Showing papers in "F1000Research in 2021"

Sustainable data analysis with Snakemake.

Abstract: 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 can be used to guarantee this, and how it enables an ergonomic, combined, unified representation of all steps involved in data analysis, ranging from raw data processing, to quality control and fine-grained, interactive exploration and plotting of final results.

Doublet identification in single-cell sequencing data using scDblFinder

Abstract: 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.

Anosmia and dysgeusia in SARS-CoV-2 infection: Incidence and effects on COVID-19 severity and mortality, and the possible pathobiology mechanisms - a systematic review and meta-analysis

Abstract: 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 prevalence of 38.2% (95% CI: 36.5%, 47.2%); whereas, dysgeusia was reported in 11,337 patients out of 30,901 COVID-19 patients from 101 studies, with prevalence of 36.6% (95% CI: 35.2%, 45.2%), worldwide. Furthermore, the prevalence of anosmia was 10.2-fold higher (OR: 10.21; 95% CI: 6.53, 15.96, p < 0.001) and that of dysgeusia was 8.6-fold higher (OR: 8.61; 95% CI: 5.26, 14.11, p < 0.001) in COVID-19 patients compared to those with other respiratory infections or COVID-19 like illness. To date, no study has assessed the association of anosmia and dysgeusia with severity and mortality of COVID-19. Conclusion: Anosmia and dysgeusia are prevalent in COVID-19 patients compared to those with the other non-COVID-19 respiratory infections. Several possible mechanisms have been hypothesized; however, future studies are warranted to elucidate the definitive mechanisms of anosmia and dysgeusia in COVID-19. Protocol registration: PROSPERO CRD42020223204.

Digital screen time during the COVID-19 pandemic: a public health concern

Abstract: 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 available guidelines and incorporate evidence-based interventions for preventing unhealthy screen time among the affected individuals Such interventions may address harmful behaviors associated with screen time and promote active lifestyles that may improve health across populations during and after this pandemic

SARS-CoV-2 and the role of fomite transmission: A systematic review

Abstract: 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 SARS-CoV-2 tests across 51 studies (using RT-PCR) ranged from 0.5% to 75%. Cycle threshold values ranged from 20.8 to 44.1. Viral concentrations were reported in 17 studies; however, discrepancies in the methods for estimation prevented comparison. Eleven studies (17.5%) attempted viral culture, but none found a cytopathic effect. Results of the systematic review showed that healthcare settings were most frequently tested (25/35, 71.4%), but laboratories reported the highest frequency of contaminated surfaces (20.5%, 17/83). Conclusions: The majority of studies report identification of SARS-CoV-2 RNA on inanimate surfaces; however, there is a lack of evidence demonstrating the recovery of viable virus. Lack of positive viral cultures suggests that the risk of transmission of SARS-CoV-2 through fomites is low. Heterogeneity in study designs and methodology prevents comparisons of findings across studies. Standardized guidelines for conducting and reporting research on fomite transmission is warranted.

Global prevalence of prolonged gastrointestinal symptoms in COVID-19 survivors and potential pathogenesis: A systematic review and meta-analysis

Abstract: 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%) and prolonged diarrhea was found in 34 of 1,073 survivors (4.12%, 95% CI: 1.07%-14.64%). A total of 156 patients among 2,238 COVID-19 survivors (4.41%, 95% CI: 1.91%-9.94%) complained of persistent decreased or loss of appetite. The cumulative prevalence of prolonged abdominal pain was 1.68% (95% CI: 0.84%-3.32%), whereas persistent dysgeusia was identified in 130 cases among 1,887 COVID-19 survivors (7.04%, 95% CI: 5.96%-8.30%). Data was insufficient to assess the relationship between COVID-19 severity and the occurrence of all prolonged GI symptoms. Conclusion: Persistent GI symptoms among COVID-19 survivors after discharge or recovery raises a concern regarding the long-term impact of the COVID-19 infection on the quality of life of the survivors. Despite several potential explanations proposed, studies that aim to follow patients after recovery from COVID-19 and determine the pathogenesis of the prolonged symptoms of COVID-19 survivors are warranted. PROSPERO registration: CRD42021239187.

