Life Sciences Commons^™

Understanding Events Through Analysis Of Social Media, Amit P. Sheth, Hemant Purohit, Ashutosh Sopan Jadhav, Pavan Kapanipathi, Lu Chen

Kno.e.sis Publications

Users are sharing vast amounts of social data through social networking platforms accessible by Web and increasingly via mobile devices. This opens an exciting opportunity to extract social perceptions as well as obtain insights relevant to events around us. We discuss the significant need and opportunity for analyzing event-centric user generated content on social networks, present some of the technical challenges and our approach to address them. This includes aggregating social data related to events of interest, along with Web resources (news, Wikipedia pages, multimedia) related to an event of interest, and supporting analysis along spatial, temporal, thematic, and sentiment …

Mobicloud - Making Clouds Reachable: A Toolkit For Easy And Efficient Development Of Customized Cloud Mobile Hybrid Applications, Ashwin Manjunatha, Ajith Harshana Ranabahu, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The advancements in computing have resulted in a boom of cheap, ubiquitous, connected mobile devices, as well as seemingly unlimited, utility style, pay as you go computing resources, commonly referred to as Cloud computing. However, taking full advantage of this mobile and cloud computing landscape, especially for the data intensive domains, has been hampered by the many heterogeneities that exist in the mobile space, as well as the Cloud space. Our research attempts to exploit the capabilities of the mobile and cloud landscape by introducing MobiCloud, an online toolkit to efficiently develop Cloud-mobile hybrid (CMH) applications. We define a CMH …

Nominal Schemas For Integrating Rules And Ontologies, Frederick Maier, Adila A. Krisnadhi, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We propose a description-logic style extension of OWL DL, which includes DL-safe variable SWRL and seamlessly integrates datalog rules. Our language also sports a tractable fragment, which we call ELP 2, covering OWL EL, OWL RL, most of OWL QL, and variable restricted datalog.

Scale: A Scalable Framework For Efficiently Clustering Transactional Data, Hua Yan, Keke Chen, Ling Liu, Zhang Yi

Kno.e.sis Publications

This paper presents SCALE, a fully automated transactional clustering framework. The SCALE design highlights three unique features. First, we introduce the concept of Weighted Coverage Density as a categorical similarity measure for efficient clustering of transactional datasets. The concept of weighted coverage density is intuitive and it allows the weight of each item in a cluster to be changed dynamically according to the occurrences of items. Second, we develop the weighted coverage density measure based clustering algorithm, a fast, memory-efficient, and scalable clustering algorithm for analyzing transactional data. Third, we introduce two clustering validation metrics and show that these domain …

From Questions To Effective Answers: On The Utility Of Knowledge-Driven Querying Systems For Life Sciences Data, Amir H. Asiaee, Prashant Doshi, Todd Minning, Satya S. Sahoo, Priti Parikh, Amit P. Sheth, Rick L. Tarleton

Kno.e.sis Publications

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data. These interfaces could be seen as implementing a set of 'pre-canned' queries commonly used by the life science researchers that we study. The second approach is based on semantic Web technologies and is knowledge (model) driven. It utilizes a large OWL ontology and same datasets as before but associated as RDF instances of the ontology concepts. An intuitive interface is provided that allows the …

Sensor Discovery On Linked Data, Josh Pschorr, Cory Andrew Henson, Harshal Kamlesh Patni, Amit P. Sheth

Kno.e.sis Publications

There has been a drive recently to make sensor data accessible on the Web. However, because of the vast number of sensors collecting data about our environment, finding relevant sensors on the Web is a non-trivial challenge. In this paper, we present an approach to discovering sensors through a standard service interface over Linked Data. This is accomplished with a semantic sensor network middleware that includes a sensor registry on Linked Data and a sensor discovery service that extends the OGC Sensor Web Enablement. With this approach, we are able to access and discover sensors that are positioned near named-locations …

Sensor Data And Perception: Can Sensors Play 20 Questions, Cory Andrew Henson

Kno.e.sis Publications

Currently, there are many sensors collecting information about our environment, leading to an overwhelming number of observations that must be analyzed and explained in order to achieve situation awareness. As perceptual beings, we are also constantly inundated with sensory data, yet we are able to make sense of our environment with relative ease. Why is the task of perception so easy for us, and so hard for machines; and could this have anything to do with how we play the game 20 Questions?

