The 100 most-cited articles in PeerJ, 2021

Abstract The coefficient of determination R 2 quantifies the amount of variance explained by regression coefficients in a linear model. It can be seen as the fixed-effects complement to the repeatability R (intra-class correlation) for the variance explained by random effects and thus as a tool for variance decomposition. The R 2 of a model can be further partitioned into the variance explained by a particular predictor or a combination of predictors using semi-partial (part) R 2 and structure coefficients, but this is rarely done due to a lack of software implementing these statistics. Here, we introduce partR2 , an R package that quantifies part R 2 for fixed effect predictors based on (generalized) linear mixed-effect model fits. The package iteratively removes predictors of interest from the model and monitors the change in the variance of the linear predictor. The difference to the full model gives a measure of the amount of variance explained uniquely by a particular predictor or a set of predictors. partR2 also estimates structure coefficients as the correlation between a…

Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98% greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub (https://github.com/adamhockenberry/bacphlip) and the code used to build and test the classifier is provided in a separate repository (https://github.com/adamhockenberry/bacphlip-model-dev) for users wishing…

Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells' genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.

Background The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all ( n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces,…

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.

The risk of plastic debris, and specifically micro(nano)plastic particles, to ecosystems remains to be fully characterized. One particular issue that warrants further characterization is the hazards associated with chemical additives within micro(nano)plastic as they are not chemically bound within the polymers and can be persistent and biologically active. Most plastics contain additives and are therefore potential vectors for the introduction of these chemicals into the environment as they leach from plastic, a process that can be accelerated through degradation and weathering processes. There are knowledge gaps on the ecotoxicological effects of plastic additives and how they are released from parent plastic materials as they progressively fragment from the meso to micro and nano scale. This review summarizes the current state of knowledge of the ecotoxicity of plastic additives and identifies research needs to characterize the hazard they present to exposed biota. The potential ecological risk of chemical additives is of international concern so key differences in governance…

BACKGROUND: Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). RESULTS: -mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ∼5% for virome and ∼75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were…

Abstract Minimizers are widely used to select subsets of fixed-length substrings ( k -mers) from biological sequences in applications ranging from read mapping to taxonomy prediction and indexing of large datasets. The minimizer of a string of w consecutive k -mers is the k -mer with smallest value according to an ordering of all k -mers. Syncmers are a family of alternative methods which select k -mers by inspecting the position of the smallest-valued substring of length s within the k -mer. For example, a closed syncmer selected if its smallest s -mer is at the start of end of the k -mer. At least one closed syncmer must be found in every window of length ( k – s ) k -mers. Unlike a minimizer, a syncmer is identified by its sequence alone, and is therefore synchronized in the following sense: if a given k -mer is selected from one sequence, it will also be selected from any other sequence. Also, minimizers can be deleted by mutations in flanking sequence, which cannot happen with syncmers. Experiments on minimizers with parameters used in the minimap2 read mapper and Kraken…

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii . Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs…

The practice of sourdough bread-making is an ancient science that involves the development, maintenance, and use of a diverse and complex starter culture. The sourdough starter culture comes in many different forms and is used in bread-making at both artisanal and commercial scales, in countries all over the world. While there is ample scientific research related to sourdough, there is no standardized approach to using sourdough starters in science or the bread industry; and there are few recommendations on future directions for sourdough research. Our review highlights what is currently known about the microbial ecosystem of sourdough (including microbial succession within the starter culture), methods of maintaining sourdough (analogous to land management) on the path to bread production, and factors that influence the sensory qualities of the final baked product. We present new hypotheses for the successful management of sourdough starters and propose future directions for sourdough research and application to better support and engage the sourdough baking community.

Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of…

BACKGROUND: Coronavirus disease has provoked much discussion since its first appearance. Despite it being widely studied all over the world, little is known about the impact of the disease on functional ability related to performing activities of daily living (ADL) in patients post COVID-19 infection. OBJECTIVES: To understand the impact of COVID-19 on ADL performance of adult patients and to describe the common scales used to assess performance of ADL on patients post-COVID-19. METHODS: A systematic review was conducted. We included studies that applied a physical capacity test in COVID-19 patients, post-infection. Two independent reviewers analyzed the studies, extracted the data, and assessed the quality of the evidence. RESULTS: A total of 1,228 studies were included, after removing duplicates, 1,005 abstracts were screened and of those 983 were excluded. A final number of nine studies which met the eligibility criteria were included. The findings revealed worsening of physical function and ADL performance in all patients post COVID-19 infection. CONCLUSION: All included studies…

Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70% ethanol. Both methods preserve taxonomically informative exoskeletal structures well but are suboptimal for preserving DNA for molecular biology. Highly concentrated ethanol (95-100%), preferred as a DNA preservative, has generally been assumed to make specimens brittle and prone to breaking. However, systematic studies on the correlation between ethanol concentration and specimen preservation are lacking. Here, we tested how preservative ethanol concentration in combination with different sample handling regimes affect the integrity of seven insect species representing four orders, and differing substantially in the level of sclerotization. After preservation and treatments (various levels of disturbance), we counted the number of appendages (legs, wings, antennae, or heads) that each specimen had lost. Additionally, we assessed the preservation of DNA after long-term storage by comparing the ratio of PCR amplicon copy numbers to an added artificial standard. We found that high…

Background As of the present, the twenty-first century is experiencing what may be one of its most devastating events, in respect to infected and dead people by the virus. Now known to the world as COVID-19, the devastating disease of what has become a pandemic started its spread from Wuhan, China and swiftly engulfed the whole world with almost 11 million cases, in a span of around six months. It has not only increased the global burden of disease but has heavily dented many social institutions, including education. Methods This study investigates how the COVID-19 pandemic and subsequent measures of lockdown, quarantine, and social distancing have affected students. We look specifically into the effects on individuals’ mental health, that is, the stress and anxiety levels of college and university students using the Zung Self-rating Anxiety Scale (SAS). Results Among 494 respondents, 61% were females, and the majority (77.3%) of the students were in the age group of 19–25 years. Among the respondents, 125 (25.3%), 45 (9.1%) and 34 (6.9%) experienced minimal to moderate, severe, and…

Background Uric acid (UA) is the end product of purine metabolism in the liver and is excreted by the kidneys. When purine metabolism is impaired, the serum UA level will be elevated (hyperuricemia) and eventually lead to gout. During evolution, humans and some primates have lost the gene encoding uricase, which is vital in UA metabolism. With the advances of human society, the prevalence of hyperuricemia has dramatically increased because of the refined food culture. Hyperuricemia can be controlled by drugs, such as allopurinol and probenecid. However, these drugs have no preventive effect and are associated with unpleasant side effects. An increasing number of probiotic strains, which are able to regulate host metabolism and prevent chronic diseases without harmful side effects, have been characterized. The identification of probiotic strains, which are able to exert beneficial effects on UA metabolism, will provide an alternative healthcare strategy for patients with hyperuricemia, especially for those who are allergic to anti-hyperuricemia drugs. Methods To elicit hyperuricemia,…

The significant attention gained by food-sourced vitamins has provided insights into numerous current researches; for instance, the potential reversal of epigenetic age using a diet and lifestyle intervention, the balance between food and dietary supplements in the general population, the role of diet and food intake in age-related macular degeneration, and the association of dietary supplement use, nutrient intake and mortality among adults. As relevant literature about food-sourced vitamin increases, continuous synthesis is warranted. To supplement existing information, this perspective review discussed food-sourced vitamins for consumer diet and health needs, scoping from vitamin absorption, metabolic functions, utilization, to balancing nutritional requirements. Relevant literatures were identified through a search of databases like Google Scholar, Web of Science, the Interscience Online Library, ScienceDirect, and PubMed. We demonstrated that vitamins whether from plant- and animal-based sources are prerequisites for the metabolic functions of the human body. The fat- and…

Soil microbial carbon utilization efficiency (CUE) is the efficiency with which microorganisms convert absorbed carbon (C) into their own biomass C, also referred to as microorganism growth efficiency. Soil microbial CUE is a critical physiological and ecological parameter in the ecosystem's C cycle, influencing the processes of C retention, turnover, soil mineralization, and greenhouse gas emission. Understanding the variation of soil microbial CUE and its influence mechanism in the context of global environmental change is critical for a better understanding of the ecosystem's C cycle process and its response to global changes. In this review, the definition of CUE and its measurement methods are reviewed, and the research progress of soil microbial CUE variation and influencing factors is primarily reviewed and analyzed. Soil microbial CUE is usually expressed as the ratio of microbial growth and absorption, which is divided into methods based on the microbial growth rate, microbial biomass, substrate absorption rate, and substrate concentration change, and varies from 0.2 to…

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.