Epidemiology of Alzheimer’s disease and other dementias: rising global burden and forecasted trends

Abstract: 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, Slovenia, Monaco, Greece and Germany. The prevalence is higher in high-income regions such as Western Europe compared to Asia and Africa. However, total number of affected individuals is substantial in South and East Asian regions, in particular China, Japan and India. Dementia related deaths are projected to increase from the current 2.4 million per year to 5.8 million by 2040. Women are more likely to be affected by dementia than men. Age-standardized rates have not changed indicating possible stability of risk factors. Conclusions : Alzheimer’s disease and other dementias are rising rapidly and will more than double in mortality burden over the next 20 years. The tremendous burden in high- and middle-income countries can potentially overwhelm communities and health systems. Urgent measures are needed to allocate funding and provide residential care for affected persons.

Make Interactive Complex Heatmaps in R

Abstract: Heatmap is a powerful visualization method on two-dimensional data to reveal patterns shared by subsets of rows and columns. In R, there are many packages that make heatmaps. Among them, ComplexHeatmap provides rich tools for constructing highly customizable heatmaps. It can easily establish connections between information from multiple sources by automatically concatenating and adjusting multiple heatmaps as well as complex annotations, which makes it widely applied in data analysis in various fields, especially in Bioinformatics. Nevertheless, the limit of ComplexHeatmap still exists. It only generates static plots which restricts deeper inspections on complex heatmaps, e.g., to look into a subset of rows and columns when a specific pattern of interest is observed from the heatmap. In this work, we described a new R/Bioconductor package InteractiveComplexHeatmap that brings interactivity to ComplexHeatmap. InteractiveComplexHeatmap is designed with an easy-to-use interface where static complex heatmaps can be directly exported to an interactive Shiny web application only with one extra line of code. The interactive application contains comprehensive tools for manipulating heatmaps. Besides common tools as supported in other interactive heatmap packages, InteractiveComplexHeatmap additionally supports, e.g., selecting over multiple heatmaps and searching heatmaps via row or column labels. Also, InteractiveComplexHeatmap provides methods for exporting static heatmaps from other popular heatmap functions, e.g., heatmap.2() or pheatmap(), to interactive heatmap applications. Finally, InteractiveComplexHeatmap provides flexible functionalities for integrating interactive heatmap widgets into other Shiny applications. InteractiveComplexHeatmap provides a user interface for self-defining response to the selection events on heatmaps, which helps to implement more complex Shiny web applications.

SARS-CoV-2 and the role of airborne transmission: a systematic review

Abstract: Background: Airborne transmission is the spread of an infectious agent caused by the dissemination of droplet nuclei (aerosols) that remain infectious when suspended in the air. We carried out a systematic review to identify, appraise and summarise the evidence from studies of the role of airborne transmission of SARS-CoV-2. Methods: We searched LitCovid, MedRxiv, Google Scholar and the WHO Covid-19 database from 1 February to 20 December 2020 and included studies on airborne transmission. Data were dual extracted and we assessed quality using a modified QUADAS 2 risk of bias tool. Results: We included 67 primary studies and 22 reviews on airborne SARS-CoV-2. Of the 67 primary studies, 53 (79%) reported data on RT-PCR from air samples, 12 (18%) report cycle threshold values and 18 (127%) copies per sample volume. All primary studies were observational and of low quality. The research often lacked standard methods, standard sampling sizes and reporting items. We found 36 descriptions of different air samplers deployed. Of the 42 studies conducted in-hospital that reported binary RT-PCR tests, 24 (57%) reported positive results for SARs-CoV-2 (142 positives out of 1,403 samples: average 10.1%, range 0% to 100%). There was no pattern between the type of hospital setting (ICU versus non-ICU) and RT-PCR positivity. Seventeen studies reported potential air transmission in the outdoors or in the community, of which seven performed RT-PCR sampling, and two studies reported weak positive RNA samples for 2 or more genes (5 of 125 samples positive: average 4.0%). Ten studies attempted viral culture with no serial passage. Conclusion: SARS-CoV-2 RNA is detected intermittently in the air in various settings. Standardized guidelines for conducting and reporting research on airborne transmission are needed. The lack of recoverable viral culture samples of SARS-CoV-2 prevents firm conclusions from being drawn about airborne transmission.

