Data Harmonization Guidelines to Combine Multi-platform Genomic Data from Admixed Populations and Boost Power in Genome-Wide Association Studies.

Data harmonization involves combining data from multiple independent sources and processing the data to produce one uniform dataset. Merging separate genotypes or whole-genome sequencing datasets has been proposed as a strategy to increase the statistical power of association tests by increasing the effective sample size. However, data harmonization is not a widely adopted strategy due to the difficulties with merging data (including confounding produced by batch effects and population stratification). Detailed data harmonization protocols are scarce and are often conflicting. Moreover, data harmonization protocols that accommodate samples of admixed ancestry are practically non-existent. Existing data harmonization procedures must be modified to ensure the heterogeneous ancestry of admixed individuals is incorporated into additional downstream analyses without confounding results. Here, we propose a set of guidelines for merging multi-platform genetic data from admixed samples that can be adopted by any investigator with elementary bioinformatics experience. We have applied these guidelines to aggregate 1544 tuberculosis (TB) case-control samples from six separate in-house datasets and conducted a genome-wide association study (GWAS) of TB susceptibility. The GWAS performed on the merged dataset had improved power over analyzing the datasets individually and produced summary statistics free from bias introduced by batch effects and population stratification. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Processing separate datasets comprising array genotype data Alternate Protocol 1: Processing separate datasets comprising array genotype and whole-genome sequencing data Alternate Protocol 2: Performing imputation using a local reference panel Basic Protocol 2: Merging separate datasets Basic Protocol 3: Ancestry inference using ADMIXTURE and RFMix Basic Protocol 4: Batch effect correction using pseudo-case-control comparisons.

Neighborhood disadvantage is associated with working memory and hippocampal volumes among older adults.

It is not well understood how neighborhood disadvantage is associated with specific domains of cognitive function and underlying brain health within older adults. Thus, the objective was to examine associations between neighborhood disadvantage, brain health, and cognitive performance, and examine whether associations were more pronounced among women. The study included 136 older adults who underwent cognitive testing and MRI. Neighborhood disadvantage was characterized using the Area Deprivation Index (ADI). Descriptive statistics, bivariate correlations, and multiple regressions were run. Multiple regressions, adjusted for age, sex, education, and depression, showed that higher ADI state rankings (greater disadvantage) were associated with poorer working memory performance (p < .01) and lower hippocampal volumes (p < .01), but not total, frontal, and white matter lesion volumes, nor visual and verbal memory performance. There were no significant sex interactions. Findings suggest that greater neighborhood disadvantage may play a role in working memory and underlying brain structure.

Prostate cancer genetic risk and associated aggressive disease in men of African ancestry.

African ancestry is a significant risk factor for prostate cancer and advanced disease. Yet, genetic studies have largely been conducted outside the context of Sub-Saharan Africa, identifying 278 common risk variants contributing to a multiethnic polygenic risk score, with rare variants focused on a panel of roughly 20 pathogenic genes. Based on this knowledge, we are unable to determine polygenic risk or differentiate prostate cancer status interrogating whole genome data for 113 Black South African men. To further assess for potentially functional common and rare variant associations, here we interrogate 247,780 exomic variants for 798 Black South African men using a case versus control or aggressive versus non-aggressive study design. Notable genes of interest include HCP5, RFX6 and H3C1 for risk, and MKI67 and KLF5 for aggressive disease. Our study highlights the need for further inclusion across the African diaspora to establish African-relevant risk models aimed at reducing prostate cancer health disparities.

Stem Cell Therapy for Aging Related Diseases and Joint Diseases in Companion Animals.

Stem cell therapy is an attractive treatment for diseases in companion animals that cannot be treated by conventional veterinary medicine practices. The unique properties of stem cells, particularly the ability to differentiate into specific cell types, makes them a focal point in regenerative medicine treatments. Stem cell transplantation, especially using mesenchymal stem cells, has been proposed as a means to treat a wide range of injuries and ailments, resulting in tissue regeneration or repair. This review aims to summarize the veterinary use of stem cells for treating age-related and joint diseases, which are common conditions in pets. While additional research is necessary and certain limitations exist, the potential of stem cell therapy for companion animals is immense.

Learning to estimate heart rate from accelerometer and user's demographics during physical exercises.

