A Case Demonstration of the Open Health Natural Language Processing Toolkit From the National COVID-19 Cohort Collaborative and the Researching COVID to Enhance Recovery Programs for a Natural Language Processing System for COVID-19 or Postacute Sequelae of SARS CoV-2 Infection: Algorithm Development and Validation.

Background: A wealth of clinically relevant information is only obtainable within unstructured clinical narratives, leading to great interest in clinical natural language processing (NLP). While a multitude of approaches to NLP exist, current algorithm development approaches have limitations that can slow the development process. These limitations are exacerbated when the task is emergent, as is the case currently for NLP extraction of signs and symptoms of COVID-19 and postacute sequelae of SARS-CoV-2 infection (PASC).

The N3C governance ecosystem: A model socio-technical partnership for the future of collaborative analytics at scale.

The National COVID Cohort Collaborative (N3C) is a public-private-government partnership established during the Coronavirus pandemic to create a centralized data resource called the "N3C data enclave." This resource contains individual-level health data from participating healthcare sites nationwide to support rapid collaborative analytics. N3C has enabled analytics within a cloud-based enclave of data from electronic health records from over 17 million people (with and without COVID-19) in the USA.

Investigation of commonly used aortic aneurysm growth rate metrics: Comparing their suitability for clinical and research applications.

An aneurysm is a pathological widening of a blood vessel. Aneurysms of the aorta are often asymptomatic until they rupture, killing approximately 10,000 Americans per year. Fortunately, rupture can be prevented through early detection and surgical repair.

Effect of SARS-CoV-2 Infection and Infection Severity on Longer-Term Glycemic Control and Weight in People With Type 2 Diabetes.

Objective: To evaluate the association of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and severity of infection with longer-term glycemic control and weight in people with type 2 diabetes (T2D) in the U.S.

Research Design And Methods: We conducted a retrospective cohort study using longitudinal electronic health record data of patients with SARS-CoV-2 infection from the National COVID Cohort Collaborative (N3C).

Glycemic Control and Clinical Outcomes in U.S. Patients With COVID-19: Data From the National COVID Cohort Collaborative (N3C) Database.

Objective: The purpose of the study is to evaluate the relationship between HbA1c and severity of coronavirus disease 2019 (COVID-19) outcomes in patients with type 2 diabetes (T2D) with acute COVID-19 infection.

Research Design And Methods: We conducted a retrospective study using observational data from the National COVID Cohort Collaborative (N3C), a longitudinal, multicenter U.S.

A Large-Scale Observational Study on the Temporal Trends and Risk Factors of Opioid Overdose: Real-World Evidence for Better Opioids.

Background: The USA is in the midst of an opioid overdose epidemic. To address the epidemic, we conducted a large-scale population study on opioid overdose.

Objectives: The primary objective of this study was to evaluate the temporal trends and risk factors of inpatient opioid overdose.

Identifying risk of opioid use disorder for patients taking opioid medications with deep learning.

Objective: The United States is experiencing an opioid epidemic. In recent years, there were more than 10 million opioid misusers aged 12 years or older annually. Identifying patients at high risk of opioid use disorder (OUD) can help to make early clinical interventions to reduce the risk of OUD.

Predicting opioid overdose risk of patients with opioid prescriptions using electronic health records based on temporal deep learning.

The US is experiencing an opioid epidemic, and opioid overdose is causing more than 100 deaths per day. Early identification of patients at high risk of Opioid Overdose (OD) can help to make targeted preventative interventions. We aim to build a deep learning model that can predict the patients at high risk for opioid overdose and identify most relevant features.

A large-scale retrospective study of opioid poisoning in New York State with implications for targeted interventions.

Opioid overdose related deaths have increased dramatically in recent years. Combating the opioid epidemic requires better understanding of the epidemiology of opioid poisoning (OP). To discover trends and patterns of opioid poisoning and the demographic and regional disparities, we analyzed large scale patient visits data in New York State (NYS).

Detecting Miscoded Diabetes Diagnosis Codes in Electronic Health Records for Quality Improvement: Temporal Deep Learning Approach.

Background: Diabetes affects more than 30 million patients across the United States. With such a large disease burden, even a small error in classification can be significant. Currently billing codes, assigned at the time of a medical encounter, are the "gold standard" reflecting the actual diseases present in an individual, and thus in aggregate reflect disease prevalence in the population.

Association of Proteinuria and Hematuria with Acute Kidney Injury and Mortality in Hospitalized Patients with COVID-19.

