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1.
Sensors (Basel) ; 21(5)2021 Mar 07.
Artículo en Inglés | MEDLINE | ID: mdl-33799930

RESUMEN

BACKGROUND: In the dental field, digital technology has created new opportunities for orthodontists to integrate their clinical practice, and for patients to collect information about orthodontics and their treatment, which is called "teledentistry." Dental monitoring (DM) is a recently introduced orthodontic application that combines safe teledentistry with artificial intelligence (AI) using a knowledge-based algorithm, allowing an accurate semi-automatic monitoring of the treatment. Dental Monitoring is the world's first SaaS (Software as a Service) application designed for remote monitoring of dental treatment, developed in Paris, France, with Philippe Salah as the Co-founder and CEO. CASES PRESENTATION: This report describes two cases in which DM system was essential to achieve the control of certain movements: it was possible to follow the movement, even if complex, such as the anterior cross of an adult patient and a lack of space in the canine of the growing patient. The software analyzed the fit and retention of the aligner, thus ensuring correct biomechanics. They were treated during the COVID-19 pandemic lockdown with aligners. The first case is a growing patient who was monitored during an interceptive orthodontic treatment to manage a retained upper canine. The second case is an adult patient forced to finalize his treatment of upper lateral incisor crossbite. The software analyzed the fit and retention of the aligner, thus ensuring correct biomechanics. CONCLUSIONS: DM system appears to be a promising method, useful for improving the interaction between doctor and patient, generally acceptable and useful to patients, even in critical clinical situations, at least in cases with optimal compliance and ability to use the tool properly.


Asunto(s)
Inteligencia Artificial , Diseño de Aparato Ortodóncico , Programas Informáticos , Telemedicina , Técnicas de Movimiento Dental , Adulto , Control de Enfermedades Transmisibles , Francia , Humanos , Pandemias
2.
Sensors (Basel) ; 21(7)2021 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-33808468

RESUMEN

High stress levels and sleep deprivation may cause several mental or physical health issues, such as depression, impaired memory, decreased motivation, obesity, etc. The COVID-19 pandemic has produced unprecedented changes in our lives, generating significant stress, and worries about health, social isolation, employment, and finances. To this end, nowadays more than ever, it is crucial to deliver solutions that can help people to manage and control their stress, as well as to reduce sleep disturbances, so as to improve their health and overall quality of life. Technology, and in particular Ambient Intelligence Environments, can help towards that direction, when considering that they are able to understand the needs of their users, identify their behavior, learn their preferences, and act and react in their interest. This work presents two systems that have been designed and developed in the context of an Intelligent Home, namely CaLmi and HypnOS, which aim to assist users that struggle with stress and poor sleep quality, respectively. Both of the systems rely on real-time data collected by wearable devices, as well as contextual information retrieved from the ambient facilities of the Intelligent Home, so as to offer appropriate pervasive relaxation programs (CaLmi) or provide personalized insights regarding sleep hygiene (HypnOS) to the residents. This article will describe the design process that was followed, the functionality of both systems, the results of the user studies that were conducted for the evaluation of their end-user applications, and a discussion about future plans.


Asunto(s)
Higiene del Sueño , Estrés Psicológico/prevención & control , Humanos , Pandemias , Calidad de Vida , Terapia por Relajación , Programas Informáticos , Dispositivos Electrónicos Vestibles
3.
Wiad Lek ; 74(2): 327-333, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33813496

RESUMEN

Through a broad literature review, analysis of EU, USA, Ukraine regulation acts, scientific research, and opinions of progressive-minded people in this sphere, this paper provides a guide to understanding the essence of classification of stand-alone software with medical purpose and specifics of its regulation. This research is based on dialectical, comparative, analytic, synthetic, and comprehensive methods.


Asunto(s)
Programas Informáticos , Unión Europea , Humanos , Ucrania
4.
Zhongguo Yi Liao Qi Xie Za Zhi ; 45(2): 159-162, 2021 Apr 08.
Artículo en Chino | MEDLINE | ID: mdl-33825374

RESUMEN

Aiming at the low efficiency and low quality detection level of the manual infusion set, a gas detection system for infusion set based on STM32 single-chip microcomputer was designed. The detection system includes hardware system design and software system design. The hardware system is based on the STM32F103 single-chip microcomputer. It mainly designs the gas pressure sensor acquisition circuit and the multi-way solenoid valve control circuit. The software system uses a C ++ real-time operating system to ensure system monitoring's real-time performance and validity. Test data is transmitted to the upper computer and displayed via USB serial communication. The experiment proves that the infusion set gas detection system can perform gas detection on the infusion set. The system has the characteristics of stability and high accuracy. The relative error of the experimental measurement is within ±5%, and the detection efficiency is better than manual detection.