Getting prompt insights about health and well-being in a non-invasive way is one of the most popular features available on wearable devices. Among all vital signs available, heart rate (HR) monitoring is one of the most important since other measurements are based on it. Real-time HR estimation in wearables mostly relies on photoplethysmography (PPG), which is a fair technique to handle such a task. However, PPG is vulnerable to motion artifacts (MA). As a consequence, the HR estimated from PPG signals is strongly affected during physical exercises. Different approaches have been proposed to deal with this problem, however, they struggle to handle exercises with strong movements, such as a running session. In this paper, we present a new method for HR estimation in wearables that uses an accelerometer signal and user demographics to support the HR prediction when the PPG signal is affected by motion artifacts. This algorithm requires a tiny memory allocation and allows on-device personalization since the model parameters are finetuned in real time during workout executions. Also, the model may predict HR for a few minutes without using a PPG, which represents a useful contribution to an HR estimation pipeline. We evaluate our model on five different exercise datasets - performed on treadmills and in outdoor environments - and the results show that our method can improve the coverage of a PPG-based HR estimator while keeping a similar error performance, which is particularly useful to improve user experience.

Clinical guideline highlights for the hospitalist: 2022 American Heart Association/American Stroke Association Guideline for the management of patients with spontaneous intracerebral hemorrhage.

GUIDELINE TITLE: 2022 Guideline for the Management of Patients with Spontaneous Intracerebral Hemorrhage: A Guideline From the American Heart Association/American Stroke Association RELEASE DATE: May 2022 PRIOR VERSION: Guidelines for the Management of Spontaneous Intracerebral Hemorrhage: A Guideline for Healthcare Professionals from the American Heart Association/American Stroke Association 2015 DEVELOPER: American Heart Association and American Stroke Association FUNDING SOURCE: None TARGET POPULATION: Adult Patients with Spontaneous Intracerebral Hemorrhage.

Monitoring of Autoantibodies Following Autologous Hematopoietic Stem Cell Transplantation in 6 Children with Recently Diagnosed Type 1 Diabetes Mellitus.

BACKGROUND Bone marrow stem cells have been shown to be a promising therapeutic strategy for autoimmune diseases. This study aimed to assess the safety and efficacy of autologous hematopoietic stem cell (ABMSC) transplantation without immunoablation used to suppress the autoimmune reaction in 6 children with newly diagnosed autoimmune diabetes mellitus. We monitored the levels of islet cell antibodies (ICA), antibodies against islet antigen-related tyrosine phosphatase 2 (IA2), glutamic acid-decarboxylase (GAD) antibodies, and anti-insulin antibodies (AIA). MATERIAL AND METHODS Between 2018 and 2022, 6 children (age 6-10 years, average 8 years) recently diagnosed with type 1 diabetes mellitus with the presence of ICA, IA2, GAD, AIA and ketoacidosis, were treated with an ABMSC stimulated with Filgrastim, granulocyte colony-stimulating factor (G-CSF), 10 ug/kg/day for 4 days. Bone marrow was harvested on day 5, collected by puncture and identified as mononuclear cells >180×106/kg, CD34+ >0.22%, and transplanted by intravenous (i.v.) infusion. Patients were monitored with ICA, IA2, GAD, AIA, C-peptide, blood glucose, and glycosylated hemoglobin A1c (HbA1C) 6 months after the procedure. RESULTS At 6-month follow-up, we observed a negative value of the ICA, which was previously positive (P<0.001). The IA2 (p=0.037) and GAD (P=0.377) antibodies decreased slowly but were significantly lower. AIA remained high. A decrease in blood glucose and HbA1C levels was observed (P<0.001). No complications occurred during follow-up. CONCLUSIONS Autologous hematopoietic stem cell transplantation without immunoablation was safe and effective in significantly decreasing the production and effect of autoantibodies against ICA, GAD, and IA2, as well as decreasing blood sugar levels and HbA1c.

The immunogenetics of tuberculosis (TB) susceptibility.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of death due to a single bacterial agent, with approximately 10.6 million people developing active disease and 1.6 million deaths reported globally in 2021. After exposure, some, but not all individuals, will become infected with the bacillus. However, only a small fraction (approximately 5 to 15%) of these individuals will progress to clinical disease, while in the remainder, infection is seemingly contained, and no signs of clinical disease are shown. Numerous observations have advocated for the role of host genetics in the display of these inter-individual variabilities in infection and disease phenotypes. In this review, we will provide an overview of the approaches, findings and limitations of the very first studies investigating TB genetic susceptibility to more recent studies. Lastly, we highlight several approaches, namely, linkage analyses and association studies, proposed to discover genetic markers associated with TB susceptibility. This review also explored the concept of polygenic risk scores (PRS) for prediction of tuberculosis susceptibility. The identification of host genetic factors influencing TB susceptibility/resistance is paramount to not only better understand the physiopathology of the disease but also explore more effective approaches for the development of both optimal preventive measures (i.e. better vaccines) and treatments of TB disease.

A Knock-In Mouse Model of Thymoma With the GTF2I L424H Mutation.

