ABSTRACT
The current COVID-19 pandemic has already claimed more than 3.7 million victims and it will cause more deaths in the coming months. Tools that track the number and locations of cases are critical for surveillance and help in making policy decisions for controlling the outbreak. However, the current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We developed a user-friendly web tool, named OUTBREAK, that facilitates epidemic surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. We applied our tool to visualize the SARS 2003, MERS, and COVID19 epidemics, and provided them as examples on the website. Through the zoom feature, it is also possible to visualize cases at city and even neighborhood levels. We made the tool freely available at https://outbreak.sysbio.tools/. OUTBREAK has the potential to guide and help health authorities to intervene and minimize the effects of outbreaks.
Subject(s)
Humans , Pandemics , COVID-19 , Disease Outbreaks , Geographic Mapping , SARS-CoV-2ABSTRACT
Non-coding RNAs (ncRNAs) were recently given much higher attention due to technical advances in sequencing which expanded the characterization of transcriptomes in different organisms. ncRNAs have different lengths (22 nt to >1, 000 nt) and mechanisms of action that essentially comprise a sophisticated gene expression regulation network. Recent publication of schistosome genomes and transcriptomes has increased the description and characterization of a large number of parasite genes. Here we review the number of predicted genes and the coverage of genomic bases in face of the public ESTs dataset available, including a critical appraisal of the evidence and characterization of ncRNAs in schistosomes. We show expression data for ncRNAs in Schistosoma mansoni. We analyze three different microarray experiment datasets: (1) adult worms' large-scale expression measurements; (2) differentially expressed S. mansoni genes regulated by a human cytokine (TNF-α) in a parasite culture; and (3) a stage-specific expression of ncRNAs. All these data point to ncRNAs involved in different biological processes and physiological responses that suggest functionality of these new players in the parasite's biology. Exploring this world is a challenge for the scientists under a new molecular perspective of host-parasite interactions and parasite development.
RNAs não codificadores (ncRNAs) têm sido recentemente objeto de atenção muito maior devido aos avanços técnicos no sequenciamento que expandiram a caracterização dos transcritomas em diferentes organismos. ncRNAs possuem diferentes comprimentos (22 nt a >1.000 nt) e mecanismos de ação que essencialmente compreendem uma sofisticada rede de regulação de expressão gênica. A publicação recente dos genomas e transcritomas dos esquistossomos aumentou a descrição e caracterização de um grande número de genes do parasita. Aqui nós revisamos o número de genes preditos e a cobertura das bases do genoma em face dos ESTs públicos disponíveis, incluindo uma avaliação crítica da evidência e caracterização de ncRNAs em esquistossomos. Nós mostramos dados de expressão de ncRNAs em Schistosoma mansoni. Nós analisamos três conjuntos diferentes de dados de experimentos com microarranjos: (1) medidas de expressão em larga escala de vermes adultos; (2) genes diferencialmente expressos de S. mansoni regulados por uma citocina humana (TNF-α) no parasita em cultura; e (3) expressão estágio-especifica de ncRNAs. Todos estes dados apontam para ncRNAs envolvidos em diferentes processos biológicos e respostas fisiológicas que sugerem funcionalidade destes novos personagens na biologia do parasita. Explorar este mundo é um desafio para os cientistas sob uma nova perspectiva molecular da interação parasita-hospedeiro e do desenvolvimento do parasita.