Background Probiotics can release bioactive substances known as postbiotics, which can inhibit pathogenic microorganisms, improve immunomodulation, reduce antioxidant production, and modulate the gut microbiota. Methods In this study, we evaluated the in vitro antimicrobial effects, antioxidant activity, and anti-inflammatory potential of 10 lyophilized cell-free supernatants (LCFS) of Lactobacillus isolates. LCFS was obtained via centrifugation and subsequent lyophilization of the supernatant collected from the culture medium ofeach isolate. The antibacterial and antibiofilm activities of the LCFS were determined using broth microdilution. The antioxidant potential was evaluated by measuring the total phenolic and flavonoid contents and 2,2-Diphennyl-1-picrylhydrazyl (DPPH) and 2,2’-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) radical cation (ABTS + ) radical scavenging activities. Results All the isolates were able to inhibit the four tested pathogens. The isolates exhibited strong antibiofilm activity and eradicated the biofilms formed by Acinetobacter buamannii and…

Objective Lung 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. Methods Three 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. Results By difference…

Insects are the most widespread group of organisms and more than one million species have been described. These animals have significant ecological functions, for example they are pollinators of many types of plants. However, they also have direct influence on human life in different manners. They have high medical and veterinary significance, stemming from their role as vectors of disease and infection of wounds and necrotic tissue; they are also plant pests, parasitoids and predators whose activities can influence agriculture. In addition, their use in medical treatments, such as maggot therapy of gangrene and wounds, has grown considerably. They also have many uses in forensic science to determine the minimum post-mortem interval and provide valuable information about the movement of the body, cause of the death, drug use, or poisoning. It has also been proposed that they may be used as model organisms to replace mammal systems in research. The present review describes the role of free fatty acids (FFAs) in key physiological processes in insects. By focusing on insects of…

Desulfovibrio (DSV) is frequently found in the human intestine but limited knowledge is available regarding the relationship between DSV and host health. In this study, we analyzed large-scale cohort data from the Guangdong Gut Microbiome Project to study the ecology of DSV and the associations of DSV and host health parameters. Phylogenetic analysis showed that Desulfovibrio piger might be the most common and abundant DSV species in the GGMP. Predominant sub-OTUs of DSV were positively associated with bacterial community diversity. The relative abundance of DSV was positively correlated with beneficial genera, including Oscillospira , Coprococcus , Ruminococcus , Akkermansia, Roseburia , Faecalibacterium , and Bacteroides , and was negatively associated with harmful genera, such as Clostridium , Escherichia , Klebsiella , and Ralstonia. Moreover, the relative abundance of DSV was negatively correlated with body mass index, waist size, triglyceride levels, and uric acid levels. This suggests that DSV is associated with healthy hosts in some human populations.

Ornithischians form a large clade of globally distributed Mesozoic dinosaurs, and represent one of their three major radiations. Throughout their evolutionary history, exceeding 134 million years, ornithischians evolved considerable morphological disparity, expressed especially through the cranial and osteodermal features of their most distinguishable representatives. The nearly two-century-long research history on ornithischians has resulted in the recognition of numerous diverse lineages, many of which have been named. Following the formative publications establishing the theoretical foundation of phylogenetic nomenclature throughout the 1980s and 1990s, many of the proposed names of ornithischian clades were provided with phylogenetic definitions. Some of these definitions have proven useful and have not been changed, beyond the way they were formulated, since their introduction. Some names, however, have multiple definitions, making their application ambiguous. Recent implementation of the International Code of Phylogenetic Nomenclature ( ICPN , or PhyloCode ) offers the…

PURPOSE: Breast cancer (BC) is characterized by concealed onset, delayed diagnosis, and high fatality rates making it particularly dangerous to patients' health. The purpose of this study was to use comprehensive bioinformatics analysis and experimental verification to find a new biomarker for BC diagnosis. METHODS: We comprehensively analyzed microRNA (miRNA) and mRNA expression profiles from the Gene Expression Omnibus (GEO) and screened out differentially-expressed (DE) miRNAs and mRNAs. We used the miRNet website to predict potential DE-miRNA target genes. Using the Database for Annotation, Visualization and Integrated Discovery (DAVID), we performed Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on overlapping potential target genes and DE-mRNAs. The protein-protein interaction (PPI) network was then established. The miRNA-mRNA regulatory network was constructed using Cytoscape and the analysis results were visualized. We verified the expression of the most up-regulated DE-miRNA using reverse transcription and a quantitative polymerase chain…

Accumulating evidence has suggested the importance of gut microbiota in the development of type 2 diabetes mellitus (T2DM). In the present study, 40 patients with T2DM were treated with liraglutide for 4 months. Feces samples and clinical characteristics were collected from these 40 T2DM patients before and after the liraglutide treatment. The diversity and composition of gut microbiota in the two groups were determined by sequencing the V4 region of bacterial 16S rRNA genes. Meanwhile, blood glucose, insulin, hemoglobin A1c (HbA1c), and lipid metabolism were also measured in the pre- and post-liraglutide-treatment groups. We find that Baseline HbA1c was associated with liraglutide treatment response ( R 2 = 0.527, β = − 0.726, p < 0.0001). After adjusted for baseline HbA1c, blood urea nitrogen was associated with liraglutide treatment response. Besides, our results showed reduced gut microbial alpha diversity, different community structure distribution and altered microbial interaction network in patients treated with liraglutide. The liner discriminant analysis (LDA) effect size…

ABSTRACT The Asian giant hornet (AGH, Vespa mandarinia ) is the world’s largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian giant hornets was detected outside of Vancouver, British Columbia and in May 2020 an individual was detected nearby in Washington state, indicating that the AGH successfully overwintered in North America. Because hornets tend to spread rapidly and become pests, reliable estimates of the potential invasive range of V. mandarinia in North America are needed to assess likely human and economic impacts, and to guide future eradication attempts. Here, we assess climatic suitability for AGH in North America, and suggest that, without control, this species could establish populations across the Pacific Northwest and much of eastern North America. Predicted suitable areas for AGH in North America overlap broadly with areas where honey production is highest, as well as with species-rich areas for native bumble bees and stingless bees of the genus…

Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia , which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia , of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters…

BACKGROUND: Skin aging is the most common dermatological problem caused by intrinsic and extrinsic factor, such as exposure to (ultraviolet) UV rays. Chlorogenic acid (CA) is a phenolic compound which is known for its antioxidant properties against oxidative stress. OBJECTIVE: This study investigates the antiaging and anti-inflammatory properties of CA on UV-induced skin fibroblast cells. METHODS: Anti-inflammatory properties of CA were assessed by measuring inflammatory-related proteins IL-1β and TNF-α, while antiaging properties of CA were assessed by measuring reactive oxygen species (ROS), apoptosis, live and necrotic cells, and COL-3 gene expression level. RESULTS: Treating UV-induced skin fibroblast cells with CA decreased the level of ROS, IL-1β, TNF-α, apoptotic cells, and necrotic cells and increased live cells and COL-3 gene expression. CONCLUSION: CA has the potential as the protective compound against inflammation and aging by decreasing the level ROS, pro-inflammatory cytokines IL-1β and TNF-α, apoptotic cells, and necrotic cells and by increasing live cells and COL-3…

Artificial intelligence has been emerging as an increasingly important aspect of our daily lives and is widely applied in medical science. One major application of artificial intelligence in medical science is medical imaging. As a major component of artificial intelligence, many machine learning models are applied in medical diagnosis and treatment with the advancement of technology and medical imaging facilities. The popularity of convolutional neural network in dental, oral and craniofacial imaging is heightening, as it has been continually applied to a broader spectrum of scientific studies. Our manuscript reviews the fundamental principles and rationales behind machine learning, and summarizes its research progress and its recent applications specifically in dental, oral and craniofacial imaging. It also reviews the problems that remain to be resolved and evaluates the prospect of the future development of this field of scientific study.

