Life Sciences Commons^™

Caenorhabditis Briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility And The Evolution Of Recombination, Joseph A. Ross, Daniel C. Koboldt, Julia E. Staisch, Helen M. Chamberlin, Bhagwati P. Gupta, Raymond D. Miller, Scott Everet Baird, Eric S. Haag

Biological Sciences Faculty Publications

The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by …

Local Closed World Semantics: Keep It Simple, Stupid!, Adila Krishnadhi, Kunal Sengupta, Pascal Hitzler

Computer Science and Engineering Faculty Publications

A combination of open and closed-world reasoning (usually called local closed world reasoning) is a desirable capability of knowledge representation formalisms for Semantic Web applications. However, none of the proposals made to date for extending description logics with local closed world capabilities has had any significant impact on applications. We believe that one of the key reasons for this is that current proposals fail to provide approaches which are intuitively accessible for application developers at the same time are applicable, as extensions, to expressive description logics as SROIQ, which underlies the Web Ontology Language OWL.

In this paper, we propose …

Web Wisdom: An Essay On How Web 2.0 And Semantic Web Can Foster A Global Knowledge Society, Christopher Thomas, Amit P. Sheth

Kno.e.sis Publications

Admittedly this is a presumptuous title that should never be used when reporting on individual research advances. Wisdom is just not a scientific concept. In this case, though, we are reporting on recent developments on the web that lead us to believe that the web is on the way to providing a platform for not only information acquisition and business transactions but also for large scale knowledge development and decision support. It is likely that by now every web user has participated in some sort of social function or knowledge accumulating function on the web, many times without even being …

Loss Of Expression Of Neutrophil Proteinase-3: A Factor Contributing To Thrombotic Risk In Paroxysmal Nocturnal Hemoglobinuria, Anna M. Jankowska, Hadrian Szpurka, Mark Calabro, Sanjay Mohan, Andrew E. Schade, Michael Clemente, Roy L. Silverstein, Jaroslaw P. Maciejewski

Biological Sciences Faculty Publications

Background: A deficiency of specific glycosylphosphatidyl inositol-anchored proteins in paroxysmal nocturnal hemoglobinuria may be responsible for most of the clinical features of this disease, but some functional consequences may be indirect. For example, the absence of certain glycosylphosphatidyl inositol-anchored proteins in paroxysmal nocturnal hemoglobinuria cells may influence expression of other membrane proteins. Membrane-bound proteinase 3 co-localizes with glycosylphosphatidyl inositol-linked neutrophil antigen 2a, which is absent in patients with paroxysmal nocturnal hemoglobinuria. Design and Methods: We compared expression of proteinase 3 and neutrophil antigen 2a by flow cytometry and western blotting in normal and paroxysmal nocturnal hemoglobinuria cells and measured cytoplasmic …

The Effects Of Arbuscular Mycorrhizal (Am) Fungal And Garlic Mustard Introductions On Native Am Fungal Diversity, Alexander M. Koch, Pedro M. Antunes, Kathryn Barto, Don Cipollini, Daniel L. Mummey, John N. Klironomos

Biological Sciences Faculty Publications

Introduced, non-native organisms are of global concern, because biological invasions can negatively affect local communities. Arbuscular mycorrhizal (AM) fungal communities have not been well studied in this context. AM fungi are abundant in most soils, forming symbiotic root-associations with many plant species. Commercial AM fungal inocula are increasingly spread worldwide, because of potentially beneficial effects on plant growth. In contrast, some invasive plant species, such as the non-mycorrhizal Alliaria petiolata, can negatively influence AM fungi. In a greenhouse study we examined changes in the structure of a local Canadian AM fungal community in response to inoculation by foreign AM fungi …

Smob: The Best Of Both Worlds, Alexandre Passant, Julia Anaya, Owen Sacco, Pavan Kapanipathi

Kno.e.sis Publications

This paper presents the architecture of SMOB and the way it combines Semantic Web standards (RDF(S) / SPARQL) and new protocols such as PubSubHubbub to enable a Federated and Privacy-Aware Social Web.

Automatic Domain Model Creation Using Pattern-Based Fact Extraction, Christopher Thomas, Pankaj Mehra, Wenbo Wang, Amit P. Sheth, Gerhard Weikum, Victor Chan

Kno.e.sis Publications

This paper describes a minimally guided approach to automatic domain model creation. The first step is to carve an area of interest out of the Wikipedia hierarchy based on a simple query or other starting point. The second step is to connect the concepts in this domain hierarchy with named relationships. A starting point is provided by Linked Open Data, such as DBPedia. Based on these community-generated facts we train a pattern-based fact-extraction algorithm to augment a domain hierarchy with previously unknown relationship occurrences. Pattern vectors are learned that represent occurrences of relationships between concepts. The process described can be …

Privacy-By-Design In Federated Social Web Applications, Alexandre Passant, Owen Sacco, Julia Anaya, Pavan Kapanipathi

Kno.e.sis Publications

No abstract provided.

