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1,068 full-text articles. Page 1 of 26.

An Analysis Of Mayo Clinic Search Query Logs For Cardiovascular Diseases, Ashutosh Sopan Jadhav, Amit P. Sheth, Jyotishman Pathak 2014 Wright State University

An Analysis Of Mayo Clinic Search Query Logs For Cardiovascular Diseases, Ashutosh Sopan Jadhav, Amit P. Sheth, Jyotishman Pathak

Kno.e.sis Publications

Increasingly, individuals are taking active participation in learning and managing their health by leveraging online resources. Understanding online health information searching behavior can help us to study what health topics users search for and how search queries are formulated. In this work, we analyzed 10 million cardiovascular diseases (CVD) related search queries from MayoClinic.com. We performed semantic analysis on the queries using UMLS MetaMap and analyzed structural and textual properties as well as linguistic characteristics of the queries.


Online Information Searching For Cardiovascular Diseases: An Analysis Of Mayo Clinic Search Query Logs, Ashutosh Sopan Jadhav, Amit P. Sheth, Jyotishman Pathak 2014 Wright State University

Online Information Searching For Cardiovascular Diseases: An Analysis Of Mayo Clinic Search Query Logs, Ashutosh Sopan Jadhav, Amit P. Sheth, Jyotishman Pathak

Kno.e.sis Publications

Since the early 2000’s, Internet usage for health information searching has increased significantly. Studying search queries can help us to understand users “information need” and how do they formulate search queries (“expression of information need”). Although cardiovascular diseases (CVD) affect a large percentage of the population, few studies have investigated how and what users search for CVD. We address this knowledge gap in the community by analyzing a large corpus of 10 million CVD related search queries from MayoClinic.com. Using UMLS MetaMap and UMLS semantic types/concepts, we developed a rule-based approach to categorize the queries into 14 ...


Graphical User Interface On Analysis Of Mechanics And Dynamics Of Biopolymers In Living Cells, Peter D. Russel, Shubham Agrawal, Taeyoon Kim, Abdel-Rahman Hassan 2014 Purdue University

Graphical User Interface On Analysis Of Mechanics And Dynamics Of Biopolymers In Living Cells, Peter D. Russel, Shubham Agrawal, Taeyoon Kim, Abdel-Rahman Hassan

The Summer Undergraduate Research Fellowship (SURF) Symposium

The mechanical properties of cells depend on the qualities of filamentous-actin (f-actin for short), among other cytoskeletal polymers. The ability to quickly determine f-actin qualities in a sample will help cellular biologists with cytoskeletal protein research. The goal of this project is to create a Matlab program which would allow researchers to determine, with limited manual input, the average filament length and persistence lengths of selected filaments. Through the graphical user interface, the user loads the image stack and can optimize the tracking result by altering several expectations of the program such as the expected contrast between the filament and ...


Analysis Of Mechanics And Dynamics Of Biopolymers In Living Cells, Shubham Agrawal, Peter D. Russel, Abdel-Rahman Hassan, Taeyoon Kim 2014 Purdue University

Analysis Of Mechanics And Dynamics Of Biopolymers In Living Cells, Shubham Agrawal, Peter D. Russel, Abdel-Rahman Hassan, Taeyoon Kim

The Summer Undergraduate Research Fellowship (SURF) Symposium

F-actin polymers in the cytoskeleton provide mechanical strength and deformability to cells. Thus, understanding their dynamic responses to intracellular and extracellular cues is of critical importance for studying the biological and mechanical behaviors of cells. Unfortunately, to date, no computer software can provide researchers with adequate means to measure these responses since in vivo F-actin cytoskeleton is quite dynamic and complex unlike in vitro actin networks. We aim at developing a tool which would allow researchers to semi-automatically analyze time-lapse microscope images of these F-actin polymers and thus evaluate the length and stochastic dynamics of F-actins (filament elongation, shrinkage and ...


Applying Novel Tree-Based Frameworks To Big Data For Classification Of Heart Failure Patients And Prediction Of Clinical Responses, Yan Zhang, Nicholas Downing, Emily Bucholz, Suganthi Balasubramanian, Shu-Xia Li, Tara Liptak, Harlan Krumholz, Mark Gerstein 2014 Yale University

Applying Novel Tree-Based Frameworks To Big Data For Classification Of Heart Failure Patients And Prediction Of Clinical Responses, Yan Zhang, Nicholas Downing, Emily Bucholz, Suganthi Balasubramanian, Shu-Xia Li, Tara Liptak, Harlan Krumholz, Mark Gerstein

Yale Day of Data

Over 5 million Americans suffer from heart failure, a condition with a 5-year survival that eclipses all cancers apart from that of lung cancer. Conventional understanding of heart failure is simplistic: it is viewed as a single syndrome, despite real heterogeneity. In addition, models predicting outcomes focus on dichotomous results, like 30-day readmission. A novel approach to classification of heart failure may improve our ability to target interventions, improve patient experiences, and predict outcomes.

