The 100 most-cited articles in PeerJ, 2020

Background The COVID-19 pandemic is found to affect the mental health of the population. Undergraduate medical students are especially prone to mental health disorders and hence could be more vulnerable to the impact of the pandemic. Methods A prospective longitudinal study was conducted on 217 undergraduate medical students in a medical college at Chennai, India. Depression, anxiety, and stress levels were recorded using Depression Anxiety Stress Scale 21 Items (DASS21) before and during the COVID-19 outbreak in India in December 2019 and June 2020, respectively. In the follow-up survey, in addition to DASS21, the Pittsburgh Sleep Quality Index to assess sleep quality and a self-administered questionnaire to assess the impact of COVID-19 related stressors were used. The self-administered questionnaire assessed the status of COVID-19 testing, interactions with COVID-19 patients, self-perceived levels of concerns and worries related to academics (COVID-19-AA (academic apprehensions)) and those pertaining to the self and family/friends (COVID-19-GA (general apprehensions)).…

Many researchers in the behavioral sciences depend on research software that presents stimuli, and records response times, with sub-millisecond precision. There are a large number of software packages with which to conduct these behavioural experiments and measure response times and performance of participants. Very little information is available, however, on what timing performance they achieve in practice. Here we report a wide-ranging study looking at the precision and accuracy of visual and auditory stimulus timing and response times, measured with a Black Box Toolkit. We compared a range of popular packages: PsychoPy, E-Prime®, NBS Presentation®, Psychophysics Toolbox, OpenSesame, Expyriment, Gorilla, jsPsych, Lab.js and Testable. Where possible, the packages were tested on Windows, MacOS, and Ubuntu, and in a range of browsers for the online studies, to try to identify common patterns in performance. Among the lab-based experiments, Psychtoolbox, PsychoPy, Presentation and E-Prime provided the best timing, all with mean precision under 1 millisecond across the visual, audio…

Multiple comparisons tests (MCTs) include the statistical tests used to compare groups (treatments) often following a significant effect reported in one of many types of linear models. Due to a variety of data and statistical considerations, several dozen MCTs have been developed over the decades, with tests ranging from very similar to each other to very different from each other. Many scientific disciplines use MCTs, including >40,000 reports of their use in ecological journals in the last 60 years. Despite the ubiquity and utility of MCTs, several issues remain in terms of their correct use and reporting. In this study, we evaluated 17 different MCTs. We first reviewed the published literature for recommendations on their correct use. Second, we created a simulation that evaluated the performance of nine common MCTs. The tests examined in the simulation were those that often overlapped in usage, meaning the selection of the test based on fit to the data is not unique and that the simulations could inform the selection of one or more tests when a researcher has choices. Based on…

Background Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. Here we introduce a normalization method for species count data called scaling with ranked subsampling (SRS) and demonstrate its suitability for the analysis of microbial communities. Methods SRS consists of two steps. In the scaling step, the counts for all species or operational taxonomic units (OTUs) are divided by a scaling factor chosen in such a way that the sum of scaled counts equals the selected total number of counts C min . The relative frequencies of all OTUs remain unchanged. In the subsequent ranked subsampling step, non-integer count values are converted into integers by an algorithm that minimizes subsampling error with regard to the population…

In the past decade, researchers have carried out a massive amount of research on the application of biochar for contaminants removal from aqueous solutions. As an emerging sorbent with great potential, biochar has shown significant advantages such as the broad sources of feedstocks, easy preparation process, and favorable surface and structural properties. This review provides an overview of recent advances in biochar application in water and wastewater treatment, including a brief discussion of the involved sorption mechanisms of contaminants removal, as well as the biochar modification methods. Furthermore, environmental concerns of biochar that need to be paid attention to and future research directions are put forward to promote the further application of biochar in practical water and wastewater treatment.

BACKGROUND: The Shannon diversity index has been widely used in population genetics studies. Recently, it was proposed as a unifying measure of diversity at different levels-from genes and populations to whole species and ecosystems. The index, however, was proven to be negatively biased at small sample sizes. Modifications to the original Shannon's formula have been proposed to obtain an unbiased estimator. METHODS: In this study, the performance of four different estimators of Shannon index-the original Shannon's formula and those of Zahl, Chao and Shen and Chao et al.-was tested on simulated microsatellite data. Both the simulation and analysis of the results were performed in the R language environment. A new R function was created for the calculation of all four indices from the genind data format. RESULTS: Sample size dependence was detected in all the estimators analysed; however, the deviation from parametric values was substantially smaller in the derived measures than in the original Shannon's formula. Error rate was negatively associated with population heterozygosity.…

Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the 'Global Museum') is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often…

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression found in more than 200 diverse organisms. Although it is still not fully established if RNA viruses could generate miRNAs, there are examples of miRNA like sequences from RNA viruses with regulatory functions. In the case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with viral replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA-based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Overall, 950 hairpin structured sequences were extracted from the virus genome and based on the prediction results, 29 of them could be precursor miRNAs. Targeting analysis showed that 30 viral mature miRNA-like sequences could target 1,367 different human genes. PANTHER gene function analysis results…

Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; http://www.gbif.org), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of…

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and…

Beer is the most popular low-alcohol beverage consumed in large amounts in many countries each year. The brewing industry is an important global business with huge annual revenues. It is profitable and important for the economies of many countries around the world. The brewing process involves several steps, which lead to fermentation of sugars contained in malt and conversion thereof into alcohol and carbon dioxide by yeasts. Beer brewing generates substantial amounts of by-products. The three main brewing industry wastes include brewer's spent grain, hot trub, and residual brewer's yeast. Proper management of these wastes may bring economical benefits and help to protect the environment from pollution caused by their excessive accumulation. The disposal of these wastes is cumbersome for the producers, however they are suitable for reuse in the food industry. Given their composition, they can serve as a low-cost and highly nutritional source of feed and food additives. They also have a potential to be a cheap material for extraction of compounds valuable for the food industry and a…

Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon…

RNA-fluorescence in situ hybridization (FISH) is a powerful tool to visualize target messenger RNA transcripts in cultured cells, tissue sections or whole-mount preparations. As the technique has been developed over time, an ever-increasing number of divergent protocols have been published. There is now a broad selection of options available to facilitate proper tissue preparation, hybridization, and post-hybridization background removal to achieve optimal results. Here we review the technical aspects of RNA-FISH, examining the most common methods associated with different sample types including cytological preparations and whole-mounts. We discuss the application of commonly used reagents for tissue preparation, hybridization, and post-hybridization washing and provide explanations of the functional roles for each reagent. We also discuss the available probe types and necessary controls to accurately visualize gene expression. Finally, we review the most recent advances in FISH technology that facilitate both highly multiplexed experiments and signal amplification for individual…

have high capacity to absorb metals; thus, leachates of sargasso may contribute to contamination by potentially toxic metals when they drain into the sea and into the groundwater when dumped in inadequate land deposits. Valorization of sargasso would contribute to sustainable management; therefore, knowledge on potentially toxic metal content is necessary to define possible uses of the algae. We present concentrations of 28 elements measured using a non-destructive X-ray fluorescence analyzer (XRF) in 63 samples of sargasso collected between August 2018 and June 2019 from eight localities along ∼370 km long coastline of the Mexican Caribbean Sea. The sargasso tissues contained detectable concentrations of Al, As, Ca, Cl, Cu, Fe, K, Mg, Mn, Mo, P, Pb, Rb, S, Si, Sr, Th, U, V, and Zn. The element concentration in sargasso varied on spatial and temporal scales, which likely depended on the previous trajectory of the pelagic masses, and whether these had (or had not) passed through contaminated areas. Total arsenic concentration varied between 24-172 ppm DW, exceeding the maximum limit…

Background The gut microbiome and microbiome-gut-brain (MGB) axis have been receiving increasing attention for their role in the regulation of mental behavior and possible biological basis of psychiatric disorders. With the advance of next-generation sequencing technology, characterization of the gut microbiota in schizophrenia (SZ) patients can provide rich clues for the diagnosis and prevention of SZ. Methods In this study, we compared the differences in the fecal microbiota between 82 SZ patients and 80 demographically matched normal controls (NCs) by 16S rRNA sequencing and analyzed the correlations between altered gut microbiota and symptom severity. Results The alpha diversity showed no significant differences between the NC and SZ groups, but the beta diversity revealed significant community-level separation in microbiome composition between the two groups (pseudo- F =3.337, p < 0.001, uncorrected). At the phylum level, relatively more Actinobacteria and less Firmicutes ( p < 0.05, FDR corrected) were found in the SZ group. At the genus level, the relative abundances of…

A decline in soil biodiversity is generally considered to be the reduction of forms of life living in soils, both in terms of quantity and variety. Where soil biodiversity decline occurs, it can significantly affect the soils' ability to function, respond to perturbations and recover from a disturbance. Several soil threats have been identified as having negative effects on soil biodiversity, including human intensive exploitation, land-use change and soil organic matter decline. In this review we consider what we mean by soil biodiversity, and why it is important to monitor. After a thorough review of the literature identified on a Web of Science search concerning threats to soil biodiversity (topic search: threat* "soil biodiversity"), we compiled a table of biodiversity threats considered in each paper including climate change, land use change, intensive human exploitation, decline in soil health or plastic; followed by detailed listings of threats studied. This we compared to a previously published expert assessment of threats to soil biodiversity. In addition, we identified…

Background Obesity is a global epidemic in the industrialized and developing world, and many children suffer from obesity-related complications. Gut microbiota dysbiosis might have significant effect on the development of obesity. The microbiota continues to develop through childhood and thus childhood may be the prime time for microbiota interventions to realize health promotion or disease prevention. Therefore, it is crucial to understand the structure and function of pediatric gut microbiota. Methods According to the inclusion criteria and exclusion criteria, twenty-three normal weight and twenty-eight obese children were recruited from Nanjing, China. Genomic DNA was extracted from fecal samples. The V4 region of the bacterial 16S rDNA was amplified by PCR, and sequencing was applied to analyze the gut microbiota diversity and composition using the Illumina HiSeq 2500 platform. Results The number of operational taxonomic units (OTUs) showed a decrease in the diversity of gut microbiota with increasing body weight. The alpha diversity indices showed that the normal weight group…