Local Closed-World Reasoning With Description Logics Under The Well-Founded Semantics, Matthias Knorr, Jose Julio Alferes, Pascal Hitzler

Computer Science and Engineering Faculty Publications

An important question for the upcoming Semantic Web is how to best combine open world ontology languages, such as the OWL-based ones, with closed world rule-based languages. One of the most mature proposals for this combination is known as hybrid MKNF knowledge bases (Motik and Rosati, 2010 [52]), and it is based on an adaptation of the Stable Model Semantics to knowledge bases consisting of ontology axioms and rules. In this paper we propose a well-founded semantics for nondisjunctive hybrid MKNF knowledge bases that promises to provide better efficiency of reasoning, and that is compatible with both the OWL-based …

What's Happening In Semantic Web ... And What Fca Could Have To Do With It, Pascal Hitzler

Computer Science and Engineering Faculty Publications

The Semantic Web is gaining momentum. Driven by over 10 years of focused project funding in the US and the EU, Semantic Web Technologies are now entering application areas in industry, academia, government, and the open Web.

The Semantic Web is based on the idea of describing the meaning - or semantics - of data on the Web using metadata - data that describes other data - in the form of ontologies, which are represented using logic-based knowledge representation languages. Central to the transfer of Semantic Web into practice is the Linked Open Data effort, which has already resulted in …

Trust Networks: Interpersonal, Social, And Sensor, Krishnaprasad Thirunarayan, Pramod Anantharam

Kno.e.sis Publications

Trust relationships occur naturally in many diverse contexts such as ecommerce, interpersonal interactions, social networks, sensor web, etc. As agents providing content and services become increasingly removed from the agents that consume them, the issue of robust trust inference and update become critical. Unfortunately, there is neither a universal notion of trust that is applicable to all domains nor a clear explication of its semantics or computation in many situations. In this beginner's level tutorial, we motivate the trust problem, explain the relevant concepts, summarize research in modeling trust and gleaning trustworthiness, and discuss challenges confronting us in this process.

Avian Community Ecology And The Shifting Baseline In Sugarcreek Metropark, Jennifer Lynne Hays, Thomas P. Rooney, Jeffrey L. Peters

Biological Sciences Faculty Publications

No abstract provided.

Abundance And Trends Of Woodpecker Populations In The Wright State Biology Preserve, Brittany Damron, Thomas P. Rooney

Biological Sciences Faculty Publications

No abstract provided.

Carbon Sequestration In Soils Of The Wright State University Biology Preserve, Laurie Wissler, Thomas P. Rooney

Biological Sciences Faculty Publications

No abstract provided.

Wright State University Celebration Of Research, Scholarship And Creative Activities Book Of Abstracts Friday, April 8, 2011, Wright State University Office Of Undergraduate Research And Stemm Activities

Celebration of Undergraduate & Graduate Research, Scholarship, and Creative Activities Materials

The student abstract booklet is a compilation of abstracts from students' oral and poster presentations at Wright State University's second annual Celebration of Research, Scholarship and Creative Activities on April 8, 2011.

Role Of The 3'Lghrr In Tcdd-Induced Suppression Of The Immunoglobulin Heavy Chain, Jayharsh L. Panchal, Eric J. Romer, David Ellis, Tharu Fernando, Courtney E. W. Sulentic

Celebration of Undergraduate & Graduate Research, Scholarship, and Creative Activities Materials

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) inhibits antibody secretion and immunoglobulin heavy chain (IgH) expression. Our previous work has shown that a possible mechanism for inhibition of IgH expression could be inhibition of the 3’IgH regulatory region (3’IgHRR). The 3’IgHRR has four enhancer regions (hs3a; hs1,2; hs3b; hs4) which are purported to control IgH gene expression. Previously we demonstrated a sensitive inhibition by TCDD of LPS-induced 3’IgHRR activity which is correlated with an inhibition of LPS-induced hs1,2 enhancer activity; however, the hs4 enhancer showed TCDD-induced activation following the co-treatment of TCDD and LPS. Therefore, the objective of the current study was to determine if …

Identifying And Implementing The Underlying Operators For Nuclear Magnetic Resonance Based Metabolomics Data Analysis, Ashwin Manjunatha, Ajith H. Ranabahu, Paul E. Anderson, Amit P. Sheth

Kno.e.sis Publications

The science of metabolomics is a relatively young field that requires intensive signal processing and multivariate data analysis for interpretation of experimental results. The lack of integration and standardization for metabolomics compounded by the complexity of the experimental data has lead to a fragmented research community. While efforts have been undertaken to approach these problems, the efforts to develop a set of standards for reporting processing and analysis procedures has stalled.

