The 50 most-cited articles in F1000Research, 2021

Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that data analyses should ideally be conducted in a reproducible way. Reproducibility enables technical validation and regeneration of results on the original or even new data. However, reproducibility alone is by no means sufficient to deliver an analysis that is of lasting impact (i.e., sustainable) for the field, or even just one research group. We postulate that it is equally important to ensure adaptability and transparency. The former describes the ability to modify the analysis to answer extended or slightly different research questions. The latter describes the ability to understand the analysis in order to judge whether it is not only technically, but methodologically valid. Here, we analyze the properties needed for data analysis to become reproducible, adaptable, and transparent. We show how the popular workflow management system Snakemake can…

Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed to detect them. Building on the strengths of existing approaches, we developed scDblFinder , a fast, flexible and accurate Bioconductor-based doublet detection method. Here we present the method, justify its design choices, demonstrate its performance on both single-cell RNA and accessibility sequencing data, and provide some observations on doublet formation, detection, and enrichment analysis. Even in complex datasets, scDblFinder can accurately identify most heterotypic doublets, and was already found by an independent benchmark to outcompete alternatives.

Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R or Python for the generation of plots and tables. It is widely recognized that data analyses should ideally be conducted in a reproducible way. Reproducibility enables technical validation and regeneration of results on the original or even new data. However, reproducibility alone is by no means sufficient to deliver an analysis that is of lasting impact (i.e., sustainable) for the field, or even just one research group. We postulate that it is equally important to ensure adaptability and transparency. The former describes the ability to modify the analysis to answer extended or slightly different research questions. The latter describes the ability to understand the analysis in order to judge whether it is not only technically, but methodologically valid. Here, we analyze the properties needed for a data analysis to become reproducible, adaptable, and transparent. We show how the popular workflow management system Snakemake…

Quality control is an essential first step in sequencing data analysis, and software tools for quality control are deeply entrenched in standard pipelines at most sequencing centers. Although the associated computations are straightforward, in many settings the total computing effort required for quality control is appreciable and warrants optimization. We present falco, an emulation of the popular FastQC tool that runs on average three times faster while generating equivalent results. Compared to FastQC, falco also provides greater scalability for datasets with longer reads and more flexible visualization of HTML reports.

Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of eight long-read assemblers (Canu, Flye, Miniasm/Minipolish, NECAT, NextDenovo/NextPolish, Raven, Redbean and Shasta) across a wide variety of genomes and read parameters. Assemblies were assessed on their structural accuracy/completeness, sequence identity, contig circularisation and computational resources used. Results: Canu v2.1 produced reliable assemblies and was good with plasmids, but it performed poorly with circularisation and had the longest runtimes of all assemblers tested. Flye v2.8 was also reliable and made the…

Background: The COVID-19 pandemic has caused considerable morbidity, mortality and disruption to people’s lives around the world. There are concerns that rates of suicide and suicidal behaviour may rise during and in its aftermath. Our living systematic review synthesises findings from emerging literature on incidence and prevalence of suicidal behaviour as well as suicide prevention efforts in relation to COVID-19, with this iteration synthesising relevant evidence up to 19 th October 2020. Method: Automated daily searches feed into a web-based database with screening and data extraction functionalities. Eligibility criteria include incidence/prevalence of suicidal behaviour, exposure-outcome relationships and effects of interventions in relation to the COVID-19 pandemic. Outcomes of interest are suicide, self-harm or attempted suicide and suicidal thoughts. No restrictions are placed on language or study type, except for single-person case reports. We exclude one-off cross-sectional studies without either pre-pandemic measures or comparisons of COVID-19 positive vs. unaffected…

Background : The unpredictability of the progression of coronavirus disease 2019 (COVID-19) may be attributed to the low precision of the tools used to predict the prognosis of this disease. Objective : To identify the predictors associated with poor clinical outcomes in patients with COVID-19. Methods : Relevant articles from PubMed, Embase, Cochrane, and Web of Science were searched as of April 5, 2020. The quality of the included papers was appraised using the Newcastle-Ottawa scale (NOS). Data of interest were collected and evaluated for their compatibility for the meta-analysis. Cumulative calculations to determine the correlation and effect estimates were performed using the Z test. Results : In total, 19 papers recording 1,934 mild and 1,644 severe cases of COVID-19 were included. Based on the initial evaluation, 62 potential risk factors were identified for the meta-analysis. Several comorbidities, including chronic respiratory disease, cardiovascular disease, diabetes mellitus, and hypertension were observed more frequent among patients with severe COVID-19 than with the…