Introduction: Acute kidney injury (AKI) is strongly associated with poor outcomes in hospitalized patients with coronavirus disease 2019 (COVID-19), but data on the association of proteinuria and hematuria are limited to non-US populations. In addition, admission and in-hospital measures for kidney abnormalities have not been studied separately.

Methods: This retrospective cohort study aimed to analyze these associations in 321 patients sequentially admitted between March 7, 2020 and April 1, 2020 at Stony Brook University Medical Center, New York.

Machine Learning Based Opioid Overdose Prediction Using Electronic Health Records.

Opioid addiction in the United States has come to national attention as opioid overdose (OD) related deaths have risen at alarming rates. Combating opioid epidemic becomes a high priority for not only governments but also healthcare providers. This depends on critical knowledge to understand the risk of opioid overdose of patients.

Deep Learning on Electronic Health Records to Improve Disease Coding Accuracy.

Characterization of a patient's clinical phenotype is central to biomedical informatics. ICD codes, assigned to inpatient encounters by coders, is important for population health and cohort discovery when clinical information is limited. While ICD codes are assigned to patients by professionals trained and certified in coding there is substantial variability in coding.

Geographic, Temporal, and Sociodemographic Differences in Opioid Poisoning.

Introduction: Not enough is known about the epidemiology of opioid poisoning to tailor interventions to help address the growing opioid crisis in the U.S. The objective of this study is to expand the current understanding of opioid poisoning through the use of data analytics to evaluate geographic, temporal, and sociodemographic differences of opioid poisoning- related hospital visits in a region of New York State with high opioid poisoning rates.

Social Media Based Analysis of Opioid Epidemic Using Reddit.

Opioid-abuse epidemic in the United States has escalated to national attention due to the dramatic increase of opioid overdose deaths. Analyzing opioid-related social media has the potential to reveal patterns of opioid abuse at a national scale, understand opinions of the public, and provide insights to support prevention and treatment. Reddit is a community based social media with more reliable content curated by the community through voting.

Serverless OpenHealth at data commons scale-traversing the 20 million patient records of New York's SPARCS dataset in real-time.

In a previous report, we explored the serverless OpenHealth approach to the Web as a Global Compute space. That approach relies on the modern browser full stack, and, in particular, its configuration for application assembly by code injection. The opportunity, and need, to expand this approach has since increased markedly, reflecting a wider adoption of Open Data policies by Public Health Agencies.

Large-scale Analysis of Opioid Poisoning Related Hospital Visits in New York State.

Opioid related deaths are increasing dramatically in recent years, and opioid epidemic is worsening in the United States. Combating opioid epidemic becomes a high priority for both the U.S.

A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images.

Well-curated sets of pathology image features will be critical to clinical studies that aim to evaluate and predict treatment responses. Researchers require information synthesized across multiple biological scales, from the patient to the molecular scale, to more effectively study cancer. This article describes a suite of services and web applications that allow users to select regions of interest in whole slide tissue images, run a segmentation pipeline on the selected regions to extract nuclei and compute shape, size, intensity, and texture features, store and index images and analysis results, and visualize and explore images and computed features.

Spatio-temporal Analysis for New York State SPARCS Data.

Increased accessibility of health data provides unique opportunities to discover spatio-temporal patterns of diseases. For example, New York State SPARCS (Statewide Planning and Research Cooperative System) data collects patient level detail on patient demographics, diagnoses, services, and charges for each hospital inpatient stay and outpatient visit. Such data also provides home addresses for each patient.

Towards Generation, Management, and Exploration of Combined Radiomics and Pathomics Datasets for Cancer Research.

Cancer is a complex multifactorial disease state and the ability to anticipate and steer treatment results will require information synthesis across multiple scales from the host to the molecular level. Radiomics and Pathomics, where image features are extracted from routine diagnostic Radiology and Pathology studies, are also evolving as valuable diagnostic and prognostic indicators in cancer. This information explosion provides new opportunities for integrated, multi-scale investigation of cancer, but also mandates a need to build systematic and integrated approaches to manage, query and mine combined Radiomics and Pathomics data.

OpenHealth Platform for Interactive Contextualization of Population Health Open Data.

The financial incentives for data science applications leading to improved health outcomes, such as DSRIP (bit.ly/dsrip), are well-aligned with the broad adoption of Open Data by State and Federal agencies. This creates entirely novel opportunities for analytical applications that make exclusive use of the pervasive Web Computing platform.