Comparing commercial pharmacogenetic testing results and recommendations for antidepressants with established CPIC guidelines.

Introduction: Increasingly, pharmacogenetic testing helps providers with medication selection based upon patient-specific DNA results. While several government-funded organizations work towards consensus and standardization for testing and interpretation, compliance to these best practices remains inconsistent. Pharmacogenetic testing companies often develop proprietary practices for interpreting and reporting, which can lead to incongruency of reported results among companies and potential discrepancies in interpretation.

Exploring prognostic implications of miRNA signatures and telomere maintenance genes in kidney cancer.

Kidney cancer, particularly clear cell renal cell carcinoma (KIRC), presents significant challenges in disease-specific survival. This study investigates the prognostic potential of microRNAs (miRNAs) in kidney cancers, including KIRC and kidney papillary cell carcinoma (KIRP), focusing on their interplay with telomere maintenance genes. Utilizing data from The Cancer Genome Atlas, miRNA expression profiles of 166 KIRC and 168 KIRP patients were analyzed.

Facilitating integrative and personalized oncology omics analysis with UCSCXenaShiny.

The continuous generation of multi-omics and phenotype data is propelling advancements in precision oncology. UCSCXenaShiny was developed as an interactive tool for exploring thousands of cancer datasets available on UCSC Xena. However, its capacity for comprehensive and personalized pan-cancer data analysis is being challenged by the growing demands.

Phenome-wide association study identifies new clinical phenotypes associated with Staphylococcus aureus infections.

Background: Phenome-Wide Association study (PheWAS) is a powerful tool designed to systematically screen clinical observations derived from medical records (phenotypes) for association with a variable of interest. Despite their usefulness, no systematic screening of phenotypes associated with Staphylococcus aureus infections (SAIs) has been done leaving potential novel risk factors or complications undiscovered.

Method And Cohorts: We tailored the PheWAS approach into a two-stage screening procedure to identify novel phenotypes correlating with SAIs.

The PocketPerio application significantly increases the accuracy of diagnosing periodontal conditions in didactic and chairside settings.

The study aimed to determine the accuracy of diagnosing periodontal conditions using the developed web-based PocketPerio application and evaluate the user's perspective on the use of PocketPerio. First, 22 third-year dental students (DS3) diagnosed ten cases without PocketPerio (control) and with PocketPerio (test) during a mock examination. Then, 105 DS3, 13 fourth-year dental students (DS4), and 32 senior second-year International Standing Program students (ISP2) used PocketPerio chairside.

Automated osteoporosis classification and -score prediction using hip radiographs deep learning algorithm.

Background: Despite being the gold standard for diagnosing osteoporosis, dual-energy X-ray absorptiometry (DXA) is an underutilized screening tool for osteoporosis.

Objectives: This study proposed and validated a controllable feature layer of a convolutional neural network (CNN) model with a preprocessing image algorithm to classify osteoporosis and predict -score on the proximal hip region simple hip radiographs.

Design: This was a single-center, retrospective study.

A retrospective analysis of the role of age and sex in outcomes of non-surgical periodontal therapy at a single academic dental center.

The present study examined the role of age and sex in the outcomes of non-surgical periodontal therapy (NSPT). De-identified demographic and periodontal characteristics of patients who presented for baseline periodontal evaluation, NSPT, and periodontal re-evaluation were abstracted from electronic health records. Independent associations of age and sex with severe periodontitis defined as ≥ 5 mm clinical attachment loss (CAL) and ≥ 6 mm probing depth (PD) were determined using multinomial logistic regression.

Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits.

Methylation quantitative trait loci (mQTLs) are essential for understanding the role of DNA methylation changes in genetic predisposition, yet they have not been fully characterized in East Asians (EAs). Here we identified mQTLs in whole blood from 3,523 Chinese individuals and replicated them in additional 1,858 Chinese individuals from two cohorts. Over 9% of mQTLs displayed specificity to EAs, facilitating the fine-mapping of EA-specific genetic associations, as shown for variants associated with height.

Dry and liquid formulations of IBT-V02, a novel multi-component toxoid vaccine, are effective against isolates from low-to-middle income countries.

is the leading cause of skin and soft tissue infections (SSTIs) in the U.S. as well as more serious invasive diseases, including bacteremia, sepsis, endocarditis, surgical site infections, osteomyelitis, and pneumonia.

Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes.

Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period.

Quantitative Foveal Structural Metrics as Predictors of Visual Acuity in Human Albinism.

Purpose: To assess the degree to which quantitative foveal structural measurements account for variation in best-corrected visual acuity (BCVA) in human albinism.

Methods: BCVA was measured and spectral domain optical coherence tomography (SD-OCT) images were acquired for 74 individuals with albinism. Categorical foveal hypoplasia grades were assessed using the Leicester Grading System for Foveal Hypoplasia.

Assessment of the current status of real-world pharmacogenomic testing: informed consent, patient education, and related practices.