Hemorrhagic and ischemic stroke in patients with coronavirus disease 2019: Incidence, risk factors, and pathogenesis - a systematic review and meta-analysis

Abstract: 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 hemorrhagic stroke (incidence: 28.42%) in COVID-19 patients who experienced a stroke. In COVID-19 patients who experienced a stroke, hospital admission with respiratory symptoms was more commonly reported than that with neurological symptoms (20.83% for hemorrhagic stroke and 5.51% for ischemic stroke versus 6.94% for hemorrhagic stroke and 5.33% for ischemic stroke, respectively). The pooled mortality rate of COVID-19 patients who experienced a hemorrhagic and ischemic stroke was 44.72% (95% CI 36.73%-52.98%) and 36.23% (95% CI 30.63%-42.24%), respectively. Conclusions: Although the occurrence of hemorrhagic and ischemic stroke is low, the mortality rates of both stroke types in patients with COVID-19 are concerning, and therefore, despite several potential pathogeneses that have been proposed, studies aimed at definitively elucidating the mechanisms of hemorrhagic and ischemic stroke in individuals with COVID-19 are warranted. PROSPERO registration: CRD42020224470 (04/12/20) © 2021 Syahrul S et al.

SARS-CoV-2 and the role of orofecal transmission: a systematic review

Abstract: 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 their contacts and 46 (96%) detected binary RT-PCR with 535 out of 1358 samples positive for SARS-CoV-2 (average 39.4%). The results suggest a long duration of fecal shedding, often recorded after respiratory samples tested negative, and symptoms of gastrointestinal disease were reported in several studies. Twenty-nine studies reported finding SARS-CoV-2 RNA in wastewater, river water or toilet areas. Six studies attempted viral culture from COVID-19 patients’ fecal samples: culture was successful in 3 of 6 studies, and one study demonstrated invasion of the virus into intestinal epithelial cells. Conclusions: Varied observational and mechanistic evidence suggests SARS-CoV-2 can infect and be shed from the gastrointestinal tract, including some data demonstrating viral culture in fecal samples. To fully assess these risks, quantitative data on infectious virus in these settings and infectious dose are needed.

Rationality over fashion and hype in drug design.

Abstract: The current hype associated with machine learning and artificial intelligence often confuses scientists and students and may lead to uncritical or inappropriate applications of computational approaches. Even the field of computer-aided drug design (CADD) is not an exception. The situation is ambivalent. On one hand, more scientists are becoming aware of the benefits of learning from available data and are beginning to derive predictive models before designing experiments. However, on the other hand, easy accessibility of in silico tools comes at the risk of using them as “black boxes” without sufficient expert knowledge, leading to widespread misconceptions and problems. For example, results of computations may be taken at face value as “nothing but the truth” and data visualization may be used only to generate “pretty and colorful pictures”. Computational experts might come to the rescue and help to re-direct such efforts, for example, by guiding interested novices to conduct meaningful data analysis, make scientifically sound predictions, and communicate the findings in a rigorous manner. However, this is not always ensured. This contribution aims to encourage investigators entering the CADD arena to obtain adequate computational training, communicate or collaborate with experts, and become aware of the fundamentals of computational methods and their given limitations, beyond the hype. By its very nature, this Opinion is partly subjective and we do not attempt to provide a comprehensive guide to the best practices of CADD; instead, we wish to stimulate an open discussion within the scientific community and advocate rational rather than fashion-driven use of computational methods. We take advantage of the open peer-review culture of F1000Research such that reviewers and interested readers may engage in this discussion and obtain credits for their candid personal views and comments. We hope that this open discussion forum will contribute to shaping the future practice of CADD.

A multidimensional quality model: an opportunity for patients, their kin, healthcare providers and professionals to coproduce health

Abstract: 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 of people involved in the interdependent work. The change of Person Centred Care to Kin Centred Care introduces a broader concept of the person and ensures that Person Centred Care is included in every domain of quality rather than as a separate domain. The concentration on the technological aspects of quality is an example of the problem in the past. This is a more expansive view of what "person-centredness" began. The delivery of health and healthcare requires people working in differing roles, with explicit attention to the lived realities of the people in the roles of professional and patient. The new model will provide a construct that may make the attainment of equity in healthcare more possible with a focus on kindness for all.

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

Abstract: 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 MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

Current market rates for scholarly publishing services.

