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1.
Surg Clin North Am ; 101(4): 693-701, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34242610

RESUMO

Continued advancement has forced medical education to accept new ways in which to incorporate technology into its curriculum. As a result, technology has become a cornerstone to all levels of the medical education. This article compiles and discusses various avenues in which technology serves and betters education, ranging from administrative databases to cloud-based storage. Overall, technology can serve various educational purposes, including compilation, circulation, and integration of educational materials. The modalities discussed within this article, while numerous and adaptable, are a small portion of what the technological world has to offer.


Assuntos
Educação de Pós-Graduação em Medicina/métodos , Tecnologia Educacional/métodos , Cirurgia Geral/educação , Coleta de Dados/métodos , Educação à Distância/métodos , Educação à Distância/organização & administração , Educação de Pós-Graduação em Medicina/organização & administração , Tecnologia Educacional/organização & administração , Humanos , Armazenamento e Recuperação da Informação/métodos , América do Norte , Software , Comunicação por Videoconferência
2.
Psychol Assess ; 33(7): 610-618, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34060864

RESUMO

Depression is a leading mental health concern across the U.S. and worldwide. There are myriad assessments to evaluate depressive symptoms, including the Edinburgh Postnatal Depression Scale (EPDS), which is widely used to evaluate women's pre- and postnatal depression but not as prevalent at other timepoints in adulthood, limiting its utility for longitudinal research. As part of the National Institutes of Health's (NIH) Environmental influences on Child Health Outcomes (ECHO) Research Program, the current study sought to develop a common metric so that scores on the EPDS can be converted to the standardized Patient-Reported Measurement Information System (PROMIS®) T-score metric. Drawing on data from the ECHO-Prenatal Alcohol in SIDS and Stillbirth cohort, this study used a single-group linking design, where 1,263 mothers completed the EPDS and PROMIS-Depression measures at the same time. Score linking was conducted using equipercentile and item response theory (IRT) methods. Results showed both linking methods provide robust, congruent results, and subgroup invariance held across age, race, ethnicity, education, and geographic location. The IRT-based unidimensional fixed-parameter calibration was selected due to its model simplicity, and a crosswalk table was established to convert scores from the EPDS to PROMIS T-scores. Overall, this study provides a way to aggregate data across various depression measures and timepoints, such that researchers and clinicians now have the ability to directly compare and combine EPDS data with PROMIS and other depression measures already score-linked to PROMIS. (PsycInfo Database Record (c) 2021 APA, all rights reserved).


Assuntos
Depressão/diagnóstico , Armazenamento e Recuperação da Informação/métodos , Escalas de Graduação Psiquiátrica , Adulto , Fatores Etários , Calibragem , Depressão/psicologia , Feminino , Humanos , Estudos Longitudinais , Pessoa de Meia-Idade , Fatores de Tempo
3.
Nat Commun ; 12(1): 3518, 2021 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-34112775

RESUMO

DNA holds significant promise as a data storage medium due to its density, longevity, and resource and energy conservation. These advantages arise from the inherent biomolecular structure of DNA which differentiates it from conventional storage media. The unique molecular architecture of DNA storage also prompts important discussions on how data should be organized, accessed, and manipulated and what practical functionalities may be possible. Here we leverage thermodynamic tuning of biomolecular interactions to implement useful data access and organizational features. Specific sets of environmental conditions including distinct DNA concentrations and temperatures were screened for their ability to switchably access either all DNA strands encoding full image files from a GB-sized background database or subsets of those strands encoding low resolution, File Preview, versions. We demonstrate File Preview with four JPEG images and provide an argument for the substantial and practical economic benefit of this generalizable strategy to organize data.