Background: The burden associated with Alzheimer’s disease is recognized as one of the most pressing issues in healthcare. This study aimed to examine the global and regional burden of Alzheimer’s disease and related dementias. Methods : Epidemiological data from the latest Global Burden of Disease (GBD) dataset were analysed to determine the prevalence, incidence and mortality rates from 1990 to 2019 for 204 countries and world regions. This dataset derives estimates for health metrics by collating primary data from research studies, disease registries and government reports. Temporal forecasting was conducted using the GBD Foresight tool. Results : An estimated 0.7% of the global population has dementia, translating to 51.6 million people worldwide. The total number of persons affected has more than doubled from 1990 to 2019. Dementia metrics showed a continuous increase in prevalence, incidence, mortality, and disability adjusted life years (DALYs) rates worldwide during the last three decades. Japan has the highest prevalence (3,079 cases per 100,000), followed by Italy,…

'Long Covid', or medical complications associated with post SARS-CoV-2 infection, is a significant post-viral complication that is being more and more commonly reported in patients. Therefore, there is an increasing need to understand the disease mechanisms, identify drug targets and inflammatory processes associated with a SARS-CoV-2 infection. To address this need, we created a targeted mass spectrometry based multiplexed panel of 96 immune response associated proteins. We applied the multiplex assay to a cohort of serum samples from asymptomatic and moderately affected patients. All patients had tested positive for a SARS-CoV-2 infection by PCR and were determined to be subsequently positive for antibodies. Even 40-60 days post-viral infection, we observed a significant remaining inflammatory response in all patients. Proteins that were still affected were associated with the anti-inflammatory response and mitochondrial stress. This indicates that biochemical and inflammatory pathways within the body can remain perturbed long after SARS-CoV-2 infections have subsided even in…

Background : The present study aimed to determine the global prevalence of anosmia and dysgeusia in coronavirus disease 2019 (COVID-19) patients and to assess their association with severity and mortality of COVID-19. Moreover, this study aimed to discuss the possible pathobiological mechanisms of anosmia and dysgeusia in COVID-19. Methods : Available articles from PubMed, Scopus, Web of Science, and preprint databases (MedRxiv, BioRxiv, and Researchsquare) were searched on November 10th, 2020. Data on the characteristics of the study (anosmia, dysgeusia, and COVID-19) were extracted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Newcastle–Ottawa scale was used to assess research quality. Moreover, the pooled prevalence of anosmia and dysgeusia were calculated, and the association between anosmia and dysgeusia in presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was assessed using the Z test. Results : Out of 32,142 COVID-19 patients from 107 studies, anosmia was reported in 12,038 patients with a…

Lipidomics increasingly describes the quantitation using mass spectrometry of all lipids present in a biological sample. As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment. Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways. As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging. BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways. BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.

Human enamel once formed cannot be biologically repaired or replaced. Saliva has a significant role in remineralization of dental enamel. It not only has a buffering capacity to neutralize the oral cavity's low pH generated after acidic encounters, but also acts as a carrier of essential ions, such as fluoride, calcium and phosphate, which have a positive role in enamel's remineralization. This review discusses how salivary contents, like proteins and enzymes, have a natural role in enamel's mineralization. In addition, the presence of ions, such as fluoride, calcium and phosphate, in saliva further enhances its capability to remineralize the demineralized enamel surface. The review further examines modern innovative technologies, based on biomimetic regeneration systems, including dentin phosphoproteins, aspartate-serine-serine, recombinant porcine amelogenin, leucine-rich amelogenin peptide and nano-hydroxyapatite, that promote enamel remineralization. Fluoride boosters like calcium phosphates, polyphosphates, and certain natural products can also play an important role in enamel…

Background: The reliable and usable (semi) automation of data extraction can support the field of systematic review by reducing the workload required to gather information about the conduct and results of the included studies. This living systematic review examines published approaches for data extraction from reports of clinical studies. Methods: databases. Full text screening and data extraction are conducted using a mix of open-source and commercial tools. This living review update includes publications up to August 2024 and OpenAlex content up to September 2024. Results: 117 publications are included in this review. Of these, 30 (26%) used full texts while the rest used titles and abstracts. A total of 112 (96%) publications developed classifiers for randomised controlled trials. Over 30 entities were extracted, with PICOs (population, intervention, comparator, outcome) being the most frequently extracted. Data are available from 53 (45%), and code from 49 (42%) publications. Nine (8%) implemented publicly available tools. Conclusions: This living systematic review presents an…