A Qualitative Examination Of Topical Tweet And Retweet Practices, Meenakshi Nagarajan, Hemant Purohit, Amit P. Sheth

Kno.e.sis Publications

This work contributes to the study of retweet behavior on Twitter surrounding real-world events. We analyze over a million tweets pertaining to three events, present general tweet properties in such topical datasets and qualitatively analyze the properties of the retweet behavior surrounding the most tweeted/viral content pieces. Findings include a clear relationship between sparse/dense retweet patterns and the content and type of a tweet itself; suggesting the need to study content properties in link-based diffusion models.

Provenance Aware Linked Sensor Data, Harshal Kamlesh Patni, Satya S. Sahoo, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

Provenance, from the French word “provenir”, describes the lineage or history of a data entity. Provenance is critical information in the sensors domain to identify a sensor and analyze the observation data over time and geographical space. In this paper, we present a framework to model and query the provenance information associated with the sensor data exposed as part of the Web of Data using the Linked Open Data conventions. This is accomplished by developing an ontology-driven provenance management infrastructure that includes a representation model and query infrastructure. This provenance infrastructure, called Sensor Provenance Management System (PMS), is …

Getting Code Near The Data: A Study Of Generating Customized Data Intensive Scientific Workflows With Domain Specific Language, Ashwin Manjunatha, Ajith Harshana Ranabahu, Paul E. Anderson, Amit P. Sheth

Kno.e.sis Publications

The amount of data produced in modern biological experiments such as Nuclear Magnetic Resonance (NMR) analysis far exceeds the processing capability of a single machine. The present state-of-the-art is taking the ”data to code”, the philosophy followed by many of the current service oriented workflow systems. However this is not feasible in some cases such as NMR data analysis, primarily due to the large scale of data.

The objective of this research is to bring ”code to data”, preferred in the cases when the data is extremely large. We present a DSL based approach to develop customized data intensive scientific …

Loqus: Linked Open Data Sparql Querying System, Prateek Jain, Kunal Verma, Peter Z. Yeh, Pascal Hitzler, Amit P. Sheth

Kno.e.sis Publications

The LOD cloud is gathering a lot of momentum, with the number of contributors growing manifold. Many prominent data providers have submitted and linked their data to other dataset with the help of manual mappings. The potential of the LOD cloud is enormous ranging from challenging AI issues such as open domain question answering to automated knowledge discovery. We believe that there is not enough technology support available to effectively query the LOD cloud. To this effect, we present a system called Linked Open Data SPARQL Querying System (LOQUS), which automatically maps users queries written in terms of a conceptual …

Computing For The Human Experience: Semantics-Empowered Sensors, Services, And Social Computing On The Ubiquitous Web, Amit P. Sheth

Kno.e.sis Publications

People are on the verge of an era in which the human experience can be enriched in ways they couldn't have imagined two decades ago. Rather than depending on a single technology, people progressed with several whose semantics-empowered convergence and integration will enable us to capture, understand, and reapply human knowledge and intellect. Such capabilities will consequently elevate our technological ability to deal with the abstractions, concepts, and actions that characterize human experiences. This will herald computing for human experience (CHE). The CHE vision is built on a suite of technologies that serves, assists, and cooperates with humans to nondestructively …