Assuntos
DNA/química , Processamento de Imagem Assistida por Computador/métodos , Armazenamento e Recuperação da Informação/métodos , Simulação por Computador , Primers do DNA/química , Bases de Dados de Ácidos Nucleicos , Sequenciamento de Nucleotídeos em Larga Escala , Reação em Cadeia da Polimerase em Tempo Real/métodos , Software , Temperatura , Termodinâmica
4.
PLoS One ; 16(5): e0234221, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33956834

RESUMO

This study compared the results of data collected from a longitudinal query analysis of the MEDLINE database hosted on multiple platforms that include PubMed, EBSCOHost, Ovid, ProQuest, and Web of Science. The goal was to identify variations among the search results on the platforms after controlling for search query syntax. We devised twenty-nine cases of search queries comprised of five semantically equivalent queries per case to search against the five MEDLINE database platforms. We ran our queries monthly for a year and collected search result count data to observe changes. We found that search results varied considerably depending on MEDLINE platform. Reasons for variations were due to trends in scholarly publication such as publishing individual papers online first versus complete issues. Some other reasons were metadata differences in bibliographic records; differences in the levels of specificity of search fields provided by the platforms and large fluctuations in monthly search results based on the same query. Database integrity and currency issues were observed as each platform updated its MEDLINE data throughout the year. Specific biomedical bibliographic databases are used to inform clinical decision-making, create systematic reviews, and construct knowledge bases for clinical decision support systems. They serve as essential information retrieval and discovery tools to help identify and collect research data and are used in a broad range of fields and as the basis of multiple research designs. This study should help clinicians, researchers, librarians, informationists, and others understand how these platforms differ and inform future work in their standardization.


Assuntos
Armazenamento e Recuperação da Informação , MEDLINE , Pesquisa Biomédica , Humanos , Armazenamento e Recuperação da Informação/métodos , Ferramenta de Busca/métodos
5.
Curr Oncol ; 28(2): 1153-1160, 2021 03 08.
Artigo em Inglês | MEDLINE | ID: covidwho-1167436

RESUMO

In a prospective study, we sought to determine acceptability of linkage of administrative and clinical trial data among Canadian patients and Research Ethics Boards (REBs). The goal is to develop a more harmonized approach to data, with potential to improve clinical trial conduct through enhanced data quality collected at reduced cost and inconvenience for patients. On completion of the original LY.12 randomized clinical trial in lymphoma (NCT00078949), participants were invited to enrol in the Long-term Innovative Follow-up Extension (LIFE) component. Those consenting to do so provided comprehensive identifying information to facilitate linkage with their administrative data. We prospectively designed a global assessment of this innovative approach to clinical trial follow-up including rates of REB approval and patient consent. The pre-specified benchmark for patient acceptability was 80%. Of 16 REBs who reviewed the research protocol, 14 (89%) provided approval; two in Quebec declined due to small patient numbers. Of 140 patients invited to participate, 115 (82%, 95% CI 76 to 88%) from across 9 Canadian provinces provided consent and their full name, date of birth, health insurance number and postal code to facilitate linkage with their administrative data for long-term follow-up. Linkage of clinical trial and administrative data is feasible and acceptable. Further collaborative work including many stakeholders is required to develop an optimized secure approach to research. A more coordinated national approach to health data could facilitate more rapid testing and identification of new effective treatments across multiple jurisdictions and diseases from diabetes to COVID-19.


Assuntos
Armazenamento e Recuperação da Informação/métodos , Ensaios Clínicos Controlados Aleatórios como Assunto , Sistema de Registros , Canadá , Comitês de Ética em Pesquisa , Feminino , Hospitais/estatística & dados numéricos , Humanos , Armazenamento e Recuperação da Informação/estatística & dados numéricos , Masculino , Estudos Prospectivos
6.
J Med Internet Res ; 23(5): e24294, 2021 05 07.
Artigo em Inglês | MEDLINE | ID: covidwho-1197468

RESUMO

Digital technology has been widely used in health care systems and disease management, as well as in controlling the spread of COVID-19. As one of the most successful countries in combating the COVID-19 pandemic, Taiwan has successfully used digital technology to strengthen its efforts in controlling the COVID-19 pandemic. Taiwan has a well-established National Health Insurance System (NHIS), which provides a great opportunity to develop a nationwide data linkage model in an agile manner. Here we provide an overview of the application of data linkage models for strategies in combating COVID-19 in Taiwan, including NHIS centralized data linkage systems and "from border to community" information-driven data linkage systems during the COVID-19 pandemic. Furthermore, we discuss the dual role of digital technologies in being an "enabler" and a "driver" in early disease prevention. Lastly, Taiwan's experience in applying digital technology to enhance the control of COVID-19 potentially highlights lessons learned and opportunities for other countries to handle the COVID-19 situation better.


