title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2021-03 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Sinomacrops bondei, a new anurognathid pterosaur from the Jurassic of China and comments on the group link: https://peerj.com/articles/11161 last-modified: 2021-03-31 description: Anurognathids are an elusive group of diminutive, potentially arboreal pterosaurs. Even though their monophyly has been well-supported, their intrarelationships have been obscure, and their phylogenetic placement even more. In the present work, we present a new genus and species from the Middle-Late Jurassic Tiaojishan Formation, the third nominal anurognathid species from the Jurassic of China. The new species provides new information concerning morphological diversity for the group. Furthermore, we provide a new phylogenetic analysis incorporating into a single data set characters from diverging phylogenetic proposals. Our results place them as the sister-group of Darwinoptera + Pterodactyloidea, as basal members of the Monofenestrata. creator: Xuefang Wei creator: Rodrigo Vargas Pêgas creator: Caizhi Shen creator: Yanfang Guo creator: Waisum Ma creator: Deyu Sun creator: Xuanyu Zhou uri: https://doi.org/10.7717/peerj.11161 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wei et al. title: eDNAir: proof of concept that animal DNA can be collected from air sampling link: https://peerj.com/articles/11030 last-modified: 2021-03-31 description: Environmental DNA (eDNA) is one of the fastest developing tools for species biomonitoring and ecological research. However, despite substantial interest from research, commercial and regulatory sectors, it has remained primarily a tool for aquatic systems with a small amount of work in substances such as soil, snow and rain. Here we demonstrate that eDNA can be collected from air and used to identify mammals. Our proof of concept successfully demonstrated that eDNA sampled from air contained mixed templates which reflect the species known to be present within a confined space and that this material can be accessed using existing sampling methods. We anticipate this demonstration will initiate a much larger research programme in terrestrial airDNA sampling and that this may rapidly advance biomonitoring approaches. Lastly, we outline these and potential related applications we expect to benefit from this development. creator: Elizabeth L. Clare creator: Chloe K. Economou creator: Chris G. Faulkes creator: James D. Gilbert creator: Frances Bennett creator: Rosie Drinkwater creator: Joanne E. Littlefair uri: https://doi.org/10.7717/peerj.11030 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Clare et al. title: Use of conditioned media (CM) and xeno-free serum substitute on human adipose-derived stem cells (ADSCs) differentiation into urothelial-like cells link: https://peerj.com/articles/10890 last-modified: 2021-03-31 description: BackgroundCongenital abnormalities, cancers as well as injuries can cause irreversible damage to the urinary tract, which eventually requires tissue reconstruction. Smooth muscle cells, endothelial cells, and urothelial cells are the major cell types required for the reconstruction of lower urinary tract. Adult stem cells represent an accessible source of unlimited repertoire of untransformed cells.AimFetal bovine serum (FBS) is the most vital supplement in the culture media used for cellular proliferation and differentiation. However, due to the increasing interest in manufacturing xeno-free stem cell-based cellular products, optimizing the composition of the culture media and the serum-type used is of paramount importance. In this study, the effects of FBS and pooled human platelet (pHPL) lysate were assessed on the capacity of human adipose-derived stem cells (ADSCs) to differentiate into urothelial-like cells. Also, we aimed to compare the ability of both conditioned media (CM) and unconditioned urothelial cell media (UCM) to induce urothelial differentiation of ADCS in vitro.MethodsADSCs were isolated from human lipoaspirates and characterized by flow cytometry for their ability to express the most common mesenchymal stem cell (MSCs) markers. The differentiation potential was also assessed by differentiating them into osteogenic and adipogenic cell lineages. To evaluate the capacity of ADSCs to differentiate towards the urothelial-like lineage, cells were cultured with either CM or UCM, supplemented with either 5% pHPL, 2.5% pHPL or 10% FBS. After 14 days of induction, cells were utilized for gene expression and immunofluorescence analysis.ResultsADSCs cultured in CM and supplemented with FBS exhibited the highest upregulation levels of the urothelial cell markers; cytokeratin-18 (CK-18), cytokeratin-19 (CK-19), and Uroplakin-2 (UPK-2), with a 6.7, 4.2- and a 2-folds increase in gene expression, respectively. Meanwhile, the use of CM supplemented with either 5% pHPL or 2.5% pHPL, and UCM supplemented with either 5% pHPL or 2.5% pHPL showed low expression levels of CK-18 and CK-19 and no upregulation of UPK-2 level was observed. In contrast, the use of UCM with FBS has increased the levels of CK-18 and CK-19, however to a lesser extent compared to CM. At the cellular level, CK-18 and UPK-2 were only detected in CM/FBS supplemented group. Growth factor analysis revealed an increase in the expression levels of EGF, VEGF and PDGF in all of the differentiated groups.ConclusionEfficient ADSCs urothelial differentiation is dependent on the use of conditioned media. The presence of high concentrations of proliferation-inducing growth factors present in the pHPL reduces the efficiency of ADSCs differentiation towards the urothelial lineage. Additionally, the increase in EGF, VEGF and PDGF during the differentiation implicates them in the mechanism of urothelial cell differentiation. creator: Ban Al- kurdi creator: Nidaa A. Ababneh creator: Nizar Abuharfeil creator: Saddam Al Demour creator: Abdalla S. Awidi uri: https://doi.org/10.7717/peerj.10890 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Alkurdi et al. title: Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application link: https://peerj.com/articles/10897 last-modified: 2021-03-31 description: Molecular profiling of tumor samples has acquired importance in cancer research, but currently also plays an important role in the clinical management of cancer patients. Rapid identification of genomic aberrations improves diagnosis, prognosis and effective therapy selection. This can be attributed mainly to the development of next-generation sequencing (NGS) methods, especially targeted DNA panels. Such panels enable a relatively inexpensive and rapid analysis of various aberrations with clinical impact specific to particular diagnoses. In this review, we discuss the experimental approaches and bioinformatic strategies available for the development of an NGS panel for a reliable analysis of selected biomarkers. Compliance with defined analytical steps is crucial to ensure accurate and reproducible results. In addition, a careful validation procedure has to be performed before the application of NGS targeted assays in routine clinical practice. With more focus on bioinformatics, we emphasize the need for thorough pipeline validation and management in relation to the particular experimental setting as an integral part of the NGS method establishment. A robust and reproducible bioinformatic analysis running on powerful machines is essential for proper detection of genomic variants in clinical settings since distinguishing between experimental noise and real biological variants is fundamental. This review summarizes state-of-the-art bioinformatic solutions for careful detection of the SNV/Indels and CNVs for targeted sequencing resulting in translation of sequencing data into clinically relevant information. Finally, we share our experience with the development of a custom targeted NGS panel for an integrated analysis of biomarkers in lymphoproliferative disorders. creator: Jakub Hynst creator: Veronika Navrkalova creator: Karol Pal creator: Sarka Pospisilova uri: https://doi.org/10.7717/peerj.10897 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Hynst et al. title: New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics link: https://peerj.com/articles/11019 last-modified: 2021-03-31 description: Despite many bioinformatic solutions for analyzing sequencing data, few options exist for targeted sequence retrieval from whole genomic sequencing (WGS) data with the ultimate goal of generating a phylogeny. Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, which may increase rates of false positive results. Many tools are also difficult to install and may lack adequate user resources. Here, we describe a program that uses freely available similarity search tools to find homologs in assembled WGS data with unparalleled freedom to modify parameters. We evaluate its performance compared to other commonly used bioinformatics tools on two divergent insect species (>200 My) for which annotated genomes exist, and on one large set each of highly conserved and more variable loci. Our software is capable of retrieving orthologs from well-curated or unannotated, low or high depth shotgun, and target capture assemblies as well or better than other software as assessed by recovering the most genes with maximal coverage and with a low rate of false positives throughout all datasets. When assessing this combination of criteria, ALiBaSeq is frequently the best evaluated tool for gathering the most comprehensive and accurate phylogenetic alignments on all types of data tested. The software (implemented in Python), tutorials, and manual are freely available at https://github.com/AlexKnyshov/alibaseq. creator: Alexander Knyshov creator: Eric R.L. Gordon creator: Christiane Weirauch uri: https://doi.org/10.7717/peerj.11019 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Knyshov et al. title: Learning to perform role-filler binding with schematic knowledge link: https://peerj.com/articles/11046 last-modified: 2021-03-31 description: Through specific experiences, humans learn the relationships that underlie the structure of events in the world. Schema theory suggests that we organize this information in mental frameworks called “schemata,” which represent our knowledge of the structure of the world. Generalizing knowledge of structural relationships to new situations requires role-filler binding, the ability to associate specific “fillers” with abstract “roles.” For instance, when we hear the sentence Alice ordered a tea from Bob, the role-filler bindings customer:Alice, drink:tea and barista:Bob allow us to understand and make inferences about the sentence. We can perform these bindings for arbitrary fillers—we understand this sentence even if we have never heard the names Alice, tea, or Bob before. In this work, we define a model as capable of performing role-filler binding if it can recall arbitrary fillers corresponding to a specified role, even when these pairings violate correlations seen during training. Previous work found that models can learn this ability when explicitly told what the roles and fillers are, or when given fillers seen during training. We show that networks with external memory learn to bind roles to arbitrary fillers, without explicitly labeled role-filler pairs. We further show that they can perform these bindings on role-filler pairs that violate correlations seen during training, while retaining knowledge of training correlations. We apply analyses inspired by neural decoding to interpret what the networks have learned. creator: Catherine Chen creator: Qihong Lu creator: Andre Beukers creator: Christopher Baldassano creator: Kenneth A. Norman uri: https://doi.org/10.7717/peerj.11046 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: Post-emergence seedling damage due to vertebrate pests and its impact on soybean establishment link: https://peerj.com/articles/11106 last-modified: 2021-03-31 description: The quality of field crop establishment is an indicator of the productivity and yield quality of a given crop. Several biotic and abiotic factors, as well as cropping practices, affect the quality of field crop establishment. More specifically to soybean, recent studies quantified pre-emergence seedling losses and identified the associated causes of non-emergence. However, little is known about post-emergence seedling damage, mainly due to vertebrate pests, which represent an important problem for growers. A 2-year field observation was conducted to quantify near- and post-emergence seedling damage due to vertebrate pests. The common wood pigeon (Columba palumbus) and the European hare (Lepus europaeus) were associated with this kind of damage. The characteristic damage due to the common wood pigeon consisted of either partially-damaged cotyledons during emergence or completely uprooted seedlings at emergence. In contrast, damage due to the European hare consisted of chewed seedling or seedling parts. There was significant effect of year (p < 0.001) on the final rates of post-emergence seedling damage due to the wood pigeon but not on those due to the European hare. The final rates of post-emergence damage due to the wood pigeon were higher (32% for 2018 and 22% for 2020) compared with those owing to the European hare (18% for 2018 and 17% for 2020). The severity of damage due to vertebrate pests was related to the type of seedling damage that, in turn, affected the capacity of soybean to compensate for post-emergence seedling damage. creator: Jay Ram Lamichhane uri: https://doi.org/10.7717/peerj.11106 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Lamichhane title: Ameliorative effect of apelin-13 against renal complications in L-NAME-induced preeclampsia in rats link: https://peerj.com/articles/11110 last-modified: 2021-03-31 description: Pre-eclampsia (PE) accompanying acute liver and kidney injury has remained a master cause of both fetal and maternal mortality and morbidity. Vasoactive mediators, oxidative stress and inflammatory imbalanceshave an important role in PE pathogenesis. Apelin is an adipokine that improves endothelial dysfunction; has anti-inflammatory and antioxidant effects; moreover, its level reduced during PE. This study aimed to explore the effects of apelin-13 administration on preeclampsia-associated renal dysfunction and proteinuria. Thirty-three pregnant female rats were divided into three groups; group: 1 (normal pregnant rats), group: 2 (preeclamptic rats); where rats were injected subcutaneously with 75 mg L-NAME/ kg body weight/day beginning from 9th to 20th day of pregnancy andgroup 3 (apelin-13 treated preeclamptic rats); In which L-NAME-induced preeclamptic rats were subcutaneously injected with 6 × 10−8 mol apelin-13/kg body weight/twice daily starting from 6th to 20th day of pregnancy. In all groups, mean arterial blood pressure, total urine protein, serum urea, creatinine, nitric oxide (NO), endothelin-1 (ET-1), interleukin–6 (IL-6) and malondialdhyde (MDA) were measured. Histopathological examination of kidney tissues was also done. preeclamptic rats showed significantly increased mean arterial blood pressure, total urine proteins, serum urea, creatinine, ET-1, IL-6, and MDA, but revealed a significantly decreased serum NO level. On the other hand, apelin treatment significantly improved these parameters together with amelioration of kidney histoarchitecture in the treated group. In conclusion, apelin may be a potentially curative candidate for prohibiting kidney damage and have a therapeutic benefit in PE rat models. creator: Reham Z. Hamza creator: Abdel Aziz A. Diab creator: Mansour H. Zahra creator: Ali K. Asalah creator: Mai S. Attia creator: Suzan MM Moursi uri: https://doi.org/10.7717/peerj.11110 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Hamza et al. title: Ligninolytic activity of the Penicillium chrysogenum and Pleurotus ostreatus fungi involved in the biotransformation of synthetic multi-walled carbon nanotubes modify its toxicity link: https://peerj.com/articles/11127 last-modified: 2021-03-31 description: Multi-walled carbon nanotubes (MWCNTs) are of multidisciplinary scientific interest due to their exceptional physicochemical properties and a broad range of applications. However, they are considered potentially toxic nanoparticles when they accumulate in the environment. Given their ability to oxidize resistant polymers, mycorremediation with lignocellulolytic fungi are suggested as biological alternatives to the mineralization of MWCNTs. Hence, this study involves the ability of two fungi specie to MWCNTs biotransformation by laccase and peroxidases induction and evaluation in vivo of its toxicity using Caenorhabditis elegans worms as a model. Results showed that the fungi Penicillium chrysogenum and Pleurotus ostreatus were capable to grow on media with MWCNTs supplemented with glucose or lignin. Activities of lignin-peroxidase, manganese-peroxidase, and laccase in cultures of both fungi were induced by MWCNTs. Raman, FTIR spectroscopy, HR-TEM, and TGA analyses of the residue from the cultures of both fungi revealed structural modifications on the surface of MWCNTs and its amount diminished, correlating the MWCNTs structural modifications with the laccase-peroxidase activities in the fungal cultures. Results indicate that the degree of toxicity of MWCNTs on the C. elegans model was enhanced by the structure modification associated with the fungal ligninolytic activity. The toxic effect of MWCNTs on the in vivo model of worms reveals the increment of reactive oxygen species as a mechanism of toxicity. Findings indicate that the MWCNTs can be subject in nature to biotransformation processes such as the fungal metabolism, which contribute to modify their toxicity properties on susceptible organisms and contributing to environmental elimination. creator: Gladys Juárez-Cisneros creator: Jesús Campos-García creator: Sharel Pamela Díaz-Pérez creator: Javier Lara-Romero creator: Dhirendra Kumar Tiwari creator: Juan Manuel Sánchez-Yáñez creator: Homero Reyes-De la Cruz creator: Sergio Jiménez-Sandoval creator: Javier Villegas uri: https://doi.org/10.7717/peerj.11127 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Juárez-Cisneros et al. title: Nutritional content of Totoaba macdonaldi (Gilbert, 1890), Antioxidants and lipid peroxidation in muscle link: https://peerj.com/articles/11129 last-modified: 2021-03-31 description: BackgroundTotoaba, Totoaba macdonaldi, is an endemic species of the Gulf of California, where wide variations in sea temperature throughout the year, surface salinities that gradually increase towards the north, and contamination by discharge of wastewater have been recorded. In addition to the challenges of reproduction and swimming, its characteristic biannual migration presents totoaba with changes in environmental factors that could affect oxidative stress indicators. The objective of this study was to assess spatial and seasonal changes in the oxidative stress indicators in muscle samples of totoaba.MethodsReactive oxygen species production, antioxidant enzyme activities and lipid peroxidation levels were quantified by spectrophotometry.ResultsResults suggest spatial-temporal variations of the oxidative stress indicators in muscle of totoaba that may be associated to a complex interaction between environmental and biological factors, including reproduction and nutrient availability. These results contribute to explain the appeal of totoaba as a marketable meat and suggest totoaba may provide antioxidant nutrients to consumers. creator: Priscila Conde-Guerrero creator: Lia C. Méndez-Rodríguez creator: Juan A. de Anda-Montañez creator: Tania Zenteno-Savín uri: https://doi.org/10.7717/peerj.11129 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Conde-Guerrero et al. title: Comparison of metastatic castration-resistant prostate cancer in bone with other sites: clinical characteristics, molecular features and immune status link: https://peerj.com/articles/11133 last-modified: 2021-03-31 description: Metastatic castration-resistant prostate cancer (mCRPC) is the lethal stage and the leading cause of death in prostate cancer patients, among which bone metastasis is the most common site. Here in this article, we downloaded the gene expression data and clinical information from online dataset. We found that prostate cancer metastasis in bone is prone to have higher prostate-specific antigen (PSA) and longer time on first-line androgen receptor signaling inhibitors (ARSI). A total of 1,263 differentially expressed genes (DEGs) were identified and results of functional enrichment analysis indicated the enrichment in categories related to cell migration, cancer related pathways and metabolism. We identified the top 20 hub genes from the PPI network and analyzed the clinical characteristics correlated with these hub genes. Finally, we analyzed the immune cell abundance ratio of each sample in different groups. Our results reveal the different clinical characteristics, the immune cell infiltration pattern in different sites of mCRPC, and identify multiple critical related genes and pathways, which provides basis for individualized treatment. creator: Zhengquan Xu creator: Yanhong Ding creator: Wei Lu creator: Ke Zhang creator: Fei Wang creator: Guanxiong Ding creator: Jianqing Wang uri: https://doi.org/10.7717/peerj.11133 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: Transcriptome analysis revealed gene regulatory network involved in PEG-induced drought stress in Tartary buckwheat (Fagopyrum Tararicum) link: https://peerj.com/articles/11136 last-modified: 2021-03-31 description: Tartary buckwheat is a nutritious pseudo-cereal crop that is resistant to abiotic stresses, such as drought. However, the buckwheat’s mechanisms for responding to drought stress remains unknown. We investigated the changes in physiology and gene expression under drought stress, which was simulated by treatment with polyethylene glycol (PEG). Five physiological indexes, namely MDA content, H2O2 content, CAT activity, SOD activity, and POD activity, were measured over time after 20% PEG treatment. All indexes showed dramatic changes in response to drought stress. A total of 1,190 differentially expressed genes (DEGs) were identified using RNA-seq and the most predominant were related to a number of stress-response genes and late embryogenesis abundant (LEA) proteins. DEGs were gathered into six clusters and were found to be involved in the ABA biosynthesis and signal pathway based on hierarchical clustering and GO and KEGG pathway enrichment. Transcription factors, such as NAC and bZIP, also took part in the response to drought stress. We determined an ABA-dependent and ABA-independent pathway in the regulation of drought stress in Tartary buckwheat. To the best of our knowledge, this is the first transcriptome analysis of drought stress in Tartary buckwheat, and our results provide a comprehensive gene regulatory network of this crop in response to drought stress. creator: Juan Huang creator: Qijiao Chen creator: Yuping Rong creator: Bin Tang creator: Liwei Zhu creator: Rongrong Ren creator: Taoxiong Shi creator: Qingfu Chen uri: https://doi.org/10.7717/peerj.11136 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Huang et al. title: Systematic analysis of JmjC gene family and stress­-response expression of KDM5 subfamily genes in Brassica napus link: https://peerj.com/articles/11137 last-modified: 2021-03-31 description: BackgroundJumonji C (JmjC) proteins exert critical roles in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization by Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean. In JmjC proteins of Brassica species, the structure and function and its relationship with the parents and model plant Arabidopsis thaliana remain uncharacterized. Systematic identification and analysis for JmjC family in Brassica crops can facilitate the future functional characterization and oilseed crops improvement.MethodsBasing on the conserved JmjC domain, JmjC homologs from the three Brassica species, B. rapa (AA), B. oleracea (CC) and B. napus, were identified from the Brassica database. Some methods, such as phylogenic analysis, chromosomal mapping, HMMER searching, gene structure display and Logos analysis, were used to characterize relationships of the JmjC homologs. Synonymous and nonsynonymous nucleotide substitutions were used to infer the information of gene duplication among homologs. Then, the expression levels of BnKDM5 subfamily genes were checked under abiotic stress by qRT-PCR.ResultsSixty-five JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades based on the phylogenetic analysis, and their catalytic activities of demethylation were predicted. The average retention rate of B. napus JmjC genes (B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%)) exceeded whole genome level. JmjC sequences demonstrated high conservation in domain origination, chromosomal location, intron/exon number and catalytic sites. The gene duplication events were confirmed among the homologs. Many of the BrKDM5 subfamily genes showed higher expression under drought and NaCl treatments, but only a few genes were involved in high temperature stress.ConclusionsThis study provides the first genome-wide characterization of JmjC genes in Brassica species. The BnJmjC exhibits higher conservation during the formation process of allotetraploid than the average retention rates of the whole B. napus genome. Furthermore, expression profiles of many genes indicated that BnKDM5 subfamily genes are involved in stress response to salt, drought and high temperature. creator: Xinghui He creator: Qianwen Wang creator: Jiao Pan creator: Boyu Liu creator: Ying Ruan creator: Yong Huang uri: https://doi.org/10.7717/peerj.11137 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 He et al. title: Research progress on the application of feed additives in ruminal methane emission reduction: a review link: https://peerj.com/articles/11151 last-modified: 2021-03-31 description: BackgroundRuminal methane (CH4) emissions from ruminants not only pollute the environment and exacerbate the greenhouse effect, but also cause animal energy losses and low production efficiency. Consequently, it is necessary to find ways of reducing methane emissions in ruminants. Studies have reported that feed additives such as nitrogen-containing compounds, probiotics, prebiotics, and plant extracts significantly reduce ruminant methane; however, systematic reviews of such studies are lacking. The present article summarizes research over the past five years on the effects of nitrogen-containing compounds, probiotics, probiotics, and plant extracts on methane emissions in ruminants. The paper could provide theoretical support and guide future research in animal production and global warming mitigation.MethodsThis review uses the Web of Science database to search keywords related to ruminants and methane reduction in the past five years, and uses Sci-Hub, PubMed, etc. as auxiliary searchers. Read, filter, list, and summarize all the retrieved documents, and finally complete this article.ResultsMost of the extracts can not only significantly reduce CH4 greenhouse gas emissions, but they will not cause negative effects on animal and human health either. Therefore, this article reviews the mechanisms of CH4 production in ruminants and the application and effects of N-containing compounds, probiotics, prebiotics, and plant extracts on CH4 emission reduction in ruminants based on published studies over the past 5 years.ConclusionOur review provides a theoretical basis for future research and the application of feed additives in ruminant CH4 emission reduction activities. creator: Kang Sun creator: Huihui Liu creator: Huiyu Fan creator: Ting Liu creator: Chen Zheng uri: https://doi.org/10.7717/peerj.11151 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sun et al. title: The classification of EEG-based winking signals: a transfer learning and random forest pipeline link: https://peerj.com/articles/11182 last-modified: 2021-03-31 description: Brain Computer-Interface (BCI) technology plays a considerable role in the control of rehabilitation or peripheral devices for stroke patients. This is particularly due to their inability to control such devices from their inherent physical limitations after such an attack. More often than not, the control of such devices exploits electroencephalogram (EEG) signals. Nonetheless, it is worth noting that the extraction of the features and the classification of the signals is non-trivial for a successful BCI system. The use of Transfer Learning (TL) has been demonstrated to be a powerful tool in the extraction of essential features. However, the employment of such a method towards BCI applications, particularly in regard to EEG signals, are somewhat limited. The present study aims to evaluate the effectiveness of different TL models in extracting features for the classification of wink-based EEG signals. The extracted features are classified by means of fine-tuned Random Forest (RF) classifier. The raw EEG signals are transformed into a scalogram image via Continuous Wavelet Transform (CWT) before it was fed into the TL models, namely InceptionV3, Inception ResNetV2, Xception and MobileNet. The dataset was divided into training, validation, and test datasets, respectively, via a stratified ratio of 60:20:20. The hyperparameters of the RF models were optimised through the grid search approach, in which the five-fold cross-validation technique was adopted. The optimised RF classifier performance was compared with the conventional TL-based CNN classifier performance. It was demonstrated from the study that the best TL model identified is the Inception ResNetV2 along with an optimised RF pipeline, as it was able to yield a classification accuracy of 100% on both the training and validation dataset. Therefore, it could be established from the study that a comparable classification efficacy is attainable via the Inception ResNetV2 with an optimised RF pipeline. It is envisaged that the implementation of the proposed architecture to a BCI system would potentially facilitate post-stroke patients to lead a better life quality. creator: Jothi Letchumy Mahendra Kumar creator: Mamunur Rashid creator: Rabiu Muazu Musa creator: Mohd Azraai Mohd Razman creator: Norizam Sulaiman creator: Rozita Jailani creator: Anwar P.P. Abdul Majeed uri: https://doi.org/10.7717/peerj.11182 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mahendra Kumar et al. title: Aggressiveness-related behavioural types in the pearly razorfish link: https://peerj.com/articles/10731 last-modified: 2021-03-30 description: Behavioural types (i.e., personalities or temperament) are defined as among individual differences in behavioural traits that are consistent over time and ecological contexts. Behavioural types are widespread in nature and play a relevant role in many ecological and evolutionary processes. In this work, we studied for the first time the consistency of individual aggressiveness in the pearly razorfish, Xyrichtys novacula, using a mirror test: a classic method to define aggressive behavioural types. The experiments were carried out in semi-natural behavioural arenas and monitored through a novel Raspberry Pi-based recording system. The experimental set up allowed us to obtain repeated measures of individual aggressivity scores during four consecutive days. The decomposition of the phenotypic variance revealed a significant repeatability score (R) of 0.57 [0.44–0.60], suggesting high predictability of individual behavioural variation and the existence of different behavioural types. Aggressive behavioural types emerged irrespective of body size, sex and the internal condition of the individual. Razorfishes are a ubiquitous group of fish species that occupy sedimentary habitats in most shallow waters of temperate and tropical seas. These species are known for forming strong social structures and playing a relevant role in ecosystem functioning. Therefore, our work provides novel insight into an individual behavioural component that may play a role in poorly known ecological and evolutionary processes occurring in this species. creator: Martina Martorell-Barceló creator: Júlia Mulet creator: Javier Sanllehi creator: Marco Signaroli creator: Arancha Lana creator: Margarida Barcelo-Serra creator: Eneko Aspillaga creator: Josep Alós uri: https://doi.org/10.7717/peerj.10731 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Martorell-Barceló et al. title: Combined use of Bacillus strains and Miscanthus for accelerating biodegradation of poly(lactic acid) and poly(ethylene terephthalate) link: https://peerj.com/articles/10957 last-modified: 2021-03-30 description: BackgroundThe aim of this study was to verify whether the presence of Bacillus strains and of miscanthus influence biodegradation and formed of biofilm of poly(lactic acid) (PLA) and poly(ethylene terephthalate) (PET).MethodsThe experiment conducted in compost soil showed that strains Bacillus subtilis and Bacillus cereus isolated from heavy metal contaminated environment have biochemical activity and accelerate biodegradation of both plastic materials.ResultsFor PLA film it was found that the carbonyl index dropped by over 15% in the presence of B. subtilis, while the film tensile strength decreased by 35% and the oxygen to carbon O/C ratio was higher by 3% in the presence of B. cereus, and the presence of miscanthus resulted in a loss of weight. For PET film, a decrease in the carbonyl index by 16% was observed following inoculation with B. cereus. The metabolic activity of this strain contributed to the reduction of the film’s tensile strength by 17% and to the increase in the permeability to O2 and CO2. The most intense degradation of PET film was observed in the presence of bacteria and plants. B. subtilis strain combined with miscanthus plantings may be a promising method for accelerating PLA and PET degradation in compost soil. creator: Grażyna B. Dąbrowska creator: Katarzyna Janczak creator: Agnieszka Richert uri: https://doi.org/10.7717/peerj.10957 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dąbrowska et al. title: Stimulus–response complexity influences task-set inhibition in task switching link: https://peerj.com/articles/10988 last-modified: 2021-03-30 description: Previous studies have found that inhibiting a task set plays an important role in task switching. However, the impact of stimulus–response (S–R) complexity on this inhibition processing has not been explored. In this study, we applied the backward inhibition paradigm (switching between tasks A, B, and C, presented in sets of three) in order to investigate inhibition performance under different S–R complexities caused by corresponding S–R mappings. The results showed that the difficult condition resulted in a greater switch cost than the moderate and easy conditions. Furthermore, we found a significant n−2 repetition cost under the easy S–R complexity that was reversed under the difficult S–R complexity. To verify stability of the reversed n−2 repetition cost in the difficult condition, we recruited another independent sample to conduct an additional experiment with the difficult condition. These results replicated the reversed n−2 repetition cost. These findings suggest that S–R complexity affects task-set inhibition in task switching because the effect of the task-set inhibition was insignificant when the S–R complexity increased; it was only significant under the easy condition. This result was caused by the different cognitive resource assignments. creator: Li Zhao creator: Saisai Hu creator: Yingying Xia creator: Jinyu Li creator: Jingjing Zhao creator: Ya Li creator: Yonghui Wang uri: https://doi.org/10.7717/peerj.10988 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhao et al. title: In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci link: https://peerj.com/articles/11059 last-modified: 2021-03-30 description: Vancomycin-resistant enterococci (VRE) are a serious public health threat and a leading cause of healthcare-associated infections. Bacterial resistance to antibiotics recommended for the treatment of enterococcal infections complicates the management of these infections. Hence, there is a critical need for the discovery of new anti-VRE agents. We previously reported carbonic anhydrase inhibitors (CAIs) as new potent VRE inhibitors. In the present study, the activity of the CAI, dorzolamide was evaluated against VRE both in vitro and in vivo. Dorzolamide exhibited potent activity against a panel of clinical VRE isolates, with minimum inhibitory concentration (MIC) values ranging from 1 µg/mL to 8 µg/mL. A killing kinetics experiment determined that dorzolamide exhibited a bacteriostatic effect against VRE, which was similar to the drug of choice (linezolid). Dorzolamide interacted synergistically with gentamicin against four strains of VRE, and exhibited an additive interaction with gentamicin against six VRE strains, reducing gentamicin’s MIC by several folds. Moreover, dorzolamide outperformed linezolid in an in vivo VRE colonization reduction mouse model. Dorzolamide significantly reduced the VRE burden in fecal samples of mice by 2.9-log10 (99.9%) and 3.86-log10 (99.99%) after 3 and 5 days of treatment, respectively. Furthermore, dorzolamide reduced the VRE count in the cecal (1.74-log10 (98.2%) reduction) and ileal contents (1.5-log10 (96.3%)) of mice, which was superior to linezolid. Collectively, these results indicate that dorzolamide represents a promising treatment option that warrants consideration as a supplement to current therapeutics used for VRE infections. creator: Nader S. Abutaleb creator: Ahmed E.M. Elhassanny creator: Daniel P. Flaherty creator: Mohamed N. Seleem uri: https://doi.org/10.7717/peerj.11059 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Abutaleb et al. title: Maternal depressive symptoms and early childhood development: the role of mother–child interactions among mother–child dyads in rural areas of Central and Western China link: https://peerj.com/articles/11060 last-modified: 2021-03-30 description: BackgroundThe associations among maternal depressive symptoms (MDS), mother–child interactions and early child development are poorly understood. This study aimed to explore the role of mother–child interactions on the associations between MDS and child development.MethodsA cross-sectional study with a multistage sampling method was conducted in rural areas of Central and Western China. MDS, child development outcomes (communication, gross motor function, fine motor function, problem solving and personal social skills) and mother–child interactions were assessed by The Edinburgh Postpartum Depression Scale, the Chinese version of the Ages and Stages Questionnaires and the Multiple Indicator Cluster Surveys, respectively. Regression-based statistical mediation and moderation were conducted using the PROCESS macro for SPSS.ResultsA total of 2,548 participants (mothers: 1,274; children: 1,274) were included in our analyses. MDS was negatively associated with child development outcomes and mother–child interactions partly mediated these associations. The proportion of the mediating effect of mother–child interactions was 7.7% for communication, 8.2% for gross motor, 10.3% for fine motor, 10.1% for problem-solving and 9.5% for personal social domains. In addition, the interaction effects of MDS and mother–child interactions on the communication domain were significant (β = 0.070, 95% CI 0.016, 0.124; p = 0.011). The associations between MDS and child communication abilities were weaker at the high level (simple slope = −0.019, t =  − 0.458, p = 0.647) of mother–child interactions than at the mean level (simple slope = −0.089, t =  − 3.190, p = 0.002) and the low level (simple slope = −0.158, t =  − 4.231, p < 0.001). Similar moderating effects were not observed in the other child development outcomes.ConclusionOur results suggest the important role of mother–child interactions on the associations between MDS and early childhood development. Due to the cross-sectional design of this study, these associations require further investigation in prospective studies. creator: Xiaoli Liu creator: Chenlu Yang creator: Yuning Yang creator: Xiaona Huang creator: Yinping Wang creator: Yaqing Gao creator: Qiying Song creator: Yan Wang creator: Hong Zhou uri: https://doi.org/10.7717/peerj.11060 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Insomnia partially mediates the relationship between pathological personality traits and depression: a case-control study link: https://peerj.com/articles/11061 last-modified: 2021-03-30 description: Background and ObjectivePersonality disorders are frequently associated with insomnia and depression, but little is known about the inter-relationships among these variables. Therefore, this study examined these inter-relationships and the possible mediating effect of insomnia on the association between specific personality pathologies and depression severity.MethodsThere were 138 study participants, including 69 individuals with depression and 69 healthy controls. The main variables were measured by the Hamilton Depression Rating Scale-24 (HAMD-24), Athens Sleep Insomnia Scale (AIS), and the Personality Diagnostic Questionnaire (PDQ-4+). Multivariate linear regression and mediation analysis were conducted.ResultsWith the exception of the antisocial personality score, all the PDQ-4+ scores and AIS scores were significantly higher in the depression group than in the healthy control group (p < 0.001). In the total sample, all personality pathology scores (p < 0.001), except the antisocial personality score, had significant positive correlations with the AIS scores and HAMD-24 scores, and the AIS scores and HAMD-24 scores were positively correlated (r = 0.620, p < 0.001). Regression analysis revealed that borderline personality, passive-aggressive personality, and insomnia positively predicted the severity of depression, after adjusting for sociodemographic covariates, and that insomnia partially mediated the associations of borderline personality and passive-aggressive personality with depression severity.ConclusionsBorderline personality, passive-aggressive personality, and insomnia tend to increase the severity of depression, and the effect of borderline and passive-aggressive personality on depression severity may be partially mediated by insomnia. This is the first study to report these findings in a Chinese sample, and they may help researchers to understand the pathways from specific personality pathologies to the psychopathology of depression better, which should be useful for designing interventions to relieve depression severity, as the impact of specific personality pathology and insomnia should be considered. creator: Fenglan Chen creator: Xiujin Lin creator: Yuli Pan creator: Xuan Zeng creator: Shengjie Zhang creator: Hong Hu creator: Miaoyu Yu creator: Junduan Wu uri: https://doi.org/10.7717/peerj.11061 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature link: https://peerj.com/articles/11088 last-modified: 2021-03-30 description: Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology. creator: Olivier Zablocki creator: Michelle Michelsen creator: Marie Burris creator: Natalie Solonenko creator: Joanna Warwick-Dugdale creator: Romik Ghosh creator: Jennifer Pett-Ridge creator: Matthew B. Sullivan creator: Ben Temperton uri: https://doi.org/10.7717/peerj.11088 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zablocki et al. title: AbhemC encoding porphobilinogen deaminase plays an important role in chlorophyll biosynthesis and function in albino Ananas comosus var. bracteatus leaves link: https://peerj.com/articles/11118 last-modified: 2021-03-30 description: BackgroundThe chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts (Grs) and albino white parts (Whs). Although the underlying mechanism of albinism in A. comosus var. bracteatus leaves is not fully understood, it is likely associated with the chlorophyll (Chl) biosynthesis. In this biosynthetic process, porphobilinogen deaminase (PBGD) plays a crucial role by catalyzing the conversion of porphobilinogen (PBG) to uroporphyrinogen III (Urogen III). Therefore, its encoding gene AbhemC was investigated here in association with Chl biosynthesis and albinism in chimeric A. comosus var. bracteatus leaves.MethodsThe Chl content, main Chl biosynthesis precursor content, and main enzyme activity were determined and compared between the Whs and Grs of A. comosus var. bracteatus leaves. In addition, AbhemC was cloned and its transcriptional expression and prokaryotic protein expression were analyzed. Furthermore, RNAi-mediated silencing of AbhemC was produced and assessed in tobacco plants.ResultsThe concentration of Chl a and Chl b in the Grs was significantly higher than that in the Whs, respectively. Additionally, the content of the Chl biosynthesis precursor Urogen III decreased significantly in the Whs compared with the Grs. Thus, the transition of PBG to Urogen III may be the first rate-limiting step leading to albinism in the chimeric leaves of A. comosus var. bracteatus. The gene AbhemC comprised 1,135 bp and was encoded into a protein with 371 amino acids; phylogenetically, AbhemC was most closely related to hemC of pineapple. Prokaryotic expression and in vitro enzyme activity analysis showed that the cloned mRNA sequence of AbhemC was successfully integrated and had PBGD activity. Compared with control plants, transgenic tobacco leaves with pFGC5941-AbhemC-RNAi vector were substantially less green with significantly reduced hemC expression and Chl content, as well as reduced PBGD enzyme activity and significantly decreased content of Chl biosynthesis precursors from Urogen III onwards. Our results suggest that the absence of hemC expression reduces the enzyme activity of PBGD, which blocks the transition of PBG to Urogen III, and in turn suppresses Chl synthesis leading to the pale-green leaf color. Therefore, we suggest that AbhemC plays an important role in Chl synthesis and may be an important factor in the albinism of A. comosus var. bracteatus leaves. creator: Yanbin Xue creator: Xia Li creator: Meiqin Mao creator: Yehua He creator: Mark Owusu Adjei creator: Xuzixin Zhou creator: Hao Hu creator: Jiawen Liu creator: Xi Li creator: Jun Ma uri: https://doi.org/10.7717/peerj.11118 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xue et al. title: COL1A1 is a prognostic biomarker and correlated with immune infiltrates in lung cancer link: https://peerj.com/articles/11145 last-modified: 2021-03-30 description: ObjectiveLung cancer (LC) is one of the top ten malignant tumors and the first leading cause of cancer-related death among both men and women worldwide. It is imperative to identify immune-related biomarkers for early LC diagnosis and treatment.MethodsThree Gene Expression Omnibus (GEO) datasets were selected to acquire the differentially expressed genes(DEGs) between LC and normal lung samples through GEO2R tools of NCBI. To identify hub genes, the DEGs were performed functional enrichment analysis, the protein–protein interaction (PPI) network construction, and Lasso regression. Then, a nomogram was constructed to predict the prognosis of patients with carcinoma based on hub genes. We further evaluated the influence of COL1A1 on clinical prognosis using GSE3141, GSE31210, and TCGA database. Also, the correlations between COL1A1 and cancer immune infiltrates and the B7-CD28 family was investigated via TIMER and GEPIA. Further analysis of immunohistochemistry shown that the COL1A1 expression level is positively correlated with CD276 expression level.ResultsBy difference analysis, there were 340 DEGs between LC and normal lung samples. Then, we picked out seven hub genes, which were identified as components of the risk signature to divide LC into low and high-risk groups. Among them, the expression of COL1A1 is highly correlated with overall survival(OS) and progression-free survival (PFS) (p < 0.05). Importantly, there is a moderate to strong positive relationships between COL1A1 expression level and infiltration level of CD4+ T cells, Macrophage, Neutrophil, and Dendritic cell, as well as CD276 expression level.ConclusionThese findings suggest that COL1A1 is correlated with prognosis and immune infiltrating levels, including CD4+ T cells, Macrophage, Neutrophil, and Dendritic cell, as well as CD276 expression level, indicating COL1A1 can be a potential immunity-related biomarker and therapeutic target in LC. creator: Qishun Geng creator: Zhibo Shen creator: Lifeng Li creator: Jie Zhao uri: https://doi.org/10.7717/peerj.11145 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Geng et al. title: COVID-19 simulation study—the effect of strict non-pharmaceutical interventions (NPIs) on controlling the spread of COVID-19 link: https://peerj.com/articles/11172 last-modified: 2021-03-30 description: BackgroundFrom the beginning of 2020, COVID-19 infection has changed our lives in many aspects and introduced limitations in the way people interact and communicate. In this paper, we are evaluating the effect of non-pharmaceutical interventions (NPI) in limiting the spread of the Severe Acute Respiratory Syndrome Coronavirus 2 pandemic during a wedding ceremony from Irbid, Northern Jordan. Agent-based modeling was used in a real wedding event that occurred at the beginning of the spread of the pandemic in Jordan. Two infected nationals of Jordan, who arrived in Jordan about a week before the event, initiated the spread of the pandemic within the contact community.MethodsIn this work, a strict national NPI that the government implemented is developed by using an abstract model with certain characteristics similar to the Jordanian community. Thus, the Jordanian community is represented in terms of ages, occupations, and population movements. After that, the extent of the impact of the NPI measures on the local community is measured.ResultsWe observed the deterioration of the state of society while the epidemic is spreading among individuals in the absence of preventive measures. Also, the results show that the herd immunity case was an epidemic, with a high level of spread among the community with 918 cases during a short interval of time. On the other hand, the preventive measures scenario shows a totally controlled spread with only 74 cases applied on the same interval of time. Furthermore, a convergence in the actual results of the real system with the hypothetical system were detected in the case of applying the strict NPI measures. Finally, strict NPI at the community level following social gatherings seem to be effective measures to control the spread of the COVID- 19 pandemic. creator: Amal Alzu’bi creator: Sanaa Abu Alasal creator: Khalid A. Kheirallah creator: Valerie Watzlaf uri: https://doi.org/10.7717/peerj.11172 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Alzu’bi et al. title: Effectiveness of isolation policies in schools: evidence from a mathematical model of influenza and COVID-19 link: https://peerj.com/articles/11211 last-modified: 2021-03-30 description: BackgroundNon-pharmaceutical interventions such as social distancing, school closures and travel restrictions are often implemented to control outbreaks of infectious diseases. For influenza in schools, the Center of Disease Control (CDC) recommends that febrile students remain isolated at home until they have been fever-free for at least one day and a related policy is recommended for SARS-CoV-2 (COVID-19). Other authors proposed using a school week of four or fewer days of in-person instruction for all students to reduce transmission. However, there is limited evidence supporting the effectiveness of these interventions.MethodsWe introduced a mathematical model of school outbreaks that considers both intervention methods. Our model accounts for the school structure and schedule, as well as the time-progression of fever symptoms and viral shedding. The model was validated on outbreaks of seasonal and pandemic influenza and COVID-19 in schools. It was then used to estimate the outbreak curves and the proportion of the population infected (attack rate) under the proposed interventions.ResultsFor influenza, the CDC-recommended one day of post-fever isolation can reduce the attack rate by a median (interquartile range) of 29 (13–59)%. With 2 days of post-fever isolation the attack rate could be reduced by 70 (55–85)%. Alternatively, shortening the school week to 4 and 3 days reduces the attack rate by 73 (64–88)% and 93 (91–97)%, respectively. For COVID-19, application of post-fever isolation policy was found to be less effective and reduced the attack rate by 10 (5–17)% for a 2-day isolation policy and by 14 (5–26)% for 14 days. A 4-day school week would reduce the median attack rate in a COVID-19 outbreak by 57 (52–64)%, while a 3-day school week would reduce it by 81 (79–83)%. In both infections, shortening the school week significantly reduced the duration of outbreaks.ConclusionsShortening the school week could be an important tool for controlling influenza and COVID-19 in schools and similar settings. Additionally, the CDC-recommended post-fever isolation policy for influenza could be enhanced by requiring two days of isolation instead of one. creator: Adam A.C. Burns creator: Alexander Gutfraind uri: https://doi.org/10.7717/peerj.11211 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Burns and Gutfraind title: Transcriptome-wide and expression analysis of the NAC gene family in pepino (Solanum muricatum) during drought stress link: https://peerj.com/articles/10966 last-modified: 2021-03-29 description: Solanum muricatum (Pepino) is an increasingly popular solanaceous crop and is tolerant of drought conditions. In this study, 71 NAC transcription factor family genes of S. muricatum were selected to provide a theoretical basis for subsequent in-depth study of their regulatory roles in the response to biological and abiotic stresses, and were subjected to whole-genome analysis. The NAC sequences obtained by transcriptome sequencing were subjected to bioinformatics prediction and analysis. Three concentration gradient drought stresses were applied to the plants, and the target gene sequences were analyzed by qPCR to determine their expression under drought stress. The results showed that the S. muricatum NAC family contains 71 genes, 47 of which have conserved domains. The protein sequence length, molecular weight, hydrophilicity, aliphatic index and isoelectric point of these transcription factors were predicted and analyzed. Phylogenetic analysis showed that the S. muricatum NAC gene family is