A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders.

Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN) cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generate single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers.

Plasma metabolites in childhood Burkitt lymphoma cases and cancer-free controls in Uganda.

Introduction: Burkitt lymphoma (BL) is an aggressive non-Hodgkin lymphoma associated with Plasmodium falciparum and Epstein-Barr virus, both of which affect metabolic pathways. The metabolomic patterns of BL is unknown.

Materials And Methods: We measured 627 metabolites in pre-chemotherapy treatment plasma samples from 25 male children (6-11 years) with BL and 25 cancer-free area- and age-frequency-matched male controls from the Epidemiology of Burkitt Lymphoma in East African Children and Minors study in Uganda using liquid chromatography-tandem mass spectrometry.

Generation of human alveolar epithelial type I cells from pluripotent stem cells.

Alveolar epithelial type I cells (AT1s) line the gas exchange barrier of the distal lung and have been historically challenging to isolate or maintain in cell culture. Here, we engineer a human in vitro AT1 model system via directed differentiation of induced pluripotent stem cells (iPSCs). We use primary adult AT1 global transcriptomes to suggest benchmarks and pathways, such as Hippo-LATS-YAP/TAZ signaling, enriched in these cells.

Hierarchically Structured Metal-Organic Framework Polymer Composites for Chemical Warfare Agent Degradation.

Metal-organic frameworks (MOFs) have captured the imagination of researchers for their highly tunable properties and many potential applications, including as catalysts for a variety of transformations. Even though MOFs possess significant potential, the challenges associated with processing of these crystalline powders into usable form factors while retaining their functional properties limit their end use applications. Herein, we introduce a new approach to construct MOF-polymer composites via 3D photoprinting to overcome these limitations.

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders.

Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN) cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generated single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers.

Human leukocyte antigen-DQA1*04:01 and rs2040406 variants are associated with elevated risk of childhood Burkitt lymphoma.

Burkitt lymphoma (BL) is responsible for many childhood cancers in sub-Saharan Africa, where it is linked to recurrent or chronic infection by Epstein-Barr virus or Plasmodium falciparum. However, whether human leukocyte antigen (HLA) polymorphisms, which regulate immune response, are associated with BL has not been well investigated, which limits our understanding of BL etiology. Here we investigate this association among 4,645 children aged 0-15 years, 800 with BL, enrolled in Uganda, Tanzania, Kenya, and Malawi.

Adaptation of the brainwriting premortem technique to inform the co-creation of COVID-19 testing strategies in underserved communities in South San Diego.

Introduction: Meaningful engagement of partners in co-creating and refining health-related programs can increase the initial uptake, sustained implementation, broad reach, and effectiveness of these programs. This is especially important for underserved communities where resources are limited and need to be prioritized. Brainwriting premortem is a novel qualitative approach to partner engagement that combines the strengths of individual idea generation with the concept of premortem exercise that addresses failure points prior to the implementation of new programs.

Risk Factors for Stroke Development After Thoracic Aortic Surgery.

Objectives: Stroke after thoracic aortic surgery is a complication that is associated with poor outcomes. The aim is to characterize the intraoperative risk factors for stroke development.

Design: A retrospective analysis.

The emergence of SARS-CoV-2 lineages and associated saliva antibody responses among asymptomatic individuals in a large university community.

SARS-CoV-2 (CoV2) infected, asymptomatic individuals are an important contributor to COVID transmission. CoV2-specific immunoglobulin (Ig)-as generated by the immune system following infection or vaccination-has helped limit CoV2 transmission from asymptomatic individuals to susceptible populations (e.g.

Gamma secretase activating protein promotes end-organ dysfunction after bacterial pneumonia.

Pneumonia elicits the production of cytotoxic beta amyloid (Aβ) that contributes to end-organ dysfunction, yet the mechanism(s) linking infection to activation of the amyloidogenic pathway that produces cytotoxic Aβ is unknown. Here, we tested the hypothesis that gamma-secretase activating protein (GSAP), which contributes to the amyloidogenic pathway in the brain, promotes end-organ dysfunction following bacterial pneumonia. First-in-kind knockout rats were generated.

Using ethnographic approaches to document, evaluate, and facilitate virtual community-engaged implementation research.

Background: Community Advisory Boards (CABs) have been frequently used to engage diverse partners to inform research projects. Yet, evaluating the quality of engagement has not been routine. We describe a multi-method ethnographic approach documenting and assessing partner engagement in two "virtual" CABs, for which we conducted all meetings remotely.

