Sep. 19, 2016

Diabetes Self-Management Applications: Focus Group Findings from Elderly Diabetic Patients

The number of mobile diabetes self-management (DSM) apps has risen. However, it is not certain whether these apps provide effective DSM for elderly diabetic patients. The purpose of this study was to identify barriers in functionality and usability related to needs of elderly diabetic patients for DSM apps. We conducted two focus groups with 10 older diabetic patients. Participants completed a set of DSM tasks using nine representative DSM apps on iPads. They answered a questionnaire which included basic information, System Usability Scale (SUS), app specific questions, and open-ended questions. We found DSM apps did not adhere to diabetes guidelines.

April 11, 2016

Botanical treatments to inhibit endometriosis: A next generation RNA-seq data analysis

Endometriosis is a benign but complex gynecologic disorder associated with pelvic pain and infertility and is characterized by the implantation of endometrial tissue outside of the uterus. To date, the reason remains unknown, though the immune dysfunction has been implicated. Hormonal interventions are widely used as effective treatment but with undesirable side effects. Botanical treatments can be alternative options with fewer side effects. In this study, we employed RNA-seq technology to assess the effects of two different botanical treatments, quercetin, and elderberry juice over vehicle (control), to inhibit the growth of endometriotic lesions in a mouse model (C57BL/6) of endometriosis.

March 21, 2016

Mining for epigenetic patterns across species

Exponential growth of next-generation sequencing technologies has made the epigenomics analysis a big data science, which poses the challenges to its translation into knowledge. This has led to the emergence of a new field called “Comparative Epigenomics.” Comparative epigenomics has three major directions, namely comparison across species, across time-course of a biological process, and across individuals. In this study we focus on comparing the epi-modifications across species (particularly between Human and Mouse). We compared different epi-genomic factors and where/how they concur or differ among species. We have used histone modification data from various publicly available data sets in Human and…

March 14, 2016

Sequence mining of EMR log data to understand clinician workflow

Modeling clinical workflow is an important pre-cursor to understanding how clinicians interact with an EMR and its features. Common methods of assessing clinical workflow include video recording or direct observations, or through directed user experience testing in a controlled environment. Assessing clinical workflow within an EMR can also be accomplished by analyzing EMR log data, which can provide an unbiased view of EMR use. Using log data to build workflow patterns requires appropriate pre-processing of the log data, and the use of several types of data mining techniques: frequent pattern mining, sequence mining, and sub-graph mining. This talk will…

March 7, 2016

Transformation of the advance care planning process through the use of an online computer-assisted instruction program and electronic health record enhancements at the University of Missouri

The Institute of Medicine report (1997) defines a good death as “good care at the end of life…depend[ant] on strong interpersonal skills, clinical knowledge, and technical proficiency, and it is informed by scientific evidence, values, and personal and professional experience” [1]. With only one-third of Americans having an advance directive [2], the failure to identify, choose, and define personal health preferences in end-of-life care has largely prevented the United States healthcare system from providing “good deaths” to many. The central hypothesis of this study is that through the development and deployment of a novel and meaningful tool, users will…

Feb. 29, 2016

Visualization of Female Breast Cancer Burden in Missouri

Background: In 2011, the female breast cancer incidence rate was about 120 per 100,000 population and the mortality rate was 24 per 100,000 population in Missouri. There is a critical need to build fact sheets in the form of interactive and dynamic map reports of accurate breast cancer burden among Missouri resident women at the sub-state and state level. Cancer incidence and mortality rates were traditionally displayed in data tables. Data tables meet the needs of some users. Aim: Use data visualization software to produce easily understood interactive reports with maps that display breast cancer incidence, survival and mortality…

Feb. 22, 2016

Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation

It has long been a challenge to determine the genetic origin of new characters in the evolution. The molecular mechanisms behind many morphological innovations are still unknown, including such striking evolutionary transitions as the appearance of the placenta. Our approach is based on using orthology to link genotype to phenotype. Orthology describes a relation between homologous genes (or chromosomal segments) that last diverged by a speciation event. Orthologous genes are often used to study evolutionary history because they tend to be conservative in molecular and biological functions. Using our orthology assignment pipeline, we have inferred orthologs in 38, primarily mammalian,…

Feb. 8, 2016

A Computational Pipeline for Comparative Study of Guide RNAs for CRISPR-CAS Genome Editing Systems

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR Associated Proteins ) systems were recently developed into genome editing tools. Given their strength in multiplex targeting and  easy programmability, CRISPR-CAS systems are already widely applied in academia and industry. While existing detection approaches could capture CRISPR arrays based on prior knowledge of sequence features, such predicted CRISPR arrays may lack essential structural features to enable RNA-processing for further immunity mechanism.  Moreover,  for efficient design of single guided RNA, unmet needs may remain to comprehensively discover structural features of CAS-nuclease/guide RNA complexes Here, we discuss a two-step seed-and-extend approach using a distributed computing environment, to detect CRISPR…

Feb. 8, 2016

A Deep Neural Network Method for Predicting Mitochondria-Localized Proteins in Plants

Targeting and translocation of proteins to the appropriate subcellular compartments is crucial for cell organization and function. Newly synthesized proteins are transported to mitochondria with the assistance of targeting sequences, which are complex, containing either an N-terminal presequence or a multitude of internal signals to target this organelle. Compared with experimental approaches, computational predictions provide an efficient and cost-effective way to infer subcellular localization for any given protein. However, it is still challenging to predict plant mitochondrial localized proteins accurately due to various limitations, and the performance of current tools is unsatisfactory. We present a novel computational approach for large-scale…