MOTIVATION: Antimicrobial peptides (AMPs) have the potential to tackle multidrug-resistant pathogens in both clinical and non-clinical contexts. The recent growth in the availability of genomes and metagenomes provides an opportunity for in silico prediction of novel AMP molecules. However, due to the small size of these peptides, standard gene prospection methods cannot be applied in this domain and alternative approaches are necessary. In particular, standard gene prediction methods have low precision for short peptides, and functional classification by homology results in low recall. RESULTS: Here, we present Macrel (for metagenomic AMP classification and retrieval), which is an end-to-end pipeline for the prospection of high-quality AMP candidates from (meta)genomes. For this, we introduce a novel set of 22 peptide features. These were used to build classifiers which perform similarly to the state-of-the-art in the prediction of both antimicrobial and hemolytic activity of peptides, but with enhanced precision (using standard benchmarks as well as a stricter testing regime). We…

Background Especially on commodities crops like soybean, maize, cotton, coffee and others, high yields are reached mainly by the intensive use of pesticides and fertilizers. The biological management of crops is a relatively recent concept, and its application has increased expectations about a more sustainable agriculture. The use of fungi as plant bioinoculants has proven to be a useful alternative in this process, and research is deepening on genera and species with some already known potential. In this context, the present study focused on the analysis of the plant growth promotion potential of Purpureocillium lilacinum , Purpureocillium lavendulum and Metarhizium marquandii aiming its use as bioinoculants in maize, bean and soybean. Methods Purpureocillium spp. and M. marquandii strains were isolated from soil samples. They were screened for their ability to solubilize phosphorus (P) and produce indoleacetic acid (IAA) and the most promising strains were tested at greenhouse in maize, bean and soybean plants. Growth promotion parameters including plant height, dry mass and…

There is evidence that COVID-19, the disease caused by the betacoronavirus SARS-CoV-2, is sensitive to environmental conditions. However, such conditions often correlate with demographic and socioeconomic factors at larger spatial extents, which could confound this inference. We evaluated the effect of meteorological conditions (temperature, solar radiation, air humidity and precipitation) on 292 daily records of cumulative number of confirmed COVID-19 cases across the 27 Brazilian capital cities during the 1st month of the outbreak, while controlling for an indicator of the number of tests, the number of arriving flights, population density, proportion of elderly people and average income. Apart from increasing with time, the number of confirmed cases was mainly related to the number of arriving flights and population density, increasing with both factors. However, after accounting for these effects, the disease was shown to be temperature sensitive: there were more cases in colder cities and days, and cases accumulated faster at lower temperatures. Our best estimate indicates that…

Abstract Polyethylene (PE) plastic mulch films are used globally in crop production but incur considerable disposal and environmental pollution issues. Biodegradable plastic mulch films (BDMs), an alternative to PE-based films, are designed to be tilled into the soil where they are expected to be mineralized to carbon dioxide, water and microbial biomass. However inadequate research regarding the impacts of repeated incorporation of BDMs on soil microbial communities has partly contributed to limited adoption of BDMs. In this study, we evaluated the effects of BDM incorporation on soil microbial community structure and function over two years in two geographical locations: Knoxville, TN, and in Mount Vernon, WA. Treatments included four plastic BDMs, a completely biodegradable cellulose mulch, a non-biodegradable PE mulch and a no mulch plot. Bacterial community structure determined using 16S rRNA amplicon sequencing revealed significant differences by location and season. Differences in bacterial communities by mulch treatment were not significant for any season in either location,…

BACKGROUND: Acquisition of procedures is an important element in health professions education. Traditionally procedures are taught using a "see one - do one" approach. That is a teacher demonstrates and describes a procedure and afterwards the students practice the procedure. A more recent teaching approach for the acquisition of procedural skills was presented by Walker and Peyton. Peyton's teaching approach is a stepwise teaching approach and consists of the following four steps: demonstration, deconstruction, comprehension and performance. The aims of this study were (i) to systematically evaluate the effectiveness of Peyton's 4-step teaching approach on the acquisition of procedural skills in health professions education and (ii) to evaluate whether studies with fewer students per teacher showed a larger between group difference than studies with more students per teacher. METHODS: We searched in Medline, PsycInfo, Embase and ERIC for eligible studies. Records were screened by two independent reviewers. A random effects meta-analysis was performed to evaluate skill acquisition…

Background The co-inoculation of soybean with Bradyrhizobium and other plant growth-promoting rhizobacteria (PGPR) is considered a promising technology. However, there has been little quantitative analysis of the effects of this technique on yield variables. In this context, the present study aiming to provide a quantification of the effects of the co-inoculation of Bradyrhizobium and PGPR on the soybean crop using a meta-analysis approach. Methods A total of 42 published articles were examined, all of which considered the effects of co-inoculation of PGPR and Bradyrhizobium on the number of nodules, nodule biomass, root biomass, shoot biomass, shoot nitrogen content, and grain yield of soybean. We also determined whether the genus of the PGPR used as co-inoculant, as well as the experimental conditions, altered the effect size of the PGPR. Results The co-inoculation technology resulted in a significant increase in nodule number (11.40%), nodule biomass (6.47%), root biomass (12.84%), and shoot biomass (6.53%). Despite these positive results, no significant increase was observed in…

Some studies on the hyperuricemia (HUA) have focused on intestinal bacteria. To better understand the correlation between gut microbiota and HUA, we established a HUA rat model with high-purine diet, and used 16S rRNA genes sequencing to analyze gut microbiota changes in HUA rats. To analyze the potential role played by gut microbiota in HUA, we altered the gut microbiota of HUA rats with antibiotics, and compared the degree of uric acid elevation between HUA and antibiotic-fed HUA rats (Ab+HUA). Finally, we established a recipient rat model, in which we transplanted fecal microbiota of HUA and normal rats into recipient rats. Three weeks later, we compared the uric acid content of recipient rats. As a result, the diversity and abundance of the gut microbiota had changed in HUA rats. The Ab-fed HUA rats had significantly lower uric acid content compared to the HUA rats, and gut microbiota from HUA rats increased uric acid content of recipient rats. The genera Vallitalea , Christensenella and Insolitispirillum may associate with HUA. Our findings highlight the association between gut…

Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki's utility for exploring biological and ecological trends in sequencing data was demonstrated through a…

Abstract Since 2014, Stony Coral Tissue Loss Disease (SCTLD) has led to mass mortality of the majority of hard coral species on the Florida Reef Tract. Following the successful treatment of SCTLD lesions on corals in closed aquaria using water dosed with antibiotics, two pastes were developed as vehicles for direct antibiotic treatments on wild corals. These pastes were tested as placebos and with additions of amoxicillin via topical applications over active SCTLD margins on multiple coral species. The effectiveness of the pastes without antibiotics (placebo treatments) was less than 10%. Adding amoxicillin to both pastes increased effectiveness. For one of the two pastes, which was silicone based with a time-release mechanism for the antibiotics, effectiveness in halting disease lesions reached 86% when amoxicillin was added. Topical antibiotic application is a viable tool for the preservation of priority corals affected by SCTLD.

Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana , Populus trichocarpa , and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous…

Monkeypox (MPX) is a zoonotic disease similar to smallpox. Its fatality rate is about 11% and it is endemic to the Central and West African countries. In this paper, we analyze a compartmental model of MPX dynamics. Our goal is to see whether MPX can be controlled and eradicated by voluntary vaccinations. We show that there are three equilibria-disease free, fully endemic and previously neglected semi-endemic (with disease existing only among humans). The existence of semi-endemic equilibrium has severe implications should the MPX virus mutate to increased viral fitness in humans. We find that MPX is controllable and can be eradicated in a semi-endemic equilibrium by vaccination. However, in a fully endemic equilibrium, MPX cannot be eradicated by vaccination alone.

Background Various perceptions and practices have been associated with the COVID-19 pandemic. In this study, we assessed the perception and practices regarding COVID-19 among residents in selected urban communities of Ibadan, Oyo State, Nigeria. Methods A descriptive cross-sectional study design using a multi-stage sampling technique was used to recruit 360 respondents (Mean age: 33.2 ± 10.6 years; 62.5% females) from households in Ibadan. Data were collected using an interviewer-administered questionnaire from 3rd to 6th June 2020. Those who demonstrated washing of the palm, back of the hand, spaces between the fingers, fingernails, wrist, and thumbs had six points and were categorized to have had a good practice of handwashing. Descriptive statistics were conducted. Bivariate analyses of sociodemographic characteristics and good handwashing practices were conducted using Chi-square test. Logistic regression was conducted to identify the determinants of good handwashing practices. P -values < 0.05 were statistically significant. Results Going to the hospital (95%) and calling the…

Chlorophyll fluorescence (ChlF) has been used to understand photosynthesis and its response to climate change, particularly with satellite-based data. However, it remains unclear how the ChlF ratio and photosynthesis are linked at the leaf level under drought stress. Here, we examined the link between ChlF ratio and photosynthesis at the leaf level by measuring photosynthetic traits, such as net CO 2 assimilation rate (A n ), the maximum carboxylation rate of Rubisco (V cmax ), the maximum rate of electron transport (J max ), stomatal conductance (g s ) and total chlorophyll content (Chl t ). The ChlF ratio of the leaf level such as maximum quantum efficiency of PSII (F v /F m ) is based on fluorescence kinetics. ChlF intensity ratio (LD 685 /LD 740 ) based on spectrum analysis was obtained. We found that a combination of the stomatal limitation, non-stomatal limitation, and Chl t regulated leaf photosynthesis under drought stress, while J max and Chl t governed the ChlF ratio. A significant link between the ChlF ratio and A n was found under drought stress while no significant…