Due to the restrictions imposed to contain the coronavirus disease 2019 (COVID-19) pandemic, different population groups have adapted to varying screen time levels, which may have profound implications on their physical and mental wellbeing . Several empirical studies included in this review reported a sudden upward change in screen time across different population groups. A higher number of people with increased screen time compared to their pre-pandemic state and prolonged duration of total screen time substantiates such assertions. The available evidence suggests that screen time is associated with obesity, hypertension, type 2 diabetes, myopia, depression, sleep disorders, and several non-communicable diseases. This elevated burden of diseases is more prevalent among individuals who have sedentary lifestyles and other unhealthy behaviors that are likely to increase during quarantine or isolation due to COVID-19. Hence, it is critical to assess the adverse health outcomes that may appear as long-term consequences of such behavior. Researchers and practitioners need to revisit the…

Lipidomics increasingly describes the quantification using mass spectrometry of all lipids present in a biological sample. As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment. Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways. As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging. BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways. BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.

Introduction: Systematic reviews involve synthesis of research to inform decision making by clinicians, consumers, policy makers and researchers. While guidance for synthesis often focuses on meta-analysis, synthesis begins with specifying the ’PICO for each synthesis’ (i.e. the criteria for deciding which populations, interventions, comparators and outcomes are eligible for each analysis). Synthesis may also involve the use of statistical methods other than meta-analysis (e.g. vote counting based on the direction of effect, presenting the range of effects, combining P values) augmented by visual display, tables and text-based summaries. This study examines these two aspects of synthesis. Objectives: To identify and describe current practice in systematic reviews of health interventions in relation to: (i) approaches to grouping and definition of PICO characteristics for synthesis; and (ii) methods of summary and synthesis when meta-analysis is not used. Methods: We will randomly sample 100 systematic reviews of the quantitative effects of public health and health systems…

We describe a web and standalone Shiny app for calculating the common, linear within-individual association for repeated assessments of paired measures with multiple individuals: repeated measures correlation (rmcorr). This tool makes rmcorr more widely accessible, providing a graphical interface for performing and visualizing the output of analysis with rmcorr. In contrast to rmcorr, most widely used correlation techniques assume paired data are independent. Incorrectly analyzing repeated measures data as independent will likely produce misleading results. Using aggregation or separate models to address the issue of independence may obscure meaningful patterns and will also tend to reduce statistical power. rmcorrShiny (repeated measures correlation Shiny) provides a simple and accessible solution for computing the repeated measures correlation. It is available at: https://lmarusich.shinyapps.io/shiny_rmcorr/.

Background:SARS-CoV-2 RNA has been detected in fomites which suggests the virus could be transmitted via inanimate objects. However, there is uncertainty about the mechanistic pathway for such transmissions. Our objective was to identify, appraise and summarise the evidence from primary studies and systematic reviews assessing the role of fomites in transmission. Methods:This review is part of an Open Evidence Review on Transmission Dynamics of SARS-CoV-2. We conduct ongoing searches using WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar; assess study quality based on five criteria and report important findings on an ongoing basis. Results:We found 64 studies: 63 primary studies and one systematic review (n=35). The settings for primary studies were predominantly in hospitals (69.8%) including general wards, ICU and SARS-CoV-2 isolation wards. There were variations in the study designs including timing of sample collection, hygiene procedures, ventilation settings and cycle threshold. The overall quality of reporting was low to moderate. The frequency of positive…

The wood industry is facing many challenges. The high variability of raw material and the complexity of manufacturing processes results in a wide range of visible structure defects, which have to be controlled by trained specialists. These manual processes are not only tedious and biased, but also less effective. To overcome the drawbacks of the manual quality control processes, several automated vision-based systems have been proposed. Even though some conducted studies achieved a higher recognition rate than trained experts, researchers have to deal with a lack of large-scale databases and authentic data in this field. To address this issue, we performed a data acquisition experiment set in the industrial environment, where we were able to acquire an extensive set of authentic data from a production line. For this purpose, we designed and implemented a complex technical solution suitable for high-speed acquisition during harsh manufacturing conditions. In this data note, we present a large-scale dataset of high-resolution sawn timber surface images containing more than 43 000…

Invasive fungal diseases due to resistant yeasts and molds are an important and increasing public health threat, likely due to a growing population of immunosuppressed hosts, increases in antifungal resistance, and improvements in laboratory diagnostics. The significant morbidity and mortality associated with these pathogens bespeaks the urgent need for novel safe and effective therapeutics. This review highlights promising investigational antifungal agents in clinical phases of development: fosmanogepix, ibrexafungerp, rezafungin, encochleated amphotericin B, oteseconazole (VT-1161), VT-1598, PC945, and olorofim. We examine three first-in-class members of three novel antifungal classes, as well as new agents within existing antifungal classes with improved safety and tolerability profiles due to enhanced pharmacokinetic and pharmacodynamic properties.