divided into seven subfamilies. Some NAC genes of S. muricatum are closely related to the NAC genes of Solanaceae crops such as tomato, pepper and potato. The seedlings of S. muricatum were grown under different gradients of drought stress conditions and qPCR was used to analyze the NAC expression in roots, stems, leaves and flowers. The results showed that 13 genes did not respond to drought stress while 58 NAC genes of S. muricatum that responded to drought stress had obvious tissue expression specificity. The overall expression levels in the root were found to be high. The number of genes at extremely significant expression levels was very large, with significant polarization. Seven NAC genes with significant responses were selected to analyze their expression trend in the different drought stress gradients. It was found that genes with the same expression trend also had the same or part of the same conserved domain. Seven SmNACs that may play an important role in drought stress were selected for NAC amino acid sequence alignment of Solanaceae crops. Four had strong similarity to other Solanaceae NAC amino acid sequences, and SmNAC has high homology with the Solanum pennellii. The NAC transcription factor family genes of S. muricatum showed strong structural conservation. Under drought stress, the expression of NAC transcription factor family genes of S. muricatum changed significantly, which actively responded to and participated in the regulation process of drought stress, thereby laying foundations for subsequent in-depth research of the specific functions of NAC transcription factor family genes of S. muricatum. creator: Shipeng Yang creator: Haodong Zhu creator: Liping Huang creator: Guangnan Zhang creator: Lihui Wang creator: Xiaoting Jiang creator: Qiwen Zhong uri: https://doi.org/10.7717/peerj.10966 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: Plasma BDNF concentrations and the antidepressant effects of six ketamine infusions in unipolar and bipolar depression link: https://peerj.com/articles/10989 last-modified: 2021-03-29 description: ObjectivesAccumulating evidence has implicated that brain derived neurotrophic factor (BDNF) is thought to be involved in the pathophysiology of depression, but its correlation with ketamine’s antidepressant efficacy focusing on Chinese individuals with depression is not known. This study was aim to determine the correlation of plasma BDNF (pBDNF) concentrations and ketamine’s antidepressant efficacy.MethodsNinety-four individuals with depression received six intravenous infusions ketamine (0.5 mg/kg). Remission and response were defined as Montgomery-Asberg Depression Rating Scale (MADRS) scores less than 10 and a reduction of 50% or more in MADRS scores, respectively. Plasma was collected at baseline and at 24 h and 2 weeks after completing six ketamine infusions (baseline, 13 d and 26 d).ResultsA significant improvement in MADRS scores and pBDNF concentrations was found after completing six ketamine infusions compared to baseline (all ps < 0.05). Higher baseline pBDNF concentrations were found in ketamine responders/remitters (11.0 ± 6.2/10.1 ± 5.8 ng/ml) than nonresponders/nonremitters (8.0 ± 5.5/9.2 ± 6.4 ng/ml) (all ps < 0.05). Baseline pBDNF concentrations were correlated with MADRS scores at 13 d (t =  − 2.011, p = 0.047) or 26 d (t =  − 2.398, p = 0.019) in depressed patients (all ps < 0.05). Subgroup analyses found similar results in individuals suffering from treatment refractory depression.ConclusionThis preliminary study suggests that baseline pBDNF concentrations appeared to be correlated with ketamine’s antidepressant efficacy in Chinese patients with depression. creator: Wei Zheng creator: Yan-Ling Zhou creator: Cheng-Yu Wang creator: Xiao-Feng Lan creator: Bin Zhang creator: Su-Miao Zhou creator: Su Yan creator: Yu-Ping Ning uri: https://doi.org/10.7717/peerj.10989 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zheng et al. title: Incorporation of feeding functional group information informs explanatory patterns of long-term population changes in fish assemblages link: https://peerj.com/articles/11032 last-modified: 2021-03-29 description: The objective of this study was to evaluate long term trends of fish taxa in southern Lake Michigan while incorporating their functional roles to improve our understanding of ecosystem level changes that have occurred in the system over time. The approach used here highlighted the ease of incorporating ecological mechanisms into population models so researchers can take full advantage of available long-term ecosystem information. Long term studies of fish assemblages can be used to inform changes in community structure resulting from perturbations to aquatic systems and understanding these changes in fish assemblages can be better contextualized by grouping species according to functional groups that are grounded in niche theory. We hypothesized that describing the biological process based on partial pooling of information across functional groups would identify shifts in fish assemblages that coincide with major changes in the ecosystem (e.g., for this study, shifts in zooplankton abundance over time). Herein, we analyzed a long-term Lake Michigan fisheries dataset using a multi-species state space modeling approach within a Bayesian framework. Our results suggested the population growth rates of planktivores and benthic invertivores have been more variable than general invertivores over time and that trends in planktivores can be partially explained by ecosystem changes in zooplankton abundance. Additional work incorporating more ecosystem parameters (e.g., primary production, etc.) should be incorporated into future iterations of this novel modeling concept. creator: Jason C. Doll creator: Stephen J. Jacquemin uri: https://doi.org/10.7717/peerj.11032 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Doll and Jacquemin title: A taxonomically detailed and large-scale view of the factors affecting the distribution and abundance of tree species planted in private gardens of Christchurch city, New Zealand link: https://peerj.com/articles/10588 last-modified: 2021-03-26 description: A city’s planted trees, the great majority of which are in private gardens, play a fundamental role in shaping a city’s wild ecology, ecosystem functioning, and ecosystem services. However, studying tree diversity across a city’s many thousands of separate private gardens is logistically challenging. After the disastrous 2010–2011 earthquakes in Christchurch, New Zealand, over 7,000 homes were abandoned and a botanical survey of these gardens was contracted by the Government’s Canterbury Earthquake Recovery Authority (CERA) prior to buildings being demolished. This unprecedented access to private gardens across the 443.9 hectares ‘Residential Red Zone’ area of eastern Christchurch is a unique opportunity to explore the composition of trees in private gardens across a large area of a New Zealand city. We analysed these survey data to describe the effects of housing age, socio-economics, human population density, and general soil quality, on tree abundance, species richness, and the proportion of indigenous and exotic species. We found that while most of the tree species were exotic, about half of the individual trees were local native species. There is an increasing realisation of the native tree species values among Christchurch citizens and gardens in more recent areas of housing had a higher proportion of smaller/younger native trees. However, the same sites had proportionately more exotic trees, by species and individuals, amongst their larger planted trees than older areas of housing. The majority of the species, and individuals, of the larger (≥10 cm DBH) trees planted in gardens still tend to be exotic species. In newer suburbs, gardens in wealthy areas had more native trees than gardens from poorer areas, while in older suburbs, poorer areas had more native big trees than wealthy areas. In combination, these describe, in detail unparalleled for at least in New Zealand, how the tree infrastructure of the city varies in space and time. This lays the groundwork for better understanding of how wildlife distribution and abundance, wild plant regeneration, and ecosystem services, are affected by the city’s trees. creator: Wei Quan creator: Jon J. Sullivan creator: Colin D. Meurk creator: Glenn H. Stewart uri: https://doi.org/10.7717/peerj.10588 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Quan et al. title: The prospective COVID-19 vaccine: willingness to pay and perception of community members in Ibadan, Nigeria link: https://peerj.com/articles/11153 last-modified: 2021-03-26 description: BackgroundThe introduction of the COVID-19 vaccine necessitates the assessment of individual perception regarding the vaccine. This study aimed to assess the perception of community members and willingness to pay for the prospective COVID-19 vaccine in Ibadan, Nigeria.MethodsA descriptive cross-sectional study design was used. Data were collected using an interviewer-administered questionnaire in September 2020. We studied community members aged 15 years and above using a multi-stage sampling technique. The perceptions of respondents about the COVID-19 vaccine were assessed on eight questions using the five-point Likert scale with a score point of “1” assigned for “Strongly Agree”, “2” for “Agree”, “3” for “Not decided”, “4” for “Disagree”, and “5” for “Strongly disagree”. During analysis, we reverse-coded the options by assigning a point of “1” for “Strongly disagree”, “2” for “Disagree”, “3” for “Not decided”, “4” for “Agree”, and “5” for “Strongly disagree”. However, questions asked in the negative directions were not reverse-coded during analysis. Eight questions were used to assess the perception of community members regarding the prospective COVID-19 vaccine, and overall, the maximum point was 40. Points greater than or equal to 32 points (80%) implied positive perception. Descriptive statistics were done. Chi-square tests were used for the assessment of associations between sociodemographic characteristics and willingness to pay for the prospective COVID-19 vaccine. We conducted logistic regression tests on statistically significant variables at p-values <0.05.ResultsThe mean age of the 440 respondents studied was 37.22 ± 15.36 years, 193 (49.00%) were males, and 292 (67.30%) of the respondents had heard of the prospective COVID-19 vaccine. Among them, 232 (79.50%) respondents had positive perception regarding COVID-19 vaccine. Individuals in the fifth wealth quintile were ten times more likely to be willing to pay for the prospective COVID-19 vaccine compared to those in the first wealth quintile (Adjusted Odds Ratio = 9.57, 95% CI [2.88–31.82], p = <0.01).ConclusionThe prospective COVID-19 vaccine should be subsidized or made freely available to everyone. creator: Olayinka Ilesanmi creator: Aanuoluwapo Afolabi creator: Obioma Uchendu uri: https://doi.org/10.7717/peerj.11153 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ilesanmi et al. title: The disturbance leg-lift response (DLR): an undescribed behavior in bumble bees link: https://peerj.com/articles/10997 last-modified: 2021-03-25 description: BackgroundBumble bees, primarily Bombus impatiens and B. terrestris, are becoming increasingly popular organisms in behavioral ecology and comparative psychology research. Despite growing use in foraging and appetitive conditioning experiments, little attention has been given to innate antipredator responses and their ability to be altered by experience. In this paper, we discuss a primarily undescribed behavior, the disturbance leg-lift response (DLR). When exposed to a presumably threatening stimulus, bumble bees often react by lifting one or multiple legs. We investigated DLR across two experiments.MethodsIn our first experiment, we investigated the function of DLR as a prerequisite to later conditioning research. We recorded the occurrence and sequence of DLR, biting and stinging in response to an approaching object that was either presented inside a small, clear apparatus containing a bee, or presented directly outside of the subject’s apparatus. In our second experiment, we investigated if DLR could be altered by learning and experience in a similar manner to many other well-known bee behaviors. We specifically investigated habituation learning by repeatedly presenting a mild visual stimulus to samples of captive and wild bees.ResultsThe results of our first experiment show that DLR and other defensive behaviors occur as a looming object approaches, and that the response is greater when proximity to the object is lower. More importantly, we found that DLR usually occurs first, rarely precedes biting, and often precedes stinging. This suggests that DLR may function as a warning signal that a sting will occur. In our second experiment, we found that DLR can be altered as a function of habituation learning in both captive and wild bees, though the captive sample initially responded more. This suggests that DLR may be a suitable response for many other conditioning experiments. creator: Christopher A. Varnon creator: Noelle Vallely creator: Charlie Beheler creator: Claudia Coffin uri: https://doi.org/10.7717/peerj.10997 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Varnon et al. title: Large-scale movements of common bottlenose dolphins in the Atlantic: dolphins with an international courtyard link: https://peerj.com/articles/11069 last-modified: 2021-03-25 description: Wide-ranging connectivity patterns of common bottlenose dolphins (Tursiops truncatus) are generally poorly known worldwide and more so within the oceanic archipelagos of Macaronesia in the North East (NE) Atlantic. This study aimed to identify long-range movements between the archipelagos of Macaronesia that lie between 500 and 1,500 km apart, and between Madeira archipelago and the Portuguese continental shelf, through the compilation and comparison of bottlenose dolphin’s photo-identification catalogues from different regions: one from Madeira (n = 363 individuals), two from different areas in the Azores (n = 495 and 176), and four from different islands of the Canary Islands (n = 182, 110, 142 and 281), summing up 1791 photographs. An additional comparison was made between the Madeira catalogue and one catalogue from Sagres, on the southwest tip of the Iberian Peninsula (n = 359). Results showed 26 individual matches, mostly between Madeira and the Canary Islands (n = 23), and between Azores and Madeira (n = 3). No matches were found between the Canary Islands and the Azores, nor between Madeira and Sagres. There were no individuals identified in all three archipelagos. The minimum time recorded between sightings in two different archipelagos (≈ 460 km apart) was 62 days. Association patterns revealed that the individuals moving between archipelagos were connected to resident, migrant and transient individuals in Madeira. The higher number of individuals that were re-sighted between Madeira and the Canary Islands can be explained by the relative proximity of these two archipelagos. This study shows the first inter-archipelago movements of bottlenose dolphins in the Macaronesia region, emphasizing the high mobility of this species and supporting the high gene flow described for oceanic dolphins inhabiting the North Atlantic. The dynamics of these long-range movements strongly denotes the need to review marine protected areas established for this species in each archipelago, calling for joint resolutions from three autonomous regions belonging to two EU countries. creator: Ana Dinis creator: Carlota Molina creator: Marta Tobeña creator: Annalisa Sambolino creator: Karin Hartman creator: Marc Fernandez creator: Sara Magalhães creator: Rui Peres dos Santos creator: Fabian Ritter creator: Vidal Martín creator: Natacha Aguilar de Soto creator: Filipe Alves uri: https://doi.org/10.7717/peerj.11069 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dinis et al. title: Effects of functional correction training on injury risk of athletes: a systematic review and meta-analysis link: https://peerj.com/articles/11089 last-modified: 2021-03-25 description: BackgroundWe explored functional correction training using the Functional Movement Screen (FMS™) tool. We also analyzed the effects of training on the injuries of athletes in a systematic review and meta-analysis of non-randomized clinical trials.MethodologyWe collected twenty-four articles from PubMed, CENTRAL, Scopus, ProQuest, Web of Science, EBSCOhost, SPORTDiscus, Embase, WanFang, and CNKI that were published between January 1997 to September 2020. Articles were selected based on the following inclusion criteria: randomized and non-randomized controlled trials, studies with functional correction training screened by FMS™ as the independent variable, and studies with injury risk to the athlete as the dependent variable. Data conditions included the sample size, mean, standard deviation, total FMS™ scores, number of injuries, and asymmetry movement patterns after interventions in the experimental and control groups. Exclusion criteria included: conference abstracts, cross-sectional studies, articles with retrospective study design.ResultsTwelve non-randomized trials were included in the meta-analysis. The injury risk ratio of athletes after functional correction training was 0.39 RR (95 CI [1.50–1.93]; Z = 15.53; P < 0.0001; I2 = 2.6%), indicating an improvement of athletes functional patterns.ConclusionGrade B evidence indicates that functional correction training based on FMS™ may improve the functional patterns of athletes and Grade D evidence indicates that it may reduce the risk of sports injury. However, the true effect is likely to be different from the estimate of the effect. Therefore, further studies are needed to explore the influence of functional correction training on the injury risks of athletes. Protocol registration: CRD42019145287. creator: Junxia Chen creator: Chunhe Zhang creator: Sheng Chen creator: Yuhua Zhao uri: https://doi.org/10.7717/peerj.11089 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Warming resistant corals from the Gulf of Aqaba live close to their cold-water bleaching threshold link: https://peerj.com/articles/11100 last-modified: 2021-03-25 description: Global climate change is causing increasing variability and extremes in weather worldwide, a trend set to continue. In recent decades both anomalously warm and cold seawater temperatures have resulted in mass coral bleaching events. Whilst corals’ response to elevated temperature has justifiably attracted substantial research interest, coral physiology under cold water stress is relatively unfamiliar. The response to below typical winter water temperature was tested for two common reef building species from the Gulf of Aqaba in an ex situ experiment. Stylophora pistillata and Acropora eurystoma were exposed to 1 or 3 °C below average winter temperature and a suite of physiological parameters were assessed. At 3 °C below winter minima (ca. 18.6 °C), both species had significant declines in photosynthetic indices (maximum quantum yield, electron transport rate, saturation irradiance, and photochemical efficiency) and chlorophyll concentration compared to corals at ambient winter temperatures. It was previously unknown that corals at this site live close to their cold-water bleaching threshold and may be vulnerable as climate variability increases in magnitude. In order to determine if a cold winter reduces the known heat resistance of this population, the corals were subsequently exposed to an acute warm period at 30 °C the following summer. Exposed to above typical summer temperatures, both species showed fewer physiological deviations compared to the cold-water stress. Therefore, the cold winter experience did not increase corals’ susceptibility to above ambient summer temperatures. This study provides further support for the selection of heat tolerant genotypes colonising the Red Sea basin and thereby support the mechanism behind the Reef Refuge Hypothesis. creator: Jessica Bellworthy creator: Maoz Fine uri: https://doi.org/10.7717/peerj.11100 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bellworthy and Fine title: Needs of family members of patients admitted to a university hospital critical care unit, Izmir Turkey: comparison of nurse and family perceptions link: https://peerj.com/articles/11125 last-modified: 2021-03-25 description: Purpose:This study aims to compare the perceptions of nurses and families on the needs of the relatives of the patients in Intensive Care Unit (ICU).MethodsThis cross-sectional study was conducted in the ICU of a university hospital. The study comprised 213 critical care patients’ relatives and 54 nurses working in the same ICU. Data were collected using the Turkish version of Critical Care Family Needs Inventory (CCFNI) and a questionnaire on the characteristics of the participants. The difference between the perceptions of families and nurses was analyzed using Student t-test. Results: CCFNI’s assurance/proximity subscale mean scores ranked first among bothpatients and nurses. The item “To be assured the best care possible is being given to the patient” was the top priority for both groups. Mean assurance/proximity and information dimensions of relatives were significantly higher compared to nurses (p < 0.001). No significant difference was found between the perception of patient relatives and nurses related to support and comfort dimensions (p < 0.05).ConclusionThe needs of the relatives of patients are underestimated by nurses. This inhibited the performance of ICU nurses in line with the holistic care approach. Educational objectives that include the needs of ICU patients’ relatives should be incorporated into the undergraduate and in-service training of nurses. Policies should be established to create space and time for effective relative-nurse communication. creator: Sibel Büyükçoban creator: Zehra Mermi Bal creator: Ozlem Oner creator: Necmiye Kilicaslan creator: Necati Gökmen creator: Meltem Ciçeklioğlu uri: https://doi.org/10.7717/peerj.11125 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Büyükçoban et al. title: Genetic signatures of population bottlenecks, relatedness, and inbreeding highlight recent and novel conservation concerns in the Egyptian vulture link: https://peerj.com/articles/11139 last-modified: 2021-03-25 description: The assessment of temporal variation in genetic features can be particularly informative on the factors behind demography and viability of wildlife populations and species. We used molecular methods to evaluate neutral genetic variation, relatedness, bottlenecks, and inbreeding in a declining population of Egyptian vulture (Neophron percnopterus) in central Spain. The results show that the genetic diversity remained relatively stable over a period of twelve years despite the decline in census and effective population sizes in the last decades. A relatively high proportion of nestlings from different and distant territories showed high relatedness in each study year. We also found support for an increasing impact of severe recent (contemporary) rather than distant (historical) past demographic bottlenecks, and the first evidence of inbred mating between full siblings coinciding with lethal malformations in offspring. The inbred nestling with feather malformations was positive to beak and feather disease virus recorded for the first time in this species. These results alert on recent and novel threats potentially affecting health and reducing the adaptive potential of individuals in this threatened species. creator: Guillermo Blanco creator: Francisco Morinha uri: https://doi.org/10.7717/peerj.11139 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Blanco and Morinha title: Integrating morphological and molecular approaches for characterizing four species of Dactylogyrus (Monogenea: Dactylogyridae) from Moroccan cyprinids, with comments on their host specificity and phylogenetic relationships link: https://peerj.com/articles/10867 last-modified: 2021-03-24 description: Cyprinid fishes are known to harbour highly host-specific gill-associated parasites of Dactylogyrus. High similarity in the morphology of sclerotized structures among Dactylogyrus species, especially those parasitizing congeneric cyprinoids, makes their identification difficult. In this paper, four previously known species of Dactylogyrus are characterized and illustrated under a reliable taxonomic framework integrating morphological and molecular evidence, and their phylogenetic relationships are investigated using molecular data. The species are as follows: D. borjensis from Luciobarbus zayanensis; D. draaensis from Luciobarbus lepineyi; D. ksibii from Luciobarbus ksibi and Luciobarbus rabatensis; and D. marocanus from Carasobarbus fritschii, L. ksibi, L. zayanensis and Pterocapoeta maroccana. Our results revealed intraspecific genetic variability among specimens of D. ksibii collected from two different hosts and geographically distant basins. Phylogenetic reconstruction showed that Dactylogyrus spp. parasitizing Moroccan cyprinids are representatives of three main lineages corresponding to morphological differences and host specificity. Our records of D. marocanus on L. zayanensis and P. maroccana increase the range of available host species i.e.,eight species of four cyprinid genera representing two phylogenetic lineages (i.e., Barbinae and Torinae). creator: Eva Řehulková creator: Imane Rahmouni creator: Antoine Pariselle creator: Andrea Šimková uri: https://doi.org/10.7717/peerj.10867 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Řehulková et al. title: LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes link: https://peerj.com/articles/10906 last-modified: 2021-03-24 description: BackgroundComputing genomic similarity between strains is a prerequisite for genome-based prokaryotic classification and identification. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments. Since this is computationally expensive, faster and computationally cheaper alignment-free methods have been developed to estimate ANI. However, these methods do not reach the level of accuracy of alignment-based methods.MethodsHere we introduce LINflow, a computational pipeline that infers pairwise genomic similarity in a set of genomes. LINflow takes advantage of the speed of the alignment-free sourmash tool to identify the genome in a dataset that is most similar to a query genome and the precision of the alignment-based pyani software to precisely compute ANI between the query genome and the most similar genome identified by sourmash. This is repeated for each new genome that is added to a dataset. The sequentially computed ANI values are stored as Life Identification Numbers (LINs), which are then used to infer all other pairwise ANI values in the set. We tested LINflow on four sets, 484 genomes in total, and compared the needed time and the generated similarity matrices with other tools.ResultsLINflow is up to 150 times faster than pyani and pairwise ANI values generated by LINflow are highly correlated with those computed by pyani. However, because LINflow infers most pairwise ANI values instead of computing them directly, ANI values occasionally depart from the ANI values computed by pyani. In conclusion, LINflow is a fast and memory-efficient pipeline to infer similarity among a large set of prokaryotic genomes. Its ability to quickly add new genome sequences to an already computed similarity matrix makes LINflow particularly useful for projects when new genome sequences need to be regularly added to an existing dataset. creator: Long Tian creator: Reza Mazloom creator: Lenwood S. Heath creator: Boris A. Vinatzer uri: https://doi.org/10.7717/peerj.10906 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tian et al. title: Characteristics of the gut microbiome in patients with prediabetes and type 2 diabetes link: https://peerj.com/articles/10952 last-modified: 2021-03-24 description: BackgroundGut microbiome has recently been identified as a new potential risk factor in addition to well-known diabetes risk factors. The aim of this study was to analyze the differences in the composition of gut microbiome in prediabetes(PreDM), type 2 diabetes mellitus (T2DM) and non-diabetic controls.MethodsA total of 180 participants were recruited for this study: 60 with T2DM, 60 with PreDM and 60 non-diabetics (control group). Fecal samples were collected from the participants and genomic DNA was extracted. The composition and diversity of gut microbiome were investigated in fecal DNA samples using Illumina sequencing of the V3∼V4 regions of 16sRNA.ResultsThere were significant differences in the number of bacteria among patients with PreDM and T2DM and the control group. Compared with the control group, Proteobacteria bacteria were significantly higher in the PreDM group (P = 0.006). On the genus level, Compared with the control group, the relative abundance of Prevotella and Alloprevotella was significantly higher in the T2DM group (P = 0.016, P = 0.018), and the relative abundance of Paraprevotella in T2DM and PreDM groups was lower than that in the control group (P = 0.011, P = 0.045). Compared with the PreDM group and the control group, the relative abundance of Bacteroides in the T2DM group was significantly lower (P = 0.019, P = 0.002).ConclusionsThe present study found significant differences in the gut microbiome between PreDM, T2DM and non-diabetic individuals, specifically at the genus level, suggesting that early intervention in PreDM patients could have implications for gut flora transitioning to T2DM. In addition, these results may be valuable for developing strategies to control T2DM by modifying the gut microbiome. creator: Zewen Zhang creator: Tian Tian creator: Zhen Chen creator: Lirong Liu creator: Tao Luo creator: Jianghong Dai uri: https://doi.org/10.7717/peerj.10952 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Association between uric acid lowering and renal function progression: a longitudinal study link: https://peerj.com/articles/11073 last-modified: 2021-03-24 description: BackgroundThis study aimed to explore the association between uric acid lowering and renal function.Materials and MethodsWe conducted a population-based cohort study with 1,534 subjects for 4 years from 2012 to 2016. The population was divided into four groups according to the interquartile range of changes in serum uric acid with quartile 1 representing lower quarter. Renal function decline was defined as eGFR decreased more than 10% from baseline in 2016. Renal function improvement was defined as eGFR increased more than 10% from baseline in 2016. Cox regression analysis was used to calculate the hazard ratio (HR) and 95% confidence interval (CI).ResultsIn the adjusted Cox regression models, compared to quartile 4, quartile 1 (HR = 0.64, 95% CI [0.49–0.85]), quartile 2 (HR = 0.65, 95% CI [0.50–0.84]) and quartile 3 (HR = 0.75, 95% CI [0.58–0.96]) have reduced risk of renal function decline. An increasing hazard ratio of renal function improvement was shown in quartile 1 (HR = 2.27, 95% CI [1.45–3.57]) and quartile 2 (HR = 1.78, 95% CI [1.17–2.69]) compared with quartile 4.ConclusionsUric acid lowering is associated with changes in renal function. The management of serum uric acid should receive attention in clinical practice and is supposed to be part of the treatment of chronic kidney disease. creator: Liyi Liu creator: Lili You creator: Kan Sun creator: Feng Li creator: Yiqin Qi creator: Chaogang Chen creator: Chuan Wang creator: Guojuan Lao creator: Shengneng Xue creator: Juying Tang creator: Na Li creator: Wanting Feng creator: Chuan Yang creator: Mingtong Xu creator: Yan Li creator: Li Yan creator: Meng Ren creator: Diaozhu Lin uri: https://doi.org/10.7717/peerj.11073 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Subsoiling increases aggregate-associated organic carbon, dry matter, and maize yield on the North China Plain link: https://peerj.com/articles/11099 last-modified: 2021-03-24 description: BackgroundSoil degradation is one of the main problems in agricultural production and leads to decreases in soil quality and productivity. Improper farming practices speed this process and are therefore not conducive to food security. The North China Plain (NCP) is a key agricultural area that greatly influences food security in China. To explore the effects of different tillage measures on aggregate-associated organic carbon (AOC), the accumulation and transport of dry matter, and maize yield, and to identify the most suitable tillage method for use on the NCP, a field experiment was conducted at Shandong Agricultural University from 2016–2017 using plots that have been farmed using conservation tillage since 2002.MethodsIn this study, Zhengdan 958 summer maize was used as the test material and undisturbed soil and plant samples were obtained under four tillage methods—no-tillage (NT, tillage depth: 0 cm); rotary tillage (RT, tillage depth: 10 cm); conventional tillage (CT, tillage depth: 20 cm); subsoiling (SS, tillage depth: 40 cm)—which were used to determine the AOC and dry matter contents, as well as the yields of two summer maize growing seasons. Each sample was replicated three times and the AOC content was determined via potassium dichromate oxidation colorimetry. Potassium dichromate oxidized organic carbon in organic matter was employed to reduce hexadecent chromium into green trivalent chromium. Colorimetry was then used to determine the amount of reduced trivalent chromium and calculate the organic matter content.ResultsThe resulting data were statistically analyzed and the results showed that, compared with CT, the AOC contents with NT and SS increased by 5.65% and 9.73%, respectively, while that with RT decreased by 0.12%. Conventional tillage resulted in the highest mean dry matter weight when the maize reached maturity, which was 19.19%, 9.83%, and 3.38% higher than those achieved using NT, RT, and SS, respectively. No significant difference was found between CT and SS treatments, both of which tended to increase the accumulation of dry matter as well as its contribution of assimilates to grain yield post-anthesis. Compared with CT, the mean yield increased at a rate of 0.18% with SS, while yields declined at rates of 17.17% and 11.15 with NT and RT, respectively. The yield with NT was the lowest, though the harvest indices with NT and SS were higher than those with RT and CT. Overall, SS increased the accumulation of dry matter and its contribution of assimilates to grain yields post-anthesis, as well as the AOC content and yields, making it the ideal tillage method for the NCP. creator: Ying Shen creator: Tingting Zhang creator: Jichao Cui creator: Siyu Chen creator: Huifang Han creator: Tangyuan Ning uri: https://doi.org/10.7717/peerj.11099 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Shen et al. title: Characterization of spray-dried Gac aril extract and estimated shelf life of β-carotene and lycopene link: https://peerj.com/articles/11134 last-modified: 2021-03-24 description: BackgroundFresh Gac (Momordica cochinchinensis) fruit is rich in carotenoids, mainly β-carotene and lycopene, but these compounds are sensitive to degradation. Spray drying is used to encapsulate the sensitive β-carotene and lycopene with different materials. Only a few reports of using highly branched cyclodextrin (HBCD) have been published. Additionally, studies of β-carotene and lycopene losses in Gac powders during storage are limited. Therefore, the encapsulation of β-carotene and lycopene of Gac aril with HBCD by spray drying at different inlet temperatures were compared. The shelf life of β-carotene and lycopene during storage was also calculated.MethodsThe fresh Gac aril was separated and kept frozen before the experiment. Gac aril and water (1:5 w/v) were centrifuged at 8,000 g at 20 °C for 15 min using a high-speed centrifuge (Sorval; Dupont, Wilmington, DE, USA). The supernatant was filtered twice and concentrated until 15° Brix using a rotary evaporator (R-200; Buchi, Flawil, Switzerland). The mixture of concentrated aril extract and highly branched cyclodextrin at 5% (w/v) was dried at three inlet temperatures by a spray dryer (B-290; Buchi, Flawil, Switzerland) with drying air flow rate, compressor air pressure, and feed rate set at 473 L/h, 40 m3/h, and 3 mL/min, respectively . The physicochemical qualities, particle image morphology, and estimated storage time of β-carotene and lycopene were determined.ResultsIncreased inlet temperatures of spray drying decreased the bulk density, β-carotene, and lycopene content of spray-dried powders significantly. The color values of dried powders had significant differences in yellowness (b*) and chroma, but not lightness (L*), redness (a*), and hue when the inlet temperature increased from 160 °C to 180 °C. The maximum reduction of β-carotene and lycopene observed during storage at 55 °C was 90.88% and 91.11% for 33 and 18 days. For β-carotene, the estimated shelf-life (retention of 50% of β-carotene) was 9.9, 48.4, and 91.6 days at 25 °C, 10 °C, and 4 °C. The shelf-life of lycopene was 26, 176, and 357 days at 25 °C, 10 °C, and 4 °C, respectively. HBCD could be potentially used as an encapsulating agent in spray-dried Gac aril, but the shelf-life of β-carotene and lycopene needs to be improved to be useful as a food ingredient. creator: Benjawan Thumthanaruk creator: Natta Laohakunjit creator: Grady W. Chism uri: https://doi.org/10.7717/peerj.11134 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Thumthanaruk et al. title: Using demographic data to understand the distribution of H1N1 and COVID-19 pandemics cases among federal entities and municipalities of Mexico link: https://peerj.com/articles/11144 last-modified: 2021-03-24 description: BackgroundThe novel coronavirus disease (COVID-19) pandemic is the second global health emergency the world has faced in less than two decades, after the H1N1 Influenza pandemic in 2009–2010. Spread of pandemics is frequently associated with increased population size and population density. The geographical scales (national, regional or local scale) are key elements in determining the correlation between demographic factors and the spread of outbreaks. The aims of this study were: (a) to collect the Mexican data related to the two pandemics; (b) to create thematic maps using federal and municipal geographic scales; (c) to investigate the correlations between the pandemics indicators (numbers of contagious and deaths) and demographic patterns (population size and density).MethodsThe demographic patterns of all Mexican Federal Entities and all municipalities were taken from the database of “Instituto Nacional de Estadística y Geografía” (INEGI). The data of “Centro Nacional de Programas Preventivos y Control de Enfermedades” (CENAPRECE) and the geoportal of Mexico Government were also used in our analysis. The results are presented by means of tables, graphs and thematic maps. A Spearman correlation was used to assess the associations between the pandemics indicators and the demographic patterns. Correlations with a p value < 0.05 were considered significant.ResultsThe confirmed cases (ccH1N1) and deaths (dH1N1) registered during the H1N1 Influenza pandemic were 72.4 thousand and 1.2 thousand respectively. Mexico City (CDMX) was the most affected area by the pandemic with 8,502 ccH1N1 and 152 dH1N1. The ccH1N1 and dH1N1 were positively correlated to demographic patterns; p-values higher than the level of marginal significance were found analyzing the % ccH1N1 and the % dH1N1 vs the population density. The COVID-19 pandemic data indicated 75.0 million confirmed cases (ccCOVID-19) and 1.6 million deaths (dCOVID-19) worldwide, as of date. The CDMX, where 264,330 infections were recorded, is the national epicenter of the pandemic. The federal scale did not allow to observe the correlation between demographic data and pandemic indicators; hence the next step was to choose a more detailed geographical scale (municipal basis). The ccCOVID-19 and dCOVID-19 (municipal basis) were highly correlated with demographic patterns; also the % ccCOVID-19 and % dCOVID-19 were moderately correlated with demographic patterns.ConclusionThe magnitude of COVID-19 pandemic is much greater than the H1N1 Influenza pandemic. The CDMX was the national epicenter in both pandemics. The federal scale did not allow to evaluate the correlation between exanimated demographic variables and the spread of infections, but the municipal basis allowed the identification of local variations and “red zones” such as the delegation of Iztapalapa and Gustavo A. Madero in CDMX. creator: Yohanna Sarria-Guzmán creator: Jaime Bernal creator: Michele De Biase creator: Ligia C. Muñoz-Arenas creator: Francisco Erik González-Jiménez creator: Clemente Mosso creator: Arit De León-Lorenzana creator: Carmine Fusaro uri: https://doi.org/10.7717/peerj.11144 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sarria-Guzmán et al. title: The effect of carbon monoxide on meiotic maturation of porcine oocytes link: https://peerj.com/articles/10636 last-modified: 2021-03-23 description: Oxidative stress impairs the correct course of meiotic maturation, and it is known that the oocytes are exposed to increased oxidative stress during meiotic maturation in in vitro conditions. Thus, reduction of oxidative stress can lead to improved quality of cultured oocytes. The gasotransmitter carbon monoxide (CO) has a cytoprotective effect in somatic cells. The CO is produced in cells by the enzyme heme oxygenase (HO) and the heme oxygenase/carbon monoxide (HO/CO) pathway has been shown to have an antioxidant effect in somatic cells. It has not yet been investigated whether the CO has an antioxidant effect in oocytes as well. We assessed the level of expression of HO mRNA, using reverse transcription polymerase chain reaction. The HO protein localization was evaluated by the immunocytochemical method. The influence of CO or HO inhibition on meiotic maturation was evaluated in oocytes cultured in a culture medium containing CO donor (CORM-2 or CORM-A1) or HO inhibitor Zn-protoporphyrin IX (Zn-PP IX). Detection of reactive oxygen species (ROS) was performed using the oxidant-sensing probe 2′,7′-dichlorodihydrofluorescein diacetate. We demonstrated the expression of mRNA and proteins of both HO isoforms in porcine oocytes during meiotic maturation. The inhibition of HO enzymes by Zn-PP IX did not affect meiotic maturation. CO delivered by CORM-2 or CORM-A1 donors led to a reduction in the level of ROS in the oocytes during meiotic maturation. However, exogenously delivered CO also inhibited meiotic maturation, especially at higher concentrations. In summary, the CO signaling molecule has antioxidant properties in porcine oocytes and may also be involved in the regulation of meiotic maturation. creator: David Němeček creator: Eva Chmelikova creator: Jaroslav Petr creator: Tomas Kott creator: Markéta Sedmíková uri: https://doi.org/10.7717/peerj.10636 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Němeček et al. title: The effects of parental age difference on the offspring sex and fitness of European blackbirds link: https://peerj.com/articles/10858 last-modified: 2021-03-23 description: BackgroundMany studies of birds have indicated that offspring sex ratios can vary with environmental and parental traits. On the basis of long-term research, we first evaluated the possible influence of parental age difference and brood characteristics on offspring sex and fitness in multi-brooded Blackbirds Turdus merula.MethodologyThe study was conducted in the city-centre Stefan Żeromski Park in Szczecin, NW Poland, where the local population of Blackbirds has been studied since 1996. Data on the offspring sex and fitness were collected in five years, 2005–2007 and 2016–2017. During the breeding season we inspected the study area to locate the pairs’ territories and to track their nests and clutches.ResultsWe found that the overall sex ratio did not differ statistically from 50:50, but that younger females bonded with older mates did tend to produce more sons, probably because of the greater fitness of male descendants. Accordingly, the sons’ breeding success increased with the father’s age, but this relationship was close to non-linear, which may indicate that the transgenerational effect of paternal senescence could negatively affect progeny fitness despite the high-quality of older fathers. Older females mated with younger males produced more daughters, which could have been due to the lesser attractiveness of the males and the mothers’ poorer condition caused by accelerated senescence. We found that neither offspring hatching sequence nor hatching date or clutch sequence were significant for sex determination.ConclusionsWe consider that in our Blackbird population, parental age could make a more significant contribution to shaping offspring sex and reproductive success. creator: Marta Cholewa creator: Łukasz Jankowiak creator: Magdalena Szenejko creator: Andrzej Dybus creator: Przemysław Śmietana creator: Dariusz Wysocki uri: https://doi.org/10.7717/peerj.10858 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cholewa et al. title: ITS secondary structure reconstruction to resolve taxonomy and phylogeny of the Betula L. genus link: https://peerj.com/articles/10889 last-modified: 2021-03-23 description: The taxonomy and phylogeny of the Betula L. genus remain unresolved and are very difficult to assess due to several factors, especially because of frequent hybridization among different species. In the current study, we used nucleotide sequences of two internal transcribed spacer regions (ITS1 and ITS2), which are commonly used as phylogenetic markers. In addition to their nucleotide variation we reconstructed their secondary structure and used it to resolve phylogenetic relationships of some birch species. We explored whether consideration of secondary structure in phylogenetic analyses based on neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods would help us obtain more solid support of the reconstructed phylogenetic trees. The results were not unambiguous. There were only a few clades with higher support when secondary structure was included into analysis. The phylogenetic trees generated using different methods were mostly in agreement with each other. However, the resolving power of these markers is still insufficient to reliably discriminate some closely related species. To achieve this aim more reliably there is a need for application of modern genomic approaches in combination with traditional ones. creator: Andrii S. Tarieiev creator: Oliver Gailing creator: Konstantin V. Krutovsky uri: https://doi.org/10.7717/peerj.10889 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tarieiev et al. title: Differences between adjusted vs. non-adjusted loads in velocity-based training: consequences for strength training control and programming link: https://peerj.com/articles/10942 last-modified: 2021-03-23 description: Strength and conditioning specialists commonly deal with the quantification and selection the setting of protocols regarding resistance training intensities. Although the one repetition maximum (1RM) method has been widely used to prescribe exercise intensity, the velocity-based training (VBT) method may enable a more optimal tool for better monitoring and planning of resistance training (RT) programs. The aim of this study was to compare the effects of two RT programs only differing in the training load prescription strategy (adjusting or not daily via VBT) with loads from 50 to 80% 1RM on 1RM, countermovement (CMJ) and sprint. Twenty-four male students with previous experience in RT were randomly assigned to two groups: adjusted loads (AL) (n = 13) and non-adjusted loads (NAL) (n = 11) and carried out an 8-week (16 sessions) RT program. The performance assessment pre- and post-training program included estimated 1RM and full load-velocity profile in the squat exercise; countermovement jump (CMJ); and 20-m sprint (T20). Relative intensity (RI) and mean propulsive velocity attained during each training session (Vsession) was monitored. Subjects in the NAL group trained at a significantly faster Vsession than those in AL (p < 0.001) (0.88–0.91 vs. 0.67–0.68 m/s, with a ∼15% RM gap between groups for the last sessions), and did not achieve the maximum programmed intensity (80% RM). Significant differences were detected in sessions 3–4, showing differences between programmed and performed Vsession and lower RI and velocity loss (VL) for the NAL compared to the AL group (p < 0.05). Although both groups improved 1RM, CMJ and T20, NAL experienced greater and significant changes than AL (28.90 vs.12.70%, 16.10 vs. 7.90% and −1.99 vs. −0.95%, respectively). Load adjustment based on movement velocity is a useful way to control for highly individualised responses to training and improve the implementation of RT programs. creator: Pedro Jiménez-Reyes creator: Adrian Castaño-Zambudio creator: Víctor Cuadrado-Peñafiel creator: Jorge M. González-Hernández creator: Fernando Capelo-Ramírez creator: Luis M. Martínez-Aranda creator: Juan J. González-Badillo uri: https://doi.org/10.7717/peerj.10942 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jiménez-Reyes et al. title: Two predicted models based on ceRNAs and immune cells in lung adenocarcinoma link: https://peerj.com/articles/11029 last-modified: 2021-03-23 description: BackgroundIt is well accepted that both competitive endogenous RNAs (ceRNAs) and immune microenvironment exert crucial roles in the tumor prognosis. The present study aimed to find prognostic ceRNAs and immune cells in lung adenocarcinoma (LUAD).Materials and MethodsMore specifically, we explored the associations of crucial ceRNAs with the immune microenvironment. The Cancer Genome Atlas (TCGA) database was employed to obtain expression profiles of ceRNAs and clinical data. CIBERSORT was utilized to quantify the proportion of 22 immune cells in LUAD.ResultsWe constructed two cox regression models based on crucial ceRNAs and immune cells to predict prognosis in LUAD. Subsequently, seven ceRNAs and seven immune cells were involved in prognostic models. We validated both predicted models via an independent cohort GSE72094. Interestingly, both predicted models proved that the longer patients were smoking, the higher risk scores would be obtained. We further investigated the relationships between seven genes and immune/stromal scores via the ESTIMATE algorithm. The results indicated that CDC14A and H1F0 expression were significantly related to stromal scores/immune scores in LUAD. Moreover, based on the result of the ceRNA model, single-sample gene set enrichment analysis (ssGSEA) suggested that differences in immune status were evident between high- and low-risk groups. creator: Miaomiao Zhang creator: Peiyan Zheng creator: Yuan Wang creator: Baoqing Sun uri: https://doi.org/10.7717/peerj.11029 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Immunoinformatic approach to design a multiepitope vaccine targeting non-mutational hotspot regions of structural and non-structural proteins of the SARS CoV2 link: https://peerj.com/articles/11126 last-modified: 2021-03-23 description: BackgroundThe rapid Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV2) outbreak caused severe pandemic infection worldwide. The high mortality and morbidity rate of SARS CoV2 is due to the unavailability of vaccination and mutation in this virus. The present article aims to design a potential vaccine construct VTC3 targeting the non-mutational region of structural and non-structural proteins of SARS CoV2.MethodsIn this study, vaccines were designed using subtractive proteomics and reverse vaccinology. To target the virus adhesion and evasion, 10 different structural and non-structural proteins have been selected. Shortlisted proteins have been screened for B cell, T cell and IFN gamma interacting epitopes. 