Asunto(s)
Microcomputadores , Programas Informáticos , Computadores , Diseño de Equipo
5.
Zhongguo Yi Liao Qi Xie Za Zhi ; 45(2): 194-199, 2021 Apr 08.
Artículo en Chino | MEDLINE | ID: mdl-33825381

RESUMEN

OBJECTIVE: To understand the current situation of artificial intelligence production enterprise quality management system, so as to provide reference basis for the research and standardization of Artificial Intelligence Medical Device (AIMD) product quality management. METHODS: Based on YY/T 0287-2017 Medical Device Quality Management System for Regulatory Requirements, Medical Equipment Production and the Quality Control Standard for Independent Software Appendix and Xavier GMLP report, the relevant factors were screened and the questionnaire was designed by combining expert consultation and literature review. Then, a total of 32 representative AIMD enterprises were invited to fill in the questionnaire. Descriptive statistical analysis was performed on the data results using Excel 2016. RESULTS: Through in-depth analysis of the four themes in product planning and design, result output, product quality control and product change, it was found that it was necessary for enterprises participating in the survey to improve the quality management system of AIMD products to different degrees. CONCLUSIONS: This study is the first time to systematically investigate the status quo of quality management of AIMD enterprises. The result will be useful for the establishment and continuous improvement of product quality management system. It will also provide a reference for the research of AIMD product quality management and the establishment of the standard.


Asunto(s)
Inteligencia Artificial , Programas Informáticos , Control de Calidad , Estándares de Referencia
6.
Zhongguo Yi Liao Qi Xie Za Zhi ; 45(2): 228-230, 2021 Apr 08.
Artículo en Chino | MEDLINE | ID: mdl-33825388

RESUMEN

This study established a rapid ECG screening system through the application of wearable ECG equipment. The closed-loop and self-service process of ECG inspection, data collection, transmission and printing have been realized. The new rapid ECG screening system docking with HIS system in the hospital, forming a new intelligent mode of rapid ECG screening. This paper introduces the design of the intelligent mode of ECG rapid screening from the aspects of hardware, software, wearable ECG examination equipment, and briefly describes its implementation path and technical scheme. With the rapid ECG screening system, human power can be saved, the timeliness of ECG examination can be enhanced. The level of ECG diagnosis in the basic units can be improved through building a multiple medical centers which is rely on the cloud platform.


Asunto(s)
Electrocardiografía , Dispositivos Electrónicos Vestibles , Diseño de Equipo , Humanos , Investigación , Programas Informáticos
7.
BMC Bioinformatics ; 22(1): 179, 2021 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-33827413

RESUMEN

BACKGROUND: The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past decade, several computational pipelines have been developed to efficiently process and annotate these microbiome data. However, most of these pipelines require an implementation of additional tools for downstream analyses as well as advanced programming skills. RESULTS: Here we introduce a user-friendly microbiome analysis platform, EzMAP (Easy Microbiome Analysis Platform), which was developed using Java Swings, Java Script and R programming language. EzMAP is a standalone package providing graphical user interface, enabling easy access to all the functionalities of QIIME2 (Quantitative Insights Into Microbial Ecology) as well as streamlined downstream analyses using QIIME2 output as input. This platform is designed to give users the detailed reports and the intermediate output files that are generated progressively. The users are allowed to download the features/OTU table (.biom;.tsv;.xls), representative sequences (.fasta) and phylogenetic tree (.nwk), taxonomy assignment file (optional). For downstream analyses, users are allowed to perform relative abundances (at all taxonomical levels), community comparison (alpha and beta diversity, core microbiome), differential abundances (DESeq2 and linear discriminant analysis) and functional prediction (PICRust, Tax4Fun and FunGuilds). Our case study using a published rice microbiome dataset demonstrates intuitive user interface and great accessibility of the EzMAP. CONCLUSIONS: This EzMAP allows users to consolidate the microbiome analysis processes from raw sequence processing to downstream analyses specific for individual projects. We believe that this will be an invaluable tool for the beginners in their microbiome data analysis. This platform is freely available at https://github.com/gnanibioinfo/EzMAP and will be continually updated for adoption of changes in methods and approaches.


Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento , Microbiota , Programas Informáticos , Filogenia , Lenguajes de Programación
8.
J Integr Bioinform ; 18(1): 19-26, 2021 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-33721918

RESUMEN

SARS-CoV-2 has spread worldwide and caused social, economic, and health turmoil. The first genome assembly of SARS-CoV-2 was produced in Wuhan, and it is widely used as a reference. Subsequently, more than a hundred additional SARS-CoV-2 genomes have been sequenced. While the genomes appear to be mostly identical, there are variations. Therefore, an alignment of all available genomes and the derived consensus sequence could be used as a reference, better serving the science community. Variations are significant, but representing them in a genome browser can become, especially if their sequences are largely identical. Here we summarize the variation in one track. Other information not currently found in genome browsers for SARS-CoV-2, such as predicted miRNAs and predicted TRS as well as secondary structure information, were also added as tracks to the consensus genome. We believe that a genome browser based on the consensus sequence is better suited when considering worldwide effects and can become a valuable resource in the combating of COVID-19. The genome browser is available at http://cov.iaba.online.


Asunto(s)
Genoma Viral/genética , /genética , Secuencia de Bases , Humanos , Programas Informáticos
9.
Artículo en Chino | MEDLINE | ID: mdl-33781037

RESUMEN

Objective: To summarize the research progress of medical emotional labor in China, and provide data reference for medical workers in the field of emotional labor. Methods: In March 2020, we searched the research content of emotional labor of medical workers through CNKI system, and analyzed it by using CiteSpace software. We visualized the topic of emotional labor of medical workers by using the knowledge map formed by keyword co-occurrence and keyword clustering, as well as the emergent words and time zone map. The analysis contents include the basic information characteristics of the selected literature, research hotspots and topics, research trends and frontiers. Results: The first related literature was published in 2008, and 126 related literatures were retrieved. Research hotspots include 'emotional labor', 'nurse', 'work burnout', 'medical staff' and 'work satisfaction', etc. Topics can be divided into three categories: research objects, variables affecting factors and medical workplace. There are 24 emergent words. In 2008, 2011, 2013, and 2015, important turning points for research changes exist. Conclusion: In the future, researchers in China can try to broaden the scope of medical subjects and influencing factors, etc., and be closely linked to the results of existing studies.


Asunto(s)
Satisfacción en el Trabajo , Publicaciones , China , Humanos , Cuerpo Médico , Programas Informáticos
10.
Hum Genomics ; 15(1): 18, 2021 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-33726831

RESUMEN

BACKGROUND: In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people's health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein-protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in. RESULTS: In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients. CONCLUSIONS: In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.


Asunto(s)
Bronquios/virología , Regulación de la Expresión Génica , Bronquios/fisiología , Quimiocina CXCL10/genética , Factor de Crecimiento Epidérmico/genética , Interacciones Huésped-Patógeno/genética , Humanos , Interleucina-8/genética , Organoides , Mapas de Interacción de Proteínas/genética , Programas Informáticos
11.
Biomed Eng Online ; 20(1): 27, 2021 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-33743707

RESUMEN

BACKGROUND: Lung ultrasound (LUS) can be an important imaging tool for the diagnosis and assessment of lung involvement. Ultrasound sonograms have been confirmed to illustrate damage to a person's lungs, which means that the correct classification and scoring of a patient's sonogram can be used to assess lung involvement. METHODS: The purpose of this study was to establish a lung involvement assessment model based on deep learning. A novel multimodal channel and receptive field attention network combined with ResNeXt (MCRFNet) was proposed to classify sonograms, and the network can automatically fuse shallow features and determine the importance of different channels and respective fields. Finally, sonogram classes were transformed into scores to evaluate lung involvement from the initial diagnosis to rehabilitation. RESULTS AND CONCLUSION: Using multicenter and multimodal ultrasound data from 104 patients, the diagnostic model achieved 94.39% accuracy, 82.28% precision, 76.27% sensitivity, and 96.44% specificity. The lung involvement severity and the trend of COVID-19 pneumonia were evaluated quantitatively.