The germination of cotton ( Gossypium hirsutum L.) seeds is affected by drought stress; however, little is known about the physiological mechanism affecting germination and the effect of melatonin (MT) on cotton seed germination under drought stress. Therefore, we studied the effects of exogenous MT on the antioxidant capacity and epidermal microstructure of cotton under drought stress. The results demonstrated a retarded water absorption capacity of testa under drought stress, significantly inhibiting germination and growth in cotton seeds. Drought stress led to the accumulation of reactive oxygen species (ROS), malondialdehyde (MDA), and osmoregulatory substances (e.g., proline, soluble protein, and soluble sugars); it also decreased the activity of antioxidant enzymes and α-amylase. Drought stress inhibited gibberellin acid (GA 3 ) synthesis and increased abscisic acid (ABA) content, seriously affecting seed germination. However, seeds pre-soaked with MT (100 µM) showed a positive regulation in the number and opening of stomata in cotton testa. The exogenous application of MT…

In mid-December 2019, a novel atypical pneumonia broke out in Wuhan, Hubei Province, China and was caused by a newly identified coronavirus, initially termed 2019 Novel Coronavirus and subsequently severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of 19 May 2020, a total of 4,731,458 individuals were reported as infected with SARS-CoV-2 among 213 countries, areas or territories with recorded cases, and the overall case-fatality rate was 6.6% (316,169 deaths among 4,731,458 recorded cases), according to the World Health Organization. Studies have shown that SARS-CoV-2 is notably similar to (severe acute respiratory syndrome coronavirus) SARS-CoV that emerged in 2002-2003 and Middle East respiratory syndrome coronavirus (MERS-CoV) that spread during 2012, and these viruses all contributed to global pandemics. The ability of SARS-CoV-2 to rapidly spread a pneumonia-like disease from Hubei Province, China, throughout the world has provoked widespread concern. The main symptoms of coronavirus disease 2019 (COVID-19) include fever, cough, myalgia, fatigue and lower…

BACKGROUND: This study aimed to develop a deep-learning model and a risk-score system using clinical variables to predict intensive care unit (ICU) admission and in-hospital mortality in COVID-19 patients. METHODS: This retrospective study consisted of 5,766 persons-under-investigation for COVID-19 between 7 February 2020 and 4 May 2020. Demographics, chronic comorbidities, vital signs, symptoms and laboratory tests at admission were collected. A deep neural network model and a risk-score system were constructed to predict ICU admission and in-hospital mortality. Prediction performance used the receiver operating characteristic area under the curve (AUC). RESULTS: The top ICU predictors were procalcitonin, lactate dehydrogenase, C-reactive protein, ferritin and oxygen saturation. The top mortality predictors were age, lactate dehydrogenase, procalcitonin, cardiac troponin, C-reactive protein and oxygen saturation. Age and troponin were unique top predictors for mortality but not ICU admission. The deep-learning model predicted ICU admission and mortality with an AUC of 0.780 (95% CI…

BACKGROUND: Concerns have been raised about whether self-report measures of pain catastrophizing reflect the construct as defined in the cognitive-behavioral literature. We investigated the content of these self-report measures; that is, whether items assess the construct 'pain catastrophizing' and not other theoretical constructs (i.e., related constructs or pain outcomes) using the discriminant content validity method. METHOD: = 34) from questionnaires measuring pain-related worrying, vigilance, pain severity, distress, and disability. Via an online survey, 94 participants rated to what extent each item was relevant for assessing pain catastrophizing, defined as "to view or present pain or pain-related problems as considerably worse than they actually are" and other relevant constructs (pain-related worrying, vigilance, pain severity, distress, and disability). RESULTS: Data were analyzed using Bayesian hierarchical models. The results revealed that the items from pain-related worrying, vigilance, pain severity, distress, and disability questionnaires were distinctively related to…

The implementation of policies promoting the adoption of an open science (OS) culture must be accompanied by indicators that allow monitoring the uptake of such policies and their potential effects on research publishing and sharing practices. This study presents indicators of open access (OA) at the institutional level for universities worldwide. By combining data from Web of Science, Unpaywall and the Leiden Ranking disambiguation of institutions, we track OA coverage of universities' output for 963 institutions. This paper presents the methodological challenges, conceptual discrepancies and limitations and discusses further steps needed to move forward the discussion on fostering OA and OS practices and policies.

BACKGROUND: The recent pandemic of CoVID-19 has emerged as a threat to global health security. There are very few prognostic models on CoVID-19 using machine learning. OBJECTIVES: To predict mortality among confirmed CoVID-19 patients in South Korea using machine learning and deploy the best performing algorithm as an open-source online prediction tool for decision-making. MATERIALS AND METHODS: = 3,524) between January 20, 2020 and May 30, 2020 was predicted using five machine learning algorithms (logistic regression, support vector machine, K nearest neighbor, random forest and gradient boosting). The performance of the algorithms was compared, and the best performing algorithm was deployed as an online prediction tool. RESULTS: The logistic regression algorithm was the best performer in terms of discrimination (area under ROC curve = 0.830), calibration (Matthews Correlation Coefficient = 0.433; Brier Score = 0.036) and. The best performing algorithm (logistic regression) was deployed as the online CoVID-19 Community Mortality Risk Prediction tool named CoCoMoRP…

Currently, ~65% of extant primate species (ca 512 species) distributed in 91 countries in the Neotropics, mainland Africa, Madagascar, South Asia and Southeast Asia are threatened with extinction and 75% have declining populations as a result of deforestation and habitat loss resulting from increasing global market demands, and land conversion for industrial agriculture, cattle production and natural resource extraction. Other pressures that negatively impact primates are unsustainable bushmeat hunting, the illegal trade of primates as pets and as body parts, expanding road networks in previously isolated areas, zoonotic disease transmission and climate change. Here we examine current and future trends in several socio-economic factors directly or indirectly affecting primates to further our understanding of the interdependent relationship between human well-being, sustainable development, and primate population persistence. We found that between 2001 and 2018 ca 191 Mha of tropical forest (30% canopy cover) were lost as a result of human activities in the five primate range…

BACKGROUND: The novel coronavirus disease (COVID-19) is a new viral respiratory illness, first identified in Wuhan province, China. Dental professionals and dental students are at an increased risk for these viruses from dental patients, as dental practice involves face-to-face communication with the patients and frequent exposure to saliva, blood, and other body fluids. Dental education can play an important role in the training of dental students, adequate knowledge and adopting attitudes regarding infection control measures. The aim of this study was to evaluate knowledge, attitudes, and clinical education of dental students about COVID-19 pandemic. METHODS: A total of 355 pre-clinical and clinical dental students (242 and 113, respectively, comprising 190 females and 165 males) at Fırat University Dentistry Faculty, in Elazığ, Turkey answered an online questionnaire about the biosafety procedures for and their attitudes to and knowledge of COVID-19. The study was conducted in March 2020, Turkey. The data gained were analyzed using descriptive statistical methods and chi-square…

Abstract As the world economies get out of the lockdown imposed by the COVID-19 pandemic, there is an urgent need to assess the suitability of known technologies to mitigate COVID-19 transmission in confined spaces such as buildings. This feasibility study looks at the method of upper-room ultraviolet (UV) air disinfection that has already proven its efficacy in preventing the transmission of airborne diseases such as measles and tuberculosis. Using published data from various sources it is shown that the SARS-CoV-2 virus, which causes COVID-19, is highly likely to be susceptible to UV damage while suspended in air irradiated by UV-C at levels that are acceptable and safe for upper-room applications. This is while humans are present in the room. Both the expected and worst-case scenarios are investigated to show the efficacy of the upper-room UV-C approach to reduce COVID-19 air transmission in a confined space with moderate but sufficient height. Discussion is given on the methods of analysis and the differences between virus susceptibility to UV-C when aerosolised or in liquid or…

Host miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses through several possible mechanisms including direct binding of viral RNA. Identification of human miRNAs involved in coronavirus-host interplay becomes important due to the ongoing COVID-19 pandemic. In this article we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. As a result, we identified six miRNAs (miR-21-3p, miR-195-5p, miR-16-5p, miR-3065-5p, miR-424-5p and miR-421) with high binding probability across all analyzed viruses. Further bioinformatic analysis of binding sites revealed high conservativity of miRNA binding regions within RNAs of human coronaviruses and their strains. In order to discover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse…

Abstract The pandemic state of COVID-19 caused by the SARS CoV-2 put the world in quarantine, led to hundreds of thousands of deaths and is causing an unprecedented economic crisis. However, COVID-19 is spreading in different rates at different countries. Here, we tested the effect of three classes of predictors, i.e., socioeconomic, climatic and transport, on the rate of daily increase of COVID-19. We found that global connections, represented by countries’ importance in the global air transportation network, is the main explanation for the growth rate of COVID-19 in different countries. Climate, geographic distance and socioeconomics had a milder effect in this big picture analysis. Geographic distance and climate were significant barriers in the past but were surpassed by the human engine that allowed us to colonize most of our planet land surface. Our results indicate that the current claims that the growth rate of COVID-19 may be lower in warmer and humid tropical countries should be taken very carefully, at risk to disturb well-established and effective policy of social…

Background Previous work has validated consumer-grade electroencephalography (EEG) systems for use in research. Systems in this class are cost-effective and easy to set up and can facilitate neuroscience outside of the laboratory. The aim of the current study was to determine if a new consumer-grade system, the Emotiv EPOC Saline Flex, was capable of capturing research-quality data. Method The Emotiv system was used simultaneously with a research-grade EEG system, Neuroscan Synamps2, to collect EEG data across 16 channels during five well-established paradigms: (1) a mismatch negativity (MMN) paradigm that involved a passive listening task in which rare deviant (1,500 Hz) tones were interspersed amongst frequent standard tones (1,000 Hz), with instructions to ignore the tones while watching a silent movie; (2) a P300 paradigm that involved an active listening task in which participants were asked to count rare deviant tones presented amongst frequent standard tones; (3) an N170 paradigm in which participants were shown images of faces and watches and asked to indicate whether the…