In this paper, we focus on providing a narrative review of healthcare services in which artificial intelligence (AI) based services are used as part of the operations and analyze key elements to create successful AI-based services for healthcare. The benefits of AI in healthcare are measured by how AI is improving the healthcare outcomes, help caregivers in work, and reducing healthcare costs. AI market in healthcare sector have also a high market potential with 28% global compound annual growth rate. This paper will collect outcomes from multiple perspectives of healthcare sector including financial, health improvement, and care outcome as well as provide proposals and key factors for successful implementation of AI methods in healthcare. It is shown in this paper that AI implementation in healthcare can provide cost reduction and same time provide better health outcome for all.

Background: It is twenty years since the US Institute of Medicine (IOM) defined quality in healthcare, as comprising six domains: person-centredness, timeliness, efficiency, effectiveness, safety and equity. Since then, a new quality movement has emerged, with the development of numerous interventions aimed at improving quality, with a focus on accessibility, safety and effectiveness of care. Further gains in equity and timeliness have proven even more challenging. The challenge: With the emergence of “service-oriented” systems, complexity science, the challenges of climate change, the growth of social media and the internet and the new reality of COVID-19, the original domains proposed by the IOM invite reflection on their relevance and possibility for improvement. The possible solution: In this paper, we propose a revised model of quality that is built on never-ending learning and includes new domains, such as Ecology and Transparency, which reflect the changing worldview of healthcare. We also introduce the concept of person- or “kin-centred care” to emphasise the shared humanity…

For decades, the supra-inflation increase of subscription prices for scholarly journals has concerned scholarly institutions. After years of fruitless efforts to solve this “serials crisis”, open access has been proposed as the latest potential solution. However, the prices for open access publishing are also high and are rising well beyond inflation. What has been missing from the public discussion so far is a quantitative approach to determine the actual costs of efficiently publishing a scholarly article using state-of-the-art technologies, such that informed decisions can be made as to appropriate price levels. Here we provide a granular, step-by-step calculation of the costs associated with publishing primary research articles, from submission, through peer-review, to publication, indexing and archiving. We find that these costs range from less than US$200 per article in modern, large-scale publishing platforms using post-publication peer-review, to about US$1,000 per article in prestigious journals with rejection rates exceeding 90%. The publication costs for a representative…

Background: Ongoing efforts attempt to define farms as regenerative to aid marketers, policymakers, farmers, etc. The approach needs to balance precision with function, and must be transparent, simple, scalable, transferable, incorruptible, and replicable. Methods: We developed practice-based scoring systems to distinguish regenerative cropland and rangeland, and validate them based on whether these scores scaled with regenerative goals on actual farm operations. Study systems included cornfields of the Upper Midwest, almond orchards of California, and rangeland systems of the Northern Plains. Response variables included soil carbon and organic matter, soil micronutrients, water infiltration rates, soil microbial communities, plant community structure, invertebrate community structure, pest populations, yields, and profit. Results: Regenerative outcomes were strongly correlated with our approach to farm scoring. Soil organic matter, fine particulate organic matter, total soil carbon, total soil nitrogen, phosphorous, calcium and sulfur all increased alongside regenerative matrix…

Bioinformatic tools for marker gene sequencing data analysis are continuously and rapidly evolving, thus integrating most recent techniques and tools is challenging. We present an R package for data analysis of 16S and ITS amplicons based sequencing. This workflow is based on several R functions and performs automatic treatments from fastq sequence files to diversity and differential analysis with statistical validation. The main purpose of this package is to automate bioinformatic analysis, ensure reproducibility between projects, and to be flexible enough to quickly integrate new bioinformatic tools or statistical methods. rANOMALY is an easy to install and customizable R package, that uses amplicon sequence variants (ASV) level for microbial community characterization. It integrates all assets of the latest bioinformatics methods, such as better sequence tracking, decontamination from control samples, use of multiple reference databases for taxonomic annotation, all main ecological analysis for which we propose advanced statistical tests, and a cross-validated differential…

