Persistence of intact HIV-1 proviruses in the brain during antiretroviral therapy.

HIV-1 reservoir cells that circulate in peripheral blood during suppressive antiretroviral therapy (ART) have been well characterized, but little is known about the dissemination of HIV-1-infected cells across multiple anatomical tissues, especially the CNS. Here, we performed single-genome, near full-length HIV-1 next-generation sequencing to evaluate the proviral landscape in distinct anatomical compartments, including multiple CNS tissues, from 3 ART-treated participants at autopsy. While lymph nodes and, to a lesser extent, gastrointestinal and genitourinary tissues represented tissue hotspots for the persistence of intact proviruses, we also observed intact proviruses in CNS tissue sections, particularly in the basal ganglia.

Persistence of intact HIV-1 proviruses in the brain during antiretroviral therapy.

HIV-1 reservoir cells that circulate in peripheral blood during suppressive antiretroviral therapy (ART) have been well characterized, but little is known about the dissemination of HIV-1-infected cells across multiple anatomical tissues, especially the central nervous system (CNS). Here, we performed single-genome, near full-length HIV-1 next-generation sequencing to evaluate the proviral landscape in distinct anatomical compartments, including multiple CNS tissues, from 3 ART-treated participants at autopsy. While lymph nodes and, to a lesser extent, gastrointestinal and genitourinary tissues represented tissue hotspots for the persistence of intact proviruses, we also observed intact proviruses in CNS tissue sections, particularly in the basal ganglia.

Classification of neurologic outcomes from medical notes using natural language processing.

Neurologic disability level at hospital discharge is an important outcome in many clinical research studies. Outside of clinical trials, neurologic outcomes must typically be extracted by labor intensive manual review of clinical notes in the electronic health record (EHR). To overcome this challenge, we set out to develop a natural language processing (NLP) approach that automatically reads clinical notes to determine neurologic outcomes, to make it possible to conduct larger scale neurologic outcomes studies.

Identifying Patients With Delirium Based on Unstructured Clinical Notes: Observational Study.

Background: Delirium in hospitalized patients is a syndrome of acute brain dysfunction. Diagnostic (International Classification of Diseases [ICD]) codes are often used in studies using electronic health records (EHRs), but they are inaccurate.

Objective: We sought to develop a more accurate method using natural language processing (NLP) to detect delirium episodes on the basis of unstructured clinical notes.

Clinical and neuroradiologic characteristics in varicella zoster virus reactivation with central nervous system involvement.

Objective: To investigate the clinical and magnetic resonance imaging (MRI) characteristics of patients with varicella zoster virus (VZV) reactivation involving the cranial nerves and central nervous system (CNS).

Methods: This is a retrospective, multi-center case-series of 37 patients with VZV infection affecting the cranial nerves and CNS.

Results: The median age was 71 years [IQR 51.

Intrathecal inflammatory responses in the absence of SARS-CoV-2 nucleic acid in the CSF of COVID-19 hospitalized patients.

Objective: Little is known about CSF profiles in patients with acute COVID-19 infection and neurological symptoms. Here, CSF was tested for SARS-CoV-2 RNA and inflammatory cytokines and chemokines and compared to controls and patients with known neurotropic pathogens.

Methods: CSF from twenty-seven consecutive patients with COVID-19 and neurological symptoms was assayed for SARS-CoV-2 RNA using quantitative reverse transcription PCR (RT-qPCR) and unbiased metagenomic sequencing.

Skeletal Muscle and Peripheral Nerve Histopathology in COVID-19.

Objective: To explore the spectrum of skeletal muscle and nerve pathology of patients who died after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and to assess for direct viral invasion of these tissues.

Methods: Psoas muscle and femoral nerve sampled from 35 consecutive autopsies of patients who died after SARS-CoV-2 infection and 10 SARS-CoV-2-negative controls were examined under light microscopy. Clinical and laboratory data were obtained by chart review.

Prolonged Intubation in Patients With Prior Cerebrovascular Disease and COVID-19.

Patients with comorbidities are at increased risk for poor outcomes in COVID-19, yet data on patients with prior neurological disease remains limited. Our objective was to determine the odds of critical illness and duration of mechanical ventilation in patients with prior cerebrovascular disease and COVID-19. A observational study of 1,128 consecutive adult patients admitted to an academic center in Boston, Massachusetts, and diagnosed with laboratory-confirmed COVID-19.

Classification of the Disposition of Patients Hospitalized with COVID-19: Reading Discharge Summaries Using Natural Language Processing.

Background: Medical notes are a rich source of patient data; however, the nature of unstructured text has largely precluded the use of these data for large retrospective analyses. Transforming clinical text into structured data can enable large-scale research studies with electronic health records (EHR) data. Natural language processing (NLP) can be used for text information retrieval, reducing the need for labor-intensive chart review.

Eastern equine encephalitis and use of IV immunoglobulin therapy and high-dose steroids.

Objective: To determine the clinical presentation and patient outcomes after treatment with IV immunoglobulin (IVIG), high-dose steroids, or standard of care alone in Eastern equine encephalitis (EEE), a mosquito-borne viral infection with significant neurologic morbidity and mortality.

Methods: A retrospective observational study of patients admitted to 2 tertiary academic medical centers in Boston, Massachusetts, with EEE from 2005 to 2019.

Results: Of 17 patients (median [IQR] age, 63 [36-70] years; 10 (59%) male, and 16 (94%) White race), 17 patients had fever (100%), 15 had encephalopathy (88%), and 12 had headache (71%).

CoVA: An Acuity Score for Outpatient Screening that Predicts Coronavirus Disease 2019 Prognosis.

Background: We sought to develop an automatable score to predict hospitalization, critical illness, or death for patients at risk for coronavirus disease 2019 (COVID-19) presenting for urgent care.

Methods: We developed the COVID-19 Acuity Score (CoVA) based on a single-center study of adult outpatients seen in respiratory illness clinics or the emergency department. Data were extracted from the Partners Enterprise Data Warehouse, and split into development (n = 9381, 7 March-2 May) and prospective (n = 2205, 3-14 May) cohorts.

COVID-19 Outpatient Screening: a Prediction Score for Adverse Events.

Background: We sought to develop an automatable score to predict hospitalization, critical illness, or death in patients at risk for COVID-19 presenting for urgent care during the Massachusetts outbreak.

Methods: Single-center study of adult outpatients seen in respiratory illness clinics (RICs) or the emergency department (ED), including development (n = 9381, March 7-May 2) and prospective (n = 2205, May 3-14) cohorts. Data was queried from Partners Enterprise Data Warehouse.