Kenaf (Hibiscus cannabinus L.) is a fibrous crop, grown in tropical climate having huge biomass and can be a good candidate for the phytoremediation of different heavy metals. Consequently, the present study was conducted to explore morpho-physiological traits, photosynthetic pigments, gaseous exchange attributes, antioxidative response and phytoextraction of copper (Cu) in H. cannabinus grown under different levels of Cu i.e. 0 (control), 60, 120 and 180 µmol L−1 in Hoagland nutrient solution (pH 6.2). The results from the present study revealed that Cu toxicity reduced plant height, plant diameter, plant fresh weight, plant dry weight, photosynthetic pigments and gaseous exchange attributes compared to control. Moreover, excess Cu in the nutrient solution ameliorates contents of malondialdehyde (MDA), hydrogen peroxide (H2O2) and electrolyte leakage (EL) which showed that Cu induced oxidative damage in the roots and leaves of H. cannabinus. The oxidative stress which was induced by a high concentration of Cu in the nutrient solution is overcome by enzymatic activities of…

The excessive use of synthetic nitrogen (N) fertilizers in rice ( Oryza sativa L.) has resulted in high N loss, soil degradation, and environmental pollution in a changing climate. Soil biochar amendment is proposed as a climate change mitigation tool that supports carbon sequestration and reduces N losses and greenhouse gas (GHG) emissions from the soil. The current study evaluated the impact of four different rates of biochar (B) (C/B 0 -0 t ha −1 , B 1 -20 t ha −1 , B 2 -40 t ha −1 , and B 3 -60 t ha −1 ) and two N levels (N 1 ; low (270 kg N ha −1 ) and N 2 ; high (360 kg N ha −1 )), on rice (cultivar Zhenguiai) grown in pots. Significant increases in the average soil microbial biomass N (SMBN) (88%) and carbon (87%) were recorded at the highest rate of 60-ton ha −1 B and 360 kg N ha −1 compared to the control (N 1 C) during both seasons (S1 and S2). The photochemical efficiency (Fv/Fm), quantum yield of the photosystem (PS) II (ΦPS II), electron transport rate (ETR), and photochemical quenching ( qP ) were enhanced at low rates of biochar applications (20 to 40 t B ha −1 ) for…

This paper presents the performance of two eukaryotic genomic ribosomal regions, ITS1 and ITS2, in describing fungal diversity in aerosol samples using amplicon-based High-Throughput Sequencing (HTS). Composting sites, biomethanization facilities, and dairy farms, all affected by the presence of fungi, were visited to collect air samples. The amplicon-based HTS approach is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of amplification. For this reason, the authors of this paper used a shotgun metagenomic approach to compare its outcome with the amplicon-based method. Indeed, shotgun metagenomic does not rely on any amplification prior to sequencing, because all genes are sequenced without a specific target. In addition, culture methods were added to the analyses in biomethanization and dairy farms samples to validate their contribution to fungal diversity of aerosols. The results obtained are unequivocal towards ITS1 outperformance to ITS2 in terms of…

Biological systems, at all scales of organisation from nucleic acids to ecosystems, are inherently complex and variable. Biologists therefore use statistical analyses to detect signal among this systemic noise. Statistical models infer trends, find functional relationships and detect differences that exist among groups or are caused by experimental manipulations. They also use statistical relationships to help predict uncertain futures. All branches of the biological sciences now embrace the possibilities of mixed-effects modelling and its flexible toolkit for partitioning noise and signal. The mixed-effects model is not, however, a panacea for poor experimental design, and should be used with caution when inferring or deducing the importance of both fixed and random effects. Here we describe a selection of the perils and pitfalls that are widespread in the biological literature, but can be avoided by careful reflection, modelling and model-checking. We focus on situations where incautious modelling risks exposure to these pitfalls and the drawing of incorrect conclusions. Our…

Abstract The Rio Doce estuary in Brazil was impacted by the deposition of mine tailings caused by the collapse of a mining dam in 2015. Since the disaster, the estuary is experiencing chronic trace metal contamination effects, but potential trace metal accumulation in fishes has not been reported. Trace metals in aquatic ecosystems pose severe threats to the aquatic biota, so we hypothesized that the accumulation of trace metals in estuarine sediments nearly two years after the disaster would cause contaminant bioaccumulation, resulting in the biosynthesis of metal-responsive proteins in fishes. We determined trace metal concentrations in sediment samples, metal concentrations, and quantified stress protein concentrations in the liver and muscle tissue of five different fish species in the estuary. Our results revealed high concentrations of trace metals in estuarine sediments when compared to published baseline values for this estuary. The demersal fish species Cathorops spixii and Genidens genidens had the highest Hg, As, Se, Cr, and Mn concentrations in both hepatic and muscle…

The flow state is defined by intense involvement in an activity with high degrees of concentration and focused attention accompanied by a sense of pleasure. Video games are effective tools for inducing flow, and keeping players in this state is considered to be one of the central goals of game design. Many studies have focused on the underlying physiological and neural mechanisms of flow. Results are inconsistent when describing a unified mechanism underlying this mental state. This paper provides a comprehensive review of the physiological and neural correlates of flow and explains the relationship between the reported physiological and neural markers of the flow experience. Despite the heterogeneous results, it seems possible to establish associations between reported markers and the cognitive and experiential aspects of flow, particularly regarding arousal, attention control, reward processing, automaticity, and self-referential processing.

Background Pancreatic adenocarcinoma (PAAD) is among the most lethal diseases and has a dismal prognosis; however, efficient treatment is currently limited. Several studies have observed epigenetic variation during tumorigenesis, suggesting the potential role of RNA methylation, especially N6-methyladenosine (m6A) modification, as a novel epigenetic modification mediating PAAD prognosis. Methods The expression levels of m6A-related genes were downloaded from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA) and Genotype-Tissue Expression (GTEx) projects, and the findings were validated in four Expression Omnibus (GEO) datasets. A predictive model was constructed using a lasso regression and evaluated by a survival analysis and receiver operating characteristic curve. Consensus clustering identified two distinct subgroups with different immune activity signatures based on the expression pattern of m6A-related genes. The relationship between the mutation state of m6A-related genes and infiltration of immune cells was established and visualized using Tumor Immune Estimation…

Amidst recent industrialization in South Korea, Seoul has experienced high levels of air pollution, an issue that is magnified due to a lack of effective air pollution prediction techniques. In this study, the Prophet forecasting model (PFM) was used to predict both short-term and long-term air pollution in Seoul. The air pollutants forecasted in this study were PM 2.5 , PM 10 , O 3 , NO 2 , SO 2 , and CO, air pollutants responsible for numerous health conditions upon long-term exposure. Current chemical models to predict air pollution require complex source lists making them difficult to use. Machine learning models have also been implemented however their requirement of meteorological parameters render the models ineffective as additional models and infrastructure need to be in place to model meteorology. To address this, a model needs to be created that can accurately predict pollution based on time. A dataset containing three years worth of hourly air quality measurements in Seoul was sourced from the Seoul Open Data Plaza. To optimize the model, PFM has the following…

Background Botrytis cinerea causes serious gray mold disease in many plants. This pathogen has developed resistance to many fungicides. Thus, it has become necessary to look for new safe yet effective compounds against B. cinerea . Methods Essential oils (EOs) from 17 plant species were assayed against B. cinerea , of which Origanum vulgare essential oil (OVEO) showed strong antifungal activity, and accordingly its main components were detected by GC/MS. Further study was conducted on the effects of OVEO, carvacrol and thymol in vitro on mycelium growth and spore germination, mycelium morphology, leakages of cytoplasmic contents, mitochondrial injury and accumulation of reactive oxygen species (ROS) of B. cinerea . The control efficacies of OVEO, carvacrol and thymol on tomato gray mold were evaluated in vivo. Results Of all the 17 plant EOs tested, Cinnamomum cassia , Litsea cubeba var. formosana and O. vulgare EOs had the best inhibitory effect on B. cinerea , with 0.5 mg/mL completely inhibiting the mycelium growth of B. cinerea . Twenty-one different compounds of OVEO were…

Background Metagenome next-generation sequencing (mNGS) is a valuable diagnostic tool that can be used for the identification of early pathogens of acute respiratory distress syndrome (ARDS) in severe pneumonia. Little is known about the use of this technology in clinical application and the evaluation of the prognostic value of ARDS. Methods We performed a retrospective cohort study of patients with ARDS caused by severe pneumonia. Samples were collected from patients in the intensive care unit (ICU) of Jiangmen Central Hospital from January 2018 to August 2019. The no-next generation sequencing (NGS) group was composed of patients given conventional microbiological tests to examine sputum, blood, or bronchoalveolar lavage fluid. The NGS group was composed of patients tested using mNGS and conventional microbiological tests. We evaluated the etiological diagnostic effect and clinical prognostic value of mNGS in patients with ARDS caused by severe pneumonia. Results The overall positive rate (91.1%) detected by the mNGS method was significantly higher than that of the culture method…

Background During the growth of complex multicellular organisms, chronological age, size and morphology change together in a hierarchical and coordinated pattern. Among extinct species, the growth of Tyrannosaurus rex has received repeated attention through quantitative analyses of relative maturity and chronological age. Its growth series shows an extreme transformation from shallow skulls in juveniles to deep skulls in adults along with a reduction in tooth count, and its growth curve shows that T. rex had a high growth rate in contrast to its closest relatives. However, separately, these sets of data provide an incomplete picture of the congruence between age, size, and relative maturity in this exemplar species. The goal of this work is to analyze these data sets together using cladistic analysis to produce a single hypothesis of growth that includes all of the relevant data. Methods The three axes of growth were analyzed together using cladistic analysis, based on a data set of 1,850 morphological characters and 44 specimens. The analysis was run in TNT v.1.5 under a New…

