cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14320554.v1
title: Human induced pluripotent stem cells as a tool for disease modeling and drug screening for COVID-19

description: Abstract The emergence of the new corona virus (SARS-CoV-2) and the resulting COVID-19 pandemic requires fast development of novel prevention and therapeutic strategies. These rely on understanding the biology of the virus and its interaction with the host, and on agnostic phenotypic screening for compounds that prevent viral infection. In vitro screenings of compounds are usually performed in human or animal-derived tumor or immortalized cell lines due to their ease of culturing. However, these platforms may not represent the tissues affected by the disease in vivo, and therefore better models are needed to validate and expedite drug development, especially in face of the COVID-19 pandemic. In this scenario, human induced pluripotent stem cells (hiPSCs) are a powerful research tool due to their ability to generate normal differentiated cell types relevant for the disease. Here we discuss the different ways hiPSCs can contribute to COVID-19 related research, including modeling the disease in vitro and serving as a platform for drug screening.
DOI: 10.6084/m9.figshare.14320555
title: Host-shift as the cause of emerging infectious diseases: Experimental approaches using Drosophila-virus interactions

description: Abstract Host shifts, when a cross-species transmission of a pathogen can lead to successful infections, are the main cause of emerging infectious diseases, such as COVID-19. A complex challenge faced by the scientific community is to address the factors that determine whether the cross-species transmissions will result in spillover or sustained onwards infections. Here we review recent literature and present a perspective on current approaches we are using to understand the mechanisms underlying host shifts. We highlight the usefulness of the interactions between Drosophila species and viruses as an ideal study model. Additionally, we discuss how cross-infection experiments — when pathogens from a natural reservoir are intentionally injected in novel host species— can test the effect cross-species transmissions may have on the fitness of virus and host, and how the host phylogeny may influence this response. We also discuss experiments evaluating how cooccurrence with other viruses or the presence of the endosymbiont bacteria Wolbachia may affect the performance of new viruses in a novel host. Finally, we discuss the need of surveys of virus diversity in natural populations using next-generation sequencing technologies. In the long term, these approaches can contribute to a better understanding of the basic biology of host shifts.
DOI: 10.6084/m9.figshare.14320555.v1
title: Host-shift as the cause of emerging infectious diseases: Experimental approaches using Drosophila-virus interactions

description: Abstract Host shifts, when a cross-species transmission of a pathogen can lead to successful infections, are the main cause of emerging infectious diseases, such as COVID-19. A complex challenge faced by the scientific community is to address the factors that determine whether the cross-species transmissions will result in spillover or sustained onwards infections. Here we review recent literature and present a perspective on current approaches we are using to understand the mechanisms underlying host shifts. We highlight the usefulness of the interactions between Drosophila species and viruses as an ideal study model. Additionally, we discuss how cross-infection experiments — when pathogens from a natural reservoir are intentionally injected in novel host species— can test the effect cross-species transmissions may have on the fitness of virus and host, and how the host phylogeny may influence this response. We also discuss experiments evaluating how cooccurrence with other viruses or the presence of the endosymbiont bacteria Wolbachia may affect the performance of new viruses in a novel host. Finally, we discuss the need of surveys of virus diversity in natural populations using next-generation sequencing technologies. In the long term, these approaches can contribute to a better understanding of the basic biology of host shifts.
DOI: 10.6084/m9.figshare.14320556
title: Molecular mechanisms and pharmacological interventions in the replication cycle of human coronaviruses

