Estimating Visual Acuity With Spectacle Correction From Fundus Photos Using Artificial Intelligence.

Importance: Determining spectacle-corrected visual acuity (VA) is essential when managing many ophthalmic diseases. If artificial intelligence (AI) evaluations of macular images estimated this VA from a fundus image, AI might provide spectacle-corrected VA without technician costs, reduce visit time, or facilitate home monitoring of VA from fundus images obtained outside of the clinic.

Objective: To estimate spectacle-corrected VA measured on a standard eye chart among patients with diabetic macular edema (DME) in clinical practice settings using previously validated AI algorithms evaluating best-corrected VA from fundus photographs in eyes with DME.

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci.

Motivation: Genome-wide association studies (GWAS) have identified genetic variants, usually single-nucleotide polymorphisms (SNPs), associated with human traits, including disease and disease risk. These variants (or causal variants in linkage disequilibrium with them) usually affect the regulation or function of a nearby gene. A GWAS locus can span many genes, however, and prioritizing which gene or genes in a locus are most likely to be causal remains a challenge.

Brain Network Alterations in Chronic Spinal Cord Injury: Multilayer Community Detection Approach.

Neurological recovery in individuals with spinal cord injury (SCI) is multifaceted, involving mechanisms such as remyelination and perilesional spinal neuroplasticity, with cortical reorganization being one contributing factor. Cortical reorganization, in particular, can be evaluated through network (graph) analysis of interregional functional connectivity. This study aimed to investigate cortical reorganization patterns in persons with chronic SCI using a multilayer community detection approach on resting-state functional MRI data.

Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages.

Objective: The objectives of this study were to: (1) create a corpus of synthetic drug-related patient portal messages to address the current lack of publicly available datasets for model development, (2) assess differences in language used and linguistics among the synthetic patient portal messages, and (3) assess the accuracy of patient-reported drug side effects for different racial groups.

Methods: We leveraged a taxonomy for patient- and clinician-generated content to guide prompt engineering for synthetic drug-related patient portal messages. We generated two groups of messages: the first group (200 messages) used a subset of the taxonomy relevant to a broad range of drug-related messages and the second group (250 messages) used a subset of the taxonomy relevant to a narrow range of messages focused on side effects.

Addressing the mean-variance relationship in spatially resolved transcriptomics data with .

An important task in the analysis of spatially resolved transcriptomics data is to identify spatially variable genes (SVGs), or genes that vary in a 2D space. Current approaches rank SVGs based on either -values or an effect size, such as the proportion of spatial variance. However, previous work in the analysis of RNA-sequencing identified a technical bias, referred to as the "mean-variance relationship", where highly expressed genes are more likely to have a higher variance.

Spatial-temporal attention for video-based assessment of intraoperative surgical skill.

Accurate, unbiased, and reproducible assessment of skill is a vital resource for surgeons throughout their career. The objective in this research is to develop and validate algorithms for video-based assessment of intraoperative surgical skill. Algorithms to classify surgical video into expert or novice categories provide a summative assessment of skill, which is useful for evaluating surgeons at discrete time points in their training or certification of surgeons.

Enhancement of a social risk score in the electronic health record to identify social needs among medically underserved patients: using structured data and free-text provider notes.

Objective: To improve the performance of a social risk score (a predictive risk model) using electronic health record (EHR) structured and unstructured data.

Materials And Methods: We used EPIC-based EHR data from July 2016 to June 2021 and linked it to community-level data from the US Census American Community Survey. We identified predictors of interest within the EHR structured data and applied natural language processing (NLP) techniques to identify patients' social needs in the EHR unstructured data.

Metabolite T relaxation times decrease across the adult lifespan in a large multi-site cohort.

Purpose: Relaxation correction is crucial for accurately estimating metabolite concentrations measured using in vivo MRS. However, the majority of MRS quantification routines assume that relaxation values remain constant across the lifespan, despite prior evidence of T changes with aging for multiple of the major metabolites. Here, we comprehensively investigate correlations between T and age in a large, multi-site cohort.

Big data in visual field testing for glaucoma.

Recent technological advancements and the advent of ever-growing databases in health care have fueled the emergence of "big data" analytics. Big data has the potential to revolutionize health care, particularly ophthalmology, given the data-intensive nature of the medical specialty. As one of the leading causes of irreversible blindness worldwide, glaucoma is an ocular disease that receives significant interest for developing innovations in eye care.

Gene regulatory network inference from CRISPR perturbations in primary CD4 T cells elucidates the genomic basis of immune disease.

The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation has been challenging due to small effects, but experimental perturbations offer a complementary approach.

HuBMAPR: an R Client for the HuBMAP Data Portal.

Summary: The Human BioMolecular Atlas Program (HuBMAP) constructs the worldwide available platform to research the human body at the cellular level. The HuBMAP Data Portal encompasses a wide range of data resources measured on emerging experimental technologies at a spatial resolution. To broaden access to the HuBMAP Data Portal, we introduce an R client called HuBMAPR available on Bioconductor.

Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.

Background: Understanding the genetic causes for variability in chromatin accessibility can shed light on the molecular mechanisms through which genetic variants may affect complex traits. Thousands of ATAC-seq samples have been collected that hold information about chromatin accessibility across diverse cell types and contexts, but most of these are not paired with genetic information and come from diverse distinct projects and laboratories.

Results: We report here joint genotyping, chromatin accessibility peak calling, and discovery of quantitative trait loci which influence chromatin accessibility (caQTLs), demonstrating the capability of performing caQTL analysis on a large scale in a diverse sample set without pre-existing genotype information.

A global transcriptional atlas of the effect of acute sleep deprivation in the mouse frontal cortex.

Sleep deprivation (SD) has negative effects on brain and body function. Sleep problems are prevalent in a variety of disorders, including neurodevelopmental and psychiatric conditions. Thus, understanding the molecular consequences of SD is of fundamental importance in biology.

Comparison of test-retest reproducibility of DESPOT and 3D-QALAS for water and mapping.

Purpose: Relaxometry, specifically and mapping, has become an essential technique for assessing the properties of biological tissues related to various physiological and pathological conditions. Many techniques are being used to estimate and relaxation times, ranging from the traditional inversion or saturation recovery and spin-echo sequences to more advanced methods. Choosing the appropriate method for a specific application is critical since the precision and accuracy of and measurements are influenced by a variety of factors including the pulse sequence and its parameters, the inherent properties of the tissue being examined, the MRI hardware, and the image reconstruction.

Integrating spatially-resolved transcriptomics data across tissues and individuals: challenges and opportunities.

Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. As the cost of generating these data decreases, these technologies provide an exciting opportunity to create large-scale atlases that integrate SRT data across multiple tissues, individuals, species, or phenotypes to perform population-level analyses. Here, we describe unique challenges of varying spatial resolutions in SRT data, as well as highlight the opportunities for standardized preprocessing methods along with computational algorithms amenable to atlas-scale datasets leading to improved sensitivity and reproducibility in the future.

Detecting Visual Field Worsening From Optic Nerve Head and Macular Optical Coherence Tomography Thickness Measurements.

Purpose: Compare the use of optic disc and macular optical coherence tomography measurements to predict glaucomatous visual field (VF) worsening.

Methods: Machine learning and statistical models were trained on 924 eyes (924 patients) with circumpapillary retinal nerve fiber layer (cp-RNFL) or ganglion cell inner plexiform layer (GC-IPL) thickness measurements. The probability of 24-2 VF worsening was predicted using both trend-based and event-based progression definitions of VF worsening.