RESUMO
The allele frequency net database (AFND, http://www.allelefrequencies.net ) is an online web-based repository that contains information on the frequencies of immune-related genes and their corresponding alleles in worldwide human populations. At present, the website contains data from 1784 population samples in more than 14 million individuals from 129 countries on the frequency of genes from different polymorphic regions including data for the human leukocyte antigen (HLA) system. In addition, over the last four years, AFND has also incorporated genotype raw data from 85,000 individuals comprising 215 population samples from 39 countries. Moreover, more population data sets containing next generation sequencing data spanning >3 million individuals have been added. This resource has been widely used in a variety of contexts such as histocompatibility, immunology, epidemiology, pharmacogenetics, epitope prediction algorithms for population coverage in vaccine development, population genetics, among many others. In this chapter, we present an update of the most used searching mechanisms as described in a previous volume and some of the latest developments included in AFND.
Assuntos
Bases de Dados Genéticas , Frequência do Gene , Genética Populacional , Humanos , Genética Populacional/métodos , Antígenos HLA/genética , Alelos , Biologia Computacional/métodos , Internet , Navegador , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala/métodosRESUMO
En el año 2020 en el Hospital Nacional Profesor Alejandro Posadas, cuando comenzó la pandemia de Covid 2019, se comenzó a realizar seguimiento clínico de pacientes y a sus contactos, en forma telefónica, debido a la gran demanda de asistencia y para evitar el desborde del sistema sanitario. Conformándose así el equipo de Seguimiento Telefónico. Consecuencia de aquello comprobamos que era una herramienta valiosa que podría ser utilizada en otros procesos. En el año 2021 el equipo de Seguimiento Telefónico continuó en funcionamiento adaptándose a nuevas líneas de trabajo en donde el monitoreo de la trazabilidad del cuidado de los pacientes es imprescindible para garantizarles acceso al sistema y al mismo tiempo realizar evaluación y monitoreo de procesos asistenciales que involucran a personas con criterios de vulnerabilidad y/o salud que les confieran riesgo. Este artículo explora el papel que puede desempeñar la "Navegación del Paciente" en la mejora de los resultados de salud1 . Los navegadores pueden facilitar un mejor acceso y calidad de la atención médica para las poblaciones desatendidas. En el mes de febrero de 2023 se institucionalizó el dispositivo de Seguimiento Telefónico como sector de Revinculación Asistencial, un arma más para beneficiar a los pacientes, aumentando su Seguridad y mejorando día a día la Calidad de atención.
In 2020, when the Covid-19 pandemic began, the Professor Alejandro Posadas National Hospital implemented clinical monitoring of patients and their contacts by telephone to manage the overwhelming demand for assistance and avoid overcrowding. This led to the formation of a Telephone Monitoring team. The team's success prompted the hospital to explore other areas where the tool could be applied. In 2021, the hospital continued to use the Telephone Monitoring team, adapting it to new lines of work where patient care traceability was critical for ensuring access to the healthcare system. This article examines the role of patient navigation in improving healthcare outcomes, including better access and quality of care for underserved populations. The hospital institutionalized the Telephone Monitoring device in February 2023 as a sector of Assistance Relinking, adding another weapon to benefit patients by increasing their safety and improving the quality of care.
Assuntos
Humanos , Masculino , Feminino , Avaliação de Processos e Resultados em Cuidados de Saúde , Qualidade da Assistência à Saúde , Registros Eletrônicos de Saúde , Navegador/estatística & dados numéricosRESUMO
BACKGROUND: The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue with the same common implementation difficulties that plague researchers who are not computer specialists. RESULTS: Here, we have developed the VisualDynamics-a WEB tool developed to automate biological simulations performed in Gromacs using a graphical interface to make molecular dynamics simulation user-friendly task. In this new application the researcher can submit a simulation of the protein in the free form or complexed with a ligand. Can also download the graphics analysis and log files at the end of the simulation. CONCLUSIONS: VisualDynamics is a tool that will accelerate implementations and learning in the area of molecular dynamics simulation. Freely available at https://visualdynamics.fiocruz.br/login , is supported by all major web browsers. VisualDynamics was developed with Flask, which is a Python-based free and open-source framework for web development. The code is freely available for download at GitHub https://github.com/LABIOQUIM/visualdynamics .