Background Climatic changes are the most important abiotic factor affecting plant growth, crop quality and nutritional value. Plants exposed to thermal stress respond by accumulation of secondary metabolites/molecules (SMs). Tomato ( Solanum lycopersicum ) is a cosmopolitan crop, eaten by most of the world’s people because it is highly nutritious plant. It is cultivated in more than 16 thousand hectares in Saudi Arabia and thus is influenced by extreme climatic changes. Objective In the current study, the phytochemical effect of thermal stress was investigated in seedlings of S. lycopersicum . Such information will be very helpful in developing more tolerant tomato cultivars in a climate change scenario. Methods Seedlings of S. lycopersicum were subjected to heat shock; HS1 and HS2 (45 and 50 °C) and cold shock; CS (4 °C) in comparison to control; Con (25 °C). Phenolic compounds, flavonoids, total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity were estimated under the four temperature treatments. Results Using 23 standards (17 phenolic and six…

Scientific experiments and research practices vary across disciplines. The research practices followed by scientists in each domain play an essential role in the understandability and reproducibility of results. The "Reproducibility Crisis", where researchers find difficulty in reproducing published results, is currently faced by several disciplines. To understand the underlying problem in the context of the reproducibility crisis, it is important to first know the different research practices followed in their domain and the factors that hinder reproducibility. We performed an exploratory study by conducting a survey addressed to researchers representing a range of disciplines to understand scientific experiments and research practices for reproducibility. The survey findings identify a reproducibility crisis and a strong need for sharing data, code, methods, steps, and negative and positive results. Insufficient metadata, lack of publicly available data, and incomplete information in study methods are considered to be the main reasons for poor reproducibility. The survey results…

Background Gut 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. Methods A 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. Results There 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…

Background Gut microbiota (GM) dysbiosis is closely related to bone loss and the occurrence of osteoporosis in animals and human. However, little is known about the effect and the mechanisms of fecal microbiota transplantation (FMT) on bone in the treatment of senile osteoporosis. Methods Aged female rats were randomly divided into the FMT group and the control group. 3-month-old female rats were used as fecal donors. The rats were sacrificed at 12 and 24 weeks following transplantation and the serum, intestine, bone, and feces were collected for subsequent analyses. Results The bone turnover markers of osteocalcin, procollagen type 1 N-terminal propeptide (P1NP), and carboxy-terminal peptide (CTX) decreased significantly at 12 and 24 weeks following FMT (P < 0.05). At 12 weeks following transplantation, histomorphometric parameters including the bone volume (BV), trabecular bone volume fraction (BV/TV), trabecular number (Tb.N), and trabecular thickness (Tb.Th) of the FMT group were comparable to the control group. However, at 24 weeks following transplantation, these parameters of…

The Convention on Biological Diversity (CBD) pathways classification framework used in the implementation of the European Union’s (EU) Regulation 1143/2014 on invasive alien species (IAS Regulation) has recently been adopted by the European Alien Species Information Network (EASIN), the official information system supporting the implementation of the IAS Regulation. In the current paper, the result of an alignment of the primary introduction pathways of all alien plants in Europe included in the EASIN catalogue is presented, based on the CBD framework. In total, 6,250 alien plant taxa (marine plants excluded), both alien to Europe (native range outside Europe) and alien in Europe (native range partially in Europe) are reported. Altogether 5,175 plant taxa had their primary introduction pathway aligned based on the CBD framework, while for the rest the pathway remains unknown. In addition, the taxonomy, year and country of its first record in the wild are provided for each taxon. Our analyses reveal that the main primary introduction pathways of alien plants into Europe are linked to…

Mapping metagenome reads to reference databases is the standard approach for assessing microbial taxonomic and functional diversity from metagenomic data. However, public reference databases often lack recently generated genomic data such as metagenome-assembled genomes (MAGs), which can limit the sensitivity of read-mapping approaches. We previously developed the Struo pipeline in order to provide a straight-forward method for constructing custom databases; however, the pipeline does not scale well enough to cope with the ever-increasing number of publicly available microbial genomes. Moreover, the pipeline does not allow for efficient database updating as new data are generated. To address these issues, we developed Struo2, which is >3.5 fold faster than Struo at database generation and can also efficiently update existing databases. We also provide custom Kraken2, Bracken, and HUMAnN3 databases that can be easily updated with new genomes and/or individual gene sequences. Efficient database updating, coupled with our pre-generated databases, enables "assembly-enhanced" profiling,…

The Mahalanobis distance is a statistical technique that has been used in statistics and data science for data classification and outlier detection, and in ecology to quantify species-environment relationships in habitat and ecological niche models. Mahalanobis distances are based on the location and scatter of a multivariate normal distribution, and can measure how distant any point in space is from the centre of this kind of distribution. Three different methods for calculating the multivariate location and scatter are commonly used: the sample mean and variance-covariance, the minimum covariance determinant, and the minimum volume ellipsoid. The minimum covariance determinant and minimum volume ellipsoid were developed to be robust to outliers by minimising the multivariate location and scatter for a subset of the full sample, with the proportion of the full sample forming the subset being controlled by a user-defined parameter. This outlier robustness means the minimum covariance determinant and the minimum volume ellipsoid are highly relevant for ecological niche analyses,…

Abstract Background: Preprints are preliminary reports that have not been peer-reviewed. On Dec 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 regarding pharmacological interventions against COVID-19 were cited, in spite of the fact that some of these preprints remained unpublished.Methods: We conducted a search on medRxiv and bioRxiv to identify preprints related to pharmacological interventions against SARS-CoV-2 from Jan 1st to Mar 31, 2020. We gathered metadata on included preprints and identified if they had been published in a peer-reviewed journal. We performed Mann-Whitney U tests to evaluate if published articles had differences in citation numbers or usage, as defined by PDF downloads and abstract views, when compared to preprints that were not published.Results: Our sample included 97 preprints, of which only 14 were published on peer-reviewed journals and 83 remained unpublished. The most common study designs we found among…

(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…

Abstract Evidence-based decision making is most effective with comprehensive access to scientific studies. If studies face delays or barriers to being published, the useful information they contain may not reach decision-makers in a timely manner. This represents a potential problem for mission-oriented disciplines where access to the latest data is paramount to ensure effective actions are deployed. We sought to analyse the severity of publication delay in conservation science — a field that requires urgent action to prevent the loss of biodiversity. We used the Conservation Evidence database to assess the length of publication delay (time from finishing data collection to publication) in the literature that tests the effectiveness of conservation interventions. From 7,415 peer-reviewed and non-peer-reviewed studies of conservation interventions published over eleven decades, we find that the mean publication delay (time from completing data collection to publication) was 3.6 years and varied by conservation subject — a smaller delay was observed for studies focussed on the…

OBJECTIVE: To explore the association between health behaviors and habits of university students and academic achievement. PARTICIPANTS: Six hundred fourteen undergraduate students at a state university in the United States. METHODS: Students were invited over a 2-year period to participate in an anonymous online survey that asked questions concerning a wide range of health behaviors and habits; participants were asked to report their current grade point average (GPA). Standard Least Squares Models were used to examine differences in self-reported GPA across the different health behaviors and habits, with individuals as replicates. RESULTS: The study found positive associations between breakfast consumption, physical activity, and strength training and self-reported GPA, and negative associations between the hours of sleep per night, hours worked per week, fast food and energy drinks consumption, and use of marijuana, alcohol and electronic vaping products. CONCLUSIONS: While there is an association for some of the studied health behaviors and habits with self-reported GPA, the…

Background The UNESP-Botucatu multidimensional feline pain assessment scale (UFEPS) is a valid and reliable instrument for acute pain assessment in cats. However, its limitations are that responsiveness was not tested using a negative control group, it was validated only for ovariohysterectomy, and it can be time-consuming. We aimed to evaluate the construct and criterion validity, reliability, sensitivity, and specificity of the UFEPS and its novel short form (SF) in various clinical or painful surgical conditions. Methods Ten client-owned healthy controls (CG) and 40 client-owned cats requiring pain management for clinical or surgical care (20 clinical and 20 surgery group (12 orthopedic and eight soft tissue surgeries) were recruited. Three evaluators assessed pain, in real-time, in clinical cases before and 20 min after rescue analgesia and in surgical cases before and up to 6.5 hours postoperatively, by using the visual analog, numerical ratio, and a simple descriptive scale, in this order, followed by the UFEPS-SF, UFEPS and Glasgow multidimensional feline pain (Glasgow…

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…

Many agricultural regions in arid and semiarid climate zone need to deal with increased soil salinity. Legumes are classified as salt-sensitive crops. A field experiment was performed to examine the application of phosphorus (P) fertilizer source and rate on growth, chlorophylls and carotenoid content, DNA and RNA content and ion accumulation in common bean ( Phaseolus vulgaris L.) cultivated under salinity stress. An experimental design was split-plot with three replicates. The main plots included two P sources, namely single superphosphate (SP) and urea phosphate (UP). The sub-plots covered four P rates, i.e., 0.0, 17.5, 35.0, and 52.5 kg P ha –1 . All applied P fertilization rates, in both forms, increased plant height, leaf area, dry weight of shoots and roots per plant, and total dry weight (TDW) in t ha −1 . The highest accumulation of N, P, K + , Mg 2+ , Mn 2+ , Zn 2+ , and Cu 2+ was determined in the shoot and root of common bean, while 35 kg of P per ha −1 was used compared to the other levels of P fertilizer. The highest P rate (52.5 kg ha −1 ) resulted in a significant…