Background : In this study, we aimed to determine the global prevalence, chronological order of symptom appearance, and mortality rates with regard to hemorrhagic and ischemic stroke in patients with coronavirus disease 2019 (COVID-19) and to discuss possible pathogeneses of hemorrhagic and ischemic stroke in individuals with the disease. Methods : We searched the PubMed, Scopus, and Web of Science databases for relevant articles published up to November 8, 2020. Data regarding study characteristics, hemorrhagic stroke, ischemic stroke, and COVID-19 were retrieved in accordance with the PRISMA guidelines. The Newcastle-Ottawa scale was used to assess the quality of the eligible studies. The pooled prevalence and mortality rate of hemorrhagic and ischemic stroke were calculated. Results : The pooled estimate of prevalence of hemorrhagic stroke was 0.46% (95% CI 0.40%–0.53%; I 2 =89.81%) among 67,155 COVID-19 patients and that of ischemic stroke was 1.11% (95% CI 1.03%–1.22%; I 2 =94.07%) among 58,104 COVID-19 patients. Ischemic stroke was more predominant (incidence: 71.58%) than…

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience. This article (and those community-specific versions) are aimed at authors citing software, including software developed by the authors or by others. We also include brief instructions on how software can be made citable, directing readers to more comprehensive guidance published elsewhere. The guidance presented in this article helps to support proper attribution and credit, reproducibility, collaboration and reuse, and encourages building on the work of others to further research.

BACKGROUND: Modes of transmission of SARS-CoV-2 are of key public health importance. SARS-CoV-2 has been detected in the feces of some COVID-19 patients, suggesting the possibility that the virus could, in addition to droplet and fomite transmission, be transmitted via the orofecal route. METHODS: This review is part of an Open Evidence Review on Transmission Dynamics of COVID-19. We conduct ongoing searches using WHO COVID-19 Database, LitCovid, medRxiv, and Google Scholar; assess study quality based on five criteria and report important findings. Where necessary, authors are contacted for further details on the content of their articles. RESULTS: We include searches up until 20 December 2020. We included 110 relevant studies: 76 primary observational studies or reports, and 35 reviews (one cohort study also included a review) examining the potential role of orofecal transmission of SARS-CoV-2. Of the observational studies, 37 were done in China. A total of 48 studies (n=9,081 patients) reported single cases, case series or cohort data on individuals with COVID-19 diagnosis or…

Background: This study aimed to determine the cumulative prevalence of prolonged gastrointestinal (GI) symptoms, including nausea, vomiting, diarrhea, lack of appetite, abdominal pain, and dysgeusia, in survivors of both mild and severe COVID-19 worldwide and to discuss the potential pathogenesis. Methods: Three databases (PubMed, Scopus, and Web of Science) were searched for relevant articles up to January 30, 2021. Data on study characteristics, clinical characteristics during follow-up, the number of patients with prolonged GI symptoms, and total number of COVID-19 survivors were retrieved according to PRISMA guidelines. The quality of eligible studies was assessed using the Newcastle-Ottawa scale. The pooled prevalence of specific prolonged GI symptoms was calculated and the association between COVID-19 severity and the occurrence of prolonged GI symptoms was assessed if appropriate. Results: The global prevalence of prolonged nausea was 3.23% (95% CI: 0.54%–16.53%) among 527 COVID-19 survivors. Vomiting persisted in 93 of 2,238 COVID-19 survivors (3.19%, 95% CI: 1.62%–6.17%)…

Background: Up-to-date guidance on comprehensive study identification for systematic reviews is crucial. According to current recommendations, systematic searching should combine electronic database searching with supplementary search methods. One such supplementary search method is citation tracking. It aims at collecting directly and/or indirectly cited and citing references from "seed references". Tailored and evidence-guided recommendations concerning the use of citation tracking are strongly needed. Objective: We intend to develop recommendations for the use of citation tracking in systematic literature searching for health-related topics. Our study will be guided by the following research questions: What is the benefit of citation tracking for systematic literature searching for health-related topics? Which methods, citation indexes, and other tools are used for citation tracking? What terminology is used for citation tracking methods? Methods: Our study will have two parts: a scoping review and a Delphi study. The scoping review aims at identifying methodological studies on…

For decades, the supra-inflation increase of subscription prices for scholarly journals has concerned scholarly institutions. After years of fruitless efforts to solve this “serials crisis”, open access has been proposed as the latest potential solution. However, also the prices for open access publishing are high and are rising well beyond inflation. What has been missing from the public discussion so far is a quantitative approach to determine the actual costs of efficiently publishing a scholarly article using state-of-the-art technologies, such that informed decisions can be made as to appropriate price levels. Here we provide a granular, step-by-step calculation of the costs associated with publishing primary research articles, from submission, through peer-review, to publication, indexing and archiving. We find that these costs range from less than US$200 per article in modern, large scale publishing platforms using post-publication peer-review, to about US$1,000 per article in prestigious journals with rejection rates exceeding 90%. The publication costs for a representative…

