Contextualized race and ethnicity annotations for clinical text from MIMIC-III.

Observational health research often relies on accurate and complete race and ethnicity (RE) patient information, such as characterizing cohorts, assessing quality/performance metrics of hospitals and health systems, and identifying health disparities. While the electronic health record contains structured data such as accessible patient-level RE data, it is often missing, inaccurate, or lacking granular details. Natural language processing models can be trained to identify RE in clinical text which can supplement missing RE data in clinical data repositories.

Auditing Learned Associations in Deep Learning Approaches to Extract Race and Ethnicity from Clinical Text.

Complete and accurate race and ethnicity (RE) patient information is important for many areas of biomedical informatics research, such as defining and characterizing cohorts, performing quality assessments, and identifying health inequities. Patient-level RE data is often inaccurate or missing in structured sources, but can be supplemented through clinical notes and natural language processing (NLP). While NLP has made many improvements in recent years with large language models, bias remains an often-unaddressed concern, with research showing that harmful and negative language is more often used for certain racial/ethnic groups than others.

Investigating Racial Disparities in Drug Prescriptions for Patients with Endometriosis.

Background: Endometriosis is a chronic disease with a long time to diagnosis and several known comorbidities that requires a range of treatments including of pain management and hormone-based medications. Racial disparities specific to endometriosis treatments are unknown.

Objective: We aim to investigate differences in patterns of drug prescriptions specific to endometriosis management in Black and White patients prior to diagnosis and after diagnosis of endometriosis and compare these differences to racial disparities established in the general population.

Large-scale characterization of gender differences in diagnosis prevalence and time to diagnosis.

We carry out an analysis of gender differences in patterns of disease diagnosis across four large observational health datasets and find that women are routinely older when first assigned most diagnoses. Among 112 acute and chronic diseases, women experience longer lengths of time between symptom onset and disease diagnosis than men for most diseases regardless of metric used, even when only symptoms common to both genders are considered. These findings are consistent for patients with private as well as government insurance.

Identification of ADAR1 p150 and p110 Associated Edit Sites.

Adenosine deaminase acting on RNA 1 (ADAR1) catalyzes adenosine-to-inosine editing on double-stranded RNA molecules and is involved in regulating cellular responses to endogenous and exogenous RNA. ADAR1 is the primary A-to-I editor of RNA in humans, and the majority of edit sites are found in a class of short interspersed nuclear elements called Alu elements, many of which are located in introns and 3' untranslated regions. Two ADAR1 protein isoforms, p110 (110 kDa) and p150 (150 kDa), are known to be coupled in expression, and decoupling the expression of these isoforms has revealed that the p150 isoform edits a broader range of targets compared to p110.

Edinburgh_UCL_Health@SMM4H'22: From Glove to Flair for handling imbalanced healthcare corpora related to Adverse Drug Events, Change in medication and self-reporting vaccination.

This paper reports on the performance of Edin-burgh_UCL_Health's models in the Social Media Mining for Health (SMM4H) 2022 shared tasks. Our team participated in the tasks related to the Identification of Adverse Drug Events (ADEs), the classification of change in medication (change-med) and the classification of selfreport of vaccination (self-vaccine). Our best performing models are based on DeepADEM-iner (with respective F1= 0.

Clinically relevant pretraining is all you need.

Clinical notes present a wealth of information for applications in the clinical domain, but heterogeneity across clinical institutions and settings presents challenges for their processing. The clinical natural language processing field has made strides in overcoming domain heterogeneity, while pretrained deep learning models present opportunities to transfer knowledge from one task to another. Pretrained models have performed well when transferred to new tasks; however, it is not well understood if these models generalize across differences in institutions and settings within the clinical domain.

Revisiting the remember-know task: Replications of Gardiner and Java (1990).

One of the most evidential behavioral results for two memory processes comes from Gardiner and Java (Memory & Cognition, 18, 23-30 1990). Participants provided more "remember" than "know" responses for old words but more know than remember responses for old nonwords. Moreover, there was no effect of word/nonword status for new items.

Mechanistic Modeling of Soluble Aβ Dynamics and Target Engagement in the Brain by Anti-Aβ mAbs in Alzheimer's Disease.

Background: Anti-amyloid-β (Aβ) monoclonal antibodies (mAbs) are currently in development for treating Alzheimer's disease.

Objectives: To address the complexity of Aβ target engagement profiles, improve the understanding of crenezumab Pharmacokinetics (PK) and Aβ Pharmacodynamics (PD) in the brain, and facilitate comparison of anti-Aβ therapies with different binding characteristics.