Background Inappropriate disposal of the plastic mulching debris could create macroplastics (MaPs) and microplastics (MiPs) pollution in agricultural soil. Methods To study the effects of farming systems on accumulation and distribution of agricultural plastic debris, research was carried out on two farming systems in Northwest China. Farming in Wutong Village (S1) is characterized by small plots and low-intensity machine tillage while farming in Shihezi (S2) is characterized by large plots and high-intensity machine tillage. In September 2017, we selected six fields in S1, three fields with 6–8 years of continuous plastic mulching (CM) as well as three fields with over 30 years of intermittent mulching (IM). In S2, we selected five cotton fields with 6, 7, 8, 15 and 18 years of continuous mulching. In both regions, MaPs and MiPs from soil surface to 30 cm depth (0–30 cm) were sampled. Results The results showed that in S1, MaPs mass in fields with 6–8 years CM (i.e., 97.4kg·ha −1 ) were significantly higher than in fields with 30 years IM (i.e., 53.7 kg·ha −1 ). MaPs in size…

A variety of practices have recently emerged which relate to both video games and gambling. These range from opening loot boxes, to esports betting, real-money video gaming, token wagering, and social casino spending. It is unknown either how harmful or how widespread many of these activities are. A sample of 1,081 adults from the UK aged 18+ was therefore recruited. This sample was purposively recruited via quota sampling to represent the UK population in terms of sex, age, and ethnicity. Engagement in all forms of gaming-related practices were significantly associated with both problem gambling and disordered gaming. A total of 18.5% of the sample had engaged in these activities at least once in the new year. These results suggest a convergent ecosystem of practices that relate to both video games and gambling. Engagement in each of these activities is linked to problem gambling. However, it remains unclear whether engagement in these activities causes problem gambling.

BACKGROUND: Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated water systems. The Bayesian SourceTracker approach uses deep-sequencing marker gene libraries (16S ribosomal RNA) to determine the proportional contributions of bacteria from many potential source environments to a given sink environment simultaneously. Since its development, SourceTracker has been applied to an extensive diversity of studies, from beach contamination to human behavior. METHODS: Here, we demonstrate a novel application of SourceTracker to work with metagenomic datasets and tested this approach using sink samples from a study of coastal marine environments. Source environment metagenomes were obtained from metagenomics studies of gut, freshwater, marine, sand and soil environments. As part of this effort, we implemented features for determining the stability of source proportion estimates, including precision visualizations for performance optimization, and performed domain-specific source-tracking analyses…

Background WRKY proteins play a vital role in the plants response to different stresses, growth and development. Studies of WRKY proteins have been mainly focused on model plant Arabidopsis and a few other vegetable plants. However, the systematical study of eggplant WRKY transcription factor superfamily is scarce. Methods Bioinformatics has been used to identify and characterize the eggplant WRKY gene family. For the exploration of the differentially expressed WRKY genes, two cultivars with different cold-tolerance were used. Finally, we performed a virus-induced gene silencing (VIGS) experiment to verify the functions of SmWRKY26 and SmWRKY32. Results Fifty eight (58) genes encoding eggplant WRKY proteins were identified through searching the eggplant genome. Eggplant WRKY proteins could be classified into three groups or seven subgroups in accordance with other plants. WRKY variants were identified from the eggplant. Gene structure analysis showed that the number of intron in eggplant WRKY family was from 0 to 11, with an average of 4.4. Conserved motif analysis suggested that…

BACKGROUND: Infectious diseases are a significant threat in both healthcare and community settings. Healthcare associated infections (HCAIs) in particular are a leading cause of complications during hospitalisation. Contamination of the healthcare environment is recognised as a source of infectious disease yet the significance of porous surfaces including healthcare textiles as fomites is not well understood. It is currently assumed there is little infection risk from textiles due to a lack of direct epidemiological evidence. Decontamination of healthcare textiles is achieved with heat and/or detergents by commercial or in-house laundering with the exception of healthcare worker uniforms which are laundered domestically in some countries. The emergence of the COVID-19 pandemic has increased the need for rigorous infection control including effective decontamination of potential fomites in the healthcare environment. This article aims to review the evidence for the role of textiles in the transmission of infection, outline current procedures for laundering healthcare textiles and…

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), has been declared a global pandemic by the World Health Organization. With no standard of care for the treatment of COVID-19, there is an urgent need to identify therapies that may be effective in treatment. Recent evidence has implicated the development of cytokine release syndrome as the major cause of fatality in COVID-19 patients, with elevated levels of interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) observed in patients. Galectin-3 (Gal-3) is an animal lectin that has been implicated in the disease process of a variety of inflammatory conditions. Inhibitors of the small molecule Gal-3 have been shown to reduce the levels of both IL-6 and TNF-α in vitro and have shown anti-inflammatory effects in vivo. Additionally, a key domain in the spike protein of β-coronaviridae, a genus which includes SARS-CoV2, is nearly identical in morphology to human Gal-3. These spike proteins are critical for the virus' entry into host cells. Here we…

Ecological data often violate common assumptions of traditional parametric statistics (e.g., that residuals are Normally distributed, have constant variance, and cases are independent). Modern statistical methods are well equipped to handle these complications, but they can be challenging for non-statisticians to understand and implement. Rather than default to increasingly complex statistical methods, resampling-based methods can sometimes provide an alternative method for performing statistical inference, while also facilitating a deeper understanding of foundational concepts in frequentist statistics (e.g., sampling distributions, confidence intervals, p -values). Using simple examples and case studies, we demonstrate how resampling-based methods can help elucidate core statistical concepts and provide alternative methods for tackling challenging problems across a broad range of ecological applications.

Teleosauroidea was a clade of ancient crocodylomorphs that were a key element of coastal marine environments during the Jurassic. Despite a 300-year research history and a recent renaissance in the study of their morphology and taxonomy, macroevolutionary studies of teleosauroids are currently limited by our poor understanding of their phylogenetic interrelationships. One major problem is the genus Steneosaurus , a wastebasket taxon recovered as paraphyletic or polyphyletic in phylogenetic analyses. We constructed a newly updated phylogenetic data matrix containing 153 taxa (27 teleosauroids, eight of which were newly added) and 502 characters, which we analysed under maximum parsimony using TNT 1.5 (weighted and unweighted analyses) and Bayesian inference using MrBayes v3.2.6 (standard, gamma and variation). The resulting topologies were then analysed to generate comprehensive higher-level phylogenetic hypotheses of teleosauroids and shed light on species-level interrelationships within the clade. The results from our parsimony and Bayesian analyses are largely consistent. Two…

COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral genome over time as it spread across the world. An important question that still needs to be answered is whether any of the common mutations affect the viral properties, and therefore the disease characteristics. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C>T mutation, on mutation rate and viral spread. By focusing on mutations in the slowly evolving M or E genes, we aimed to minimize the effects of selective pressure. Our results indicate that 14408C>T mutation increases the mutation rate, while the third-most common RdRp mutation, 15324C>T, has the opposite effect. It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere.

High external nitrogen (N) inputs can maximize maize yield but can cause a subsequent reduction in N use efficiency (NUE). Thus, it is necessary to identify the minimum effective N fertilizer input that does not affect maize grain yield (GY) and to investigate the photosynthetic and root system consequences of this optimal dose. We conducted a 4-year field experiment from 2014 to 2017 with four N application rates: 300 (N 300 ), 225 (N 225 ), 150 (N 150 ), and 0 Kg ha −1 (N 0 ) in the Northwest of China. GY was assessed by measuring the photosynthetic capacity and root system (root volume, surface area, length density and distribution). Grain yield decreased by −3%, 7.7%, and 21.9% when the N application rates decreased by 25%, 50%, and 100% from 300 Kg ha −1 . We found that yield reduction driven by N reduction was primarily due to decreased radiation use efficiency (RUE) and WUE instead of intercepted photosynthetically active radiation and evapotranspiration. In the N 225 treatment, GY, WUE, and RUE were not significantly reduced, or in some cases, were greater than those of the…

Background Osteoarthritis (OA) is the most common chronic degenerative joint disease and is mainly characterized by cartilage degeneration, subcartilage bone hyperplasia, osteophyte formation and joint space stenosis. Recent studies showed that synovitis might also be an important pathological change of OA. However, the molecular mechanisms of synovitis in OA are still not well understood. Objective This study was designed to identify key biomarkers and immune infiltration in the synovial tissue of osteoarthritis by bioinformatics analysis. Materials and Methods The gene expression profiles of GSE12021 , GSE55235 and GSE55457 were downloaded from the GEO database. The differentially expressed genes (DEGs) were identified by the LIMMA package in Bioconductor, and functional enrichment analyses were performed. A protein-protein interaction network (PPI) was constructed, and module analysis was performed using STRING and Cytoscape. The CIBERSORT algorithm was used to analyze the immune infiltration of synovial tissue between OA and normal controls. Results A total of 106 differentially…

Melatonin is a small-molecule indole hormone that plays an important role in participating in biotic and abiotic stress resistance. Melatonin has been confirmed to promote the normal development of plants under adversity stress by mediating physiological regulation mechanisms. However, the mechanisms by which exogenous melatonin mediates salt tolerance via regulation of antioxidant activity and osmosis in cotton seedlings remain largely unknown. In this study, the regulatory effects of melatonin on reactive oxygen species (ROS), the antioxidant system, and osmotic modulators of cotton seedlings were determined under 0–500 µM melatonin treatments with salt stress induced by 150 mM NaCl treatment. Cotton seedlings under salt stress exhibited an inhibition of growth, excessive hydrogen peroxide (H 2 O 2 ), superoxide anion (O 2 − ), and malondialdehyde (MDA) accumulations in leaves, increased activity levels of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), and elevated ascorbic acid (AsA) and glutathione (GSH) content in leaves. However,…

The 'big data' revolution has enabled novel types of analyses in the life sciences, facilitated by public sharing and reuse of datasets. Here, we review the prodigious potential of reusing publicly available datasets and the associated challenges, limitations and risks. Possible solutions to issues and research integrity considerations are also discussed. Due to the prominence, abundance and wide distribution of sequencing data, we focus on the reuse of publicly available sequence datasets. We define 'successful reuse' as the use of previously published data to enable novel scientific findings. By using selected examples of successful reuse from different disciplines, we illustrate the enormous potential of the practice, while acknowledging the respective limitations and risks. A checklist to determine the reuse value and potential of a particular dataset is also provided. The open discussion of data reuse and the establishment of this practice as a norm has the potential to benefit all stakeholders in the life sciences.

