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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 ...


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 ...


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 ...


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 ...


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 ...


Semantics-Enhanced Geoscience Interoperability, Analytics, And Applications, Krishnaprasad Thirunarayan, Amit P. Sheth 2014 Wright State University

Semantics-Enhanced Geoscience Interoperability, Analytics, And Applications, Krishnaprasad Thirunarayan, 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 ...


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.


An Examination Of The Phylogenetic Diversity Of Green Algae (Chlorophyceae) That Symbiose With Spotted Salamanders (Ambystoma Maculatum) In The Egg Stage., Crystal Xue 2014 University of Connecticut

An Examination Of The Phylogenetic Diversity Of Green Algae (Chlorophyceae) That Symbiose With Spotted Salamanders (Ambystoma Maculatum) In The Egg Stage., Crystal Xue

Honors Scholar Theses

In 1909, the species Oophila amblystomatis Lambert ex Wille was described for green algae that symbiose with salamanders in the egg stage (Wille). There are two hypotheses about the source of algae: 1) that algae enter from the surrounding water once the egg clutch is laid in a pond, and 2) that they are acquired from the maternal reproductive tract. We developed a third hypothesis developed to account for the salamander reproductive cycle. Male salamanders lay spermatophores, which are protein-filled capsules, on plant matter in and around ponds. Spermatophores are exposed to the environment before use by females in internal ...


Transcriptome Analysis Of Sea Lamprey Embryogenesis, Zakary Ilya Yermolenko 2014 Seton Hall University

Transcriptome Analysis Of Sea Lamprey Embryogenesis, Zakary Ilya Yermolenko

Seton Hall University Dissertations and Theses (ETDs)

The sea lamprey (Petromyzon marinus) has survived throughout evolution for hundreds of millions of years. It is considered an invasive species to the Great Lakes that has caused dramatic changes in the ecosystem for fish communities resulting in the collapse of a fishing industry that was previously valued at billions of dollars. Successful management of the sea lamprey is essential to a sustainable fishing industry and biodiversity. Therefore sea lamprey embryos were studied at various stages of development by growing them in a simulated habitat. RNAs from adult female ovaries and embryos at different time points during embryogenesis were extracted ...


The Association Between The Il-1 Pathway, Isaac C. Wun 2014 Texas Medical Center Library

The Association Between The Il-1 Pathway, Isaac C. Wun

UT GSBS Dissertations and Theses (Open Access)

Cutaneous malignant melanoma (CMM) is a potentially lethal malignancy that warrants attention and further research, as it is known to that there is an increasing rate of incidence in theUnited States, and it is also known that exposure to UV light is its most crucial risk factor, and family history of melanoma is also an important risk factor. Melanoma is an aggressive and lethal cancer in humans. There are an estimated new 132,000 melanoma cases annually worldwide, and the trend has doubled in the past 20 years. However, attempts to treat melanoma have encountered considerable resistance and remained ineffective ...


Numerical Assessment Of Sequence Conservation In Flu-Virus Hemagglutinin, Scott S. Norton 2014 University of Connecticut

Numerical Assessment Of Sequence Conservation In Flu-Virus Hemagglutinin, Scott S. Norton

Honors Scholar Theses

The flu virus was investigated to find a common recognition domain to which an antibody against human-infected viruses can bind. If such a target site is structurally and electrostaticly conserved or invariant, only a single antibody would be required to attack the virus in all cases. The sequence of one of the viral surface proteins contains 24 amino acids that do not vary through mutation. However, these amino acids are neither contiguous in sequence or in space, and the ones that are associated with each other are not readily accessible to an antibody. They do provide a first impression of ...


R-Fap: Rapid Functional Annotation Of Prokaryotes Using Taxon-Specific Pan-Genomes And 10-Mer Peptides, Jordan Matthew Utley 2014 University of Tennessee, Knoxville

R-Fap: Rapid Functional Annotation Of Prokaryotes Using Taxon-Specific Pan-Genomes And 10-Mer Peptides, Jordan Matthew Utley

Masters Theses

The growing implementation of next-generation sequencing technologies presents numerous fields with the opportunity to identify bacteria in near real-time. Fields such as counter-terrorism, forensics, medicine, and even microbial ecology are positioned to benefit from such advances and implementation. However, with the ability to rapidly produce high-quality sequence data comes the need to interpret this data as quickly as it is produced. While gene prediction algorithms have kept pace, functional prediction methods have not.