description: Abstract SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), as well as SARS-CoV from 2003 along with MERS-CoV from 2012, is a member of the Betacoronavirus genus of the Nidovirales order and is currently the cause of the pandemic called COVID-19 (or Coronavirus disease 2019). COVID-19, which is characterized by cough, fever, fatigue, and severe cases of pneumonia, has affected more than 23 million people worldwide until August 25th, 2020. Here, we present a review of the cellular mechanisms associated with human coronavirus replication, including the unique molecular events related to the replication transcription complex (RTC) of coronaviruses. We also present information regarding the interactions between each viral protein and cellular proteins associated to known host-pathogen implications for the coronavirus biology. Finally, a specific topic addresses the current attempts for pharmacological interventions against COVID-19, highlighting the possible effects of each drug on the molecular events of viral replication. This review intends to aid future studies for a better understanding of the SARS-CoV-2 replication cycle and the development of pharmacological approaches targeting COVID-19.
DOI: 10.6084/m9.figshare.14320556.v1
title: Molecular mechanisms and pharmacological interventions in the replication cycle of human coronaviruses

description: Abstract SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), as well as SARS-CoV from 2003 along with MERS-CoV from 2012, is a member of the Betacoronavirus genus of the Nidovirales order and is currently the cause of the pandemic called COVID-19 (or Coronavirus disease 2019). COVID-19, which is characterized by cough, fever, fatigue, and severe cases of pneumonia, has affected more than 23 million people worldwide until August 25th, 2020. Here, we present a review of the cellular mechanisms associated with human coronavirus replication, including the unique molecular events related to the replication transcription complex (RTC) of coronaviruses. We also present information regarding the interactions between each viral protein and cellular proteins associated to known host-pathogen implications for the coronavirus biology. Finally, a specific topic addresses the current attempts for pharmacological interventions against COVID-19, highlighting the possible effects of each drug on the molecular events of viral replication. This review intends to aid future studies for a better understanding of the SARS-CoV-2 replication cycle and the development of pharmacological approaches targeting COVID-19.
DOI: 10.6084/m9.figshare.14320559
title: Control and prevention of infectious diseases from a One Health perspective

description: Abstract The ongoing COVID-19 pandemic has caught the attention of the global community and rekindled the debate about our ability to prevent and manage outbreaks, epidemics, and pandemics. Many alternatives are suggested to address these urgent issues. Some of them are quite interesting, but with little practical application in the short or medium term. To realistically control infectious diseases, human, animal, and environmental factors need to be considered together, based on the One Health perspective. In this article, we highlight the most effective initiatives for the control and prevention of infectious diseases: vaccination; environmental sanitation; vector control; social programs that encourage a reduction in the population growth; control of urbanization; safe sex stimulation; testing; treatment of sexually and vertically transmitted infections; promotion of personal hygiene practices; food safety and proper nutrition; reduction of the human contact with wildlife and livestock; reduction of social inequalities; infectious disease surveillance; and biodiversity preservation. Subsequently, this article highlights the impacts of human genetics on susceptibility to infections and disease progression, using the SARS-CoV-2 infection as a study model. Finally, actions focused on mitigation of outbreaks and epidemics and the importance of conservation of ecosystems and translational ecology as public health strategies are also discussed.
DOI: 10.6084/m9.figshare.14320559.v1
title: Control and prevention of infectious diseases from a One Health perspective

description: Abstract The ongoing COVID-19 pandemic has caught the attention of the global community and rekindled the debate about our ability to prevent and manage outbreaks, epidemics, and pandemics. Many alternatives are suggested to address these urgent issues. Some of them are quite interesting, but with little practical application in the short or medium term. To realistically control infectious diseases, human, animal, and environmental factors need to be considered together, based on the One Health perspective. In this article, we highlight the most effective initiatives for the control and prevention of infectious diseases: vaccination; environmental sanitation; vector control; social programs that encourage a reduction in the population growth; control of urbanization; safe sex stimulation; testing; treatment of sexually and vertically transmitted infections; promotion of personal hygiene practices; food safety and proper nutrition; reduction of the human contact with wildlife and livestock; reduction of social inequalities; infectious disease surveillance; and biodiversity preservation. Subsequently, this article highlights the impacts of human genetics on susceptibility to infections and disease progression, using the SARS-CoV-2 infection as a study model. Finally, actions focused on mitigation of outbreaks and epidemics and the importance of conservation of ecosystems and translational ecology as public health strategies are also discussed.
DOI: 10.6084/m9.figshare.14320562.v1
title: Extreme phenotypes approach to investigate host genetics and COVID-19 outcomes

