The impact of treatment adjustment in breast cancer by Cerner Real-World Data during pandemic

The global burden of the ongoing COVID-19 pandemic has predominantly been measured using metrics like case numbers, hospitalizations and deaths. However, the short-term health impacts are more difficult to capture, especially for breast cancer(BC) patients. An expert opinion formulated by multiple national organizations provided preliminary guidance on the prioritization and treatment of breast cancer(BC) during this covid outbreak. Most breast surgery and adjuvant treatment for malignant conditions have been postponed or adjusted. As we know, BC treatment is time-dependent. How standard treatment modifications and surgery postponement would affect BC patients are unknown. Currently, there is no research that has applied…

The Soybean Allele Catalog Tool: A Web-Based Interactive Tool for Gene Alleles Discovery

The advancement of sequencing technologies has made a plethora of whole genome sequenced (WGS) data publicly available. However, utilizing the raw WGS data will not generate promising research outcomes for agriculture. To solve this problem, the Soybean Allele Catalog Tool (https://soykb.org/SoybeanAlleleCatalogTool/search.php) has been developed to assist researchers in gaining insights into soybean genotypes associated with phenotypes and selecting accessions based on comprehensive soybean SNPs and InDels data organized into alleles of genes. A variant calling pipeline (SnakyVC, https://github.com/yenon118/snakyVC) and an Allele Catalog pipeline (AlleleCatalog, https://github.com/yenon118/AlleleCatalog) were developed to prepare the datasets for the tool. The variant calling pipeline processes…

Understanding Common Key Indicators of Successful and Unsuccessful Cancer Drug Trials Using Contrast Mining

Clinical trials are essential in the process of new drug development. As clinical trials involve significant investments of time and money, it is crucial for trial designers to carefully investigate trial settings prior to designing the trial. Utilizing trial documents from ClinicalTrials.gov, we aim at understanding common characteristics of successful and unsuccessful cancer drug trials to provide insights about what to learn and what to avoid. In this research, we first computationally classified cancer drug trials into successful and unsuccessful cases and then utilized natural language processing to extract information of eligibility criteria from the trial documents. Contrast mining was…

Do viruses experience culture shock?

Viruses have the potential to cause enormous health, social, and economic burdens. These burdens are demonstrated by influenza viruses, which cause seasonal epidemics, and SARS-CoV-2 viruses, which caused the ongoing COVID-19 pandemic resulting in over 4.55 million deaths. Virus research and vaccine strain selection often require viruses to be propagated in cell lines or embryonated chicken eggs. However, viruses may acquire culture-adapted mutations during this process, biasing our understanding of the viruses and consequently affecting disease prevention and control strategies. We determined whether culture-adaptations occur during influenza B virus (IBV) and SARS-CoV-2 virus propagation and their phenotypic implications. To do this,…

A COVID-19 Geospatial Population Health Risk Assessment for Missouri

Aim: Design and analyze a multifactor spatial database to assess COVID-19 risk across individual, community, social, infrastructure and culture contexts at the county level to provide quantitative insight and statistical support for potential mitigation areas. Methods: COVID-19 studies require vast amounts of integrated data to create understanding. MU’s Geospatial Analytical Research Knowledgebase (GeoARK) is a spatially integrated database to support spatial and contextual analytics. Utilizing GeoARK we created six distinct risk databases covering individual susceptibility; transmission; socioeconomic; accessibility; health culture; and exposure. Ordinary least squares regression was used to evaluate combinations of explanatory variables. Selected variables within each risk category…

SEE-Diabetes, a Patient-Centered Diabetes Self-Management Education and Support for Older Adults: Findings and Information Needs from Patients’ Perspectives

Objectives: This study seeks to understand the information needs of people with diabetes aged 65 and older gathered through survey and focus groups to inform development of an educational decision aid, SEE-Diabetes (Support-Engage-Empower-Diabetes). The SEE-Diabetes aid provides patient-centered self-management education and support for older people with diabetes. Methods: We surveyed 82 University of Missouri Health Care patients with diabetes Thirty seven surveys were completed. The survey collected demographics, diabetes duration, insulin usage, and the accessibility of clinic notes through a patient portal. For focus groups, nine participants aged 65 and over accepted an invitation to participate. We asked participants to evaluate three randomly selected deidentified representative clinic…

P3DB-4.0: a large-scale plant protein phosphorylation database from diverse species to phosphosite conservation

Since the last version (version 3) of the P3DB was published in 2014, we are very encouraged to see that more and more plant scientists have been using our database including reanalysis of our data collections. In this new version (version 4.0), we extensively re-innovated our database to a brand-new platform (https://www.p3db.org) for accommodating much more data sets and new bioinformatic modules, many of which are suggested by our users and collaborators. In detail, we would like to highlight our novel development from the following aspects: (1) The new P3DB altogether harvests ~220,000 phosphosites in ~57,000 phosphoproteins curated across…

Predictive Models for Early Detection of Glaucoma using Electronic Health Records

Glaucoma is the second leading cause of irreversible blindness across the world. Around 70 million people have glaucoma, and 4.4 million people are blind due to undiagnosed glaucoma by optic nerve damage worldwide. Studies suggest that early detection of glaucoma is critically essential for the prevention of irreversible blindness. Effective use of electronic health records (EHR) provides data-driven, evidence-based risk factors for glaucoma progression that would also enable applying a practical machine learning (ML) model to predict glaucoma before the onset of clinical symptoms. Predictive models for the early detection of glaucoma are critical steps for subsequent actionable/preventable interventions. We…

Regulation of gene expression by DNA methylation with cytotoxic T lymphocytes evaluation in consensus molecular subtypes of colorectal cancer

Background: Low cytotoxic T lymphocyte (CTLs) infiltration in colorectal cancer (CRC) tumors is a challenge to treatment with immune checkpoint inhibitors. Consensus molecular subtypes (CMS) classify patients based on tumor attributes, and CMS1 patients include the majority of patients with high CTL infiltration and “inflamed” tumors. Epigenetic modification plays a critical role in gene expression and therapy resistance. Therefore, in this study we compared DNA methylation, gene expression, and CTL infiltration of CMS1 patients to other CMS groups to determine targets for improving immunotherapy in CRC. Furthermore, we used transcriptome of 91,103 unsorted scRNAseq to validate bulk RNA finding. Results…