Background The importance of organic farming has increased through the years to promote food security allied with minimal harm to the ecosystem. Besides the environmental benefits, a recurring problem associated with organic management is the unsatisfactory yield. A possible solution may rely on the soil microbiome, which presents a crucial role in the soil system. Here, we aimed to evaluate the soil bacterial community structure and composition under organic and conventional farming, considering the tropical climate and tropical soil. Methodology Our organic management treatments were composed by composted poultry manure and green manure with Bokashi. Both organic treatments were based on low nitrogen inputs. We evaluated the soil bacterial community composition by high-throughput sequencing of 16S rRNA genes, soil fertility, and soil enzyme activity in two organic farming systems, one conventional and the last transitional from conventional to organic. Results We observed that both organic systems evaluated in this study, have higher yield than the conventional treatment, even in…

BACKGROUND: Maximal strength is a critical determinant of performance in numerous sports. Autoregulation is a resistance training prescription approach to adjust training variables based on the individuals' daily fluctuations in performance, which are a result of training-induced fitness and fatigue, together with readiness from daily non-training stressors. OBJECTIVE: This review aimed to summarise the effects of different subjective and objective autoregulation methods for intensity and volume on enhancing maximal strength. MATERIALS AND METHODS: A comprehensive literature search was conducted through SPORTDiscus, PubMed and Google Scholar. Studies had to meet the following criteria to be included in the review: (1) estimation of 1-RM or a 1-RM test for both pre-test and post-test to measure progression in strength assessment during the training intervention, (2) a training comparison group, (3) participants were healthy, (4) the article had a detailed description of training intensity, training volume, and training frequency during the training intervention, (5) the training…

Soluble sugar is known to improve the sweetness and increase tomato sauce yield. Studies have focused on improving the content of soluble sugar in tomato fruits, usually by promoting functional genes. We studied two genes ( SlINVINH1 and SlVPE5 ) that inhibited the accumulation of soluble sugar in tomato fruits and obtained two genes’ knocked-out lines (CRISPR- invinh1 or CRISPR- vpe5 ) using CRISPR/Cas9. Aggregated lines with CRISPR- invinh1 and CRISPR- vpe5 were gained by hybridization and self-pollination. Compared to wild-type lines, the glucose, fructose, and total soluble solid (TSS) contents of CRISPR- invinh1 and CRISPR- vpe5 increased significantly. Glucose, fructose, and TSS levels further improved simultaneously with CRISPR- invinh1 and CRISPR- vpe5 than with single gene knock-out lines. This indicates that these genes have a synergistic effect and will increase the soluble sugar content. Thus, the knock-out SlINVINH1 and SlVPE5 may provide a practical basis for improving the sweetness of tomato fruits and their processing quality.

Drought is a common yield limiting factor in wheat production and has become a significant threat to global food security. Root system is the organ responsible for water uptake from soil and root growth is closely associated with yield and quality of wheat. However, the relationship between morphological and structural characteristics of root growth and caryopsis enrichment in wheat under drought stress is unclear. In this study, two wheat cultivars (YM13 and YN19) were treated with drought from flowering to caryopsis maturity stage. The changes in morphological structure of roots and characteristics of endosperm enrichment were investigated. Drought stress significantly reduced the root length, plant height, root dry weight and aboveground parts dry weight, whereas the root-shoot ratio of YM13 and YN19 increased by 17.65% and 8.33% under drought stress, respectively. The spike length, spike weight, grains number per spike and 1,000-grains weight of mature wheat also significantly declined under drought stress. Meanwhile, the cross section structure of roots was changed with the…

Aerosol optical depth (AOD) is a key parameter that reflects aerosol characteristics. However, research on the AOD of dust aerosols and various environmental variables is scarce. Therefore, we conducted in-depth studies on the distributions and variations of AOD in the Taklimakan Desert and its margins, China. We examined the correlation characteristics between AOD and meteorological factors combined with satellite remote sensing detection methods using MCD19A2-MODIS AOD products (from 2000, 2005, 2010, and 2015), MOD13Q1-MODIS normalized difference vegetation index products, and meteorological data. We analyzed the temporal and spatial distributions of AOD, periodic change trends, and important impacts of meteorological factors on AOD in the Taklimakan Desert and its margins. To explore the relationships between desert aerosols and meteorological factors, a random forest model was used along with environmental variables to predict AOD and rank factor contributions. Results indicated that the monthly average AOD exhibited a clear unimodal curve that reached its maximum in April. The…

ABSTRACT DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences. However, existing tools for…

BACKGROUND: The global spreading of the COVID-19 coronavirus is still a serious public health challenge. Although there are a large number of public resources that provide statistics data, tools for retrospective historical data and convenient visualization are still valuable. To provide convenient access to data and visualization on the pandemic we developed an R package, nCov2019 (https://github.com/YuLab-SMU/nCov2019). METHODS: We collect stable and reliable data of COVID-19 cases from multiple authoritative and up-to-date sources, and aggregate the most recent and historical data for each country or even province. Medical progress information, including global vaccine development and therapeutics candidates, were also collected and can be directly accessed in our package. The nCov2019 package provides an R language interfaces and designed functions for data operation and presentation, a set of interfaces to fetch data subset intuitively, visualization methods, and a dashboard with no extra coding requirement for data exploration and interactive analysis. RESULTS: As of January…

The historical clade “Protorosauria” represents an important group of archosauromorph reptiles that had a wide geographic distribution between the Late Permian and Late Triassic. “Protorosaurs” are characterized by their long necks, which are epitomized in the genus Tanystropheus and in Dinocephalosaurus orientalis . Recent phylogenetic analyses have indicated that “Protorosauria” is a polyphyletic clade, but the exact relationships of the various “protorosaur” taxa within the archosauromorph lineage is currently uncertain. Several taxa, although represented by relatively complete material, have previously not been assessed phylogenetically. We present a new phylogenetic hypothesis that comprises a wide range of archosauromorphs, including the most exhaustive sample of “protorosaurs” to date and several “protorosaur” taxa from the eastern Tethys margin that have not been included in any previous analysis. The polyphyly of “Protorosauria” is confirmed and therefore we suggest the usage of this term should be abandoned. Tanystropheidae is recovered as a monophyletic group and the…

The Myers-Briggs Type Indicator (MBTI) is a well-known personality test that assigns a personality type to a user by using four traits dichotomies. For many years, people have used MBTI as an instrument to develop self-awareness and to guide their personal decisions. Previous researches have good successes in predicting Extraversion-Introversion (E/I), Sensing-Intuition (S/N) and Thinking-Feeling (T/F) dichotomies from textual data but struggled to do so with Judging-Perceiving (J/P) dichotomy. J/P dichotomy in MBTI is a non-separable part of MBTI that have significant inference on human behavior, perception and decision towards their surroundings. It is an assessment on how someone interacts with the world when making decision. This research was set out to evaluate the performance of the individual features and classifiers for J/P dichotomy in personality computing. At the end, data leakage was found in dataset originating from the Personality Forum Café, which was used in recent researches. The results obtained from the previous research on this dataset were suggested to be overly…

Background Autism 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. Methods The 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. Results We 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,…

Background Expanding fisheries in developing nations like Sri Lanka have a significant impact on threatened marine species such as elasmobranchs. Manta and devil (mobulid) rays have some of the most conservative life history strategies of any elasmobranch, and even low to moderate levels of bycatch from gillnet fisheries may lead to significant population declines. A lack of information on life history, demographics, population trends, and fisheries impacts hinders effective management measures for these species. Method We report on mobulid fishery landings over nine years between 2011 and 2020 across 38 landing sites in Sri Lanka. We collected data on catch numbers, body sizes, sex, and maturity status for five mobulid species. We used a Bayesian state-space model to estimate monthly country-wide catch rates and total annual landings of mobulid rays. We used catch curve analyses to estimate total mortality for Mobula mobular , and evaluated trends in recorded body sizes across the study period for M. mobular, M. birostris, M. tarapacana and M. thurstoni . Results We find that catch…

Many pollination studies with honey bees have examined the effect of colony density on crop yield and yet overlook the effect of variation in the population size of these colonies. High colony density in northern highbush blueberry has been met with concerns from beekeepers who feel higher densities will intensify outbreaks of European foulbrood (EFB, Melissococcus plutonius , Truper and dé Clari), a honey bee brood disease. The purpose of this study was to confirm the prevalence of EFB in colonies pollinating blueberries and to determine whether field-level variation in the population of adult workers in colonies explained variation in blueberry fruit set and/or yield. We addressed these objectives over the course of two production seasons at 13 commercial blueberry fields in Oregon, USA, stocked with identical densities of 10 colonies/ha. We confirmed that all colonies had negligible symptoms of EFB at the start of blueberry pollination, but 53% of colonies in 2019 and 41% in 2020 had symptoms immediately following the pollination season. We also validated a method for rapidly…

