A5007963072- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Electronic Health Records Systems
- Computational Drug Discovery Methods
- Scientific Computing and Data Management
- Natural Language Processing Techniques
- Machine Learning in Healthcare
- Topic Modeling
- Pharmacovigilance and Adverse Drug Reactions
- Data Quality and Management
- Bioinformatics and Genomic Networks
- Artificial Intelligence in Healthcare
- AI in cancer detection
- Clinical practice guidelines implementation
- Cancer Genomics and Diagnostics
- Ovarian cancer diagnosis and treatment
- Genomics and Rare Diseases
- Rough Sets and Fuzzy Logic
- Radiomics and Machine Learning in Medical Imaging
- Atrial Fibrillation Management and Outcomes
- Cardiac Arrhythmias and Treatments
- MicroRNA in disease regulation
- Nursing Diagnosis and Documentation
- Lung Cancer Diagnosis and Treatment
- Biosimilars and Bioanalytical Methods
Yanshan University
2024
Mayo Clinic in Florida
2014-2023
Mayo Clinic
2011-2023
Mayo Clinic in Arizona
2013-2023
Mercy Health
2022
University of Minnesota
2020
WinnMed
2007-2016
Jining First People's Hospital
2015
Wuhan University of Technology
2013
Hokkaido University
2003-2006
Electronic health records (EHRs) are increasingly used for clinical and translational research through the creation of phenotype algorithms. Currently, algorithms most commonly represented as noncomputable descriptive documents knowledge artifacts that detail protocols querying diagnoses, symptoms, procedures, medications, and/or text-driven medical concepts, primarily meant human comprehension. We present desiderata developing a computable representation model (PheRM).A team clinicians...
Background MicroRNAs (miRNAs) are known to be important regulators of both organ development and tumorigenesis. MiRNA networks their regulation messenger RNA (mRNA) translation protein expression in specific biological processes poorly understood. Methods We explored the dynamic miRNAs mouse lung organogenesis. Comprehensive miRNA mRNA profiling was performed encompassing all recognized stages beginning at embryonic day 12 continuing adulthood. analyzed patterns dynamically regulated mRNAs...
Abstract Several parameters of preoperative complete blood count (CBC) and inflammation-associated cell markers derived from them have been reported to correlate with prognosis in patients epithelial ovarian cancer (EOC), but their prognostic importance optimal cutoffs are still needed be elucidated. Clinic/pathological parameters, 5-year follow-up data CBC were obtained retrospectively 654 EOC underwent primary surgery at Mayo Clinic. Cutoffs for neutrophil-to-lymphocyte ratio (NLR),...
Bronchopulmonary dysplasia is a chronic lung disease of premature neonates characterized by arrested pulmonary alveolar development. There increasing evidence that microRNAs (miRNAs) regulate translation messenger RNAs (mRNAs) during organogenesis. The potential role miRNAs in the pathogenesis BPD unclear.Following exposure neonatal mice to 80% O2 or room air (RA) for either 14 29 days, lungs hyperoxic displayed histological changes consistent with BPD. Comprehensive miRNA and mRNA profiling...
The clinical element model (CEM) is an information designed for representing in electronic health records (EHR) systems across organizations. current representation of CEMs does not support formal semantic definitions and therefore it possible to perform reasoning consistency checking on derived models. This paper introduces our efforts represent the CEM specification using Web Ontology Language (OWL). CEM-OWL connects content with Semantic environment, which provides authoring, reasoning,...
Abstract Objective To design, develop, and evaluate a scalable clinical data normalization pipeline for standardizing unstructured electronic health record (EHR) leveraging the HL7 Fast Healthcare Interoperability Resources (FHIR) specification. Methods We established an FHIR-based known as NLP2FHIR that mainly comprises: (1) module core natural language processing (NLP) engine with type system; (2) integrating structured data; (3) content normalization. evaluated FHIR modeling capability...
PURPOSE The Fast Healthcare Interoperability Resources (FHIR) is emerging as a next-generation standards framework developed by HL7 for exchanging electronic health care data. modeling capability of FHIR in standardizing cancer data has been gaining increasing attention the research informatics community. However, few studies have conducted to examine capture (EDC) applications effective clinical trials. objective this study was design, develop, and evaluate an FHIR-based method that enables...
