title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1001 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effects of food type and abundance on begging and sharing in Asian small-clawed otters (Aonyx cinereus) link: https://peerj.com/articles/10369 last-modified: 2020-11-30 description: Begging for food, a conspicuous solicitation display, is common in a variety of taxa, and it has received extensive research attention in a parent-offspring context. Both theoretical models and empirical evidence suggest that offspring begging can be an honest signal of hunger or a mediator of competition between siblings. At a behavioural mechanistic level, begging for food can be a form of harassment aimed at persuading those in possession of food to share. Food sharing, defined as the transfer of a defendable food item from one individual to another, can vary considerably between species, age-classes and food type and abundance. We investigated the determinants of begging and food-sharing behaviours in Asian small-clawed otters (Aonyx cinereus), a group-living species that commonly exhibits begging in captivity. We presented two captive otter populations with three food types that varied in exploitation complexity, in three different abundances. We predicted that begging rates would be highest when food was in lowest abundance and hardest to exploit, and that increased begging would lead to increased food sharing. We found that, over time, increased begging rates were indeed correlated with increased food transfers, but neither food type complexity nor abundance affected begging or sharing rates. However, age category was significantly associated with begging and food sharing rates: juvenile otters begged more and shared less than adult otters. The results from this first experimental study on begging and food sharing within the Mustelid family begin to reveal some of the drivers of these behaviours. creator: Madison Bowden-Parry creator: Erik Postma creator: Neeltje J. Boogert uri: https://doi.org/10.7717/peerj.10369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bowden-Parry et al. title: Effects of platelet-rich plasma on mesenchymal stem cells isolated from rat uterus link: https://peerj.com/articles/10415 last-modified: 2020-11-30 description: BackgroundPlatelet-rich plasma (PRP), which represents a valuable source of growth factors, is increasingly being applied in regenerative medicine. Recent findings suggest the feasibility of using PRP in the treatment of infertility secondary to refractory thin endometrium. Mesenchymal stem/stromal cells (MSCs) of the endometrium are an essential cellular component responsible for extracellular matrix remodeling, angiogenesis, cell-to-cell communication, and postmenstrual tissue repair. Using a rat model, we examine the effects of autologous PRP on MSCs isolated from the uterus and compare them with the effects of autologous ordinary plasma (OP) and complete growth medium.MethodsMSCs were isolated from uterine tissues via enzymatic disaggregation. Flow cytometry immunophenotyping of the primary cell cultures was complemented by immunocytochemistry for Ki-67 and vimentin. The ability of MSCs to differentiate in osteo-, chondro-, and adipogenic directions was assessed using differentiation-inducing media. The levels of autophagy and apoptosis markers, as well as the levels of matrix metalloproteinase 9 (MMP9) and estrogen receptor α, were assessed by western blotting.ResultsAfter 24 h incubation, the proliferation index of the PRP-treated MSC cultures was significantly higher than that of the MSC cultures treated with complete growth medium. PRP treatment elevated production of LC3B protein, an autophagy marker, while OP treatment upregulated the expression of stress-induced protein p53 and extracellular enzyme MMP9. The results indicate practical relevance and validity for PRP use in the treatment of infertility. creator: Polina Vishnyakova creator: Daria Artemova creator: Andrey Elchaninov creator: Zulfiia Efendieva creator: Inna Apolikhina creator: Gennady Sukhikh creator: Timur Fatkhudinov uri: https://doi.org/10.7717/peerj.10415 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Vishnyakova et al. title: Repurposing FDA-approved phytomedicines, natural products, antivirals and cell protectives against SARS-CoV-2 (COVID-19) RNA-dependent RNA polymerase link: https://peerj.com/articles/10480 last-modified: 2020-11-30 description: Following the recent emergence of SARS-CoV-2 or coronavirus disease 2019 (COVID-19), drug discovery and vaccine design to combat this fatal infection are critical. In this study, an essential enzyme in the SARS-CoV-2 replication machinery, RNA-dependent RNA polymerase (RDRP), is targeted in a virtual screening assay using a set of 1,664 FDA-approved drugs, including sets of botanical and synthetic derivatives. A set of 22 drugs showed a high docking score of >−7. Notably, approximately one-third of the top