerj.com/articles/8456 last-modified: 2020-02-03 description: Machine learning and weighted gene co-expression network analysis (WGCNA) have been widely used due to its well-known accuracy in the biological field. However, due to the nature of a gene’s multiple functions, it is challenging to locate the exact genes involved in complex diseases such as asthma. In this study, we combined machine learning and WGCNA in order to analyze the gene expression data of asthma for better understanding of associated pathogenesis. Specifically, the role of machine learning is assigned to screen out the key genes in the asthma development, while the role of WGCNA is to set up gene co-expression network. Our results indicated that hormone secretion regulation, airway remodeling, and negative immune regulation, were all regulated by critical gene modules associated with pathogenesis of asthma progression. Overall, the method employed in this study helped identify key genes in asthma and their roles in the asthma pathogenesis. creator: Yuyi Huang creator: Hui Liu creator: Li Zuo creator: Ailin Tao uri: https://doi.org/10.7717/peerj.8456 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Larger contactor area increases low-frequency vibratory sensitivity in hairy skin link: https://peerj.com/articles/8479 last-modified: 2020-02-03 description: BackgroundIn research, assessing vibratory cutaneous sensitivity is an important research branch to quantify various diseases or to develop devices for pattern recognition. The measured vibration perception thresholds (VPTs), however, are subjective and usually result in a large data variability. This might induce difficulties to detect differences, for example, when comparing different anatomical locations. Hence, a higher ability to detect changes is desirable. Another feature of VPTs is spatial summation, but in the literature it is controversially discussed whether or not this phenomenon is also present in the lower frequency range. For these reasons, the present study aimed to investigate whether an enlarged matrix contactor area (measured at the hairy skin) induces improvements in subjective sensitivity using high and low frequencies, and whether a large contactor area is better able to identify changes of VPTs than a small contactor area of a single contactor. For each frequency, we hypothesized an increased sensitivity for the matrix compared to the single contactor. We also hypothesized that changes can be better-detected between the anatomical locations when using the matrix than the single contactor.MethodsTwenty healthy and young participants voluntarily took part in this study. Three anatomical locations at the torso were measured at the middle aspect of the lower back, middle lateral aspect of the upper arm, and the region just below the armpit. At each location, two frequencies (30, 200 Hz) and two contactor conditions (single contactor: 0.48 cm2 , contactor matrix: 9 × 0.48 cm2 = 4.32 cm2) were tested in a randomized order.ResultsSupporting our hypothesis, we found that improved cutaneous sensitivity after increasing the contactor size occurs not only at high, but also at low frequencies at all anatomical locations. Large contactor sizes resulted in higher sensitivity and in a superior ability to detect changes. The superior behavior of the matrix to exhibit a lower variability could not always be proven. This work may be relevant for future studies aiming to identify changes of VPTs in various patient groups, for example. creator: Daniel Schmidt creator: Guenther Schlee creator: Andresa M.C. Germano creator: Thomas L. Milani uri: https://doi.org/10.7717/peerj.8479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Schmidt et al. title: EMT-related gene expression is positively correlated with immunity and may be derived from stromal cells in osteosarcoma link: https://peerj.com/articles/8489 last-modified: 2020-02-03 description: BackgroundOsteosarcoma is the most common type of bone cancer in children and young adults. Recent studies have shown a correlation between epithelial–mesenchymal transition (EMT)-related gene expression and immunity in human cancers. Here, we investigated the relationship among EMT, immune activity, stromal activity and tumor purity in osteosarcoma.MethodsWe defined EMT gene signatures and evaluated immune activity and stromal activity based on the gene expression and clinical data from three independent microarray datasets. These factors were evaluated by single sample Gene Set Enrichment Analyses and the ESTIMATE tool. Finally, we analyzed the key source of EMT gene expression in osteosarcoma using microarray datasets from the Gene Expression Omnibus and human samples that we collected.ResultsEMT-related gene expression was positively correlated with immune and stromal activity in osteosarcoma. Tumor purity was negatively correlated with EMT, immune activity and stromal cells. We further demonstrated that high EMT gene expression could significantly predict poor overall survival (OS) and recurrence-free survival (RFS) in osteosarcoma patients, while high immune activity cannot. However, combining these factors could have further prognostic value for osteosarcoma patients in terms of OS and RFS. Finally, we found that stromal cells may serve as a key source of EMT gene expression in osteosarcoma.ConclusionThe results of this study reveal that the expression of EMT genes and immunity are positively correlated, but these signatures convey disparate prognostic information. Furthermore, the results indicate that EMT-related gene expression may be derived from stromal rather than epithelial cancer cells. creator: Yin-xiao Peng creator: Bin Yu creator: Hui Qin creator: Li Xue creator: Yi-jian Liang creator: Zheng-xue Quan uri: https://doi.org/10.7717/peerj.8489 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Peng et al. title: Radiotherapy after mastectomy has significant survival benefits for inflammatory breast cancer: a SEER population-based retrospective study link: https://peerj.com/articles/8512 last-modified: 2020-02-03 description: ObjectivesThe survival benefit of postmastectomy radiotherapy (PMRT) has not been fully proven