In this paper, we propose a set of fundamental operators for nuclear magnetic resonance(NMR) based metabolomics. These operators are implementation independent, and can be used to easily and precisely …

Performance And Reproduction Of An Exotic Invader Across Temperate Forest Gradients, Robert J. Warren Ii, Volker Bahn, Timothy D. Kramer, Yaya Tang, Mark A. Bradford

Biological Sciences Faculty Publications

Widespread colonization by invasive species often obscures their underlying niche requirements. A robust inference into habitat requirements demands direct measures of invasive species performance linked with associated environmental conditions. In the context of general ecological theory, we investigated the niche requirements of Microstegium vimineum, an invasive grass in the U.S. that overruns native vegetation in forest understories. We examined M. vimineum’s performance and reproduction as a function of environmental drivers across forested and unforested habitats along a 100-km regional and climatic gradient in the southeastern U.S. from the southern Appalachian Mountains to the Georgia piedmont. We then measured M. vimineum …

Unsupplemented Artemia Diet Results In Reduced Growth And Jaw Dysmorphogenesis In Zebrafish, Michael P. Craig, Mitul B. Desai, Kate E. Olukalns, Scott E. Afton, Joseph A. Caruso, Jay R. Hove

Biochemistry and Molecular Biology Faculty Publications

The number of laboratories using zebrafish as an experimental animal model has risen tremendously over the past two decades (Craig et al., 2006). As a result, the number of zebrafish facilities around the world has dramatically increased to meet the elevated demand for proper animal care and maintenance. In order to meet this demand, aquaculture facilities must employ husbandry protocols designed to produce a constant supply of healthy, viable eggs. Surprisingly, many husbandry strategies, particularly feeding protocols, are frequently passed down from members of one lab to another in a colloquial fashion without rigorous experimental validation. An ideal diet should …

A Genetic Optimization Approach For Isolating Translational Efficiency Bias, Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

The study of codon usage bias is an important research area that contributes to our understanding of molecular evolution, phylogenetic relationships, respiratory lifestyle, and other characteristics. Translational efficiency bias is perhaps the most well studied codon usage bias, as it is frequently utilized to predict relative protein expression levels. We present a novel approach to isolating translational efficiency bias in microbial genomes. There are several existent methods for isolating translational efficiency bias. Previous approaches are susceptible to the confounding influences of other potentially dominant biases. Additionally, existing approaches to identifying translational efficiency bias generally require both genomic sequence information and …

A Systematic Property Mapping Using Category Hierarchy And Data, Kalpa Gunaratna, Sarasi Lalithsena, Prateek Jain, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

Relationships play a key role in Semantic Web to connect the dots between entities (concepts or instances in a way that enables to absorb the real sense of the entities. Even though relationships are important, it is difficult to categorize or identify them because they consist of complex knowledge in the schema. Therefore systematically identifying relationships yield many advantages and open doors for new research avenues. In this work, we try to identify a specific type of relationship (part of) in a multi-domain dataset and devised an algorithm using Wikipedia to identify patterns of part of relationships in the dataset. …

Utilization Of A Custom-Designed Microbiota Array To Determine The Distal Gut Microbiota Of Healthy Human Adults, Richard Thomas Agans

Browse all Theses and Dissertations

The human microbiota is an essential component of human health and disease. It is involved in metabolism of dietary components and is at the forefront of the intestinal immune response. Classical techniques applied to study intestinal microbiota illustrated higher presences of aerobic and facultative-anaerobic bacteria, however; the levels of obligate anaerobes had been underrepresented. Modern technologies based on DNA and RNA analysis have circumvented previous challenges allowing researchers to gain more extensive insight into the complex intestinal environment. In this work, a recently developed Microbiota Array was used to assess intestinal microbiota of 10 healthy adults (age 22-61, ave. 34.3yrs). …

Cloudvista: Visual Cluster Exploration For Extreme Scale Data In The Could, Keke Chen, Huiqi Xi, Fengguang Tian, Shumin Guo

Kno.e.sis Publications

The problem of efficient and high-quality clustering of extreme scale datasets with complex clustering structures continues to be one of the most challenging data analysis problems. An innovate use of data cloud would provide unique opportunity to address this challenge. In this paper, we propose the CloudVista framework to address (1) the problems caused by using sampling in the existing approaches and (2) the problems with the latency caused by cloud-side processing on interactive cluster visualization. The CloudVista framework aims to explore the entire large data stored in the cloud with the help of the data structure visual frame and …

Analysis On Partial Relationship In Lod, Kalpa Gunaratna, Sarasi Lalithsena, Cory Andrew Henson, Prateek Jain