hits were either from natural products or biological molecules. The FDA-approved phytochemicals were sennosides, digoxin, asiaticoside, glycyrrhizin, neohesperidin, taxifolin, quercetin and aloin. These approved natural products and phytochemicals are used as general tonics, antioxidants, cell protectives, and immune stimulants (nadid, thymopentin, asiaticoside, glycyrrhizin) and in other miscellaneous systemic or topical applications. A comprehensive analysis was conducted on standard precision and extra precision docking, two-step molecular dynamics simulations, binding energy calculations and a post dynamics analysis. The results reveal that two drugs, docetaxel and neohesperidin, showed strong binding profiles with SARS CoV-2 RdRP. These results can be used as a primer for further drug discovery studies in the treatment of COVID-19. This initiative repurposes safe FDA-approved drugs against COVID-19 RdRP, providing a rapid channel for the discovery and application of new anti-CoV therapeutics. creator: Mahmoud Kandeel creator: Yukio Kitade creator: Abdullah Almubarak uri: https://doi.org/10.7717/peerj.10480 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kandeel et al. title: Molecular phylogeny and species delimitation of the freshwater prawn Macrobrachium pilimanus species group, with descriptions of three new species from Thailand link: https://peerj.com/articles/10137 last-modified: 2020-11-27 description: Specific status and species boundaries of several freshwater prawns in the Macrobrachium pilimanus species group remain ambiguous, despite the taxonomic re-description of type materials and additional specimens collected to expand the boundaries of some species. In this study, the “pilimanus” species group of Macrobrachium sensu Johnson (1958) was studied using specimens collected from montane streams of Thailand. Molecular phylogenetic analyses based on sequences of three molecular markers (COI, 16S and 18S rRNA) were performed. The phylogenetic results agreed with morphological identifications, and indicated the presence of at least nine putative taxa. Of these, six morphospecies were recognised as M. malayanum, M. forcipatum, M. dienbienphuense, M. hirsutimanus, M. eriocheirum, and M. sirindhorn. Furthermore, three morphologically and genetically distinct linages were detected, and are described herein as M. naiyanetri Siriwut sp. nov., M. palmopilosum Siriwut sp. nov. and M. puberimanus Siriwut sp. nov. The taxonomic comparison indicated wide morphological variation in several species and suggested additional diagnostic characters that are suitable for use in species diagnoses, such as the shape and orientation of fingers, the rostrum form, and the presence or absence of velvet pubescence hairs and tuberculated spinulation on each telopodite of the second pereiopods. The “pilimanus” species group was portrayed as non-monophyletic in both ML and BI analyses. The genetic structure of different geographical populations in Thailand was detected in some widespread species. The species delimitation based on the four delimitation methods (BIN, ABGD, PTP and GMYC) suggested high genetic diversity of the “pilimanus” species group and placed the candidate members much higher than in previous designations based on traditional morphology. This finding suggests that further investigation of morphological and genetic diversity of Southeast Asian freshwater prawns in the genus Macrobrachium is still required to provide a comprehensive species list to guide efforts in conservation and resource management. creator: Warut Siriwut creator: Ekgachai Jeratthitikul creator: Somsak Panha creator: Ratmanee Chanabun creator: Chirasak Sutcharit uri: https://doi.org/10.7717/peerj.10137 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Siriwut et al. title: Effectiveness of specific stabilization exercise compared with traditional trunk exercise in women with non-specific low back pain: a pilot randomized controlled trial link: https://peerj.com/articles/10304 last-modified: 2020-11-27 description: BackgroundNon-specific low back pain (LBP) is the leading cause of disability worldwide. The primary physiotherapeutic treatment for LBP is physical exercise, but evidence suggesting a specific exercise as most appropriate for any given case is limited.ObjectiveTo determine if specific stabilization exercise (SSE) is more effective than traditional trunk exercise (TTE) in reducing levels of pain, disability and inflammation in women with non-specific low back pain (LBP).DesignA pilot randomized controlled trial was conducted in Rovira i Virgili University, Catalonia.MethodsThirty-nine females experiencing non-specific LBP were included in two groups: the TTE program and SSE program, both were conducted by a physiotherapist during twenty sessions. The primary outcome was pain intensity (10-cm Visual Analogue Scale). Secondary outcomes were disability (Roland Morris Disability Questionnaire), and