Soil erosion is a critical environmental problem of the Chinese Loess Plateau (CLP). The effects of vegetation cover on soil erosion reduction under different rainfall types are not well understood especially in the eastern Chinese Loess Plateau (ECLP). In this study, we monitored runoff and sediment yield at the Fengjiagou water and soil conservation station with five types of vegetation cover (arbor trees (ARC), shrubs (SHC), arable (ABC), natural vegetation (NVC), and artificial grass (APC)) and three slope gradients (10°, 15°, and 20°) in the ECLP. Based on long-term monitoring data, five rainfall types were classified by the maximum 30 min rainfall intensity (I30). We also quantitatively revealed the interactive effects of different types precipitation, vegetation cover and slope gradients on regional soil erosion. The results showed that (1) The RII (13 times) and RIII (eight times) type are the most threatening erosive rainfall in this region. (2) The ARC and SHC type were most beneficial for soil and water conservation in the ECLP; The APC and ABC are not conductive to the…

Background Hepatocellular carcinoma (HCC) with high heterogeneity is one of the most frequent malignant tumors throughout the world. However, there is no research to establish a ferroptosis-related lncRNAs (FRlncRNAs) signature for the patients with HCC. Therefore, this study was designed to establish a novel FRlncRNAs signature to predict the survival of patients with HCC. Method The expression profiles of lncRNAs were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. FRlncRNAs co-expressed with ferroptosis-related genes were utilized to establish a signature. Cox regression was used to construct a novel three FRlncRNAs signature in the TCGA cohort, which was verified in the GEO validation cohort. Results Three differently expressed FRlncRNAs significantly associated with prognosis of HCC were identified, which composed a novel FRlncRNAs signature. According to the FRlncRNAs signature, the patients with HCC could be divided into low- and high-risk groups. Patients with HCC in the high-risk group displayed shorter overall survival (OS)…

The cranial circulation and innervation systems of turtles have been studied for more than two centuries and extensively used to understand turtle systematics. Although a significant number of studies related to these structures exists, a broader comprehension of variation across the tree has been hindered by poor sampling and a lack of synthetic studies that addressed both systems together. We here provide new insights regarding the carotid circulation and facial nerve innervation systems in a broad set of extant turtles using CT (computed tomography) scans, which allow us to trace the canals these structures form in bone and understand the interaction between both systems. We document that the palatine artery, including the lateral carotid canal, is absent in all pleurodires and carettochelyids and was likely reduced or lost several times independently within Testudinoidea. We also highlight osteological correlates for the location of the mandibular artery. We finally summarize variation regarding the placement of the mandibular artery, location of the geniculate ganglion,…

BACKGROUND: Facial fracture is one of the most common injuries globally. Some types of facial fractures may cause irreversible damage and can be life-threatening. This study aimed to investigate the health burden of facial fractures at the global, regional, and national levels from 1990 to 2017. METHODS: Facial fracture data, including the incidence, prevalence, and years lived with disability (YLDs) from 1990 to 2017, were obtained from the Global Burden of Disease study. We calculated the estimated annual percentage changes (EAPCs) to assess the changes of facial fractures in 195 countries or territories and 21 regions. RESULTS: From 1990 to 2017, the change in cases of facial fracture incidence was 39% globally, while the age-standardized incidence rate showed a downtrend with an EAPC of 0.00. Syria experienced a ten-fold increase in incidence cases with an EAPC of 9.2, and this condition is largely responsible for the global health burden of facial fractures. The prevalence and YLDs showed a similar trend worldwide as the incidence. Additionally, we found that the incidence,…

SARS-CoV-2 RNA in wastewater settled solids is associated with COVID-19 incidence in sewersheds and therefore, there is a strong interest in using these measurements to augment traditional disease surveillance methods. A wastewater surveillance program should provide rapid turn around for sample measurements (ideally within 24 hours), but storage of samples is necessary for a variety of reasons including biobanking. Here we investigate how storage of wastewater solids at 4 °C, -20 °C, and -80 °C affects measured concentrations of SARS-CoV-2 RNA. We find that short term (7 or 8 d) storage of raw solids at 4 °C has little effect on measured concentrations of SARS-CoV-2 RNA, whereas longer term storage at 4 °C (35-122 d) or freezing reduces measurements by 60%, on average. We show that normalizing SARS-CoV-2 RNA concentrations by concentrations of pepper mild mottle virus (PMMoV) RNA, an endogenous wastewater virus, can correct for changes during storage as storage can have a similar effect on PMMoV RNA as on SARS-CoV-2 RNA. The reductions in SARS-CoV-2 RNA in solids during freeze…

Reptiles are the most species-rich terrestrial vertebrate group with a broad diversity of life history traits. Biotelemetry is an essential methodology for studying reptiles as it compensates for several limitations when studying their natural history. We evaluated trends in terrestrial reptile spatial ecology studies focusing upon quantifying home ranges for the past twenty years. We assessed 290 English-language reptile home range studies published from 2000-2019 via a structured literature review investigating publications' study location, taxonomic group, methodology, reporting, and analytical techniques. Substantial biases remain in both location and taxonomic groups in the literature, with nearly half of all studies (45%) originating from the USA. Snakes were most often studied, and crocodiles were least often studied, while testudines tended to have the greatest within study sample sizes. More than half of all studies lacked critical methodological details, limiting the number of studies for inclusion in future meta-analyses (55% of studies lacked information on individual…

Microplastics (MP) are now considered ubiquitous across global aquatic environments. The ingestion of MP by fish and other marine vertebrates is well studied, but the ingestion of MP by marine invertebrates is not. Sponges (Phylum Porifera) are particularly understudied when it comes to MP ingestion, even though they are widely distributed across benthic habitats, can process large volumes of seawater, and can retain small particles within their water filtration systems. This study examines the presence of potential MP (PMP) in wild marine sponges and seawater collected in Bocas del Toro, Panamá. Subsurface seawater and tissue from six common Caribbean sponge species was collected in Saigon Bay, a heavily impacted, shallow-water coral reef. Seawater samples were filtered onto glass fiber filters to retain any PMP present and sponge tissue was digested with bleach, heated and filtered. Filters were examined using fluorescence microscopy to quantify PMP. An average of 107 ± 25 PMP L –1 was detected in seawater from Saigon Bay with particles ranging in size between 10 μm and ~3,000 μm.…

Background The dehydration responsive element-binding (DREB) gene family plays a crucial role as transcription regulators and enhances plant tolerance to abiotic stresses. Although the DREB gene family has been identified and characterized in many plants, knowledge about it in Solanum tuberosum (Potato) is limited. Results In the present study, StDREB gene family was comprehensively analyzed using bioinformatics approaches. We identified 66 StDREB genes through genome wide screening of the Potato genome based on the AP2 domain architecture and amino acid conservation analysis (Valine at position 14th). Phylogenetic analysis divided them into six distinct subgroups (A1–A6). The categorization of StDREB genes into six subgroups was further supported by gene structure and conserved motif analysis. Potato DREB genes were found to be distributed unevenly across 12 chromosomes. Gene duplication proved that StDREB genes experienced tandem and segmental duplication events which led to the expansion of the gene family. The Ka/Ks ratios of the orthologous pairs also demonstrated the StDREB…

Population increase and the demand for infrastructure development such as construction of highways and road widening are intangible, leading up to mass land clearing. As flat terrains become scarce, infrastructure expansions have moved on to hilly terrains, cutting through slopes and forests. Unvegetated or bare slopes are prone to erosion due to the lack of or insufficient surface cover. The combination of exposed slope, uncontrolled slope management practices, poor slope planning and high rainfall as in Malaysia could steer towards slope failures which then results in landslides under acute situation. Moreover, due to the tropical weather, the soils undergo intense chemical weathering and leaching that elevates soil erosion and surface runoff. Mitigation measures are vital to address slope failures as they lead to economic loss and loss of lives. Since there is minimal or limited information and investigations on slope stabilization methods in Malaysia, this review deciphers into the current slope management practices such as geotextiles, brush layering, live poles, rock buttress…

Background Globally, there is a large amount of salinized land. These soils have varying degrees of salt stress, causing ionic toxicity and osmotic stress on plants. However, it is not clear how different degrees of salt stress affect plant nutrients and microbial communities. Thus, a comprehensive understanding of plant major nutrients and microbial communities response to salt stress is desirable. Results We analyzed the main nutrients of the salt-tolerant ZhongMu No. 3 alfalfa variety planted in a salt stress environment. In mild and moderate group, the protein content and fatty acid content of alfalfa were the highest, indicating the best nutritional value. The severe group of salt stress affected the growth and development of alfalfa, as manifested by a decrease in the nutritional quality of alfalfa. Pseudomonas and Sphingobacterium that from alfalfa stem and leaf endophytes also increased with an increase in salt stress. In contrast, Sphingomonas, Methylobacterium, and Rhizobium decrease with increasing salt stress. Methylobacterium and Rhizobium have extremely significant…