Provenance Context Entity (Pace): Scalable Provenance Tracking For Scientific Rdf Data, Satya S. Sahoo, Olivier Bodenreider, Pascal Hitzler, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The Resource Description Framework (RDF) format is being used by a large number of scientific applications to store and disseminate their datasets. The provenance information, describing the source or lineage of the datasets, is playing an increasingly significant role in ensuring data quality, computing trust value of the datasets, and ranking query results. Current provenance tracking approaches using the RDF reification vocabulary suffer from a number of known issues, including lack of formal semantics, use of blank nodes, and application-dependent interpretation of reified RDF triples. In this paper, we introduce a new approach called Provenance Context Entity (PaCE) that uses …

A Study In Hadoop Streaming With Matlab For Nmr Data Processing, Kalpa Gunaratna, Paul E. Anderson, Ajith Harshana Ranabahu, Amit P. Sheth

Kno.e.sis Publications

Applying Cloud computing techniques for analyzing large data sets has shown promise in many data-driven scientific applications. Our approach presented here is to use Cloud computing for Nuclear Magnetic Resonance (NMR)data analysis which normally consists of large amounts of data. Biologists often use third party or commercial software for ease of use. Enabling the capability to use this kind of software in a Cloud will be highly advantageous in many ways. Scripting languages especially designed for clouds may not have the flexibility biologists need for their purposes. Although this is true, they are familiar with special software packages that allow …

Twitris 2.0 : Semantically Empowered System For Understanding Perceptions From Social Data, Ashutosh Sopan Jadhav, Hemant Purohit, Pavan Kapanipathi, Pramod Anantharam, Ajith H. Ranabahu, Vinh Nguyen, Pablo N. Mendes, Alan Gary Smith, Michael Cooney, Amit P. Sheth

Kno.e.sis Publications

We present Twitris 2.0, a Semantic Web application that facilitates understanding of social perceptions by Semantics-based processing of massive amounts of event-centric data. Twitris 2.0 addresses challenges in large scale processing of social data, preserving spatio-temporal-thematic properties. Twitris 2.0 also covers context based semantic integration of multiple Web resources and expose semantically enriched social data to the public domain. Semantic Web technologies enable the systematic integration and analysis abilities.

Power Of Clouds In Your Pocket: An Efficient Approach For Cloud Mobile Hybrid Application Development, Ashwin Manjunatha, Ajith Harshana Ranabahu, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The advancements in computing have resulted in a boom of cheap, ubiquitous, connected mobile devices as well as seemingly unlimited, utility style, pay as you go computing resources, commonly referred to as Cloud computing. However, taking full advantage of this mobile and cloud computing landscape, especially for the data intensive domains has been hampered by the many heterogeneities that exist in the mobile space as well as the Cloud space. Our research focuses on exploiting the capabilities of the mobile and cloud landscape by defining a new class of applications called cloud mobile hybrid (CMH) applications and a Domain Specific …

Semantic Web – Interoperability, Usability, Applicability, Pascal Hitzler, Krzysztof Janowicz

Computer Science and Engineering Faculty Publications

No abstract provided.

Approximate Instance Retrieval On Ontologies, Tuvshintur Tserendorj, Stephan Grimm, Pascal Hitzler

Computer Science and Engineering Faculty Publications

With the development of more expressive description logics (DLs) for the Web Ontology Language OWL the question arises how we can properly deal with the high computational complexity for efficient reasoning. In application cases that require scalable reasoning with expressive ontologies, non-standard reasoning solutions such as approximate reasoning are necessary to tackle the intractability of reasoning in expressive DLs. In this paper, we are concerned with the approximation of the reasoning task of instance retrieval on DL knowledge bases, trading correctness of retrieval results for gain of speed. We introduce our notion of an approximate concept extension and we provide …

Diversity Of Interactions: A Metric For Studies Of Biodiversity, Lee A. Dyer, Thomas R. Walla, Harold F. Greeney, John O. Stireman Iii, Rebecca F. Hazen

Biological Sciences Faculty Publications

Multitrophic interactions play key roles in the origin and maintenance of species diversity, and the study of these interactions has contributed to important theoretical advances in ecology and evolutionary biology. Nevertheless, most biodiversity inventories focus on static species lists, and prominent theories of diversity still ignore trophic interactions. The lack of a simple interaction metric that is analogous to species richness is one reason why diversity of interactions is not examined as a response or predictor variable in diversity studies. Using plant-herbivore-enemy trophic chains as an example, we develop a simple metric of diversity in which richness, diversity indices (e.g., …

