Mapping the topography of spatial gene expression with interpretable deep learning.

Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of these data complicates analysis of spatial gene expression patterns. We address this issue by deriving a topographic map of a tissue slice-analogous to a map of elevation in a landscape-using a quantity called the isodepth. Contours of constant isodepths enclose domains with distinct cell type composition, while gradients of the isodepth indicate spatial directions of maximum change in expression.

Environmental Exposures Associated with Enteropathogen Infection in Six-Month-Old Children Enrolled in the ECoMiD Cohort along a Rural-Urban Gradient in Northern Ecuador†.

Enteropathogens are major contributors to mortality and morbidity, particularly in settings with limited access to water, sanitation, and hygiene infrastructure. To assess transmission pathways associated with enteropathogen infection, we measured household environmental conditions and assayed 22 enteropathogens using TaqMan Array Cards in stool samples from 276 six-month-old children living in communities along a rural-urban gradient in Northern Ecuador. We utilized multivariable models, risk factor importance, and distance-based statistical methods to test factors associated with infection.

Water, sanitation, handwashing, and nutritional interventions can reduce child antibiotic use: evidence from Bangladesh and Kenya.

Antibiotics can trigger antimicrobial resistance and microbiome alterations. Reducing pathogen exposure and undernutrition can reduce infections and antibiotic use. We assess effects of water, sanitation, handwashing (WSH) and nutrition interventions on caregiver-reported antibiotic use in Bangladesh and Kenya, longitudinally measured at three timepoints among birth cohorts (ages 3-28 months) in a cluster-randomized trial.

Quality of Life in Patients With Acquired Anophthalmia Using an Ocular Prosthesis.

Purpose: To employ a validated survey for evaluation of quality of life (QoL) outcomes and associated factors in a US cohort of adult patients with acquired anophthalmia wearing a prosthesis.

Methods: A retrospective cohort study was performed at a single, US academic institution of patients cared for between 2012 and 2021. The electronic medical record database was queried for adult patients with a history of evisceration or enucleation surgery and placement of an orbital implant.

Recombinant zoster vaccine and the risk of dementia.

Background: Herpes zoster is a potential risk factor for dementia. The effectiveness of the recombinant zoster vaccine for preventing dementia is uncertain.

Methods: This retrospective cohort study used de-identified claims data from the Optum Labs Data Warehouse database from January 1, 2017, to December 31, 2022, to determine whether the recombinant zoster vaccine is associated with a reduced risk of dementia.