To bypass the need for large-scale queries to multiple databases for each newly-sequenced genome, the project detailed herein seeks to identify the genes shared within a taxonomic ...


With Whom To Coordinate, Why And How In Ad-Hoc Social Media Communications During Crisis Reponse, Hemant Purohit, Shreyansh Bhatt, Andrew Hampton, Valerie L. Shalin, Amit P. Sheth, John Flach 2014 Wright State University

With Whom To Coordinate, Why And How In Ad-Hoc Social Media Communications During Crisis Reponse, Hemant Purohit, Shreyansh Bhatt, Andrew Hampton, Valerie L. Shalin, Amit P. Sheth, John Flach

Kno.e.sis Publications

During crises affected people, well-wishers, and observers join social media communities to discuss the event. They often share useful information relevant to response coordination, for example, specific resource needs. However, responders face the challenge of massive data overload and lack the time to monitor social media traffic for important information. Analysis shows that only a small number of event related conversations are actionable. Moreover, responders do not know which sources are trustworthy. To address these challenges, response teams may apply manual filtering methods, resulting in limited coverage and quality. We propose a framework and interface for extracting specific resource-related information ...


Mining Contrast Subspaces, Lei Duan, Guanting Tang, Jian Pei, James Bailey, Guozhu Dong, Akiko Campbell, Changjie Tang 2014 Wright State University

Mining Contrast Subspaces, Lei Duan, Guanting Tang, Jian Pei, James Bailey, Guozhu Dong, Akiko Campbell, Changjie Tang

Kno.e.sis Publications

In this paper, we tackle a novel problem of mining contrast subspaces. Given a set of multidimensional objects in two classes C  +  and C  − and a query object o, we want to find top-ksubspaces S that maximize the ratio of likelihood of o in C  +  against that in C  −. We demonstrate that this problem has important applications, and at the same time, is very challenging. It even does not allow polynomial time approximation. We present CSMiner, a mining method with various pruning techniques. CSMiner is substantially faster than the baseline method. Our experimental results on real data sets ...


Disease Name Extraction From Clinical Text Using Conditional Random Fields, Omid Ghiasvand 2014 University of Wisconsin Milwaukee

Disease Name Extraction From Clinical Text Using Conditional Random Fields, Omid Ghiasvand

Theses and Dissertations

The aim of the research done in this thesis was to extract disease and disorder names from clinical texts. We utilized Conditional Random Fields (CRF) as the main method to label diseases and disorders in clinical sentences. We used some other tools such as MetaMap and Stanford Core NLP tool to extract some crucial features. MetaMap tool was used to identify names of diseases/disorders that are already in UMLS Metathesaurus. Some other important features such as lemmatized versions of words, and POS tags were extracted using the Stanford Core NLP tool. Some more features were extracted directly from UMLS ...


Defining Functional Dna Elements In The Human Genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, ENCODE Project Consortium 2014 University of Massachusetts Medical School

Defining Functional Dna Elements In The Human Genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, Encode Project Consortium

Program in Systems Biology Publications and Presentations

With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily ...


Isolation & Characterization Of The Novel Bacteriophage Gaius, Rohan Khazanchi, John A. Nahon, Anna M. Kolasa, Elisa S. De Togni 2014 Washington University in St. Louis

Isolation & Characterization Of The Novel Bacteriophage Gaius, Rohan Khazanchi, John A. Nahon, Anna M. Kolasa, Elisa S. De Togni

Undergraduate Research Symposium Posters & Abstracts

There are an estimated 1031 species of bacteriophages in the Earth’s biome. As a result, understanding the immense diversity of bacteriophages is a topic of great interest. We isolated a novel mycobacteriophage, called Gaius, from soil collected near the Watershed Nature Center in Edwardsville, IL. We enriched our soil sample using Mycobacterium smegmatis, and after purification, its plaque morphology was characteristic of a temperate phage. Following purification, we used electron microscope imaging to find Gaius’ physical structure to be similar to other members of the A4 subcluster. We sequenced Gaius’ genome using the Pacific Biosystems Sequencing technique, making ...


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