Asunto(s)
/diagnóstico por imagen , Pulmón/diagnóstico por imagen , Neumonía/diagnóstico por imagen , Ultrasonografía , Algoritmos , Bases de Datos Factuales , Reacciones Falso Positivas , Humanos , Procesamiento de Imagen Asistido por Computador/métodos , Modelos Estadísticos , Redes Neurales de la Computación , Lenguajes de Programación , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Programas Informáticos
12.
Math Biosci Eng ; 18(2): 1513-1528, 2021 01 28.
Artículo en Inglés | MEDLINE | ID: mdl-33757196

RESUMEN

The internet of things (IoT) and deep learning are emerging technologies in diverse research fields, including the provision of IT services in medical domains. In the COVID-19 era, intelligent medication behavior monitoring systems for stable patient monitoring are further required, because many patients cannot easily visit hospitals. Several previous studies made use of wearable devices to detect medication behaviors of patients. However, the wearable devices cause inconvenience while equipping the devices. In addition, they suffer from inconsistency problems due to errors of measured values. We devise a medication behavior monitoring system that uses the IoT and deep learning to avoid sensing errors and improve user experiences by effectively detecting various activities of patients. Based on the real-time operation of our proposed IoT device, the proposed solution processes captured images of patents via OpenPose to check medication situations. The proposed system identifies medication status on time by using a human activity recognition scheme and provides various notifications to patients' mobile devices. To support reliable communication between our system and doctors, we employ MQTT protocol with periodic data transmissions. Thus, the measured information of patient's medication status is transmitted to the doctors so that they can periodically perform remote treatments. Experimental results show that all medication behaviors are accurately detected and notified to the doctor efficiently, improving the accuracy of monitoring the patient's medication behavior.


Asunto(s)
/tratamiento farmacológico , Aprendizaje Profundo , Cumplimiento de la Medicación , Monitoreo Fisiológico/métodos , Ingeniería Biomédica , Sistemas de Computación , Terapia por Observación Directa , Diseño de Equipo , Humanos , Internet de las Cosas , Cumplimiento de la Medicación/psicología , Cumplimiento de la Medicación/estadística & datos numéricos , Monitoreo Fisiológico/instrumentación , Monitoreo Fisiológico/estadística & datos numéricos , Redes Neurales de la Computación , Pandemias , Programas Informáticos , Dispositivos Electrónicos Vestibles
13.
Biomed Eng Online ; 20(1): 30, 2021 Mar 25.
Artículo en Inglés | MEDLINE | ID: mdl-33766034

RESUMEN

BACKGROUND: The regulation and control of pressure stimuli is useful for many studies of pain and nociception especially those in the visceral pain field. In many in vivo experiments, distinct air and liquid stimuli at varying pressures are delivered to hollow organs such as the bladder, vagina, and colon. These stimuli are coupled with behavioral, molecular, or physiological read-outs of the response to the stimulus. Care must be taken to deliver precise timed stimuli during experimentation. For example, stimuli signals can be used online to precisely time-lock the stimulus with a physiological output. Such precision requires the development of specialized hardware to control the stimulus (e.g., air) while providing a precise read-out of pressure and stimulus signal markers. METHODS: In this study, we designed a timed pressure regulator [termed visceral pressure stimulator (VPS)] to control air flow, measure pressure (in mmHg), and send stimuli markers to online software. The device was built using a simple circuit and primarily off-the-shelf parts. A separate custom inline analog-to-digital pressure converter was used to validate the real pressure output of the VPS. RESULTS: Using commercial physiological software (Spike2, CED), we were able to measure mouse bladder pressure continuously during delivery of unique air stimulus trials in a mouse while simultaneously recording an electromyogram (EMG) of the overlying abdominal muscles. CONCLUSIONS: This device will be useful for those who need to (1) deliver distinct pressure stimuli while (2) measuring the pressure in real-time and (3) monitoring stimulus on-off using physiological software.


Asunto(s)
Colon/diagnóstico por imagen , Electromiografía , Vejiga Urinaria/diagnóstico por imagen , Vagina/diagnóstico por imagen , Animales , Femenino , Ratones , Proyectos Piloto , Presión , Procesamiento de Señales Asistido por Computador , Programas Informáticos , Dolor Visceral
14.
An Acad Bras Cienc ; 93(1): e20190346, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33787750