Background: Frontline doctors are the most vulnerable and high-risk population to get the novel coronavirus disease 2019 (COVID-19) infection. Hence, we aimed to evaluate the anxiety, depression, sleep disturbance and fear of COVID-19 among frontline doctors of Bangladesh during the pandemic, and the associated factors for these psychological symptoms. Methods: In total, 370 frontline doctors who were involved in the treatment of suspected or confirmed COVID-19 patients during the pandemic took part in an online cross-sectional study. Recruitment was completed using convenience sampling and the data were collected after the start of community transmission of COVID-19 in the country. Anxiety and depression, sleep disturbance, and fear of COVID-19 were assessed by the Patient Health Questionnaire-4, two-item version of the Sleep Condition Indicator, and the Fear of Coronavirus-19 scale, respectively. Socio-demographic information, health service-related information, co-morbidity, and smoking history were collected for evaluating risk factors. The proportion of psychological symptoms…

Background : In recent times, digitization is gaining importance in different domains of knowledge such as agriculture, medicine, recommendation platforms, the Internet of Things (IoT), and weather forecasting. In agriculture, crop yield estimation is essential for improving productivity and decision-making processes such as financial market forecasting, and addressing food security issues. The main objective of the article is to predict and improve the accuracy of crop yield forecasting using hybrid machine learning (ML) algorithms. Methods: This article proposes hybrid ML algorithms that use specialized ensembling methods such as stacked generalization, gradient boosting, random forest, and least absolute shrinkage and selection operator (LASSO) regression. Stacked generalization is a new model which learns how to best combine the predictions from two or more models trained on the dataset. To demonstrate the applications of the proposed algorithm, aerial-intel datasets from the github data science repository are used. Results: Based on the experimental results done on the…

Background: There is increasing evidence that nephrolithiasis is a systemic disease, as opposed to an isolated urinary metabolic problem, after considerable links were found between nephrolithiasis and systemic diseases such as hypertension, obesity, dyslipidemia, and insulin resistance. The interplay between these four factors defines metabolic syndrome (MetS). In this review we aim to clarify the associations of MetS and its components to kidney stone incident. Methods: Online databases of EMBASE, MEDLINE, and Google Scholar were searched from January 1998 up to October 2020 to identify observational studies examining the association between metabolic syndrome components and kidney stone incident. Bayesian random-effects meta-analysis and meta-regression were performed to observe the association. Linear dose-response analysis was conducted to shape the direction of the association. Data analysis was performed using STATA, and R statistics. Results: A total of 25 potentially relevant studies (n = 934,588 participants) were eventually identified. The pooled results suggested that…

Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z . marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the…

Background: SARS-CoV-2 has been detected in fomites which suggests the virus could be transmitted via inanimate objects. However, there is uncertainty about the mechanistic pathway for such transmissions. Our objective was to identify, appraise and summarise the evidence from primary studies and systematic reviews assessing the role of fomites in transmission. Methods: This review is part of an Open Evidence Review on Transmission Dynamics of SARS-CoV-2. We conduct ongoing searches using WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar; assess study quality based on five criteria and report important findings on an ongoing basis. Results: We found 64 studies: 63 primary studies and one systematic review (n=35). The settings for primary studies were predominantly in hospitals (69.8%) including general wards, ICU and SARS-CoV-2 isolation wards. There were variations in the study designs including timing of sample collection, hygiene procedures, ventilation settings and cycle threshold. The overall quality of reporting was low to moderate. The frequency of positive…

Although the antimicrobial potential of nitric oxide (NO) is widely published, it is little used clinically. NO is a key signalling molecule modulating vascular, neuronal, inflammatory and immune responses. Endogenous antimicrobial activity is largely mediated by high local NO concentrations produced by cellular inducible nitric oxide synthase, and by derivative reactive nitrogen oxide species including peroxynitrite and S-nitrosothiols. NO may be taken as dietary substrate (inorganic nitrate, L-arginine), and therapeutically as gaseous NO, and transdermal, sublingual, oral, intranasal and intravenous nitrite or nitrate. Numerous preclinical studies have demonstrated that NO has generic static and cidal activities against viruses (including β-coronaviruses such as SARS-CoV-2), bacteria, protozoa and fungi/yeasts in vitro . Therapeutic effects have been seen in animal models in vivo , and phase II trials have demonstrated that NO donors can reduce microbial infection. Nevertheless, excess NO, as occurs in septic shock, is associated with increased morbidity and mortality. In view of…