Xinjiang is a major part of China's arid region and its water resource is extremely scarcity. The change in precipitation amounts and extremes is of significant importance for the reliable management of regional water resources in this region. Thus, this study explored the spatiotemporal changes in extreme precipitation using the Mann-Kendall (M-K) trend analysis, mutation test, and probability distribution functions, based on the observed daily precipitation data from 89 weather stations in Xinjiang, China during 1961-2018. We also examined the correlations between extreme precipitation and climate indices using the cross-wavelet analysis. The results indicated that the climate in Xinjiang is becoming wetter and the intensity and frequency of extreme precipitation has begun to strengthen, with these trends being more obvious after the 1990s. Extreme precipitation trends displayed spatial heterogeneity in Xinjiang. Extreme precipitation was mainly concentrated in mountainous areas, northern Xinjiang, and western Xinjiang. The significant increasing trend of extreme precipitation was…

The tumor microenvironment (TME) influences the occurrence and progression of tumors, and hypoxia is an important characteristic of the TME. The expression of programmed death 1 (PD1)/programmed death-ligand 1 (PDL1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA4), and other immune checkpoints in hypoxic malignant tumors is often significantly increased, and is associated with poor prognosis. The application of immune checkpoint inhibitors (ICIs) for treating lung cancer, urothelial carcinoma, and gynecological tumors has achieved encouraging efficacy; however, the rate of efficacy of ICI single-drug treatment is only about 20%. In the present review, we discuss the possible mechanisms by which the hypoxic TME regulates immune checkpoints. By activating hypoxia-inducible factor-1α(HIF-1α), regulating the adenosine (Ado)-A2aR pathway, regulating the glycolytic pathway, and driving epithelial-mesenchymal transition (EMT) and other biological pathways, hypoxia regulates the expression levels of CTLA4, PD1, PDL1, CD47, lymphocyte activation gene 3 (LAG3), T-cell immunoglobulin and…

Background China 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. Methods A 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. Results The 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…

Jasmonic acid (JA) and its derivatives called jasmonates (JAs) are lipid-derived signalling molecules that are produced by plants and certain fungi. Beside this function, JAs have a great variety of applications in flavours and fragrances production. In addition, they may have a high potential in agriculture. JAs protect plants against infections. Although there is much information on the biosynthesis and function of JA concerning plants, knowledge on these aspects is still scarce for fungi. Taking into account the practical importance of JAs, the objective of this review is to summarize knowledge on the occurrence of JAs from fungal culture media, their biosynthetic pathways and the culture conditions for optimal JA production as an alternative source for the production of these valuable metabolites.

Many studies investigating the human microbiome-cancer interface have focused on the gut microbiome and gastrointestinal cancers. Outside of human papillomavirus driving cervical cancer, little is known about the relationship between the vaginal microbiome and other gynecological cancers, such as ovarian cancer. In this retrospective study, we investigated the relationship between ovarian cancer, platinum-free interval (PFI) length, and vaginal and gut microbiomes. We observed that Lactobacillus -dominated vaginal communities were less common in women with ovarian cancer, as compared to existing datasets of similarly aged women without cancer. Primary platinum-resistance (PPR) disease is strongly associated with survivability under one year, and we found over one-third of patients with PPR (PFI < 6 months, n = 17) to have a vaginal microbiome dominated by Escherichia (>20% relative abundance), while only one platinum super-sensitive (PFI > 24 months, n = 23) patient had an Escherichia -dominated microbiome. Additionally, L. iners was associated with little, or no, gross residual…

BACKGROUND: Plastic pollution affects all ecosystems, and detrimental effects to animals have been reported in a growing number of studies. However, there is a paucity of evidence for effects on terrestrial animals in comparison to those in the marine realm. METHODS: to study the effects that exposure to plastics may have on life history traits and immune response. We reared flies in four conditions: In media containing 1% virgin polyethylene, with no chemical additives; in media supplemented with 1% or 4% polyvinyl chloride, known to have a high content of added chemicals; and control flies in non-supplemented media. Plastic particle size ranged from 23-500 µm. We studied fly survival to viral infection, the length of the larval and pupal stage, sex ratios, fertility and the size of the resultant adult flies. We then performed crossings of F1 flies in non-supplemented media and looked at the life history traits of the F2. RESULTS: Flies treated with plastics in the food media showed changes in fertility and sex ratio, but showed no differences in developmental times, adult size or…

DNA-binding proteins (DBPs) play pivotal roles in many biological functions such as alternative splicing, RNA editing, and methylation. Many traditional machine learning (ML) methods and deep learning (DL) methods have been proposed to predict DBPs. However, these methods either rely on manual feature extraction or fail to capture long-term dependencies in the DNA sequence. In this paper, we propose a method, called PDBP-Fusion, to identify DBPs based on the fusion of local features and long-term dependencies only from primary sequences. We utilize convolutional neural network (CNN) to learn local features and use bi-directional long-short term memory network (Bi-LSTM) to capture critical long-term dependencies in context. Besides, we perform feature extraction, model training, and model prediction simultaneously. The PDBP-Fusion approach can predict DBPs with 86.45% sensitivity, 79.13% specificity, 82.81% accuracy, and 0.661 MCC on the PDB14189 benchmark dataset. The MCC of our proposed methods has been increased by at least 9.1% compared to other advanced prediction models.…

Previous research has highlighted that Emotional Intelligence (EI) is related to an array of positive interpersonal behaviours, including greater human empathy. Nonetheless, although animals are an integral part of our lives, there is still a lack of clarity regarding the way in which EI relates to empathy towards animals. The aim of this study was to investigate the relationship between EI and empathy towards humans and animals. We used the Trait-Meta Mood Scale to assess EI, the Interpersonal Reactivity Index to assess empathy for humans, and the Animal Empathy Scale to assess empathy for animals. Our findings revealed a positive relationship between empathy for humans and animals. The results also supported the idea that EI is positively related to empathy for humans, while the relationship between EI and empathy for animals was dependent on whether or not the participants had experience with pets. In addition, multiple regression analysis showed that the variables that best predicted empathy for animals were having a pet (or not), age, gender and human empathic concern. Finally,…

PURPOSE: Status 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. METHODS: 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. RESULTS: EpCAM 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…

Background The sugarcane/peanut intercropping system is a specific and efficient cropping pattern in South China. Intercropping systems change the bacterial diversity of soils and decrease disease rates. It can not only utilized light, heat, water and land resources efficiently, but also increased yield and economic benefits of farmers. Methods We determined soil nutrients, enzymes and microbes in sugarcane/peanut intercropping system, and analyzed relevance of the soil physicochemical properties and the genes involved in N and P cycling and organic matter turnover by metagenome sequencing. Results The results showed that sugarcane/peanut intercropping significantly boosted the content of total nitrogen, available phosphorus, total potassium, organic matter, pH value and bacteria and enhanced the activity of acid phosphatase compared to monocropping. Especially the content of available nitrogen, available phosphorus and organic matter increased significantly by 20.1%, 65.3% and 56.0% in root zone soil of IP2 treatment than monocropping treatment. The content of available potassium…

BACKGROUND: Tooth whitening is one of the most requested dental treatments, but it still presents some side effects. Indeed, the bleaching agent can generate patients' discomfort and dental hard tissue damages, not achieving an efficient and long-lasting treatment with optimum whitening effect. To overcome these limitations, the bleaching agents containing nano-hydroxyapatite can represent a reliable solution to avoid these detrimental effects. METHODS: In this study, human third molars were treated with commercial bleaching agents, containing nano-hydroxyapatite (nHA) and 6% (at-home treatment), 12% and 18% (in-office treatments) of hydrogen peroxide (HP), named respectively G1, G2 and G3. The results were evaluated descriptively and analytically using Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR), Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray spectroscopy (EDS), comparing the treated groups with a commercial gel containing 10% carbamide peroxide (CONV) and with a non-treated control group (CTRL). RESULTS: ATR-FTIR analysis…

BACKGROUND: The Human Leukocyte Antigen (HLA) gene locus plays a fundamental role in human immunity, and it is established that certain HLA alleles are disease determinants. METHODS: By combining the predictive power of multiple in silico HLA predictors, we have previously identified prevalent HLA class I and class II alleles, including DPA1*02:02, in two small cohorts at the COVID-19 pandemic onset. Since then, newer and larger patient cohorts with controls and associated demographic and clinical data have been deposited in public repositories. Here, we report on HLA-I and HLA-II alleles, along with their associated risk significance in one such cohort of 126 patients, including COVID-19 positive (n=100) and negative patients (n=26). RESULTS: We recapitulate an enrichment of DPA1*02:02 in the COVID-19 positive cohort (29%) when compared to the COVID-negative control group (Fisher's exact test [FET] p=0.0174). Having this allele, however, does not appear to put this cohort's patients at an increased risk of hospitalization. Inspection of COVID-19 disease severity outcomes reveal…

