Oct. 17, 2018

Challenges for the analysis of healthcare reports using natural language processing

Healthcare professionals generate, transmit, and store healthcare records as free-text documents these are the traditional“physician’s reports” or “physician’s notes”. These reports contain complex biomedical data, demographic information, location data, etc. However, free text data are a poor starting point for complex data management, aggregation and processing tasks with computational models. For data-based applications, information from healthcare reports, biomedical tests, radiology impressions and the like should be available in discrete and machine-processable form. Natural language processing (NLP), a subfield of artificial intelligence, includes techniques for manipulating and interpreting free text data for analyses with computers. Here, we briefly discuss free-textpreprocessing, an…

Oct. 16, 2018

Applying Blockchain Technology for Health Information Exchange and Persistent Monitoring for Clinical Trials

“Blockchain” is a distributed ledger technology originally applied in the financial sector. This technology ensures the integrity of transactions without third-party validation. Its functions of decentralized transaction validation, data provenance, data sharing, and data integration are a good fit for the needs of health information exchange and clinical trials. We investigated the current workflow of Health Information Exchange and clinical trials; conducted design thinking processes with clinicians, trial managers, informaticians, and blockchain professionals; and implemented a blockchain model to tackle known issues. We used coded Smart Contract regulations to simulate several scenarios in healthcare processes. This proof-of-concept work provides a…

Oct. 4, 2018

The promise of precision medicine: A focus on genomics and bioinformatics

Chromosomal rearrangements leading to the generation of gene fusions are more common in pediatric malignancies compared to adults and possess diagnostic and prognostic value. Identification of novel gene fusions provides a means for patient stratification and the foundation for the development of targeted therapeutics. The innovations discussed will include: the development of custom Next Generation Sequencing (NGS) gene panels for pediatric leukemias, and a newborn screening assay that detects germline events in high-risk populations.

Oct. 2, 2018

Development and Application of a high throughput multiomics pipeline to uncover molecular signatures in drought stressed Maize Nodal Roots

One of the major focus areas in agricultural research is reducing the major limiting factor of drought for agricultural production worldwide. In the maize plant, water uptake is mainly acquired by the nodal root system after the seedling stage. These roots grow from multiple stem nodes, initially from below-ground and later from above-ground nodes. In drought conditions, nodal roots have shown to grow through dry topsoil to access water found at significant depth and transport water to other parts. This means these roots are able to grow under low water potential levels which normally inhibit leaf and stem growth. However,…

Sep. 28, 2018

Promoting Healthy Coping in seniors 72 years or older with Type 2 Diabetes: A feasibility study of a mobile diabetes self-management and support application on functionality, readability, and usability

One out of four Americans older than 65 years old has diabetes.Type 2 diabetes accounts for about 90% to 95% of all diagnosed cases of diabetes. Mobile health technology provides possible solutions for seniors with type 2 diabetes to manage their daily lives. However, our preliminary research shows that only 10% of diabetes apps provided features related to Healthy Coping, which is one principle from the American Association of Diabetes Educators Self-Care Behaviors™, enables people with diabetes to find healthy ways to cope with stress. To alleviate this problem, we have designed a prototype of Healthy Coping mobile…

Sep. 18, 2018

Using Deep learning method (CNN/RNN) for prediction of ubiquitination protein

Ubiquitination, as a post-translational modification, is a crucial biological process presented in cell signaling, death and localization. Identification of ubiquitination protein is of fundamental importance for understanding molecular mechanisms in biological systems and diseases. Although high-throughput experimental studies using mass spectrometry have identified many ubiquitination proteins and ubiquitination sites, the vast majority of ubiquitination proteins remain undiscovered, even in well studied model organisms. To reduce experimental costs, computational (in silico) methods have been introduced to predict ubiquitination sites. If we can predict whether a query protein can be ubiquitinated or not, it is meaningful by itself and helpful for predicting…

Sep. 18, 2018

Discovering novel risk factors for age-related eye diseases using subgroup data mining

In the United States, the Medicare cost for the treatment of cataract is continually increasing due to an increased number of cataract surgery done in each year, for example, more than 3 million cataract surgeries were performed in 2017. A study by the World Health Organization reported that a delay of 10 years of the onset of cataracts would cut the number of people who need cataract surgery in half. Henceforth we ventured to investigate potential risk factors for the development of cataract to tackle this growing problem. On the other hand, comorbidities of multiple risk factors and its cumulative…

Sep. 10, 2018

eCaregiving 2.0: Feasibility, Data Quality and Cost of Collecting Continuous Self-reported and Passive Data Using a Personal Health Management System

This project aims to demonstrate if self-reported and passive data can be continuously collected from a cohort of 55 study participants using Personal Health Management Information System (PHMS).  We estimated measures of data quality, feasibility and cost of data collection after asking participants to wear Fitbit and download the app to manage data transmission from passive (daily) and active data collection through a monthly survey. In this six-month cohort study, we expected to capture 100% of survey-based self-reported data and 100% of passive data parameters totaling 9,848 days of measurement. With minimal instruction to participants, we captured 66% number of days of…

Sep. 6, 2018

Immunogenomic Pathway and Survival Analysis in Colorectal Cancer Patients Based on Tumor Location and Microsatellite Status

Despite the advancement of available therapies (surgery, chemotherapy and immunotherapy, etc.), colorectal cancer (CRC) as the third most common cancer still remains the second leading cause of cancer-related death worldwide. Typically, CRC patients could be categorized into microsatellite stable (MSS, approximately80-85% in CRC) or microsatellite instability (MSI, approximately 10-15% in CRC) type. An extensive literature has shown that CRC patients with MSI status have more T cells in the primary tumor than those with MSS status. This is believed to contribute to the 78% of the MSI patients who had cancer progression-free survival after receiving immunotherapy (Pembrolizumab, an anti-PD-1 immunotherapy)…