Assuntos
COVID-19/epidemiologia , COVID-19/prevenção & controle , Armazenamento e Recuperação da Informação/métodos , COVID-19/transmissão , Gerenciamento Clínico , Transmissão de Doença Infecciosa/prevenção & controle , Humanos , Pandemias , SARS-CoV-2/isolamento & purificação , Taiwan/epidemiologia
7.
Nat Commun ; 12(1): 2371, 2021 04 22.
Artigo em Inglês | MEDLINE | ID: mdl-33888693

RESUMO

DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency. Previous studies have used artificially synthesized DNA to store data and automated next-generation sequencing to read it back. Here, we report digital Nucleic Acid Memory (dNAM) for applications that require a limited amount of data to have high information density, redundancy, and copy number. In dNAM, data is encoded by selecting combinations of single-stranded DNA with (1) or without (0) docking-site domains. When self-assembled with scaffold DNA, staple strands form DNA origami breadboards. Information encoded into the breadboards is read by monitoring the binding of fluorescent imager probes using DNA-PAINT super-resolution microscopy. To enhance data retention, a multi-layer error correction scheme that combines fountain and bi-level parity codes is used. As a prototype, fifteen origami encoded with 'Data is in our DNA!\n' are analyzed. Each origami encodes unique data-droplet, index, orientation, and error-correction information. The error-correction algorithms fully recover the message when individual docking sites, or entire origami, are missing. Unlike other approaches to DNA-based data storage, reading dNAM does not require sequencing. As such, it offers an additional path to explore the advantages and disadvantages of DNA as an emerging memory material.


Assuntos
DNA de Cadeia Simples/química , Armazenamento e Recuperação da Informação/métodos , Nanoestruturas/química , Nanotecnologia/métodos , Algoritmos , Conformação de Ácido Nucleico , Estudo de Prova de Conceito
8.
J Med Internet Res ; 23(5): e24294, 2021 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-33882019

RESUMO

Digital technology has been widely used in health care systems and disease management, as well as in controlling the spread of COVID-19. As one of the most successful countries in combating the COVID-19 pandemic, Taiwan has successfully used digital technology to strengthen its efforts in controlling the COVID-19 pandemic. Taiwan has a well-established National Health Insurance System (NHIS), which provides a great opportunity to develop a nationwide data linkage model in an agile manner. Here we provide an overview of the application of data linkage models for strategies in combating COVID-19 in Taiwan, including NHIS centralized data linkage systems and "from border to community" information-driven data linkage systems during the COVID-19 pandemic. Furthermore, we discuss the dual role of digital technologies in being an "enabler" and a "driver" in early disease prevention. Lastly, Taiwan's experience in applying digital technology to enhance the control of COVID-19 potentially highlights lessons learned and opportunities for other countries to handle the COVID-19 situation better.


Assuntos
COVID-19/epidemiologia , COVID-19/prevenção & controle , Armazenamento e Recuperação da Informação/métodos , COVID-19/transmissão , Gerenciamento Clínico , Transmissão de Doença Infecciosa/prevenção & controle , Humanos , Pandemias , SARS-CoV-2/isolamento & purificação , Taiwan/epidemiologia
9.
Nucleic Acids Res ; 49(10): 5451-5469, 2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-33836076

RESUMO

Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.


Assuntos
DNA , Genes Sintéticos , Armazenamento e Recuperação da Informação/métodos , DNA/síntese química , DNA/química
10.
Rev Bras Epidemiol ; 24: e210011, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33825773

RESUMO

OBJECTIVE: To develop a linkage algorithm to match anonymous death records of cancer of the larynx (ICD-10 C32X), retrieved from the Mortality Information System (SIM) and the Hospital Information System of the Brazilian Unified National Health System (SIH-SUS) in Brazil. METHODOLOGY: Death records containing ICD-10 C32X codes were retrieved from SIM and SIH-SUS, limited to individuals aged 30 years and over, between 2002 and 2012, in the state of São Paulo. The databases were linked using a unique key identifier developed with sociodemographic data shared by both systems. Linkage performance was ascertained by applying the same procedure to similar non-anonymous databases. True pairs were those having the same identification variables. RESULTS: A total of 14,311 eligible death records were found. Most records, 10,674 (74.6%), were exclusive to SIM. Only 1,853 (12.9%) deaths were registered in both systems, representing true pairs. A total of 1,784 (12.5%) cases of laryngeal cancer in the SIH-SUS database were tracked in SIM with different causes of death. The linkage failed to match 167 (9.4%) records due to inconsistencies in the key identifier. CONCLUSION: The authors found that linking anonymous data from mortality and hospital records is a feasible measure to track missing records and may improve cancer statistics.