3D structure of vaccine construct was modeled and evaluated for its physicochemical properties, immunogenicity, allergenicity, toxicity and antigenicity. The finalized construct was implemented for docking and molecular dynamics simulation (MDS) with different toll-like receptors (TLRs) and human leukocyte antigen (HLA). The binding energy and dissociation construct of the vaccine with HLA and TLR was also calculated. Mutational sensitivity profiling of the designed vaccine was performed, and mutations were reconfirmed from the experimental database. Antibody production, clonal selection, antigen processing, immune response and memory generation in host cells after injection of the vaccine was also monitored using immune simulation.ResultsSubtractive proteomics identified seven (structural and non-structural) proteins of this virus that have a role in cell adhesion and infection. The different epitopes were predicted, and only extracellular epitopes were selected that do not have similarity and cross-reactivity with the host cell. Finalized epitopes of all proteins with minimum allergenicity and toxicity were joined using linkers to designed different vaccine constructs. Docking different constructs with different TLRs and HLA demonstrated a stable and reliable binding affinity of VTC3 with the TLRs and HLAs. MDS analysis further confirms the interaction of VTC3 with HLA and TLR1/2 complex. The VTC3 has a favorable binding affinity and dissociation constant with HLA and TLR. The VTC3 does not have similarities with the human microbiome, and most of the interacting residues of VTC3 do not have mutations. The immune simulation result showed that VTC3 induces a strong immune response. The present study designs a multiepitope vaccine targeting the non-mutational region of structural and non-structural proteins of the SARS CoV2 using an immunoinformatic approach, which needs to be experimentally validated. creator: Vandana Solanki creator: Monalisa Tiwari creator: Vishvanath Tiwari uri: https://doi.org/10.7717/peerj.11126 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Solanki et al. title: Structure and comparative analysis of the mitochondrial genomes of Liolaemus lizards with different modes of reproduction and ploidy levels link: https://peerj.com/articles/10677 last-modified: 2021-03-22 description: Liolaemus is the most specious genus of the Squamata lizards in South America, presenting exceptional evolutionary radiation and speciation patterns. This recent diversification complicates the formal taxonomic treatment and the phylogenetic analyses of this group, causing relationships among species to remain controversial. Here we used Next-Generation Sequencing to do a comparative analysis of the structure and organization of the complete mitochondrial genomes of three differently related species of Liolaemus and with different reproductive strategies and ploidy levels. The annotated mitochondrial genomes of ca. 17 kb are the first for the Liolaemidae family. Despite the high levels of sequence similarity among the three mitochondrial genomes over most of their lengths, the comparative analyses revealed variations at the stop codons of the protein coding genes and the structure of the tRNAs among species. The presence of a non-canonical dihydrouridine loop is a novelty for the pleurodonts iguanians. But the highest level of variability was observed in two repetitive sequences of the control region, which were responsible for most of the length heterogeneity of the mitochondrial genomes. These tandem repeats may be useful markers to analyze relationships of closely related species of Liolaemus and related genera and to conduct population and phylogenetic studies. creator: Julian Valdes creator: Sergio Sebastian Samoluk creator: Cristian Simón Abdala creator: Diego Baldo creator: Guillermo Seijo uri: https://doi.org/10.7717/peerj.10677 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Valdes et al. title: Spatiotemporal dynamics of habitat suitability for the Ethiopian staple crop, Eragrostis tef (teff), under changing climate link: https://peerj.com/articles/10965 last-modified: 2021-03-22 description: Teff (Eragrostis tef (Zucc.) Trotter) is a staple, ancient food crop in Ethiopia. Its growth is affected by climate change, so it is essential to understand climatic effects on its habitat suitability in order to design countermeasures to ensure food security. Based on the four Representative Concentration Pathway emission scenarios (i.e., RCP2.6, RCP4.5, RCP6.0 and RCP8.5) set by the Intergovernmental Panel on Climate Change (IPCC), we predicted the potential distribution of teff under current and future scenarios using a maximum entropy model (Maxent). Eleven variables were selected out of 19, according to correlation analysis combined with their contribution rates to the distribution. Simulated accuracy results validated by the area under the curve (AUC) had strong predictability with values of 0.83–0.85 for current and RCP scenarios. Our results demonstrated that mean temperature in the coldest season, precipitation seasonality, precipitation in the cold season and slope are the dominant factors driving potential teff distribution. Proportions of suitable teff area, relative to the total study area were 58% in current climate condition, 58.8% in RCP2.6, 57.6% in RCP4.5, 59.2% in RCP6.0, and 57.4% in RCP8.5, respectively. We found that warmer conditions are correlated with decreased land suitability. As expected, bioclimatic variables related to temperature and precipitation were the best predictors for teff suitability. Additionally, there were geographic shifts in land suitability, which need to be accounted for when assessing overall susceptibility to climate change. The ability to adapt to climate change will be critical for Ethiopia’s agricultural strategy and food security. A robust climate model is necessary for developing primary adaptive strategies and policy to minimize the harmful impact of climate change on teff. creator: Dinka Zewudie creator: Wenguang Ding creator: Zhanlei Rong creator: Chuanyan Zhao creator: Yapeng Chang uri: https://doi.org/10.7717/peerj.10965 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zewudie et al. title: De novo assembly of Amorpha fruticosa L. transcriptome in response to drought stress provides insight into the tolerance mechanisms link: https://peerj.com/articles/11044 last-modified: 2021-03-22 description: BackgroundAmorpha fruticosa L. is a deciduous shrub that is native to North America and has been introduced to China as an ornamental plant. In order to clarify the drought resistance characteristics of Amorpha fruticosa L. and excavate the related genes involved in drought resistance regulation pathway, the mechanism of drought resistance stress of Amorpha fruticosa L. was revealed by the changes of transcriptome of Amorpha fruticosa L. under drought stress.Through the changes of the transcriptome of Amorpha fruticosa L. under drought stress, the mechanism of anti-stress of Amorpha fruticosa L. could be revealed.MethodsDifferent concentrations of polyethylene glycol-6000 (PEG-6000) was used to simulate drought stress, and transcriptomic analysis was used to reveal the changes of gene expression patterns in Amorpha fruticosa L. seedlings.ResultsResults showed that Amorpha fruticosa L. seedlings were seriously affected by PEG-6000. As for the differently expressed genes (DEGs), most of them were up-regulated. The additional Go and KEGG analysis results showed that DEGs were functionally enriched in cell wall, signal transduction and hormonal regulation related pathways. DEGs like AfSOD, AfHSP, AfTGA, AfbZIP and AfGRX play roles in response to drought stress.ConclusionIn conclusion, Amorpha fruticosa L. seedlings were sensitive to drought, which was different from Amorpha fruticosa L. tree, and the genes functions in drought stress responses via ABA-independent pathways. The up-regulation of Salicylic acid signal related DEGs (AfTGA and AfPR-1) indicated that Salicylic acid play a key role in response to drought stress in Amorpha fruticosa L. creator: Xinzhu Sun creator: Songmiao Hu creator: Xin Wang creator: He Liu creator: Yun wei Zhou creator: Qingjie Guan uri: https://doi.org/10.7717/peerj.11044 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Sun et al. title: Effects of the cranial parasite Tylodelphys sp. on the behavior and physiology of puye Galaxias maculatus (Jenyns, 1842) link: https://peerj.com/articles/11095 last-modified: 2021-03-22 description: Diplostomatid digeneans are well-known manipulators of the behavior of their intermediate hosts. Unencysted metacercariae of Tylodelphys sp. inhabit the cranial cavity of the fish Galaxias maculatus; however, to date they have not been documented to alter their host behavior. The goal of this study was to evaluate the potential effects of Tylodelphys sp. inhabiting the cranial cavity of Galaxias maculatus on host physiology and swimming behavior as well as its reaction to a simulated predation attempt. Blind experiments in the lab were carried out on 56 fish that were filmed individually. The Fulton condition factor (K) was used as an approximation of nutritional status and a respirometry chamber was used to evaluate oxygen consumption rates of fish. Of the 56 fish, 21 were parasitized by Tylodelphys sp. (mean intensity = 30, range from 1 to 101). Parasitized and non-parasitized fish were similar in condition factor and oxygen consumption rates. Furthermore, the oxygen consumption rate of G. maculatus was not correlated with the abundance of Tylodelphys sp. However, parasitized fish more frequently swam close to the water surface, whereas non-parasitized fish more frequently swam at intermediate depths. When faced with a simulated predator attack, unparasitized fish showed more frequent fleeing behavior as well as a more intense post-fleeing activity. Collectively, these results suggest that Tylodelphys sp. inhabiting the cranial cavity of fish may alter their behavior predisposing them to predation by birds. creator: Ruby López-Rodríguez creator: Mario George-Nascimento creator: Konrad Górski uri: https://doi.org/10.7717/peerj.11095 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 López-Rodríguez et al. title: Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana-Fusarium oxysporum pathosystem link: https://peerj.com/articles/11135 last-modified: 2021-03-22 description: Vascular wilt, caused by the pathogen Fusarium oxysporum f. sp. physali (Foph), is a major disease of cape gooseberry (Physalis peruviana L.) in Andean countries. Despite the economic losses caused by this disease, there are few studies related to molecular mechanisms in the P. peruviana—Foph pathosystem as a useful tool for crop improvement. This study evaluates eight candidate genes associated with this pathosystem, using real-time quantitative PCR (RT-qPCR). The genes were identified and selected from 1,653 differentially expressed genes (DEGs) derived from RNA-Seq analysis and from a previous genome-wide association study (GWAS) of this plant-pathogen interaction. Based on the RT-qPCR analysis, the tubuline (TUB) reference gene was selected for its highly stable expression in cape gooseberry. The RT-qPCR validation of the candidate genes revealed the biological variation in their expression according to their known biological function. Three genes related to the first line of resistance/defense responses were highly expressed earlier during infection in a susceptible genotype, while three others were overexpressed later, mostly in the tolerant genotype. These genes are mainly involved in signaling pathways after pathogen recognition, mediated by hormones such as ethylene and salicylic acid. This study provided the first insight to uncover the molecular mechanism from the P. peruviana—Foph pathosystem. The genes validated here have important implications in the disease progress and allow a better understanding of the defense response in cape gooseberry at the molecular level. Derived molecular markers from these genes could facilitate the identification of tolerant/susceptible genotypes for use in breeding schemes. creator: Gina A. Garzón-Martínez creator: Francy L. García-Arias creator: Felix E. Enciso-Rodríguez creator: Mauricio Soto-Suárez creator: Carolina González creator: Aureliano Bombarely creator: Luz Stella Barrero creator: Jaime A. Osorio Guarín uri: https://doi.org/10.7717/peerj.11135 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Garzón-Martínez et al. title: Mating system of Datura inoxia: association between selfing rates and herkogamy within populations link: https://peerj.com/articles/10698 last-modified: 2021-03-19 description: Plant mating system determines, to a great extent, the demographic and genetic properties of populations, hence their potential for adaptive evolution. Variation in plant mating system has been documented between phylogenetically related species as well between populations of a species. A common evolutionary transition, from outcrossing to selfing, is likely to occur under environmental spatial variation in the service of pollinators. Here, we studied two phenotypically (in floral traits) and genetically (in neutral molecular markers) differentiated populations of the annual, insect-pollinated, plant Datura inoxia in Mexico, that differ in the service of pollinators (Mapimí and Cañada Moreno). First, we determined the populations’ parameters of phenotypic in herkogamy, outcrossing and selfing rates with microsatellite loci, and assessed between generation (adults and seedlings) inbreeding, and inbreeding depression. Second, we compared the relationships between parameters in each population. Results point strong differences between populations: plants in Mapimí have, on average, approach herkogamy, higher outcrossing rate (tm = 0.68), lower primary selfing rate (r = 0.35), and lower inbreeding at equilibrium (Fe = 0.24) and higher inbreeding depression (δ = 0.25), than the populations of Cañada. Outcrossing seems to be favored in Mapimí while selfing in Cañada. The relationship between r and Fe were negatively associated with herkogamy in Mapimí; here, progenies derived from plants with no herkogamy or reverse herkogamy had higher selfing rate and inbreeding coefficient than plants with approach herkogamy. The difference Fe–F is positively related to primary selfing rate (r) only in Cañada Moreno which suggests inbreeding depression in selfing individuals and then genetic purging. In conclusion, mating system evolution may occur differentially among maternal lineages within populations of Datura inoxia, in which approach herkogamy favors higher outcrossing rates and low levels of inbreeding and inbreeding depression, while no herkogamy or reverse herkogamy lead to the evolution of the “selfing syndrome” following the purge of deleterious alleles despite high inbreeding among individuals. creator: Vania Jiménez-Lobato creator: Juan Núñez-Farfán uri: https://doi.org/10.7717/peerj.10698 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jiménez-Lobato and Núñez-Farfán title: Characteristic changes in malt, wort, and beer produced from different Nigerian rice varieties as influenced by varying malting conditions link: https://peerj.com/articles/10968 last-modified: 2021-03-19 description: Gluten-free beer could be produced with rice, although the latter would primarily serve as adjunct in combination with barley malt in today’s brewing. However, the recent growing realisation of the potential and applications of rice malt for brewing an all-rice malt beer through varying malting conditions cannot be overlooked. In this study, therefore, the characteristic changes in malt, wort, and beer from different Nigerian rice varieties (FARO 44, FARO 57, NERICA 7) as influenced by varying malting conditions (steeping duration (18, 24 and 30 h), germination periods (2, 3 and 4 days) and kilning temperatures (50 and 55 °C)), were investigated. Rice (grain) samples were examined by thousand kernel weight (TKW), germinative energy (GE), germinative capacity (GC), and degree of steeping (DoS). To ensure that rice wort/beer with unique beer style and enhanced attributes, comparable to barley wort/beer is produced, malting conditions that produced rice malts with peak diastatic power (DP), cold water extract (CWE), and hot water extract (HWE) were selected. Peak DP, CWE and HWE were obtained at FARO 44 (18 h steeping, 3 days germination, 55 °C kilning (S18G3K55°)), FARO 57 (30 h steeping, 2 days germination, 50 °C kilning (S30G2K50°)) and NERICA 7 (24 h steeping, 3 days germination, 55 °C kilning (S24G3K55°)). Selected malts were further tested for moisture content, total nitrogen, malt yield and malting loss and subsequently progressed to wort and beer production. Wort’s pH, total soluble nitrogen (TSN), brix, kolbach index (KI), free amino nitrogen (FAN), dextrose equivalent (DE), original extract (OE) and sugar profile were determined, as well as beer’s pH, colour, apparent extract (AE), alcohol by volume (%ABV), turbidity and sensory attributes. Rice grain varied significantly (p < 0.05) in TKW, GE, GC and DoS across varieties. Despite wort’s pH, TSN, DE, OE as well as beer pH, colour, AE and turbidity resembling (p > 0.05) across varieties, wort’s brix, KI, FAN, sugar profile as well as beer’s %ABV, differed significantly (p < 0.05). Sensory attributes of appearance, colour, mouthfeel, and overall acceptability in beer differed noticeably (p < 0.05), except for aroma and taste (p > 0.05). Overall, the rice beer, though very slightly hazy, represented a pale yellow light lager, which is indicative of its peculiar beer style. Besides increased DP and enhanced hydrolysis, varying malting conditions of current study could serve as a pathway of reducing the cost of exogenous (commercial) enzymes or barley malt imports, together with decreasing barley’s dependency for brewing in the tropics. creator: Chigozie E. Ofoedu creator: Chibugo Q. Akosim creator: Jude O. Iwouno creator: Chioma D. Obi creator: Ivan Shorstkii creator: Charles Odilichukwu R. Okpala uri: https://doi.org/10.7717/peerj.10968 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ofoedu et al. title: A fresh look at an old concept: home-range estimation in a tidy world link: https://peerj.com/articles/11031 last-modified: 2021-03-19 description: A rich set of statistical techniques has been developed over the last several decades to estimate the spatial extent of animal home ranges from telemetry data, and new methods to estimate home ranges continue to be developed. Here we investigate home-range estimation from a computational point of view and aim to provide a general framework for computing home ranges, independent of specific estimators. We show how such a workflow can help to make home-range estimation easier and more intuitive, and we provide a series of examples illustrating how different estimators can be compared easily. This allows one to perform a sensitivity analysis to determine the degree to which the choice of estimator influences qualitative and quantitative conclusions. By providing a standardized implementation of home-range estimators, we hope to equip researchers with the tools needed to explore how estimator choice influences answers to biologically meaningful questions. creator: Johannes Signer creator: John R. Fieberg uri: https://doi.org/10.7717/peerj.11031 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Signer and Fieberg title: Median nerve travel and deformation in the transverse carpal tunnel increases with chuck grip force and deviated wrist position link: https://peerj.com/articles/11038 last-modified: 2021-03-19 description: BackgroundWe assessed median nerve travel and deformation concurrently to better understand the influence of occupational risk factors on carpal tunnel dynamics, including forceful chuck gripping and deviated wrist positions.MethodsFourteen healthy right-hand dominant participants performed a chuck grip in 6 experimental conditions: two relative force levels (10% and 40% of maximum voluntary effort); three wrist positions (15° radial deviation, 0° neutral, 30° ulnar deviation). Chuck grip forces were measured with a load cell while the transverse cross-section of the carpal tunnel was imaged via ultrasound at the distal wrist crease. Images of the median nerve were analyzed in ImageJ to assess cross-sectional area, circularity, width, and height as well as travel in the anterior-posterior and medial-lateral axes.ResultsWe found a main effect of deviated wrist position on both anterior-posterior and medial-lateral travel, with the greatest nerve travel occurring in 30° ulnar deviation. There was also a significant interaction between chuck grip force and deviated wrist position on cross-sectional area. Specifically, the area decreased with 40% vs. 10% chuck grip force when the wrist was in 30° ulnar deviation; however, there were no changes in 0° neutral and 15° radial deviation.DiscussionOverall, we demonstrated that forceful chuck gripping in deviated wrist positions influenced carpal tunnel dynamics, resulting in both migratory and morphological changes to the median nerve. These changes may, in turn, increase local strain and stress with adjacent structures in the carpal tunnel. Future studies mapping contact stress between structures may further elucidate injury development of work-related carpal tunnel syndrome. creator: Kaylyn E. Turcotte creator: Aaron M. Kociolek uri: https://doi.org/10.7717/peerj.11038 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Turcotte and Kociolek title: DNA metabarcoding of zooplankton communities: species diversity and seasonal variation revealed by 18S rRNA and COI link: https://peerj.com/articles/11057 last-modified: 2021-03-19 description: BackgroundZooplankton is an important component of aquatic organisms and has important biological and economical significance in freshwater ecosystems. However, traditional methods that rely on morphology to classify zooplankton require expert taxonomic skills. Moreover, traditional classification methods are time-consuming and labor-intensive, which is not practical for the design of conservation measures and ecological management tools based on zooplankton diversity assessment.MethodsWe used DNA metabarcoding technology with two different markers: the nuclear small subunit ribosomal RNA (18S rRNA) and mitochondrial cytochrome c oxidase (COI), to analyze 72 zooplankton samples collected in 4 seasons and 9 locations from the Sanmenxia Reservoir. We investigated seasonal changes in the zooplankton community and their relationship with water environmental factors.ResultsA total of 190 species of zooplankton were found, belonging to 12 phyla, 24 classes, 61 orders, 111 families, and 174 genera. Protozoa, especially ciliates, were the most diverse taxa. Richness and relative abundance of zooplankton showed significant seasonal changes. Both alpha and beta diversity showed seasonal trends: the diversity in summer and autumn was higher than that in winter and spring. The zooplankton diversity was most similar in winter and spring. By correlating metabarcoding data and water environmental factors, we proved that water temperature, chemical oxygen demand, total nitrogen and ammoniacal nitrogen were the main environmental factors driving the seasonal changes in zooplankton in the Sanmenxia Reservoir. Water temperature, followed by total nitrogen, were the most influential factors. This study highlights the advantages and some limitations of zooplankton molecular biodiversity assessment using two molecular markers. creator: Lina Zhao creator: Xue Zhang creator: Mengyue Xu creator: Ying Mao creator: Yuan Huang uri: https://doi.org/10.7717/peerj.11057 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhao et al. title: Enzymatic and transcriptomic analysis reveals the essential role of carbohydrate metabolism in freesia (Freesia hybrida) corm formation link: https://peerj.com/articles/11078 last-modified: 2021-03-19 description: Starch and sucrose metabolism plays a crucial role in the formation and development of bulbs in bulbous plants. However, these mechanisms remain unclear and unexplored in the corms of Freesia hybrida. Herein, we investigated the dynamics of the major form of carbohydrates and related enzyme activities and profiled the transcriptome of freesia corms at four developmental stages with the aim to reveal the relation between the expression of genes involved in the metabolism of carbohydrates and the accumulation of carbohydrates in corm developmental stages for further exploring the mechanism on the starch and sucrose metabolism regulating the formation and development of corms in F. hybrida. The content of starch, sucrose and soluble sugars followed an overall upward trend across the corm developmental stages. Activities of the adenosine diphosphoglucose pyrophosphorylase, starch branching enzyme and β-amylase generally followed the pattern of the starch and sucrose levels. Activities of sucrose phosphate synthase increased from corm formation till the initial swelling stage and subsequently reached a plateau. Activities of invertase and sucrose synthase peaked at the later rapid swelling stage. These suggested that the starch and sucrose dynamics paralleled corm swelling under the action of metabolic enzymes. A total of 100,999 unigenes were assembled in the transcriptomic analysis, and 44,405 unigenes of them were annotated. Analysis based on Clusters of Orthologous Groups suggested that carbohydrate transport and metabolism (9.34% of the sequences) was prominent across the corm developmental process. In total 3,427 differentially expressed genes (DEGs) were identified and the enrichment analysis detected starch and sucrose metabolism as a critical pathway in corm development, especially at the rapid swelling stage. Further, DEGs encoding key carbohydrate-metabolizing enzymes were identified and correlated to enzyme activities and carbohydrate accumulation. The results construct a valuable resource pool for further molecular-level studies, which are helpful for metabolic regulation of carbohydrates and improvement in F. hybrida. creator: Li Ma creator: Suqin Ding creator: Xueqing Fu creator: Zi Yan creator: Dongqin Tang uri: https://doi.org/10.7717/peerj.11078 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ma et al. title: Network based multifactorial modelling of miRNA-target interactions link: https://peerj.com/articles/11121 last-modified: 2021-03-19 description: Competing endogenous RNA (ceRNA) regulations and crosstalk between various types of non-coding RNA in humans is an important and under-explored subject. Several studies have pointed out that an alteration in miRNA:target interaction can result in unexpected changes due to indirect and complex interactions. In this article, we defined a new network-based model that incorporates miRNA:ceRNA interactions with expression values. Our approach calculates network-wide effects of perturbations in the expression level of one or more nodes in the presence or absence of miRNA interaction factors such as seed type, binding energy. We carried out the analysis of large-scale miRNA:target networks from breast cancer patients. Highly perturbing genes identified by our approach coincide with breast cancer-associated genes and miRNAs. Our network-based approach takes the sponge effect into account and helps to unveil the crosstalk between nodes in miRNA:target network. The model has potential to reveal unforeseen regulations that are only evident in the network context. Our tool is scalable and can be plugged in with emerging miRNA effectors such as circRNAs, lncRNAs, and available as R package ceRNAnetsim: https://www.bioconductor.org/packages/release/bioc/html/ceRNAnetsim.html. creator: Selcen Ari Yuka creator: Alper Yilmaz uri: https://doi.org/10.7717/peerj.11121 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ari Yuka and Yilmaz title: Evaluation of risk factors associated with the development of MDR- and XDR-TB in a tertiary care hospital: a retrospective cohort study link: https://peerj.com/articles/10826 last-modified: 2021-03-18 description: BackgroundDrug resistant tuberculosis (DR-TB) infringes substantial burden in terms of longer treatment duration, morbidity and mortality. Timely identification of patients at risks of DR-TB will aid individualized treatment. Current study was aimed to ascertain several factors associated with DR-TB among patients attending a tertiary care hospital.MethodsThis retrospective study was conducted among patients with confirmed diagnosis of DR-TB and drug susceptible TB (DS-TB) seeking medical care from a tertiary care hospital during 2014–2019. The types of DR-TB included were rifampicin resistant tuberculosis (RR-TB), Multidrug resistant tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB). Appropriate statistical methods were implied to evaluate the factors associated with DR-TB.ResultsOut of 580 patients, DS-TB was diagnosed in 198 (34.1%) patients while DR-TB was present in 382 patients. Of resistance cases, RR-TB, MDR-TB and XDR-TB were diagnosed in 176 (30.3%), 195 (33.6%) and 11 (1.9%) patients, respectively. Significant differences (P < 0.05) in demographics and clinico-laboratory characteristics were observed between patients with DS-TB and DR-TB. Logistic regression analysis revealed age ≤38 years (OR: 2.5), single marital status (OR: 11.1), tobacco use (OR: 2.9), previous treatment (OR: 19.2), treatment failure (OR: 9.2) and cavity on chest X-ray (OR: 30.1) as independent risk factors for MDR-TB. However, XDR-TB was independently associated with age group of ≤38 years (OR: 13.6), students (OR: 13.0), previous treatment (OR: 12.5), cavity on chest X-ray (OR: 59.6). The independent risk factors associated with RR-TB are age ≤38 years (OR: 2.8), females (OR: 5.7), unemployed (OR: 41.5), treatment failure (OR: 4.9), previous treatment (OR: 38.2) and cavity on chest X-ray (OR: 4.3). ROC curve analysis accentuate the excellent predictive accuracy of all logistic regression models as shown by AUC (0.968, P < 0.001) for MDR-TB, AUC (0.941, P < 0.001) for XDR-TB and AUC (0.962, P < 0.001) for RR-TB.ConclusionsCurrent study demonstrates a sizeable extent of resistant cases among pulmonary TB patients. This study presaged significant risk of DR-TB among females, young adults, unemployed, smokers, patients with previous treatment failure and cavitation on chest X-ray. Timely identification of high risk patients will give pronounced advantages regarding appropriate choices of prevention, treatment and disease control. creator: Amna Saifullah creator: Tauqeer Hussain Mallhi creator: Yusra Habib Khan creator: Muhammad Shahid Iqbal creator: Nasser Hadal Alotaibi creator: Abdulaziz Ibrahim Alzarea creator: Maria Rasheed uri: https://doi.org/10.7717/peerj.10826 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Saifullah et al. title: Identification of fibroblast activation-related genes in two acute kidney injury models link: https://peerj.com/articles/10926 last-modified: 2021-03-18 description: BackgroundIschemia-reperfusion injury and drug-induced nephrotoxicity are the two most common reasons for acute kidney injury (AKI). However, little attention has been paid to early activation of fibroblasts in the progression of AKI to chronic kidney disease (CKD). The present study aimed to identify related genes and pathways on fibroblast activation in two mouse models of AKI: ischemia-reperfusion injury (IRI) model and folic acid (FA)-induced injury model.MethodsThe microarray expression profiles of GSE62732 and GSE121190 were downloaded from the GEO database, and the differentially expressed genes (DEGs) was analyzed using the Limma package of R software. Principal component analysis (PCA) was also performed using R. The functional information of gene products was annotated by Gene Ontology (GO) and DAVID online database, and the pathway analysis was carried out by using the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) database. Protein-protein interactions (PPI) network was constructed by STRING and Cytoscape. Furthermore, in the Hypoxia/Reoxygenation (H/R) model, the morphological changes of cells were observed under microscope and the expression of the hub genes in NRK-49F cells were validated by qRT-PCR assays.ResultsA total of 457 DEGs were identified. Among these, 215 DEGs were upregulated and 242 DEGs were downregulated in the acute injured samples compared with uninjured samples. The GO enrichment analysis indicated that these DEGs were mainly involved in transport, the oxidation-reduction process, the metabolic process, metal ion binding, hydrolase activity, and oxidoreductase activity. The KEGG analysis revealed that these DEGs were significantly enriched in the PI3K-Akt signaling pathway, protein digestion and absorption pathway, and focal adhesion pathway. The hub genes including Hnf4α, Pck1 and Timp1 were validated by the qRT-PCR assay in NRK-49F cells in the H/R model.ConclusionsHnf4α, Pck1 and Timp-1 may play a pivotal role in the early activation of fibroblasts, providing novel therapeutic strategies for early prediction and treatment of renal fibrosis. creator: Weiming Deng creator: Xiangling Wei creator: Zhanwen Dong creator: Jinhua Zhang creator: Zhengyu Huang creator: Ning Na uri: https://doi.org/10.7717/peerj.10926 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Deng et al. title: Molecular barcode and morphological analysis of Smilax purhampuy Ruiz, Ecuador link: https://peerj.com/articles/11028 last-modified: 2021-03-18 description: Smilax plants are distributed in tropical, subtropical, and temperate regions in both hemispheres of the world. They are used extensively in traditional medicines in a number of countries. However, morphological and molecular barcodes analysis, which may assist in the taxonomic identification of species, are lacking in Ecuador. In order to evaluate the micromorphological characteristics of these plants, cross sections of Smilax purhampuy leaves were obtained manually. The rhizome powder, which is typically used in traditional medicines, was analyzed for micromorphological characteristics. All samples were clarified with 1% sodium hypochlorite. Tissues were colored with 1% safranin in water and were fixed with glycerinated gelatin. DNA was extracted from the leaves using a modified CTAB method for molecular barcode characterization and PCR was performed using primers to amplify the different loci including the plastid genome regions atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer; and the nuclear DNA sequence ITS2. A DNA sequence similarity search was performed using BLAST in the GenBank nr database and phylogenetic analysis was performed using the maximum likelihood method according to the best model identified by MEGAX using a bootstrap test with 1,000 replicates. Results showed that the micromorphological evaluation of a leaf cross section depicted a concave arrangement of the central vein, which was more pronounced in the lower section and had a slight protuberance. The micromorphological analysis of the rhizome powder allowed the visualization of a group of cells with variable sizes in the parenchyma and revealed thickened xylematic vessels associated with other elements of the vascular system. Specific amplicons were detected in DNA barcoding for all the barcodes tested except for the trnH–psbA spacer. BLAST analysis revealed that the Smilax species was predominant in all the samples for each barcode; therefore, the genus Smilax was confirmed through DNA barcode analysis. The barcode sequences psbK-psbI, atpF-atpH, and ITS2 had a better resolution at the species level in phylogenetic analysis than the other barcodes we tested. creator: Pilar Soledispa creator: Efrén Santos-Ordóñez creator: Migdalia Miranda creator: Ricardo Pacheco creator: Yamilet Irene Gutiérrez Gaiten creator: Ramón Scull uri: https://doi.org/10.7717/peerj.11028 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Soledispa et al. title: Supplementary feeding of cattle-yak in the cold season alters rumen microbes, volatile fatty acids, and expression of SGLT1 in the rumen epithelium link: https://peerj.com/articles/11048 last-modified: 2021-03-18 description: Cattle-yak, a hybrid offspring of yak (Bos grunniens) and cattle (Bos taurus), inhabit the Qinghai-Tibet Plateau at an altitude of more than 3,000 m and obtain nutrients predominantly through grazing on natural pastures. Severe shortages of pasture in the cold season leads to reductions in the weight and disease resistance of grazing cattle-yak, which then affects their production performance. This study aimed to investigate the effect of supplementary feeding during the cold season on the rumen microbial community of cattle-yak. Six cattle-yak (bulls) were randomly divided into two groups—“grazing + supplementary feeding” (G+S) (n = 3) and grazing (G) (n = 3)—and rumen microbial community structure (based on 16S rRNA sequencing), volatile fatty acids (VFAs), and ruminal epithelial sodium ion-dependent glucose transporter 1 (SGLT1) expression were assessed. There were significant differences in the flora of the two groups at various taxonomic classification levels. For example, Bacteroidetes, Rikenellaceae, and Rikenellaceae_RC9_gut_group were significantly higher in the G+S group than in the G group (P < 0.05), while Firmicutes and Christensenellaceae_R-7_group were significantly lower in the G+S group than in the G group (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) analyses revealed that functions related to carbohydrate metabolism and energy production were significantly enriched in the G+S group (P < 0.05). In addition, the concentration of total VFAs, along with concentrations of acetate, propionate, and butyrate, were significantly higher in the G+S group than in the G group (P < 0.05). Furthermore, SGLT1 expression in ruminal epithelial tissue was significantly lower in the G+S group (P < 0.01). Supplementary feeding of cattle-yak after grazing in the cold season altered the microbial community structure and VFA contents in the rumen of the animals, and decreased ruminal epithelial SGLT1 expression. This indicated that supplementary feeding after grazing aids rumen function, improves adaptability of cattle-yak to the harsh environment of the Qinghai-Tibet Plateau, and enhances ability of the animals to overwinter. creator: Yuzhu Sha creator: Jiang Hu creator: Bingang Shi creator: Renqing Dingkao creator: Jiqing Wang creator: Shaobin Li creator: Wei Zhang creator: Yuzhu Luo creator: Xiu Liu uri: https://doi.org/10.7717/peerj.11048 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sha et al. title: Specific and sensitive, ready-to-use universal fungi detection by visual color using ITS1 loop-mediated isothermal amplification combined hydroxynaphthol blue link: https://peerj.com/articles/11082 last-modified: 2021-03-18 description: Being ubiquitous, fungi are common opportunistic pathogens to humans that can lead to invasive and life-threatening infections in immunocompromised individuals. Eukaryote-resembling cell membrane and filamentous branches make the fungal diagnosis difficult. This study therefore developed a ready-to-use ITS1 loop-mediated isothermal amplification combined with hydroxynaphthol blue (LAMP-HNB) for rapid, sensitive and specific colorimetric detection of universal fungi in all phyla. The ITS1 LAMP-HNB could identify every evolutionary phylum of fungi according to sequence analyses. We tested a total of 30 clinically relevant fungal isolates (representing three major human pathogenic phyla of fungi, namely Zygomycota, Ascomycota and Basidiomycota) and 21 non-fungal isolates, and the ITS1 LAMP-HNB properly identified all isolates, with a detection limit of as low as 4.6 ag (9.6 copies), which was identical to ITS1 and 18S rDNA PCR. The assays were also validated on the feasibility of point-of-care diagnostic with real food (dry peanuts, chili and garlics) and blood samples. Furthermore, the shelf life of our ready-to-use ITS1 LAMP activity (≥50%) was more than 40 days at 30 °C with 3–5% polyvinyl alcohol or glycerol additive. The results supported the ready-to-use ITS1 LAMP-HNB for simple detection of fungi contamination with high sensitivity in local and resource-constrained areas to prevent opportunistic fungal species infections. creator: Ilada Choopara creator: Yothin Teethaisong creator: Narong Arunrut creator: Sudaluck Thunyaharn creator: Wansika Kiatpathomchai creator: Naraporn Somboonna uri: https://doi.org/10.7717/peerj.11082 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Choopara et al. title: Habitat suitability of cetaceans in the Gulf of Mexico using an ecological niche modeling approach link: https://peerj.com/articles/10834 last-modified: 2021-03-17 description: BackgroundThe Gulf of Mexico (GOM) is a semi-enclosed sea where the waters of the United States, Mexico and Cuba converge. Al least 21 species of cetaceans inhabit it. The only mysticete (baleen whale) is found in the northeast (U.S. waters). The distribution of the 20 species of odontocetes (toothed cetaceans) is well understood in U.S. waters, but practically unknown in Mexican and Cuban waters. In this study we used sighting data from several odontocete species to construct habitat suitability maps in order to identify geographical regions suitable for high diversity throughout the GOM.MethodsHistorical datasets of georeferenced sightings from across the GOM were used to implement the maximum entropy algorithm (MaxEnt) to model the habitat suitability of each species. Five environmental predictors were used, selected for their influence over the occurrence of cetaceans: two oceanographic predictors (sea surface temperature and chlorophyll-a concentration), and three bathymetric predictors (depth, slope, and distance to 200-m isobath). A spatial approach based on the habitat suitability maps was used to identify the suitable regions.ResultsOnly 12 species were modeled, which were the ones with the minimum sample size required. The models performed well, showing good discriminatory power and slight overfitting. Overall, depth, minimum sea surface temperature, and bottom slope were the most contributing predictor in the models. High suitability areas of 10 species were located on the continental slope, and four suitable regions were identified: (1) the Mississippi Canyon and the Louisiana-Texas slope in the northern GOM, (2) the west Florida slope in the east-northeastern GOM, (3) the Rio Grande slope in the west-northwestern GOM, and (4) the Tamaulipas-Veracruz slope in the west-southwestern GOM.ConclusionsWe were able to detect four geographic regions in the GOM where a high diversity of odontocetes is expected, all located on the continental slope. Although the methodology to identify them (spatial overlap) is a very conservative approach, it is useful for conservation and management purposes. The paucity of data did not allow all species to be modeled, which highlights the importance of establishing transboundary monitoring programs. creator: M. Rafael Ramírez-León creator: María C. García-Aguilar creator: Alfonsina E. Romo-Curiel creator: Zurisaday Ramírez-Mendoza creator: Arturo Fajardo-Yamamoto creator: Oscar Sosa-Nishizaki uri: https://doi.org/10.7717/peerj.10834 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ramírez-León et al. title: Impact of work environment perceptions and communication satisfaction on the intention to quit: an empirical analysis of nurses in Saudi Arabia link: https://peerj.com/articles/10949 last-modified: 2021-03-17 description: ObjectiveIn consideration of the current nursing shortage in Saudi Arabia, we aimed to investigate the association among perceptions of work environment, communication satisfaction, and intentions to quit nursing profession among nurses. In addition, we aimed to investigate the mediating effect of communication satisfaction on the association between nurses’ perception of work environment and their intentions to quit nursing profession.MethodsThis predictive correlational study was conducted at one of the major hospitals in Saudi Arabia from January 2020 to March 2020. It included a convenience sample of 367 full-time registered nurses who completed three types of close-ended questionnaires. We used IBM SPSS version 24.0 to analyze the collected data. Regression analyses were used to test the study’s hypotheses. All regression assumptions were assessed and confirmed. Significance for all tests was set at p ≤ .05.ResultsThe findings indicated an affirmative association between work environment perception and communication satisfaction (b = .764, p < .05) among nurses. In addition, findings showed that work environment perception (b = −.187, p < .05) and communication satisfaction (b = −.226, p < .05) have negative impacts on the nurses’ intentions to quit; indicating that as work environment perception or communication satisfaction increases, the intention to quit decreases among nurses. Further, a mediation effect of communication satisfaction on the relationship between work environment perception and intention to quit was confirmed.ConclusionThis study presents a novel conceptual framework developed based on the literature about the predisposing factors for nurses’ intentions to quit nursing profession. Our results suggest that work environment perception and communication satisfaction among the most contributing factors for nurses resignation. Effective communication was established as a crucial factor for establishing attractive and healthy working environment. Nursing managers can benefit by applying these findings to develop appropriate strategies to inhibit the shortage of nurses in Saudi Arabia. creator: Abdulaziz M. Alsufyani creator: Khalid E. Almalki creator: Yasir M. Alsufyani creator: Sayer M. Aljuaid creator: Abeer M. Almutairi creator: Bandar O. Alsufyani creator: Abdullah S. Alshahrani creator: Omar G. Baker creator: Ahmad Aboshaiqah uri: https://doi.org/10.7717/peerj.10949 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Alsufyani et al. title: Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma link: https://peerj.com/articles/11067 last-modified: 2021-03-17 description: BackgroundCholangiocarcinoma (CCA) is a malignancy that originates from bile duct cells. The incidence and mortality of CCA are very high especially in Southeast Asian countries. Moreover, most CCA patients have a very poor outcome. Presently, there are still no effective treatment regimens for CCA. The resistance to several standard chemotherapy drugs occurs frequently; thus, searching for a novel effective treatment for CCA is urgently needed.MethodsIn this study, comprehensive bioinformatics analyses for identification of novel target genes for CCA therapy based on three microarray gene expression profiles (GSE26566, GSE32225 and GSE76297) from the Gene Expression Omnibus (GEO) database were performed. Based on differentially expressed genes (DEGs), gene ontology and pathway enrichment analyses were performed. Protein-protein interactions (PPI) and hub gene identifications were analyzed using STRING and Cytoscape software. Then, the expression of candidate genes from bioinformatics analysis was measured in CCA cell lines using real time PCR. Finally, the anti-tumor activity of specific inhibitor against candidate genes were investigated in CCA cell lines cultured under 2-dimensional and 3-dimensional cell culture models.ResultsThe three microarray datasets exhibited an intersection consisting of 226 DEGs (124 up-regulated and 102 down-regulated genes) in CCA. DEGs were significantly enriched in cell cycle, hemostasis and metabolism pathways according to Reactome pathway analysis. In addition, 20 potential hub genes in CCA were identified using the protein-protein interaction (PPI) network and sub-PPI network analysis. Subsequently, CDC20 was identified as a potential novel targeted drug for CCA based on a drug prioritizing program. In addition, the anti-tumor activity of a potential CDC20 inhibitor, namely dinaciclib, was investigated in CCA cell lines. Dinaciclib demonstrated huge anti-tumor activity better than gemcitabine, the standard chemotherapeutic drug for CCA.ConclusionUsing integrated bioinformatics analysis, CDC20 was identified as a novel candidate therapeutic target for CCA. creator: Prin Sungwan creator: Worachart Lert-itthiporn creator: Atit Silsirivanit creator: Nathakan Klinhom-on creator: Seiji Okada creator: Sopit Wongkham creator: Wunchana Seubwai uri: https://doi.org/10.7717/peerj.11067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sungwan et al. title: RNA-seq analysis of antibacterial mechanism of Cinnamomum camphora essential oil against Escherichia coli link: https://peerj.com/articles/11081 last-modified: 2021-03-17 description: BackgroundTranscriptome analysis plays a central role in elucidating the complexity of gene expression regulation in Escherichia coli. In recent years, the overuse of antibiotics has led to an increase in antimicrobial resistance, which greatly reduces the efficacy of antibacterial drugs and affects people’s health. Therefore, several researchers are focused on finding other materials, which could replace or supplement antibiotic treatment.MethodsE. coli was treated with water, acetone and Cinnamomum camphora essential oils, respectively. The antibacterial activity was assessed using the minimum inhibitory concentration (MIC), the minimum bactericidal concentration (MBC), the dry weight and the wet weight of the cells. To explore the antibacterial mechanism of the oil, the RNA-Seq analysis was adopted under three different treatments. Finally, the expression of related genes was verified by Quantitative PCR.ResultsIn this study, we showed that the C. Camphora essential oil exerted a strong antibacterial effect. Our results showed that the inhibitory efficiency increased with increasing of the concentration of essential oil. RNA-seq analysis indicated that the essential oil inhibited the growth of E. coli by inhibiting the metabolism, chemotaxis, and adhesion, meanwhile, life activities were maintained by enhancing E. coli resistance reactions. These results are contributed to uncover the antimicrobial mechanisms of essential oils against E. coli, and the C. Camphora essential oil could be applied as an antibacterial agent to replace or ally with antibiotic. creator: Yutian Yu creator: Jie Dong creator: Yanlu Wang creator: Xi Gong uri: https://doi.org/10.7717/peerj.11081 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yu et al. title: Surveillance of tuberculosis and treatment outcomes following screening and therapy interventions among marriage-migrants and labor-migrants from high TB endemic countries in Taiwan link: https://peerj.com/articles/10332 last-modified: 2021-03-16 description: BackgroundTuberculosis (TB) among migrants from high-risk countries and underling interventions were concerned for disease control. This study aimed to assess the TB trends among marriage-migrants with the 1–2-round vs. labor-migrants with the four-round TB screenings in the period of the first four post-entry years; pre-entry screenings by an initial chest X-ray (CXR) were conducted during 2012–2015, and a friendly treatment policy was introduced in 2014.MethodsTB data of migrants during 2012–2015 were obtained from the National TB Registry Database and analyzed. The incidences, clinical characteristics, and treatment outcomes were assessed to explore the impact of underlying interventions.ResultsDuring post-entry 0–4 years, the TB incidence rates among marriage-migrants ranged 11–90 per 100,000 person-years, with 60.8% bacteria-positive and 28.2% smear-positive cases. Whereas among labor migrants, the incidence rates ranged 67–120 per 100,000 person-years, with 43.6% bacteria-positive and 13.7% smear-positive cases. All migrants originated from Southeast Asia following pre-entry health screening in 2012–2015. The TB cases among marriage-migrants were with a higher proportion of sputum-smear-positivity (SS+) (OR: 4.82, 95% CI [3.7–6.34]) and CXR cavitation (OR: 2.90, 95% CI [2.10–4.01]). Marriage-migrants with TB had treatment completion rate of >90%, which was above the WHO target. For labor-migrants with TB, when compared the period of post- vs. pre-implementation of the friendly therapy policy that eliminated compulsory repatriation, the overall treatment completion rate of those who stayed in Taiwan improved by 30.9% (95% CI [24.3–37.6]) vs. 6.7% (95% CI [3.8–9.7]), which exceeded a 4.88-fold (95% CI: 3.83–6.22) improvement. Additionally, the treatment initiation rate within 30 days of diagnosis for SS- TB and B- TB cases during post- vs. pre-implementation of the therapy policy was increased, that is, 77.1% vs. 70.9% (OR: 1.38, 95% CI [1.12–1.70]) and 78% vs. 77% (OR: 1.64, 95% CI [1.38–1.95]).ConclusionMultiple CXR screenings could identify more TB cases with sputum-smear-negativity (SS-) TB at the early-stage, introducing latent tuberculosis infection (LTBI) screening might save underlying efforts. For those labor-migrants with TB who stayed in the receiving country, the friendly TB therapy policy not only significantly improved the treatment completion but also the early treatment initiation. creator: Mei-Mei Kuan uri: https://doi.org/10.7717/peerj.10332 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kuan title: Phylogeny and evolution of Lasiopodomys in subfamily Arvivolinae based on mitochondrial genomics link: https://peerj.com/articles/10850 last-modified: 2021-03-16 description: The species of Lasiopodomys Lataste 1887 with their related genera remains undetermined owing to inconsistent morphological characteristics and molecular phylogeny. To investigate the phylogenetic relationship and speciation among species of the genus Lasiopodomys, we sequenced and annotated the whole mitochondrial genomes of three individual species, namely Lasiopodomys brandtii Radde 1861, L. mandarinus Milne-Edwards 1871, and Neodon (Lasiopodomys) fuscus Büchner 1889. The nucleotide sequences of the circular mitogenomes were identical for each individual species of L. brandtii, L. mandarinus, and N. fuscus. Each species contained 13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs, with mitochondrial genome lengths of 16,557 bp, 16,562 bp, and 16,324 bp, respectively. The mitogenomes and PCGs showed positive AT skew and negative GC skew. Mitogenomic phylogenetic analyses suggested that L. brandtii, L. mandarinus, and L. gregalis Pallas 1779 belong to the genus Lasiopodomys, whereas N. fuscus belongs to the genus Neodon grouped with N. irene. Lasiopodomys showed the closest relationship with Microtus fortis Büchner 1889 and M. kikuchii Kuroda 1920, which are considered as the paraphyletic species of genera Microtus. TMRCA and niche model analysis revealed that Lasiopodomys may have first appeared during the early Pleistocene epoch. Further, L. gregalis separated from others over 1.53 million years ago (Ma) and then diverged into L. brandtii and L. mandarinus 0.76 Ma. The relative contribution of climatic fluctuations to speciation and selection in this group requires further research. creator: Luye Shi creator: Likuan Liu creator: Xiujuan Li creator: Yue Wu creator: Xiangyu Tian creator: Yuhua Shi creator: Zhenlong Wang uri: https://doi.org/10.7717/peerj.10850 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Shi et al. title: Direct-acting antiviral treatment for Hepatitis C Virus in geriatric patients: a real-world retrospective comparison between early and late elderly patients link: https://peerj.com/articles/10944 last-modified: 2021-03-16 description: IntroductionChronic hepatitis C virus (HCV) infection rates are high in the geriatric population considering that interferon-based therapy is usually intolerable. With the introduction of oral antiviral therapy for HCV, increased treatment tolerability and good treatment responses have been observed. However, treatment data regarding the geriatric population have been limited. Therefore, this retrospective study aimed to evaluate the efficacy and safety of direct-acting antiviral therapy for HCV in the geriatric population.Materials and MethodsThe primary end point was sustained virologic response (SVR) 12 weeks after treatment completion, whereas the secondary end points were treatment-related side effects and short-term survival rate following treatment.ResultsIn total, 492 patients (median age, 73 years; 43.9% males), including 278 early elderly patients, were enrolled. Among the included patients, 45% had cirrhosis. HCV genotypes 1 (72.4%) and 2 (25.4%) were the most common. The overall SVR rate was 96.7%, with no difference in SVR rates observed between early and late elderly groups (96.8% vs. 96.7%; p = 0.983). Both groups showed similar side effects, including dizziness (11.4%), and fatigue (8.7%), with three patients discontinuing therapy owing to side effects. Both groups had a similar 3-year survival rate. Significant factors associated with post-treatment survival included cirrhosis, albumin, and creatinine level.ConclusionsOur real-world data showed that both early and late elderly patients could undergo direct-acting antiviral treatment for HCV with excellent treatment outcomes. creator: Hsu-Heng Yen creator: Pei-Yuan Su creator: I-Ling Liu creator: Ya-Yuei Zeng creator: Siou-Ping Huang creator: Yu-Chun Hsu creator: Chia-Wei Yang creator: Yang-Yuan Chen uri: https://doi.org/10.7717/peerj.10944 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yen et al. title: Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager link: https://peerj.com/articles/10947 last-modified: 2021-03-16 description: The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields. creator: James A. Fellows Yates creator: Thiseas C. Lamnidis creator: Maxime Borry creator: Aida Andrades Valtueña creator: Zandra Fagernäs creator: Stephen Clayton creator: Maxime U. Garcia creator: Judith Neukamm creator: Alexander Peltzer uri: https://doi.org/10.7717/peerj.10947 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Fellows Yates et al. title: Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots link: https://peerj.com/articles/10976 last-modified: 2021-03-16 description: BackgroundThe peanut (Arachis hypogaea) is a crop plant of high economic importance, but the epigenetic regulation of its root growth and development has not received sufficient attention. Research on Arabidopsis thaliana has shown that histone deacetylases (HDACs) are involved in cell growth, cell differentiation, and stress response. Few studies have focused on the role of HDACs in the root development of other plants, particularly crop plants. In earlier studies, we found large accumulations of A. hypogaea histone deacetylase 1 (AhHDA1) mRNA in peanut roots. However, we did not explore the role of AhHDA1 in peanut root development.MethodsIn this paper, we investigated the role of the peanut AhHDA1 gene and focused on the effect of altered AhHDA1 expression in hairy roots at both the phenotypic and transcriptional levels. We analyzed the transformation of A. hypogaea hairy roots using Agrobacterium rhizogenes and RNA sequencing to identify differentially expressed genes that were assigned to specific metabolic pathways. Transgenic hairy roots were used as experimental material to analyze the downstream genes expression and histone acetylation levels. To thoroughly understand AhHDA1 function, we also simultaneously screened the AhHDA1-interacting proteins using a yeast two-hybrid system.ResultsAhHDA1-overexpressing hairy roots were growth-retarded after 20 d in vitro cultivation, and they had a greater accumulation of superoxide anions and hydrogen peroxide than the control and RNAi groups. AhHDA1 overexpression in hairy roots accelerated flux through various secondary synthetic metabolic pathways, as well as inhibited the primary metabolism process. AhHDA1 overexpression also caused a significant upregulation of genes encoding the critical enzyme chalcone synthase (Araip.B8TJ0, CHS) in the flavonoid biosynthesis pathway, hydroxyisoflavanone synthase (Araip.0P3RJ) in the isoflavonoid biosynthesis pathway, and caffeoyl-CoA O-methyltransferase (Aradu.M62BY, CCoAOMT) in the phenylpropanoid biosynthesis pathway. In contrast, ferredoxin 1 (Araip.327XS), the polypeptide of the oxygen-evolving complex of photosystem II (Araip.N6ZTJ), and ribulose bisphosphate carboxylase (Aradu.5IY98) in the photosynthetic pathway were significantly downregulated by AhHDA1 overexpression. The expression levels of these genes had a positive correlation with histone acetylation levels.ConclusionOur results revealed that the relationship between altered gene metabolism activities and AhHDA1 overexpression was mainly reflected in flavonoid, isoflavonoid, and phenylpropanoid metabolism. AhHDA1 overexpression retarded the growth of transgenic hairy roots and may be associated with cell metabolism status. Future studies should focus on the function of AhHDA1-interacting proteins and their effect on root development. creator: Liangchen Su creator: Shuai Liu creator: Xing Liu creator: Baihong Zhang creator: Meijuan Li creator: Lidan Zeng creator: Ling Li uri: https://doi.org/10.7717/peerj.10976 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Su et al. title: Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon link: https://peerj.com/articles/11015 last-modified: 2021-03-16 description: BackgroundIn December 2019, the COVID-19 pandemic initially erupted from a cluster of pneumonia cases of unknown origin in the city of Wuhan, China. Presently, it has almost reached 94 million cases worldwide. Lebanon on the brink of economic collapse and its healthcare system thrown into turmoil, has previously managed to cope with the initial SARS-CoV-2 wave. In this study, we sequenced 11 viral genomes from positive cases isolated between 2 February 2020 and 15 March 2020.MethodsSequencing data was quality controlled, consensus sequences generated, and a maximum-likelihood tree was generated with IQTREE v2. Genetic lineages were assigned with Pangolin v1.1.14 and single nucleotide variants (SNVs) were called from read files and manually curated from consensus sequence alignment through JalView v2.11 and the genomic mutational interference with molecular diagnostic tools was assessed with the CoV-GLUE pipeline. Phylogenetic analysis of whole genome sequences confirmed a multiple introduction scenario due to international travel.ResultsThree major lineages were identified to be circulating in Lebanon in the studied period. The B.1 (20A clade) was the most prominent, followed by the B.4 lineage (19A clade) and the B.1.1 lineage (20B clade). SNV analysis showed 15 novel mutations from which only one was observed in the spike region. creator: Rita Feghali creator: Georgi Merhi creator: Aurelia Kwasiborski creator: Veronique Hourdel creator: Nada Ghosn creator: Sima Tokajian uri: https://doi.org/10.7717/peerj.11015 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Feghali et al. title: Evaluating and improving simulations of diurnal variation in land surface temperature with the Community Land Model for the Tibetan Plateau link: https://peerj.com/articles/11040 last-modified: 2021-03-16 description: This study evaluated and improved the ability of the Community Land Model version 5.0 (CLM5.0) in simulating the diurnal land surface temperature (LST) cycle for the whole Tibetan Plateau (TP) by comparing it with Moderate Resolution Imaging Spectroradiometer satellite observations. During daytime, the model underestimated the LST on sparsely vegetated areas in summer, whereas cold biases occurred over the whole TP in winter. The lower simulated daytime LST resulted from weaker heat transfer resistances and greater soil thermal conductivity in the model, which generated a stronger heat flux transferred to the deep soil. During nighttime, CLM5.0 overestimated LST for the whole TP in both two seasons. These warm biases were mainly due to the greater soil thermal inertia, which is also related to greater soil thermal conductivity and wetter surface soil layer in the model. We employed the sensible heat roughness length scheme from Zeng, Wang & Wang (2012), the recommended soil thermal conductivity scheme from Dai et al. (2019), and the modified soil evaporation resistance parameterization, which was appropriate for the TP soil texture, to improve simulated daytime and nighttime LST, evapotranspiration, and surface (0–10 cm) soil moisture. In addition, the model produced lower daytime LST in winter because of overestimation of the snow cover fraction and an inaccurate atmospheric forcing dataset in the northwestern TP. In summary, this study reveals the reasons for biases when simulating LST variation, improves the simulations of turbulent fluxes and LST, and further shows that satellite-based observations can help enhance the land surface model parameterization and unobservable land surface processes on the TP. creator: Xiaogang Ma creator: Jiming Jin creator: Lingjing Zhu creator: Jian Liu uri: https://doi.org/10.7717/peerj.11040 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ma et al. title: Simultaneous determination of two galangin metabolites from Alpinia Officinarum Hance in rat plasma by UF LC-MS/MS and its application in pharmacokinetics study link: https://peerj.com/articles/11041 last-modified: 2021-03-16 description: Galangin has multiple pharmacological efficacies, such as anti-cancer, anti-inflammation and anti-oxidation. Galangin can be rapidly converted into glucuronidated metabolites in vivo. This study aimed to establish an UFLC-MS/MS analytical method to simultaneously determine the concentrations of two glucuronidated metabolites of galangin, galangin-3-O-β-D-glucuronic acid (GG-1) and galangin-7-O-β-D-glucuronic acid (GG-2) in rat plasma. After oral administration of galangal extract (0.3 g/kg), blood samples were collected from the orbital sinus, then treated by methanol precipitation and further gradient-eluted with Phenomenex Kinetex 2.6 µm XB-C18 column. The mass spectrometer was manipulated in the negative electrospray ionization (ESI) and selected multiple reaction monitoring (MRM) mode for the analytes. The precursor-to-product ion pairs applied for GG-1, GG-2 and chrysin (as the internal standard, IS) were m/z 445.2→269.0, 445.2→268.9 and 253.0→142.9, respectively. The results showed that the linear ranges for both GG-1 and GG-2 were 2.0–2000.0 ng/mL (r2 > 0.995). The inter- and intra-day precision were 89.3%–109.2%, RSD was less than 15%, and the repeatability was good. The recoveries of both metabolites and IS were over 89%, and matrix effect was within 15%. The validated analytical method was further applied to study the pharmacokinetic profiles of GG-1 and GG-2 in vivo. The pharmacokinetic parameters suggested that Tmax of GG-1 was equivalent to that of GG-2, and MRT0-t, t1/2 of GG-2 were a little higher than those of GG-1. Importantly, AUC0-t and Cmax of GG-2 were almost twice as those of GG-1. In short, the validated UFLCMS/MS analytical method was feasible to simultaneously determine two galangin metabolites GG-1 and GG-2 in rat plasma and further analyze in vivo metabolism of galangin. creator: Rangru Liu creator: Hailong Li creator: Na Wei creator: Yinfeng Tan uri: https://doi.org/10.7717/peerj.11041 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Photosymbiosis in Late Triassic scleractinian corals from the Italian Dolomites link: https://peerj.com/articles/11062 last-modified: 2021-03-16 description: During the Carnian, oligotrophic shallow-water regions of the western Tethys were occupied by small, coral-rich patch reefs. Scleractinian corals, which already contributed to the formation of the reef structure, owed their position most probably to the symbiosis with dinoflagellate algae (zooxanthellae). Using microstructural (regularity of growth increments) and geochemical (oxygen and carbon stable isotopes) criteria of zooxanthellae symbiosis, we investigated whether this partnership was widespread among Carnian scleractinians from the Italian Dolomites (locality Alpe di Specie). Although corals from this locality are renowned from excellent mineralogical preservation (aragonite), their skeletons were rigorously tested against traces of diagenesis Irrespective of their growth forms, well preserved skeletons of corals from the Dolomites, most frequently revealed regular growth bands (low values of coefficient of variation) typical of modern zooxanthellate corals. Paradoxically, some Carnian taxa (Thamnasteriomorpha frechi and Thamnasteriomorphasp.)with highly integrated thamnasterioid colonies which today are formed exclusively by zooxanthellate corals, showed irregular fine-scale growth bands (coefficient of variation of 40% and 41% respectively) that could suggest their asymbiotic status. However, similar irregular skeletal banding is known also in some modern agariciids (Leptoseris fragilis) which are symbiotic with zooxanthellae. This may point to a similar ecological adaptation of Triassic taxa with thamnasterioid colonies. Contrary to occasionally ambiguous interpretation of growth banding, all examined Carnian corals exhibited lack of distinct correlation between carbon (δ13C range between 0.81‰ and 5.81‰) and oxygen (δ18O values range between −4.21‰ and −1.06‰) isotope composition of the skeleton which is consistent with similar pattern in modern zooxanthellates. It is therefore highly likely, that Carnian scleractinian corals exhibited analogous ecological adaptations as modern symbiotic corals and that coral-algal symbiosis that spread across various clades of Scleractinia preceded the reef bloom at the end of the Triassic. creator: Katarzyna Frankowiak creator: Ewa Roniewicz creator: Jarosław Stolarski uri: https://doi.org/10.7717/peerj.11062 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Frankowiak et al. title: Nitrogen fertilizer reduction in combination with Azolla cover for reducing ammonia volatilization and improving nitrogen use efficiency of rice link: https://peerj.com/articles/11077 last-modified: 2021-03-16 description: BackgroundExcessive nitrogen (N) application rate with low N use efficiency (NUE) caused a considerable amount of N losses, especially ammonia volatilization (AV). Proper N fertilizer reduction (RN) could significantly reduce AV. However, continuous RN led to a nutrient deficiency in the soil and therefore negatively impacted the NUE and rice yield. Paddy Azolla, a good green manure, is considered as a promising measure to decrease AV and improve NUE and grain yield of rice. However, there is limited information on the integrated effects of RN and Azolla cover on the AV, NUE, and rice yield, especially in the highly fertilized rice-growing systems.MethodsThe experiment was conducted including eight treatments: the control (without N fertilizer and Azolla cover), Azolla cover without N fertilizer (A), farmer’s N application rate (FN), FN + Azolla cover (FNA), 15% RN from FN (RN15), RN15 + Azolla cover (RN15A). 30% RN from FN (RN30), RN30 + Azolla cover (RN30A). The integrated effects of N fertilizer reduction and Azolla cover on AV, NUE, and rice grain was evaluated.ResultsRN15A and RN30A substantially reduced total AV by 50.3 and 66.9% compared with FN, respectively, primarily due to the lower surface water ammonia concentrations and pH. RN improved the efficiency of Azolla cover on reducing AV, with 4.1–9.9% higher than for FN. Compared with the FN, RN15A and RN30A enhanced apparent N recovery efficiency (ANRE) by 46.5 and 39.1%, which might be responsible for the lower NH3 emission and the increased total N uptake / total chemical N applied. Furthermore, RN15A and RN30A reduced yield-scaled volatilization by 52.3 and 64.3% than for FN, respectively. Thus, combining 15–30% RN with Azolla cover may be a way to reduce AV and improve ANRE without decreasing rice grain yield. creator: Guoying Yang creator: Hongting Ji creator: Hongjiang Liu creator: Yanfang Feng creator: Yuefang Zhang creator: Liugen Chen creator: Zhi Guo uri: https://doi.org/10.7717/peerj.11077 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al. title: Effects of dietary inorganic chromium supplementation on broiler growth performance: a meta-analysis link: https://peerj.com/articles/11097 last-modified: 2021-03-16 description: BackgroundA meta-analysis was conducted to assess dietary inorganic chromium supplementation on broiler growth performance and determine if these effects are regulated by strains, sex, or contextual factors such as study area and time.MethodsEligible studies were identified by searching Web of Science, Springer, Elsevier, Science Direct, Taylor & Francis online databases. The weighted average difference with corresponding 95% confidence interval was computed with a random-effects model. We performed subgroup analyses stratified by study locations, published years, broiler sex, and strains. The publication bias was assessed with Egger’s test method. A total of nine studies were eligible for inclusion.ResultsThe meta-analysis results indicated that inorganic chromium supplementation significantly improved the broiler’s growth performance, with a lower feed conversion ratio (FCR) and a higher average daily feed intake (ADFI). Through subgroup analyses, we found that the result of average daily gain (ADG) in Iran or published in the 2010s, the results of ADFI in Egypt, and the results of FCR in China had significant responses to chromium supplementation. We also found that Cobb 500 broilers and male broilers might be more sensitive to the addition of inorganic chromium by subgroup analyses. A model was used to obtain the amount of chromium addition under the optimal growth performance. The results showed that the adjusted ADFI and FCR presented a quadratic relationship with chromium supplementation except for average daily gain (ADG). The growth performance improved when the inorganic chromium addition ranged from 1.6 to 2.3 mg/kg. The result of sensitivity analyses showed low sensitivity and high stability. Also, there was little indication of publication bias for studies.ConclusionsOur study showed that the males and Cobb 500 broilers might be more sensitive to chromium supplementation and provided more accurate inorganic chromium supplementation for broiler management practice. The fewer included studies may lead to higher heterogeneity, and no subgroup analyses of environmental stress conditions was conducted due to the lack of related information. Therefore, this study still has some limitations, and we look forward to the follow-up researches. creator: Chao Feng creator: Hua Lin creator: Jie Li creator: Bin Xie uri: https://doi.org/10.7717/peerj.11097 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Feng et al. title: Myofascial release versus Mulligan sustained natural apophyseal glides’ immediate and short-term effects on pain, function, and mobility in non-specific low back pain link: https://peerj.com/articles/10706 last-modified: 2021-03-15 description: BackgroundMyofascial release (MFR) and Mulligan Sustained Natural Apophyseal Glides (SNAGs) are manual therapy techniques routinely practiced in the management of non-specific low back pain (NSLBP). As a solo intervention or along with other therapies, both methods have reported positive results for individuals with NSLBP. However, which technique improves NSLBP-related pain, restricted range of motion (ROM) and disability, warrants further research.ObjectiveTo study the comparative effects of MFR and SNAGs on pain, disability, functional ability, and lumbar ROM in NSLBP.MethodA parallel-group study was conducted at tertiary care hospitals. Sixty-five Sub-acute or chronic NSLBP patients were allocated to receive strengthening exercises along with either MFR (n = 33) or SNAGs (n = 32) for six treatment sessions over one week. An independent assessor evaluated outcome measures such as the Visual Analog Scale (VAS), Patient-Specific Function Scale (PSFS), and ROM at baseline, immediate (after 1st treatment), and short-term (post-sixth day of the intervention). The Modified Oswestry disability index (MODI) was assessed at baseline and short-term.ResultsWithin-group analysis found clinically and statistically significant (p < 0.05) changes for VAS and PSFS at immediate and short-term for both the groups. The lumbar extension also showed improvement immediately and in the short-term. Improvement in Lumbar flexion was seen only in the SNAGs group over the short-term. A statistically significant improvement was seen for MODI in both the groups but was not clinically significant in the MFR group. The analysis observed no statistically significant difference (p < 0.05) between the groups at both the immediate and short-term.ConclusionsPain and restricted function associated with NSLBP can be improved using SNAGs or MFR, along with strengthening exercises. For limited lumbar flexion ROM, Mulligan SNAGs have a better outcome than MFR over the short-term. Hence, both manual therapy techniques can be incorporated along with exercises for immediate and short-term management of sub-acute to chronic NSLBP.Clinical Trial Registration. CTRI/2018/12/016787 (http://ctri.nic.in/Clinicaltrials/). creator: Vignesh Bhat P creator: Vivek Dineshbhai Patel creator: Charu Eapen creator: Manisha Shenoy creator: Steve Milanese uri: https://doi.org/10.7717/peerj.10706 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bhat P et al. title: Metabolite profiling of endophytic Streptomyces spp. and its antiplasmodial potential link: https://peerj.com/articles/10816 last-modified: 2021-03-15 description: BackgroundAntiplasmodial drug discovery is significant especially from natural sources such as plant bacteria. This research aimed to determine antiplasmodial metabolites of Streptomyces spp. against Plasmodium falciparum 3D7 by using a metabolomics approach.MethodsStreptomyces strains’ growth curves, namely SUK 12 and SUK 48, were measured and P. falciparum 3D7 IC50 values were calculated. Metabolomics analysis was conducted on both strains’ mid-exponential and stationary phase extracts.ResultsThe most successful antiplasmodial activity of SUK 12 and SUK 48 extracts shown to be at the stationary phase with IC50 values of 0.8168 ng/mL and 0.1963 ng/mL, respectively. In contrast, the IC50 value of chloroquine diphosphate (CQ) for antiplasmodial activity was 0.2812 ng/mL. The univariate analysis revealed that 854 metabolites and 14, 44 and three metabolites showed significant differences in terms of strain, fermentation phase, and their interactions. Orthogonal partial least square-discriminant analysis and S-loading plot putatively identified pavettine, aurantioclavine, and 4-butyldiphenylmethane as significant outliers from the stationary phase of SUK 48. For potential isolation, metabolomics approach may be used as a preliminary approach to rapidly track and identify the presence of antimalarial metabolites before any isolation and purification can be done. creator: Siti Junaidah Ahmad creator: Noraziah Mohamad Zin creator: Noor Wini Mazlan creator: Syarul Nataqain Baharum creator: Mohd Shukri Baba creator: Yee Ling Lau uri: https://doi.org/10.7717/peerj.10816 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ahmad et al. title: Predicting maximal oxygen uptake from a 3-minute progressive knee-ups and step test link: https://peerj.com/articles/10831 last-modified: 2021-03-15 description: BackgroundCardiorespiratory fitness assessment is crucial for diagnosing health risks and assessing interventions. Direct measurement of maximum oxygen uptake (V̇O2 max) yields more objective and accurate results, but it is practical only in a laboratory setting. We therefore investigated whether a 3-min progressive knee-up and step (3MPKS) test can be used to estimate peak oxygen uptake in these settings.MethodThe data of 166 healthy adult participants were analyzed. We conducted a V̇O2 max test and a subsequent 3MPKS exercise test, in a balanced order, a week later. In a multivariate regression model, sex; age; relative V̇O2 max; body mass index (BMI); body fat percentage (BF); resting heart rate (HR0); and heart rates at the beginning as well as at the first, second, third, and fourth minutes (denoted by HR0, HR1, HR2, HR3, and HR4, respectively) during a step test were used as predictors. Moreover, R2 and standard error of estimate (SEE) were used to evaluate the accuracy of various body composition models in predicting V̇O2max.ResultsThe predicted and actual V̇O2 max values were significantly correlated (BF% model: R2 = 0.624, SEE = 4.982; BMI model: R2 = 0.567, SEE = 5.153). The BF% model yielded more accurate predictions, and the model predictors were sex, age, BF%, HR0, ΔHR3−HR0, and ΔHR3−HR4.ConclusionIn our study, involving Taiwanese adults, we constructed and verified a model to predict V̇O2 max, which indicates cardiorespiratory fitness. This model had the predictors sex, age, body composition, and heart rate changes during a step test. Our 3MPKS test has the potential to be widely used in epidemiological research to measure V̇O2 max and other health-related parameters. creator: Yu-Chun Chung creator: Ching-Yu Huang creator: Huey-June Wu creator: Nai-Wen Kan creator: Chin-Shan Ho creator: Chi-Chang Huang creator: Hung-Ting Chen uri: https://doi.org/10.7717/peerj.10831 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chung et al. title: Divergent morphological responses to millennia of climate change in two species of bats from Hall’s Cave, Texas, USA link: https://peerj.com/articles/10856 last-modified: 2021-03-15 description: How species will respond to ongoing and future climate change is one of the most important questions facing biodiversity scientists today. The fossil record provides unparalleled insight into past ecological and evolutionary responses to climate change, but the resource remains virtually untapped for many organisms. We use geometric morphometrics and a 25,000 year fossil record to quantify changes in body size and mandible shape through time and across climate regimes for two bat species present in Quaternary paleontological deposits of central Texas: Myotis velifer, a bat distributed throughout the Southwestern US and Mexico that is still found in central Texas today, and Eptesicus fuscus, a bat widely distributed throughout North America that has been extirpated in central Texas. Because of ecogeographic rules like Bergmann’s rule, which posits that endotherms are larger in colder environments, we hypothesized that both species were larger during cooler time intervals. Additionally, we hypothesized that both species would show variation in dental morphology across the studied sequence as a response to climate change. While we found a decrease in centroid size–a proxy for ­­body size–through time for both species, we could not establish a clear relationship between centroid size and temperature alone. However, we did find that specimens from drier environments were significantly larger than those from wetter ones. Furthermore, we found significant dental shape variation between environments reflecting different temperature levels for both species. Yet only M. velifer exhibited significant variation between environments of varying precipitation levels. This result was surprising because present-day populations of E. fuscus are highly variable across both temperature and precipitation gradients. We determined that the morphological change experienced by M. velifer through time, and between warmer and cooler temperatures, was associated with the coronoid process, condylar process, and the mandibular symphysis. These parts play a pivotal role in bite force, so changes in these features might relate to changes in diet. We show that long-term datasets derived from fossil material provide invaluable insight not only into the validity of ecogeographic rules, but also into the adaptive capacities of extant taxa when faced with environmental changes. Our results highlight diverging responses to a variety of climate factors that are relevant to consider in biodiversity research given ongoing global change. creator: Molly Moroz creator: Illiam S.C. Jackson creator: Daniel Ramirez creator: Melissa E. Kemp uri: https://doi.org/10.7717/peerj.10856 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Moroz et al. title: Associations with monetary values do not influence access to awareness for faces link: https://peerj.com/articles/10875 last-modified: 2021-03-15 description: Human faces can convey socially relevant information in various ways. Since the early detection of such information is crucial in social contexts, socially meaningful information might also have privileged access to awareness. This is indeed suggested by previous research using faces with emotional expressions. However, the social relevance of emotional faces is confounded with their physical stimulus characteristics. Here, we sought to overcome this problem by manipulating the relevance of face stimuli through classical conditioning: Participants had to learn the association between different face exemplars and high or low amounts of positive and negative monetary outcomes. Before and after the conditioning procedure, the time these faces needed to enter awareness was probed using continuous flash suppression, a variant of binocular rivalry. While participants successfully learned the association between the face stimuli and the respective monetary outcomes, faces with a high monetary value did not enter visual awareness faster than faces with a low monetary value after conditioning, neither for rewarding nor for aversive outcomes. Our results tentatively suggest that behaviorally relevant faces do not have privileged access to awareness when the assessment of the faces’ relevance is dependent on the processing of face identity, as this requires complex stimulus processing that is likely limited at pre-conscious stages. creator: Marcus Rothkirch creator: Maximilian Wieser creator: Philipp Sterzer uri: https://doi.org/10.7717/peerj.10875 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rothkirch et al. title: Depression of the soil arbuscular mycorrhizal fungal community by the canopy gaps in a Japanese cedar (Cryptomeria japonica) plantation on Lushan Mountain, subtropical China link: https://peerj.com/articles/10905 last-modified: 2021-03-15 description: Both canopy gaps (CG) and arbuscular mycorrhizal fungi (AMF) play key roles in seedling establishment and increasing species diversity in forests. The response of AMF to canopy gaps is poorly understood. To assess the long-term effects of canopy gaps on soil AMF community, we sampled soil from plots in a 50-year Cryptomeria japonica (L.f.) D. Don. plantation, located in Lushan Mountain, subtropical China. We analyzed the AMF community, identified through 454 pyrosequencing, in soil and edaphic characteristics. Both richness and diversity of AMF in CG decreased significantly compared to the closed canopy (CC). The differences of the AMF community composition between CG and CC was also significant. The sharp response of the AMF community appears to be largely driven by vegetation transformation. Soil nutrient content also influenced some taxa, e.g., the low availability of phosphorus increased the abundance of Acaulospora. These results demonstrated that the formation of canopy gaps can depress AMF richness and alter the AMF community, which supported the plant investment hypothesis and accentuated the vital role of AMF–plant symbioses in forest management. creator: Guiwu Zou creator: Yuanqiu Liu creator: Fanqian Kong creator: Liqin Liao creator: Guanghua Deng creator: Xueru Jiang creator: Junhuo Cai creator: Wei Liu uri: https://doi.org/10.7717/peerj.10905 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zou et al. title: Force-velocity relationship profile of elbow flexors in male gymnasts link: https://peerj.com/articles/10907 last-modified: 2021-03-15 description: BackgroundThe theoretical maximum force (F0), velocity (V0), and power (Pmax) of athletes calculated from the relationship between force and velocity (F-V relationship) and the slope of the F-V relationship, reflect their competitive and training activity profiles. Evaluating the F-V relationship of athletes facilitates categorizing the profiles of dynamic muscle functions in relation to long-term sport-specific training. For gymnastics, however, no studies have tried to examine the profiles of F-V relation and power output for upper limb muscles in relation to the muscularity, while the use of the upper extremities in this sport is very unique as described earlier.PurposeIt was hypothesized that the F-V relationship of the elbow flexion in gymnasts might be characterized by low capacity for generating explosive force, notably in terms of the force normalized to muscle size.MethodsThe F0, V0, and Pmax derived from the force-velocity relationship during explosive elbow flexion against six different loads (unloaded condition, 15, 30, 45, 60, and 75% of maximal voluntary isometric elbow flexion force (MVFEF)) for 16 gymnasts (GYM) and 22 judo athletes (JD). F0 and Pmax were expressed as values relative to the cross-sectional area index (CSAindex) of elbow flexors (F0/CSAindex and Pmax/CSAindex, respectively), which was calculated from muscle thickness in the anterior upper arm. The electromyogram (EMG) activities of the biceps brachii (BB) during the maximal isometric and dynamic tasks were also determined.ResultsThere were no significant differences in CSAindex of elbow flexors between GYM and JD. MVFEF/CSAindex for GYM was significantly lower than that for JD. Force was linearly associated with velocity in the dynamic elbow flexion for all the participants (r =  − 0.997 to −0.905 for GYM, r =  − 0.998 to −0.840 for JD). F0, F0/ CSAindex, V0, Pmax, Pmax/CSAindex, and MVFEF were significantly lower in GYM than in JD. The activity levels of BB during the dynamic tasks tended to be lower in GYM than in JD at load of <45%MVC.ConclusionGymnasts cannot generate explosive elbow flexion force corresponding to their muscle size. This may be due to low neuromuscular activities during the maximal dynamic tasks against relatively low loads. creator: Miyuki Nakatani creator: Kensuke Murata creator: Hiroaki Kanehisa creator: Yohei Takai uri: https://doi.org/10.7717/peerj.10907 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Nakatani et al. title: Measurement invariance of the distress tolerance scale among university students with and without a history of non-suicidal self-injury link: https://peerj.com/articles/10915 last-modified: 2021-03-15 description: Non-suicidal self-injury (NSSI) is the intentional damage to one’s body tissue in the absence of suicidal intent. NSSI primarily serves an emotion regulation function, with individuals engaging in self-injury to escape intense or unwanted emotion. Low distress tolerance has been identified as a mechanism that underlies self-injury, and is commonly assessed using the self-report Distress Tolerance Scale. There are mixed findings regarding the factor structure of the Distress Tolerance Scale, with some researchers utilising a higher-order distress tolerance score (derived from the scores on the four lower-order subscales) and other researchers using the four subscales as unique predictors of psychological outcomes. Neither of these factor structures have been assessed among individuals with a history of self-injury. Of note, an inability to tolerate distress (thought to underlie NSSI) may limit an individual’s capacity to accurately observe and report specific thoughts and emotions experienced in a state of heightened distress, which may impact the validity of scores on the Distress Tolerance Scale. Therefore, measurement invariance should be established before attributing NSSI-related differences on the scale to true differences in distress tolerance. We compared the Distress Tolerance Scale higher-order model with the lower-order four factor model among university students with and without a history of NSSI. Our results indicated that the lower-order four factor model was a significantly better fit to the data than the higher-order model. We then tested the measurement invariance of this lower-order factor model among individuals with and without a history of NSSI, and established configural and full metric invariance, followed by partial scalar and full residual error invariance. These results suggest the four subscales of the Distress Tolerance Scale can be used to confidently discern NSSI-related differences in distress tolerance. creator: Ashley Slabbert creator: Penelope Hasking creator: Danyelle Greene creator: Mark Boyes uri: https://doi.org/10.7717/peerj.10915 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Slabbert et al. title: Preparation and characterization of gelatin-polysaccharide composite hydrogels for tissue engineering link: https://peerj.com/articles/11022 last-modified: 2021-03-15 description: BackgroundTissue engineering, which involves the selection of scaffold materials, presents a new therapeutic strategy for damaged tissues or organs. Scaffold design based on blends of proteins and polysaccharides, as mimicry of the native extracellular matrix, has recently become a valuable strategy for tissue engineering.ObjectiveThis study aimed to construct composite hydrogels based on natural polymers for tissue engineering.MethodsComposite hydrogels based on blends of gelatin with a polysaccharide component (chitosan or alginate) were produced and subsequently enzyme crosslinked. The other three hydrogels, chitosan hydrogel, sodium alginate hydrogel, and microbial transglutaminase-crosslinked gelatin (mTG/GA) hydrogel were also prepared. All hydrogels were evaluated for in vitro degradation property, swelling capacity, and mechanical property. Rat adipose-derived stromal stem cells (ADSCs) were isolated and seeded on (or embedded into) the above-mentioned hydrogels. The morphological features of ADSCs were observed and recorded. The effects of the hydrogels on ADSC survival and adhesion were investigated by immunofluorescence staining. Cell proliferation was tested by thiazolyl blue tetrazolium bromide (MTT) assay.ResultsCell viability assay results showed that the five hydrogels are not cytotoxic. The mTG/GA and its composite hydrogels showed higher compressive moduli than the single-component chitosan and alginate hydrogels. MTT assay results showed that ADSCs proliferated better on the composite hydrogels than on the chitosan and alginate hydrogels. Light microscope observation and cell cytoskeleton staining showed that hydrogel strength had obvious effects on cell growth and adhesion. The ADSCs seeded on chitosan and alginate hydrogels plunged into the hydrogels and could not stretch out due to the low strength of the hydrogel, whereas cells seeded on composite hydrogels with higher elastic modulus, could spread out, and grew in size.ConclusionThe gelatin-polysaccharide composite hydrogels could serve as attractive biomaterials for tissue engineering due to their easy preparation and favorable biophysical properties. creator: Jing Ye creator: Gang Yang creator: Jing Zhang creator: Zhenghua Xiao creator: Ling He creator: Han Zhang creator: Qi Liu uri: https://doi.org/10.7717/peerj.11022 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ye et al. title: The montane trees of the Cameroon Highlands, West-Central Africa, with Deinbollia onanae sp. nov. (Sapindaceae), a new primate-dispersed, Endangered species link: https://peerj.com/articles/11036 last-modified: 2021-03-15 description: We test the hypothesis that the tree species previously known as Deinbollia sp. 2. is a new species for science. We formally characterise and name this species as Deinbollia onanae (Sapindaceae-Litchi clade) and we discuss it in the context of the assemblage of montane tree species in the Cameroon Highlands of West-Central Africa. The new species is a shade-bearing, non-pioneer understorey forest tree species reaching 15 m high and a trunk diameter that can attain over 40 cm at 1.3 m above the ground. Seed dispersal has been recorded by chimpanzees (Pan troglodytes ellioti) and by putty-nose monkeys (Cercopithecus nictitans) and the species is used by chimpanzees for nesting. Cameroon has the highest species-diversity and species endemism known in this African-Western Indian Ocean genus of 42, mainly lowland species. Deinbollia onanae is an infrequent tree species known from six locations in surviving islands of montane (sometimes also upper submontane) forest along the line of the Cameroon Highlands, including one at Ngel Nyaki in Mambilla, Nigeria. Deinbollia onanae is here assessed as Endangered according to the IUCN 2012 standard, threatened by severe fragmentation of its mountain forest habitat due to extensive and ongoing clearance for agriculture. The majority of the 28 tree species of montane forest (above 2000 m alt.) in the Cameroon Highlands are also widespread in East African mountains (i.e. are Afromontane wide). Deinbollia onanae is one of only seven species known to be endemic (globally restricted to) these highlands. It is postulated that this new species is morphologically closest to Deinbollia oreophila, a frequent species at a lower (submontane) altitudinal band of the same range. Detailed ecological data on Deinbollia onanae from the Nigerian location, Ngel Nyaki, where it has been known under the name Deinbollia “pinnata”, is reviewed. creator: Martin Cheek creator: Jean Michel Onana creator: Hazel M. Chapman uri: https://doi.org/10.7717/peerj.11036 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cheek et al. title: Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily link: https://peerj.com/articles/11052 last-modified: 2021-03-15 description: The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases. creator: Sushma Naithani creator: Daemon Dikeman creator: Priyanka Garg creator: Noor Al-Bader creator: Pankaj Jaiswal uri: https://doi.org/10.7717/peerj.11052 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Naithani et al. title: The kinematic analysis of the lower limb during topspin forehand loop between different level table tennis athletes link: https://peerj.com/articles/10841 last-modified: 2021-03-12 description: BackgroundTopspin is one of the most attacking stroke in table tennis sport. The aim of this research was to investigate the kinematic characteristics of the lower limb (driving leg) during topspin forehand loop in different playing level table tennis athletes.MethodsTen male table tennis athletes performed topspin forehand loop shots with maximal force to hit the ball that was played by a professional table tennis coach. The three-dimensional Vicon motion analysis system was used to capture the kinematic information.ResultsThe key findings from this research indicate that there were no significant differences in motion time between elite athletes (EA) and medium athletes (MA) during the entire phase (P = 0.784). EA showed significantly less knee (P < 0.001) as well as hip (P < 0.001) flexion in the BS stage when contrasted to MA, with a significant larger ankle varus (P = 0.003) as well as eversion (P < 0.001) than MA in the BS and FS phase, respectively. EA displayed a significant larger angular changing rate of ankle dorsiflexion (P < 0.001) and varus (P < 0.001) in the BS stage with ankle plantar flexion as well as eversion during the FS stage, with a significant larger ankle internal rotation (P = 0.003) and external rotation (P < 0.001) than MA in the BS and FS phase, respectively. Furthermore, EA showed significantly larger ankle dorsiflexion (P = 0.001) as well as plantarflexion (P < 0.001) ROM in the BS and FS phase respectively compared with MA.ConclusionAnkle activities in the all plane displayed significant differences in kinematic characteristics between EA and MA. MA should pay attention to the function that ankle played in the kinetic chain, such as training the lower limb muscle rapid reaction ability to improve the energy transfer efficiency and capability of the kinetic chain. creator: Yuqi He creator: Xiang Lyu creator: Dong Sun creator: Julien S. Baker creator: Yaodong Gu uri: https://doi.org/10.7717/peerj.10841 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 He et al. title: Positive emotion induction improves cardiovascular coping with a cognitive task link: https://peerj.com/articles/10904 last-modified: 2021-03-12 description: Feeling positive emotions seems to favour an adaptive cardiovascular response (greater heart rate variability, HRV), associated with improved cognitive performance. This study aims to test whether the induction of a positive emotional state produce such cardiovascular response and therefore, enhance coping and performance in Tower of Hanoi (ToH). Forty-two Participants were randomly distributed into two groups (Experimental and Control). Experimental group was subjected to the evocation of a memory of success, while control group was subjected to an attentional task before performing ToH. Heart Rate Variability (HRV), activity of the zygomatic major muscle (ZEMG) and emotions were measured. Emotional induction increased ZEMG activity, feelings of emotional valence and HRV, but the performance in ToH was not different from control. Experiencing positive emotions seems to favour an adaptive psychophysiological response when faced with a complex cognitive task. These results are discussed in relation to clinical practice and health. creator: Francisco Molins creator: Tania Pérez-Calleja creator: Diana Abad-Tortosa creator: Adrian Alacreu-Crespo creator: Miguel Ángel Serrano-Rosa uri: https://doi.org/10.7717/peerj.10904 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Molins et al. title: Genome-wide identification of HSF family in peach and functional analysis of PpHSF5 involvement in root and aerial organ development link: https://peerj.com/articles/10961 last-modified: 2021-03-12 description: BackgroundHeat shock factors (HSFs) play important roles during normal plant growth and development and when plants respond to diverse stressors. Although most studies have focused on the involvement of HSFs in the response to abiotic stresses, especially in model plants, there is little research on their participation in plant growth and development or on the HSF (PpHSF) gene family in peach (Prunus persica).MethodsDBD (PF00447), the HSF characteristic domain, was used to search the peach genome and identify PpHSFs. Phylogenetic, multiple alignment and motif analyses were conducted using MEGA 6.0, ClustalW and MEME, respectively. The function of PpHSF5 was confirmed by overexpression of PpHSF5 into Arabidopsis.ResultsEighteen PpHSF genes were identified within the peach genome. The PpHSF genes were nonuniformly distributed on the peach chromosomes. Seventeen of the PpHSFs (94.4%) contained one or two introns, except PpHSF18, which contained three introns. The in silico-translated PpHSFs were classified into three classes (PpHSFA, PpHSFB and PpHSFC) based on multiple alignment, motif analysis and phylogenetic comparison with HSFs from Arabidopsis thaliana and Oryza sativa. Dispersed gene duplication (DSD at 67%) mainly contributed to HSF gene family expansion in peach. Promoter analysis showed that the most common cis-elements were the MYB (abiotic stress response), ABRE (ABA-responsive) and MYC (dehydration-responsive) elements. Transcript profiling of 18 PpHSFs showed that the expression trend of PpHSF5 was consistent with shoot length changes in the cultivar ‘Zhongyoutao 14’. Further analysis of the PpHSF5 was conducted in 5-year-old peach trees, Nicotiana benthamiana and Arabidopsis thaliana, respectively. Tissue-specific expression analysis showed that PpHSF5 was expressed predominantly in young vegetative organs (leaf and apex). Subcellular localization revealed that PpHSF5 was located in the nucleus in N. benthamiana cells. Two transgenic Arabidopsis lines were obtained that overexpressed PpHSF5. The root length and the number of lateral roots in the transgenic seedlings were significantly less than in WT seedlings and after cultivation for three weeks. The transgenic rosettes were smaller than those of the WT at 2–3 weeks. The two transgenic lines exhibited a dwarf phenotype three weeks after transplanting, although there was no significant difference in the number of internodes. Moreover, the PpHSF5-OE lines exhibited enhanced thermotolerance. These results indicated that PpHSF5 might be act as a suppresser of growth and development of root and aerial organs. creator: Bin Tan creator: Liu Yan creator: Huannan Li creator: Xiaodong Lian creator: Jun Cheng creator: Wei Wang creator: Xianbo Zheng creator: Xiaobei Wang creator: Jidong Li creator: Xia Ye creator: Langlang Zhang creator: Zhiqian Li creator: Jiancan Feng uri: https://doi.org/10.7717/peerj.10961 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tan et al. title: Effect of Bacillus subtilis on antioxidant enzyme activities in tomato grafting link: https://peerj.com/articles/10984 last-modified: 2021-03-12 description: Grafting generally means stress to a plant and this triggers antioxidant defense systems. An imbalance in reactive oxygen species may negatively affect the grafting success. Several research projects have studied the association with plant growth-promoting rhizobacteria (PGPR) and it has been documented that they enhance nutrient acquisition, regulate hormone levels, and influence the antioxidant response in crops. However, little is known about the strategy of inoculating grafted herbaceous plants with PGPR and its effect on the antioxidant response. The effects of inoculating a strain of Bacillus subtilis on the antioxidant metabolism of grafted tomato were evaluated. In this study, two different rootstocks were used for tomato (Solanum lycopersicum L. var. Rio Grande (RG)): [S. lycopersicum L. var. cerasiforme (Ch)] and eggplant [(Solanum melanogena L. (Ber)] to establish a compatible graft (RGCh) and a semicompatible graft (RGBer). Enzyme activities involved in the antioxidant defense system: superoxide dismutase (SOD), catalase (CAT), phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), peroxidase (POD), and total phenols were measured during 4 weeks after grafting. The results show that for RGCh, during the first two weeks after grafting, the tendency was a decrease of the enzyme activity for SOD, CAT, PAL when inoculated with B. subtilis; while in the semicompatible graft RGBer, PPO and PAL decreased their activity after inoculation. For both combinations, the quantity of total phenols varied depending on the day. In both graft combinations, applications of B. subtilis resulted in 86 and 80% callusing compared with the uninoculated control where the percentages were 74 and 70% for RGCh and RGBer, respectively. The highest significant graft success (95%) was recorded 28 days after grafting for inoculated RGBer. These findings imply that B. subtilis induced antioxidant mechanisms in grafted plants and suggest that inoculation with this growth-promoting bacterium can represent a biotechnological approach to improve success in tomato grafting. creator: Maria D. Arias Padró creator: Emilia Caboni creator: Karla Azucena Salazar Morin creator: Marco Antonio Meraz Mercado creator: Víctor Olalde-Portugal uri: https://doi.org/10.7717/peerj.10984 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Arias Padró et al. title: High throughput microRNAs sequencing profile of serum exosomes in women with and without polycystic ovarian syndrome link: https://peerj.com/articles/10998 last-modified: 2021-03-12 description: BackgroundPolycystic ovary syndrome (PCOS) is the most common type of endocrine disorder, affecting 5–11% of women of reproductive age worldwide. microRNAs (miRNAs) stably exist in circulating blood encapsulated in extracellular vesicles such as exosomes; therefore, serum miRNAs have the potential to serve as novel PCOS biomarkers.MethodsTo identify miRNA biomarkers that are associated with PCOS, we performed a comprehensive sequence-based characterization of the PCOS serum miRNA landscape. The serum exosomes were successfully isolated and characterized in a variety of ways. Next, sequence-based analysis was performed on serum exosomes to screen the differentially expressed miRNAs in women with and without PCOS.ResultsThe sequence data revealed that the levels of 54 miRNAs significantly differed between PCOS patients and normal controls. The levels of these miRNAs were detected by RT-qPCR. The results show that hsa-miR-1299, hsa-miR-6818-5p hsa-miR-192-5p, and hsa-miR-145-5p are significantly differentially expressed in PCOS patients serum exosomes and identify these microRNAs as potential biomarkers for PCOS. Furthermore, Gene Ontology (GO) analyses and KEGG pathway analyses of the miRNA targets further allowed to explore the potential implication of the miRNAs in PCOS.ConclusionOur findings suggest that serum exosomal miRNAs serve important roles in PCOS and may be used as novel molecular biomarkers for clinical diagnosis. creator: Feng Zhang creator: Su-Ping Li creator: Tao Zhang creator: Bin Yu creator: Juan Zhang creator: Hai-Gang Ding creator: Fei-Jun Ye creator: Hua Yuan creator: Ying-Ying Ma creator: Hai-Tao Pan creator: Yao He uri: https://doi.org/10.7717/peerj.10998 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Screening and identification of endometrial proteins as novel potential biomarkers for repeated implantation failure link: https://peerj.com/articles/11009 last-modified: 2021-03-12 description: Inadequate endometrial receptivity may be responsible for the low implantation rate of transferred embryos in in vitro fertilization (IVF) treatments. Patients with repeated implantation failure (RIF) impact the clinical pregnancy rate for IVF. We collected endometrial tissue during the implantation window of hysteroscopy biopsies from September 2016 to December 2019 and clinical data were collected simultaneously. Patients were divided into RIF and pregnant controls group according to pregnancy outcomes. A total of 82 differentially expressed endometrial proteins were identified, including 55 up-regulated proteins (>1.50-fold, P < 0.05) and 27 down-regulated proteins (<0.67-fold, P < 0.05) by iTRAQ labeling coupled with the 2D LC MS/MS technique in the RIF group. String analysis found interactions between these proteins which assembled in two bunches: ribosomal proteins and blood homeostasis proteins. The most significant enriched Gene Ontology terms were negative regulation of hydrolase activity, blood microparticle, and enzyme inhibitor activity. Our results emphasized the corticosteroid-binding globulin and fetuin-A as the specific proteins of endometrial receptivity by Western-blot. Our study provided experimental data to establish the objective indicator of endometrial receptivity, and also provided new insight into the pathogenesis of RIF. creator: Chong Wang creator: Ying Feng creator: Wen-Jing Zhou creator: Zhao-Jun Cheng creator: Mei-Yan Jiang creator: Yan Zhou creator: Xiao-Yang Fei uri: https://doi.org/10.7717/peerj.11009 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: ­­Effect of multimodal cues from a predatory fish on refuge use and foraging on an amphidromous shrimp link: https://peerj.com/articles/11011 last-modified: 2021-03-12 description: BackgroundPrey can alter their behavior when detecting predator cues. Little is known about which sensory channel, number of channels, or the interaction among channels that shrimp species use to evaluate the threat from predators. The amphidromous shrimp Xiphocaris elongata has an induced defense, an elongated rostrum, where predatory fishes are present. We sought to test if kairomones or visual cues when presented singly from fish either eating flakes or shrimp, had more effect on altering the temporal feeding and refuge use patterns of long-rostrum (LR) X. elongata. We were also interested in elucidating potential interactions among cues when presented simultaneously in different combinations (kairomones + visual + mechanosensory, kairomones + alarm + visual, kairomones + alarm, kairomones + visual) on the same response variables. We expected that when presented alone kairomones