Assuntos
Simulação de Dinâmica Molecular , Software , Proteínas/química , Cinética , NavegadorRESUMO
OBJECTIVE: To explore trends and patterns of laypeople's activity for seeking telephone number of emergency medical services (EMS) based on analysis of online search traffic, including changes of the search activity with onset of the coronavirus disease 2019 (COVID-19) outbreak, in five countries - the United States of America (USA), India, Brazil, the United Kingdom (UK) and Russia. METHODS: Google Trends (GT) country-level data on weekly relative search volumes (RSV) for top queries to seek EMS number were examined for January 2018-October 2021, including a comparison of RSVs between pre-COVID-19 period (January 2018-October 2019) and COVID-19 period (January 2020-October 2021), and evaluation of temporal associations of RSVs with weekly numbers of new COVID-19 cases. RESULTS: The countries demonstrated diverse patterns of the search activity with significantly different mean RSVs (the USA 1.76, India 10.20, Brazil 2.51, the UK 6.42, Russia 56.79; p < 0.001). For all countries excepting the USA mean RSVs of the COVID-19 period were significantly higher compared with the pre-COVID-19 ones (India +74%, Brazil +148%, the UK +22%, Russia +9%; p ≤ 0.034), and exhibited positive correlations with numbers of new COVID-19 cases, more pronounced for 2021 (India rS = 0.538, Brazil 0.307, the UK 0.434, Russia 0.639; p ≤ 0.045). CONCLUSION: Laypeople's activity for seeking EMS telephone number greatly varies between countries. It clearly responds to the spread of COVID-19 and could be reflective of public need for obtaining emergency help. Further studies are required to establish the role of GT for conducting real-time surveillance of population demand for EMS.
Assuntos
COVID-19/psicologia , Serviços Médicos de Emergência/estatística & dados numéricos , Linhas Diretas/estatística & dados numéricos , Comportamento de Busca de Informação , Brasil , COVID-19/terapia , Serviços Médicos de Emergência/métodos , Linhas Diretas/métodos , Humanos , Índia , Federação Russa , Estados Unidos , Navegador/estatística & dados numéricosRESUMO
Promoter annotation is an important task in the analysis of a genome. One of the main challenges for this task is locating the border between the promoter region and the transcribing region of the gene, the transcription start site (TSS). The TSS is the reference point to delimit the DNA sequence responsible for the assembly of the transcribing complex. As the same gene can have more than one TSS, so to delimit the promoter region, it is important to locate the closest TSS to the site of the beginning of the translation. This paper presents TSSFinder, a new software for the prediction of the TSS signal of eukaryotic genes that is significantly more accurate than other available software. We currently are the only application to offer pre-trained models for six different eukaryotic organisms: Arabidopsis thaliana, Drosophila melanogaster, Gallus gallus, Homo sapiens, Oryza sativa and Saccharomyces cerevisiae. Additionally, our software can be easily customized for specific organisms using only 125 DNA sequences with a validated TSS signal and corresponding genomic locations as a training set. TSSFinder is a valuable new tool for the annotation of genomes. TSSFinder source code and docker container can be downloaded from http://tssfinder.github.io. Alternatively, TSSFinder is also available as a web service at http://sucest-fun.org/wsapp/tssfinder/.
Assuntos
Biologia Computacional/métodos , Eucariotos/genética , Genoma , Genômica/métodos , Regiões Promotoras Genéticas , Software , Sítio de Iniciação de Transcrição , Algoritmos , Bases de Dados Genéticas , Reprodutibilidade dos Testes , Análise de Sequência de DNA , NavegadorRESUMO
Learning metabolic pathways is vital for understanding biochemical processes and all of their implications for life. Their learning in the virtual environment is complex and generative learning strategies, such as the construction of online conceptual maps, can help in this process. This article presents a proposal for the collaborative construction of virtual concept maps on metabolism by students in the CMap Cloud browser application (free). A sequence of steps is suggested, which include online group brainstorming and discussions, peer assessment, and teachers feedback. This proposal is flexible and can be adapted to the didactic and technological reality of each teacher.