RESUMEN

Based on the leakage of the coalbed methane (CBM) drilling engineering practice of Luan mining area in China, the author determines the safe drilling fluid density range for the stable borehole wall based on borehole wall collapse and fracture pressure. Such parameters as the drilling fluid hydraulic parameters (including pump pressure, pump power and displacement, nozzle diameter, bit pressure drop, bit hydraulic horsepower, circulation pressure drop, impact force and jet velocity) and drilling parameters (including weight-on-bit, drilling rotary speed, bit tooth wear) in each borehole section are optimized. Taking the lowest drilling cost as the controlling target, the drilling parameter optimization model is designed and solved by the genetic algorithm. Furthermore, a software named "CBM borehole wall stability parameter design and optimization" characterized by visualization and applicable for drilling formation condition, which can be used to design and optimize the borehole drilling technological parameters, is developed. This program includes such modules as drilling fluid density prediction, drilling technology design, database management, user management and help. The developed software is proven to solve the drilling leakage effectively in the No.67 borehole practice, which can help drilling engineers to optimize CBM drilling technological parameters safely and quickly.


Asunto(s)
Metano , Minería , China , Fenómenos Mecánicos , Programas Informáticos
15.
Nat Commun ; 12(1): 1387, 2021 03 02.
Artículo en Inglés | MEDLINE | ID: mdl-33654082

RESUMEN

Wearable sensors to continuously measure blood pressure and derived cardiovascular variables have the potential to revolutionize patient monitoring. Current wearable methods analyzing time components (e.g., pulse transit time) still lack clinical accuracy, whereas existing technologies for direct blood pressure measurement are too bulky. Here we present an innovative art of continuous noninvasive hemodynamic monitoring (CNAP2GO). It directly measures blood pressure by using a volume control technique and could be used for small wearable sensors integrated in a finger-ring. As a software prototype, CNAP2GO showed excellent blood pressure measurement performance in comparison with invasive reference measurements in 46 patients having surgery. The resulting pulsatile blood pressure signal carries information to derive cardiac output and other hemodynamic variables. We show that CNAP2GO can self-calibrate and be miniaturized for wearable approaches. CNAP2GO potentially constitutes the breakthrough for wearable sensors for blood pressure and flow monitoring in both ambulatory and in-hospital clinical settings.


Asunto(s)
Determinación de la Presión Sanguínea/métodos , Adulto , Algoritmos , Presión Sanguínea , Calibración , Femenino , Hemodinámica , Humanos , Masculino , Persona de Mediana Edad , Miniaturización , Monitoreo Fisiológico/instrumentación , Pulso Arterial , Procesamiento de Señales Asistido por Computador , Programas Informáticos , Adulto Joven
16.
Nat Commun ; 12(1): 1485, 2021 03 05.
Artículo en Inglés | MEDLINE | ID: mdl-33674578

RESUMEN

Yeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow-it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.


Asunto(s)
Ingeniería Genética/métodos , Genoma Fúngico , Saccharomyces cerevisiae/genética , Secuenciación Completa del Genoma/métodos , Secuencia de Bases , Cromosomas , Cromosomas Artificiales de Levadura , Clonación Molecular , Simulación por Computador , Mapeo Contig/métodos , Metagenoma , Metagenómica , Plásmidos , Programas Informáticos , Transformación Genética
17.
BMC Bioinformatics ; 22(1): 119, 2021 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-33706720

RESUMEN

BACKGROUND: Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in which longer contigs, ideally whole chromosomes/genomes, are formed from shorter NGS reads. However, the contigs generated from the de novo assembly are often very fragmented and rarely longer than a few kilo base pairs (kb). Therefore, a time-consuming extension process is routinely performed on the de novo assembled contigs. RESULTS: To facilitate this process, we propose a new tool for metagenome contig extension after de novo assembly. ContigExtender employs a novel recursive extending strategy that explores multiple extending paths to achieve highly accurate longer contigs. We demonstrate that ContigExtender outperforms existing tools in synthetic, animal, and human metagenomics datasets. CONCLUSIONS: A novel software tool ContigExtender has been developed to assist and enhance the performance of metagenome de novo assembly. ContigExtender effectively extends contigs from a variety of sources and can be incorporated in most viral metagenomics analysis pipelines for a wide variety of applications, including pathogen detection and viral discovery.


