March 17, 2021
Virtual Campus Visit with NSF CISE AD Dr. Margaret Martonosi
The National Science Foundation (NSF) supports a majority of US academic research in the Computer and Information Science and Engineering (CISE) topic areas. Since February, 2020, Dr. Margaret Martonosi serves as NSF CISE AD, stewarding the CISE directorate’s $1B annual budget on behalf of research, education, workforce and infrastructure funding in CISE topic areas and for science as a whole. Martonosi is conducting a series of “virtual campus visits” to engage in conversation about a vision for CISE research going forward, and to field Q&A from the CISE community. Please join us for this highly-interactive session and please bring your input and questions! BioMargaret Martonosi is the US…
March 11, 2021
Dissertation Defense – Utilizing Blockchain Technology for Clinical Trial Optimization
Clinical trials are the cornerstone of treatment discovery because they provide comprehensive scientific evidence on the safety, efficacy, and optimal use of therapeutics. However, current clinical trials are facing multiple challenges such as patient recruitment, data capture, and overall management. There are various causes of patient recruitment challenges such as inefficient advertising models, complex protocols, and distant trial sites. Data inconsistency is the main challenge of the data capture process. Source data verification, a standard method used for data monitoring, is resource-intensive that can cost up to 25% of the total budget. The current clinical trial management system market is…
March 11, 2021
Comprehensive Exam Announcement – A Case-Control based Genomic Analysis of Chronic Obstructive Pulmonary Disease
Chronic Obstructive Pulmonary Disease (COPD) is a respiratory illness that affects millions of people all over the world. It is a major cause of chronic morbidity and mortality and a serious global public health problem. COPD is the fourth leading cause of death worldwide. Although the environmental causes of COPD which predominantly include cigarette smoking are well-documented, to this date the genetic underpinnings of COPD remain largely unknown. Furthermore, in the current landscape of a respiratory pandemic, COPD patients are at a much higher risk for developing other respiratory illnesses and co-morbidities. In this study we use genomic data from…
March 11, 2021
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…
March 11, 2021
Leveraging Unsupervised Machine Learning To Find Trends In The Textual Warnings Generated Using Multi-Modality Time Series Sensor Data
With technology and the internet of things (IoT), smart health care is no longer a dream. The devices that wouldn’t usually be generally expected to have an internet connection can communicate with the network independent of human action, and this is referred to as the internet of things. These devices, in our case, are the sensors placed in the elderly assisted living facility Tiger Place. Sensors include the ballistocardiogram (bed sensor) and motion sensors placed in the living room, bathroom, kitchen, etc. These sensors help in measuring nine major features, which defines the per-day activities of each elderly resident in the…
March 2, 2021
Information Extraction Framework for Facilitating the Assessment of the Quality of Radiology Interpretations
Assessing the quality of imaging interpretations requires that the results of radiological interpretations be compared with those of subsequent surgical-pathology results, when available. The manual process is inherently slow, tedious and expensive, and unless systematic errors occur in the interpretations, discrepancies are unlikely to be detected. Classical computational methods using Natural Language Processing entail using a corpus of annotated documents for model development and evaluation. However, developing such a corpus is also very expensive and time consuming, and the output is usually not portable between medical institutions. To alleviate these issues we are proposing a statistical learning method for textual…
March 2, 2021
Abnormal liver function and adverse health outcomes in COVID-19: A multicenter, retrospective analysis of 14,872 patients from the Cerner Real-World DataTM de-identified COVID-19 cohort
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been associated with liver impairment and abnormalities in liver function tests. However, associations between hepatic impairment and patient health outcomes have not been well-studied in large cohorts. In this US-based, multicenter retrospective cohort study, we analyze the impact of abnormalities in liver function tests at admission on mortality and adverse health outcomes in patients with laboratory-confirmed COVID-19 infection. Propensity score analysis and a full matching algorithm were used to minimize dissimilarity in covariates thought to impact outcomes of interest and to isolate the effect of liver abnormalities on patient…
Feb. 17, 2021
Purdue’s New Plant Sensor Technologies for Improved Phenotyping Quality
Plant phenotyping technologies have been developing rapidly over the last 2 decades. Plant sensors are becoming more precise, faster, easier to use and with lower cost. However, there are still several bottleneck issues in plant sensing, including the changing environmental conditions, the great variances on the plant, and the complicated GxTxEinteractions. These issues keep phenotyping difficult and limit further application of the sensor technologies. The Purdue plant sensor developers have been working innovatively to address these issues and develop the next generation plant sensing technologies. In this seminar, Dr. Jin will firstly introduce the 4 newly constructed phenotyping facilities at Purdue,…
Feb. 11, 2021
Thyroid Cancer Informatics
Survival prediction is important both to clinicians and patients; ensuring the best course of treatment is selected to manage the thyroid cancer. In 2018, there was an estimated half a million new thyroid cancer diagnoses and 41,071 deaths. Unlike other tumors whose mortality has decreased over the last two decades, thyroid cancer mortality rates have increased. Existing risk stratification systems fail to account for microcarcinomas, which accounted for 28.6 percent of thyroid cancer diagnoses and 32.5 percent of papillary thyroid cancer diagnoses. They are also based upon a varying combination of 10 variables and have not considered newly identified variables available in current research. Additionally,…