will significantly increase refuge use and decrease foraging, particularly late at night, in comparison to visual cues alone, and that multiple cues when presented simultaneously will further increase refuge use and decrease foraging at night.MethodsWe exposed shrimp to individual or multiple cues from the predatory fish mountain mullet, Augonostomus monticola. We examined shrimp behavior with respect to refuge use and foraging activity during four time periods (after sunset, nighttime, sunrise, and sunset) in a 24-hour period.ResultsShrimp presented fish visual and chemical cues singly did not differ from one another but differed from control shrimp (no cues) with respect to refuge use or foraging. The number of shrimp using refuge in the treatment with most cues (KVM: kairomones+ visual + mechanosensory) was higher than in all the treatments with less cues. A significant decline in foraging was observed when multiple cues were presented simultaneously. The highest number of shrimp foraged one hour after sunset and at nighttime. A significant interaction was observed between cue treatments and time periods, with shrimp in the KVM treatment foraging less and using more refuge late at night and at sunrise than shrimp in other treatments or time periods.ConclusionsThe observation that fish chemical and visual cues when presented singly produced similar refuge use and foraging patterns was contrary to expectation and suggests that visual and chemical cues, when presented alone, provide redundant information to X. elongata with regards to predation threat. The significant increase in refuge use and reduction in foraging observed in the KVM treatment suggest multimodal signal enhancement in the perception of threat. This makes evolutionary sense in “noisy” environments, such as streams, where detection, localization, and intention of predators is much improved when cues are received through multiple sensory channels. creator: Maria E. Ocasio-Torres creator: Todd A. Crowl creator: Alberto M. Sabat uri: https://doi.org/10.7717/peerj.11011 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ocasio-Torres et al. title: Heparin-binding protein and procalcitonin in the diagnosis of pathogens causing community-acquired pneumonia in adult patients: a retrospective study link: https://peerj.com/articles/11056 last-modified: 2021-03-12 description: The performance of inflammatory markers in community-acquired pneumonia (CAP) caused by different pathogens has not been fully studied. We sought to find the differences in the concentrations of procalcitonin (PCT) and heparin-binding protein (HBP) between patients with CAP caused by different pathogens. We enrolled 162 patients with CAP, divided into three groups on the basis of bacterial (n = 108), fungal (n = 21) and viral (n = 33) infection. Complete leukocyte counts and the concentration of HBP and PCT were measured, and the differences were compared with nonparametric tests. The receiver operating characteristic (ROC) curve was used to evaluate the significant differences in the sensitivity and specificity of the indicators. The leukocyte and neutrophils counts and the concentrations of HBP and PCT in the viral group were significantly lower than those in the other two groups (p < 0.001). The area under the ROC curve (AUC) of the concentration of HBP and PCT as well as leukocyte and neutrophils counts were 0.927, 0.892, 0.832 and 0.806 for distinguishing bacterial from viral infection, respectively. The best cut-off value was 20.05 ng/mL for HBP, with a sensitivity of 0.861 and specificity of 0.939. The best cut-off value was 0.195 ng/mL for PCT, with a sensitivity of 0.991 and specificity of 0.636. The best cut-off value was 5.195 × 109/L and 4.000 × 109/L for leukocyte and neutrophils counts, with sensitivity of 0.694 and 0.880 and specificity of 0.667 and 0.636, respectively. The AUC of HBP, PCT and leukocyte and neutrophil counts for distinguishing fungal from viral infection were 0.851, 0.883, 0.835 and 0.830, respectively. The best cut-off values were 29.950 ng/mL, 0.560 ng/mL, 5.265 × 109/L and 3.850 × 109/L, with sensitivity of 0.667, 0.714, 0.905 and 0.952 and specificity of 0.970, 0.879 0.667 and 0.606, respectively. There were no significant differences in the three indicators between the bacterial and fungal infection groups. The concentration of CRP showed no significant differences among the three groups. Consequently, the stronger immune response characterized by higher inflammation markers including HBP and PCT can help distinguish bacterial and fungal CAP from viral CAP. creator: Rentian Cai creator: Huihui Li creator: Zhen Tao uri: https://doi.org/10.7717/peerj.11056 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Cai et al. title: Segmental analysis by speckle-tracking echocardiography of the left ventricle response to isoproterenol in male and female mice link: https://peerj.com/articles/11085 last-modified: 2021-03-12 description: We studied by conventional and speckle-tracking echocardiography, the response of the left ventricle (LV) to a three-week continuous infusion of isoproterenol (Iso), a non-specific beta-adrenergic receptor agonist in male and female C57Bl6/J mice. Before and after Iso (30 mg/kg/day), we characterized LV morphology and function as well as global and segmental strain. We observed that Iso reduced LV ejection in both male (−8.7%) and female (−14.7%) mice. Several diastolic function parameters were negatively regulated in males and females such as E/A, E/E′, isovolumetric relaxation time. Global longitudinal (GLS) and circumferential (GCS) strains were reduced by Iso in both sexes, GLS by 31% and GCS by about 20%. For the segmental LV analysis, we measured strain, strain rate, reverse strain rate, peak speckle displacement and peak speckle velocity in the parasternal long axis. We observed that radial strain of the LV posterior segments were more severely modulated by Iso than those of the anterior wall in males. In females, on the other hand, both posterior and anterior wall segments were negatively impacted by Iso. Longitudinal strain showed similar results to the radial strain for both sexes. Strain rate, on the other hand, was only moderately changed by Iso. Reverse strain rate measurements (an index of diastolic function) showed that posterior LV segments were negatively regulated by Iso. We then studied the animals 5 and 17 weeks after Iso treatment. Compared to control mice, LV dilation was still present in males. Ejection fraction was decreased in mice of both sex compared to control animals. Diastolic function parameters, on the other hand, were back to normal. Taken together, our study indicates that segmental strain analysis can identify LV regions that are more negatively affected by a cardiotoxic agent such as Iso. In addition, cessation of Iso was not accompanied with a complete restoration of cardiac function after four months. creator: Elisabeth Walsh-Wilkinson creator: Marie Arsenault creator: Jacques Couet uri: https://doi.org/10.7717/peerj.11085 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Walsh-Wilkinson et al. title: Molecular characteristic of treatment failure clinical isolates of Leishmania major link: https://peerj.com/articles/10969 last-modified: 2021-03-11 description: BackgroundLeishmaniasis is a prevalent tropical disease caused by more than 20 Leishmania species (Protozoa, Kinetoplastida and Trypanosomatidae). Among different clinical forms of the disease, cutaneous leishmaniasis is the most common form, with an annual 0.6–1 million new cases reported worldwide. This disease’s standard treatment is pentavalent antimonial (SbV) that have been used successfully since the first half of the 20th century as a first-line drug. However, treatment failure is an increasing problem that is persistently reported from endemic areas. It is important to define and standardize tests for drug resistance in cutaneous leishmaniasis. SbV must be reduced to its trivalent active form (SbIII). This reduction occurs within the host macrophage, and the resultant SbIIIenters amastigotes via the aquaglyceroporin1 (AQP1) membrane carrier. Overexpression of AQP1 results in hypersensitivity of the parasites to SbIII, but resistant phenotypes accompany reduced expression, inactivation mutations, or deletion of AQP1. Hence, in this study, a phylogenetic analysis using barcode gene COXII and kDNA minicircle and expression analysis of AQP1 were performed in treatment failure isolates to assess the isolates’ molecular characteristics and to verify possible association with drug response.MethodsSamples in this study were collected from patients with cutaneous leishmaniasis referred to the Diagnosis Laboratory Center in Isfahan Province, Iran, from October 2017 to December 2019. Among them, five isolates (code numbers 1–5) were categorized as treatment failures. The PCR amplification of barcode gene COXII and kDNA minicircle were done and subsequently analyzed using MEGA (10.0.5) to perform phylogenetics analysis of Treatment failures (TF) and Treatment response (TR) samples. Relative quantification of the AQP1 gene expression of TF and TR samples was assessed by real-time PCR.ResultsAll samples were classified as L. major. No amplification failure was observed in the cases of barcode gene COXII and kDNA minicircle amplification. Having excluded the sequences with complete homology using maximum parsimony with the Bootstrap 500 method, four major groups were detected to perform phylogenetic analysis using COXII. The phylogenetic analysis using the barcode target of minicircle showed that all five treatment failure isolates were grouped in a separate sub-clade.ConclusionsWe concluded that the barcode gene COXII and the minicircle kDNA were suitable for identification, differentiation and phylogenetic analysis in treatment failure clinical isolates of Leishmania major. Also, AQP1 gene expression analyses showed that treatment failure isolates had less expression than TR isolates. The isolate with TF and overexpression of the AQP1 gene of other molecular mechanisms such as overexpression of ATP-binding cassette may be involved in the TR, such as overexpression of ATP-binding cassette which requires further research. creator: Gilda Eslami creator: Samira Hatefi creator: Vahid Ramezani creator: Masoud Tohidfar creator: Tatyana V. Churkina creator: Yuriy L. Orlov creator: Saeedeh Sadat Hosseini creator: Mohammad Javad Boozhmehrani creator: Mahmood Vakili uri: https://doi.org/10.7717/peerj.10969 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Eslami et al. title: In silico candidate variant and gene identification using inbred mouse strains link: https://peerj.com/articles/11017 last-modified: 2021-03-11 description: Mice are the most widely used animal model to study genotype to phenotype relationships. Inbred mice are genetically identical, which eliminates genetic heterogeneity and makes them particularly useful for genetic studies. Many different strains have been bred over decades and a vast amount of phenotypic data has been generated. In addition, recently whole genome sequencing-based genome-wide genotype data for many widely used inbred strains has been released. Here, we present an approach for in silico fine-mapping that uses genotypic data of 37 inbred mouse strains together with phenotypic data provided by the user to propose candidate variants and genes for the phenotype under study. Public genome-wide genotype data covering more than 74 million variant sites is queried efficiently in real-time to provide those variants that are compatible with the observed phenotype differences between strains. Variants can be filtered by molecular consequences and by corresponding molecular impact. Candidate gene lists can be generated from variant lists on the fly. Fine-mapping together with annotation or filtering of results is provided in a Bioconductor package called MouseFM. In order to characterize candidate variant lists under various settings, MouseFM was applied to two expression data sets across 20 inbred mouse strains, one from neutrophils and one from CD4+ T cells. Fine-mapping was assessed for about 10,000 genes, respectively, and identified candidate variants and haplotypes for many expression quantitative trait loci (eQTLs) reported previously based on these data. For albinism, MouseFM reports only one variant allele of moderate or high molecular impact that only albino mice share: a missense variant in the Tyr gene, reported previously to be causal for this phenotype. Performing in silico fine-mapping for interfrontal bone formation in mice using four strains with and five strains without interfrontal bone results in 12 genes. Of these, three are related to skull shaping abnormality. Finally performing fine-mapping for dystrophic cardiac calcification by comparing 9 strains showing the phenotype with eight strains lacking it, we identify only one moderate impact variant in the known causal gene Abcc6. In summary, this illustrates the benefit of using MouseFM for candidate variant and gene identification. creator: Matthias Munz creator: Mohammad Khodaygani creator: Zouhair Aherrahrou creator: Hauke Busch creator: Inken Wohlers uri: https://doi.org/10.7717/peerj.11017 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Munz et al. title: Effects of temperature frequency trends on projected japonica rice (Oryza sativa L.) yield and dry matter distribution with elevated carbon dioxide link: https://peerj.com/articles/11027 last-modified: 2021-03-11 description: In this study, we investigated the effects of temperature frequency trends on the projected yield and dry matter distribution of japonica rice (Oryza sativa L.) with elevated carbon dioxide (CO2) under future climate change scenarios in northwestern China. The Crop Environment Resource Synthesis (CERES)-Rice model was forced with the outputs from three general circulation models (GCMs) to project the rice growth and yield. Future temperature trends had the most significant impact on rice growth, and the frequency of higher than optimal temperatures (∼24–28 oC) for rice growth showed a marked increase in the future, which greatly restricted photosynthesis. The frequency of extreme temperatures (>35 oC) also increased, exerting a strong impact on rice fertilization and producing a significantly reduced yield. Although the increased temperature suppressed photosynthetic production, the elevated CO2 stimulated this production; therefore, the net result was determined by the dominant process. The aboveground biomass at harvest trended downward when temperature became the major factor in photosynthetic production and trended upward when CO2-fertilization dominated the process. The trends for the leaf and stem dry matter at harvest were affected not only by changes in photosynthesis but also by the dry matter distribution to the panicles. The trends for the rice panicle dry matter at harvest were closely related to the effects of temperature and CO2 on photosynthetic production, and extreme temperatures also remarkably affected these trends by reducing the number of fertilized spikelets. The trends of rice yield were very similar to those of panicle dry matter because the panicle dry matter is mostly composed of grain weight (yield). This study provides a better understanding of the japonica rice processes, particularly under extreme climate scenarios, which will likely become more frequent in the future. creator: Zeyu Zhou creator: Jiming Jin creator: Libing Song creator: Ling Yan uri: https://doi.org/10.7717/peerj.11027 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhou et al. title: Rapid and cost-effective nutrient content analysis of cotton leaves using near-infrared spectroscopy (NIRS) link: https://peerj.com/articles/11042 last-modified: 2021-03-11 description: The development of portable near-infrared spectroscopy (NIRS) combined with smartphone cloud-based chemometrics has increased the power of these devices to provide real-time in-situ crop nutrient analysis. This capability provides the opportunity to address nutrient deficiencies early to optimise yield. The agriculture sector currently relies on results delivered via laboratory analysis. This involves the collection and preparation of leaf or soil samples during the growing season that are time-consuming and costly. This delays farmers from addressing deficiencies by several weeks which impacts yield potential; hence, requires a faster solution. This study evaluated the feasibility of using NIRS in estimating different macro- and micronutrients in cotton leaf tissues, assessing the accuracy of a portable handheld NIR spectrometer (wavelength range of 1,350–2,500 nm). This study first evaluated the ability of NIRS to predict leaf nutrient levels using dried and ground cotton leaf samples. The results showed the high accuracy of NIRS in predicting essential macronutrients (0.76 ≤ R2 ≤ 0.98 for N, P, K, Ca, Mg and S) and most micronutrients (0.64 ≤ R2 ≤ 0.81 for Fe, Mn, Cu, Mo, B, Cl and Na). The results showed that the handheld NIR spectrometer is a practical option to accurately measure leaf nutrient concentrations. This research then assessed the possibility of applying NIRS on fresh leaves for potential in-field applications. NIRS was more accurate in estimating cotton leaf nutrients when applied on dried and ground leaf samples. However, the application of NIRS on fresh leaves was still quite accurate. Using fresh leaves, the prediction accuracy was reduced by 19% for macronutrients and 11% for micronutrients, compared to dried and ground samples. This study provides further evidence on the efficacy of using NIRS for field estimations of cotton nutrients in combination with a nutrient decision support tool, with an accuracy of 87.3% for macronutrients and 86.6% for micronutrients. This application would allow farmers to manage nutrients proactively to avoid yield penalties or environmental impacts. creator: Jeremy Aditya Prananto creator: Budiman Minasny creator: Timothy Weaver uri: https://doi.org/10.7717/peerj.11042 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Prananto et al. title: pmparser and PMDB: resources for large-scale, open studies of the biomedical literature link: https://peerj.com/articles/11071 last-modified: 2021-03-11 description: PubMed is an invaluable resource for the biomedical community. Although PubMed is freely available, the existing API is not designed for large-scale analyses and the XML structure of the underlying data is inconvenient for complex queries. We developed an R package called pmparser to convert the data in PubMed to a relational database. Our implementation of the database, called PMDB, currently contains data on over 31 million PubMed Identifiers (PMIDs) and is updated regularly. Together, pmparser and PMDB can enable large-scale, reproducible, and transparent analyses of the biomedical literature. pmparser is licensed under GPL-2 and available at https://pmparser.hugheylab.org. PMDB is available in both PostgreSQL (DOI 10.5281/zenodo.4008109) and Google BigQuery (https://console.cloud.google.com/bigquery?project=pmdb-bq&d=pmdb). creator: Joshua L. Schoenbachler creator: Jacob J. Hughey uri: https://doi.org/10.7717/peerj.11071 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Schoenbachler and Hughey title: The association between prior physical fitness and depression in young adults during the COVID-19 pandemic—a cross-sectional, retrospective study link: https://peerj.com/articles/11091 last-modified: 2021-03-11 description: BackgroundThe COVID-19 pandemic has led to a spike in deleterious mental health. This dual-center retrospective cross-sectional study assessed the prevalence of depression in young adults during this pandemic and explored its association with various physical fitness measures.MethodsThis study enrolled 12,889 (80% female) young adults (mean age 20 ± 1) who performed a National Student Physical Fitness battery from December 1st, 2019, to January 20th, 2020, and completed a questionnaire including Beck’s Depression Inventory in May 2020. Independent associations between prior physical fitness and depression during the pandemic were assessed using multivariable linear and binary logistic regressions accordingly, covariates including age, dwelling location, economic level, smoking, alcohol, living status, weight change, and exercise volume during the pandemic. Sex- and baseline stress-stratified analyses were performed.ResultsOf the study population 13.9% of men and 15.0% of women sampled qualified for a diagnosis of depression. After multivariable adjustment, anaerobic (mean change 95% CI −3.3 [−4.8 to 1.8]) aerobic (−1.5 [−2.64 to −0.5]), explosive (−1.64 [−2.7 to −0.6]) and muscular (−1.7 [−3.0 to −0.5]) fitness were independently and inversely associated with depression for the overall population. These remained consistent after sex- and baseline stress-stratification. In binary logistic regression, the combined participants with moderate, high or excellent fitness also showed a much lower risk compared to those least fit in anaerobic (odd ratio (OR) 95% CI 0.68 [0.55–0.82]), aerobic (0.80 [0.68–0.91]), explosive (0.72 [0.61–0.82]), and muscular (0.66 [0.57–0.75]) fitness.ConclusionsThese findings suggest that prior physical fitness may be inversely associated with depression in young adults during a pandemic. creator: Yaoshan Dun creator: Jeffrey W. Ripley-Gonzalez creator: Nanjiang Zhou creator: Qiuxia Li creator: Meijuan Chen creator: Zihang Hu creator: Wenliang Zhang creator: Randal J. Thomas creator: Thomas P. Olson creator: Jie Liu creator: Yuchen Dong creator: Suixin Liu uri: https://doi.org/10.7717/peerj.11091 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Dun et al. title: Short-term variation in abundance of four Acartia species (Copepoda, Calanoida) in a eutrophic bay link: https://peerj.com/articles/10835 last-modified: 2021-03-10 description: The short-term variation in the abundance of Acartia copepods in the eutrophic Gamak Bay of South Korea was investigated with weekly measurements from October 2007 to September 2008. During this period, four Acartia species (A. erythraea, A. ohtsukai, A. omorii, and A. sinjiensis) were recorded as showing seasonally different peak abundance. The abundance of A. erythraea and A. sinjiensis was high in autumn, whereas that of A. omorii was high from winter to spring. In summer, A. erythraea, A. ohtsukai, and A. sinjiensis coexisted at peak abundance significantly related to water temperature and salinity. Results from the response curves of the four Acartia species to water temperature and salinity suggest that A. erythraea and A. sinjiensis increased in abundance at water temperatures >18 °C, whereas A. ohtsukai increased in abundance at water temperatures >27 °C. The occurrence of A. erythraea, A. ohtsukai, and A. sinjiensis decreased with increasing salinity, but chlorophyll-a concentration showed no effect on occurrence. Despite these findings, the coexistence of the three ecologically similar species may be due to prey abundance in summer and autumn (chlorophyll-a concentration >10 µg L−1). Notably, the wide range of the response curve of A. omorii indicates its occurrence at higher salinity levels than other species. creator: Seo Yeol Choi creator: Min Ho Seo creator: Ho Young Soh uri: https://doi.org/10.7717/peerj.10835 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Choi et al. title: Settling taxonomic and nomenclatural problems in brine shrimps, Artemia (Crustacea: Branchiopoda: Anostraca), by integrating mitogenomics, marker discordances and nomenclature rules link: https://peerj.com/articles/10865 last-modified: 2021-03-10 description: High morphological plasticity in populations of brine shrimp subjected to different environmental conditions, mainly salinity, hindered for centuries the identification of the taxonomic entities encompassed within Artemia. In addition, the mismatch between molecular and morphological evolution rates complicates the characterization of evolutionary lineages, generating taxonomic problems. Here, we propose a phylogenetic hypothesis for Artemia based on two new complete mitogenomes, and determine levels of congruence in the definition of evolutionary units using nuclear and mtDNA data. We used a fossil of Artemia to calibrate the molecular clock and discuss divergence times within the genus. The hypothesis proposed herein suggests a more recent time frame for lineage splitting than previously considered. Phylogeographic analyses were performed using GenBank available mitochondrial and nuclear markers. Evidence of gen e flow, identified through discordances between nuclear and mtDNA markers, was used to reconsider the specific status of some taxa. As a result, we consider Artemia to be represented by five evolutionary units: Southern Cone, Mediterranean—South African, New World, Western Asian, and Eastern Asian Lineages. After an exhaustive bibliographical revision, unavailable names for nomenclatural purposes were discarded. The remaining available names have been assigned to their respective evolutionary lineage. The proper names for the evolutionary units in which brine shrimps are structured remain as follows: Artemia persimilis Piccinelli & Prosdocimi, 1968 for the Southern Cone Lineage, Artemia salina (Linnaeus, 1758) for the Mediterranean-SouthAfrican Lineage, Artemia urmiana Günther, 1899 for the Western Asian Lineage, and Artemia sinica Cai, 1989 for the Eastern Asian Lineage. The name Artemia monicaVerrill, 1869 has nomenclatural priority over A. franciscanaKellogg, 1906 for naming the New World Lineage. New synonymies are proposed for A. salina (= C. dybowskiiGrochowski, 1896n. syn., and A. tunisianaBowen & Sterling, 1978n. syn.), A. monica (= A. franciscanaKellogg, 1906n. syn., and A. salina var. pacificaSars, 1904n. syn.); A. urmiana (= B. milhauseniiFischer de Waldheim, 1834n. syn., A. koeppenianaFischer, 1851n. syn., A. proximaKing, 1855n. syn., A. s. var. biloba Entz, 1886n. syn., A. s. var. furcataEntz, 1886n. syn., A. asiaticaWalter, 1887n. syn., A. parthenogeneticaBowen & Sterling, 1978n. syn., A. ebinurica Qian & Wang, 1992 n. syn., A. murae Naganawa, 2017 n. syn., and A. frameshiftaNaganawa & Mura, 2017n. syn.). Internal deep nuclear structuring within the A. monica and A. salina clades, might suggest the existence of additional evolutionary units within these taxa. creator: Lucía Sainz-Escudero creator: E. Karen López-Estrada creator: Paula Carolina Rodríguez-Flores creator: Mario García-París uri: https://doi.org/10.7717/peerj.10865 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sainz-Escudero et al. title: Genome-wide identification and expression pattern of SnRK gene family under several hormone treatments and its role in floral scent emission in Hedychium coronarium link: https://peerj.com/articles/10883 last-modified: 2021-03-10 description: The SnRK (Snf1-Related protein Kinase) gene family plays crucial roles in various plant signaling pathways and stress-adaptive responses including biotic and abiotic stresses via activating protein phosphorylation pathways. However, there is no information available on the role of the SnRK gene family in Hedychium coronarium. H. coronarium is an important crop widely cultivated as an ornamental plant, herb, spice, or condiment. In this study, 60 HcSnRK genes were identified from the H. coronarium genomic and transcriptome data. Phylogenetic and gene structure analysis showed that the HcSnRK genes were divided into three groups (HcSnRK1, HcSnRK2 and HcSnRK3) and among them HcSnRK3 subfamily was further subdivided into two clades according to the number of introns. Chromosome localization analysis showed that HcSnRK genes were unevenly mapped onto all chromosomes, and the Ka/Ks ratio of 24 paralogues includes four tandems and 20 segmental duplications indicated that the HcSnRK gene family underwent a purifying selection. Cis-regulatory elements analysis suggested that the HcSnRK genes respond to multiple hormones and other stresses. The responsiveness of HcSnRK genes to several hormones was analyzed by quantitative real-time PCR. Based on the different transcriptome data, two candidates HcSnRK genes (HcSnRK2.2 and HcSnRK2.9) were screened out for further characterization . The subcellular localization experiment revealed that both genes were located in the nucleus and cytoplasm. Moreover, virus-induced gene silencing (VIGS) of HcSnRK2.2 and HcSnRK2.9 significantly reduced the floral volatile contents by suppressing the expression of terpene synthase genes (HcTPS1, HcTPS3, and HcTPS5), indicating that HcSnRK2.2 and HcSnRK2.9 genes play an important role in the regulatory mechanism of floral aroma. These results will provide novel insights into the functional dissection of H. coronarium SnRK gene family. creator: Chutian Wang creator: Farhat Abbas creator: Yiwei Zhou creator: Yanguo Ke creator: Xinyue Li creator: Yuechong Yue creator: Yunyi Yu creator: Rangcai Yu creator: Yanping Fan uri: https://doi.org/10.7717/peerj.10883 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Forbidden links, trait matching and modularity in plant-hummingbird networks: Are specialized modules characterized by higher phenotypic floral integration? link: https://peerj.com/articles/10974 last-modified: 2021-03-10 description: BackgroundPlant-pollinator mutualistic networks show non-random structural properties that promote species coexistence. However, these networks show high variability in the interacting species and their connections. Mismatch between plant and pollinator attributes can prevent interactions, while trait matching can enable exclusive access, promoting pollinators’ niche partitioning and, ultimately, modularity. Thus, plants belonging to specialized modules should integrate their floral traits to optimize the pollination function. Herein, we aimed to analyze the biological processes involved in the structuring of plant-hummingbird networks by linking network morphological constraints, specialization, modularity and phenotypic floral integration.MethodsWe investigated the understory plant-hummingbird network of two adjacent habitats in the Lacandona rainforest of Mexico, one characterized by lowland rainforest and the other by savanna-like vegetation. We performed monthly censuses to record plant-hummingbird interactions for 2 years (2018–2020). We also took hummingbird bill measurements and floral and nectar measurements. We summarized the interactions in a bipartite matrix and estimated three network descriptors: connectance, complementary specialization (H2’), and nestedness. We also analyzed the modularity and average phenotypic floral integration index of each module.ResultsBoth habitats showed strong differences in the plant assemblage and network dynamics but were interconnected by the same four hummingbird species, two Hermits and two Emeralds, forming a single network of interaction. The whole network showed low levels of connectance (0.35) and high specialization (H2’ = 0.87). Flower morphologies ranged from generalized to specialized, but trait matching was an important network structurer. Modularity was associated with morphological specialization. The Hermits Phaethornis longirostris and P. striigularis each formed a module by themselves, and a third module was formed by the less-specialized Emeralds: Chlorestes candida and Amazilia tzacatl. The floral integration values were higher in specialized modules but not significantly higher than that formed by generalist species.ConclusionsOur findings suggest that biological processes derived from both trait matching and “forbidden” links, or nonmatched morphological attributes, might be important network drivers in tropical plant-hummingbird systems while morphological specialization plays a minor role in the phenotypic floral integration. The broad variety of corolla and bill shapes promoted niche partitioning, resulting in the modular organization of the assemblage according to morphological specialization. However, more research adding larger datasets of both the number of modules and pollination networks for a wider region is needed to conclude whether phenotypic floral integration increases with morphological specialization in plant-hummingbird systems. creator: Jaume Izquierdo-Palma creator: Maria del Coro Arizmendi creator: Carlos Lara creator: Juan Francisco Ornelas uri: https://doi.org/10.7717/peerj.10974 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Izquierdo-Palma et al. title: Activity strategy and pattern of the Siberian jerboa (Orientallactaga sibirica) in the Alxa desert region, China link: https://peerj.com/articles/10996 last-modified: 2021-03-10 description: Rodents exhibit seasonal changes in their activity patterns as an essential survival strategy. We studied the activity patterns and strategies of the Siberian jerboa (Orientallactaga sibirica) in the Alxa desert region to better understand the habitats and behavioural ecology of xeric rodents. We conducted an experiment using three plots to monitor the duration, time, and frequency of the active period of the Siberian jerboa using infrared cameras in the Alxa field workstation, Inner Mongolia, China in 2017. The relationships between the activity time and frequency, biological factors (perceived predation risk, food resources, and species composition), and abiotic factors (temperature, air moisture, wind speed) were analysed using Redundancy Analysis (RDA). Our results showed that: (1) relative humidity mainly affected activities in the springtime; temperature, relative humidity and interspecific competition mainly affected activities in the summertime; relative humidity and perceived predation risk mainly influenced activities in the autumn. (2) The activity pattern of the Siberian jerboa altered depending on the season. The activity of the Siberian jerboa was found to be bimodal in spring and summer, and was trimodal in autumn. The activity time and frequency in autumn were significantly lower than the spring. (3) Animals possess the ability to integrate disparate sources of information about danger to optimize energy gain. The jerboa adapted different responses to predation risks and competition in different seasons according to the demand for food resources. creator: Yu Ji creator: Shuai Yuan creator: Heping Fu creator: Suwen Yang creator: Fan Bu creator: Xin Li creator: Xiaodong Wu uri: https://doi.org/10.7717/peerj.10996 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ji et al. title: Determining insulin sensitivity from glucose tolerance tests in Iberian and landrace pigs link: https://peerj.com/articles/11014 last-modified: 2021-03-10 description: As insulin sensitivity may help to explain divergences in growth and body composition between native and modern breeds, metabolic responses to glucose infusion were measured using an intra-arterial glucose tolerance test (IAGTT). Iberian (n = 4) and Landrace (n = 5) barrows (47.0 ± 1.2 kg body weight (BW)), fitted with a permanent carotid artery catheter were injected with glucose (500 mg/kg BW) and blood samples collected at -10, 0, 5, 10, 15, 20, 25, 30, 45, 60, 90, 120 and 180 min following glucose infusion. Plasma samples were analysed for insulin, glucose, lactate, triglycerides, cholesterol, creatinine, albumin and urea. Insulin sensitivity indices were calculated and analysed. Mean plasma glucose, creatinine and cholesterol concentrations were lower (P < 0.01) in Iberian (14, 68 and 22%, respectively) than in Landrace pigs during the IAGTT. However, mean plasma insulin, lactate, triglycerides and urea concentrations were greater (P < 0.001) in Iberian (50, 35, 18 and 23%, respectively) than in Landrace pigs. Iberian pigs had larger area under the curve (AUC) of insulin (P < 0.05) or tended to a greater AUC of lactate (P < 0.10), and a smaller (P < 0.05) AUC for glucose 0-60 min compared with Landrace pigs. Indices for estimating insulin sensitivity in fasting conditions indicated improved β-cell function in Iberian compared with Landrace pigs, but no difference (P > 0.10) in calculated insulin sensitivity index was found after IAGTT between breeds. A time response (P < 0.05) was obtained for insulin, glucose and lactate so that maximum concentration was achieved at 10 and 15 min post-infusion for insulin (Iberian and Landrace pigs, respectively), immediately post-infusion for glucose, and 20 min post-infusion for lactate, decreasing thereafter until basal levels. There was no time effect for the rest of metabolites evaluated. In conclusion, growing Iberian pigs challenged with an IAGTT showed changes in biochemical parameters and insulin response that may indicate an early stage of insulin resistance. creator: José Miguel Rodríguez-López creator: Manuel Lachica creator: Lucrecia González-Valero creator: Ignacio Fernández-Fígares uri: https://doi.org/10.7717/peerj.11014 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rodríguez-López et al. title: T cell mediated immunity against influenza H5N1 nucleoprotein, matrix and hemagglutinin derived epitopes in H5N1 survivors and non-H5N1 subjects link: https://peerj.com/articles/11021 last-modified: 2021-03-10 description: BackgroundProtection against the influenza virus by a specific antibody is relatively strain specific; meanwhile broader immunity may be conferred by cell-mediated immune response to the conserved epitopes across influenza virus subtypes. A universal broad-spectrum influenza vaccine which confronts not only seasonal influenza virus, but also avian influenza H5N1 virus is promising.MethodsThis study determined the specific and cross-reactive T cell responses against the highly pathogenic avian influenza A (H5N1) virus in four survivors and 33 non-H5N1 subjects including 10 H3N2 patients and 23 healthy individuals. Ex vivo IFN-γ ELISpot assay using overlapping peptides spanning the entire nucleoprotein (NP), matrix (M) and hemagglutinin (HA) derived from A/Thailand/1(KAN-1)/2004 (H5N1) virus was employed in adjunct with flow cytometry for determining T cell functions. Microneutralization (microNT) assay was performed to determine the status of previous H5N1 virus infection.ResultsIFN-γ ELISpot assay demonstrated that survivors nos. 1 and 2 had markedly higher T cell responses against H5N1 NP, M and HA epitopes than survivors nos. 3 and 4; and the magnitude of T cell responses against NP were higher than that of M and HA. Durability of the immunoreactivity persisted for as long as four years after disease onset. Upon stimulation by NP in IFN-γ ELISpot assay, 60% of H3N2 patients and 39% of healthy subjects exhibited a cross-reactive T cell response. The higher frequency and magnitude of responses in H3N2 patients may be due to blood collection at the convalescent phase of the patients. In H5N1 survivors, the effector peptide-specific T cells generated from bulk culture PBMCs by in vitro stimulation displayed a polyfunction by simultaneously producing IFN-γ and TNF-α, together with upregulation of CD107a in recognition of the target cells pulsed with peptide or infected with rVac-NP virus as investigated by flow cytometry.ConclusionsThis study provides an insight into the better understanding on the homosubtypic and heterosubtypic T cell-mediated immune responses in H5N1 survivors and non-H5N1 subjects. NP is an immunodominant target of cross-recognition owing to its high conservancy. Therefore, the development of vaccine targeting the conserved NP may be a novel strategy for influenza vaccine design. creator: Pirom Noisumdaeng creator: Thaneeya Roytrakul creator: Jarunee Prasertsopon creator: Phisanu Pooruk creator: Hatairat Lerdsamran creator: Susan Assanasen creator: Rungrueng Kitphati creator: Prasert Auewarakul creator: Pilaipan Puthavathana uri: https://doi.org/10.7717/peerj.11021 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Noisumdaeng et al. title: When ecological marginality is not geographically peripheral: exploring genetic predictions of the centre-periphery hypothesis in the endemic plant Lilium pomponium link: https://peerj.com/articles/11039 last-modified: 2021-03-10 description: BackgroundQuantifying variation of genetic traits over the geographical range of species is crucial for understanding the factors driving their range dynamics. The center-periphery hypothesis postulates, and many studies support, the idea that genetic diversity decreases and genetic differentiation increases toward the geographical periphery due to population isolation. The effects of environmental marginality on genetic variation has however received much less attention.MethodsWe tested the concordance between geographical and environmental gradients and the genetic predictions of center-periphery hypothesis for endemic Lilium pomponium in the southern Alps.ResultsWe found little evidence for concordance between genetic variation and both geographical and environmental gradients. Although the prediction of increased differentiation at range limits is met, genetic diversity does not decrease towards the geographical periphery. Increased differentiation among peripheral populations, that are not ecologically marginal, may be explained by a decrease in habitat availability that reduces population connectivity. In contrast, a decrease of genetic diversity along environmental but not geographical gradients may be due to the presence of low quality habitats in the different parts of the range of a species that reduce effective population size or increase environmental constraints. As a result, environmental factors may affect population dynamics irrespective of distance from the geographical center of the range. In such situations of discordance between geographical and environmental gradients, the predictions of decreasing genetic diversity and increasing differentiation toward the geographical periphery may not be respected. creator: Gabriele Casazza creator: Carmelo Macrì creator: Davide Dagnino creator: Maria Guerrina creator: Marianick Juin creator: Luigi Minuto creator: John D. Thompson creator: Alex Baumel creator: Frédéric Médail uri: https://doi.org/10.7717/peerj.11039 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Casazza et al. title: A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution link: https://peerj.com/articles/11051 last-modified: 2021-03-10 description: The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers full understanding of the functioning of the living cells. ADP-ribosylation is a common post-translational modification of proteins; also nucleic acids and small molecules can be modified by the covalent attachment of ADP-ribose. This modification, important in cellular signalling and infection processes, is usually executed by enzymes from the large superfamily of ADP-ribosyltransferases (ARTs). Here, using bioinformatics approaches, we identify a novel putative ADP-ribosyltransferase family, conserved in eukaryotic evolution, with a divergent active site. The hallmark of these proteins is the ART domain nestled between flanking leucine-rich repeat (LRR) domains. LRRs are typically involved in innate immune surveillance. The novel family appears as putative novel ADP-ribosylation-related actors, most likely pseudoenzymes. Sequence divergence and lack of clearly detectable “classical” ART active site suggests the novel domains are pseudoARTs, yet atypical ART activity, or alternative enzymatic activity cannot be excluded. We propose that this family, including its human member LRRC9, may be involved in an ancient defense mechanism, with analogies to the innate immune system, and coupling pathogen detection to ADP-ribosyltransfer or other signalling mechanisms. creator: Zbigniew Wyżewski creator: Marcin Gradowski creator: Marianna Krysińska creator: Małgorzata Dudkiewicz creator: Krzysztof Pawłowski uri: https://doi.org/10.7717/peerj.11051 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wyżewski et al. title: Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil link: https://peerj.com/articles/11079 last-modified: 2021-03-10 description: BackgroundLactobacillus crispatus is the dominant species in the vaginal microbiota associated with health and considered a homeostasis biomarker. Interestingly, some strains are even used as probiotics. However, the genetic mechanisms of L. crispatus involved in the control of the vaginal microbiome and protection against bacterial vaginosis (BV) are not entirely known. To further investigate these mechanisms, we sequenced and characterized the first four L. crispatus genomes from vaginal samples from Brazilian women and used genome-wide association study (GWAS) and comparative analyses to identify genetic mechanisms involved in healthy or BV conditions and selective pressures acting in the vaginal microbiome.MethodsThe four genomes were sequenced, assembled using ten different strategies and automatically annotated. The functional characterization was performed by bioinformatics tools comparing with known probiotic strains. Moreover, it was selected one representative strain (L. crispatus CRI4) for in vitro detection of phages by electron microscopy. Evolutionary analysis, including phylogeny, GWAS and positive selection were performed using 46 public genomes strains representing health and BV conditions.ResultsGenes involved in probiotic effects such as lactic acid production, hydrogen peroxide, bacteriocins, and adhesin were identified. Three hemolysins and putrescine production were predicted, although these features are also present in other probiotic strains. The four genomes presented no plasmids, but 14 known families insertion sequences and several prophages were detected. However, none of the mobile genetic elements contained antimicrobial resistance genes. The genomes harbor a CRISPR-Cas subtype II-A system that is probably inactivated due to fragmentation of the genes csn2 and cas9. No genomic feature was associated with a health condition, perhaps due to its multifactorial characteristic. Five genes were identified as under positive selection, but the selective pressure remains to be discovered. In conclusion, the Brazilian strains investigated in this study present potential protective properties, although in vitro and in vivo studies are required to confirm their efficacy and safety to be considered for human use. creator: Marcelle Oliveira de Almeida creator: Rodrigo Carvalho creator: Flavia Figueira Aburjaile creator: Fabio Malcher Miranda creator: Janaína Canário Cerqueira creator: Bertram Brenig creator: Preetam Ghosh creator: Rommel Ramos creator: Rodrigo Bentes Kato creator: Siomar de Castro Soares creator: Artur Silva creator: Vasco Azevedo creator: Marcus Vinicius Canário Viana uri: https://doi.org/10.7717/peerj.11079 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Oliveira de Almeida et al. title: Fall supplemental feeding increases population growth rate of an endangered caribou herd link: https://peerj.com/articles/10708 last-modified: 2021-03-09 description: Most woodland caribou (Rangifer tarandus caribou) populations are declining primarily because of unsustainable predation resulting from habitat-mediated apparent competition. Wolf (Canis lupus) reduction is an effective recovery option because it addresses the direct effect of predation. We considered the possibility that the indirect effects of predation might also affect caribou population dynamics by adversely affecting summer foraging behaviour. If spring and/or summer nutrition was inadequate, then supplemental feeding in fall might compensate for that limitation and contribute to population growth. Improved nutrition and therefore body condition going into winter could increase adult survival and lead to improved reproductive success the next spring. To test that hypothesis, we fed high-quality food pellets to free-ranging caribou in the Kennedy Siding caribou herd each fall for six years, starting in 2014, to see if population growth rate increased. Beginning in winter 2015–16, the Province of British Columbia began a concurrent annual program to promote caribou population increase by attempting to remove most wolves within the Kennedy Siding and the adjacent caribou herds’ ranges. To evaluate the impact of feeding, we compared lambdas before and after feeding began, and to the population trend in the adjacent Quintette herd over the subsequent four years. Supplemental feeding appeared to have an incremental effect on population growth. Population growth of the Kennedy Siding herd was higher in the year after feeding began (λ = 1.06) compared to previous years (λ = 0.91) and to the untreated Quintette herd (λ = 0.95). Average annual growth rate of the Kennedy Siding herd over the subsequent four years, where both feeding and wolf reduction occurred concurrently, was higher than in the Quintette herd where the only management action in those years was wolf reduction (λ = 1.16 vs. λ = 1.08). The higher growth rate of the Kennedy Siding herd was due to higher female survival (96.2%/yr vs. 88.9%/yr). Many caribou were in relatively poor condition in the fall. Consumption of supplemental food probably improved their nutritional status which ultimately led to population growth. Further feeding experiments on other caribou herds using an adaptive management approach would verify the effect of feeding as a population recovery tool. Our results support the recommendation that multiple management actions should be implemented to improve recovery prospects for caribou. creator: Douglas C. Heard creator: Kathryn L. Zimmerman uri: https://doi.org/10.7717/peerj.10708 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Heard and Zimmerman title: Long-term storage of feces at −80 °C versus −20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome link: https://peerj.com/articles/10837 last-modified: 2021-03-09 description: The development of next-generation sequencing technologies has spurred a surge of research on bacterial microbiome diversity and function. But despite the rapid growth of the field, many uncertainties remain regarding the impact of differing methodologies on downstream results. Sample storage temperature is conventionally thought to be among the most important factors for ensuring reproducibility across marker gene studies, but to date much of the research on this topic has focused on short-term storage in the context of clinical applications. Consequently, it has remained unclear if storage at −80 °C, widely viewed as the gold standard for long-term archival of feces, is truly required for maintaining sample integrity in amplicon-based studies. A better understanding of the impacts of long-term storage conditions is important given the substantial cost and limited availability of ultra-low temperature freezers. To this end, we compared bacterial microbiome profiles inferred from 16S V3–V4 amplicon sequencing for paired fecal samples obtained from a feral horse population from Sable Island, Nova Scotia, Canada, stored at either −80 °C or −20 °C for 4 years. We found that storage temperature did not significantly affect alpha diversity measures, including amplicon sequence variant (ASV) richness and evenness, and abundance of rare sequence variants, nor presence/absence, relative abundances and phylogenetic diversity weighted measures of beta diversity. These results indicate that storage of equine feces at −20 °C for periods ranging from a few months to a few years is equivalent to storage at −80 °C for amplicon-based microbiome studies, adding to accumulating evidence indicating that standard domestic freezers are both economical and effective for microbiome research. creator: Stefan Gavriliuc creator: Mason R. Stothart creator: Astrid Henry creator: Jocelyn Poissant uri: https://doi.org/10.7717/peerj.10837 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gavriliuc et al. title: Analyzing clinical characteristics of patients with different cumulative hemodialysis durations: a cross-sectional study link: https://peerj.com/articles/10852 last-modified: 2021-03-09 description: BackgroundThe objective of this study was to examine the clinical characteristics of patients with different cumulative hemodialysis (HD) durations, so as to improve their survival rate.MethodsIn this cross-sectional study, we extracted background information and relevant clinical data from 145 patients who were undergoing maintenance HD three times a week at the Affiliated Hospital of Nantong University between January 1998 and January 2019. The study subjects were divided into four groups according to the duration of their HD: <5 years, 5–10 years, 10–15 years, and >15 years of HD. We collected the medical history and relevant clinical parameters for each subject, and measured the urea reduction ratio (URR), hemoglobin (Hb), serum calcium, phosphorus, parathyroid hormone (iPTH), and serum albumin (ALB) levels for each group.ResultsThe average patient age was 52.06 ±  11.93 years old. The average patient age in the 10–15 years and >15 years groups was significantly lower than in the <5 years and 5–10 years groups (P = 0.002, P < 0.001, P = 0.012, and P = 0.0025, respectively). The most common cause of end-stage renal disease (ESRD) was chronic glomerulonephritis. We found no significant differences in URR, Hb, serum calcium, serum phosphorus, iPTH, and ALB levels.ConclusionA prolonged HD duration was related to a younger mean age at the start of HD treatment. The leading cause of ESRD was chronic glomerulonephritis. We predominantly found diabetic nephropathy in the group with a duration of <5 years cumulative HD. Most of the indexes related to hemodialysis almost satisfied the recommended values in these patients. creator: Xu Chen creator: Li Yuan creator: Yuan Zhang creator: Houyong Dai creator: Yaping Fan creator: Xiaolan Chen uri: https://doi.org/10.7717/peerj.10852 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Expression analysis of genes related to cold tolerance in Dendroctonus valens link: https://peerj.com/articles/10864 last-modified: 2021-03-09 description: Pine beetles are well known in North America for their widespread devastation of pine forests. However, Dendroctonus valens LeConte is an important invasive forest pest in China also. Adults and larvae of this bark beetle mainly winter at the trunks and roots of Pinus tabuliformis and Pinus sylvestris; larvae, in particular, result in pine weakness or even death. Since the species was introduced from the United States to Shanxi in 1998, its distribution has spread northward. In 2017, it invaded a large area at the junction of Liaoning, Inner Mongolia and Hebei provinces, showing strong cold tolerance. To identify genes relevant to cold tolerance and the process of overwintering, we sequenced the transcriptomes of wintering and non-wintering adult and larval D. valens using the Illumina HiSeq