Loss of forest cover, rise in human populations and fragmentation of habitats leads to decline in biodiversity and extinction of large mammals globally. Elephants, being the largest of terrestrial mammals, symbolize global conservation programs and co-occur with humans within multiple-use landscapes of Asia and Africa. Within such shared landscapes, poaching, habitat loss and extent of human–elephant conflicts (HEC) affect survival and conservation of elephants. HEC are severe in South Asia with increasing attacks on humans, crop depredation and property damage. Such incidents reduce societal tolerance towards elephants and increase the risk of retaliation by local communities. We analyzed a 2-year dataset on crop depredation by Asian elephants ( N = 380) events in North Bengal (eastern India). We also explored the effect of landscape, anthropogenic factors (area of forest, agriculture, distance to protected area, area of human settlements, riverine patches and human density) on the spatial occurrence of such incidents.Crop depredation showed a distinct nocturnal pattern…

BACKGROUND: Different phenotypes of macrophages (M0, M1 and M2 Mφs) have been demonstrated to play distinct roles in regulating mesenchymal stem cells in various in vitro and in vivo systems. Our previous study also found that cell-conditioned medium (CM) derived from M1 Mφs supported the proliferation and adipogenic differentiation of bone marrow mesenchymal stem cells (BMMSCs), whereas CM derived from either M0 or M2 Mφs showed an enhanced effect on cell osteogenic differentiation. However, the underlying mechanism remains incompletely elucidated. Exosomes, as key components of Mφ-derived CM, have received increasing attention. Therefore, it is possible that exosomes may modulate the effect of Mφ-derived CM on the property of BMMSCs. This hypothesis was tested in the present study. METHODS: In this study, RAW264.7 cells were induced toward M1 or M2 polarization with different cytokines, and exosomes were isolated from the unpolarized (M0) and polarized (M1 and M2) Mφs. Mouse BMMSCs were then cultured with normal complete medium or inductive medium supplemented with M0-Exos,…

BACKGROUND: Increases in knowledge of climate change generally, and its impact on agricultural industries specifically, have led to a greater research effort aimed at improving understanding of the role of fungi in various fields. Fungi play a key role in soil ecosystems as the primary agent of decomposition, recycling of organic nutrients. Fungi also include important pathogens of plants, insects, bacteria, domestic animals and humans, thus highlighting their importance in many contexts. Temperature directly affects fungal growth and protein dynamics, which ultimately will cascade through to affect crop performance. To study changes in the global protein complement of fungi, proteomic approaches have been used to examine links between temperature stress and fungal proteomic profiles. SURVEY METHODOLOGY AND OBJECTIVES: A traditional rather than a systematic review approach was taken to focus on fungal responses to temperature stress elucidated using proteomic approaches. The effects of temperature stress on fungal metabolic pathways and, in particular, heat shock proteins (HSPs) are…

BACKGROUND: The aims of this systematic review and meta-analyses were to determine if there is a statistically reliable association between poor reading and poor self-concept, and if such an association is moderated by domain of self-concept, type of reading impairment, or contextual factors including age, gender, reading instruction, and school environment. METHODOLOGY: We searched 10 key databases for published and unpublished studies, as well as reference lists of included studies, and studies that cited included studies. We calculated standardised mean differences (SMDs) and 95% confidence intervals for one primary outcome (average self-concept) and 10 secondary outcomes (10 domains of self-concept). We assessed the data for risk of bias, heterogeneity, sensitivity, reporting bias, and quality of evidence. RESULTS: Thirteen studies with 3,348 participants met our selection criteria. Meta-analyses revealed statistically significant SMDs for average self-concept (-0.57) and five domains of self-concept (reading/writing/spelling: -1.03; academic: -0.67; math: -0.64; behaviour:…

Abstract Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, w CfeT and w CfeJ, found co-infecting cat fleas ( Ctenocephalides felis ) of the Elward Laboratory colony (Soquel, CA). w CfeT is basal to nearly all described Wolbachia supergroups, while w CfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. w CfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, w CfeJ harbors a toxin-antidote operon analogous to the w Pip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. w CfeJ cinB and immediate-5’ end genes are…

Abstract The genus Nicotiana of the family Solanaceae, commonly referred to as tobacco plants, are a group cultivated as garden ornamentals. Besides their use in the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history, which is tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species, namely N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca . De novo assembled tobacco plastid genomes showed typical quadripartite structure, consisting of a pair of inverted repeats (IR) regions (25,323–25,369 bp each) separated by a large single copy (LSC) region (86,510 –86,716 bp) and a small single copy (SSC) region (18,441–18,555 bp). Comparative analyses of Nicotiana plastid genomes showed similar GC content, gene content, codon usage, simple sequence repeats, oligonucleotide repeats, RNA editing sites and substitutions with currently available Solanaceae genomes sequences. We identified twenty highly polymorphic regions mostly belonging to intergenic…

Abstract The invasive fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a polyphagous pest that causes widespread damage particularly to maize and sorghum in Africa. The microbiome associated with S. frugiperda could play a role in their success and adaptability. However, these bacterial communities remain poorly studied, especially for S. frugiperda in Africa. We investigated the composition, abundance and diversity of microbiomes associated with larval and adult specimens of S. frugiperda collected from four maize growing regions in Kenya through high throughput sequencing of bacterial 16S rRNA gene. We identified Proteobacteria and Firmicutes as the most dominant phyla and lesser proportions of Bacteroidetes and Actinobacteria. We also observed differences in bacterial microbiome diversity between larvae and adults that are a likely indication that some prominent larval bacterial groups are lost during metamorphosis. Several bacterial groups were found in both adults and larvae suggesting that they are transmitted across developmental stages. Reads corresponding to…

Human pythiosis is an infectious condition with high morbidity and mortality. The causative agent is the oomycete microorganism Pythium insidiosum . The pathogen inhabits ubiquitously in a wet environment, and direct exposure to the pathogen initiates the infection. Most patients with pythiosis require surgical removal of the affected organ, and many patients die from the disease. Awareness of pythiosis among healthcare personnel is increasing. In this review, we summarized and updated information on the diagnosis and treatment of human pythiosis. Vascular and ocular pythiosis are common clinical manifestations. Recognition of the typical clinical features of pythiosis is essential for early diagnosis. The definitive diagnosis of the disease requires laboratory testing, such as microbiological, serological, molecular, and proteomic assays. In vascular pythiosis, surgical intervention to achieve the organism-free margin of the affected tissue, in combination with the use of antifungal drugs and P. insidiosum immunotherapy, remains the recommended treatment. Ocular pythiosis is a…

We used a constant total N application base rate to conduct a two-year field experiment comparing the effects of three organic fertilizers (rapeseed meal (RSM), soybean meal (SBM), and cattle manure (CM)) on the crop yield, economic growth, and soil quality of a winter wheat-summer maize rotation system. Winter wheat and summer maize in rapeseed meal treatment (RSMT), soybean meal treatment (SBMT), and cattle manure treatment (CMT) showed yield increases of 161%, 299%, and 256%, respectively, when compared to no organic fertilizer treatment (CK) (P < 0.05). The annual net incomes of SBMT and CMT were 1.46 and 1.42 times higher, respectively, than RSMT. Compared to the results of the CK group, RSM, SBM, and CM stimulated the soil physically, chemically, and biologically. We found the highest soil macroaggregate proportions, soil organic matter (SOM) levels, total N (TN) levels, and phospholipid fatty acid (PLFA) levels in SBMT. The highest soil pH, microbial biomass carbon (MBC) levels, and microbial biomass nitrogen (MBN) levels were observed in CMT. We used a soil quality index…

The rapid development of the SARS-CoV-2 mediated COVID-19 pandemic has been the cause of significant health concern, highlighting the immediate need for effective antivirals. SARS-CoV-2 is an RNA virus that has an inherently high mutation rate. These mutations drive viral evolution and genome variability, thereby facilitating viruses to have rapid antigenic shifting to evade host immunity and to develop drug resistance. Viral RNA-dependent RNA polymerases (RdRp) perform viral genome duplication and RNA synthesis. Therefore, we compared the available RdRp sequences of SARS-CoV-2 from Indian isolates and the 'Wuhan wet sea food market virus' sequence to identify, if any, variation between them. Our data revealed the occurrence of seven mutations in Indian isolates of SARS-CoV-2. The secondary structure prediction analysis of these seven mutations shows that three of them cause alteration in the structure of RdRp. Furthermore, we did protein modelling studies to show that these mutations can potentially alter the stability of the RdRp protein. Therefore, we propose that RdRp mutations…

BACKGROUND: Luteolin (LUT) is a flavonoid found in vegetables and fruits that has diverse functions. Doxorubicin (DOX) is an anthracycline antibiotic that is frequently used for the treatment of various cancers. Unfortunately, the clinical efficacy of DOX is limited by its dose-related cardiotoxicity. In this study, we aimed to investigate the potential mechanism through which LUT attenuates cardiotoxicity in vivo. METHODS: We evaluated the body weight, heart weight, electrocardiogram, and pathological changes before and after administration of LUT. Moreover, the effects of LUT (50 mg/kg in the low dose group, 100 mg/kg in the high dose group) on biochemical parameters (brain natriuretic peptide, creatine kinase MB, cardiac troponin T, and dehydrogenation of lactate enzyme) and oxidative stress parameters (malondialdehyde and superoxide dismutase) were studied in the sera of cardiotoxicity model rats. We also identified the apoptotic mediators whose expression was induced by LUT by quantitative real-time reverse transcription-polymerase chain reaction (RT-qPCR) evaluation. In…