INTRODUCTION: The pathogenesis of thymic epithelial tumors remains largely unknown. We previously identified GTF2I L424H as the most frequently recurrent mutation in thymic epithelial tumors. Nevertheless, the precise role of this mutation in tumorigenesis of thymic epithelial cells is unclear. METHODS: To investigate the role of GTF2I L424H mutation in thymic epithelial cells in vivo, we generated and characterized a mouse model in which the Gtf2i L424H mutation was conditionally knocked-in in the Foxn1+ thymic epithelial cells. Digital spatial profiling was performed on thymomas and normal thymic tissues with GeoMx-mouse whole transcriptome atlas. Immunohistochemistry staining was performed using both mouse tissues and human thymic epithelial tumors. RESULTS: We observed that the Gtf2i mutation impairs development of the thymic medulla and maturation of medullary thymic epithelial cells in young mice and causes tumor formation in the thymus of aged mice. Cell cycle-related pathways, such as E2F targets and MYC targets, are enriched in the tumor epithelial cells. Results of gene set variation assay analysis revealed that gene signatures of cortical thymic epithelial cells and thymic epithelial progenitor cells are also enriched in the thymomas of the knock-in mice, which mirrors the human counterparts in The Cancer Genome Atlas database. Immunohistochemistry results revealed similar expression pattern of epithelial cell markers between mouse and human thymomas. CONCLUSIONS: We have developed and characterized a novel thymoma mouse model. This study improves knowledge of the molecular drivers in thymic epithelial cells and provides a tool for further study of the biology of thymic epithelial tumors and for development of novel therapies.

The Role of Race in Relations of Social Support to Hippocampal Volumes Among Older Adults.

Evidence suggests social support may buffer brain pathology. However, neither its association with hippocampal volume, a marker of Alzheimer's disease risk, nor the role of race in this association has been fully investigated. Multiple regression analyses examined relations of total social support to magnetic resonance imaging-assessed gray matter (GM) hippocampal volumes in the total sample (n = 165; mean age = 68.48 year), and in race-stratified models of African American and White older adults, adjusting for select covariates. Results showed greater social support was associated with greater GM hippocampal volumes among African American older adults only (p < .01). Our findings suggest greater total social support may play a role in supporting the hippocampus, particularly among African American older adults, who had lower hippocampal volumes than their White counterparts. Further research is needed to test these questions longitudinally and examine which aspects of social support may promote hippocampal integrity, specifically.

Genotyping and Antimicrobial Susceptibility Profiling of Streptococcus uberis Isolated from a Clinical Bovine Mastitis Outbreak in a Dairy Farm.

Streptococcus uberis, an environmental pathogen responsible also for contagious transmission, has been increasingly implicated in clinical mastitis (CM) cases in Europe. We described a 4-month epidemiological investigation of Strep. uberis CM cases in an Italian dairy farm. We determined molecular characteristics and phenotypic antimicrobial resistance of 71 Strep. uberis isolates from dairy cows with CM. Genotypic variability was investigated via multiplex PCR of housekeeping and virulence genes, and by RAPD-PCR typing. Antimicrobial susceptibility was assessed for 14 antimicrobials by MIC assay. All the isolates carried the 11 genes investigated. At 90% similarity, two distinct clusters, grouping 69 of the 71 isolates, were detected in the dendrogram derived from the primer ERIC1. The predominant cluster I could be separated into two subclusters, containing 38 and 14 isolates, respectively. Strep. uberis strains belonging to the same RAPD pattern differed in their resistance profiles. Most (97.2%) of them were resistant to at least one of the drugs tested, but only 25.4% showed a multidrug resistance phenotype. The highest resistance rate was observed for lincomycin (93%), followed by tetracycline (85.9%). This study confirmed a low prevalence of ß-lactam resistance in Strep. uberis, with only one isolate showing resistance to six antimicrobial classes, including cephalosporins.

Clinical Guideline Highlights for the Hospitalist: Anaphylaxis Management in Adults and Children.

GUIDELINE TITLE: Anaphylaxis-A 2020 practice parameter update, systematic review, and Grading of Recommendations, Assessment, Development and Evaluation (GRADE) analysis RELEASE DATE: April 2020 PRIOR VERSION: Anaphylaxis - a 2019 practice parameter and GRADE analysis DEVELOPER: American Academy of Allergy, Asthma & Immunology (AAAAI) and the American College of Allergy, Asthma, and Immunology (ACAAI) FUNDING SOURCE: None TARGET POPULATION: Adult and pediatric patients with anaphylaxis.

Culture Negative Endocarditis Masquerading as Recurrent Supraventricular Tachycardia.

Supraventricular tachycardia are common dysrhythmias seen in hospitalized patients. Electrolyte derangements and cardiomyopathy are among the most common causes. Rarely, blood culture negative endocarditis can lead to unexplained recurrentsupraventricular tachycardia. Herein, we present a case of recurrent atrioventricular nodal reentrant tachycardia in a patient with no previous history of cardiovascular disease.