Abstract: 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 scholarly article today come to lie at around US$400. These results appear uncontroversial as they not only match previous data using different methodologies, but also conform to the costs that many publishers have openly or privately shared. We discuss the numerous additional non-publication items that make up the difference between these publication costs and final price at the more expensive, legacy publishers.

Increase of SARS-CoV-2 RNA load in faecal samples prompts for rethinking of SARS-CoV-2 biology and COVID-19 epidemiology

Abstract: Background Scientific evidence for the involvement of human microbiota in the development of COVID-19 disease has been reported recently. SARS-CoV-2 RNA presence in human faecal samples and SARS-CoV-2 activity in faeces from COVID-19 patients have been observed. Methods Starting from these observations, an experimental design was developed to cultivate in vitro faecal microbiota from infected individuals, to monitor the presence of SARS-CoV-2, and to collect data on the relationship between faecal bacteria and the virus. Results Our results indicate that SARS-CoV-2 replicates in vitro in bacterial growth medium, that the viral replication follows bacterial growth and it is influenced by the administration of specific antibiotics. SARS-CoV-2-related peptides have been detected in 30-day bacterial cultures and characterised. Discussion Our observations are compatible with a 'bacteriophage-like' behaviour of SARS-CoV-2, which, to our knowledge has not been observed or described before. These results are unexpected and hint towards a novel hypothesis on the biology of SARS-CoV-2 and on the COVID-19 epidemiology. The discovery of possible new modes of action of SARS-CoV-2 has far-reaching implications for the prevention and the treatment of the disease.

BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS.

Abstract: 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.

The effects of lactic acid bacteria and yeasts as probiotics on the growth performance, relative organ weight, blood parameters, and immune responses of broiler: A meta-analysis.

Abstract: 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. The level of probiotic increased (p <0.001) body weight, body weight gain, and feed intake of broiler. There was a reduction (p <0.01) on feed conversion ratio and mortality on the level probiotic given to broiler. Supplementation of probiotics in broiler diet increased (p <0.001) the weight of liver, spleen, gizzard, bursa of fabricius and carcass yield, while reduced (p<0.001) abdominal fat weight. The probiotic given increased the total of red and white blood cells (both at p < 0.001) but did not affect lymphocyte. Discussion : It can be concluded the yeast act as supporting agent that serves lactic acid bacteria as probiotic increases the growth performance, relative organ weight, blood parameters, and immune response of the broiler.

Perception on Online Teaching and Learning Among Health Sciences Students in Higher Education Institutions during the COVID-19 Lockdown - Ways to Improve Teaching and Learning in Saudi Colleges and Universities

Abstract: 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. © 2021 Aziz Ansari K et al.

Data extraction methods for systematic review (semi)automation: A living systematic review

Abstract: 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: We systematically and continually search MEDLINE, Institute of Electrical and Electronics Engineers (IEEE), arXiv, and the dblp computer science bibliography databases. Full text screening and data extraction are conducted within an open-source living systematic review application created for the purpose of this review. This iteration of the living review includes publications up to a cut-off date of 22 April 2020. Results: In total, 53 publications are included in this version of our review. Of these, 41 (77%) of the publications addressed extraction of data from abstracts, while 14 (26%) used full texts. A total of 48 (90%) publications developed and evaluated classifiers that used randomised controlled trials as the main target texts. Over 30 entities were extracted, with PICOs (population, intervention, comparator, outcome) being the most frequently extracted. A description of their datasets was provided by 49 publications (94%), but only seven (13%) made the data publicly available. Code was made available by 10 (19%) publications, and five (9%) implemented publicly available tools. Conclusions: This living systematic review presents an overview of (semi)automated data-extraction literature of interest to different types of systematic review. We identified a broad evidence base of publications describing data extraction for interventional reviews and a small number of publications extracting epidemiological or diagnostic accuracy data. The lack of publicly available gold-standard data for evaluation, and lack of application thereof, makes it difficult to draw conclusions on which is the best-performing system for each data extraction target. With this living review we aim to review the literature continually.