Soil salinization is a global problem closely related to the sustainable development of social economy. Compared with frequently-used satellite-borne sensors, unmanned aerial vehicles (UAVs) equipped with multispectral sensors provide an opportunity to monitor soil salinization with on-demand high spatial and temporal resolution. This study aims to quantitatively estimate soil salt content (SSC) using UAV-borne multispectral imagery, and explore the deep mining of multispectral data. For this purpose, a total of 60 soil samples (0–20 cm) were collected from Shahaoqu Irrigation Area in Inner Mongolia, China. Meanwhile, from the UAV sensor we obtained the multispectral data, based on which 22 spectral covariates (6 spectral bands and 16 spectral indices) were constructed. The sensitive spectral covariates were selected by means of gray relational analysis (GRA), successive projections algorithm (SPA) and variable importance in projection (VIP), and from these selected covariates estimation models were built using back propagation neural network (BPNN) regression, support vector…

Background Sprint performance is an essential skill to target within soccer, which can be likely achieved with a variety of methods, including different on-field training options. One such method could be heavy resisted sprint training. However, the effects of such overload on sprint performance and the related kinetic changes are unknown in a professional setting. Another unknown factor is whether violating kinematic specificity via heavy resistance will lead to changes in unloaded sprinting kinematics. We investigated whether heavy resisted sled training (HS) affects sprint performance, kinetics, sagittal plane kinematics, and spatiotemporal parameters in professional male soccer players. Methods After familiarization, a nine-week training protocol and a two-week taper was completed with sprint performance and force-velocity (FV) profiles compared before and after. Out of the two recruited homogenous soccer teams ( N = 32, age: 24.1 ± 5.1 years: height: 180 ± 10 cm; body-mass: 76.7 ± 7.7 kg, 30-m split-time: 4.63 ± 0.13 s), one was used as a control group continuing training as…

Polycystic ovary syndrome (PCOS) can cause reproductive disorders that may affect oocyte quality from punctured follicles in human follicular fluid (HFF). The non-coding RNA family includes micro RNA (miRNA), piwi-interacting RNA (piRNA) and transfer RNA (tRNA); these non-coding RNA transcripts play diverse functions and are implicated in a variety of diseases and health conditions, including infertility. In this study, to explore the role of HFF exosomes in PCOS, we extracted and sequenced RNA from HFF exosomes of PCOS patients and compared the analysis results with those of non-PCOS control group. The HFF exosomes were successfully isolated and characterized in a variety of ways. The sequencing results of the HFF exosomal RNA showed that about 6.6% of valid reads in the PCOS group and 8.6% in the non-PCOS group were successfully mapped to the human RNA database. Using a hierarchical clustering method, we found there were ten small RNA sequences whose expression was significantly different between the PCOS and non-PCOS groups. We chose six of them to predict target genes of…

Background Older adults have been reported to be a population with high-risk of death in the COVID-19 outbreak. Rapid detection of high-risk patients is crucial to reduce mortality in this population. The aim of this study was to evaluate the prognositc accuracy of the Modified Early Warning Score (MEWS) for in-hospital mortality in older adults with COVID-19. Methods A retrospective cohort study was conducted in Wuhan Hankou Hospital in China from 1 January 2020 to 29 February 2020. Receiver operating characteristic (ROC) analysis was used to evaluate the predictive value of MEWS, Acute Physiology and Chronic Health Evaluation II (APACHE II), Sequential Organ Function Assessment (SOFA), quick Sequential Organ Function Assessment (qSOFA), Pneumonia Severity Index (PSI), Combination of Confusion, Urea, Respiratory Rate, Blood Pressure, and Age ≥65 (CURB-65), and the Systemic Inflammatory Response Syndrome Criteria (SIRS) for in-hospital mortality. Logistic regression models were performed to detect the high-risk older adults with COVID-19. Results Among the 235 patients included in…

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the…

Tumour-associated macrophages (TAMs) are associated with both the progression and poor prognosis of a variety of solid tumours. This study aimed to investigate and clarify the tumour-promoting role of CXCL8 secreted by TAMs in the urothelial carcinoma microenvironment of the bladder. Immunohistochemistry ( n = 55) was used to detect Chemokine (C-X-C motif) ligand 8 (CXCL8), CD163 (a TAM marker), Matrixmetalloproteinase-9 (MMP-9), vascular endothelial growth factor (VEGF), and E-cadherin in cancerous and adjacent tissues of bladder cancer patients. TAMs-like PBM (peripheral blood mononuclear)-derived macrophages were developed using in vitro experiments. T24, 5637, and UM-UC-3 were treated with conditioned medium (CM) for the experimental intervention group, without CM for the blank control group, and with CM and an anti-CXCL8 neutralizing antibody for the experimental control group, respectively. The immunohistochemical study showed that the expression of CXCL8 was significantly upregulated as the number of infiltrating TAMs increased in the tumour tissues. A high expression of…

Drought stress hampers the growth and productivity of wheat crop worldwide. Thus far, different strategies have been proposed to improve drought tolerance in wheat but the combined application of plant growth-promoting rhizobacteria formulated bio-fertilizer (BF) and salicylic acid (SA) has not been thoroughly explored yet. Therefore, a pot experiment was conducted to observe the effect of SA, BF, and their combination on wheat plants under optimal and drought stress conditions. Seeds priming was done with BF (107CFU mL−1). After 2 weeks of germination, SA (one mM) was applied as a foliar spray. Drought stress was applied by withholding water supply at three-leaf stage (30 d old plants) for the next 15 d until soil moisture dropped to 10%. Foliar application of SA increased the bacterial population of BF significantly compared to the sole application of BF under irrigated as well as drought stress conditions. Co-application of BF and foliar spray of SA induced drought tolerance in wheat plants by enhancing plant biomass, photosynthetic pigments, relative water content and osmolytes,…

We review the concept of ecosystem resilience in its relation to ecosystem integrity from an information theory approach. We summarize the literature on the subject identifying three main narratives: ecosystem properties that enable them to be more resilient; ecosystem response to perturbations; and complexity. We also include original ideas with theoretical and quantitative developments with application examples. The main contribution is a new way to rethink resilience, that is mathematically formal and easy to evaluate heuristically in real-world applications: ecosystem antifragility. An ecosystem is antifragile if it benefits from environmental variability. Antifragility therefore goes beyond robustness or resilience because while resilient/robust systems are merely perturbation-resistant, antifragile structures not only withstand stress but also benefit from it.

DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. In the plant kingdom, cytosine - 5 DNA methyltransferase ( C5-MTase ) and DNA demethylase ( dMTase ) genes have been identified in some plant species. However, to the best of our knowledge, no investigator has focused on the identification and analysis of C5-MTase and dMTase genes in tea plants ( Camellia sinensis ) based on genome-wide levels. In this study, eight CsC5-MTases and four dMTases were identified in tea plants. These CsC5-MTase genes were divided into four subfamilies, including CsMET , CsCMT , CsDRM and CsDNMT2 . The CsdMTase genes can be classified into CsROS , CsDME and CsDML . Based on conserved domain analysis of these genes, the gene loss and duplication events occurred during the evolution of CsC5-MTase and CsdMTase . Furthermore, multiple cis -acting elements were observed in the CsC5-MTase and CsdMTase , including light responsiveness, phytohormone responsiveness, stress responsiveness,…

Discrete, ephemeral natural phenomena with low spatial or temporal predictability are incredibly challenging to study systematically. In ecology, species interactions, which constitute the functional backbone of ecological communities, can be notoriously difficult to characterise especially when taxa are inconspicuous and the interactions of interest (e.g., trophic events) occur infrequently, rapidly, or variably in space and time. Overcoming such issues has historically required significant time and resource investment to collect sufficient data, precluding the answering of many ecological and evolutionary questions. Here, we show the utility of social media for rapidly collecting observations of ephemeral ecological phenomena with low spatial and temporal predictability by using a Facebook group dedicated to collecting predation events involving reptiles and amphibians in sub-Saharan Africa. We collected over 1900 independent feeding observations using Facebook from 2015 to 2019 involving 83 families of predators and 129 families of prey. Feeding events by snakes were particularly…

Phosphate (P) availability often limits biological nitrogen fixation (BNF) by diazotrophic bacteria. In soil, only 0.1% of the total P is available for plant uptake. P solubilizing bacteria can convert insoluble P to plant-available soluble P (ionic P and low molecular-weight organic P). However, limited information is available about the effects of synergistic application of diazotrophic bacteria and P solubilizing bacteria on the nitrogenase activity of rhizosphere and nifH expression of endosphere. In this study, we investigated the effects of co-inoculation with a diazotrophic bacterium (Paenibacillus beijingensis BJ-18) and a P-solubilizing bacterium (Paenibacillus sp. B1) on wheat growth, plant and soil total N, plant total P, soil available P, soil nitrogenase activity and the relative expression of nifH in plant tissues. Co-inoculation significantly increased plant biomass (length, fresh and dry weight) and plant N content (root: 27%, shoot: 30%) and P content (root: 63%, shoot: 30%). Co-inoculation also significantly increased soil total N (12%), available P (9%) and…

Marine sediments contain a high diversity of micro- and macro-organisms which are important in the functioning of biogeochemical cycles. Traditionally, anthropogenic perturbation has been investigated by identifying macro-organism responses along gradients. Environmental DNA (eDNA) analyses have recently been advocated as a rapid and cost-effective approach to measuring ecological impacts and efforts are underway to incorporate eDNA tools into monitoring. Before these methods can replace or complement existing methods, robustness and repeatability of each analytical step has to be demonstrated. One area that requires further investigation is the selection of sediment DNA extraction method. Environmental DNA sediment samples were obtained along a disturbance gradient adjacent to a Chinook ( Oncorhynchus tshawytscha ) salmon farm in Otanerau Bay, New Zealand. DNA was extracted using four extraction kits (Qiagen DNeasy PowerSoil, Qiagen DNeasy PowerSoil Pro, Qiagen RNeasy PowerSoil Total RNA/DNA extraction/elution and Favorgen FavorPrep Soil DNA Isolation Midi Kit) and three sediment…