White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement,…

Ecosystem functioning is dependent a lot on large mammals, which are, however, vulnerable and facing extinction risks due to human impacts mainly. Megafauna of Asia has been declining for a long, not only in numbers but also in their distribution ranges. In the current study, we collected information on past and current occurrence and distribution records of Asia's megafauna species. We reconstructed the historical distribution ranges of the six herbivores and four carnivores for comparison with their present ranges, to quantify spatially explicit levels of mega-defaunation. Results revealed that historically the selected megafauna species were more widely distributed than at current. Severe range contraction was observed for the Asiatic lion, three rhino species, Asian elephant, tigers, and tapirs. Defaunation maps generated have revealed the vanishing of megafauna from parts of the East, Southeast, and Southwest Asia, even some protected Areas losing up to eight out of ten megafaunal species. These defaunation maps can help develop future conservation policies, to save the…

Background Melatonin is a hormone substance that exists in various living organisms. Since it was discovered in the pineal gland of cattle in 1956, the function of melatonin in animals has been roughly clarified. Nevertheless, in plants, the research on melatonin is still insufficient. Hulless barley ( Hordeum vulgare L. var. nudum hook. f.) is a crop that originates from cultivated barley in the east, usually grown on the Qinghai-Tibet Plateau, becoming the most important food crop in this area. Although the genome and transcriptome research of highland barley has gradually increased recently years, there are still many problems about how hulless barley adapts to the cold climate of the Qinghai-Tibet Plateau. Methods In this study, we set three temperature conditions 25°C, 15°C, 5°C hulless barley seedlings, and at the same time soaked the hulless barley seeds with a 1 µM melatonin solution for 12 hours before the hulless barley seeds germinated. Afterwards, the growth and physiological indicators of hulless barley seedlings under different treatment conditions were determined.…

BACKGROUND: Real-Time Reverse-Transcription Polymerase Chain Reaction (RT-PCR) is currently the only recommended diagnostic method for SARS-CoV-2. However, rapid immunoassays for SARS-CoV-2 antigen could significantly reduce the COVID-19 burden currently weighing on laboratories around the world. METHODS: We evaluated the performance of two rapid fluorescence immunoassays (FIAs), SOFIA SARS Antigen FIA (Quidel Corporation, San Diego, CA, USA) and STANDARD F COVID-19 Ag FIA (SD Biosensor Inc., Gyeonggi-do, Republic of Korea), which use an automated reader. The study used 64 RT-PCR characterized clinical samples (32 positive; 32 negative), which consisted of nasopharyngeal swabs in universal transport medium. RESULTS: Of the 32 positive specimens, all from patients within 5 days of symptom onset, the Quidel and SD Biosensor assays detected 30 (93.8%) and 29 (90.6%) samples, respectively. Among the 27 samples with high viral loads (Ct ≤ 25), the two tests had a sensitivity of 100%. Specificity was 96.9% for both kits. CONCLUSION: copies/mL (Ct values ≤ 25), the estimated threshold of…

The Growth-Regulating Factor (GRF) family encodes a type of plant-specific transcription factor (TF). GRF members play vital roles in plant development and stress response. Although GRF family genes have been investigated in a variety of plants, they remain largely unstudied in bread wheat ( Triticum aestivum L.). The present study was conducted to comprehensively identify and characterize the T. aestivum GRF ( TaGRF ) gene family members. We identified 30 TaGRF genes, which were divided into four groups based on phylogenetic relationship. TaGRF members within the same subgroup shared similar motif composition and gene structure. Synteny analysis suggested that duplication was the dominant reason for family member expansion. Expression pattern profiling showed that most TaGRF genes were highly expressed in growing tissues, including shoot tip meristems, stigmas and ovaries, suggesting their key roles in wheat growth and development. Further qRT-PCR analysis revealed that all 14 tested TaGRFs were significantly differentially expressed in responding to drought or salt stresses,…

BACKGROUND: Metastasis is a major event for survival and prognosis in patients with head and neck squamous cell carcinomas (HNSCC). A primary cause of metastasis is the proteolytic degradation of the extracellular matrix (ECM). The plasminogen activator urokinase (PLAU) is involved in the transformation of plasminogen to plasmin leading to hydrolyzation of ECM-related proteins. However, the role of PLAU expression in HNSCC is unclear and the worth being investigated. METHODS: PLAU expression profiles and clinical parameters from multiple HNSCC datasets were used to investigate the relationship of PLAU expression and HNSCC survival. GO and PPI network were established on PLAU-related downstream molecular. The stroma score was deconvoluted for analysis of PLAU's association with the immune environment. ROC analysis was applied to show the performance of PLAU in predicting HNSCC prognosis. RESULTS: < 0.01). Univariate and multivariate cox analysis showed PLAU could be an independent indicator for HNSCC prognosis. Combining with neck lymph node status, the AUC of PLAU in predicting…

Sumoylation is the post-translational modification that is involved in the adaption of the cells and the functional properties of a large number of proteins. Sumoylation has key importance in subcellular concentration, transcriptional synchronization, chromatin remodeling, response to stress, and regulation of mitosis. Sumoylation is associated with developmental defects in many human diseases such as cancer, Huntington's, Alzheimer's, Parkinson's, Spin cerebellar ataxia 1, and amyotrophic lateral sclerosis. The covalent bonding of Sumoylation is essential to inheriting part of the operative characteristics of some other proteins. For that reason, the prediction of the Sumoylation site has significance in the scientific community. A novel and efficient technique is proposed to predict the Sumoylation sites in proteins by incorporating Chou's Pseudo Amino Acid Composition (PseAAC) with statistical moments-based features. The outcomes from the proposed system using 10 fold cross-validation testing are 94.51%, 94.24%, 94.79% and 0.8903% accuracy, sensitivity, specificity and MCC,…

BACKGROUND: A novel coronavirus first reported in Wuhan City in China in 2019 (COVID-19) developed into a global pandemic throughout 2020. Many countries around the world implemented strict social distancing policies to curb the spread of the virus. In this study we aimed to examine potential change in mental/physical health and social relationships during a highly restrictive COVID-19 lockdown period in Australia during April 2020. METHODS: = 1, 599) included questions about concerns, social behaviour, perceived change in relationship quality, social media use, frequency of exercise, physical health, and mental health during COVID-19 lockdown (April, 2020). RESULTS: When estimating their mental health for the previous year 13% of participants reported more negative than positive emotion, whereas this increased to 41% when participants reflected on their time during COVID-19 lockdown. A substantial proportion (39-54%) of participants reported deterioration in mental health, physical health, financial situation, and work productivity. However, most of these participants reported…

Background & Objectives The massive outbreak of Novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has turned out to be a serious global health issue worldwide. Currently, no drugs or vaccines are available for the treatment of COVID-19. The current computational study was attempted to identify a novel therapeutic inhibitor against novel SARS-CoV-2 using in silico drug discovery pipeline. Methods In the present study, the human angiotensin-converting enzyme 2 (ACE2) receptor was the target for the designing of drugs against the deadly virus. The 3D structure of the receptor was modeled & validated using a Swiss-model, Procheck & Errat server. A molecular docking study was performed between a group of natural & synthetic compounds having proven anti-viral activity with ACE2 receptor using Autodock tool 1.5.6. The molecular dynamics simulation study was performed using Desmond v 12 to evaluate the stability and interaction of the ACE2 receptor with a ligand. Results Based on the lowest binding energy, confirmation, and H-bond interaction, cinnamic acid (−5.20 kcal/mol),…

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…

Background The 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). Methods Following 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 theI2statistic. The risk of bias was explored…

ABSTRACT This is the first revision in nearly 130 years of the African genus Pseudohydrosme , formerly considered endemic to Gabon. Sister to Anchomanes, Pseudohydrosme is distinct from Anchomanes because of its 2–3-locular ovary (not unilocular), peduncle concealed by cataphylls at anthesis and far shorter than the spathe (not exposed, far exceeding the spathe), stipitate fruits and viviparous (vegetatively apomictic) roots (not sessile, roots non-viviparous). Three species, one new to science, are recognised, in two sections. Although doubt has previously been cast on the value of recognising Pseudohydrosme buettneri , of Gabon, it is here accepted and maintained as a distinct species in the monotypic section, Zyganthera . However, it is considered to be probably globally extinct. Pseudohydrosme gabunensis , type species of the genus, also Gabonese, is maintained in Sect. Pseudohydrosme together with Pseudohydrosme ebo sp.nov . of the Ebo Forest, Littoral, Cameroon, the first addition to the genus since the nineteenth century, and which extends the range of the genus 450 km north…