Factors influencing COVID-19 vaccine acceptance in Indonesia: An adoption of Technology Acceptance Model

Abstract: 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 that high perceived usefulness significantly increased COVID-19 vaccine acceptance and high perceived ease of use significantly increased the perceived usefulness. Perceived religiosity did not substantially affect vaccine acceptance. The amount of information on COVID-19 also did not significantly affect vaccine acceptance. Our data suggested that vaccine acceptance was associated with age, type of occupation, marital status and monthly income to some degree. Conclusion: Since perceived usefulness affects vaccine acceptance, the government should focus on the usefulness of the vaccine when promoting the COVID-19 vaccine to Indonesian citizens. In addition, since perceived ease of use significantly affects users' acceptance to COVID-19 vaccine, the easier to acquire the vaccine in the community, the higher chance that the citizens are willing to be vaccinated.

Developing open-source software for bioimage analysis: opportunities and challenges.

Abstract: Fast-paced innovations in imaging have resulted in single systems producing exponential amounts of data to be analyzed. Computational methods developed in computer science labs have proven to be crucial for analyzing these data in an unbiased and efficient manner, reaching a prominent role in most microscopy studies. Still, their use usually requires expertise in bioimage analysis, and their accessibility for life scientists has therefore become a bottleneck. Open-source software for bioimage analysis has developed to disseminate these computational methods to a wider audience, and to life scientists in particular. In recent years, the influence of many open-source tools has grown tremendously, helping tens of thousands of life scientists in the process. As creators of successful open-source bioimage analysis software, we here discuss the motivations that can initiate development of a new tool, the common challenges faced, and the characteristics required for achieving success.

Global prevalence and pathogenesis of headache in COVID-19: A systematic review and meta-analysis [version 2;peer review: 2 approved]

Abstract: 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 2nd, 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 out of 104,751 cases). Headache was found to be more prevalent, approximately by two-fold, in COVID-19 patients than in non-COVID-19 patients (other respiratory viral infections), OR: 1.73;95% CI: 1.94, 2.5 with p=0.04. Conclusion: Headache is common among COVID-19 patients and seems to be more common in COVID-19 patients compared to thosewith the non-COVID-19 viral infection. No definitive mechanisms on how headache emerges in COVID-19 patients but several possible hypotheses have been proposed. However, extensive studies are warranted to elucidate the mechanisms. © 2021. Mutiawati E et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Novel antifungal agents in clinical trials

Abstract: 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.

Optimal use of tocilizumab for severe and critical COVID-19: A systematic review and meta-analysis

Abstract: Background: Several studies have revealed the potential use of tocilizumab in treating COVID-19 since no therapy has yet been approved for COVID-19 pneumonia. Tocilizumab may provide clinical benefits for cytokine release syndrome in COVID-19 patients. Methods: We searched for relevant studies in PubMed, Embase, Medline, and Cochrane published from March to October 2020 to evaluate optimal use and baseline criteria for administration of tocilizumab in severe and critically ill COVID-19 patients. Research involving patients with confirmed SARS-CoV-2 infection, treated with tocilizumab and compared with the standard of care (SOC) was included in this study. We conducted a systematic review to find data about the risks and benefits of tocilizumab and outcomes from different baseline criteria for administration of tocilizumab as a treatment for severe and critically ill COVID-19 patients. Results: A total of 26 studies, consisting of 23 retrospective studies, one prospective study, and two randomised controlled trials with 2112 patients enrolled in the tocilizumab group and 6160 patients in the SOC group, were included in this meta-analysis. Compared to the SOC, tocilizumab showed benefits for all-cause mortality events and a shorter time until death after first intervention but showed no difference in hospital length of stay. Upon subgroup analysis, tocilizumab showed fewer all-cause mortality events when CRP level ≥100 mg/L, P/F ratio 200-300 mmHg, and P/F ratio <200 mmHg. However, tocilizumab showed a longer length of stay when CRP <100 mg/L than the SOC. Conclusion: This meta-analysis demonstrated that tocilizumab has a positive effect on all-cause mortality. It should be cautiously administrated for optimal results and tailored to the patient's eligibility criteria.

Defining and validating regenerative farm systems using a composite of ranked agricultural practices.