False discovery rates (FDR) are an essential component of statistical inference, representing the propensity for an observed result to be mistaken. FDR estimates should accompany observed results to help the user contextualize the relevance and potential impact of findings. This paper introduces a new user-friendly R pack-age for estimating FDRs and computing adjusted p-values for FDR control. The roles of these two quantities are often confused in practice and some software packages even report the adjusted p-values as the estimated FDRs. A key contribution of this package is that it distinguishes between these two quantities while also offering a broad array of refined algorithms for estimating them. For example, included are newly augmented methods for estimating the null proportion of findings - an important part of the FDR estimation procedure. The package is broad, encompassing a variety of adjustment methods for FDR estimation and FDR control, and includes plotting functions for easy display of results. Through extensive illustrations, we strongly encourage wider reporting of…

Background Many studies have assessed the quality of news reports about the effects of health interventions, but there has been no systematic review of such studies or meta-analysis of their results. We aimed to fill this gap (PROSPERO ID: CRD42018095032). Methods We included studies that used at least one explicit, prespecified and generic criterion to assess the quality of news reports in print, broadcast, or online news media, and specified the sampling frame, and the selection criteria and technique. We assessed criteria individually for inclusion in the meta-analyses, excluding ineligible criteria and criteria with inadequately reported results. We mapped and grouped criteria to facilitate evidence synthesis. Where possible, we extracted the proportion of news reports meeting the included criterion. We performed meta-analyses using a random effects model to estimate such proportions for individual criteria and some criteria groups, and to characterise heterogeneity across studies. Results We included 44 primary studies in the review, and 18 studies and 108 quality criteria in…

Background: Online learning or E-learning are approaches to broadcasting teaching by the means of internet technology and software applications. Kingdom of Saudi Arabia is likewise embarking on the rapid growth in online education. The purpose of this study is to investigate the student’s perceptions regarding online teaching and learning during COVID 19. Methods: An online computer-based cross-sectional study was conducted between May and June 2020. A pre-validated questionnaire was used and administrated to health sciences students studying at Dammam Universities through online software QuestionPro. Results: Out of total 281, 68% of the participants were females (n=188) while 31.9% (n=88) were male students with an average age of 23.1(4.5) years. Overall, 176 (62%) of the students expressed their satisfaction with online learning. Conclusion: Findings will help academicians to identify strengths, areas of improvement, and encourage faculty to think deeply to restructure course learning objectives, teaching techniques to engage students and improve learning process.

Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Conclusions: Our study…

Background: It is critical to understand the factors that could affect the acceptance of the coronavirus disease 2019 (COVID-19) vaccine in the community. The aim of this study was to determine factors that could possibly affect the acceptance of Indonesian citizens of COVID-19 vaccination using a Technology Acceptance Model (TAM), a model how users come to accept and use a technology. Methods: An online survey was conducted between the first and fifth of November, 2020. Participants were asked to respond to questions on acceptance, perceived usefulness, perceived ease of use, perceived religiosity towards, and amount of information about COVID-19. This study used the Technology Acceptance Model (TAM) as the framework to decide factors that affect vaccine acceptance. Structural Equation Model was employed to assess the correlation between all explanatory variables and vaccine acceptance. Mann-Whitney test and Kruskal-Wallis rank were employed to assess demographic factors associated with acceptance. Results: In total, 311 responses were included for analysis. Our TAM model suggested…

Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we…

Introduction : The number of publications in Scopus on this topic increased from less than 50 in 1995 to more than 250 in 2015. In other hand, inconsistency in results about the correlation between yeast and lactic acid bacteria as probiotics has been evident since the early publications on use in broilers. Methods : A meta-analysis was conducted to determine relationship between lactic acid bacteria and yeast as probiotics to broiler diets on the growth performance, relative organ weight, blood parameters, and immune response of the broiler. A database was designed based on published data that reported the use of probiotics on the broiler. The method used for selecting articles was based on the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA) method. Articles selected were taken from PubMed, Web of science, Scopus, Google Scholar, and Science direct databases as well as individual. Results : The final database consists of 49 in vivo articles, 93 studies, and 225 treatments. The analysis statement in the system was a PROC MIXED procedure of SAS software.…

Biological agents and infectious pathogens have the potential to cause very significant harm, as the natural occurrence of disease and pandemics makes clear. As a way to better understand the risk of Global Catastrophic Biological Risks due to human activities, rather than natural sources, this paper reports on a dataset of 71 incidents involving either accidental or purposeful exposure to, or infection by, a highly infectious pathogenic agent. There has been significant effort put into both reducing the risk of purposeful spread of biological weapons, and biosafety intended to prevent the exposure to, or release of, dangerous pathogens in the course of research. Despite these efforts, there are incidents of various types that could potentially be controlled or eliminated by different lab and/or bioweapon research choices and safety procedures. The dataset of events presented here was compiled during a project conducted in 2019 to better understand biological risks from anthropic sources. The events which are listed are unrelated to clinical treatment of naturally occurring…