inflammation (IL-6 and TNF-α plasma levels). Measurements were taken at baseline, at half intervention, at post-intervention, and a month later.ResultsMean group differences in change from baseline to post-intervention for TTE were: −4.5 points (CI 3.3 to 5.6) for pain, −5.1 points (CI 3.0 to 7.3) for disability, 0.19 pg/mL (95% CI [−1.6–1.2]) for IL-6 levels, and 46.2 pg/mL (CI 13.0 to 85.3) for TNF-α levels. For SSE, differences were: −4.3 points (CI 3.1 to 5.6) for pain, −6.1 points (CI 3.7 to 8.6) for disability, 1.1 pg/mL (CI 0.0 to 2.1) for IL-6 levels , and 12.8 pg/mL (95% CI [−42.3–16.7]) for TNF-α levels. There were an insignificant effect size and no statistically significant overall mean differences between both groups.ConclusionThis study suggests that both interventions (traditional trunk and specific stabilization exercises) are effective in reducing pain and disability in non-specific LBP patients, but the two programs produce different degrees of inflammation change.Clinical trial registration numberNCT02103036. creator: Eduard Minobes-Molina creator: Maria Rosa Nogués creator: Montse Giralt creator: Carme Casajuana creator: Dyego Leandro Bezerra de Souza creator: Javier Jerez-Roig creator: Marta Romeu uri: https://doi.org/10.7717/peerj.10304 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Minobes-Molina et al. title: Eco-morphological diversity of larvae of soldier flies and their closest relatives in deep time link: https://peerj.com/articles/10356 last-modified: 2020-11-27 description: Stratiomyomorpha (soldier flies and allies) is an ingroup of Diptera, with a fossil record stretching back to the Early Cretaceous (the Barremian, about 125 MYA). Stratiomyomorpha includes at least 3,000 species in the modern fauna, with many species being crucial for ecosystem functions, especially as saprophages. Larvae of many stratiomyomorphans are especially important as scavengers and saproxyls in modern ecosystems. Yet, fossil larvae of the group are extremely scarce. Here we present 23 new records of fossil stratiomyomorphan larvae, representing six discrete morphotypes. Specimens originate from Cretaceous amber from Myanmar, Eocene Baltic amber, Miocene Dominican amber, and compression fossils from the Eocene of Messel (Germany) and the Miocene of Slovenia. We discuss the implications of these new records for our understanding of stratiomyomorphan ecomorphology in deep time as well as their palaeoecology. creator: Viktor A. Baranov creator: Yinan Wang creator: Rok Gašparič creator: Sonja Wedmann creator: Joachim T. Haug uri: https://doi.org/10.7717/peerj.10356 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Baranov et al. title: A diverse global fungal library for drug discovery link: https://peerj.com/articles/10392 last-modified: 2020-11-27 description: BackgroundSecondary fungal metabolites are important sources for new drugs against infectious diseases and cancers.MethodsTo obtain a library with enough diversity, we collected about 2,395 soil samples and 2,324 plant samples from 36 regions in Africa, Asia, and North America. The collection areas covered various climate zones in the world. We examined the usability of the global fungal extract library (GFEL) against parasitic malaria transmission, Gram-positive and negative bacterial pathogens, and leukemia cells.ResultsNearly ten thousand fungal strains were isolated. Sequences of nuclear ribosomal internal transcribed spacer (ITS) from 40 randomly selected strains showed that over 80% were unique. Screening GFEL, we found that the fungal extract from Penicillium thomii was able to block Plasmodium falciparum transmission to Anopheles gambiae, and the fungal extract from Tolypocladium album was able to kill myelogenous leukemia cell line K562. We also identified a set of candidate fungal extracts against bacterial pathogens. creator: Guodong Niu creator: Thirunavukkarasu Annamalai creator: Xiaohong Wang creator: Sheng Li creator: Stephen Munga creator: Guomin Niu creator: Yuk-Ching Tse-Dinh creator: Jun Li uri: https://doi.org/10.7717/peerj.10392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Niu et al. title: Data quantity is more important than its spatial bias for predictive species distribution modelling link: https://peerj.com/articles/10411 last-modified: 2020-11-27 description: Biological records are often the data of choice for training predictive species distribution models (SDMs), but spatial sampling bias is pervasive in biological records data at multiple spatial scales and is thought to impair the performance of SDMs. We simulated presences and absences of virtual species as well as the process of recording these species to evaluate the effect on species distribution model prediction performance of (1) spatial bias in training data, (2) sample size (the average number of observations per species), and (3) the choice of species distribution modelling method. Our approach is novel in