The practice of informed consent (IC) for pharmacogenomic testing in clinical settings varies, and there is currently no consensus on which elements of IC to provide to patients. This study aims to assess current IC practices for pharmacogenomic testing. An online survey was developed and sent to health providers at institutions that offer clinical germline pharmacogenomic testing to assess current IC practices.

An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction.

Breast cancer (BC) is one of the most commonly diagnosed cancers worldwide. As key regulatory molecules in several biological processes, microRNAs (miRNAs) are potential biomarkers for cancer. Understanding the miRNA markers that can detect BC may improve survival rates and develop new targeted therapeutic strategies.

Gene signatures associated with prognosis and chemotherapy resistance in glioblastoma treated with temozolomide.

Glioblastoma (GBM) prognosis remains extremely poor despite standard treatment that includes temozolomide (TMZ) chemotherapy. To discover new GBM drug targets and biomarkers, genes signatures associated with survival and TMZ resistance in GBM patients treated with TMZ were identified. GBM cases in The Cancer Genome Atlas who received TMZ ( = 221) were stratified into subgroups that differed by median overall survival (mOS) using network-based stratification to cluster patients whose somatic mutations affected genes in similar modules of a gene interaction network.

TCCIA: a comprehensive resource for exploring CircRNA in cancer immunotherapy.

Background: Immunotherapies targeting immune checkpoints have gained increasing attention in cancer treatment, emphasizing the need for predictive biomarkers. Circular RNAs (circRNAs) have emerged as critical regulators of tumor immunity, particularly in the PD-1/PD-L1 pathway, and have shown potential in predicting immunotherapy efficacy. Yet, the detailed roles of circRNAs in cancer immunotherapy are not fully understood.

Genetic risk score in multiple sclerosis is associated with unique gut microbiome.

Multiple sclerosis (MS) is a complex autoimmune disease in which both the roles of genetic susceptibility and environmental/microbial factors have been investigated. More than 200 genetic susceptibility variants have been identified along with the dysbiosis of gut microbiota, both independently have been shown to be associated with MS. We hypothesize that MS patients harboring genetic susceptibility variants along with gut microbiome dysbiosis are at a greater risk of exhibiting the disease.

Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.

Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases.

Prognostic microRNA signature for estimating survival in patients with hepatocellular carcinoma.

Objective: Hepatocellular carcinoma (HCC) is one of the leading cancer types with increasing annual incidence and high mortality in the USA. MicroRNAs (miRNAs) have emerged as valuable prognostic indicators in cancer patients. To identify a miRNA signature predictive of survival in patients with HCC, we developed a machine learning-based HCC survival estimation method, HCCse, using the miRNA expression profiles of 122 patients with HCC.

Validation of Gait Measurements on Short-Distance Walkways Using Azure Kinect DK in Patients Receiving Chronic Hemodialysis.

Muscle dysfunction, skeletal muscle fibrosis, and disability are associated with weakness in patients with end-stage renal disease. The main purpose of this study was to validate the effectiveness of a proposed system for gait monitoring on short-distance 1.5 m walkways in a dialysis center.

Association between hyperlipidemia and trigger finger: A nationwide population-based cohort study.

The cause of trigger fingers remains uncertain. High lipid levels in the blood may reduce blood supply to the distal fingers and promote inflammation. We aimed to explore the association between hyperlipidemia and trigger finger.

Survival associated miRNA signature in patients with head and neck carcinomas.

Head and neck carcinoma (HNSC) is often diagnosed at advanced stage, incurring poor patient outcome. Despite of advances in chemoradiation and surgery approaches, limited improvements in survival rates of HNSC have been observed over the last decade. Accumulating evidences have demonstrated the importance of microRNAs (miRNAs) in carcinogenesis.

Genetic and clinical determinants of telomere length.

Many epidemiologic studies have identified important relationships between leukocyte telomere length (LTL) with genetics and health. Most of these studies have been significantly limited in scope by focusing predominantly on individual diseases or restricted to GWAS analysis. Using two large patient populations derived from Vanderbilt University and Marshfield Clinic biobanks linked to genomic and phenomic data from medical records, we investigated the inter-relationship between LTL, genomics, and human health.

Multi-ancestry genome- and phenome-wide association studies of diverticular disease in electronic health records with natural language processing enriched phenotyping algorithm.

Objective: Diverticular disease (DD) is one of the most prevalent conditions encountered by gastroenterologists, affecting ~50% of Americans before the age of 60. Our aim was to identify genetic risk variants and clinical phenotypes associated with DD, leveraging multiple electronic health record (EHR) data sources of 91,166 multi-ancestry participants with a Natural Language Processing (NLP) technique.

Materials And Methods: We developed a NLP-enriched phenotyping algorithm that incorporated colonoscopy or abdominal imaging reports to identify patients with diverticulosis and diverticulitis from multicenter EHRs.

Dairy Farm Work and Protection from Gastrointestinal Illness.

Gastrointestinal (GI) disorders are a major public health burden in the United States. Due to close contact with animals, farmers may be a high risk subgroup for acute GI infections, though some studies suggest farm work is actually protective against GI illness. The purpose of this study was to examine associations between dairy farm work and GI symptoms over 3 years.