The Healthcare Cost and Utilization Project is a family of administrative claims databases that describes patient demographics, comorbidities, procedures, acute care utilization and outcomes, such as ...


Applications And Improvements In The Molecular Modeling Of Protein And Ligand Interactions, Jason Bret Harris 2014 University of Tennessee, Knoxville

Applications And Improvements In The Molecular Modeling Of Protein And Ligand Interactions, Jason Bret Harris

Doctoral Dissertations

Understanding protein and ligand interactions is fundamental to treat disease and avoid toxicity in biological organisms. Molecular modeling is a helpful but imperfect tool used in computer-aided toxicology and drug discovery. In this work, molecular docking and structural informatics have been integrated with other modeling methods and physical experiments to better understand and improve predictions for protein and ligand interactions. Results presented as part of this research include:

1.) an application of single-protein docking for an intermediate state structure, specifically, modeling an intermediate state structure of alpha-1-antitrypsin and using the resulting model to virtually screen for chemical inhibitors that can ...


World Wide Diversity Of Phytophthora Capsici, Dylan B. Storey 2014 University of Tennessee, Knoxville

World Wide Diversity Of Phytophthora Capsici, Dylan B. Storey

Doctoral Dissertations

The plant pathogen Phytophthora capsici is a genetically diverse organism that is a global problem. It effects many crops across the Solanacea, Cucurbitacea, andLeguminosea. As a result of the large diversity between individuals (and by extension populations) it has been previously near impossible to make meaningful comparisons between individuals of geographically distinct locations. Here we present the results of applying Next Generation Sequencing (NGS) technologies to a representative panel of isolates. This information and data is further used to demonstrate how this diversity has a functionally relevent effect on a class of proteins responsible for the infectious process. We ...


The Prediction Of B-Cell Epitope Via Biostatistical And Bioinformatic Methodology And Applications, Bo Yao 2014 University of Nebraska - Lincoln

The Prediction Of B-Cell Epitope Via Biostatistical And Bioinformatic Methodology And Applications, Bo Yao

Dissertations and Theses in Biological Sciences

By creating antibodies against antigens, B-cells, also named B-lymphocytes, play an important role in the immune system to fight against foreign invasion to the host body. Within the antigen specific to a certain B-cell antibody, the sections recognized and bound by antibody are called B-cell epitopes. As antigenic determinants, B-cell epitope identification is of vital importance in many immunological processes, such as vaccine design, immunodiagnostic tests, and antibody production. Towards this goal, biologists and immunologists have applied a variety of methods to identify B-cell epitopes through both experiments and bioinformatic predictions.

There are two kinds of B-cell epitopes: linear (continuous ...


Integrating Domain Knowledge To Improve Signal Detection From Electronic Health Records For Pharmacovigilance, Ning Shang 2014 Texas Medical Center Library

Integrating Domain Knowledge To Improve Signal Detection From Electronic Health Records For Pharmacovigilance, Ning Shang

UT SBMI Dissertations (Open Access)

The intent of this dissertation is to make a contribution to the field of pharmacovigilance. Pharmacovigilance, also known as post-marketing drug surveillance, is the process of continued monitoring for adverse drug reactions (ADRs) after drugs are released into the market. An ADR is a harmful or unpleasant reaction related to the use of a medical product. ADRs were reported to be between the fourth and sixth leading cause of death in the United States in 1994, accounting for 3-7% of medical hospital admissions. On account of the practice of pharmacovigilance, Vioxx (Rofecoxib) and Avandia (Rosiglitazone) are examples of high profile ...


Assisting Coordination During Crisis: A Domain Ontology Based Approach To Infer Resource Needs From Tweets, Shreyansh Bhatt, Hemant Purohit, Andrew Hampton, Valerie L. Shalin, Amit P. Sheth, John Flach 2014 Wright State University

Assisting Coordination During Crisis: A Domain Ontology Based Approach To Infer Resource Needs From Tweets, Shreyansh Bhatt, Hemant Purohit, Andrew Hampton, Valerie L. Shalin, Amit P. Sheth, John Flach

Kno.e.sis Publications

Ubiquitous social media during crises provides citizen reports on the situation, needs and supplies. Previous research extracts resource needs directly from the text (e.g. "Power cut to Coney Island and Brighton beach" indicates a power need). This approach assumes that citizens derive and write about specific needs from their observations, properly specified for the emergency response system, an assumption that is not consistent with general conversational behavior. In our study, Twitter messages (tweets) from Hurricane Sandy in 2012 clearly indicate power blackouts, but not their probable implications (e.g. loss of power to hospital life support systems). We use ...