quantifying and applying real-world spatial sampling biases to simulated data. Spatial bias in training data decreased species distribution model prediction performance, but sample size and the choice of modelling method were more important than spatial bias in determining the prediction performance of species distribution models. creator: Willson Gaul creator: Dinara Sadykova creator: Hannah J. White creator: Lupe Leon-Sanchez creator: Paul Caplat creator: Mark C. Emmerson creator: Jon M. Yearsley uri: https://doi.org/10.7717/peerj.10411 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gaul et al. title: Identification and prognostic value of DLGAP5 in endometrial cancer link: https://peerj.com/articles/10433 last-modified: 2020-11-27 description: BackgroundEndometrial cancer poses a serious threat to women’s health worldwide, and its pathogenesis, although actively explored, is not fully understood. DLGAP5 is a recently identified cell cycle-regulation gene not reported in endometrial cancer. This study was aiming to analyze the role of DLGAP5 in tumorigenesis and development and to investigate its prognostic significance of patients with endometrial cancer.MethodologyMicroarray datasets (GSE17025, GSE39099 and GSE63678) from the GEO database were used for comparative analysis, and their intersection was obtained by applying the Venn diagram, and DLGAP5 was selected as the target gene. Next, transcriptome data (n = 578) was downloaded from TCGA-UCEC to analyze the mRNA expression profile of DLGAP5. Then, immunohistochemical data provided by HPA were used to identify the different protein expression levels of DLGAP5 in tumor tissues and normal tissues. Subsequently, the prognostic meaning of DLGAP5 in patients with endometrial cancer was explored based on survival data from TCGA-UCEC (n = 541). Finally, the reliability of DLGAP5 expression was verified by RT-qPCR.ResultsTranscriptome data from TCGA-UCEC, immunohistochemical data from HPA, and RT-qPCR results from clinical samples were used for triple validation to confirm that the expression of DLGAP5 in endometrial cancer tissues was significantly higher than that in normal endometrial tissues. Kaplan–Meier survival analysis announced that the expression level of DLGAP5 was negatively correlated with the overall survival of patients with endometrial cancer.ConclusionsDLGAP5 is a potential oncogene with cell cycle regulation, and its overexpression can predict the poor prognosis of patients with endometrial cancer. As a candidate target for the diagnosis and treatment of endometrial cancer, it is worthwhile to make further study to reveal the carcinogenicity of DLGAP5 and the mechanism of its resistance of organisms. creator: Ruoyi Zheng creator: Zhengzheng Shi creator: Wenzhi Li creator: Jianqin Yu creator: Yuli Wang creator: Qing Zhou uri: https://doi.org/10.7717/peerj.10433 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zheng et al. title: The mRNA landscape profiling reveals potential biomarkers associated with acute kidney injury AKI after kidney transplantation link: https://peerj.com/articles/10441 last-modified: 2020-11-27 description: BackgroundThis study aims to identify potential biomarkers associated with acute kidney injury (AKI) post kidney transplantation.Material and MethodsTwo mRNA expression profiles from Gene Expression Omnibus repertory were downloaded, including 20 delayed graft function (DGF) and 68 immediate graft function (IGF) samples. Differentially expressed genes (DEGs) were identified between DGF and IGF group. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of DEGs were performed. Then, a protein-protein interaction analysis was performed to extract hub genes. The key genes were searched by literature retrieval and cross-validated based on the training dataset. An external dataset was used to validate the expression levels of key genes. Receiver operating characteristic curve analyses were performed to evaluate diagnostic performance of key genes for AKI.ResultsA total of 330 DEGs were identified between DGF and IGF samples, including 179 up-regulated and 151 down-regulated genes. Of these, OLIG3, EBF3 and ETV1 were transcription factor genes. Moreover, LEP, EIF4A3, WDR3, MC4R, PPP2CB, DDX21 and GPT served as hub genes in PPI network. EBF3 was significantly up-regulated in validation GSE139061 dataset, which was consistently with our initial gene differential expression analysis. Finally, we found that LEP had a great diagnostic value for AKI (AUC = 0.740).ConclusionEBF3 may be associated with the development of AKI following kidney transplantation. Furthermore, LEP had a good diagnostic value for AKI. These findings provide deeper insights into the diagnosis and management of AKI post renal transplantation. creator: Hui Bi creator: Min Zhang creator: Jialin Wang creator: Gang Long uri: https://doi.org/10.7717/peerj.10441 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Bi et al.