Kno.e.sis Publications

Relationships play a key role in Semantic Web to connect the dots between entities (concepts or instances) in a way that enables to absorb the real sense of the entities. Some interesting relationships would give proof for the existence of subject and object in triples which in tern can be defined as evidential relationships. Identifying evidential relationships will yield solutions to some existing inference problems and open doors for new applications and research. Part_of relationships are identified as a special kind of an evidential relationship out of membership, causality and etc. Linked Open data as a global data space would …

Contextual Ontology Alignment Of Lod With An Upper Ontology: A Case Study With Proton, Prateek Jain, Peter Z. Yeh, Kunal Verma, Reymonrod G. Vasquez, Mariana Darnorva, Pascal Hitzler, Amit P. Sheth

Kno.e.sis Publications

The Linked Open Data (LOD) is a major milestone towards realizing the Semantic Web vision, and can enable applications such as robust Question Answering (QA) systems that can answer queries requiring multiple, disparate information sources. However, realizing these applications requires relationships at both the schema and instance level, but currently the LOD only provides relationships for the latter. To address this limitation, we present a solution for automatically finding schema-level links between two LOD ontologies – in the sense of ontology alignment. Our solution, called BLOOMS+, extends our previous solution (i.e. BLOOMS) in two significant ways. BLOOMS+ 1) uses a …

Reconciling Owl And Rules, David Carral Martinez, Adila A. Krisnadhi, Frederick Maier, Kunal Sengupta, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We report on a recent advance in integrating Rules and OWL. We discuss a recent proposal, known as nominal schemas, which realizes a seamless integration of Datalog rules into the description logic SROIQ which underlies OWL 2 DL. We present extensions of the standardized OWL syntaxes to incorporate nominal schemas, reasoning algorithms, and a first naive implementation. And we argue why this approach goes a long way towards overcoming the present paradigm split.

Privacy-Aware An Scalable Content Dissemination In Distributed Social Networks, Pavan Kapanipathi, Julia Anaya, Amit P. Sheth, Brett Slatkin, Alexandre Passant

Kno.e.sis Publications

Centralized social networking websites raise scalability issues - due to the growing number of participants - and, as well as, policy concerns - such as control, privacy and ownership over the user's published data. Distributed Social Networks aim to solve this issue by enabling architecture where people own their data and share it their own way. However, the privacy and scalability challenge is still to be tackled. This paper presents a privacy-aware extension to Google's PubSubHubbub protocol, using Semantic Web technologies, solving both the scalability and the privacy issues in Distributed Social Networks. We enhanced the traditional feature of PubSubHubbub …

Semantic Social Mashup Approach For Designing Citizen Diplomacy, Amit P. Sheth

Kno.e.sis Publications

Advancement in technology has brought exceptional connectivity, easy and open access to communication mediums via Internet. Everyday millions of people are interactively communicating to each other and sharing multimedia content through Social Media/Networks, Web-based and mobile-based technologies. Social media provides variety of interesting, engaging applications such as Twitter, Facebook, YouTube, Flicker, Blogs. People interested in contributing to global welfare and improving humanity are connected to various NGO's like Red Cross, Ushahidi (www.ushahidi.com), eMoksha (emoksha.org), etc. Social media and NGOs are acting as an excellent medium of communication and sharing, connected diverse people irrespective of their nationality, religion, culture, etc. Social …

Effects Of Xs® Energy Drink On Aerobic Exercise Capacity Of Athletes, Kevin M. Sheehan, Lynn K. Hartzler

Biological Sciences Faculty Publications

A small increase in performance is often the difference between winning and losing for athletes, and energy supplements are marketed to give them a competitive edge. One such supplement is XS® Energy Drink which contains B vitamins, caffeine, taurine, and an herbal adaptogen blend. XS® Energy Drink is primarily designed and marketed as an alertness stimulus; however, it is also marketed to athletes as a performance enhancing supplement. The hypothesis of this investigation was that the consumption of XS® Energy Drink before exercise would increase aerobic capacity (an increase in Vo2max) and time to fatigue, and would decrease time for …

Citizen Sensor Data Mining, Social Media Analytics And Development Centric Web Applications, Meenakshi Nagarajan, Amit P. Sheth, Selvam Velmuru

Kno.e.sis Publications

With the rapid rise in the popularity of social media (500M+ Facebook users, 100M+ twitter users), and near ubiquitous mobile access (4.1 billion actively-used mobile phones), the sharing of observations and opinions has become common-place (nearly 100M tweets a day, 1.8 trillion SMSs in US last year). This has given us an unprecedented access to the pulse of a populace and the ability to perform analytics on social data to support a variety of socially intelligent applications -- be it towards targeted online content delivery, crisis management, organizing revolutions or promoting social development in underdeveloped and developing countries. This tutorial …