Assuntos
Armazenamento e Recuperação da Informação , Neoplasias Laríngeas , Adulto , Algoritmos , Brasil/epidemiologia , Bases de Dados Factuais , Atestado de Óbito , Estudos de Viabilidade , Sistemas de Informação Hospitalar , Humanos , Armazenamento e Recuperação da Informação/métodos , Sistemas de Informação , Neoplasias Laríngeas/mortalidade
11.
Curr Oncol ; 28(2): 1153-1160, 2021 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-33800281

RESUMO

In a prospective study, we sought to determine acceptability of linkage of administrative and clinical trial data among Canadian patients and Research Ethics Boards (REBs). The goal is to develop a more harmonized approach to data, with potential to improve clinical trial conduct through enhanced data quality collected at reduced cost and inconvenience for patients. On completion of the original LY.12 randomized clinical trial in lymphoma (NCT00078949), participants were invited to enrol in the Long-term Innovative Follow-up Extension (LIFE) component. Those consenting to do so provided comprehensive identifying information to facilitate linkage with their administrative data. We prospectively designed a global assessment of this innovative approach to clinical trial follow-up including rates of REB approval and patient consent. The pre-specified benchmark for patient acceptability was 80%. Of 16 REBs who reviewed the research protocol, 14 (89%) provided approval; two in Quebec declined due to small patient numbers. Of 140 patients invited to participate, 115 (82%, 95% CI 76 to 88%) from across 9 Canadian provinces provided consent and their full name, date of birth, health insurance number and postal code to facilitate linkage with their administrative data for long-term follow-up. Linkage of clinical trial and administrative data is feasible and acceptable. Further collaborative work including many stakeholders is required to develop an optimized secure approach to research. A more coordinated national approach to health data could facilitate more rapid testing and identification of new effective treatments across multiple jurisdictions and diseases from diabetes to COVID-19.


Assuntos
Armazenamento e Recuperação da Informação/métodos , Ensaios Clínicos Controlados Aleatórios como Assunto , Sistema de Registros , Canadá , Comitês de Ética em Pesquisa , Feminino , Hospitais/estatística & dados numéricos , Humanos , Armazenamento e Recuperação da Informação/estatística & dados numéricos , Masculino , Estudos Prospectivos
12.
J Am Med Inform Assoc ; 28(6): 1275-1283, 2021 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-33674830

RESUMO

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 SignSym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.


Assuntos
COVID-19/diagnóstico , Registros Eletrônicos de Saúde , Armazenamento e Recuperação da Informação/métodos , Processamento de Linguagem Natural , Aprendizado Profundo , Humanos , Avaliação de Sintomas/métodos
13.
Sci Eng Ethics ; 27(2): 23, 2021 03 29.
Artigo em Inglês | MEDLINE | ID: covidwho-1155325

RESUMO

At the beginning of the COVID-19 pandemic, high hopes were placed on digital contact tracing. Digital contact tracing apps can now be downloaded in many countries, but as further waves of COVID-19 tear through much of the northern hemisphere, these apps are playing a less important role in interrupting chains of infection than anticipated. We argue that one of the reasons for this is that most countries have opted for decentralised apps, which cannot provide a means of rapidly informing users of likely infections while avoiding too many false positive reports. Centralised apps, in contrast, have the potential to do this. But policy making was influenced by public debates about the right app configuration, which have tended to focus heavily on privacy, and are driven by the assumption that decentralised apps are "privacy preserving by design". We show that both types of apps are in fact vulnerable to privacy breaches, and, drawing on principles from safety engineering and risk analysis, compare the risks of centralised and decentralised systems along two dimensions, namely the probability of possible breaches and their severity. We conclude that a centralised app may in fact minimise overall ethical risk, and contend that we must reassess our approach to digital contact tracing, and should, more generally, be cautious about a myopic focus on privacy when conducting ethical assessments of data technologies.