Burkitt lymphoma risk shows geographic and temporal associations with infections in Uganda, Tanzania, and Kenya.

Endemic Burkitt lymphoma (eBL) is a pediatric cancer coendemic with malaria in sub-Saharan Africa, suggesting an etiological link between them. However, previous cross-sectional studies of limited geographic areas have not found a convincing association. We used spatially detailed data from the Epidemiology of Burkitt Lymphoma in East African Children and Minors (EMBLEM) study to assess this relationship.

Accuracy of whole slide image based image analysis is adversely affected by preanalytical factors such as stained tissue slide and paraffin block age.

Background: Personalized medicine and accurate quantification of tumor and biomarker expression have become the cornerstone of cancer diagnostics. This requires Quality Control (QC) of research tissue samples to confirm adequate targeted tumor tissue sampling. Digitalization of stained tissue slides offer a precious way to archive, preserve, and retrieve necessary information when needed.

Epstein-Barr Virus in Burkitt Lymphoma in Africa Reveals a Limited Set of Whole Genome and Sequence Patterns: Analysis of Archival Datasets and Field Samples From Uganda, Tanzania, and Kenya.

Unlabelled: Epstein-Barr virus (EBV) is associated with endemic Burkitt lymphoma (eBL), but the contribution of EBV variants is ill-defined. Studies of EBV whole genome sequences (WGS) have identified phylogroups that appear to be distinct for Asian versus non-Asian EBV, but samples from BL or Africa, where EBV was first discovered, are under-represented. We conducted a phylogenetic analysis of EBV WGS and sequences obtained primarily from BL patients in Africa and representative non-African EBV from other conditions or regions using data from GenBank, Sequence Read Archive, or Genomic Data Commons for the Burkitt Lymphoma Genome Sequencing Project (BLGSP) to generate data to support the use of a simpler biomarker of geographic or phenotypic associations.

Integrative Toolkit to Analyze Cellular Signals: Forces, Motion, Morphology, and Fluorescence.

Quantitative assessment of cellular forces and motion advanced considerably over the last four decades. These advancements provided the framework to examine insightful mechanical signaling processes in cell culture systems. However, the field currently faces three problems: lack of quality standardization of the acquired data, technical errors in data analysis and visualization, and perhaps most importantly, the technology remains largely out of reach for common cell biology laboratories.

Co-creating a Theory of Change to advance COVID-19 testing and vaccine uptake in underserved communities.

Objectives: To describe the use of a Theory of Change to meaningfully engage community members from or support underserved communities in two National Institutes of Health-funded implementation science projects aimed at promoting equitable access to COVID-19 testing and vaccination for underserved communities.

Study Setting: Both projects focused on Latino, Black, and immigrant and refugee communities in South/Central San Diego and/or individuals accessing care at a federally qualified health center near the US/Mexico border during December 2020-April 2021.

Study Design: By using a participatory action research design, Community Advisory Boards (CABs) were established for each project with 11 and 22 members.

Resolving the polygenic aetiology of a late onset combined immune deficiency caused by NFKB1 haploinsufficiency and modified by PIK3R1 and TNFRSF13B variants.

Genetic variants in PIK3CD, PIK3R1 and NFKB1 cause the primary immune deficiencies, activated PI3Kδ syndrome (APDS) 1, APDS2 and NFκB1 haploinsufficiency, respectively. We have identified a family with known or potentially pathogenic variants NFKB1, TNFRSF13B and PIK3R1. The study's aim was to describe their associated immune and cellular phenotypes and compare with individuals with monogenic disease.

Impact of Na+ permeation on collective migration of pulmonary arterial endothelial cells.

Collective migration of endothelial cells is important for wound healing and angiogenesis. During such migration, each constituent endothelial cell coordinates its magnitude and direction of migration with its neighbors while retaining intercellular adhesion. Ensuring coordination and cohesion involves a variety of intra- and inter-cellular signaling processes.

Dermoscopic Lotus of Learning: Implementation and Dissemination of a Multimodal Dermoscopy Curriculum for Primary Care.

Dermoscopy is a cost-effective tool for detection of skin cancers yet there is limited training available for primary care. The goal of this project was to develop, implement, and disseminate a multimodal curriculum for primary care across a health system based on a previously validated algorithm (Triage Amalgamated Dermoscopic Algorithm; TADA). This cross-sectional study analyzes the dermoscopy workshop intervention of a dermoscopy multimodal curriculum.