Aims: To evaluate the prevalence and risk factors of type 2 diabetes mellitus (T2DM) from 2000-2020 in various parts of Nepal. Methods: PubMed, Embase, Scopus, and Google Scholar were searched using the appropriate keywords. All Nepalese studies mentioning the prevalence of T2DM and/or details such as risk factors were included. Studies were screened using Covidence. Two reviewers independently selected studies based on the inclusion criteria. Meta-analysis was conducted using Comprehensive Meta-Analysis Software v.3. Results: Total 15 studies met the inclusion criteria. The prevalence of T2DM, pre-diabetes, and impaired glucose tolerance in Nepal in the last two decades was 10% (CI, 7.1%- 13.9%), 19.4% (CI, 11.2%- 31.3%), and 11.0% (CI, 4.3%- 25.4%) respectively. The prevalence of T2DM in the year 2010-15 was 7.75% (CI, 3.67-15.61), and it increased to 11.24% between 2015-2020 (CI, 7.89-15.77). There were 2.19 times higher odds of having T2DM if the body mass index was ≥24.9 kg/m 2 . Analysis showed normal waist circumference, normal blood pressure, and no history of T2DM in a…

Background : At the time of publication, the most devastating desert locust crisis in decades is affecting East Africa, the Arabian Peninsula and South-West Asia. The situation is extremely alarming in East Africa, where Kenya, Ethiopia and Somalia face an unprecedented threat to food security and livelihoods. Most of the time, however, locusts do not occur in swarms, but live as relatively harmless solitary insects. The phenotypically distinct solitarious and gregarious locust phases differ markedly in many aspects of behaviour, physiology and morphology, making them an excellent model to study how environmental factors shape behaviour and development. A better understanding of the extreme phenotypic plasticity in desert locusts will offer new, more environmentally sustainable ways of fighting devastating swarms. Methods : High molecular weight DNA derived from two adult males was used for Mate Pair and Paired End Illumina sequencing and PacBio sequencing. A reliable reference genome of Schistocerca gregaria was assembled using the ABySS pipeline, scaffolding was improved using…

Background : This study was conducted to determine the prevalence of headache in coronavirus disease 2019 (COVID-19) and to assess its association as a predictor for COVID-19. This study also aimed to discuss the possible pathogenesis of headache in COVID-19. Methods : Available articles from PubMed, Scopus, and Web of Science were searched as of September 2 nd , 2020. Data on characteristics of the study, headache and COVID-19 were extracted following the PRISMA guidelines. Biases were assessed using the Newcastle-Ottawa scale. The cumulative prevalence of headache was calculated for the general population (i.e. adults and children). The pooled odd ratio (OR) with 95% confidence intervals (95%CI) was calculated using the Z test to assess the association between headache and the presence of COVID-19 cases. Results : We included 104,751 COVID-19 cases from 78 eligible studies to calculate the global prevalence of headache in COVID-19 and 17 studies were included to calculate the association of headache and COVID-19. The cumulative prevalence of headache in COVID-19 was 25.2% (26,464…

Background: The COVID-19 pandemic has brought about many changes in all sectors of life, especially in the field of education. These changes aim to make the learning process more effective in the pandemic environment. However, it can be challenging, as some students do not give positive responses to these changes, especially those in remote areas. This article aims to identify and report students' perceptions about the effectiveness of online learning during the COVID-19 pandemic in the remote North Tapanuli region of Indonesia. Methods: In this study, data were obtained using an online survey involving 30 students from three levels of education, namely junior high school, senior high school, and college. The data gathered from the survey were analyzed using quantitative descriptive methods. Results: Results show that online learning is considered less effective by students in remote areas; this happens because communication networks and infrastructure do not adequately support them to follow online learning. Conclusion: Teachers need to evaluate how to teach as well as re-design…

Abstract Alternative splicing produces multiple functional transcripts from a single gene. Dysregulation of splicing is known to be associated with disease and as a hallmark of cancer. Existing tools for differential transcript usage (DTU) analysis either lack in performance, cannot account for complex experimental designs or do not scale to massive scRNA-seq data. We introduce satuRn, a fast and flexible quasi-binomial generalized linear modelling framework that is on par with the best performing DTU methods from the bulk RNA-seq realm, while providing good false discovery rate control, addressing complex experimental designs and scaling to scRNA-seq applications.