Assuntos
Confidencialidade/ética , Busca de Comunicante/ética , Busca de Comunicante/métodos , Tecnologia Digital , Armazenamento e Recuperação da Informação/métodos , Aplicativos Móveis , Privacidade , COVID-19/epidemiologia , Política de Saúde , Humanos , Armazenamento e Recuperação da Informação/ética , Saúde Pública , SARS-CoV-2 , Smartphone
14.
JMIR Public Health Surveill ; 7(3): e26719, 2021 03 24.
Artigo em Inglês | MEDLINE | ID: covidwho-1148274

RESUMO

BACKGROUND: Patient travel history can be crucial in evaluating evolving infectious disease events. Such information can be challenging to acquire in electronic health records, as it is often available only in unstructured text. OBJECTIVE: This study aims to assess the feasibility of annotating and automatically extracting travel history mentions from unstructured clinical documents in the Department of Veterans Affairs across disparate health care facilities and among millions of patients. Information about travel exposure augments existing surveillance applications for increased preparedness in responding quickly to public health threats. METHODS: Clinical documents related to arboviral disease were annotated following selection using a semiautomated bootstrapping process. Using annotated instances as training data, models were developed to extract from unstructured clinical text any mention of affirmed travel locations outside of the continental United States. Automated text processing models were evaluated, involving machine learning and neural language models for extraction accuracy. RESULTS: Among 4584 annotated instances, 2659 (58%) contained an affirmed mention of travel history, while 347 (7.6%) were negated. Interannotator agreement resulted in a document-level Cohen kappa of 0.776. Automated text processing accuracy (F1 85.6, 95% CI 82.5-87.9) and computational burden were acceptable such that the system can provide a rapid screen for public health events. CONCLUSIONS: Automated extraction of patient travel history from clinical documents is feasible for enhanced passive surveillance public health systems. Without such a system, it would usually be necessary to manually review charts to identify recent travel or lack of travel, use an electronic health record that enforces travel history documentation, or ignore this potential source of information altogether. The development of this tool was initially motivated by emergent arboviral diseases. More recently, this system was used in the early phases of response to COVID-19 in the United States, although its utility was limited to a relatively brief window due to the rapid domestic spread of the virus. Such systems may aid future efforts to prevent and contain the spread of infectious diseases.


Assuntos
Doenças Transmissíveis Emergentes/diagnóstico , Registros Eletrônicos de Saúde , Armazenamento e Recuperação da Informação/métodos , Vigilância em Saúde Pública/métodos , Viagem/estatística & dados numéricos , Algoritmos , COVID-19/epidemiologia , Doenças Transmissíveis Emergentes/epidemiologia , Estudos de Viabilidade , Feminino , Humanos , Aprendizado de Máquina , Masculino , Pessoa de Meia-Idade , Processamento de Linguagem Natural , Reprodutibilidade dos Testes , Estados Unidos/epidemiologia
16.
JMIR Public Health Surveill ; 7(3): e26719, 2021 03 24.
Artigo em Inglês | MEDLINE | ID: mdl-33759790

RESUMO

BACKGROUND: Patient travel history can be crucial in evaluating evolving infectious disease events. Such information can be challenging to acquire in electronic health records, as it is often available only in unstructured text. OBJECTIVE: This study aims to assess the feasibility of annotating and automatically extracting travel history mentions from unstructured clinical documents in the Department of Veterans Affairs across disparate health care facilities and among millions of patients. Information about travel exposure augments existing surveillance applications for increased preparedness in responding quickly to public health threats. METHODS: Clinical documents related to arboviral disease were annotated following selection using a semiautomated bootstrapping process. Using annotated instances as training data, models were developed to extract from unstructured clinical text any mention of affirmed travel locations outside of the continental United States. Automated text processing models were evaluated, involving machine learning and neural language models for extraction accuracy. RESULTS: Among 4584 annotated instances, 2659 (58%) contained an affirmed mention of travel history, while 347 (7.6%) were negated. Interannotator agreement resulted in a document-level Cohen kappa of 0.776. Automated text processing accuracy (F1 85.6, 95% CI 82.5-87.9) and computational burden were acceptable such that the system can provide a rapid screen for public health events. CONCLUSIONS: Automated extraction of patient travel history from clinical documents is feasible for enhanced passive surveillance public health systems. Without such a system, it would usually be necessary to manually review charts to identify recent travel or lack of travel, use an electronic health record that enforces travel history documentation, or ignore this potential source of information altogether. The development of this tool was initially motivated by emergent arboviral diseases. More recently, this system was used in the early phases of response to COVID-19 in the United States, although its utility was limited to a relatively brief window due to the rapid domestic spread of the virus. Such systems may aid future efforts to prevent and contain the spread of infectious diseases.