Asunto(s)
Genoma Viral , Metagenoma , Metagenómica , Programas Informáticos , Algoritmos , Animales , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Análisis de Secuencia de ADN
18.
BMC Bioinformatics ; 22(1): 150, 2021 Mar 23.
Artículo en Inglés | MEDLINE | ID: mdl-33757425

RESUMEN

BACKGROUND: Currently, no proven effective drugs for the novel coronavirus disease COVID-19 exist and despite widespread vaccination campaigns, we are far short from herd immunity. The number of people who are still vulnerable to the virus is too high to hamper new outbreaks, leading a compelling need to find new therapeutic options devoted to combat SARS-CoV-2 infection. Drug repurposing represents an effective drug discovery strategy from existing drugs that could shorten the time and reduce the cost compared to de novo drug discovery. RESULTS: We developed a network-based tool for drug repurposing provided as a freely available R-code, called SAveRUNNER (Searching off-lAbel dRUg aNd NEtwoRk), with the aim to offer a promising framework to efficiently detect putative novel indications for currently marketed drugs against diseases of interest. SAveRUNNER predicts drug-disease associations by quantifying the interplay between the drug targets and the disease-associated proteins in the human interactome through the computation of a novel network-based similarity measure, which prioritizes associations between drugs and diseases located in the same network neighborhoods. CONCLUSIONS: The algorithm was successfully applied to predict off-label drugs to be repositioned against the new human coronavirus (2019-nCoV/SARS-CoV-2), and it achieved a high accuracy in the identification of well-known drug indications, thus revealing itself as a powerful tool to rapidly detect potential novel medical indications for various drugs that are worth of further investigation. SAveRUNNER source code is freely available at https://github.com/giuliafiscon/SAveRUNNER.git , along with a comprehensive user guide.


Asunto(s)
Antivirales/farmacología , Reposicionamiento de Medicamentos , Programas Informáticos , Humanos , Uso Fuera de lo Indicado
19.
BMC Bioinformatics ; 22(1): 149, 2021 Mar 23.
Artículo en Inglés | MEDLINE | ID: mdl-33757430

RESUMEN

BACKGROUND: A common approach for sequencing studies is to do joint-calling and store variants of all samples in a single file. If new samples are continually added or controls are re-used for several studies, the cost and time required to perform joint-calling for each analysis can become prohibitive. RESULTS: We present ATAV, an analysis platform for large-scale whole-exome and whole-genome sequencing projects. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and singletons, as well as rare-variant collapsing analyses for finding disease associations in complex diseases. Runtime logs ensure full reproducibility and the modularized ATAV framework makes it extensible to continuous development. Besides helping with the identification of disease-causing variants for a range of diseases, ATAV has also enabled the discovery of disease-genes by rare-variant collapsing on datasets containing more than 20,000 samples. Analyses to date have been performed on data of more than 110,000 individuals demonstrating the scalability of the framework. To allow users to easily access variant-level data directly from the database, we provide a web-based interface, the ATAV data browser ( http://atavdb.org/ ). Through this browser, summary-level data for more than 40,000 samples can be queried by the general public representing a mix of cases and controls of diverse ancestries. Users have access to phenotype categories of variant carriers, as well as predicted ancestry, gender, and quality metrics. In contrast to many other platforms, the data browser is able to show data of newly-added samples in real-time and therefore evolves rapidly as more and more samples are sequenced. CONCLUSIONS: Through ATAV, users have public access to one of the largest variant databases for patients sequenced at a tertiary care center and can look up any genes or variants of interest. Additionally, since the entire code is freely available on GitHub, ATAV can easily be deployed by other groups that wish to build their own platform, database, and user interface.


Asunto(s)
Genética de Población/instrumentación , Genómica , Programas Informáticos , Secuenciación del Exoma Completo , Bases de Datos Genéticas , Humanos , Fenotipo , Reproducibilidad de los Resultados
20.
An Acad Bras Cienc ; 93(1): e20200511, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33759953

RESUMEN

Dynamic loads continue to draw the interest of structural engineers. The sources of these loads can be earthquakes, blast effects or transportation loads from railroads or highways. Especially for blast loads, terrorist attacks or military actions have caused many loses of lives and damages in several buildings. The verification of structural behavior is necessary to help designers to plan structures that support these loads and reduce damages. Although computer simulation with, specific software, have helped these designers, full-scale tests can provide valuable information about the real response of the structure. This paper presents damage diagram from ten full-scale field tests using approximately 2.70 kg of non-confined plastic bonded explosive against reinforced concrete slabs with different scaled distance, reinforcement ratio and concrete strength. The damage diagram is expected to be a help tool for designers to understand the effects of blast loads on slabs.


Asunto(s)
Materiales de Construcción , Terremotos , Simulación por Computador , Programas Informáticos
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