description: Abstract COVID-19 comprises clinical outcomes of SARS-CoV-2 infection and is highly heterogeneous, ranging from asymptomatic individuals to deceased young adults without comorbidities. There is growing evidence that host genetics play an important role in COVID-19 severity, including inborn errors of immunity, age-related inflammation and immunosenescence. Here we present a brief review on the known order of events from infection to severe system-wide disturbance due to COVID-19 and summarize potential candidate genes and pathways. Finally, we propose a strategy of subject’s ascertainment based on phenotypic extremes to take part in genomic studies and elucidate intrinsic risk factors involved in COVID-19 severe outcomes.
DOI: 10.6084/m9.figshare.14320561
title: Challenges in estimating virus divergence times in short epidemic timescales with special reference to the evolution of SARS-CoV-2 pandemic

description: Abstract The estimation of evolutionary parameters provides essential information for designing public health policies. In short time intervals, however, nucleotide substitutions are ineffective to record all complexities of virus population dynamics. In this sense, the current SARS-CoV-2 pandemic poses a challenge for evolutionary analysis. We used computer simulation to evolve populations in scenarios of varying temporal intervals to evaluate the impact of the age of an epidemic on estimates of time and geography. Before estimating virus timescales, the shape of tree topologies can be used as a proxy to assess the effectiveness of the virus phylogeny in providing accurate estimates of evolutionary parameters. In short timescales, estimates have larger uncertainty. We compared the predictions from simulations with empirical data. The tree shape of SARS-CoV-2 was closer to shorter timescales scenarios, which yielded parametric estimates with larger uncertainty, suggesting that estimates from these datasets should be evaluated cautiously. To increase the accuracy of the estimates of virus transmission times between populations, the uncertainties associated with the age estimates of both the crown and stem nodes should be communicated. We place the age of the common ancestor of the current SARS-CoV-2 pandemic in late September 2019, corroborating an earlier emergence of the virus.
DOI: 10.6084/m9.figshare.14320561.v1
title: Challenges in estimating virus divergence times in short epidemic timescales with special reference to the evolution of SARS-CoV-2 pandemic

description: Abstract The estimation of evolutionary parameters provides essential information for designing public health policies. In short time intervals, however, nucleotide substitutions are ineffective to record all complexities of virus population dynamics. In this sense, the current SARS-CoV-2 pandemic poses a challenge for evolutionary analysis. We used computer simulation to evolve populations in scenarios of varying temporal intervals to evaluate the impact of the age of an epidemic on estimates of time and geography. Before estimating virus timescales, the shape of tree topologies can be used as a proxy to assess the effectiveness of the virus phylogeny in providing accurate estimates of evolutionary parameters. In short timescales, estimates have larger uncertainty. We compared the predictions from simulations with empirical data. The tree shape of SARS-CoV-2 was closer to shorter timescales scenarios, which yielded parametric estimates with larger uncertainty, suggesting that estimates from these datasets should be evaluated cautiously. To increase the accuracy of the estimates of virus transmission times between populations, the uncertainties associated with the age estimates of both the crown and stem nodes should be communicated. We place the age of the common ancestor of the current SARS-CoV-2 pandemic in late September 2019, corroborating an earlier emergence of the virus.
DOI: 10.6084/m9.figshare.14320562
title: Extreme phenotypes approach to investigate host genetics and COVID-19 outcomes