Abstract: 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 scores in one or both of the cropping systems. Water infiltration rates were significantly faster in more regenerative almond orchards. Soil bacterial biomass and Haney soil health test scores were higher as cropland incorporated more regenerative practices. Plant species diversity and biomass increased significantly with the number of regenerative practices employed on almonds and rangelands. Invertebrate species diversity and richness were positively associated with regenerative practices in corn, almonds, and rangelands, whereas pest populations and almond yields were unaffected by the number of regenerative practices. Corn yields were negatively associated with more regenerative practices, while almond yields were unaffected by the number of regenerative practices. Profit was significantly higher on more regenerative corn and almond operations. Conclusions: Our scoring system scaled positively with desired regenerative outcomes, and provides the basis for predicting ecosystem responses with minimal information about the farming operation. Natural clusters in the number of regenerative practices used can be used to distinguish regenerative and conventional operations.

AI in healthcare: A narrative review

Abstract: 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.

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

Abstract: 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 highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans

Risk factors for mortality in hospitalized patients with COVID-19 from three hospitals in Peru: A retrospective cohort study

Abstract: Background: Peru was one of the countries with the highest COVID-19 mortality worldwide during the first stage of the pandemic. It is then relevant to evaluate the risk factors for mortality in patients hospitalized for COVID-19 in three hospitals in Peru in 2020, from March to May, 2020. Methods: We carried out a retrospective cohort study. The population consisted of patients from three Peruvian hospitals hospitalized for a diagnosis of COVID-19 during the March-May 2020 period. Independent sociodemographic variables, medical history, symptoms, vital functions, laboratory parameters and medical treatment were evaluated. In-hospital mortality was assessed as the outcome. We performed Cox regression models (crude and adjusted) to evaluate risk factors for in-hospital mortality. Hazard ratios (HR) with their respective 95% confidence intervals (95% CI) were calculated. Results: We analyzed 493 hospitalized adults; 72.8% (n=359) were male and the mean age was 63.3 ± 14.4 years. COVID-19 symptoms appeared on average 7.9 ± 4.0 days before admission to the hospital, and the mean oxygen saturation on admission was 82.6 ± 13.8. While 67.6% (n=333) required intensive care unit admission, only 3.3% (n=16) were admitted to this unit, and 60.2% (n=297) of the sample died. In the adjusted regression analysis, it was found that being 60 years old or older (HR=1.57; 95% CI: 1.14-2.15), having two or more comorbidities (HR=1.53; 95% CI: 1.10-2.14), oxygen saturation between 85-80% (HR=2.52; 95% CI: 1.58-4.02), less than 80% (HR=4.59; 95% CI: 3.01-7.00), and being in the middle (HR=1.65; 95% CI: 1.15-2.39) and higher tertile (HR=2.18; 95% CI: 1.51-3.15) of the neutrophil-to-lymphocyte ratio, increased the risk of mortality. Conclusions: The risk factors found agree with what has been described in the literature and allow the identification of vulnerable groups in whom monitoring and early identification of symptoms should be prioritized in order to reduce mortality.

Philympics 2021: Prophage Predictions Perplex Programs

Abstract: Background Most bacterial genomes contain integrated bacteriophages—prophages—in various states of decay. Many are active and able to excise from the genome and replicate, while others are cryptic prophages, remnants of their former selves. Over the last two decades, many computational tools have been developed to identify the prophage components of bacterial genomes, and it is a particularly active area for the application of machine learning approaches. However, progress is hindered and comparisons thwarted because there are no manually curated bacterial genomes that can be used to test new prophage prediction algorithms. Methods We present a library of gold-standard bacterial genome annotations that include manually curated prophage annotations, and a computational framework to compare the predictions from different algorithms. We use this suite to compare all extant stand-alone prophage prediction algorithms to identify their strengths and weaknesses. We provide a FAIR dataset for prophage identification, and demonstrate the accuracy, precision, recall, and f 1 score from the analysis of seven different algorithms for the prediction of prophages. Results We identified different strengths and weaknesses between the prophage prediction tools. Several tools exhibit exceptional f 1 scores, while others have better recall at the expense of more false positives. The tools vary greatly in runtime performance with few exhibiting all desirable qualities for large-scale analyses. Conclusions Our library of gold-standard prophage annotations and benchmarking framework provide a valuable resource for exploring strengths and weaknesses of current and future prophage annotation tools. We discuss caveats and concerns in this analysis, how those concerns may be mitigated, and avenues for future improvements. This framework will help developers identify opportunities for improvement and test updates. It will also help users in determining the tools that are best suited for their analysis.