Assuntos
Doenças Transmissíveis Emergentes/diagnóstico , Registros Eletrônicos de Saúde , Armazenamento e Recuperação da Informação/métodos , Vigilância em Saúde Pública/métodos , Viagem/estatística & dados numéricos , Algoritmos , COVID-19/epidemiologia , Doenças Transmissíveis Emergentes/epidemiologia , Estudos de Viabilidade , Feminino , Humanos , Aprendizado de Máquina , Masculino , Pessoa de Meia-Idade , Processamento de Linguagem Natural , Reprodutibilidade dos Testes , Estados Unidos/epidemiologia
17.
Nat Methods ; 18(3): 262-271, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33649586

RESUMO

Single-cell technologies have made it possible to profile millions of cells, but for these resources to be useful they must be easy to query and access. To facilitate interactive and intuitive access to single-cell data we have developed scfind, a single-cell analysis tool that facilitates fast search of biologically or clinically relevant marker genes in cell atlases. Using transcriptome data from six mouse cell atlases, we show how scfind can be used to evaluate marker genes, perform in silico gating, and identify both cell-type-specific and housekeeping genes. Moreover, we have developed a subquery optimization routine to ensure that long and complex queries return meaningful results. To make scfind more user friendly, we use indices of PubMed abstracts and techniques from natural language processing to allow for arbitrary queries. Finally, we show how scfind can be used for multi-omics analyses by combining single-cell ATAC-seq data with transcriptome data.


Assuntos
Gerenciamento de Dados/métodos , Armazenamento e Recuperação da Informação/métodos , Análise de Célula Única/métodos , Transcriptoma/genética , Algoritmos , Animais , Análise de Dados , Bases de Dados Genéticas , Regulação da Expressão Gênica , Camundongos , Processamento de Linguagem Natural , PubMed , Interface Usuário-Computador
18.
Sci Eng Ethics ; 27(2): 23, 2021 03 29.
Artigo em Inglês | MEDLINE | ID: mdl-33779818

RESUMO

At the beginning of the COVID-19 pandemic, high hopes were placed on digital contact tracing. Digital contact tracing apps can now be downloaded in many countries, but as further waves of COVID-19 tear through much of the northern hemisphere, these apps are playing a less important role in interrupting chains of infection than anticipated. We argue that one of the reasons for this is that most countries have opted for decentralised apps, which cannot provide a means of rapidly informing users of likely infections while avoiding too many false positive reports. Centralised apps, in contrast, have the potential to do this. But policy making was influenced by public debates about the right app configuration, which have tended to focus heavily on privacy, and are driven by the assumption that decentralised apps are "privacy preserving by design". We show that both types of apps are in fact vulnerable to privacy breaches, and, drawing on principles from safety engineering and risk analysis, compare the risks of centralised and decentralised systems along two dimensions, namely the probability of possible breaches and their severity. We conclude that a centralised app may in fact minimise overall ethical risk, and contend that we must reassess our approach to digital contact tracing, and should, more generally, be cautious about a myopic focus on privacy when conducting ethical assessments of data technologies.


Assuntos
Confidencialidade/ética , Busca de Comunicante/ética , Busca de Comunicante/métodos , Tecnologia Digital , Armazenamento e Recuperação da Informação/métodos , Aplicativos Móveis , Privacidade , COVID-19/epidemiologia , Política de Saúde , Humanos , Armazenamento e Recuperação da Informação/ética , Saúde Pública , SARS-CoV-2 , Smartphone
19.
Nurs Res ; 70(2): 132-141, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33630536