Calmodulation Meta-Analysis: Predicting Calmodulin Binding Via Canonical Motif Clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, William R. Kobertz 2014 University of Massachusetts Medical School

Calmodulation Meta-Analysis: Predicting Calmodulin Binding Via Canonical Motif Clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, William R. Kobertz

Biochemistry and Molecular Pharmacology Publications and Presentations

The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM-peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator ...


Semantic Modelling Of Smart City Data, Stefan Bischof, Athanasios Karapantelakis, Cosmin-Septimiu Nechifor, Amit P. Sheth, Alessandra Mileo, Payam Barnaghi 2014 Wright State University

Semantic Modelling Of Smart City Data, Stefan Bischof, Athanasios Karapantelakis, Cosmin-Septimiu Nechifor, Amit P. Sheth, Alessandra Mileo, Payam Barnaghi

Kno.e.sis Publications

Cities present an opportunity for rendering Web of Things-enabled services. According to the World Health Organization, population in cities will double by the middle of this century, while cities deal with increasingly pressing issues such as environmental sustainability, economic growth and citizen mobility. In this paper, we propose a discussion around the need for common semantic descriptions for smart city data to facilitate future services in "smart cities". We present examples of data that can be collected from cities, discuss issues around this data and put forward some preliminary thoughts for creating a semantic description model to describe and help ...


Active Learning With Efficient Feature Weighting Methods For Improving Data Quality And Classification Accuracy, Justin Martineau, Lu Chen, Doreen Cheng, Amit P. Sheth 2014 Wright State University

Active Learning With Efficient Feature Weighting Methods For Improving Data Quality And Classification Accuracy, Justin Martineau, Lu Chen, Doreen Cheng, Amit P. Sheth

Kno.e.sis Publications

Many machine learning datasets are noisy with a substantial number of mislabeled instances. This noise yields sub-optimal classification performance. In this paper we study a large, low quality annotated dataset, created quickly and cheaply using Amazon Mechanical Turk to crowdsource annotations. We describe computationally cheap feature weighting techniques and a novel non-linear distribution spreading algorithm that can be used to iteratively and interactively correcting mislabeled instances to significantly improve annotation quality at low cost. Eight different emotion extraction experiments on Twitter data demonstrate that our approach is just as effective as more computationally expensive techniques. Our techniques save a considerable ...


Semantics-Enhanced Geoscience Interoperability, Analytics, And Applications, T. K. Prasad, Amit P. Sheth 2014 Wright State University

Semantics-Enhanced Geoscience Interoperability, Analytics, And Applications, T. K. Prasad, Amit P. Sheth

Kno.e.sis Publications

We present our research ideas for developing cyberinfrastructure for Geoscience applications developed in the context of the EarthCube initiative, and our NSF-sponsored work on incorporating spatial-temporal-thematic semantics for enhanced querying and feature extraction from sensor data streams.


Utilization Of Molecular Inversion Probes In Malaria Sequencing, Ozkan Aydemir, Alice Tran, Yasin Kaymaz, Nicholas J. Hathaway, Jeffrey A. Bailey 2014 University of Massachusetts Medical School

Utilization Of Molecular Inversion Probes In Malaria Sequencing, Ozkan Aydemir, Alice Tran, Yasin Kaymaz, Nicholas J. Hathaway, Jeffrey A. Bailey

UMass Center for Clinical and Translational Science Research Retreat

While massively parallel sequencing of whole genomes shed light on many previously puzzling genetic questions, the high costs associated with this approach makes its use impractical when large cohorts need to be sequenced at high coverage. Available capture technologies reduces the sequencing costs by enriching template material for the regions of interest. However, these technologies are also prohibitively costly at high sample numbers. Capture methods utilizing molecular inversion probes (MIPs) offer a flexible alternative to enrich template material that multiplex well for thousands of samples and require minimal resources. Here, for our work in malaria, we extend the utility of ...