Assuntos
COVID-19 , Aprendizagem , Pandemias , Ensino , Navegador , HumanosRESUMO
A technical overview of the High Performance Collision Cross Section (HPCCS) software for accurate and efficient calculations of collision cross sections for molecular ions ranging from small organic molecules to large protein complexes is presented. The program uses helium or nitrogen as buffer gas with considerable gains in computer time compared to publicly available codes under the Trajectory Method approximation. HPCCS is freely available under the Academic Use License at https://github.com/cepid-cces/hpccs .
Assuntos
Espectrometria de Mobilidade Iônica , Espectrometria de Massas , Software , Algoritmos , Bases de Dados Factuais , Espectrometria de Mobilidade Iônica/métodos , Íons/análise , Espectrometria de Massas/métodos , Modelos Teóricos , Compostos Orgânicos/análise , Compostos Orgânicos/química , Proteínas/análise , Proteínas/química , NavegadorRESUMO
Circular RNAs (circRNAs) are a widespread class of endogenous noncoding RNAs and they have been studied in the past few years, implying important biological functions in all kingdoms of life. Recently, circRNAs have been identified in many plant species, including cereal crops, showing differential expression during stress response and developmental programs, which suggests their role in these process. In the following years, it is expected that insights into the functional roles of circRNAs can be used by cereal scientists and molecular breeders with the aim to develop new strategies for crop improvement. Here, we briefly outline the current knowledge about circRNAs in plants and we also outline available computational resources for their validation and analysis in cereal species.
Assuntos
Biologia Computacional , Grão Comestível/genética , Regulação da Expressão Gênica de Plantas , RNA Circular , RNA de Plantas , Biologia Computacional/métodos , Bases de Dados Genéticas , Perfilação da Expressão Gênica , Melhoramento Vegetal , Software , NavegadorRESUMO
Since the early 1980s, we have witnessed considerable progress in the development and application of docking programs to assess protein-ligand interactions. Most of these applications had as a goal the identification of potential new binders to protein targets. Another remarkable progress is taking place in the determination of the structures of protein-ligand complexes, mostly using X-ray diffraction crystallography. Considering these developments, we have a favorable scenario for the creation of a computational tool that integrates into one workflow all steps involved in molecular docking simulations. We had these goals in mind when we developed the program SAnDReS. This program allows the integration of all computational features related to modern docking studies into one workflow. SAnDReS not only carries out docking simulations but also evaluates several docking protocols allowing the selection of the best approach for a given protein system. SAnDReS is a free and open-source (GNU General Public License) computational environment for running docking simulations. Here, we describe the combination of SAnDReS and AutoDock4 for protein-ligand docking simulations. AutoDock4 is a free program that has been applied to over a thousand receptor-ligand docking simulations. The dataset described in this chapter is available for downloading at https://github.com/azevedolab/sandres.
Assuntos
Biologia Computacional/métodos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Software , Sítios de Ligação , Bases de Dados Factuais , Desenho de Fármacos , Ligantes , Ligação Proteica , Proteínas/química , Interface Usuário-Computador , NavegadorRESUMO
Protein-ligand docking simulation is central in drug design and development. Therefore, the development of web servers intended to docking simulations is of pivotal importance. SwissDock is a web server dedicated to carrying out protein-ligand docking simulation intuitively and elegantly. SwissDock is based on the protein-ligand docking program EADock DSS and has a simple and integrated interface. The SwissDock allows the user to upload structure files for a protein and a ligand, and returns the results by e-mail. To facilitate the upload of the protein and ligand files, we can prepare these input files using the program UCSF Chimera. In this chapter, we describe how to use UCSF Chimera and SwissDock to perform protein-ligand docking simulations. To illustrate the process, we describe the molecular docking of the competitive inhibitor roscovitine against the structure of human cyclin-dependent kinase 2.