in inflammatory breast cancer (IBC). Thus, in the present research, we aimed at elucidating the effects of PMRT on the survival of IBC patients.MethodsEligible patients were collected from the Surveillance, Epidemiology, and End Results (SEER) dataset between 2010 and 2013. The Kaplan-Meier method along with the log-rank test was utilized for the comparison of both the overall survival (OS) andthe cancer-specific survival (CSS) in patients undergoing PMRT or not. Additionally, multivariate survival analysis of CSS and OS were performed using the Cox proportional hazard model.ResultsIn total, 293 eligible cases were identified, with the median follow-up time of 27 months (range: 5–59 months). After propensity score matching (PSM), 188 patients (94 for each) were classified intothe No-PMRT and the PMRT group. Consequently, significantly higher OS rates were detected in the PMRT group compared with the No-PMRT group prior to PSM (P = 0.034), and significantly higher CSS (P = 0.013) and OS (P = 0.0063) rates were observed following PSM. Furthermore, multivariate analysis revealed thatPMRT [CSS (HR: 0.519, 95% CI [0.287–0.939], P = 0.030); OS (HR: 0.480, 95% CI [0.269–0.859], P = 0.013)], as well as Her2+/HR+ subtype, was independent favorable prognostic factors.Besides, black ethnicity, AJCC stage IV and triple-negative subtype were independent unfavorable prognostic factors. Further subgroup analysis revealed that most of the study population could benefit from PMRT, no matter OS or CSS.ConclusionsOur findings support that PMRT could improve the survival of IBC patients. creator: Zhi-wen Li creator: Miao Zhang creator: Yong-jing Yang creator: Zi-jun Zhou creator: Yan-ling Liu creator: Hang Li creator: Bo Bao creator: Jian-dong Diao creator: Dun-wei Wang uri: https://doi.org/10.7717/peerj.8512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Glycyrrhizin suppresses epithelial-mesenchymal transition by inhibiting high-mobility group box1 via the TGF-β1/Smad2/3 pathway in lung epithelial cells link: https://peerj.com/articles/8514 last-modified: 2020-02-03 description: BackgroundEpithelial-mesenchymal transition (EMT) plays an important role in fibrosis, chronic inflammation, tumor metastasis, etc. Glycyrrhizin, an active component extracted from licorice plant, has been reported to treat a variety of inflammatory reactions through inhibiting high-mobility group box1 (HMGB1), which has been suggested to be a significant mediator in EMT process. However, whether glycyrrhizin affects the EMT process or not remains unclear.MethodsHuman alveolar epithelial cell line A549 and normal human bronchial epithelial cell line BEAS-2B were treated with extrinsic TGF-β1 to induce EMT. Elisa was used to detect HMGB1 concentrations in cell supernatant. RNA interference and lentivirus infection experiments were performed to investigate the involvement of HMGB1 in EMT process. Cell Counting Kit-8 (CCK-8) was used to detect the viability of A549 and BEAS-2B cells treated with glycyrrhizin. Finally, the effects of glycyrrhizin on EMT changes, as well as the underlying mechanisms, were evaluated via Western blot, immunofluorescence and transwell assays.ResultsOur results showed that HMGB1 expression was increased by TGF-β1, and knockdown of HMGB1 expression reversed TGF-β1-induced EMT in A549 and BEAS-2B cells. Ectopic HMGB1 expression or TGF-β1 treatment caused a significant increase in HMGB1 release. Notably, we found that glycyrrhizin treatment effectively suppressed TGF-β1-induced EMT process by inhibiting HMGB1. Also, glycyrrhizin significantly inhibited the migration of both A549 and BEAS-2B cells promoted by TGF-β1. Mechanistically, HMGB1 overexpression could activate Smad2/3 signaling in A549 and BEAS-2B cells. Glycyrrhizin significantly blocked the phosphorylation of Smad2/3 stimulated either by TGF-β1 or by ectopic HMGB1 in A549 and BEAS-2B cells.ConclusionsHMGB1 is a vital mediator of EMT changes induced by TGF-β1 in lung epithelial cells. Importantly, glycyrrhizin can effectively block Smad2/3 signaling pathway through inhibiting HMGB1, thereby suppressing the EMT progress. creator: Yanni Gui creator: Jian Sun creator: Wenjie You creator: Yuanhui Wei creator: Han Tian creator: Shujuan Jiang uri: https://doi.org/10.7717/peerj.8514 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gui et al. title: Epidemiological scenario of dengue in the state of Manipur during the last 3 years link: https://peerj.com/articles/8518 last-modified: 2020-02-03 description: BackgroundThe study of disease transmission of dengue fever (DF) is perplexing in the Indian subcontinent as all the four serotypes are circling. Also, there is no efficient epidemiological examination done on dengue cases in Manipur, a north-eastern territory of India.MethodWe utilized the dengue information extricated from the lab register of Viral Research and Diagnostic Laboratory (VRDL) from 2016 to 2018. All presumed outpatient and inpatients dengue cases from open and private health-care facilities are incorporated into the VRDL database whose informed consent were gotten.ResultsA sum of 1689 instances of associated patients with dengue infection was tried for dengue ELISA test and 272 (16.10%) samples were seen as seropositive. The month-wise conveyance of dengue cases is very intriguing as the three years of study demonstrates a variation design in perception. In all the three years dengue seropositive cases were seen higher in the male populace. Be that as it may, there is no noteworthy incentive to the inspiration of dengue seropositive towards male than female.ConclusionOur examination exhibits a comparative epidemiological investigation on seroprevelance of dengue in the province of Manipur for three years. This is an endeavour to show epidemiological dengue seroprevelance in the territory of Manipur which in future would be a reference from general wellbeing worries for making up essential move intend to shorten the spread of dengue. creator: Leimapokpam Shivadutta Singh creator: Rajkumar Manojkumar Singh creator: Huidrom Lokhendro Singh uri: https://doi.org/10.7717/peerj.8518 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Singh et al.