Methods: A mechanistic mathematical model was developed describing the distribution, elimination, and binding kinetics of anti-Aβ mAbs and Aβ (monomeric and oligomeric forms of Aβ1-40 and Aβ1-42) in the brain, Cerebrospinal Fluid (CSF), and plasma.

Developing and Testing a Personalized, Evidence-Based, Shared Decision-Making Tool for Stent Selection in Percutaneous Coronary Intervention Using a Pre-Post Study Design.

Background Drug-eluting stents reduce the risk of restenosis in patients undergoing percutaneous coronary intervention, but their use necessitates prolonged dual antiplatelet therapy, which increases costs and bleeding risk, and which may delay elective surgeries. While >80% of patients in the United States receive drug-eluting stents, less than a third report that their physicians discussed options with them. Methods and Results An individualized shared decision-making (SDM) tool for stent selection was designed and implemented at 2 US hospitals.

Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown.

Type I interferon (IFN) is produced when host sensors detect foreign nucleic acids, but how sensors differentiate self from nonself nucleic acids, such as double-stranded RNA (dsRNA), is incompletely understood. Mutations in ADAR1, an adenosine-to-inosine editing enzyme of dsRNA, cause Aicardi-Goutières syndrome, an autoinflammatory disorder associated with spontaneous interferon production and neurologic sequelae. We generated ADAR1 knockout human cells to explore ADAR1 substrates and function.

Astrocytes decrease adult neurogenesis during virus-induced memory dysfunction via IL-1.

Memory impairment following West Nile virus neuroinvasive disease (WNND) is associated with loss of hippocampal synapses with lack of recovery. Adult neurogenesis and synaptogenesis are fundamental features of hippocampal repair, which suggests that viruses affect these processes. Here, in an established model of WNND-induced cognitive dysfunction, transcriptional profiling revealed alterations in the expression of genes encoding molecules that limit adult neurogenesis, including interleukin 1 (IL-1).

Intrinsic Immunity Shapes Viral Resistance of Stem Cells.

Stem cells are highly resistant to viral infection compared to their differentiated progeny; however, the mechanism is mysterious. Here, we analyzed gene expression in mammalian stem cells and cells at various stages of differentiation. We find that, conserved across species, stem cells express a subset of genes previously classified as interferon (IFN) stimulated genes (ISGs) but that expression is intrinsic, as stem cells are refractory to interferon.

Recapitulating the Structural Evolution of Redox Regulation in Adenosine 5'-Phosphosulfate Kinase from Cyanobacteria to Plants.

In plants, adenosine 5'-phosphosulfate (APS) kinase (APSK) is required for reproductive viability and the production of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfur donor in specialized metabolism. Previous studies of the APSK from Arabidopsis thaliana (AtAPSK) identified a regulatory disulfide bond formed between the N-terminal domain (NTD) and a cysteine on the core scaffold. This thiol switch is unique to mosses, gymnosperms, and angiosperms.

Flat clathrin lattices: stable features of the plasma membrane.

Clathrin-mediated endocytosis (CME) is a fundamental property of eukaryotic cells. Classical CME proceeds via the formation of clathrin-coated pits (CCPs) at the plasma membrane, which invaginate to form clathrin-coated vesicles, a process that is well understood. However, clathrin also assembles into flat clathrin lattices (FCLs); these structures remain poorly described, and their contribution to cell biology is unclear.

Congenitally acquired persistent lymphocytic choriomeningitis viral infection reduces neuronal progenitor pools in the adult hippocampus and subventricular zone.

Lymphocytic choriomeningitis virus (LCMV) can be transmitted through congenital infection, leading to persistent infection of numerous organ systems including the central nervous system (CNS). Adult mice persistently infected with LCMV (LCMV-cgPi mice) exhibit learning deficits, such as poor performance in spatial discrimination tests. Given that deficits in spatial learning have been linked to defects in adult neurogenesis, we investigated the impact of congenital LCMV infection on generation of neuroblasts from neural progenitor cells within neurogenic zones of adult mice.

Education does pay off: pneumococcal vaccine screening and administration in hospitalized adult patients with pneumonia.

Streptococcus pneumoniae-associated infections are an important cause of hospitalization and mortality in high-risk and elderly patients. Even in the setting of appropriate therapy, the case fatality rate of invasive pneumococcal disease in the elderly may approach 40%. Since approximately 40,000 people die annually from pneumococcal-associated disease, it represents a substantial target for vaccine-preventable, bacterial fatalities.