platform. Differential expression analysis methods for other non-model organisms were used to compare transcript abundances in adults and larvae at two time periods, followed by the identification of functions and metabolic pathways related to genes associated with cold tolerance. We detected 4,387 and 6,091 differentially expressed genes (DEGs) between sampling dates in larvae and adults, respectively, and 1,140 common DEGs, including genes encoding protein phosphatase, very long-chain fatty acids protein, cytochrome P450, and putative leucine-rich repeat-containing proteins. In a Gene Ontology (GO) enrichment analysis, 1,140 genes were assigned to 44 terms, with significant enrichment for cellulase activity, hydrolase activity, and carbohydrate metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) classification and enrichment analyses showed that the lysosomal and purine metabolism pathways involved the most DEGs, the highly enriched terms included autophagy—animal, pentose and glucuronate interconversions and lysosomal processes. We identified 140 candidate genes associated with cold tolerance, including genes with established roles in this trait (e.g., genes encoding trehalose transporter, fructose-1,6-bisphosphatase, and trehalase). Our comparative transcriptome analysis of adult and larval D. valens in different conditions provides basic data for the discovery of key genes and molecular mechanisms underlying cold tolerance. creator: Dongfang Zhao creator: Chunchun Zheng creator: Fengming Shi creator: Yabei Xu creator: Shixiang Zong creator: Jing Tao uri: https://doi.org/10.7717/peerj.10864 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhao et al. title: The role of gender and academic degree on preference for smooth curvature of abstract shapes link: https://peerj.com/articles/10877 last-modified: 2021-03-09 description: BackgroundPreference for smooth contours occurs for a variety of visual stimuli. However, there are individual differences. Openness to experience, a trait associated with aesthetic appreciation, emotional sensitivity and abstract thinking, correlates with this preference. The evaluation of meaningless stimuli entails automatic associations influenced by knowledge, intellectual interests and individual experiences which are diverse. However, it is difficult to capture this variability in studies restricted to Undergraduate students in Psychology with a prevalence of female participants.MethodsHere we examined preference for curvature with 160 undergraduate students in Psychology, Mathematics, Engineering and Computer Science, balanced for gender. Participants viewed abstract shapes varying for contour (angular vs. curved). The shapes presented variations in Vertices (10, 20, 30) and Concavity (30%, 40%, 50%) to increase complexity. Participants rated how much they liked each shape on a 0 (dislike) to 100 (like) scale. Furthermore, because students in pure Science disciplines present autistic-like traits as measured with the Autism Quotient (AQ), and there is evidence that individuals with autism respond positively to edgy abstract shapes, participants also completed the AQ.ResultsOverall participants preferred curved shapes to angular shapes. We confirmed past research showing that complexity played a key role, with simple shapes with less vertices (10 vertices) being preferred over shapes with larger number of vertices (20 and 30 vertices). Furthermore, simple shapes (10 vertices) were preferred more with more concavities (50%). Importantly, an interaction between academic degree and gender revealed that preference for smooth curvature was stronger for Psychology female participants. Science students scored higher than Psychology students on the AQ. Interestingly, multilevel analyses showed that the variability of AQ traits in the sample did not contribute to this interaction. The results are discussed in relation to theories of preference formation and individual differences. creator: Letizia Palumbo creator: Giulia Rampone creator: Marco Bertamini uri: https://doi.org/10.7717/peerj.10877 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Palumbo et al. title: Sucrose synthase gene family in Brassica juncea: genomic organization, evolutionary comparisons, and expression regulation link: https://peerj.com/articles/10878 last-modified: 2021-03-09 description: Sucrose synthase (SUS) plays an important role in sucrose metabolism and plant development. The SUS gene family has been identified in many plants, however, there is no definitive study of SUS gene in Brassica juncea. In this study, 14 SUS family genes were identified and comprehensively analyzed using bioinformatics tools. The analyzed parameters included their family member characteristics, chromosomal locations, gene structures and phylogenetic as well as transcript expression profiles. Phylogenetic analysis revealed that the 14 members could be allocated into three groups: SUS I, SUS II and SUS III. Comparisons of the exon/intron structure of the mustard SUS gene indicated that its structure is highly conserved. The conserved structure is attributed to purification selection during evolution. Expansion of the SUS gene family is associated with fragment and tandem duplications of the mustard SUS gene family. Collinearity analysis among species revealed that the SUS gene family could be lost or mutated to varying degrees after the genome was doubled, or when Brassica rapa and Brassica nigra hybridized to form Brassica juncea. The expression patterns of BjuSUSs vary among different stages of mustard stem swelling. Transcriptomics revealed that the BjuSUS01-04 expression levels were the most elevated. It has been hypothesized that they play an important role in sucrose metabolism during stem development. The expression levels of some BjuSUSs were significantly up-regulated when they were treated with plant hormones. However, when subjected to abiotic stress factors, their expression levels were suppressed. This study establishes SUS gene functions during mustard stem development and stress. creator: Mengyao Li creator: Qi He creator: Ying Huang creator: Ya Luo creator: Yong Zhang creator: Qing Chen creator: Yan Wang creator: Yuanxiu Lin creator: Yunting Zhang creator: Zejing Liu creator: Xiao-Rong Wang creator: Haoru Tang uri: https://doi.org/10.7717/peerj.10878 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Conservation actions and ecological context: optimizing coral reef local management in the Dominican Republic link: https://peerj.com/articles/10925 last-modified: 2021-03-09 description: Over the past few decades, coral reef ecosystems have been lost at accelerated rates as a result of global climate change and local stressors. Local management schemes can help improve the condition of coral reefs by enhancing their ecosystem recovery capacity. Caribbean conservation efforts include mitigation of local anthropogenic stressors, and integrating social participation. Here, we analyzed the case of the Bayahibe reefs in the Southeastern (SE) Dominican Republic to identify conservation actions and illustrate a conceptual example of local seascape management. We assessed reef health indicators from 2011 to 2016. Overall, our results show increases in total fish biomass, in both commercial and herbivorous fishes. Mean live coral cover was 31% and fleshy macroalgae was 23% after multiple disturbances such as Hurricanes Sandy and Isaac (2012), Mathew (2016) and heat stress presented in the study area in 2015. We also described actions taken by stakeholders and government institutions, including the implementation of a policy declaring an area of 869,000 ha as a marine protected area (MPA), enhanced water quality treatment, local restrictions to vessel traffic, enforcement of fishing regulations, and the removal of invasive lionfish (Pterois spp.). In addition, a restoration program for the threatened staghorn coral (Acropora cervicornis) was established in 2011, and currently has eight coral nurseries and six outplanting sites. Considering the biology and ecology of these reefs, we observed good results for these indicators (live coral cover, fish biomass, and water quality) in contrast with severely degraded Caribbean reefs, suggesting that optimizing local management may be a useful example for improving reef condition. Our results provide an overview of trends in reef condition in the SE Dominican Republic and could support current strategies to better protect reefs in the region. Given that Caribbean coral reefs face extreme challenges from global climate change, management measures may improve reef conditions across the region but stronger policy processes and increased scientific knowledge are needed for the successful management of coral reefs. creator: Camilo Cortés-Useche creator: Edwin A. Hernández-Delgado creator: Johanna Calle-Triviño creator: Rita Sellares Blasco creator: Victor Galván creator: Jesús E. Arias-González uri: https://doi.org/10.7717/peerj.10925 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cortés-Useche et al. title: Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4 link: https://peerj.com/articles/10929 last-modified: 2021-03-09 description: BackgroundOligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides.MethodsTo confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis.ResultsThe QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in the QB4 genome based on the CAZy database. Eleven polysaccharide lyases and 16 glycoside hydrolases contained lipobox motif, indicating that these enzymes play an important role in degrading the polysaccharides. Fourteen of 28 polysaccharide lyases were classified into ulvan lyase, and the QB4 genome possessed the most abundant ulvan lyase genes in the CAZy database. Besides, genes involved in uronic acid metabolisms were also present in the genome. These results were consistent with the cell growth. In the pectin metabolic pathway, the strain had genes for three different pathways. However, the growth experiment using saturated galacturonate exhibited that the strain can only use the pathway related to unsaturated galacturonate. creator: Go Furusawa creator: Nor Azura Azami creator: Aik-Hong Teh uri: https://doi.org/10.7717/peerj.10929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Furusawa et al. title: Age constraint for the Moreno Hill Formation (Zuni Basin) by CA-TIMS and LA-ICP-MS detrital zircon geochronology link: https://peerj.com/articles/10948 last-modified: 2021-03-09 description: The “mid-Cretaceous” (~125–80 Ma) was punctuated by major plate-tectonic upheavals resulting in widespread volcanism, mountain-building, eustatic sea-level changes, and climatic shifts that together had a profound impact on terrestrial biotic assemblages. Paleontological evidence suggests terrestrial ecosystems underwent a major restructuring during this interval, yet the pace and pattern are poorly constrained. Current impediments to piecing together the geologic and biological history of the “mid-Cretaceous” include a relative paucity of terrestrial outcrop stemming from this time interval, coupled with a historical understudy of fragmentary strata. In the Western Interior of North America, sedimentary strata of the Turonian–Santonian stages are emerging as key sources of data for refining the timing of ecosystem transformation during the transition from the late-Early to early-Late Cretaceous. In particular, the Moreno Hill Formation (Zuni Basin, New Mexico) is especially important for detailing the timing of the rise of iconic Late Cretaceous vertebrate faunas. This study presents the first systematic geochronological framework for key strata within the Moreno Hill Formation. Based on the double-dating of (U-Pb) detrital zircons, via CA-TIMS and LA-ICP-MS, we interpret two distinct depositional phases of the Moreno Hill Formation (initial deposition after 90.9 Ma (middle Turonian) and subsequent deposition after 88.6 Ma (early Coniacian)), younger than previously postulated based on correlations with marine biostratigraphy. Sediment and the co-occurring youthful subset of zircons are sourced from the southwestern Cordilleran Arc and Mogollon Highlands, which fed into the landward portion of the Gallup Delta (the Moreno Hill Formation) via northeasterly flowing channel complexes. This work greatly strengthens linkages to other early Late Cretaceous strata across the Western Interior. creator: Charl D. Cilliers creator: Ryan T. Tucker creator: James L. Crowley creator: Lindsay E. Zanno uri: https://doi.org/10.7717/peerj.10948 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cilliers et al. title: The emotional canvas of human screams: patterns and acoustic cues in the perceptual categorization of a basic call type link: https://peerj.com/articles/10990 last-modified: 2021-03-09 description: Screams occur across taxonomically widespread species, typically in antipredator situations, and are strikingly similar acoustically, but in nonhuman primates, they have taken on acoustically varied forms in association with more contextually complex functions related to agonistic recruitment. Humans scream in an even broader range of contexts, but the extent to which acoustic variation allows listeners to perceive different emotional meanings remains unknown. We investigated how listeners responded to 30 contextually diverse human screams on six different emotion prompts as well as how selected acoustic cues predicted these responses. We found that acoustic variation in screams was associated with the perception of different emotions from these calls. Emotion ratings generally fell along two dimensions: one contrasting perceived anger, frustration, and pain with surprise and happiness, roughly associated with call duration and roughness, and one related to perceived fear, associated with call fundamental frequency. Listeners were more likely to rate screams highly in emotion prompts matching the source context, suggesting that some screams conveyed information about emotional context, but it is noteworthy that the analysis of screams from happiness contexts (n = 11 screams) revealed that they more often yielded higher ratings of fear. We discuss the implications of these findings for the role and evolution of nonlinguistic vocalizations in human communication, including consideration of how the expanded diversity in calls such as human screams might represent a derived function of language. creator: Jonathan W. M. Engelberg creator: Jay W. Schwartz creator: Harold Gouzoules uri: https://doi.org/10.7717/peerj.10990 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Engelberg et al. title: The extent of carbapenemase-encoding genes in public genome sequences link: https://peerj.com/articles/11000 last-modified: 2021-03-09 description: Genome sequences provide information on the genetic elements present in an organism, and currently there are databases containing hundreds of thousands of bacterial genome sequences. These repositories allow for mining patterns concerning antibiotic resistance gene occurrence in both pathogenic and non-pathogenic bacteria in e.g. natural or animal environments, and link these to relevant metadata such as bacterial host species, country and year of isolation, and co-occurrence with other resistance genes. In addition, the advances in the prediction of mobile genetic elements, and discerning chromosomal from plasmid DNA, broadens our view on the mechanism mediating dissemination. In this study we utilize the vast amount of data in the public database PATRIC to investigate the dissemination of carbapenemase-encoding genes (CEGs), the emergence and spread of which is considered a grave public health concern. Based on publicly available genome sequences from PATRIC and manually curated CEG sequences from the beta lactam database, we found 7,964 bacterial genomes, belonging to at least 70 distinct species, that carry in total 9,892 CEGs, amongst which blaNDM, blaOXA, blaVIM, blaIMP and blaKPC. We were able to distinguish between chromosomally located resistance genes (4,137; 42%) and plasmid-located resistance genes (5,753; 58%). We found that a large proportion of the identified CEGs were identical, i.e. displayed 100% nucleotide similarity in multiple bacterial species (8,361 out of 9,892 genes; 85%). For example, the New Delhi metallo-beta-lactamase NDM-1 was found in 42 distinct bacterial species, and present in seven different environments. Our data show the extent of carbapenem-resistance far beyond the canonical species Acetinobacter baumannii, Klebsiella pneumoniae or Pseudomonas aeruginosa. These types of data complement previous systematic reviews, in which carbapenem-resistant Enterobacteriaceae were found in wildlife, livestock and companion animals. Considering the widespread distribution of CEGs, we see a need for comprehensive surveillance and transmission studies covering more host species and environments, akin to previous extensive surveys that focused on extended spectrum beta-lactamases. This may help to fully appreciate the spread of CEGs and improve the understanding of mechanisms underlying transmission, which could lead to interventions minimizing transmission to humans. creator: Ingmar Janse creator: Rick Beeloo creator: Arno Swart creator: Michael Visser creator: Leo Schouls creator: Engeline van Duijkeren creator: Mark W.J. van Passel uri: https://doi.org/10.7717/peerj.11000 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2021 Janse et al. title: Effect of domain knowledge encoding in CNN model architecture—a prostate cancer study using mpMRI images link: https://peerj.com/articles/11006 last-modified: 2021-03-09 description: BackgroundProstate cancer is one of the most common cancers worldwide. Currently, convolution neural networks (CNNs) are achieving remarkable success in various computer vision tasks, and in medical imaging research. Various CNN architectures and methodologies have been applied in the field of prostate cancer diagnosis. In this work, we evaluate the impact of the adaptation of a state-of-the-art CNN architecture on domain knowledge related to problems in the diagnosis of prostate cancer. The architecture of the final CNN model was optimised on the basis of the Prostate Imaging Reporting and Data System (PI-RADS) standard, which is currently the best available indicator in the acquisition, interpretation, and reporting of prostate multi-parametric magnetic resonance imaging (mpMRI) examinations.MethodsA dataset containing 330 suspicious findings identified using mpMRI was used. Two CNN models were subjected to comparative analysis. Both implement the concept of decision-level fusion for mpMRI data, providing a separate network for each multi-parametric series. The first model implements a simple fusion of multi-parametric features to formulate the final decision. The architecture of the second model reflects the diagnostic pathway of PI-RADS methodology, using information about a lesion’s primary anatomic location within the prostate gland. Both networks were experimentally tuned to successfully classify prostate cancer changes.ResultsThe optimised knowledge-encoded model achieved slightly better classification results compared with the traditional model architecture (AUC = 0.84 vs. AUC = 0.82). We found the proposed model to achieve convergence significantly faster.ConclusionsThe final knowledge-encoded CNN model provided more stable learning performance and faster convergence to optimal diagnostic accuracy. The results fail to demonstrate that PI-RADS-based modelling of CNN architecture can significantly improve performance of prostate cancer recognition using mpMRI. creator: Piotr Sobecki creator: Rafał Jóźwiak creator: Katarzyna Sklinda creator: Artur Przelaskowski uri: https://doi.org/10.7717/peerj.11006 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sobecki et al. title: Development and validation of a nomogram to predict the mortality risk in elderly patients with ARF link: https://peerj.com/articles/11016 last-modified: 2021-03-09 description: BackgroundAcute respiratory failure (ARF) is a life-threatening complication in elderly patients. We developed a nomogram model to explore the risk factors of prognosis and the short-term mortality in elderly patients with ARF.MethodsA total of 759 patients from MIMIC-III database were categorized into the training set and 673 patients from our hospital were categorized into the validation set. Demographical, laboratory variables, SOFA score and APS-III score were collected within the first 24 h after the ICU admission. A 30-day follow-up was performed for all patients.ResultsMultivariate logistic regression analysis showed that the heart rate, respiratoryrate, systolic pressure, SPO2, albumin and 24 h urine output were independent prognostic factors for 30-day mortality in ARF patients. A nomogram was established based on above independent prognostic factors. This nomogram had a C-index of 0.741 (95% CI [0.7058–0.7766]), and the C-index was 0.687 (95% CI [0.6458–0.7272]) in the validation set. The calibration curves both in training and validation set were close to the ideal model. The SOFA had a C-index of 0.653 and the APS-III had a C-index of 0.707 in predicting 30-day mortality.ConclusionOur nomogram performed better than APS-III and SOFA scores and should be useful as decision support on the prediction of mortality risk in elderly patients with ARF. creator: Junnan Xu creator: Jie Weng creator: Jingwen Yang creator: Xuan Shi creator: Ruonan Hou creator: Xiaoming Zhou creator: Zhiliang Zhou creator: Zhiyi Wang creator: Chan Chen uri: https://doi.org/10.7717/peerj.11016 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: Arsenic transfer along the soil-sclerotium-stroma chain in Chinese cordyceps and the related health risk assessment link: https://peerj.com/articles/11023 last-modified: 2021-03-09 description: BackgroundChinese cordyceps (Lepidoptera: Ophiocordyceps sinensis)is a larval-fungus complex. The concentration and distribution of arsenic (As) may vary during the stroma (ST) germination process and between the sclerotium (SC) and the ST. The soil-to-Chinese cordyceps system is an environmental arsenic exposure pathway for humans. We studied the As concentration in the soil, the SC, and the ST of Chinese cordyceps, and performed a risk assessment.MethodsSoil and Chinese cordyceps samples were collected from the Tibetan Plateau in China. The samples were analyzed for the total As concentration and As species determination, which were conducted by inductively coupled plasma mass spectrometry (ICP-MS) and HPLC-ICP-MS, respectively.ResultsThe concentration of total As in the soil was much higher than in SC and ST. The major As species in the soil was inorganic AsV. In SC and ST, organic As was predominant, and the majority of As was an unknown organic form. There are significant differences in the As distribution and composition in soil, SC, and ST. Our risk assessment indicated that chronic daily ingestion was higher than inhalation and dermal exposure in children and adults. The hazard index (HI) of the non-carcinogenic and cancer risks (CR) for human health were HI ≤ 1 and CR < 1 × 10−4, respectively.ConclusionThe Chinese cordyceps possesses highly-efficient detoxifying characteristics and has a significant role in As transformation during its life cycle. We found that the levels of As in soils from the habitat of Chinese cordyceps were higher than the soil background values in China, but the probability for incurring health risks remained within the acceptable levels for humans. creator: YuGuo Liu creator: Ming Shi creator: XiaoShan Liu creator: JinYing Xie creator: RunHuang Yang creator: QiaoWei Ma creator: LianXian Guo uri: https://doi.org/10.7717/peerj.11023 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Colchicine induction of ‘Old Blush’ 2n pollen for the hybridization and breeding of tetraploid rose link: https://peerj.com/articles/11043 last-modified: 2021-03-09 description: Obtaining 2n pollen from the diploid Chinese old rose ‘Old Blush’ through artificial induction is one important means of hybridizing and breeding modern tetraploid roses. We used colchicine-induced 2n pollen to assess normal viability during hybridization and fructification. The results showed that the pollen mother cell had lagging chromosomes and parallel spindles at meiosis I stage, following which the 2n pollen was produced from dyads and triads with doubled chromosomes. We obtained 4.30% viable 2n pollen, which was significantly higher than the yield of the spontaneous 2n pollen (1.00%) using an optimal treatment combination of induction for 24 h with 0.50% colchicine. There was no significant difference between the external morphology of the induced 2n pollen and the spontaneous 2n pollen, whereas both types of 2n pollen possessed finer furrows, and fewer and smaller pores than the 1n pollen, and the external morphology of 2n pollen was more evolved. In terms of in vitro germination rate and pollen tube length, the induced 2n pollen did not differ significantly from the spontaneous 2n pollen. The survival rate of the floral buds was significantly decreased with increased colchicine concentration and treatment time. creator: Shumin Gao creator: Yahong Sun creator: Yan Zhou uri: https://doi.org/10.7717/peerj.11043 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gao et al. title: Differences in the endophytic fungal community and effective ingredients in root of three Glycyrrhiza species in Xinjiang, China link: https://peerj.com/articles/11047 last-modified: 2021-03-09 description: BackgroundEndophytic fungi influence the quality and quantity of the medicinal plant’s bioactive compounds through specific fungus-host interactions. Nevertheless, due to the paucity of information, the composition of endophytic fungal communities and the mechanism by which effective ingredients regulate endophytic fungal communities in roots remains unclear.MethodsIn this study, we collected root and soil samples (depth range: 0–20, 20–40, and 40–60 cm) of three Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, and Glycyrrhiza glabra). Glycyrrhizic acid and liquiritin content were determined using high-performance liquid chromatography (HPLC), and total flavonoid content was determined using ultraviolet spectrophotometry. High-throughput sequencing technology was employed to explore the composition and diversity of the endophytic fungal community in different root segments of three Glycyrrhiza species. Furthermore, soil samples were subjected to physicochemical analyses.ResultsWe observed that the liquiritin content was not affected by the root depth (0–20 cm, 20–40 cm, and 40–60 cm). Still, it was significantly affected by the Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, Glycyrrhiza glabra) (P < 0.05). In Glycyrrhiza root, a total of eight phyla and 140 genera were annotated so far, out of which Ascomycota and Basidiomycota phyla, and the Fusarium, Paraphoma, and Helminthosporium genera were found to be significantly dominant. Spearman correlation analysis revealed that liquiritin content was accountable for the differences in the diversity of the endophytic fungal community. Furthermore, distance-based redundancy analysis (db-RDA) showed that physicochemical properties of the soil (available potassium and ammonium nitrogen) and the root factors (liquiritin and water content) were the main contributing factors for the variations in the overall structure of the endophytic fungal community. Our results showed that the effective ingredients of Glycyrrhiza root and physicochemical properties of the soil regulated the endophytic fungal community composition and medicinal licorice diversity. creator: Hanli Dang creator: Tao Zhang creator: Zhongke Wang creator: Guifang Li creator: Wenqin Zhao creator: Xinhua Lv creator: Li Zhuang uri: https://doi.org/10.7717/peerj.11047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Dang et al. title: Luzindole and 4P-PDOT block the effect of melatonin on bovine granulosa cell apoptosis and cell cycle depending on its concentration link: https://peerj.com/articles/10627 last-modified: 2021-03-08 description: Granulosa cells play an essential physiological role in mediating the follicle development and survival or apoptosis of granulosa cells dictate the follicle development or atresia. The aim of this study was to investigate the role of high dose (10−5 M) and low dose (10−9 M) melatonin in bovine granulosa cells, and assess whether MT1 and MT2 inhibiter affect granulosa cells response to melatonin. We found that the high dose (10−5 M) and low dose (10−9 M) both could act as an essential role in modulating granulosa cells apoptosis, cell cycle and antioxidant. The beneficial effect could be related to that melatonin promoted the expression of Bcl2, Bcl-xl, SOD1 and GPX4, and inhibited Bax, caspase-3 and p53 expression. Moreover P21 expression was decreased in granulosa cells treated with the high dose (10−5 M) melatonin and increased in that treated with the low dose (10−9 M) melatonin. To further reveal the role of MT1 and MT2 in mediating the effect of melatonin on granulosa cells apoptosis, cell cycle and antioxidant, we found that the luzindole and 4P-PDOT did not affect the effect of high dose (10−5 M) melatonin on regulating Bcl2, Bax, caspase-3, SOD1, GPX4 and p53 expression, while blocked its effect on modulating Bcl-xl and P21expression. However, luzindole and 4P-PDOT disturbed the effect of low dose (10−9 M) melatonin on regulating Bcl2, Bax, caspase-3, Bcl-xl, SOD1, GPX4, and p53 expression. In conclusion, these results reveal that the effect of low dose (10−9 M) melatonin on granulosa cells apoptosis are mediated by MT1 and MT2, and the high dose (10−5 M) melatonin affect the granulosa cells apoptosis by other pathway, besides MT1 and MT2. Moreover MT1 and MT2 may work in concert to modulate bovine granulosa cells function by regulating cellular progression and apoptosis. creator: Shujuan Wang creator: Wenju Liu creator: Aiyou Wen creator: Bing Yang creator: Xunsheng Pang uri: https://doi.org/10.7717/peerj.10627 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession link: https://peerj.com/articles/10757 last-modified: 2021-03-08 description: Caves are often assumed to be static environments separated from weather changes experienced on the surface. The high humidity and stability of these subterranean environments make them attractive to many different organisms including microbes such as bacteria and protists. Cave waters generally originate from the surface, may be filtered by overlying soils, can accumulate in interstitial epikarst zones underground, and emerge in caves as streams, pools and droplets on speleothems. Water movement is the primary architect of karst caves, and depending on the hydrologic connectivity between surface and subsurface, is the most likely medium for the introduction of microbes to caves. Recently published metabarcoding surveys of karst cave soils and speleothems have suggested that the vast majority of bacteria residing in these habitats do not occur on the surface, calling into question the role of microbial transport by surface waters. The purpose of this study was to use metabarcoding to monitor the aquatic prokaryotic microbiome of a cave for 1 year, conduct longitudinal analyses of the cave’s aquatic bacterioplankton, and compare it to nearby surface water. Water samples were collected from two locations inside Panel Cave in Natural Tunnel State Park in Duffield, VA and two locations outside of the cave. Of the two cave locations, one was fed by groundwater and drip water and the other by infiltrating surface water. A total of 1,854 distinct prokaryotic ASVs were detected from cave samples and 245 (13.1%) were not found in surface samples. PCo analysis demonstrated a marginal delineation between two cave sample sites and between cave and surface microbiomes suggesting the aquatic bacterioplankton in a karst cave is much more similar to surface microbes than reported from speleothems and soils. Most surprisingly, there was a cave microbe population and diversity bloom in the fall months whereas biodiversity remained relatively steady on the surface. The cave microbiome was more similar to the surface before the bloom than during and afterwards. This event demonstrates that large influxes of bacteria and particulate organic matter can enter the cave from either the surface or interstitial zones and the divergence of the cave microbiome from the surface demonstrates movement of microbes from the epikarst zones into the cave. creator: Kendall V. Morse creator: Dylan R. Richardson creator: Teresa L. Brown creator: Robert D. Vangundy creator: Aubrey Bruce Cahoon uri: https://doi.org/10.7717/peerj.10757 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Morse et al. title: Two centuries from species discovery to diagnostic characters: molecular and morphological evidence for narrower species limits in the widespread SW Australian Anarthria gracilis complex (Restionaceae s.l./Anarthriaceae, Poales) link: https://peerj.com/articles/10935 last-modified: 2021-03-08 description: BackgroundThe extreme southwest of Australia is a biodiversity hotspot region that has a Mediterranean-type climate and numerous endemic plant and animal species, many of which remain to be properly delimited. We refine species limits in Anarthria, a Western Australian endemic genus characterised by the occurrence of the greatest number of plesiomorphic character states in the restiid clade of Poales. In contrast to many other groups of wind-pollinated Australian Poales, Anarthria was traditionally viewed as having well-established species limits. All six currently recognised species, which are conspicuous members of some Western Australian plant communities, were described in the first half of the 19th century. They are traditionally distinguished from each other mainly using quantitative characters.MethodsWe examined extensive existing herbarium specimens and made new collections of Anarthria in nature. Scanning electron microscopy and light microscopy were used to study leaf micromorphology. Molecular diversity of Anarthria was examined using a plastid (trnL-F) and a low-copy nuclear marker (at103). This is the first study of species-level molecular diversity in the restiid clade using a nuclear marker.ResultsMaterial historically classified as Anarthria gracilis R.Br. actually belongs to three distinct species, A. gracilis s.str., A. grandiflora Nees and A. dioica (Steud.) C.I.Fomichev, each of which forms a well-supported clade in phylogenetic analyses. Both segregate species were described in the first half of the 19th century but not recognised as such in subsequent taxonomic accounts. Anarthria dioica was first collected in 1826, then wrongly interpreted as a species of Juncus (Juncaceae) and described as Juncus dioicus. We provide a formal transfer of the name to Anarthria and for the first time report its clear and qualitative diagnostic characters: an extremely short leaf ligule and distinctive pattern of leaf epidermal micromorphology. A long ligule is present in A. gracilis s.str. and A. grandiflora. These species differ from each other in leaf lamina morphology and anatomy and have mostly non-overlapping distribution ranges. The narrower definition of species provides a basis for future phylogeographic analyses in Anarthria. Our study highlights a need for more extensive use of nuclear DNA markers in Restionaceae. The use of the low copy nuclear marker at103 allowed a clade comprising all three ligulate species of Anarthria to be recognised. The ligule character is used here for the first time in the taxonomy of Anarthria and merits special attention in studies of other restiids. In general, our study uncovered a superficially hidden but, in reality, conspicuous diversity in a common group of wind-pollinated plants in the southwest of Western Australia. creator: Constantin I. Fomichev creator: Terry D. Macfarlane creator: Carmen M. Valiejo-Roman creator: Tahir H. Samigullin creator: Galina V. Degtjareva creator: Barbara G. Briggs creator: Dmitry D. Sokoloff uri: https://doi.org/10.7717/peerj.10935 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Fomichev et al. title: Colorectal cancer screening behaviors link: https://peerj.com/articles/10951 last-modified: 2021-03-08 description: IntroductionColorectal cancer screening program compliance in Turkey is around 20–30%. Factors that may affect preventive health behavior, mainly individuals’ values, beliefs and attitudes, should be explored. A “Health Belief Model” (HBM) scale was developed in 1950 to explain the insufficient participation of some individuals in screening programs. The scale was adopted for colon cancer in 2002. The validity and reliability study of this scale for the Turkish language was conducted in 2007. In this study we aim to evaluate the health beliefs of relatively young individuals before the age of screening in relation to attitudes to colorectal cancer screening via the Turkish version of the scale.Materials and MethodsA questionnaire composed of 14 sociodemographic questions and 33 HBM scale questions were applied to the patients of a Family Medicine outpatient clinic where the majority of the patients are relatively young people. The data was analyzed using the IBM SPSS version 21.0.ResultsA total of 310 subjects at the age of 18 and over were informed about the study. The study was completed with 215 subjects with a participation rate of 69.3%. The average age of the participants was 35.4 ± 12.8 years; 62.8% of them were women; 26.0% were students. 94.4% of the participants did not have a history of colon cancer among their first degree relatives. 58.1% agreed that “A colonoscopy should be done every ten years starting at age 50 to screen for colon cancer.” Age, marital status, education and occupation status were found to have an effect on barrier scores. Young participants, singles, and those with a primary and/or secondary school education had statistically significant higher barrier scores. The motivation scores of high school graduates were higher than university graduates. The seriousness scores of men were found to be higher than women.ConclusionOur study points out that attitudes about preventive health measures are mainly associated with age, gender, education level and marital status. These personal characteristics should be taken into consideration while offering screening programs and preventive health measures to individuals in order to protect against colorectal cancer. It is better to give specific messages according to personal characteristics and specific barriers instead of general messages about conducting screening tests beginning from a young age. creator: Selda Tekiner creator: Gülsen Ceyhun Peker creator: Mine Ceylan Doğan uri: https://doi.org/10.7717/peerj.10951 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Tekiner et al. title: Exposure-related, global alterations in innate and adaptive immunity; a consideration for re-use of non-human primates in research link: https://peerj.com/articles/10955 last-modified: 2021-03-08 description: BackgroundNon-human primates (NHPs) play an important role in biomedical research, where they are often being re-used in multiple research studies over the course of their life-time. Researchers employ various study-specific screening criteria to reduce potential variables associated with subsequent re-use of NHPs. However, criteria set for NHP re-assignments largely neglect the impact of previous exposures on overall biology. Since the immune system is a key determinant of overall biological outcome, an altered biological state could be predicted by monitoring global changes in the immune profile. We postulate that every different exposure or a condition can generate a unique global immune profile in NHPs.MethodsChanges in the global immune profile were evaluated in three different groups of rhesus macaques previously enrolled in dengue or malaria vaccine studies over six months after their last exposure. Naïve animals served as the baseline. Fresh blood samples were stained with various immune cell surface markers and analyzed by multi-color flow-cytometry to study immune cell dynamics in the peripheral blood. Serum cytokine profile in the pre-exposed animals were analyzed by mesoscale assay using a customized U-PLEX NHP biomarker panel of 12 cytokines/chemokines.ResultsPre-exposed macaques showed altered dynamics in circulating cytokines and certain innate and adaptive immune cell subsets such as monocytes, HLA-DR+NKT cells, B cells and T cells. Some of these changes were transient, while some lasted for more than six months. Each group seemed to develop a global immune profile unique to their particular exposure.ConclusionOur data strongly suggest that re-used NHPs should be evaluated for long-term, overall immunological changes and randomly assigned to new studies to avoid study bias. creator: François A. Bates creator: Elizabeth H. Duncan creator: Monika Simmons creator: Tanisha Robinson creator: Sridhar Samineni creator: Natasa Strbo creator: Eileen Villasante creator: Elke Bergmann-Leitner creator: Wathsala Wijayalath uri: https://doi.org/10.7717/peerj.10955 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Development and validation of bioimpedance prediction equations for fat-free mass in unilateral male amputees link: https://peerj.com/articles/10970 last-modified: 2021-03-08 description: BackgroundMetabolic disease due to increased fat mass is observed in amputees (APTs), thereby restricting their activity. Systemic health management with periodic body composition (BC) testing is essential for healthy living. Bioelectrical impedance analysis (BIA) is a non-invasive and low-cost method to test BC; however, the APTs are classified as being exempted in the BIA.ObjectiveTo develop segmental estimated regression equations (sEREs) for determining the fat-free mass (FFM, kg) suitable for APTs and improve the accuracy and validity of the sERE.MethodsSeventy-five male APTs participated in this cross-sectional study. Multiple regression analysis was performed to develop highly accurate sEREs of BIA based on independent variables derived from anthropometric measurements, dual-energy X-ray absorptiometry (DXA), and BIA parameters. The difference in validity between the predicted DXA and sum of the segmentally-predicted FFM values by sEREs (Sum_sEREs) values was evaluated using bivariate linear regression analysis and the Bland–Altman plot.ResultsThe coefficient of determination (R2) and total error (TE) between DXA and Sum_sEREs were 71% and 5.4 (kg) in the cross-validation analysis.ConclusionsWe confirmed the possibility of evaluating the FFM of APTs through the sEREs developed in this study. We also identified several independent variables that should be considered while developing such sEREs. Further studies are required to determine the validity of our sEREs and the most appropriate BIA frequencies for measuring FFM in APTs. creator: Hyuk-Jae Choi creator: Chang-Yong Ko creator: Yunhee Chang creator: Gyoo-Suk Kim creator: Kyungsik Choi creator: Chul-Hyun Kim uri: https://doi.org/10.7717/peerj.10970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Choi et al. title: Three-dimensional data-tracking simulations of sprinting using a direct collocation optimal control approach link: https://peerj.com/articles/10975 last-modified: 2021-03-08 description: Biomechanical simulation and modelling approaches have the possibility to make a meaningful impact within applied sports settings, such as sprinting. However, for this to be realised, such approaches must first undergo a thorough quantitative evaluation against experimental data. We developed a musculoskeletal modelling and simulation framework for sprinting, with the objective to evaluate its ability to reproduce experimental kinematics and kinetics data for different sprinting phases. This was achieved by performing a series of data-tracking calibration (individual and simultaneous) and validation simulations, that also featured the generation of dynamically consistent simulated outputs and the determination of foot-ground contact model parameters. The simulated values from the calibration simulations were found to be in close agreement with the corresponding experimental data, particularly for the kinematics (average root mean squared differences (RMSDs) less than 1.0° and 0.2 cm for the rotational and translational kinematics, respectively) and ground reaction force (highest average percentage RMSD of 8.1%). Minimal differences in tracking performance were observed when concurrently determining the foot-ground contact model parameters from each of the individual or simultaneous calibration simulations. The validation simulation yielded results that were comparable (RMSDs less than 1.0° and 0.3 cm for the rotational and translational kinematics, respectively) to those obtained from the calibration simulations. This study demonstrated the suitability of the proposed framework for performing future predictive simulations of sprinting, and gives confidence in its use to assess the cause-effect relationships of technique modification in relation to performance. Furthermore, this is the first study to provide dynamically consistent three-dimensional muscle-driven simulations of sprinting across different phases. creator: Nicos Haralabidis creator: Gil Serrancolí creator: Steffi Colyer creator: Ian Bezodis creator: Aki Salo creator: Dario Cazzola uri: https://doi.org/10.7717/peerj.10975 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Haralabidis et al. title: A revision of Prolimulus woodwardi Fritsch, 1899 with comparison to other highly paedomorphic belinurids link: https://peerj.com/articles/10980 last-modified: 2021-03-08 description: Xiphosurida is an ingroup of marine Euchelicerata often referred to as “living fossils”. However, this oxymoronic term is inapplicable for Paleozoic and early Mesozoic forms, as during these periods the group experienced notable evolutionary radiations; particularly the diverse late Palaeozoic clade Belinurina. Despite the iconic nature of the group, select species in this clade have been left undescribed in the light of recent geometric morphometric and phylogenetic considerations and methodologies. To this end, we re-describe Prolimulus woodwardiFritsch, 1899 using new and type specimens to reveal more details on appendage anatomy and possible ecology. Furthermore, we present geometric morphometric and phylogenetic analyses that uncover relationships between P. woodwardi and other belinurids without genal spines. Both approaches highlight that a clade containing ProlimulusFritsch, 1899, LiomesaspisRaymond, 1944, AlanopsRacheboeuf, Vannier & Anderson, 2002 and StilpnocephalusSelden, Simonetto & Marsiglio, 2019 may exist. While we do not erect a new group to contain these genera, we note that these genera exemplify the extreme limits of the Belinurina radiation and a peak in horseshoe crab diversity and disparity. This evidence also illustrates how changes in heterochronic timing are a key evolutionary phenomenon that can drive radiations among animals. creator: Lorenzo Lustri creator: Lukáš Laibl creator: Russell D.C. Bicknell uri: https://doi.org/10.7717/peerj.10980 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lustri et al. title: Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis link: https://peerj.com/articles/11018 last-modified: 2021-03-08 description: BackgroundPsoriasis is a chronic immune-mediated inflammatory dermatosis. Long noncoding RNAs (lncRNAs) play an important role in immune-related diseases. This study aimed to identify potential immune-related lncRNA biomarkers for psoriasis.MethodsWe screened differentially expressed immune-related lncRNAs biomarkers using GSE13355 (skin biopsy samples of 180 cases) from Gene Expression Omnibus (GEO). Moreover, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Set Enrichment Analysis (GSEA) were performed to explore biological mechanisms in psoriasis. In addition, we performed LASSO logistic regression to identify potential diagnostic lncRNAs and further verify the diagnostic value and relationship with drug response using two validation sets: GSE30999 (skin biopsy samples of 170 cases) and GSE106992 (skin biopsy samples of 192 cases). Furthermore, we estimated the degree of infiltrated immune cells and investigated the correlation between infiltrated immune cells and diagnostic lncRNA biomarkers.ResultsA total of 394 differentially expressed genes (DEGs) were extracted from gene expression profile. GO and KEGG analysis of target genes found that immune-related lncRNAs were primarily associated with epidermis development, skin development, collagen-containing extracellular matrix, and glycosaminoglycan binding and mainly enriched in cytokine-cytokine receptor interaction and influenza A and chemokine signaling pathway. We found that LINC01137, LINC01215, MAPKAPK5-AS1, TPT1-AS1, CARMN, CCDC18-AS1, EPB41L4A-AS, and LINC01214 exhibited well diagnostic efficacy. The ROC and ROC CI were 0.944 (0.907–0.982), 0.953 (0.919–0.987), 0.822 (0.758–0.887), 0.854 (0.797–0.911), 0.957(0.929–0.985), 0.894 (0.846–0.942), and 0.964 (0.937–0.991) for LINC01137, LINC01215, MAPKAPK5-AS1, TPT1-AS1,CARMN, CCDC18-AS1, EPB41L4A-AS1, and LINC01214. LINC01137, LINC01215, and LINC01214 were correlated with drug response. LINC01137, CCDC18-AS1, and CARMN were positively correlated with activated memory CD4 T cell, activated myeloid dendritic cell (DC), neutrophils, macrophage M1, and T follicular helper (Tfh) cells, while negatively correlated with T regulatory cell (Treg). LINC01215, MAPKAPK5-AS1, TPT1-AS1, EPB41L4A-AS, and LINC01214 were negatively correlated with activated memory CD4 T cell, activated myeloid DC, neutrophils, macrophage M1, and Tfh, while positively correlated with Treg.ConclusionsThese findings indicated that these immune-related lncRNAs may be used as potential diagnostic and predictive biomarkers for psoriasis. creator: Feixiang Fan creator: Zhen Huang creator: Yongfeng Chen uri: https://doi.org/10.7717/peerj.11018 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Fan et al. title: Prevalence and correlates of low back pain among undergraduate medical students in Serbia, a cross-sectional study link: https://peerj.com/articles/11055 last-modified: 2021-03-08 description: BackgroundLow back pain (LBP) is a serious health problem among medical students. We aimed to investigate the prevalence and associated factors for LBP among Serbian medical students.MethodsA cross-sectional study was performed among medical students at one University in Serbia. Data was collected by a self-reported questionnaire. Logistic regression was used to determine the factors associated with LBP; results from the analyses were expressed as odds ratios (OR) with 95% confidence intervals (CI).ResultsThe study sample comprised 499 medical students, giving a response rate of 92.9%. The mean age of the participants was 22.0 ± 2.2 years (range 18–34). Overall, 20.8% (104/499) of medical students had LBP at the time of study. Cigarette smoking (OR = 2.5, 95% CI [1.5–4.2], p = 0.001), stress during classes (OR = 1.8, 95% CI [1.1–3.0], p = 0.039), incorrect sleeping position (OR = 1.9, 95% CI [1.2–3.1], p = 0.006) and family history of LBP (OR = 1.6, 95% CI [1.1–2.7], p = 0.047) were independently associated with high prevalence of LBP at the time of the study.ConclusionsLBP is a highly prevalent health problem in medical students in Serbia. The association between LBP and cigarette smoking, stress during classes, incorrect sleeping position and LBP in family history has been observed in medical students. creator: Irena Ilic creator: Vesna Milicic creator: Sandra Grujicic creator: Ivana Zivanovic Macuzic creator: Sanja Kocic creator: Milena D. Ilic uri: https://doi.org/10.7717/peerj.11055 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ilic et al. title: Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers link: https://peerj.com/articles/10607 last-modified: 2021-03-05 description: The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa. creator: David H. Mauki creator: Adeniyi C. Adeola creator: Said I. Ng’ang’a creator: Abdulfatai Tijjani creator: Ibikunle Mark Akanbi creator: Oscar J. Sanke creator: Abdussamad M. Abdussamad creator: Sunday C. Olaogun creator: Jebi Ibrahim creator: Philip M. Dawuda creator: Godwin F. Mangbon creator: Paul S. Gwakisa creator: Ting-Ting Yin creator: Min-Sheng Peng creator: Ya-Ping Zhang uri: https://doi.org/10.7717/peerj.10607 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Mauki et al. title: Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis link: https://peerj.com/articles/10682 last-modified: 2021-03-05 description: BackgroundGastric cancer is one of the most lethal tumors and is characterized by poor prognosis and lack of effective diagnostic or therapeutic biomarkers. The aim of this study was to find hub genes serving as biomarkers in gastric cancer diagnosis and therapy.MethodsGSE66229 from Gene Expression Omnibus (GEO) was used as training set. Genes bearing the top 25% standard deviations among all the samples in training set were performed to systematic weighted gene co-expression network analysis (WGCNA) to find candidate genes. Then, hub genes were further screened by using the “least absolute shrinkage and selection operator” (LASSO) logistic regression. Finally, hub genes were validated in the GSE54129 dataset from GEO by supervised learning method artificial neural network (ANN) algorithm.ResultsTwelve modules with strong preservation were identified by using WGCNA methods in training set. Of which, five modules significantly related to gastric cancer were selected as clinically significant modules, and 713 candidate genes were identified from these five modules. Then, ADIPOQ, ARHGAP39, ATAD3A, C1orf95, CWH43, GRIK3, INHBA, RDH12, SCNN1G, SIGLEC11 and LYVE1 were screened as the hub genes. These hub genes successfully differentiated the tumor samples from the healthy tissues in an independent testing set through artificial neural network algorithm with the area under the receiver operating characteristic curve at 0.946.ConclusionsThese hub genes bearing diagnostic and therapeutic values, and our results may provide a novel prospect for the diagnosis and treatment of gastric cancer in the future. creator: Chunyang Li creator: Haopeng Yu creator: Yajing Sun creator: Xiaoxi Zeng creator: Wei Zhang uri: https://doi.org/10.7717/peerj.10682 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis) link: https://peerj.com/articles/10934 last-modified: 2021-03-05 description: Ovate family proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive- and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species. creator: Ruihua Wang creator: Taili Han creator: Jifeng Sun creator: Ligong Xu creator: Jingjing Fan creator: Hui Cao creator: Chunxiang Liu uri: https://doi.org/10.7717/peerj.10934 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Photosynthetic responses of Halimeda scabra (Chlorophyta, Bryopsidales) to interactive effects of temperature, pH, and nutrients and its carbon pathways link: https://peerj.com/articles/10958 last-modified: 2021-03-05 description: In this study, we evaluated the interactive effects of temperature, pH, and nutrients on photosynthetic performance in the calcareous tropical macroalga Halimeda scabra. A significant interaction among these factors on gross photosynthesis (Pgross) was found. The highest values of Pgross were reached at the highest temperature, pH, and nutrient enrichment tested and similarly in the control treatment (no added nutrients) at 33 °C at the lowest pH. The Q10Pgross values confirmed the effect of temperature only under nutrient enrichment scenarios. Besides the above, bicarbonate (HCO3−) absorption was assessed by the content of carbon stable isotope (δ13C) in algae tissue and by its incorporation into photosynthetic products, as well as by carbonic anhydrase (CA) inhibitors (Acetazolamide, AZ and Ethoxyzolamide, EZ) assays. The labeling of δ13C revealed this species uses both, CO2 and HCO3− forms of Ci relying on a CO2 Concentration Mechanism (CCM). These results were validated by the EZ-AZ inhibition assays in which photosynthesis inhibition was observed, indicating the action of internal CA, whereas AZ inhibitor did not affect maximum photosynthesis (Pmax). The incorporation of 13C isotope into aspartate in light and dark treatments also confirmed photosynthetic and non-photosynthetic the HCO3−uptake. creator: Daily Zuñiga-Rios creator: Román Manuel Vásquez-Elizondo creator: Edgar Caamal creator: Daniel Robledo uri: https://doi.org/10.7717/peerj.10958 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zuñiga-Rios et al. title: Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers link: https://peerj.com/articles/10964 last-modified: 2021-03-05 description: Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogenetic relationships with related species. Recent molecular phylogenetic studies have shown a very close phylogenetic relationship between L. lankongense and the five species L. duchartrei, L. stewartianum, L. matangense, L. lophophorum, and L. nanum. However, molecular markers still lack sufficient signals for population-level research of the genus Lilium. We sequenced and compared the complete plastid sequences of L. lankongense and its five related species. The genomes ranged from 152,307 bp to 152,611 bp. There was a slight inconsistency detected in inverted repeat and single copy boundaries and there were 53 to 63 simple sequence repeats in the six species. Two of the 12 highly variable regions (trnC-petN and rpl32-trnL) were verified in 11 individuals and are promising for population-level studies. We used the complete sequence of 33 plastid genomes, the protein-coding region sequence, and the nuclear ITS sequence to reconstruct the phylogenetic tree of Lilium species. Our results showed that the plastid gene tree and nuclear gene tree were not completely congruent, which may be caused by hybridization, insufficient information contained in the nuclear ITS, or the small number of samples. The results of phylogenetic analysis based on plastid genomes indicated that the six Lilium species were closely related. Our study provides a preliminarily rebuilt backbone phylogeny that is significant for future molecular and morphological studies of Lilium. creator: Danmei Su creator: Fumin Xie creator: Haiying Liu creator: Dengfeng Xie creator: Juan Li creator: Xingjin He creator: Xianlin Guo creator: Songdong Zhou uri: https://doi.org/10.7717/peerj.10964 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Su et al. title: An exploration of the relationships of experiential avoidance (as measured by the aaq-ii and meaq) with negative affect, perceived stress, and avoidant coping styles link: https://peerj.com/articles/11033 last-modified: 2021-03-05 description: BackgroundCurrent psychotherapies seek to reduce experiential avoidance (EA) which has also been put forth as a risk factor for anxiety disorders, depression, and post-traumatic stress disorder. EA is a potentially maladaptive self-regulatory tendency to avoid negative thoughts, feelings, memories, physical sensations, and other internal experiences. One unresolved issue with the most commonly used measures of EA, the Acceptance and Action Questionnaire-II (AAQ-II) which measures EA as a single factor and the Multidimensional Experiential Avoidance Questionnaire (MEAQ) which measures EA as six subdimensions, is what exactly is being measured. The AAQ-II appears to measure negative affect (NA), some aspects of avoidant coping, and psychological distress. In addition, the relationships of all the MEAQ subscales have not been thoroughly examined with these other constructs. In the current study, the relationships of AAQ-II and MEAQ scores with NA, avoidant coping styles, and perceived stress were examined.MethodsTwo-hundred undergraduates (154 females and 46 males) completed the AAQ-II and MEAQ, the Distressed Type D Personality Scale (DS-14) which includes a measure of NA, the Brief COPE which measures coping styles, and the Perceived Stress Scale.ResultsScores on the AAQ-II had moderate positive relationships with the MEAQ total score and all MEAQ subscales with the exception of distress endurance which had a moderate negative relationship. The AAQ-II had a stronger relationship with NA, avoidant coping, and perceived stress than did the MEAQ. All MEAQ subscales had a positive relationship to NA, avoidant coping, and perceived stress with the exception of distress endurance which had a negative relationship with these constructs. While the AAQ-II is limited as a unitary measure of EA the multiple dimensions of the MEAQ may involve an extraneous factor of distress endurance. Future work should examine the relationships of the MEAQ with NA, avoidant coping and perceived stress with clinical populations. creator: M. Todd Allen uri: https://doi.org/10.7717/peerj.11033 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Allen title: Compositional and functional profiling of the rhizosphere microbiomes of the invasive weed Ageratina adenophora and native plants link: https://peerj.com/articles/10844 last-modified: 2021-03-04 description: The rhizosphere soil microbiome (RSM) plays an important role in the nutritional metabolism of the exotic weed Ageratina adenophora. However, our understanding of the composition and metabolic activity of this microbiome is limited. We used high-throughput sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer fragments in combination with transcriptome analysis to compare the composition and metabolic features of the RSMs of A. adenophora and the native plant species Artemisia indica and Imperata cylindrica. A. indica cohabitates with the weed and I. cylindrica grows in uninvaded soil areas. We found fungi belonging to the phyla Ascomycota and Basidiomycota and bacteria belonging to the phyla Proteobacteria, Acidobacteria and Bacteroidetes were highly abundant in the RSMs of A. adenophora and both native plant species. The RSM of A. adenophora differed to varying degrees in the relative abundances of bacterial and fungal phyla and genera, and in levels of expression of functional genes from those of both the native species. The RSM of A. adenophora was more metabolically active than both of these, as indicated by marked increases in the expression levels of genes associated with cell wall, membrane, and envelope biogenesis, energy production and conversion, and the transport and metabolism of carbohydrates, amino acids, coenzymes, nucleotides, and secondary metabolites. Ascomycota and Basidiomycota contributed most significantly to these differences. The composition and metabolic activities of A. adenophora RSM differed less to the RSM of A. indica than to the RSM of I. cylindrica. Fungal communities contributed most to the metabolic genes in the RSM of A. adenophora. These included the arbuscular mycorrhizal fungi Glomeromycota. The different relative abundances in the RSMs of these three plant populations may explain why A. adenophora is more successful in colonizing soils than the two native populations. creator: Yun Xia creator: Minghua Dong creator: Lei Yu creator: Lingdong Kong creator: Robert Seviour creator: Yunhong Kong uri: https://doi.org/10.7717/peerj.10844 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xia et al. title: A set of RT-PCR assays for detection of all known avian paramyxoviruses and application in surveillance of avian paramyxoviruses in China link: https://peerj.com/articles/10748 last-modified: 2021-03-04 description: BackgroundAvian paramyxoviruses (APMVs), also termed avian avulaviruses, are of a vast diversity and great significance in poultry. Detection of all known APMVs is challenging, and distribution of APMVs have not been well investigated.MethodsA set of reverse transcription polymerase chain reaction (RT-PCR) assays for detection of all known APMVs were established using degenerate primers targeting the viral polymerase L gene. The assays were preliminarily evaluated using in-vitro transcribed double-stranded RNA controls and 24 known viruses, and then they were employed to detect 4,346 avian samples collected from 11 provinces.ResultsThe assays could detect 20–200 copies of the double-stranded RNA controls, and detected correctly the 24 known viruses. Of the 4,346 avian samples detected using the assays, 72 samples were found positive. Of the 72 positives, 70 were confirmed through sequencing, indicating the assays were specific for APMVs. The 4,346 samples were also detected using a reported RT-PCR assay, and the results showed this RT-PCR assay was less sensitive than the assays reported here. Of the 70 confirmed positives, 40 were class I Newcastle disease virus (NDV or APMV-1) and 27 were class II NDV from poultry including chickens, ducks, geese, and pigeons, and three were APMV-2 from parrots. The surveillance identified APMV-2 in parrots for the first time, and revealed that prevalence of NDVs in live poultry markets was higher than that in poultry farms. The surveillance also suggested that class I NDVs in chickens could be as prevalent as in ducks, and class II NDVs in ducks could be more prevalent than in chickens, and class II NDVs could be more prevalent than class I NDVs in ducks. Altogether, we developed a set of specific and sensitive RT-PCR assays for detection of all known APMVs, and conducted a large-scale surveillance using the assays which shed novel insights into APMV epidemiology. creator: Ji-Hui Jin creator: Jing-Jing Wang creator: Ying-Chao Ren creator: Shuo Liu creator: Jin-Ping Li creator: Guang-Yu Hou creator: Hua-Lei Liu creator: Qing-Ye Zhuang creator: Su-Chun Wang creator: Wen-Ming Jiang creator: Xiao-Hui Yu creator: Jian-Min Yu creator: Li-Ping Yuan creator: Cheng Peng creator: Guo-Zhong Zhang creator: Ji-Ming Chen uri: https://doi.org/10.7717/peerj.10748 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jin et al. title: Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. link: https://peerj.com/articles/10770 last-modified: 2021-03-04 description: BackgroundSeed coat color is an important horticultural trait in Brassica crops, which is divided into two categories: brown/black and yellow. Seeds with yellow seed coat color have higher oil quality, higher protein content and lower fiber content. Yellow seed coat color is therefore considered a desirable trait in hybrid breeding of Brassica rapa, Brassica juncea and Brassica napus.MethodsComprehensive analysis of the abundance transcripts for seed coat color at three development stages by RNA-sequencing (RNA-seq) and corresponding flavonoids compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were carried out in B. rapa.ResultsWe identified 41,286 unigenes with 4,989 differentially expressed genes between brown seeds (B147) and yellow seeds (B80) at the same development stage. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified 19 unigenes associated with the phenylpropanoid, flavonoid, flavone and flavonol biosynthetic pathways as involved in seed coat color formation. Interestingly, expression levels of early biosynthetic genes (BrCHS, BrCHI, BrF3H, BrF3’H and BrFLS) in the flavonoid biosynthetic pathway were down-regulated while late biosynthetic genes (BrDFR, BrLDOX and BrBAN) were hardly or not expressed in seeds of B80. At the same time, BrTT8 and BrMYB5 were down-regulated in B80. Results of LC-MS also showed that epicatechin was not detected in seeds of B80. We validated the accuracy of our RNA-seq data by RT-qPCR of nine critical genes. Epicatechin was not detected in seeds of B80 by LC-MS/MS.ConclusionsThe expression levels of flavonoid biosynthetic pathway genes and the relative content of flavonoid biosynthetic pathway metabolites clearly explained yellow seed color formation in B. rapa. This study provides a foundation for further research on the molecular mechanism of seed coat color formation. creator: Yanjing Ren creator: Ning Zhang creator: Ru Li creator: Xiaomin Ma creator: Lugang Zhang uri: https://doi.org/10.7717/peerj.10770 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ren et al. title: CoViD-19: an automatic, semiparametric estimation method for the population infected in Italy link: https://peerj.com/articles/10819 last-modified: 2021-03-04 description: To date, official data on the number of people infected with the SARS-CoV-2—responsible for the Covid-19—have been released by the Italian Government just on the basis of a non-representative sample of population which tested positive for the swab. However a reliable estimation of the number of infected, including asymptomatic people, turns out to be crucial in the preparation of operational schemes and to estimate the future number of people, who will require, to different extents, medical attentions. In order to overcome the current data shortcoming, this article proposes a bootstrap-driven, estimation procedure for the number of people infected with the SARS-CoV-2. This method is designed to be robust, automatic and suitable to generate estimations at regional level. Obtained results show that, while official data at March the 12th report 12.839 cases in Italy, people infected with the SARS-CoV-2 could be as high as 105.789. creator: Livio Fenga uri: https://doi.org/10.7717/peerj.10819 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Fenga title: Maniraptoran pelvic musculature highlights evolutionary patterns in theropod locomotion on the line to birds link: https://peerj.com/articles/10855 last-modified: 2021-03-04 description: Locomotion is a fundamental aspect of palaeobiology and often investigated by comparing osteological structures and proportions. Previous studies document a stepwise accumulation of avian-like features in theropod dinosaurs that accelerates in the clade Maniraptora. However, the soft tissues that influenced the skeleton offer another perspective on locomotory adaptations. Examination of the pelvis for osteological correlates of hind limb and tail musculature allowed reconstruction of primary locomotory muscles across theropods and their closest extant relatives. Additionally, the areas of pelvic muscle origins were quantified to measure relative differences within and between taxa, to compare morphological features associated with cursoriality, and offer insight into the evolution of locomotor modules. Locomotory inferences based on myology often corroborate those based on osteology, although they occasionally conflict and indicate greater complexity than previously appreciated. Maniraptoran pelvic musculature underscores previous studies noting the multifaceted nature of cursoriality and suggests that a more punctuated step in caudal decoupling occurred at or near the base of Maniraptora. creator: Matthew M. Rhodes creator: Donald M. Henderson creator: Philip J. Currie uri: https://doi.org/10.7717/peerj.10855 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Rhodes et al. title: Prevalence and clinical correlates of insomnia symptoms and their association with quality of life in Chinese patients with HBV-related liver disease link: https://peerj.com/articles/10956 last-modified: 2021-03-04 description: ObjectiveThis study aimed to describe the one-month prevalence of insomnia symptoms (insomnia hereafter) and the demographic and clinical correlates, and its association with quality of life (QOL) in Chinese patients with HBV-related liver disease.MethodA total of 689 patients with HBV-related liver disease in Beijing, China formed the study sample. Three forms of insomnia including difficulty initiating sleep (DIS), difficulty maintaining sleep (DMS) and early morning awakening (EMA) were assessed using standardized questions. QOL was measured using the Medical Outcomes Study Short Form 12 (SF-12).ResultsThe one-month prevalence of at least one type of insomnia was 69.5%, while DIS, DMS and EMA were 60.4%, 54.7% and 50.9%, respectively. Only 4.8% of patients suffering from insomnia received treatment. Multiple logistic regression analyses revealed that pre-existing medical conditions were positively associated with DIS and EMA; patients with more severe depressive symptoms were more likely to have DIS, DMS and EMA; local residents were less likely to have DIS; and those who were married and older were more likely to have DMS. Insomnia was not independently associated with QOL.ConclusionsInsomnia is common in Chinese patients with HBV-related liver disease with a very low rate of treatment. Greater attention should be given to identify and treat insomnia in this patient population. creator: Jing Zhao creator: Mei Liu creator: Gabor S. Ungvari creator: Chee H. Ng creator: Ines Hang Iao Chow creator: Ting Wang creator: Yu Chen creator: Zhongping Duan creator: Yu-Tao Xiang creator: Su-Jun Zheng uri: https://doi.org/10.7717/peerj.10956 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhao et al. title: The influence of fish farm activity on the social structure of the common bottlenose dolphin in Sardinia (Italy) link: https://peerj.com/articles/10960 last-modified: 2021-03-04 description: In a wide variety of habitats, including some heavily urbanised areas, the adaptability of populations of common bottlenose dolphin (Tursiops truncatus) may depend on the social structure dynamics. Nonetheless, the way in which these adaptations take place is still poorly understood. In the present study we applied photo-identification techniques to investigate the social structure of the common bottlenose dolphin population inhabiting the Gulf of Alghero (Sardinia, Italy), analysing data recorded from 2008 to 2019. The social structure analysis showed a division of the entire population into five different communities and the presence of non-random associations, while there was no evidence of segregation between sexes. Furthermore, results highlighted an important change in social structure through time, likely due to a reduction in fish farm activity since 2015. The division of the population into different communities, the presence of segregation based on the foraging strategy (inside or outside the fish farm area) and the social network measures were evaluated by analysing independently the two datasets: the intense and low farm activity periods: 2008–2014 and 2015–2020, respectively. Segregation among individuals belonging to the same foraging strategy class was found only in the earlier period, and the composition of the four communities was consistent with this result. Our study improves the knowledge about bottlenose dolphin adaptation, as a lower complexity in social structure was linked to a reduction in anthropogenic food availability. creator: Serena Frau creator: Fabio Ronchetti creator: Francesco Perretti creator: Alberto Addis creator: Giulia Ceccherelli creator: Gabriella La Manna uri: https://doi.org/10.7717/peerj.10960 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Frau et al. title: A review of the diagnosis and geographical distribution of the recently described flea toad Brachycephalus sulfuratus in relation to B. hermogenesi (Anura: Brachycephalidae) link: https://peerj.com/articles/10983 last-modified: 2021-03-04 description: BackgroundThe flea toad Brachycephalus sulfuratus was recently described from southeastern and southern Brazil. In its description, the authors overlooked previous records of flea toads that had been identified as “Brachycephalus sp. nov.” and B. hermogenesi occurring in the same regions, which could suggest the possibility of up to three flea toads coexisting in southern Brazil. In addition, B. sulfuratus is characterized by substantial phenotypic variability, to an extent that compromises its current diagnosis with respect to its congener B. hermogenesi. Therefore, the current state-of-affairs regarding the geographical distribution of these two species and the identification of previously known populations is hitherto uncertain. Our goals are to reassess previous records of flea toads attributable to B. hermogenesi, B. sulfuratus and “Brachycephalus sp. nov.”, considering the description of B. sulfuratus, and to review the diagnosis of B. sulfuratus.MethodsA critical analysis of the species identity of flea toad specimens attributable to B. hermogenesi, B. sulfuratus, or to a potentially undescribed species from southeastern and southern Brazil was based either on the analysis of morphology or on their advertisement calls. These analyses include our independent examinations of specimens and, when not possible, examinations of published descriptions. To allow for a consistent comparison of advertisement calls between B. hermogenesi and B. sulfuratus, we made recordings of both species, including in the type locality of the former.ResultsWe found that morphological and call characters originally proposed as diagnostic for B. sulfuratus in relation to B. hermogenesi vary intraspecifically. Live individuals with ventral yellow spots correspond to B. sulfuratus; individuals without yellow spots can be either B. sulfuratus or B. hermogenesi. In preservative, they are indistinguishable. Previous records of Brachycephalus sp. nov. correspond to B. sulfuratus. We propose that the reduced number of notes per call and the presence of only isolated notes in the call of B. sulfuratus, as opposed to a high number of notes per call with isolated notes and note groups in the call of B. hermogenesi, as the only diagnostic characters between them. Regarding their distributions and based in our assessment, only B. sulfuratus occurs in southern Brazil, without any overlap with B. hermogenesi. There is a narrow gap between the distributions of these species around the southeast of the city of São Paulo. Our revision also revealed that some records previously attributed to B. hermogenesi in Rio de Janeiro and north São Paulo represent a distinct, unidentified flea toad that is not B. sulfuratus. Both species occur side by side in Corcovado, São Paulo, a locality from where five paratypes of B. hermogenesi were obtained. Biogeographic events that might have led to vicariance between B. hermogenesi and B. sulfuratus are discussed. creator: Marcos R. Bornschein creator: Luiz Fernando Ribeiro creator: Larissa Teixeira creator: Ricardo Belmonte-Lopes creator: Leonardo Amaral de Moraes creator: Leandro Corrêa creator: Giovanni Nachtigall Maurício creator: Júnior Nadaline creator: Marcio R. Pie uri: https://doi.org/10.7717/peerj.10983 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Bornschein et al. title: Changes in diversity and community assembly of jumping spiders (Araneae: Salticidae) after rainforest conversion to rubber and oil palm plantations link: https://peerj.com/articles/11012 last-modified: 2021-03-04 description: Rainforest conversion into monoculture plantations results in species loss and community shifts across animal taxa. The effect of such conversion on the role of ecophysiological properties influencing communities, and conversion effects on phylogenetic diversity and community assembly mechanisms, however, are rarely studied in the same context. Here, we compare salticid spider (Araneae: Salticidae) communities between canopies of lowland rainforest, rubber agroforest (“jungle rubber”) and monoculture plantations of rubber or oil palm, sampled in a replicated plot design in Jambi Province, Sumatra, Indonesia. Overall, we collected 912 salticid spider individuals and sorted them to 70 morphospecies from 21 genera. Salticid richness was highest in jungle rubber, followed by rainforest, oil palm and rubber, but abundance of salticids did not differ between land-use systems. Community composition was similar in jungle rubber and rainforest but different from oil palm and rubber, which in turn were different from each other. The four investigated land-use systems differed in aboveground plant biomass, canopy openness and land use intensity, which explained 12% of the observed variation in canopy salticid communities. Phylogenetic diversity based on ~850 bp 28S rDNA fragments showed similar patterns as richness, that is, highest in jungle rubber, intermediate in rainforest, and lowest in the two monoculture plantations. Additionally, we found evidence for phylogenetic clustering of salticids in oil palm, suggesting that habitat filtering is an important factor shaping salticid spider communities in monoculture plantations. Overall, our study offers a comprehensive insight into the mechanisms shaping communities of arthropod top predators in canopies of tropical forest ecosystems and plantations, combining community ecology, environmental variables and phylogenetics across a land-use gradient in tropical Asia. creator: André Junggebauer creator: Tamara R. Hartke creator: Daniel Ramos creator: Ina Schaefer creator: Damayanti Buchori creator: Purnama Hidayat creator: Stefan Scheu creator: Jochen Drescher uri: https://doi.org/10.7717/peerj.11012 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Junggebauer et al. title: Differential gene expression in a tripartite interaction: Drosophila, Spiroplasma and parasitic wasps link: https://peerj.com/articles/11020 last-modified: 2021-03-04 description: BackgroundSeveral facultative bacterial symbionts of insects protect their hosts against natural enemies. Spiroplasma poulsonii strain sMel (hereafter Spiroplasma), a male-killing heritable symbiont of Drosophila melanogaster, confers protection against some species of parasitic wasps. Several lines of evidence suggest that Spiroplasma-encoded ribosome inactivating proteins (RIPs) are involved in the protection mechanism, but the potential contribution of the fly-encoded functions (e.g., immune response), has not been deeply explored.MethodsHere we used RNA-seq to evaluate the response of D. melanogaster to infection by Spiroplasma and parasitism by the Spiroplasma-susceptible wasp Leptopilina heterotoma, and the Spiroplasma-resistant wasp Ganaspis sp. In addition, we used quantitative (q)PCR to evaluate the transcript levels of the Spiroplasma-encoded Ribosomal inactivation protein (RIP) genes.ResultsIn the absence of Spiroplasma infection, we found evidence of Drosophila immune activation by Ganaspis sp., but not by L. heterotoma, which in turn negatively influenced functions associated with male gonad development. As expected for a symbiont that kills males, we detected extensive downregulation in the Spiroplasma-infected treatments of genes known to have male-biased expression. We detected very few genes whose expression patterns appeared to be influenced by the Spiroplasma-L. heterotoma interaction, and these genes are not known to be associated with immune response. For most of these genes, parasitism by L. heterotoma (in the absence of Spiroplasma) caused an expression change that was at least partly reversed when both L. heterotoma and Spiroplasma were present. It is unclear whether such genes are involved in the Spiroplasma-mediated mechanism that leads to wasp death and/or fly rescue. Nonetheless, the expression pattern of some of these genes, which reportedly undergo expression shifts during the larva-to-pupa transition, is suggestive of an influence of Spiroplasma on the development time of L. heterotoma-parasitized flies. One of the five RIP genes (RIP2) was consistently highly expressed independently of wasp parasitism, in two substrains of sMel. Finally, the RNAseq data revealed evidence consistent with RIP-induced damage in the ribosomal (r)RNA of the Spiroplasma-susceptible, but not the Spiroplasma-resistant, wasp. Acknowledging the caveat that we lacked adequate power to detect the majority of DE genes with fold-changes lower than 3, we conclude that immune priming is unlikely to contribute to the Spiroplasma-mediated protection against wasps, and that the mechanism by which Ganaspis sp. resists/tolerates Spiroplasma does not involve inhibition of RIP transcription. creator: Victor Manuel Higareda Alvear creator: Mariana Mateos creator: Diego Cortez creator: Cecilia Tamborindeguy creator: Esperanza Martinez-Romero uri: https://doi.org/10.7717/peerj.11020 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Higareda Alvear et al. title: Characterizing avian pathogenic Escherichia coli (APEC) from colibacillosis cases, 2018 link: https://peerj.com/articles/11025 last-modified: 2021-03-04 description: Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a devastating disease of poultry that results in multi-million-dollar losses annually to the poultry industry. Disease syndromes associated with APEC includes colisepticemia, cellulitis, air sac disease, peritonitis, salpingitis, omphalitis, and osteomyelitis among others. A total of 61 APEC isolates collected during the Fall of 2018 (Aug–Dec) from submitted diagnostic cases of poultry diagnosed with colibacillosis were assessed for the presence of 44 virulence-associated genes, 24 antimicrobial resistance genes and 17 plasmid replicon types. Each isolate was also screened for its ability to form biofilm using the crystal violet assay and antimicrobial susceptibility to 14 antimicrobials using the NARMS panel. Overall, the prevalence of virulence genes ranged from 1.6% to >90% with almost all strains harboring genes that are associated with the ColV plasmid—the defining trait of the APEC pathotype. Overall, 58 strains were able to form biofilms and only three strains formed negligible biofilms. Forty isolates displayed resistance to antimicrobials of the NARMS panel ranging from one to nine agents. This study highlights that current APEC causing disease in poultry possess virulence and resistance traits and form biofilms which could potentially lead to challenges in colibacillosis control. creator: Darby M. Newman creator: Nicolle L. Barbieri creator: Aline L. de Oliveira creator: Dajour Willis creator: Lisa K. Nolan creator: Catherine M. Logue uri: https://doi.org/10.7717/peerj.11025 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Newman et al. title: An integrative approach to infer systematic relationships and define species groups in the shrub frog genus Raorchestes, with description of five new species from the Western Ghats, India link: https://peerj.com/articles/10791 last-modified: 2021-03-03 description: The genus Raorchestes is a large radiation of Old World tree frogs for which the Western Ghats in Peninsular India is the major center for origin and diversification. Extensive studies on this group during the past two decades have resolved long-standing taxonomic confusions and uncovered several new species, resulting in a four-fold increase in the number of known Raorchestes frogs from this region. Our ongoing research has revealed another five new species in the genus, formally described as Raorchestes drutaahu sp. nov., Raorchestes kakkayamensis sp. nov., Raorchestes keirasabinae sp. nov., Raorchestes sanjappai sp. nov., and Raorchestes vellikkannan sp. nov., all from the State of Kerala in southern Western Ghats. Based on new collections, we also provide insights on the taxonomic identity of three previously known taxa. Furthermore, since attempts for an up-to-date comprehensive study of this taxonomically challenging genus using multiple integrative taxonomic approaches have been lacking, here we review the systematic affinities of all known Raorchestes species and define 16 species groups based on evidence from multi-gene (2,327 bp) phylogenetic analyses, several morphological characters (including eye colouration and pattern), and acoustic parameters (temporal and spectral properties, as well as calling height). The results of our study present novel insights to facilitate a better working taxonomy for this rather speciose and morphologically conserved radiation of shrub frogs. This will further enable proper field identification, provide momentum for multi-disciplinary studies, as well as assist conservation of one of the most colourful and acoustically diverse frog groups of the Western Ghats biodiversity hotspot. creator: Sonali Garg creator: Robin Suyesh creator: Sandeep Das creator: Mark A. Bee creator: S. D. Biju uri: https://doi.org/10.7717/peerj.10791 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Garg et al. title: Detection of sexually transmitted pathogens and co-infection with human papillomavirus in women residing in rural Eastern Cape, South Africa link: https://peerj.com/articles/10793 last-modified: 2021-03-03 description: BackgroundSouth African women of reproductive age have a high burden of sexually transmitted infections (STIs), including human papillomavirus (HPV) infection. However, there is limited information on the prevalence of sexually transmitted pathogens in women from rural Eastern Cape Province, South Africa. The study aims at determining the prevalence of sexually transmitted pathogens and co-infection with high-risk (HR) HPV among women from rural Eastern Cape Province, South Africa.MethodsA total of 205 cervical specimens were collected from women aged ≥ 30 years from a rural community-based clinic. The samples were tested for a panel of pathogenic STIs [Chlamydia trachomatis (serovars A-K & L1-L3), Haemophilus ducreyi, Herpes Simplex Virus (Types 1 & 2), Neisseria gonorrhoeae, Treponema pallidum, Trichomonas vaginalis (TV), and pathobionts [Mycoplasma genitalium (MG), Mycoplasma hominis (MH) and Ureaplasma spp. (UP)] using a multiplex PCR STD direct flow chip assay through a manual Hybrispot platform (Master Diagnostica, Granada, Spain). HR-HPV detection was performed by Hybrid Capture-2 assay.ResultsHigh-risk HPV prevalence was 32.2% (66/205) and HIV-1 prevalence was 38.5% (79/205). The overall prevalence of six pathogenic STIs was 22.9% (47/205), with TV having the highest prevalence (15.6%; 32/205). UP (70.2%, 144/205) and MH (36.6%, 75/205) were the most frequently detected pathobionts. Co-infection with ≥ 2 pathogens pathobionts was observed among 52.7% (108/205) participants. Of the six pathogenic STIs, three participants had more than one STI (1.46%) with the presence of MH and UP. HSV-2 (OR: 4.17, CI [1.184–14.690]) and HIV infection (OR: 2.11, CI [1.145–3.873]) were independent STIs associated with HR-HPV infection.ConclusionsThe high prevalence of pathogenic STIs underscores the need to improve syndromic management policy by implementing effective strategies of prevention, screening tests, and management. HSV-2 and HIV positive remain strongly associated with HR-HPV infection. creator: Ongeziwe Taku creator: Adrian Brink creator: Tracy L. Meiring creator: Keletso Phohlo creator: Charles B. Businge creator: Zizipho Z.A. Mbulawa creator: Anna-Lise Williamson uri: https://doi.org/10.7717/peerj.10793 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Taku et al. title: Evaluation of female Aedes aegypti proteome via LC-ESI-MS/MS using two protein extraction methods link: https://peerj.com/articles/10863 last-modified: 2021-03-03 description: BackgroundProteomic analyses have broadened the horizons of vector control measures by identifying proteins associated with different biological and physiological processes and give further insight into the mosquitoes’ biology, mechanism of insecticide resistance and pathogens-mosquitoes interaction. Female Ae. aegypti ingests human blood to acquire the requisite nutrients to make eggs. During blood ingestion, female mosquitoes transmit different pathogens. Therefore, this study aimed to determine the best protein extraction method for mass spectrometry analysis which will allow a better proteome profiling for female mosquitoes.MethodsIn this present study, two protein extractions methods were performed to analyze female Ae. aegyti proteome, via TCA acetone precipitation extraction method and a commercial protein extraction reagent CytoBusterTM. Then, protein identification was performed by LC-ESI-MS/MS and followed by functional protein annotation analysis.ResultsThe CytoBusterTM reagent gave the highest protein yield with a mean of 475.90 µg compared to TCA acetone precipitation extraction showed 283.15 µg mean of protein. LC-ESI-MS/MS identified 1,290 and 890 proteins from the CytoBusterTM reagent and TCA acetone precipitation, respectively. When comparing the protein class categories in both methods, there were three additional categories for proteins identified using CytoBusterTM reagent. The proteins were related to scaffold/adaptor protein (PC00226), protein binding activity modulator (PC00095) and intercellular signal molecule (PC00207). In conclusion, the CytoBusterTM protein extraction reagent showed a better performance for the extraction of proteins in term of the protein yield, proteome coverage and extraction speed. creator: Abubakar Shettima creator: Intan H. Ishak creator: Syahirah Hanisah Abdul Rais creator: Hadura Abu Hasan creator: Nurulhasanah Othman uri: https://doi.org/10.7717/peerj.10863 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Shettima et al. title: Publication rate and citation counts for preprints released during the COVID-19 pandemic: the good, the bad and the ugly link: https://peerj.com/articles/10927 last-modified: 2021-03-03 description: BackgroundPreprints are preliminary reports that have not been peer-reviewed. In December 2019, a novel coronavirus appeared in China, and since then, scientific production, including preprints, has drastically increased. In this study, we intend to evaluate how often preprints about COVID-19 were published in scholarly journals and cited.MethodsWe searched the iSearch COVID-19 portfolio to identify all preprints related to COVID-19 posted on bioRxiv, medRxiv, and Research Square from January 1, 2020, to May 31, 2020. We used a custom-designed program to obtain metadata using the Crossref public API. After that, we determined the publication rate and made comparisons based on citation counts using non-parametric methods. Also, we compared the publication rate, citation counts, and time interval from posting on a preprint server to publication in a scholarly journal among the three different preprint servers.ResultsOur sample included 5,061 preprints, out of which 288 were published in scholarly journals and 4,773 remained unpublished (publication rate of 5.7%). We found that articles published in scholarly journals had a significantly higher total citation count than unpublished preprints within our sample (p < 0.001), and that preprints that were eventually published had a higher citation count as preprints when compared to unpublished preprints (p < 0.001). As well, we found that published preprints had a significantly higher citation count after publication in a scholarly journal compared to as a preprint (p < 0.001). Our results also show that medRxiv had the highest publication rate, while bioRxiv had the highest citation count and shortest time interval from posting on a preprint server to publication in a scholarly journal.ConclusionsWe found a remarkably low publication rate for preprints within our sample, despite accelerated time to publication by multiple scholarly journals. These findings could be partially attributed to the unprecedented surge in scientific production observed during the COVID-19 pandemic, which might saturate reviewing and editing processes in scholarly journals. However, our findings show that preprints had a significantly lower scientific impact, which might suggest that some preprints have lower quality and will not be able to endure peer-reviewing processes to be published in a peer-reviewed journal. creator: Diego Añazco creator: Bryan Nicolalde creator: Isabel Espinosa creator: Jose Camacho creator: Mariam Mushtaq creator: Jimena Gimenez creator: Enrique Teran uri: https://doi.org/10.7717/peerj.10927 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Añazco et al. title: iTRAQ-based comparative proteome analyses of different growth stages revealing the regulatory role of reactive oxygen species in the fruiting body development of Ophiocordyceps sinensis link: https://peerj.com/articles/10940 last-modified: 2021-03-03 description: In this study, using an isobaric tags for relative and absolute quantitation (iTRAQ ) approach coupled with LC-MS / MS and bioinformatics, the proteomes were analyzed for the crucial three stages covering the fruiting body development of Ophiocordyceps sinensis, including sclerotium (ST), primordium (PR) and mature fruiting body (MF), with a focus on fruiting body development-related proteins and the potential mechanisms of the development. A total of 1,875 proteins were identified. Principal Component Analysis (PCA) demonstrated that the protein patterns between PR and MF were more similar than ST. Differentially accumulated proteins (DAPs) analysis showed that there were 510, 173 and 514 DAPs in the comparisons of ST vs. PR, PR vs. MF and ST vs. MF, respectively. A total of 62 shared DAPs were identified and primarily enriched in proteins related to ‘carbon transport and mechanism’, ‘the response to oxidative stress’, ‘antioxidative activity’ and ‘translation’. KEGG and GO databases showed that the DAPs were enriched in terms of ‘primary metabolisms (amino acid/fatty acid/energy metabolism)’, ‘the response to oxidative stress’ and ‘peroxidase’. Furthermore, 34 DAPs involved in reactive oxygen species (ROS) metabolism were identified and clustered across the three stages using hierarchical clustering implemented in hCluster R package . It was suggested that their roles and the underlying mechanisms may be stage-specific. ROS may play a role in fungal pathogenicity in ST, the fruit-body initiation in PR, sexual reproduction and highland adaptation in MF. Crucial ROS-related proteins were identified, such as superoxide dismutase (SOD, T5A6F1), Nor-1 (T5AFX3), electron transport protein (T5AHD1), histidine phosphotransferase (HPt, T5A9Z5) and Glutathione peroxidase (T5A9V1). Besides, the accumulation of ROS at the three stages were assayed using 2,7-dichlorofuorescin diacetate (DCFH-DA) stanning. A much stronger ROS accumulation was detected at the stage MF, compared to the stages of PR and ST. Sections of ST and fruit-body part of MF were stained by DCFH-DA and observed under the fluorescencemicroscope, showing ROS was distributed within the conidiospore and ascus. Besides, SOD activity increased across the three stages, while CAT activity has a strong increasement in MF compared to the stages of ST and PR. It was suggested that ROS may act in gradient-dependent manner to regulate the fruiting body development. The coding region sequences of six DAPs were analyzed at mRNA level by quantitative real-time PCR (qRT-PCR). The results support the result of DAPs analysis and the proteome sequencing data. Our findings offer the perspective of proteome to understand the biology of fruiting body development and highland adaptation in O. sinensis, which would inform the big industry of this valuable fungus. creator: Xinxin Tong creator: Fang Wang creator: Han Zhang creator: Jing Bai creator: Qiang Dong creator: Pan Yue creator: Xinyi Jiang creator: Xinrui Li creator: Li Wang creator: Jinlin Guo uri: https://doi.org/10.7717/peerj.10940 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tong et al. title: Influence of plastic film mulch with biochar application on crop yield, evapotranspiration, and water use efficiency in northern China: A meta-analysis link: https://peerj.com/articles/10967 last-modified: 2021-03-03 description: BackgroundChina is the leading consumer of plastic film worldwide. Plastic film mulched ridge-furrow is one of the most widely adopted agronomic and field management practices in rain-fed agriculture in dry-land areas of China. The efficiency of plastic film mulching as a viable method to decrease evapotranspiration (ET), increase crop yields, and water use efficiency (WUE), has been demonstrated extensively by earlier studies.MethodsA comprehensive evaluation of how co-application of plastic-film mulch and biochar in different agro-environments under varying climatic conditions influence ET, crop yield, WUE, and soil microbial activity were assessed. We performed a meta-analysis using the PRISMA guideline to assess the effect of plastic-film mulched ridge-furrow and biochar on ET, yield, and WUE of wheat (Triticum aestivum L.), potato (Solanum tuberosum L.), and maize (Zea mays L.) in northern China.ResultsThe use of plastic film increased average yields of wheat (75.7%), potato (20.2%), and maize (12.9%) in Gansu, Ningxia, Shaanxi, and Shanxi provinces, respectively due to the reduction in ET by 12.8% in Gansu, 0.5% in Ningxia, and 4.1% in Shanxi, but increased in Shaanxi by 0.5% compared to no-mulching. These changes may be attributed to the effect of plastic film mulch application which simultaneously increased WUE by 68.5% in Gansu, 23.9% in Ningxia, 16.2% in Shaanxi, and 12.8% in Shanxi, respectively. Compared to flat planting without mulching, in three years, the yield of maize increased with the co-application of plastic film and biochar by 22.86% in the Shanxi and Shaanxi regions.ConclusionOur analysis revealed co-application of plastic film with biochar is integral for improving soil and water conservation in rain-fed agriculture and as an integrated practice to avert drought while simultaneously mitigating runoff and erosion. creator: Erastus Mak-Mensah creator: Peter Bilson Obour creator: Eunice Essel creator: Qi Wang creator: John K. Ahiakpa uri: https://doi.org/10.7717/peerj.10967 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Mak-Mensah et al. title: Inhibitory effects of α-Mangostin on T cell cytokine secretion via ORAI1 calcium channel and K+ channels inhibition link: https://peerj.com/articles/10973 last-modified: 2021-03-03 description: BackgroundAs one of the main components of mangosteen (Garcinia mangostana), a tropical fruit, α-mangostin has been reported to have numerous pharmacological benefits such as anti-cancer, anti-inflammatory, and anti-allergic effects through various mechanisms of action. The effects of α-mangostin on intracellular signaling proteins is well studied, but the effects of α-mangostin on ion channels and its physiological effects in immune cells are unknown. Generation of intracellular calcium signaling is a fundamental step for T cell receptor stimulation. This signaling is mediated not only by the ORAI1 calcium channel, but also by potassium ion channels, which provide the electrical driving forces for generating sufficient calcium ion influx. This study investigated whether α-mangosteen suppress T cell stimulation by inhibiting ORAI1 and two kinds of potassium channels (Kv1.3 and KCa3.1), which are normally expressed in human T cells.MethodsThis study analyzed the inhibitory effect of α-mangostin on immune cell activity via inhibition of calcium and potassium ion channels expressed in immune cells.Resultsα-mangostin inhibited ORAI1 in a concentration-dependent manner, and the IC50 value was 1.27 ± 1.144 µM. Kv1.3 was suppressed by 41.38 ± 6.191% at 3 µM, and KCa3.1 was suppressed by 51.16 ± 5.385% at 3 µM. To measure the inhibition of cytokine secretion by immune cells, Jurkat T cells were stimulated to induce IL-2 secretion, and α-mangostin was found to inhibit it. This study demonstrated the anti-inflammatory effect of α-mangostin, the main component of mangosteen, through the regulation of calcium signals. creator: Hyun Jong Kim creator: Seorin Park creator: Hui Young Shin creator: Yu Ran Nam creator: Phan Thi Lam Hong creator: Young-Won Chin creator: Joo Hyun Nam creator: Woo Kyung Kim uri: https://doi.org/10.7717/peerj.10973 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kim et al. title: Comparative transcriptomic analysis reveals the cold acclimation during chilling stress in sensitive and resistant passion fruit (Passiflora edulis) cultivars link: https://peerj.com/articles/10977 last-modified: 2021-03-03 description: Chilling stress (CS) is an important limiting factor for the growth and development of passion fruit (Passiflora edulis) in winter in South China. However, little is known about how the passion fruit responds and adapts to CS. In this study, we performed transcriptome sequencing of cold-susceptible cultivar Huangjinguo (HJG) and cold-tolerant cultivar Tainong 1 (TN1) under normal temperature (NT) and CS conditions, and a total of 47,353 unigenes were obtained by seven databases. Using differentially expressed unigenes (DEGs) analysis, 3,248 and 4,340 DEGs were identified at two stages, respectively. The Gene Ontology (GO) enrichment analysis showed that the DEGs were mainly related to phosphorylation, membrane protein, and catalytic activity. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the unigenes of plant-pathogen interaction, plant hormone signal transduction and fatty acid metabolism were enriched. Then, the 12,471 filtered unigenes were clustered into eight co-expression modules, and two modules were correlated with CS. In this two modules, 32 hub unigenes were obtained. Furthermore, the unigenes related to CS were validated using quantitative real-time PCR (RT-qPCR). This work showed that the expression levels of CS-related unigenes were very different in two passion fruit cultivars. The results provide information for the development of passion fruit with increased chilling tolerance. creator: Yanyan Wu creator: Weihua Huang creator: Qinglan Tian creator: Jieyun Liu creator: Xiuzhong Xia creator: Xinghai Yang creator: Haifei Mou uri: https://doi.org/10.7717/peerj.10977 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wu et al. title: Impact of organic manure on fruit set, fruit retention, yield, and nutritional status in pomegranate (Punica granatum L. “Wonderful”) under water and mineral fertilization deficits link: https://peerj.com/articles/10979 last-modified: 2021-03-03 description: This research was conducted on mature pomegranate (Punica granatum L. “Wonderful”) trees growing at a site located in North Coast, Matrouh Governorate, Egypt. The aim was to investigate the impacts of different irrigation regimes in combination with different fertilizer regimes on the fruit set, fruit retention, yield, and nutritional status of the trees. The experimental factors were arranged in a split-plot design, with four replicates per treatment combination. The results indicated that all of the characteristics measured, including leaves nutritional status, percentages of fruit set, fruit drop, fruit retention, fruit cracking, fruit sunburn, and marketable fruit, and yield were significantly affected by the interaction between the irrigation treatment which denoted by percentages of reference evapotranspiration (ETo) and fertilizer regime. The application of 75% mineral fertilizer + 25% organic manure under deficit irrigation of 80% ETo increased the yield by an average of 18.23% over the 2 years compared with 100% mineral fertilization under full irrigation, while 50% mineral fertilizer + 50% organic matter under 80% ETo gave the maximum percentage of marketable fruit (86.23% and 86.84% in 2018 and 2019, respectively). The maximum water use efficiency was obtained with the 80% ETo treatment combined with 75% mineral fertilizer + 25% organic manure in both seasons with values of 9.69 and 10.06 kg/m3 applied water, respectively. These results demonstrate that under the field conditions at the experimental site, the fruit set and retention could be improved by applying a reduced amount of mineral fertilizer in combination with organic manure and less irrigation water. creator: Mahmoud Abdel-Sattar creator: Khalid F. Almutairi creator: Abdulwahed M. Aboukarima creator: Mohamed El-Mahrouky uri: https://doi.org/10.7717/peerj.10979 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Abdel-Sattar et al. title: Estimating species sensitivity distributions on the basis of readily obtainable descriptors and toxicity data for three species of algae, crustaceans, and fish link: https://peerj.com/articles/10981 last-modified: 2021-03-03 description: Estimation of species sensitivity distributions (SSDs) is a crucial approach to predicting ecological risks and water quality benchmarks, but the amount of data required to implement this approach is a serious constraint on the application of SSDs to chemicals for which there are few or no toxicity data. The development of statistical models to directly estimate the mean and standard deviation (SD) of the logarithms of log-normally distributed SSDs has recently been proposed to overcome this problem. To predict these two parameters, we developed multiple linear regression models that included, in addition to readily obtainable descriptors, the mean and SD of the logarithms of the concentrations that are acutely toxic to one algal, one crustacean, and one fish species, as predictors. We hypothesized that use of the three species’ mean and SD would improve the accuracy of the predicted means and SDs of the logarithms of the SSDs. We derived SSDs for 60 chemicals based on quality-assured acute toxicity data. Forty-five of the chemicals were used for model fitting, and 15 for external validation. Our results supported previous findings that models developed on the basis of only descriptors such as log KOW had limited ability to predict the mean and SD of SSD (e.g., r2 = 0.62 and 0.49, respectively). Inclusion of the three species’ mean and SD, in addition to the descriptors, in the models markedly improved the predictions of the means and SDs of SSDs (e.g., r2 = 0.96 and 0.75, respectively). We conclude that use of the three species’ mean and SD is promising for more accurately estimating an SSD and thus the hazardous concentration for 5% of species in cases where limited ecotoxicity data are available. creator: Yuichi Iwasaki creator: Kiyan Sorgog uri: https://doi.org/10.7717/peerj.10981 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Iwasaki and Sorgog title: Influence of water availability and temperature on estimates of microbial extracellular enzyme activity link: https://peerj.com/articles/10994 last-modified: 2021-03-03 description: Soils are highly heterogeneous and support highly diverse microbial communities. Microbial extracellular enzymes breakdown complex polymers into small assimilable molecules representing the limiting step of soil organic matter mineralization. This process occurs on to soil particles although currently it is typically estimated in laboratory aqueous solutions. Herein, estimates of microbial extracellular enzyme activity were obtained over a broad range of temperatures and water availabilities frequently observed at soil upper layers. A Pseudomonas strain presented optimum extracellular enzyme activities at high water activity whereas a desiccation resistant bacterium (Deinococcus) and a soil thermophilic isolate (Parageobacillus) showed optimum extracellular enzyme activity under dried (i.e., water activities ranging 0.5–0.8) rather that wet conditions. Different unamended soils presented a distinctive response of extracellular enzyme activity as a function of temperature and water availability. This study presents a procedure to obtain realistic estimates of microbial extracellular enzyme activity under natural soil conditions of extreme water availability and temperature. Improving estimates of microbial extracellular enzyme activity contribute to better understand the role of microorganisms in soils. creator: Enrique J. Gomez creator: Jose A. Delgado creator: Juan M. Gonzalez uri: https://doi.org/10.7717/peerj.10994 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gomez et al. title: Cranial ornamentation in the Late Cretaceous nodosaurid ankylosaur Hungarosaurus link: https://peerj.com/articles/11010 last-modified: 2021-03-03 description: Bony cranial ornamentation is developed by many groups of vertebrates, including ankylosaur dinosaurs. To date, the morphology and ontogenetic origin of ankylosaurian cranial ornamentation has primarily focused on a limited number of species from only one of the two major lineages, Ankylosauridae. For members of the sister group Nodosauridae, less is known. Here, we provide new details of the cranial anatomy of the nodosaurid Hungarosaurus from the Santonian of Europe. Based on a number of previously described and newly identified fragmentary skulls and skull elements, we recognize three different size classes of Hungarosaurus. We interpret these size classes as representing different stages of ontogeny. Cranial ornamentation is already well-developed in the earliest ontogenetic stage represented herein, suggesting that the presence of outgrowths may have played a role in intra- and interspecific recognition. We find no evidence that cranial ornamentation in Hungarosaurus involves the contribution of coossified osteoderms. Instead, available evidence indicates that cranial ornamentation forms as a result of the elaboration of individual elements. Although individual differences and sexual dimorphism cannot be excluded, the observed variation in Hungarosaurus cranial ornamentation appears to be associated with ontogeny. creator: Attila Ősi creator: János Magyar creator: Károly Rosta creator: Matthew Vickaryous uri: https://doi.org/10.7717/peerj.11010 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ősi et al. title: Examining long-term natural vegetation dynamics in the Aral Sea Basin applying the linear spectral mixture model link: https://peerj.com/articles/10747 last-modified: 2021-03-02 description: BackgroundAssociated with the significant decrease in water resources, natural vegetation degradation has also led to many widespread environmental problems in the Aral Sea Basin. However, few studies have examined long-term vegetation dynamics in the Aral Sea Basin or distinguished between natural vegetation and cultivated land when calculating the fractional vegetation cover.MethodsBased on the multi-temporal Moderate Resolution Imaging Spectroradiometer, this study examined the natural vegetation coverage by introducing the Linear Spectral Mixture Model to the Google Earth Engine platform, which greatly reduces the experimental time. Further, trend line analysis, Sen trend analysis, and Mann–Kendall trend test methods were employed to explore the characteristics of natural vegetation cover change in the Aral Sea Basin from 2000 to 2018.ResultsAnalyses of the results suggest three major conclusions. First, the development of irrigated agriculture in the desert area is the main reason for the decrease in downstream water. Second, with the reduction of water, the natural vegetation coverage in the Aral Sea Basin showed an upward trend of 17.77% from 2000 to 2018. Finally, the main driving factor of vegetation cover changes in the Aral Sea Basin is the migration of cultivated land to the desert. creator: Yiting Su creator: Dongchuan Wang creator: Shuang Zhao creator: Jiancong Shi creator: Yanqing Shi creator: Dongying Wei uri: https://doi.org/10.7717/peerj.10747 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Su et al. title: Comparative transcriptome analyses of maize seedling root responses to salt stress link: https://peerj.com/articles/10765 last-modified: 2021-03-02 description: Salt stress affects crop yield by limiting growth and delaying development. In this study, we constructed 16 transcriptome libraries from maize seedling roots using two maize lines, with contrasting salt tolerance, that were exposed to salt stress for 0, 6, 18 and 36 h. In total, 6,584 differential expression genes (DEGs; 3,669 upregulated, 2,915 downregulated) were induced in the salt-sensitive line and 6,419 DEGs (3,876 upregulated, 2,543 downregulated) were induced in the salt-tolerant line. Several DEGs common to both lines were enriched in the ABA signaling pathway, which was presumed to coordinate the process of maize salt response. A total of 459 DEGs were specifically induced in the salt-tolerant line and represented candidate genes responsible for high salt-tolerance. Expression pattern analysis for these DEGs indicated that the period between 0 and 6 h was a crucial period for the rapid response of the tolerant genes under salt stress. Among these DEGs, several genes, Aux/IAA, SAUR, and CBL-interacting kinase have been reported to regulate salt tolerance. In addition, the transcription factors WRKY, bZIP and MYB acted as regulators in the salt-responsive regulatory network of maize roots. Our findings will contribute to understanding of the mechanism on salt response and provide references for functional gene revelation in plants. creator: Xiaoxiang Zhang creator: Peng Liu creator: Chunyan Qing creator: Cong Yang creator: Yaou Shen creator: Langlang Ma uri: https://doi.org/10.7717/peerj.10765 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Comparison of circulating tumor cell (CTC) detection rates with epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) antibodies in different solid tumors: a retrospective study link: https://peerj.com/articles/10777 last-modified: 2021-03-02 description: PurposeStatus of epithelial-mesenchymal transition (EMT) varies from tumors to tumors. Epithelial cell adhesion molecule (EpCAM) and cell surface vimentin (CSV) are the most common used targets for isolating epithelial and mesenchymal CTCs, respectively. This study aimed to identify a suitable CTC capturing antibody for CTC enrichment in each solid tumor by comparing CTC detection rates with EpCAM and CSV antibodies in different solid tumors.MethodsTreatment-naive patients with confirmed cancer diagnosis and healthy people who have performed CTC detection between April 2017 and May 2018 were included in this study. CTC detection was performed with CytoSorter® CTC system using either EpCAM or CSV antibody. In total, 853 CTC results from 690 cancer patients and 72 healthy people were collected for analysis. The performance of CTC capturing antibody was determined by the CTC detection rate.ResultsEpCAM has the highest CTC detection rate of 84.09% in CRC, followed by BCa (78.32%). CTC detection rates with EpCAM antibody are less than 40% in HCC (25%), PDAC (32.5%) and OC (33.33%). CSV has the highest CTC detection rate of 90% in sarcoma, followed by BC (85.71%), UC (84.62%), OC (83.33%) and BCa (81.82%). CTC detection rates with CSV antibody are over 60% in all 14 solid tumors. Except for CRC, CSV has better performances than EpCAM in most solid tumors regarding the CTC detection rates.ConclusionEpCAM can be used as a target to isolate CTCs in CRC, LC, GC, BCa, EC, HNSCC, CC and PCa, especially in CRC, while CSV can be used in most solid tumors for isolating CTCs. creator: Yang Gao creator: Wan-Hung Fan creator: Zhengbo Song creator: Haizhou Lou creator: Xixong Kang uri: https://doi.org/10.7717/peerj.10777 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gao et al. title: Residual dynamics and dietary exposure risk of dimethoate and its metabolite in greenhouse celery link: https://peerj.com/articles/10789 last-modified: 2021-03-02 description: This study aimed to explore the residual dynamics and dietary risk of dimethoate and its metabolite omethoate in celery. Celery was sprayed with 40% dimethoate emulsifiable concentrate (EC) at either a low concentration of 600 g a.i./ha or a high concentration of 900 g a.i./ha. Plants in the seedling, transplanting, or middle growth stages were sprayed once, and the samples were collected 90 days after transplantation. Plants in the harvesting stage were sprayed two or three times. The samples were collected on days 3, 5, 7, 10, 14 and 21 after the last pesticide application. The dimethoate and omethoate compounds were extracted from the celery samples using acetonitrile, and their concentrations were detected using ultra-performance liquid chromatography-tandem mass spectrometry. Also, the dietary risk assessments of dimethoate and omethoate were conducted in various populations and on different foods in China. The metabolism led to the formation of omethoate from dimethoate in the celery. The degradation dynamics of dimethoate and total residues in greenhouse celery followed the first-order kinetic equation. The half-lives of the compounds were 2.42 days and 2.92 days, respectively. The celery which received one application during the harvesting stage had a final residue of dimethoate after 14 days, which was lower than the maximum residue limit (MRL) 0.5 mg kg−1 for Chinese celery. The final deposition of the metabolite omethoate after 28 days was less than the maximum residue limit of 0.02 mg kg−1 for Chinese celery. Furthermore, the risk quotients of dimethoate in celery were less than 1; therefore, the level of chronic risk was acceptable after day 21. Only children aged 2–7 years had an HQ of dimethoate more than 1 (an unacceptable level of acute risk), while the acute dietary risks to other populations were within acceptable levels. It was recommended that any dimethoate applications to celery in greenhouses should happen before the celery reached the harvesting stage, with a safety interval of 28 days. creator: Chunjing Guo creator: Guang Li creator: Qiujun Lin creator: Xianxin Wu creator: Jianzhong Wang uri: https://doi.org/10.7717/peerj.10789 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Guo et al. title: The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study link: https://peerj.com/articles/10830 last-modified: 2021-03-02 description: Tumor-derived circulating tumor DNA (ctDNA) has demonstrated its excellent potential for cancer diagnosis by DNA methylome; therefore, this study aimed to identify the retinoblastoma (RB) specific methylated CpG loci as the RB diagnostic biomarkers and design a methylation specific assay to detect these biomarker from aqueous humor of RB patients. Through a genome-wide methylation profiling of tissue samples from patients with RB, normal retina and other retinal diseases, we shortlisted two CpG loci were only methylated in RB but not in normal retina or other retinal diseases. Both of these two CpG loci were located in the genome of TFAP2A. Through the screening, a primer and probe set for the two CpG loci were tested in fully methylated standards and RB tissues with a significant differentiation of RB. Our results of this assay tested in aqueous humor from RB revealed an accuracy of 92.7% for RB diagnosis. These results suggested our assay targeting the TFAP2A ctDNA methylation can be utilized for RB diagnosis and cancer monitoring. creator: Qi Zeng creator: Sha Wang creator: Jia Tan creator: Lu Chen creator: Jinwei Wang uri: https://doi.org/10.7717/peerj.10830 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zeng et al. title: The regulatory roles and mechanisms of the transcription factor FOXF2 in human diseases link: https://peerj.com/articles/10845 last-modified: 2021-03-02 description: Many studies have focused on the relationship between transcription factors and a variety of common pathological conditions, such as diabetes, stroke, and cancer. It has been found that abnormal transcription factor regulation can lead to aberrant expression of downstream genes, which contributes to the occurrence and development of many diseases. The forkhead box (FOX) transcription factor family is encoded by the FOX gene, which mediates gene transcription and follow-up functions during physiological and pathological processes. FOXF2, a member of the FOX transcription family, is expressed in various organs and tissues while maintaining their normal structural and functional development during the embryonic and adult stages. Multiple regulatory pathways that regulate FOXF2 may also be controlled by FOXF2. Abnormal FOXF2 expression induced by uncontrollable regulatory signals mediate the progression of human diseases by interfering with the cell cycle, proliferation, differentiation, invasion, and metastasis. FOXF2 manipulates downstream pathways and targets as both a pro-oncogenic and anti-oncogenic factor across different types of cancer, suggesting it may be a new potential clinical marker or therapeutic target for cancer. However, FOXF2’s biological functions and specific roles in cancer development remain unclear. In this study, we provide an overview of FOXF2’s structure, function, and regulatory mechanisms in the physiological and pathological conditions of human body. We also discussed the possible reasons why FOXF2 performs the opposite function in the same types of cancer. creator: Qiong Wu creator: Wei Li creator: Chongge You uri: https://doi.org/10.7717/peerj.10845 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wu et al. title: Undercarboxylated osteocalcin inhibits the early differentiation of osteoclast mediated by Gprc6a link: https://peerj.com/articles/10898 last-modified: 2021-03-02 description: Osteocalcin (OCN) was the most abundant noncollagen protein and considered as an endocrine factor. However, the functions of Undercarboxylated osteocalcin (ucOCN) on osteoclast and bone resorption are not well understood. In the present study, preosteoclast RAW264.7 cells and bone marrow mononuclear cells (BMMs) were treated with ucOCN purified from prokaryotic bacteria. Our results showed that ucOCN attenuated the proliferation of RAW264.7 cells with a concentration dependant manner by MTS assay. Scrape wounding assay revealed the decreased motility of RAW264.7 cells after ucOCN treatment. RT-qPCR results manifested the inhibitory effects of ucOCN on the expression of osteoclastic marker genes in RAW264.7 cells during inducing differentiation of RANKL. It was also observed that ucOCN inhibited the formation of multinucleated cells from RAW264.7 cells and BMMs detected by TRAP staining. The number and area of bone resorb pits were also decreased after treatment with ucOCN during their osteoclast induction by toluidine blue staining. The formation and integrity of the osteoclast actin ring were impaired by ucOCN by immunofluorescent staining. Time dependant treatment of ucOCN during osteoclastic induction demonstrated the inhibitory effects mainly occurred at the early stage of osteoclastogenesis. Signaling analysis of luciferase activity of the CRE or SRE reporter and ERK1/2 phosphorylation showed the selective inhibitor or siRNA of Gprc6a (a presumptive ucOCN receptor) could attenuate the promotion of ucOCN on CRE-luciferase activity. Taken together, we provided the first evidence that ucOCN had negative effects on the early differentiation and bone resorption of osteoclasts via Gprc6a. creator: Hailong Wang creator: Jinqiao Li creator: Zihan Xu creator: Feng Wu creator: Hongyu Zhang creator: Chao Yang creator: Jian Chen creator: Bai Ding creator: Xiukun Sui creator: Zhifeng Guo creator: Yinghui Li creator: Zhongquan Dai uri: https://doi.org/10.7717/peerj.10898 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Taxonomic revision of the Malagasy Aphaenogaster swammerdami group (Hymenoptera: Formicidae) link: https://peerj.com/articles/10900 last-modified: 2021-03-02 description: BackgroundMadagascar is famous for its extremely rich biodiversity; the island harbors predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Continuing ongoing efforts to inventory the Malagasy ant fauna, we revise the species currently placed in the myrmicine genus Aphaenogaster Mayr. One species described from Madagascar, Aphaenogaster friederichsi Forel, is synonymized with the Palearctic A. subterranea Latreille syn. nov. This species is considered neither native to Madagascar nor established in the region. This revision focuses on the balance of species in the A. swammerdami group which are all endemic to Madagascar.MethodsThe diversity of the Malagasy Aphaenogaster fauna was assessed via application of multiple lines of evidence involving quantitative morphometric, qualitative morphological, and DNA sequence data. (1) Morphometric investigation was based on hypothesis-free Nest Centroid clustering (NC-clustering) combined with PArtitioning based on Recursive Thresholding (PART) to estimate the number of morphological clusters and determine the most probable boundaries between them. This protocol provides a repeatable and testable approach to find patterns in continuous morphometric data. Species boundaries and the reliability of morphological clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). (2) Qualitative, external morphological characteristics (e.g., shape, coloration patterns, setae number) were subjectively evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. (3) Species delimitation analyses based on mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were carried out to test the putative species previously delimited by morphological and morphometric analyses.ResultsFive species can be inferred based on the integrated evaluation of multiple lines of evidence; of these, three are new to science: Aphaenogaster bresslerisp. n., A. gonacantha (Emery, 1899), A. makaysp. n., A. sahafinasp. n., and A. swammerdamiForel, 1886. In addition, three new synonymies were found for A. swammerdami Forel, 1886 (A. swammerdami clara Santschi, 1915 syn. n., A. swammerdami curta Forel, 1891 syn. n. and A. swammerdami spinipes Santschi, 1911 syn. n.). Descriptions and redefinitions for each taxon and an identification key for their worker castes using qualitative traits and morphometric data are given. Geographic maps depicting species distributions and biological information regarding nesting habits for the species are also provided. creator: Sandor Csősz creator: Ana C. Loss creator: Brian L. Fisher uri: https://doi.org/10.7717/peerj.10900 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Csősz et al. title: Putative carboxylesterase gene identification and their expression patterns in Hyphantria cunea (Drury) link: https://peerj.com/articles/10919 last-modified: 2021-03-02 description: The olfactory system of insects is important for behavioral activities as it recognizes internal and external volatile stimuli in the environment. Insect odorant degrading enzymes (ODEs), including antennal-specific carboxylesterases (CXEs), are known to degrade redundant odorant molecules or to hydrolyze important olfactory sex pheromone components and plant volatiles. Compared to many well-studied Type-I sex pheromone-producing lepidopteran species, the molecular mechanisms of the olfactory system of Type-II sex pheromone-producing Hyphantria cunea (Drury) remain poorly understood. In the current study, we first identified a total of ten CXE genes based on our previous H. unea antennal transcriptomic data. We constructed a phylogenetic tree to evaluate the relationship of HcunCXEs with other insects’ CXEs, and used quantitative PCR to investigate the gene expression of H. cunea CXEs (HcunCXEs). Our results indicate that HcunCXEs are highly expressed in antennae, legs and wings, suggesting a potential function in degrading sex pheromone components, host plant volatiles, and other xenobiotics. This study not only provides a theoretical basis for subsequent olfactory mechanism studies on H. cunea, but also offers some new insights into functions and evolutionary characteristics of CXEs in lepidopteran insects. From a practical point of view, these HcunCXEs might represent meaningful targets for developing behavioral interference control strategies against H. cunea. creator: Jia Ye creator: Dingze Mang creator: Ke Kang creator: Cheng Chen creator: Xiaoqing Zhang creator: Yanping Tang creator: Endang R. Purba creator: Liwen Song creator: Qing-He Zhang creator: Longwa Zhang uri: https://doi.org/10.7717/peerj.10919 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ye et al. title: Ontogeny of highly variable ceratitid ammonoids from the Anisian (Middle Triassic) link: https://peerj.com/articles/10931 last-modified: 2021-03-02 description: Ammonoids reached their greatest diversity during the Triassic period. In the early Middle Triassic (Anisian) stage, ammonoid diversity was dominated by representatives of the family Ceratitidae. High taxonomic diversity can, however, be decoupled from their morphologic disparity. Due to its high phenotypic variability, the high diversity of ceratitids of the Anisian of Nevada was initially assumed to be caused by artificial over-splitting. This study aims to contribute data to settle this issue by applying geometric morphometrics methods, using landmarks and semi-landmarks, in the study of ontogenetic cross-sections of ammonoids for the first time. The results reveal that alterations in ontogenetic trajectories, linked to heterochronic processes, lead to the morphologic diversification of the species studied herein. Our knowledge, based on these ontogenetic changes, challenge the traditional treatment of species using solely adult characters for their distinction. This study furthermore demonstrates that the high diversity of the Anisian ammonoid assemblages of Nevada based on the traditional nomenclatoric approach is regarded to be reasonably accurate. creator: Eva Alexandra Bischof creator: Nils Schlüter creator: Dieter Korn creator: Jens Lehmann uri: https://doi.org/10.7717/peerj.10931 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bischof et al. title: Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat (Triticum aestivum L.) link: https://peerj.com/articles/10963 last-modified: 2021-03-02 description: The ARF gene family plays important roles in intracellular transport in eukaryotes and is involved in conferring tolerance to biotic and abiotic stresses in plants. To explore the role of these genes in the development of wheat (Triticum aestivum L.), 74 wheat ARF genes (TaARFs; including 18 alternate transcripts) were identified and clustered into seven sub-groups. Phylogenetic analysis revealed that TaARFA1 sub-group genes were strongly conserved. Numerous cis-elements functionally associated with the stress response and hormones were identified in the TaARFA1 sub-group, implying that these TaARFs are induced in response to abiotic and biotic stresses in wheat. According to available transcriptome data and qRT-PCR analysis, the TaARFA1 genes displayed tissue-specific expression patterns and were regulated by biotic stress (powdery mildew and stripe rust) and abiotic stress (cold, heat, ABA, drought and NaCl). Protein interaction network analysis further indicated that TaARFA1 proteins may interact with protein phosphatase 2C (PP2C), which is a key protein in the ABA signaling pathway. This comprehensive analysis will be useful for further functional characterization of TaARF genes and the development of high-quality wheat varieties. creator: Yaqian Li creator: Jinghan Song creator: Guang Zhu creator: Zehao Hou creator: Lin Wang creator: Xiaoxue Wu creator: Zhengwu Fang creator: Yike Liu creator: Chunbao Gao uri: https://doi.org/10.7717/peerj.10963 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Trophic niche differentiation and utilisation of food resources in Collembola is altered by rainforest conversion to plantation systems link: https://peerj.com/articles/10971 last-modified: 2021-03-02 description: Intensively managed monoculture plantations are increasingly replacing natural forests across the tropics resulting in changes in ecological niches of species and communities, and in ecosystem functioning. Collembola are among the most abundant arthropods inhabiting the belowground system sensitively responding to changes in vegetation and soil conditions. However, most studies on the response of Collembola to land-use change were conducted in temperate ecosystems and focused on shifts in community composition or morphological traits, while parameters more closely linked to ecosystem functioning, such as trophic niches, received little attention. Here, we used stable isotope analysis (13C and 15N) to investigate changes in the trophic structure and use of food resources by Collembola in Jambi province (Sumatra, Indonesia), a region that experienced strong deforestation in the last decades. Isotopic values of Collembola from 32 sites representing four land-use systems were analyzed (rainforest, rubber agroforest, rubber (Hevea brasiliansis) and oil palm (Elaeis guineensis) monoculture plantations). Across Collembola species Δ13C values were highest in rainforest suggesting more pronounced processing of litter resources by microorganisms and consumption of these microorganisms by Collembola in this system. Lower Δ13C values, but high Δ13C variation in Collembola in oil palm plantations indicated that Collembola shifted towards herbivory and used more variable resources in this system. Small range in Δ15N values in Collembola species in monoculture plantations in comparison to rainforest indicated that conversion of rainforest into plantations is associated with simplification in the trophic structure of Collembola communities. This was further confirmed by generally lower isotopic niche differentiation among species in plantations. Across the studied ecosystems, atmobiotic species (Symphypleona and Paronellidae) occupied the lowest, whereas euedaphic Collembola species occupied the highest trophic position, resembling patterns in temperate forests. Some species of Paronellidae in rainforest and jungle rubber had Δ15N values below those of leaf litter suggesting algivory (Salina sp.1, Callyntrura sp.1 and Lepidonella sp.1), while a dominant species, Pseudosinella sp.1, had the highest Δ15N values in most of the land-use systems suggesting that this species at least in part lives as predator or scavenger. Overall, the results suggest that rainforest conversion into plantation systems is associated with marked shifts in the structure of trophic niches in soil and litter Collembola with potential consequences for ecosystem functioning and food-web stability. creator: Winda Ika Susanti creator: Rahayu Widyastuti creator: Stefan Scheu creator: Anton Potapov uri: https://doi.org/10.7717/peerj.10971 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Susanti et al. title: Formalin-induced pain prolongs sub- to supra-second time estimation in rats link: https://peerj.com/articles/11002 last-modified: 2021-03-02 description: BackgroundTemporal estimation can be influenced by pain, which is a complex psychological and physiological phenomenon. However, the time range in which perception is most sensitive to pain remains unclear.MethodsIn the present study, we explored the effects of acute inflammatory pain on time perception in the sub- to supra-second (0.6–2.4-s) and supra-second (2–8-s) ranges in rats. Plantar formalin injection was used to induce acute inflammatory pain, and a temporal bisection task was used to measure time perception. Task test sessions were held for five consecutive days (one per day): the day before injection (baseline), immediately after injection, and the three post-injection days. The point of subjective equality (PSE, which reflects the subjective duration) and Weber fraction (which reflects temporal sensitivity) were calculated and analysed.ResultsIn the 0.6–2.4-s range, the PSE was significantly lower, indicating prolonged subjective duration, in the formalin group relative to the saline group (p = 0.049) immediately after injection. Formalin-induced pain also tended to lengthened time perception in the 0.6–2.4-s range on post-injection days 2 (p = 0.06) and 3 (p = 0.054). In the 2–8-s range, formalin injection did not affect the PSE or Weber fraction.ConclusionsThe enhanced effect of pain on temporal perception in the sub- to supra-second range is observed in this study and this effect is attenuated with the prolongation of estimated time, even in rats. creator: Xinhe Liu creator: Ning Wang creator: Jinyan Wang creator: Fei Luo uri: https://doi.org/10.7717/peerj.11002 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Predictors of treatment failure during the first year in newly diagnosed type 2 diabetes patients: a retrospective, observational study link: https://peerj.com/articles/11005 last-modified: 2021-03-02 description: BackgroundDiabetes patients who fail to achieve early glycemic control may increase the future risk of complications and mortality. The aim of the study was to identify factors that predict treatment failure (TF) during the first year in adults with newly diagnosed type 2 diabetes mellitus (T2DM).MethodsThis retrospective cohort study conducted at a medical center in Taiwan enrolled 4,282 eligible patients with newly diagnosed T2DM between 2002 and 2017. Data were collected from electronic medical records. TF was defined as the HbA1c value >7% at the end of 1-year observation. A subgroup analysis of 2,392 patients with baseline HbA1c ≥8% was performed. Multivariable logistic regression analysis using backward elimination was applied to establish prediction models.ResultsOf all study participants, 1,439 (33.6%) were classified as TF during the first year. For every 1% increase in baseline HbA1c, the risk of TF was 1.17 (95% CI 1.15–1.20) times higher. Patients with baseline HbA1c ≥8% had a higher rate of TF than those with HbA1c <8% (42.0 vs 23.0%, p < 0.001). Medication adherence, self-monitoring of blood glucose (SMBG), regular exercise, gender (men), non-insulin treatment, and enrollment during 2010–2017 predicted a significant lower risk of TF in both of the primary and subgroup models.ConclusionsNewly diagnosed diabetes patients with baseline HbA1c ≥8% did have a much higher rate of TF during the first year. Subgroup analysis for them highlights the important predictors of TF, including medication adherence, performing SMBG, regular exercise, and gender, in achieving glycemic control. creator: Hon-Ke Sia creator: Chew-Teng Kor creator: Shih-Te Tu creator: Pei-Yung Liao creator: Yu-Chia Chang uri: https://doi.org/10.7717/peerj.11005 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Sia et al. title: A psychrometric model to assess the biological decay of the SARS-CoV-2 virus in aerosols link: https://peerj.com/articles/11024 last-modified: 2021-03-02 description: There is increasing evidence that the 2020 COVID-19 pandemic has been influenced by variations in air temperature and humidity. However, the impact that these environmental parameters have on survival of the SARS-CoV-2 virus has not been fully characterised. Therefore, an analytical study was undertaken using published data to develop a psychrometric model to assess the biological decay rate of the virus in aerosols. This revealed that it is possible to describe with reasonable accuracy (R2 = 0.718, p < 0.001) the biological decay constant for the SARS-CoV-2 virus using a regression model with enthalpy, vapour pressure and specific volume as predictors. Applying this to historical meteorological data from London, Paris and Milan over the pandemic period, produced results which indicate that the average half-life of the virus in aerosols outdoors was in the region 13–22 times longer in March 2020, when the outbreak was accelerating, than it was in August 2020 when epidemic in Europe was at its nadir. However, indoors, this variation is likely to be much less. As such, this suggests that changes in virus survivability due the variations in the psychrometric qualities of the air might influence the transmission of SARS-CoV-2. creator: Clive B. Beggs creator: Eldad J. Avital uri: https://doi.org/10.7717/peerj.11024 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Beggs and Avital title: A heat-shock 20 protein isolated from watermelon (ClHSP22.8) negatively regulates the response of Arabidopsis to salt stress via multiple signaling pathways link: https://peerj.com/articles/10524 last-modified: 2021-03-01 description: Heat-shock protein 20s (HSP20) were initially shown to play a role during heat shock stress; however, recent data indicated that HSP20 proteins are also involved in abiotic stress in plants. Watermelon is known to be vulnerable to various stressors; however, HSP20 proteins have yet to be investigated and characterized in the watermelon. In a previous study, we identified a negative regulator of salt stress response from watermelon: ClHSP22.8, a member of the HSP20 family. Quantitative real-time PCR (qRT-PCR) and promoter::β-glucuronidase (GUS) analysis revealed that ClHSP22.8 was expressed widely in a range of different tissues from the watermelon, but particularly in the roots of 7-day-old seedlings and flowers. Furthermore, qRT-PCR and GUS staining showed that the expression of ClHSP22.8 was significantly repressed by exogenous abscisic acid (ABA) and salt stress. The over-expression of ClHSP22.8 in Arabidopsis lines resulted in hypersensitivity to ABA and reduced tolerance to salt stress. Furthermore, the expression patterns of key regulators associated with ABA-dependent and independent pathways, and other stress-responsive signaling pathways, were also repressed in transgenic lines that over-expressed ClHSP22.8. These results indicated that ClHSP22.8 is a negative regulator in plant response to salt stress and occurs via ABA-dependent and independent, and other stress-responsive signaling pathways. creator: Yanjun He creator: Yixiu Yao creator: Lili Li creator: Yulin Li creator: Jie Gao creator: Min Fan uri: https://doi.org/10.7717/peerj.10524 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 He et al. title: Mammal-exclusion fencing improves the nesting success of an endangered native Hawaiian waterbird link: https://peerj.com/articles/10722 last-modified: 2021-03-01 description: Invasive predator control is often critical to improving the nesting success of endangered birds, but methods of control vary in cost and effectiveness. Poison-baiting or trapping and removal are relatively low-cost, but may have secondary impacts on non-target species, and may not completely exclude mammals from nesting areas. Mammal-exclusion fencing has a substantial up-front cost, but due to cost savings over the lifetime of the structure and the complete exclusion of mammalian predators, this option is increasingly being utilized to protect threatened species such as ground-nesting seabirds. However, non-mammalian predators are not excluded by these fences and may continue to impact nesting success, particularly in cases where the fence is designed for the protection of waterbirds, open to an estuary or wetland on one side. Thus, there remains a research gap regarding the potential gains in waterbird nesting success from the implementation of mammal-exclusion fencing in estuarine systems. In this study, we compared the nesting success of endangered Hawaiian Stilts (Ae‘o; Himantopus mexicanus knudseni) within a mammal-exclusion fence to that of breeding pairs in a nearby wetland where trapping was the sole means for removing invasive mammals. We predicted success would be greater for breeding pairs inside the exclusion fence and the hatchlings inside the enclosure would spend more time in the nesting area than hatchlings at the unfenced site. During a single breeding season following construction of a mammal-exclusion fence, we used motion-activated game cameras to monitor nests at two sites, one site with mammal-exclusion fencing and one site without. Clutch sizes and hatch rates were significantly greater at the fenced site than the unfenced site, but time spent by chicks in the nesting area did not differ between sites. These results add to the mounting body of evidence that demonstrates the effectiveness of mammal-exclusion fencing in protecting endangered birds and suggests it can aid endangered Hawaiian waterbirds toward recovery. These results also suggest that the single greatest predatory threat to the Hawaiian Stilt may be invasive mammals, despite a host of known non-mammalian predators including birds, crabs, turtles, and bullfrogs, as the complete exclusion of mammals resulted in significant gains in nesting success. As additional fences are built, future studies are necessary to compare nesting success among multiple sites and across multiple seasons to determine potential gains in fledging success and recruitment. creator: Dain L. Christensen creator: Kristen C. Harmon creator: Nathaniel H. Wehr creator: Melissa R. Price uri: https://doi.org/10.7717/peerj.10722 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Christensen et al. title: Homeostatic responses and growth of Leymus chinensis under incrementally increasing saline-alkali stress link: https://peerj.com/articles/10768 last-modified: 2021-03-01 description: Despite considerable tolerance to salt and alkali stress, Leymus chinensis populations on the southwestern Songnen Plain in northern China are threatened by increasing soil salinity and alkalinity. To explore the species’ responses to saline-alkali stress, we grew it in substrates with varying concentrations of nitrogen (N) and phosphorus (P) while applying varying levels of saline-alkali stress (increasing in 14-, 17- or 23 -day intervals). We measured the plants’ contents of N and P, and the N:P ratio, and calculated their homeostasis indices (HN, HP and HN:P) under each nutrient and saline-alkali stress treatment. The N content was found to be more sensitive to saline-alkali stress than the P content. The N and P contents were highest and the N:P ratio was stable at pH 8.4. At both pH 8.1 and 8.4, HN:P> HN > HP, but the indices and their relations differed at other pH values. Exposure to saline-alkali stress for the 14-day incremental interval had weaker effects on the plants. Rapid changes in salinity-alkalinity weakened both the positive effects of the weakly alkaline conditions (pH 7.5–8.4) and the negative effects of more strongly alkaline conditions (pH 8.7 or 9.3) on L. chinensis. When L. chinensis plants lack N, applying N fertilizer will be extremely efficient. The optimal concentrations of N and P appeared to be 16 and 1.2 mmol/L, respectively. When the L. chinensis plants were N- and P-limited, the specific growth rate correlated positively with N:P, when limited by N it correlated positively with the environmental N concentration, and when limited by P it was weakly positively correlated with the environmental P concentration. creator: Shujie Li creator: Yujin Huang creator: Yuefen Li uri: https://doi.org/10.7717/peerj.10768 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Li et al. title: Comparative transcriptome analysis during seeds development between two soybean cultivars link: https://peerj.com/articles/10772 last-modified: 2021-03-01 description: Soybean is one of the important economic crops, which supplies a great deal of vegetable oil and proteins for human. The content of nutrients in different soybean seeds is different, which is related to the expression of multiple genes, but the mechanisms are complicated and still largely uncertain. In this study, to reveal the possible causes of the nutrients difference in soybeans A7 (containing low oil and high protein) and A35 (containing high oil and low protein), RNA-seq technology was performed to compare and identify the potential differential expressed genes (DEGs) at different seed developmental stages. The results showed that DEGs mainly presented at the early stages of seeds development and more DEGs were up-regulated at the early stage than the late stages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs have diverged in A7 and A35. In A7, the DEGs were mainly involved in cell cycle and stresses, while in A35 were the fatty acids and sugar metabolism. Specifically, when the DEGs contributing to oil and protein metabolic pathways were analyzed, the differences between A7 and A35 mainly presented in fatty acids metabolism and seeds storage proteins (SSPs) synthesis. Furthermore, the enzymes, fatty acid dehydrogenase 2, 3-ketoacyl-CoA synthase and 9S-lipoxygenase, in the synthesis and elongation pathways of fatty acids, were revealed probably to be involved in the oil content difference between A7 and A35, the SSPs content might be due to the transcription factors: Leafy Cotyledon 2 and Abscisic acid-intensitive 3, while the sugar transporter, SWEET10a, might contribute to both oil and protein content differences. Finally, six DEGs were selected to analyze their expression using qRT-PCR, and the results were consistent with the RNA-seq results. Generally, the study provided a comprehensive and dynamic expression trends for the seed development processes, and uncovered the potential DEGs for the differences of oil in A7 and A35. creator: Li Peng creator: Linlin Qian creator: Meinan Wang creator: Wei Liu creator: Xiangting Song creator: Hao Cheng creator: Fengjie Yuan creator: Man Zhao uri: https://doi.org/10.7717/peerj.10772 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Peng et al. title: Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs link: https://peerj.com/articles/10809 last-modified: 2021-03-01 description: Biological dinitrogen (N2) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N2 fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N2 fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and 15N2 stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N2 fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N2 fixation (10–64 nmol L−1 d−1) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N2 fixation (2 nmol L−1 d−1) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO3/NO2 were significantly correlated with the highest N2 fixation rates, suggesting that N2 fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to Pseudomonas stutzeri, and Cluster 3 sulfate-reducing deltaproteobacteria. Diazotroph community composition was significantly influenced by salinity and SiO4 concentrations, reflecting the transition from UCYN-A-dominated assemblages in the continental shelf waters, to Cluster 3-dominated assemblages in the hypersaline waters of the inverse estuary. Diverse, transitional diazotrophic communities, comprised of a mixture of UCYN-A and putative heterotrophic bacteria, were observed at the mouth and southern edge of Spencer Gulf, where the highest N2 fixation rates were observed. In contrast to observations in other environments, no seasonal patterns in N2 fixation rates and diazotroph community structure were apparent. Collectively, our findings are consistent with the emerging view that N2 fixation within temperate coastal waters is a previously overlooked dynamic and potentially important component of the marine N cycle. creator: Lauren F. Messer creator: Mark V. Brown creator: Paul D. Van Ruth creator: Mark Doubell creator: Justin R. Seymour uri: https://doi.org/10.7717/peerj.10809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Messer et al. title: Phenotype study of multifoliolate leaf formation in Trifolium alexandrinum L. link: https://peerj.com/articles/10874 last-modified: 2021-03-01 description: BackgroundThe genus Trifolium is characterized by typical trifoliolate leaves. Alterations in leaf formats from trifoliolate to multifoliolate, i.e., individual plants bearing trifoliolate, quadrifoliolate, pentafoliolate or more leaflets, were previously reported among many species of the genus. The study is an attempt to develop pure pentafoliolate plants of T. alexandrinum and to understand its genetic control.MethodsThe experimental material consisted of two populations of T. alexandrinum with multifoliolate leaf expression, i.e.,interspecific hybrid progenies of T. alexandrinum with T. apertum, and T. alexandrinum genotype Penta-1. Penetrance of the multifoliolate trait was observed among multifoliolate and trifoliolate plant progenies. In vitro culture and regeneration of plantlets from the axillary buds from different plant sources was also attempted.ResultsThe inheritance among a large number of plant progenies together with in vitro micro-propagation results did not establish a definite pattern. The multifoliolate leaf formation was of chimeric nature, i.e., more than one leaf format appearing on individual branches. Reversal to normal trifoliolate from multifoliolate was also quite common. Penetrance and expression of multifoliolate leaf formation was higher among the plants raised from multifoliolate plants. Multifoliolate and pure pentafoliolate plants were observed in the progenies of pure trifoliolate plants and vice-versa. There was an apparent increase in the pentafoliolate leaf formation frequency over the years due to targeted selection. A few progenies of the complete pentafoliolate plants in the first year were true breeding in the second year. Frequency of plantlets with multifoliolate leaf formation was also higher in in vitro axillary bud multiplication when the explant bud was excised from the multifoliolate leaf node.ConclusionNumber of leaflets being a discrete variable, occurrence of multifoliolate leaves on individual branches, reversal of leaf formats on branches and developing true breeding pentafoliolates were the factors leading to a hypothesis beyond normal Mendelian inheritance. Transposable elements (TEs) involved in leaf development in combination with epigenetics were probably responsible for alterations in the expression of leaflet number. Putative TE’s movement owing to chromosomal rearrangements possibly resulted in homozygous pentafoliolate trait with evolutionary significance. The hypothesis provides a new insight into understanding the genetic control of this trait in T. alexandrinum and may also be useful in other Trifolium species where such observations are reported. creator: Devendra Ram Malaviya creator: Ajoy Kumar Roy creator: Pankaj Kaushal creator: Shalini Pathak creator: Ruslan Kalendar uri: https://doi.org/10.7717/peerj.10874 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Malaviya et al. title: Estimating the national and regional prevalence of drinking or eating more than usual during childhood diarrhea in Malawi using the bivariate sample selection copula regression link: https://peerj.com/articles/10917 last-modified: 2021-03-01 description: BackgroundEstimation of prevalence of feeding practices during diarrhea using conventional imputation methods may be biased as these methods apply to observed factors and in this study, feeding practice status was unobserved for those without diarrhea. The study aimed at re-estimating the prevalence of feeding practices using the bivariate sample selection model.MethodsThe study used 2015–2016 Malawi demographic health survey (MDHS) data which had 16,246 children records who had diarrhea or not. A bivariate Joe copula regression model with 90 degrees rotation was fitted to either drinking or eating more, with diarrhea as a sample selection outcome in the bivariate models. The prevalence of drinking more than usual and prevalence of eating more than usual were then estimated based on the fitted bivariate model. These prevalences were then compared to the prevalences estimated using the conventional imputation method.ResultsThere was a substantial increase in the re-estimated national prevalence of drinking more fluids (40.0%, 95% CI [31.7–50.5]) or prevalence of eating more food (20.46%, 95% CI [9.87–38.55]) using the bivariate model as compared to the prevalences estimated by the conventional imputation method, that is, (28.9%, 95% CI [27.0–30.7]) and (13.1%, 95% CI [12.0–15.0]) respectively. The maps of the regional prevalences showed similar results where the prevalences estimated by the bivariate model were relatively higher than those estimated by the standard imputation method. The presence of diarrhea was somehow weakly negatively correlated with either drinking more fluids or eating more food.ConclusionThe estimation of prevalence of drinking more fluids or eating more food during diarrhea should use bivariate modelling to model sample selection variable so as to minimize bias. The observed negative correlation between diarrhea presence and feeding practices implies that mothers should be encouraged to let their children drink more fluids or eat more food during diarrhea episode to avoid dehydration and malnutrition. creator: Alfred Ngwira creator: Francisco Chamera creator: Matrina Mpeketula Soko uri: https://doi.org/10.7717/peerj.10917 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Ngwira et al. title: Comparison of gut microbiota between adults with autism spectrum disorder and obese adults link: https://peerj.com/articles/10946 last-modified: 2021-03-01 description: BackgroundAutism spectrum disorder (ASD) and obesity are serious global public health problems. Studies have shown that ASD children are at a higher risk of obesity than the general population. To investigate the gut microbe characteristics of adults ASD and obese adults, we compared the gut microbiota of adults with ASD to obese adults.MethodsThe fecal samples were collected from 21 adult patients with ASD and 21 obese adults, and V3–V4 regions of 16S rRNA genes were sequenced by high-throughput DNA sequencing. The gut microbiota of adults with ASD and obese adults was compared.ResultsWe observed the proportion of Firmicutes/Bacteroidetes in ASD was significantly increased, with families Lachnospiraceae and Ruminococcaceae significantly enriched in adult ASD. Eighteen genera, including Lachnospiracea incertae sedis, Ruminococcus, Blautia, and Holdemanella were significantly increased in adult ASD, whereas Megamonas and Fusobacterium were significantly increased in obesity. At the species level, we found six species enriched in ASD and three species enriched in obesity, including Phascolarctobacterium succinatuten producing propionate. Dialister succinatiphilus may be as a biomarker for predicting obesity, as well as Prevotella copri may be a common-owned pathogens of ASD and obesity.ConclusionsSome conflicting results have been reported in microbiota studies of ASD, which may be related to age and obesity. Thus, the body mass index should be evaluated before analyzing the gut microbiota of patients with ASD, as obesity is prevalent in these individuals and gut microbiota is severally affected by obesity. creator: Qiang Zhang creator: Rong Zou creator: Min Guo creator: Mengmeng Duan creator: Quan Li creator: Huajun Zheng uri: https://doi.org/10.7717/peerj.10946 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhang et al. title: Plyometric jump training effects on the physical fitness of individual-sport athletes: a systematic review with meta-analysis link: https://peerj.com/articles/11004 last-modified: 2021-03-01 description: BackgroundThe aim of this study is to conduct a systematic review with meta-analysis to explore the effects of plyometric jump training (PJT) on the physical fitness of individual sport athletes (ISA).MethodsFollowing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, we searched through PubMed, Web of Science, and SCOPUS electronic databases. We included controlled studies that incorporated a PJT intervention among ISA (with no restriction for age or sex), that included a pre-to-post intervention assessment of physical fitness (e.g., sprint; jump). From the included studies, relevant data (e.g., PJT and participants characteristics) was extracted. We assessed the methodological quality of the included studies using the PEDro scale. Using a random-effects model, meta-analyses for a given outcome was conducted. Means and standard deviations for a measure of pre-post-intervention physical fitness from the PJT and control groups were converted to Hedges’ g effect size (ES). Heterogeneity was assessed using the I2 statistic. The risk of bias was explored using the extended Egger’s test. The statistical significance threshold was set at p < 0.05. Moderator analyses were conducted according to the sex, age and sport background of the athletes.ResultsTwenty-six studies of moderate-high methodological quality were included (total participants, n = 667). Compared to controls, PJT improved vertical jump (ES = 0.49; p < 0.001; I = 0.0%), linear sprint (ES = 0.23; p = 0.032; I2 = 10.9%), maximal strength (ES = 0.50; p < 0.001; I2 = 0.0%) and endurance performance (ES = 0.30; p = 0.028; I2 = 11.1%). No significant effect was noted for sprint with change of direction (ES = 0.34; p = 0.205; I2 = 70.9%). Athlete’s sex, age and sport background had no modulator role on the effect of PJT on vertical jump, linear sprint, maximal strength and endurance performance. Among the included studies, none reported adverse effects related to the PJT intervention.ConclusionsPJT induces small improvements on ISA physical fitness, including jumping, sprinting speed, strength and endurance. creator: Silvia Sole creator: Rodrigo Ramírez-Campillo creator: David C. Andrade creator: Javier Sanchez-Sanchez uri: https://doi.org/10.7717/peerj.11004 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Sole et al.