Semantics Centric Solutions For Application And Data Portability In Cloud Computing, Ajith Harshana Ranabahu, Amit P. Sheth

Kno.e.sis Publications

Cloud computing has become one of the key considerations both in academia and industry. Cheap, seemingly unlimited computing resources that can be allocated almost instantaneously and pay-as-you-go pricing schemes are some of the reasons for the success of Cloud computing. The Cloud computing landscape, however, is plagued by many issues hindering adoption. One such issue is vendor lock-in, forcing the Cloud users to adhere to one service provider in terms of data and application logic. Semantic Web has been an important research area that has seen significant attention from both academic and industrial researchers. One key property of Semantic Web …

Cellular And Molecular Dissection Of Pluripotent Adult Somatic Stem Cells In Planarians, Norito Shibata, Labib Rouhana, Kiyokazu Agata

Biological Sciences Faculty Publications

Freshwater planarians, Plathelminthes, have been an intriguing model animal of regeneration studies for more than 100 years. Their robust regenerative ability is one of asexual reproductive capacity, in which complete animals develop from tiny body fragments within a week. Pluripotent adult somatic stem cells, called neoblasts, assure this regenerative ability. Neoblasts give rise to not only all types of somatic cells, but also germline cells. During the last decade, several experimental techniques for the analysis of planarian neoblasts at the molecular level, such as in situ hybridization, RNAi and fluorescence activated cell sorting, have been established. Moreover, information about genes …

A Reasonable Semantic Web, Pascal Hitzler, Frank Van Harmelen

Computer Science and Engineering Faculty Publications

The realization of Semantic Web reasoning is central to substantiating the Semantic Web vision. However, current mainstream research on this topic faces serious challenges, which forces us to question established lines of research and to rethink the underlying approaches. We argue that reasoning for the Semantic Web should be understood as "shared inference," which is not necessarily based on deductive methods. Model-theoretic semantics (and sound and complete reasoning based on it) functions as a gold standard, but applications dealing with large-scale and noisy data usually cannot afford the required runtimes. Approximate methods, including deductive ones, but also approaches based on …

Automated Isolation Of Translational Efficiency Bias That Resists The Confounding Effect Of Gc(At)-Content, Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

Genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale; however, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons is preferred. Detection of this bias is an important tool …

Linked Open Social Signals, Pablo N. Mendes, Alexandre Passant, Pavan Kapanipathi, Amit P. Sheth

Kno.e.sis Publications

In this paper we discuss the collection, semantic annotation and analysis of real-time social signals from micro-blogging data. We focus on users interested in analyzing social signals collectively for sensemaking. Our proposal enables flexibility in selecting subsets for analysis, alleviating information overload. We define an architecture that is based on state-of-the-art Semantic Web technologies and a distributed publish subscribe protocol for real time communication. In addition, we discuss our method and application in a scenario related to the health care reform in the United States.

Continuous Semantics To Analyze Real-Time Data, Amit P. Sheth, Christopher Thomas, Pankaj Mehra

Kno.e.sis Publications

Increasingly we are presented with dynamic domains involved in social, mobile, and sensor webs. Such domains are spontaneous (arising suddenly), follow a period of rapid evolution, involving real-time or near real-time data, involve many distributed participants and diverse viewpoints involving topical or contentious subjects, and involve feature context colored by local knowledge and sociocultural backgrounds. This article present continuous semantics can help us model such dynamic domains and analyze the related real-time data. Capabilities include crating dynamic domain model by mining social data, and using dynamic models for semantic analysis of real-time data.