description: Abstract COVID-19 comprises clinical outcomes of SARS-CoV-2 infection and is highly heterogeneous, ranging from asymptomatic individuals to deceased young adults without comorbidities. There is growing evidence that host genetics play an important role in COVID-19 severity, including inborn errors of immunity, age-related inflammation and immunosenescence. Here we present a brief review on the known order of events from infection to severe system-wide disturbance due to COVID-19 and summarize potential candidate genes and pathways. Finally, we propose a strategy of subject’s ascertainment based on phenotypic extremes to take part in genomic studies and elucidate intrinsic risk factors involved in COVID-19 severe outcomes.
DOI: 10.6084/m9.figshare.14320564
title: SARS-CoV-2 and COVID-19: A perspective from environmental virology

description: Abstract December 2019 marked the beginning of the current Coronavirus disease pandemic (COVID-19). Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) was identified as the causative agent of a viral pneumonia outbreak in Wuhan, Hubei Province, China. The alarming spread levels and clinical severity elevated the status of COVID-19 to the global pandemic by the World Health Organization. In 6 months, more than 25 million cases of infected people and more than 890,000 deaths by COVID-19 had been reported worldwide. The main goal of this review is to shed light upon the current COVID-19 epidemic situation in Brazil with a health approach highlighting some unique environmental, animal and epidemiological aspects.
DOI: 10.6084/m9.figshare.14320564.v1
title: SARS-CoV-2 and COVID-19: A perspective from environmental virology

description: Abstract December 2019 marked the beginning of the current Coronavirus disease pandemic (COVID-19). Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) was identified as the causative agent of a viral pneumonia outbreak in Wuhan, Hubei Province, China. The alarming spread levels and clinical severity elevated the status of COVID-19 to the global pandemic by the World Health Organization. In 6 months, more than 25 million cases of infected people and more than 890,000 deaths by COVID-19 had been reported worldwide. The main goal of this review is to shed light upon the current COVID-19 epidemic situation in Brazil with a health approach highlighting some unique environmental, animal and epidemiological aspects.
DOI: 10.6084/m9.figshare.14320566.v1
title: Cytogenetic and genetic data support Crossodactylus aeneus Müller, 1924 as a new junior synonym of C. gaudichaudii Duméril and Bibron, 1841 (Amphibia, Anura)

description: Abstract The nominal anuran species Crossodactylus gaudichaudii Duméril and Bibron, 1841 and Crossodactylus aeneus Müller, 1924 are indistinguishable based on adult and larval morphology, being subject of taxonomic doubts. Here, we describe the karyotypes of C. gaudichaudii and C. aeneus, using classical and molecular cytogenetic markers. In addition, we used sequences of the H1 mitochondrial DNA to infer their phylogenetic relationships by Maximum Likelihood (ML) and Maximum Parsimony (MP) approaches and species delimitation test (by bPTP approach). The karyotypic data do not differentiate C. gaudichaudii and C. aeneus in any of the chromosome markers assessed. In both phylogenetic analyses, C. gaudichaudii and C. aeneus were recovered into a strongly supported clade. The species delimitation analysis recovered the specimens assigned to C. gaudichaudii and C. aeneus as a single taxonomic unit. Taken the cytogenetic and genetic results together with previous studies of internal and external morphology of tadpoles and biacoustic pattern, C. gaudichaudii and C. aeneus could not be differentiated, which supports the hypothesis that they correspond to the same taxonomic unit, with C. aeneus being a junior synonym of C. gaudichaudii.
DOI: 10.6084/m9.figshare.14320566
title: Cytogenetic and genetic data support Crossodactylus aeneus Müller, 1924 as a new junior synonym of C. gaudichaudii Duméril and Bibron, 1841 (Amphibia, Anura)