Bisphosphonates (BPs)-related osteonecrosis of jaw (BRONJ) is a severe complication of the long-term administration of BPs. The development of BRONJ is associated with the cell death of osteoclasts, but the underlying mechanism remains unclear. In the current study, the role of Zoledronic acid (ZA), a kind of bisphosphonates, in suppressing the growth of osteoclasts was investigated and its underlying mechanism was explored. The role of ZA in regulating osteoclasts function was evaluated in the RANKL-induced cell model. Cell viability was assessed by cell counting kit-8 (CCK-8) assay and fluorescein diacetate (FDA)-staining. We confirmed that ZA treatment suppressed cell viability of osteoclasts. Furthermore, ZA treatment led to osteoclasts death by facilitating osteoclasts ferroptosis, as evidenced by increased Fe 2+ , ROS, and malonyldialdehyde (MDA) level, and decreased glutathione peroxidase 4 (GPX4) and glutathione (GSH) level. Next, the gene expression profiles of alendronate- and risedronate-treated osteoclasts were obtained from Gene Expression Omnibus (GEO) dataset, and 18…

The sustainable development of agriculture is one of the key issues of ensuring food security and mitigating climate change. Since innovative large-scale agriculture is gaining popularity in cities in China, where the agricultural landscape is dominated by conventional smallholder farming, it is necessary to investigate the difference in carbon emissions between conventional smallholder operation and innovative largescale agriculture. This study evaluated the carbon footprint (CF) of conventional and innovative urban agriculture in Beijing using the cradle-to-consumption Life Cycle Assessment (LCA). Two modes of greenhouse vegetable and fruit production were analyzed and compared respectively: conventional smallholder operated vegetable farms that sell in local markets versus largescale home-delivery agriculture (HDA) that deliver vegetables to consumers' home directly, conventional smallholder operated fruit farms that sell in farm shops versus largescale pick-your-own (PYO) initiatives. Results showed that HDA and PYO can reduce CF per area in on-farm cultivation compared to…

Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea . The distribution in phyla revealed a majority abundance of Proteobacteria (37–89%), followed by Actinobacteria , Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72–96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO 2 fixation; although other ecological…

Background Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Delphinium grandiflorum L. is a perennial herb with high economic value and typical biological characteristics. Evolutionary analysis of D. grandiflorum can provide a rich resource of genetic information for developing hybridization resources of the genus Delphinium. Methods Synonymous codon usage (SCU) and related indices of 51 coding sequences from the D. grandiflorum chloroplast (cp) genome were calculated using Codon W, Cups of EMBOSS, SPSS and Microsoft Excel. Multivariate statistical analysis combined by principal component analysis (PCA), correspondence analysis (COA), PR2-plot mapping analysis and ENC plot analysis was then conducted to explore the factors affecting the usage of synonymous codons. Results The SCU bias of D. grandiflorum was weak and codons preferred A/T ending. A SCU imbalance between A/T and G/C at the third base position was revealed by PR2-plot mapping analysis. A total of eight codons were identified as the optimal…

Background Changing family models have resulted in a large increase in the number of single-person households. This phenomenon has certain implications for society and the economy as single people often exhibit different behaviours, including their engagement in health-related physical activity, than those who are married and living with partners. However, the results of studies on determinants of physical activity in people of different marital status have been inconclusive. The aim of this study was to identify associations between physical activity and socioeconomic status in single and married urban adults. Methods The study material consisted of 4,460 persons (1,828 single and 2,632 married and living with partners). A cross-sectional study was conducted in Wroclaw (Poland). A diagnostic survey-direct interview method was used. Two research tools were applied: the International Physical Activity Questionnaire Short Form (IPAQ-SF) and the Socioeconomic Status Questionnaire (S-ESQ). The level of respondents’ physical activity was assessed following WHO recommendations. The…

BACKGROUND: The family caregivers of patients on hemodialysis (HD) and peritoneal dialysis (PD) typically experience higher burden than the general population because of the nature of tasks these caregivers need to carry out as a part of homecare. This fact influences both the caregivers' quality of life and the quality of their care toward the patient. Thus, this study aimed to review the effectiveness and limitations of interventions in improving the well-being of family caregivers of patients on HD and PD. METHODOLOGY: A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and the Cochrane Handbook for Systematic Reviews of Interventions (version 5.1.0). The Cochrane Library, Cumulative Index to Nursing and Allied Health Literature, Embase, MEDLINE, VHL Regional Portal, Scopus, and Web of Science databases were searched queried for randomized controlled trials that developed interventions aimed at improving the well-being of family caregivers of patients undergoing HD and/or PD from 2009 to 2020. The study protocol…

A better understanding of disease development and progression mechanisms at the molecular level is critical both for the diagnosis of a disease and for the development of therapeutic approaches. The advancements in high throughput technologies allowed to generate mRNA and microRNA (miRNA) expression profiles; and the integrative analysis of these profiles allowed to uncover the functional effects of RNA expression in complex diseases, such as cancer. Several researches attempt to integrate miRNA and mRNA expression profiles using statistical methods such as Pearson correlation, and then combine it with enrichment analysis. In this study, we developed a novel tool called miRcorrNet, which performs machine learning-based integration to analyze miRNA and mRNA gene expression profiles. miRcorrNet groups mRNAs based on their correlation to miRNA expression levels and hence it generates groups of target genes associated with each miRNA. Then, these groups are subject to a rank function for classification. We have evaluated our tool using miRNA and mRNA expression profiling data downloaded…

Commercial, recreational, and indigenous fisheries are critical to coastal economies and communities in the United States. For over three decades, the federal government has formally recognized the impact of fishery disasters via federal declarations. Despite these impacts, national syntheses of the dynamics, impacts, and causes of fishery disasters are lacking. We developed a nationwide Federal Fishery Disaster database using National Oceanic and Atmospheric Administration (NOAA) fishery disaster declarations and fishery revenue data. From 1989-2020, there were 71 federally approved fishery disasters (eleven are pending), which spanned every federal fisheries management region and coastal state in the country. To date, we estimate fishery disasters resulted in $2B (2019 USD) in Congressional allocations, and an additional, conservative estimate of $3.2B (2019 USD) in direct revenue loss. Despite this scale of impact, the disaster assistance process is largely ad hoc and lacks sufficient detail to properly assess allocation fairness and benefit. Nonetheless, fishery disasters…

Background Sediments frequently exposed to dry-wet cycles are potential biogeochemical hotspots for greenhouse gas (GHG) emissions during dry, wet and transitional phases. While the effects of drying and rewetting on carbon fluxes have been studied extensively in terrestrial and aquatic systems, less is known about the effects of dry-wet cycles on N 2 O emissions from aquatic systems. As a notable part of lotic systems are temporary, and small lentic systems can substantially contribute to GHG emissions, dry-wet cycles in these ecosystems can play a major role on N 2 O emissions. Methodology This study compiles literature focusing on the effects of drying, rewetting, flooding, and water level fluctuations on N 2 O emissions and related biogeochemical processes in sediments of lentic and lotic ecosystems. Results N 2 O pulses were observed following sediment drying and rewetting events. Moreover, exposed sediments during dry phases can be active spots for N 2 O emissions. The general mechanisms behind N 2 O emissions during dry-wet cycles are comparable to those of soils and are…

Background The relationship between serum uric acid (SUA) and several diabetic complications or co-morbidities remains a matter of debate. The study aims to explore the association between SUA levels and the prevalence of non-alcoholic fatty liver disease (NAFLD), diabetic retinopathy (DR), diabetic nephropathy (DN) and diabetic peripheral neuropathy (DPN) in patients with type 2 diabetes mellitus (T2DM). Methods A total of 2,809 participants (1,784 males and 1,025 females) were included in this cross-sectional study. Clinical characteristics and the prevalence of each of the four diseases were analyzed based on gender-specific quartiles of SUA levels. The Pearson correlation analysis and linear-regression analysis were used to access the correlation between SUA levels and clinical characteristics. Furthermore, a binary logistic regression analysis was carried out to determine whether SUA was an independent risk factor for each of the four complications. Results SUA levels were positively correlated to BMI, BUN, Scr and TG, but negatively associated with eGFR, HDL, FBG, 2h-PG and…

Leaf blotch caused by Alternaria spp. is a common disease in apple-producing regions. The disease is usually associated with one phylogenetic species and one species complex, Alternaria alternata and the Alternaria arborescens species complex ( A. arborescens SC), respectively. Both taxa may include the Alternaria apple pathotype, a quarantine or regulated pathogen in several countries. The apple pathotype is characterized by the production of a host-selective toxin (HST) which is involved in pathogenicity towards the apple. A cluster of genes located on conditionally dispensable chromosomes (CDCs) is involved in the production of this HST (namely AMT in the case of the apple pathotype). Since 2016, leaf blotch and premature tree defoliation attributed to Alternaria spp. have been observed in apple-producing regions of central and south-eastern France. Our study aimed to identify the Alternaria species involved in apple tree defoliation and assess the presence of the apple pathotype in French orchards. From 2016 to 2018, 166 isolates were collected and identified by multi-locus…