2,3,7,8-Tetrachlordibenzo-P-Dioxin Mediated Immune Suppression Through Interactions At The 3'Immunoglobulin Heavy Chain Regulatory Region Enhancers, David Harold Ellis

Browse all Theses and Dissertations

2,3,7,8-Tetrachlordibenzo-p-dioxin (TCDD) is a potent toxin which inhibits the antibody response of B cells. The 3'IgHRR which is involved in transcriptional regulation of the heavy-chain polypeptide of antibodies is inhibited by TCDD. The hs1,2 enhancer region, isolated from the 3'IgHRR, is also inhibited while the isolated hs4 is activated by TCDD. This project sought to determine if that dichotomy in effects results from interactions at enhancer-specific binding sites for AhR, thought to mediate transcriptional effects of TCDD, and NFκB, a transcription factor involved in B cell activation. Here, I report a difference in the effect of TCDD on transcriptional activity …

Revision Of The Genus Erythromelana Townsend, 1919 (Diptera: Tachinidae) With Notes On Their Phylogeny And Diversification, Diego Javier Inclan Luna

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The neotropics harbor an enormous diversity of tachinid flies, yet the fauna remains poorly known. The tribe Blondeliini is particularly diverse in this region and desperately needs taxonomic attention. Here, I present a revision of the neotropical genus Erythromelana Townsend including the redescription of three previously described species and the description of 11 new species. Two species previously assigned into this genus, are resurrected as distinct genera. Erythromelana species are widely distributed from southern Mexico to northern Argentina, with the Andes being a hotspot of diversity. Erythromelana are specialized on geometrids in the genus Eois, which mainly feed on plants …

An Assessment Of White-Tailed Deer (Odocoileus Virginianus) Dynamics, Management, And Impacts In Highly Fragmented Landscapes, Bambi Shafer

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Habitat and forage selection by deer can cause local extinction of plant species. In my research, I asked: 1) How do deer population growth rates in urban parks change through time? 2) Are culling rates and deer densities correlated? 3) Are browse rates on Trillium spp. and deer densities correlated? I used FLIR deer census data from Davis Aviation and culling data from Five Rivers MetroParks (Montgomery County, Ohio). I found that deer population growth rates generally declined from 2003 to 2008. The number of deer culled was positively correlated to the deer densities. The browse rates of Trillium spp. …

The Im-9 Cell Line: A Model For Evaluating Tcdd-Induced Modulation Of The Polymorphic Human Hs1,2 Enhancer Within The 3' Immunoglobulin Heavy Chain Regulatory Region, Ruth C. Chambers-Turner

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2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a disrupter, of B-cell differentiation, induces binding of the aryl hydrocarbon receptor (AhR) nuclear complex to dioxin responsive elements (DRE) within the mouse immunoglobulin heavy chain regulatory region (3'IgHRR), and produces a marked inhibition of 3'IgHRR activation, IgH expression, and antibody secretion in a well-characterized mouse B-cell line (CH12.LX). The mouse 3'IgHRR consists of at least four enhancers (hs3a; hs1,2; hs3b; hs4), and is highly homologous with the three enhancers (hs3; hs1,2; hs4) of the human 3'IgHRR. A polymorphism of the human hs1,2 enhancer (resulting in varying numbers of tandem repeats containing a DRE and κB site) has …

Quantitative Structure-Activity Relationships For Organophosphates Binding To Trypsin And Chymotrypsin, Christopher Daniel Ruark

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Organophosphate (OP) nerve agents such as sarin, soman, tabun, and O-ethyl S-[2-(diisopropylamino) ethyl] methylphosphonothioate (VX) do not react solely with acetylcholinesterase (AChE). Evidence suggests that a wide range of cholinergic-independent pathways are also targeted, including serine proteases. These proteases comprise nearly one-third of all known proteases and play major roles in synaptic plasticity, learning, memory, neuroprotection, wound healing, cell signaling, inflammation, blood coagulation and protein processing. Inhibition of these proteases by OPs was found to exert a wide range of noncholinergic effects depending on the type of OP, the dose, and the duration of exposure. Consequently, in order to understand …