Knowledge graphs (KGs) play a key role to enable explainable artificial intelligence (AI) applications in healthcare. Constructing clinical knowledge (CKGs) against heterogeneous electronic health records (EHRs) has been desired by the research and healthcare AI communities. From standardization perspective, community-based standards such as Fast Healthcare Interoperability Resources (FHIR) Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) are increasingly used...
Objective: This study sought to develop and evaluate an approach for auditing the semantic completeness of SNOMED CT contents using a formal concept analysis (FCA)-based model. Design:We developed model formalizing normal forms expressions FCA.Anonymous nodes, identified through analyses, were retrieved from evaluation.Two quasi-Poisson regression models test whether anonymous nodes can (Model 1), testing such differs between 2 clinical domains 2).The data randomly sampled all contexts that...
Abstract Introduction We sought to assess longitudinal electronic health records (EHRs) using machine learning (ML) methods computationally derive probable Alzheimer's Disease (AD) and related dementia subphenotypes. Methods A retrospective analysis of EHR data from a cohort 7587 patients seen at large, multi‐specialty urban academic medical center in New York was conducted. Subphenotypes were derived hierarchical clustering 792 AD (cases) who had received least one diagnosis their clinical...
Left ventricular ejection fraction (EF) is a key measure in the diagnosis and treatment of heart failure (HF) many patients experience changes EF overtime. Large-scale analysis longitudinal using electronic health records (EHRs) limited. In multi-site retrospective study EHR data from three academic medical centers, we investigated measurements diagnosed with HF. We observed significant variations baseline characteristics change behavior HF cohorts previous that based on registry data. Data...
Electronic health record (EHR) algorithms for defining patient cohorts are commonly shared as free-text descriptions that require human intervention both to interpret and implement. We developed the Phenotype Execution Modeling Architecture (PhEMA, http://projectphema.org) author execute standardized computable phenotype algorithms. With PhEMA, we converted an algorithm benign prostatic hyperplasia, electronic Medical Records Genomics network (eMERGE), into a standards-based format. Eight...
The Adverse Event Reporting System (AERS) is an FDA database providing rich information on voluntary reports of adverse drug events (ADEs). Normalizing data in the AERS would improve mining capacity for safety signal detection and promote semantic interoperability between other sources. In this study, we normalize build a publicly available normalized ADE source. to RxNorm, standard terminology source medication, using natural language processing medication extraction tool, MedEx. Drug class...
A variety of data models have been developed to provide a standardized interface that supports organizing clinical research into standard structure for building the integrated repositories. HL7 Fast Healthcare Interoperability Resources (FHIR) is emerging as next generation standards framework facilitating health care and electronic records-based exchange. The objective study was design assess consensus-based approach harmonizing OHDSI CDM with FHIR. We leverage FHIR W5 (Who, What, When,...
Aberrant expression of miR-1271 plays prominent roles in progression several cancers. However, the role oral squamous cell carcinoma (OSCC) has not been elucidated. The levels and anaplastic lymphoma kinase (ALK) were measured by qRT-PCR OSCC tissues lines. effects miR-1271-mediated ALK on growth metastasis cells, transfected with or without plasmid, assessed using MTT, colony formation, migration invasion assays. Moreover, target relationship between was luciferase reporter assay, western...
This article is part of the Focus Theme METHODS Information in Medicine on "Managing Interoperability and Complexity Health Systems".Data sharing integration between clinical research data management system electronic health record remains a challenging issue. To approach issue, there emerging interest utilizing Detailed Clinical Model (DCM) across variety contexts. The Intermountain Healthcare Element Models (CEMs) have been adopted by Office National Coordinator awarded Strategic IT...
A huge amount of associations among different biological entities (e.g., disease, drug, and gene) are scattered in millions biomedical articles. Systematic analysis such heterogeneous data can infer novel the context personalized medicine translational research. Recently, network-based computational approaches have gained popularity investigating data, proposing therapeutic targets deciphering disease mechanisms. However, little effort has been devoted to drugs, diseases, genes an...