Using Next-Gen Sequencing To Estimate Strain Diversity And Frequency Within Infections, Nicholas J. Hathaway, Jeffrey A. Bailey 2014 University of Massachusetts Medical School

Using Next-Gen Sequencing To Estimate Strain Diversity And Frequency Within Infections, Nicholas J. Hathaway, Jeffrey A. Bailey

UMass Center for Clinical and Translational Science Research Retreat

Targeted deep sequencing has rapidly transformed our ability to investigate environmental and infectious microbial diversity. Our lab is focused on applying deep sequencing to diversity in malaria infections. A key challenge in all deep sequencing work is determining true sequence differences from errors. While several amplicon deep sequencing clustering tools exist these tools can be CPU intensive and/or lack the sensitivity to detect down to a single base pair difference between sequences, which is a necessity for examining intrapopulation differences in malaria. We have therefore created a novel clustering and statistical framework to overcome these limitations. Our clustering algorithm ...


Differential Gene Expression Analysis And Clinical Correlations Within Endemic Burkitt Lymphoma, Yasin Kaymaz, Cliff I. Oduor, John Vulule, Juliana A. Otieno, Ann M. Moormann, Jeffrey A. Bailey 2014 University of Massachusetts Medical School

Differential Gene Expression Analysis And Clinical Correlations Within Endemic Burkitt Lymphoma, Yasin Kaymaz, Cliff I. Oduor, John Vulule, Juliana A. Otieno, Ann M. Moormann, Jeffrey A. Bailey

Clinical and Translational Science Research Retreat

Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in equatorial Africa and is associated with malaria and Epstein-Barr virus co-infections. Molecular alterations within the eBL tumor genome and transcriptome have not been adequately investigated or compared to sporadic Burkitt lymphoma (sBL). Given that eBL has distinct clinical presentations in the jaw as opposed to the abdomen which are associated with survival, we hypothesize that transcriptome sequencing (RNA-seq) and potentially underlying genetic alterations will enhance our understanding of pathogenesis. Our results compare genome-wide RNA transcript abundances between eBL tumors from children (ages 6-7 yrs) with Stage I (Jaw tumor ...


Automatic Article Screening In Systematic Review, Tong Wang 2014 University of Massachusetts Medical School

Automatic Article Screening In Systematic Review, Tong Wang

UMass Center for Clinical and Translational Science Research Retreat

In recent years, evidence-based medicine has become increasingly important in guiding health care practices. Systematic review, which is the core component of evidence-based medicine, attempts to identify and synthesize all the empirical evidence from online resources such as pubmed to answer a given research question. Usually a clinical researcher needs to choose dozens of related articles as references to work on systematic review. However, there are usually thousand of articles retried from pubmed after keywords searching, it is time consuming to read each of the articles to find the right ones. My work is to apply text mining and machine ...


Structure-Based Design Of Broadly Neutralizing Hcv Antibody And Vaccine, Brian G. Pierce, Elisabeth N. Boucher, Heidi L. Smith, William D. Thomas Jr., Zhiping Weng, Yang Wang 2014 University of Massachusetts Medical School

Structure-Based Design Of Broadly Neutralizing Hcv Antibody And Vaccine, Brian G. Pierce, Elisabeth N. Boucher, Heidi L. Smith, William D. Thomas Jr., Zhiping Weng, Yang Wang

UMass Center for Clinical and Translational Science Research Retreat

Hepatitis C virus (HCV) chronically infects nearly 200 million people worldwide. Antibodies have the potential to prevent establishment of chronic HCV infection in individuals exposed to the virus. Several broadly neutralizing monoclonal antibodies capable of binding HCV surface glycoproteins have been identified, including HCV1 identified by MassBiologics at UMMS, which targets a highly conserved linear epitope. We utilized the recently solved structure of the HCV1-bound epitope to identify regions of the antibody that could be modified to potentially improve binding to a mutation (N415K) which facilitates escape from neutralization. Based on systematic in silico mutagenesis of HCV1 residues in the ...


Alternative Tools For Mining The Biomedical Literature, Rolando Garcia-Milian 2014 Yale University

Alternative Tools For Mining The Biomedical Literature, Rolando Garcia-Milian

Rolando Garcia-Milian

The rapid growth of experimental and computational biomedical data is being accompanied by an increase in the number of biomedical publications discussing these results. This makes retrieving relevant scientific information and identifying connections between findings, a challenging task. New literature-mining tools (e.g. KNALIJ, Quertle, NextBio, iHOP, SemMed, GoPubMed, etc) may be of help when sorting through this abundance of literature, as discovery and hypothesis generating tools. This workshop provides an introduction on how to use some of these literature-mining tools when answering research questions.


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