description: Abstract The nominal anuran species Crossodactylus gaudichaudii Duméril and Bibron, 1841 and Crossodactylus aeneus Müller, 1924 are indistinguishable based on adult and larval morphology, being subject of taxonomic doubts. Here, we describe the karyotypes of C. gaudichaudii and C. aeneus, using classical and molecular cytogenetic markers. In addition, we used sequences of the H1 mitochondrial DNA to infer their phylogenetic relationships by Maximum Likelihood (ML) and Maximum Parsimony (MP) approaches and species delimitation test (by bPTP approach). The karyotypic data do not differentiate C. gaudichaudii and C. aeneus in any of the chromosome markers assessed. In both phylogenetic analyses, C. gaudichaudii and C. aeneus were recovered into a strongly supported clade. The species delimitation analysis recovered the specimens assigned to C. gaudichaudii and C. aeneus as a single taxonomic unit. Taken the cytogenetic and genetic results together with previous studies of internal and external morphology of tadpoles and biacoustic pattern, C. gaudichaudii and C. aeneus could not be differentiated, which supports the hypothesis that they correspond to the same taxonomic unit, with C. aeneus being a junior synonym of C. gaudichaudii.
DOI: 10.6084/m9.figshare.14320526
title: Meta-review inclusion exclusion data

description: Dataset: inclusion and exclusion data and flow accompanying a herbal medicine meta-review.
DOI: 10.6084/m9.figshare.14320526.v1
title: Meta-review inclusion exclusion data

description: Dataset: inclusion and exclusion data and flow accompanying a herbal medicine meta-review.
DOI: 10.17632/5jcg5vfx58.2
title: The Moroccan Video Intelligent Transport System dataset for vehicle detection

description: Intelligent transportation systems (ITS) are composed of functionalities that aim to reduce traffic jams and detect anomalies. These functionalities include vehicle detection and classification that represent critical tasks and require a high degree of accuracy to ensure the extracted information's reliability. Therefore, we present a key data set related to the detection of vehicles in Morocco, nicknamed MoVITS. The data provided in this paper is collected using a stereo-based vision system, and it is useful for vehicle detection and classification by using different methods for many purposes. This data set is intended to support researchers, stakeholders, and the general public interested in ITS. The vehicle video dataset incorporated with deep learning, transfer learning, and fine-tuning can provide outstanding vehicle detection and classification results.
DOI: 10.6084/m9.figshare.14320572
title: Neck circumference as predictor of excess body fat and cardiovascular risk factors in adolescents

description: OBJECTIVE:To verify whether neck circumference can predict cardiovascular risk factors and excess body fat in adolescents.METHODS:This cross-sectional study included male and female adolescents aged 10 to 14 years from Viçosa, Minas Gerais. The following data were collected: anthropometric measurements, blood pressure, percentage of body fat according to dual energy X-ray absorptiometry, and levels of fasting glucose, fasting insulin, triglycerides, total cholesterol, high-density lipoprotein, and low-density lipoprotein. The anthropometric measurements were used for calculating indices and assessing nutritional status. The receiver operating characteristic curve tested whether neck circumference could predict cardiovascular risk. We also investigated how neck circumference related to the study parameters. The significance level was set at 5% (p&lt;0.05).RESULTS:A total of 260 adolescents were assessed of which 50.4% (n=131) were females, 20.4% (n=53) had excess body weight according to the body mass index-for-age index, and 42.7% (n=111) had excess body fat. Blood pressure (3.9%, n=10) and all biochemical parameters were affected, varying from 1.9% (n=5) for glucose to 65% (n=169) for total cholesterol. Neck circumference correlated with body fat, waist circumference, hip circumference, weight, height, body mass index, waist-to-height ratio, homeostasis model of assessment - insulin resistance, fasting insulin, blood pressure, and high-density lipoprotein (&lt;0.05). It predicted excess body fat and changes in fasting insulin and blood pressure in both sexes, blood glucose and high-density lipoprotein in females, and triglycerides in males (area under the curve &gt;0.5; p&lt;0.05, varying from 0.610 for high-density lipoprotein to 0.817 for blood pressure).CONCLUSION:Neck circumference was capable of predicting excess fat and cardiovascular risk factors in adolescents.
DOI: 10.6084/m9.figshare.14320568
title: R-AMSTAR quality analysis of herbal reviews

description: Dataset: R-AMSTAR quality analysis and workings accompanying a herbal medicine meta-review.