URM 3718 as a meal additive like cupcake. The biosurfactant was produced in a culture medium containing 5% sugar cane molasses, 5% residual soybean oil and 3% corn steep liquor. The surface and interfacial tension of the biosurfactant were 30.790 ± 0.04 mN/m and 0.730 ± 0.05 mN/m, respectively. The yield in isolated biosurfactant was 25 ± 1.02 g/L and the CMC was 0.5 g/L. The emulsions of the isolated biosurfactant with vegetable oils showed satisfactory results. The microphotographs of the emulsions showed that increasing the concentration of biosurfactant decreased the oil droplets, increasing the stability of the emulsions. The biosurfactant was incorporated into the cupcake dessert formulation, replacing 50%, 75% and 100% of the vegetable fat in the standard formulation. Thermal analysis showed that the biosurfactant is stable for cooking cupcakes (180 °C). The biosurfactant proved to be promising for application in foods low in antioxidants and did not show cytotoxic potential in the tested cell lines. Cupcakes with biosurfactant incorporated in their dough did not show…

L-asparaginase is an important anticancer enzyme that is used in the first line treatment of acute lymphoblastic leukemia. This study was conducted to isolate L-asparaginase-producing endophytic fungi from medicinal plants of family Asteraceae. Seven healthy medicinal plants from family Asteraceae were selected for the isolation of endophytic fungi using standard surface sterilization techniques. A total of 837 isolates belonging to 84 species were comprised of the stem (55.6%), leaf (31.1%), root (10.6%) and flower (2.7%). Initial screening of L-asparaginase-producing endophytes was performed by qualitative plate assay on modified Czapex dox’s agar medium. L-asparaginase activity of fungal endophytes was quantified by the nesslerization method. Identification of endophytic fungi was performed using both morphological characteristics and phylogenetic analyses of DNA sequence data including ribosomal DNA regions of ITS (Internal transcribed spacer) and LSU (partial large subunit rDNA), TEF1 (Translation Elongation Factor) and TUB ( β -tubulin). Of the 84 isolates, 38 were able to…

Background Conyza blinii H. Lév is a medicinal plant that has a variety of pharmacological activities, but its study is at a standstill due to the shortage of resources. Method This study utilized the surface sterilization method to isolate endophytic fungi, and they were preliminarily identified by morphology. Flavonoid-producing strains were screened by NaNO 2 -Al(NO) 3 colorimetry and further identified by the ITS sequence. Additionally, we used five antioxidant assays (DPPH, Hydroxyl radical, ABTS, FRAP and T-AOC assays) to systematically evaluate the antioxidant capacity of total flavonoids , and we also determined their antibacterial activity. Results In this study, 21 endophytic fungi were isolated from wild Conyza blinii H. Lév for the first time. There were six flavonoid-producing strains, especially CBL11, whose total flavonoid content reached 50.78 ± 2.4 mg/L. CBL12, CBL12-2 and CBL1-1 all exhibited excellent antioxidant activity. The effect of CBL12 was similar to that of ascorbic acid at low concentrations, and its radical scavenging rates for DPPH and ABTS were 94.56 ±…

Mexico has more than 750,000 ha of mangroves and more than 400,000 ha of seagrasses. However, approximately 200,000 ha of mangroves and an unknown area of seagrass have been lost due to coastal development associated with urban, industrial and tourist purposes. In 2018, the approved reforms to the General Law on Climate Change (LGCC) aligned the Mexican law with the international objectives established in the 2nd Article of the Paris Agreement. This action proves Mexico’s commitment to contributing to the global target of stabilizing the greenhouse gas emissions concentration in the planet. Thus, restoring and conserving mangrove and seagrass habitats could contribute to fulfilling this commitment. Therefore, as a first step in establishing a mitigation and adaptation plan against climate change with respect to conservation and restoration actions of these ecosystems, we evaluated Mexican blue carbon ecosystems through a systematic review of the carbon stock using the standardized method of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We used the data…

The concept of ecosystem services, especially in combination with economic valuation, can illuminate trade-offs involved in soil management, policy and governance, and thus support decision making. In this paper, we investigate and highlight the potential and limitations of the economic valuation of soil-based ecosystem services to inform sustainable soil management and policy. We formulate a definition of soil-based ecosystem services as basis for conducting a review of existing soil valuation studies with a focus on the inclusion of ecosystem services and the choice of valuation methods. We find that, so far, the economic valuation of soil-based ecosystem services has covered only a small number of such services and most studies have employed cost-based methods rather than state-of-the-art preference-based valuation methods, even though the latter would better acknowledge the public good character of soil related services. Therefore, the relevance of existing valuation studies for political processes is low. Broadening the spectrum of analyzed ecosystem services as well as using…

BACKGROUND: Non-suicidal self-injury (NSSI) among adolescents is prevalent and its rate has increased in recent years worldwide. Previous studies had investigated the association between parenting and childhood NSSI, but little is known about the relationship between parental rearing and repetition and severity of NSSI. The aim of this study was to investigate associations of parenting with NSSI and its repetition and severity in a representative adolescent sample from southwestern China. METHODS: In this cross-sectional study, a sample of 2,705 adolescents (F/M: 1,245/1,460; mean age: 13.4 ± 2.2 years) was recruited from 14 randomly selected schools in Lincang municipality, Yunnan province, China. A self-report questionnaire was used to collect data. The Adolescent Non-Suicidal Self-Injury Function Assessment Scale and the short Chinese Egna Minnen av Barndoms Uppfostran (s-EMBU-C) were used to evaluate NSSI behaviors and parenting style, respectively. Univariate and multivariate logistic regression models were adopted to examine association between parenting and NSSI. RESULTS:…

BACKGROUND: Badminton is a popular sport activity in both recreational and elite levels. A lot of biomechanical studies have investigated badminton lunge, since good lunge performance may increase the chances to win the game. This review summarized the current trends, research methods, and parameters-of-interest concerning lower-extremity biomechanics in badminton lunges. METHODOLOGY: Databases including Web of Science, Cochrane Library, Scopus, and PubMed were searched from the oldest available date to September 2020. Two independent authors screened all the articles and 20 articles were eligible for further review. The reviewed articles compared the differences among playing levels, footwear designs, and lunge directions/variations, using parameters including ground reaction forces, plantar pressure distribution, kinematics, and kinetics. RESULTS: Elite badminton players demonstrated higher impact attenuation capability, more aggressive knee and ankle strategy (higher mechanical moment), and higher medial plantar load than amateur players. Footwear modifications can influence…

BACKGROUND: In the absence of highly effective antiviral therapies against SARS-CoV-2, it is crucial to counter the known pathophysiological causes of severe COVID-19. Evaluating the efficacy existing drugs may expedite the development of such therapeutics. Severe COVID-19 is largely the result of a dysregulated immune response characterized by lymphocytopenia, neutrophilia and critical hypercytokinemia, or "cytokine storm," which is largely mediated by the cytokine interleukin-6 (IL-6). The IL-6 inhibitor tocilizumab (TCZ) could potentially suppress the effects of the pro-inflammatory cytokine and thereby lower mortality from the disease. This systematic analysis aimed to investigate and synthesize existing evidence for the efficacy of TCZ in reducing COVID-19 mortality. METHODOLOGY: PubMed and SearchWorks searches were performed to locate clinical studies with primary data on TCZ treatment for severe COVID-19. Sixteen case-control studies comparing mortality between TCZ and standard of care (SOC) were identified for quantitative synthesis. The systematic analysis was pre-approved…

BACKGROUND: Nowadays, the most widely used types of wearable sensors in gait analysis are inertial sensors. The aim of the study was to assess the agreement between two different systems for measuring gait parameters (inertial sensor vs. electronic walkway) on healthy control subjects (HC) and patients with Parkinson's disease (PD). METHODS: Forty healthy volunteers (26 men, 14 women, mean age 58.7 ± 7.7 years) participated in the study and 24 PD patients (19 men, five women, mean age 62.7 ± 9.8 years). Each participant walked across an electronic walkway, GAITRite, with embedded pressure sensors at their preferred walking speed. Concurrently a G-Walk sensor was attached with a semi-elastic belt to the L5 spinal segment of the subject. Walking speed, cadence, stride duration, stride length, stance, swing, single support and double support phase values were compared between both systems. RESULTS: The Passing-Bablock regression slope line manifested the values closest to 1.00 for cadence and stride duration (0.99 ≤ 1.00) in both groups. The slope of other parameters varied between…

Background The Feline Grimace Scale (FGS) is a facial expression-based scoring system for acute pain assessment in cats with reported validity using image assessment. The aims of this study were to investigate the clinical applicability of the FGS in real-time when compared with image assessment, and to evaluate the influence of sedation and surgery on FGS scores in cats. Methods Sixty-five female cats (age: 1.37 ± 0.9 years and body weight: 2.85 ± 0.76 kg) were included in a prospective, randomized, clinical trial. Cats were sedated with intramuscular acepromazine and buprenorphine. Following induction with propofol, anesthesia was maintained with isoflurane and cats underwent ovariohysterectomy (OVH). Pain was evaluated at baseline, 15 min after sedation, and at 0.5, 1, 2, 3, 4, 6, 8, 12 and 24 h after extubation using the FGS in real-time (FGS-RT). Cats were video-recorded simultaneously at baseline, 15 min after sedation, and at 2, 6, 12, and 24 h after extubation for subsequent image assessment (FGS-IMG), which was performed six months later by the same observer. The agreement…

"Higher" termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the…