RESUMO

OBJECTIVE: The aim of this study was to describe computational ethnography as a contemporary and supplemental methodology in EHR workflow analysis and the relevance of this method to nursing research. METHODS: We explore the use of audit logs as a computational ethnographic data source and the utility of data mining techniques, including sequential pattern mining (SPM) and Markov chain analysis (MCA), to analyze nurses' workflow within the EHRs. SPM extracts frequent patterns in a given transactional database (e.g., audit logs from the record). MCA is a stochastic process that models a sequence of states and allows for calculating the probability of moving from one state to the next. These methods can help uncover nurses' global navigational patterns (i.e., how nurses navigate within the record) and enable robust workflow analyses. RESULTS: We demonstrate hypothetical examples from SPM and MCA, such as (a) the most frequent sequential pattern of nurses' workflow when navigating the EHR using SPM and (b) transition probability from one record screen to the next using MCA. These examples demonstrate new methods to address the inflexibility of current approaches used to examine nursing EHR workflow. DISCUSSION: Within a clinical context, the use of computational ethnographic data and data mining techniques can inform the optimization of the EHR. Results from these analyses can be used to supplement the data needed in redesigning the EHR, such as organizing and combining features within a screen or predicting future navigation to improve the record that nurses use.


Assuntos
Atitude do Pessoal de Saúde , Registros Eletrônicos de Saúde/organização & administração , Armazenamento e Recuperação da Informação/métodos , Cuidados de Enfermagem/organização & administração , Carga de Trabalho/estatística & dados numéricos , Humanos , Pesquisa em Enfermagem , Interface Usuário-Computador , Fluxo de Trabalho
20.
JAMA Netw Open ; 4(2): e2037739, 2021 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-33616663

RESUMO

Importance: A cornerstone of precision medicine is the identification and use of biomarkers that help subtype patients for targeted treatment. Such an approach requires the development and subsequent interrogation of large-scale biobanks linked to well-annotated clinical data. Traditional means of creating these data-linked biobanks are costly and lengthy, especially in acute conditions that require time-sensitive clinical data and biospecimens. Objectives: To develop a virtually enabled biorepository and electronic health record (EHR)-embedded, scalable cohort for precision medicine (VESPRE) and compare the feasibility, enrollment, and costs of VESPRE with those of a traditional study design in acute care. Design, Setting, and Participants: In a prospective cohort study, the EHR-embedded screening alert was generated for 3428 patients, and 2199 patients (64%) were eligible and screened. Of these, 1027 patients (30%) were enrolled. VESPRE was developed for regulatory compliance, feasibility, internal validity, and cost in a prospective cohort of 1027 patients (aged ≥18 years) with sepsis-3 within 6 hours of presentation to the emergency department. The VESPRE infrastructure included (1) automated EHR screening, (2) remnant blood collection for creation of a virtually enabled biorepository, and (3) automated clinical data abstraction. The study was conducted at an academic institution in southwestern Pennsylvania from October 17, 2017, to June 6, 2019. Main Outcomes and Measures: Regulatory compliance, enrollment, internal validity of automated screening, biorepository acquisition, and costs. Results: Of the 1027 patients enrolled in the study, 549 were included in the proof-of-concept analysis (305 [56%] men); median (SD) age was 59 (17) years. VESPRE collected 12 963 remnant blood and urine samples and demonstrated adequate feasibility for clinical, biomarker, and microbiome analyses. Over the 20-month test, the total cost beyond the existing operations infrastructure was $39 417.50 ($14 880.00 project management, $22 717.50 laboratory supplies/staff, and $1820.00 data management)-approximately $39 per enrolled patient vs $239 per patient for a traditional cohort study. Conclusions and Relevance: Results of this study suggest that, in a large US health system that collects data using a common EHR platform and centralized laboratory system, VESPRE, a large-scale, inexpensive EHR-embedded infrastructure for precision medicine can be used. Tested in the sepsis setting, VESPRE appeared to capture a high proportion of eligible patients at low incremental cost.


Assuntos
Coleta de Dados/métodos , Registros Eletrônicos de Saúde , Medicina de Precisão , Sepse/sangue , Manejo de Espécimes/métodos , Adulto , Idoso , Automação , Bancos de Espécimes Biológicos/economia , Biomarcadores/sangue , Estudos de Coortes , Coleta de Dados/economia , Estudos de Viabilidade , Feminino , Humanos , Armazenamento e Recuperação da Informação/economia , Armazenamento e Recuperação da Informação/métodos , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Sepse/urina , Manejo de Espécimes/economia
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