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Wright State University

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Articles 1741 - 1770 of 1987

Full-Text Articles in Life Sciences

An Investigation Of Codon Usage Bias Including Visualization And Quantification In Organisms Exhibiting Multiple Biases, Douglas W. Raiford, Travis E. Doom, Dan E. Krane, Michael L. Raymer Jan 2006

An Investigation Of Codon Usage Bias Including Visualization And Quantification In Organisms Exhibiting Multiple Biases, Douglas W. Raiford, Travis E. Doom, Dan E. Krane, Michael L. Raymer

Kno.e.sis Publications

Prokaryotic genomic sequence data provides a rich resource for bioinformatic analytic algorithms. Information can be extracted in many ways from the sequence data. One often overlooked process involves investigating an organism’s codon usage. Degeneracy in the genetic code leads to multiple codons coding for the same amino acids. Organism’s often preferentially utilize specific codons when coding for an amino acid. This biased codon usage can be a useful trait when predicting a gene’s expressivity or whether the gene originated from horizontal transfer. There can be multiple biases at play in a genome causing errors in the predictive process. For this …

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A Semantic Future For Ai, Rudi Studer, Anupriya Ankolekar, Pascal Hitzler Jan 2006

A Semantic Future For Ai, Rudi Studer, Anupriya Ankolekar, Pascal Hitzler

Computer Science and Engineering Faculty Publications

In our modern information society, people need to manage ever-increasing numbers of personal devices and conduct more of their work and activities online, often making use of heterogeneous services. The amount of information to be processed by each individual is constantly growing, making it increasingly difficult to control, channel, share and make constructive use of it. To mitigate this, computing needs to become much more human-centered, e.g. by presenting personalised information to users and by respecting personal preferences in controlling multiple devices or invoking various services. Appropriate representation of the semantics of the information and functionality of devices and services …

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Predicting Domain Specific Entities With Limited Background Knowledge, Christopher Thomas, Amit P. Sheth Jan 2006

Predicting Domain Specific Entities With Limited Background Knowledge, Christopher Thomas, Amit P. Sheth

Kno.e.sis Publications

This paper proposes a framework for automatic recognition of domain-specific entities from text, given limited background knowledge, e.g. in form of an ontology. The algorithm exploits several lightweight natural language processing techniques, such as tokenization and stemming, as well as statistical techniques, such as singular value decomposition (SVD) to suggest domain relatedness of unknown entities.

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Using Query-Specific Variance Estimates To Combine Bayesian Classifiers, Chi-Hoon Lee, Russell Greiner, Shaojun Wang Jan 2006

Using Query-Specific Variance Estimates To Combine Bayesian Classifiers, Chi-Hoon Lee, Russell Greiner, Shaojun Wang

Kno.e.sis Publications

Many of today's best classification results are obtained by combining the responses of a set of base classifiers to produce an answer for the query. This paper explores a novel "query specific" combination rule: After learning a set of simple belief network classifiers, we produce an answer to each query by combining their individual responses, using weights based inversely on their respective variances around their responses. These variances are based on the uncertainty of the network parameters, which in turn depend on the training datasample. In essence, this variance quantifies the base classifier's confidence of its response to this query. …

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Clustering Similarity Comparison Using Density Profiles, Eric Bae, James Bailey, Guozhu Dong Jan 2006

Clustering Similarity Comparison Using Density Profiles, Eric Bae, James Bailey, Guozhu Dong

Kno.e.sis Publications

The unsupervised nature of cluster analysis means that objects can be clustered in many ways, allowing different clustering algorithms to generate vastly different results. To address this, clustering comparison methods have traditionally been used to quantify the degree of similarity between alternative clusterings. However, existing techniques utilize only the point memberships to calculate the similarity, which can lead to unintuitive results. They also cannot be applied to analyze clusterings which only partially share points, which can be the case in stream clustering. In this paper we introduce a new measure named ADCO, which takes into account density profiles for each …

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An Online Discriminative Approach To Background Subtraction, Li Cheng, Shaojun Wang, Terry Caelli Jan 2006

An Online Discriminative Approach To Background Subtraction, Li Cheng, Shaojun Wang, Terry Caelli

Kno.e.sis Publications

We present a simple, principled approach to detecting foreground objects in video sequences in real-time. Our method is based on an on-line discriminative learning technique that is able to cope with illumination changes due to discontinuous switching, or illumination drifts caused by slower processes such as varying time of the day. Starting from a discriminative learning principle, we derive a training algorithm that, for each pixel, computes a weighted linear combination of selected past observations with time-decay. We present experimental results that show the proposed approach outperforms existing methods on both synthetic sequences and real video data.

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Driving Deep Semantics In Middleware And Networks: What, Why And How?, Amit P. Sheth Jan 2006

Driving Deep Semantics In Middleware And Networks: What, Why And How?, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

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Knowledge Modeling And Its Application In Life Sciences: A Tale Of Two Ontologies, Satya S. Sahoo, Christopher Thomas, Amit P. Sheth, William S. York, Samir Tartir Jan 2006

Knowledge Modeling And Its Application In Life Sciences: A Tale Of Two Ontologies, Satya S. Sahoo, Christopher Thomas, Amit P. Sheth, William S. York, Samir Tartir

Kno.e.sis Publications

High throughput glycoproteomics, similar to genomics and proteomics, involves extremely large volumes of distributed, heterogeneous data as a basis for identification and quantification of a structurally diverse collection of biomolecules. The ability to share, compare, query for and most critically correlate datasets using the native biological relationships are some of the challenges being faced by glycobiology researchers. As a solution for these challenges, we are building a semantic structure, using a suite of ontologies, which supports management of data and information at each step of the experimental lifecycle. This framework will enable researchers to leverage the large scale of glycoproteomics …

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Show Me What You Mean! Exploiting Domain Semantics In Ontology Visualization, Ravi Pavagada, Christopher Thomas, Amit P. Sheth, William S. York Jan 2006

Show Me What You Mean! Exploiting Domain Semantics In Ontology Visualization, Ravi Pavagada, Christopher Thomas, Amit P. Sheth, William S. York

Kno.e.sis Publications

Ontologies build the backbone for many life-sciences applications. These ontologies, however, are represented in XML based languages that are meant for machine-consumption and hence are difficult for humans to comprehend. For a meaningful visualization of these ontologies, it is important that the display of entities and relationships captures the cognitive representation of the domain as perceived by the domain experts. In this paper we present OntoVista, an ontology visualization tool that is adaptable to the needs of different domains, especially in the life sciences. While keeping the graph structures as the predominant model, we provide a semantically enhanced graph display …

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In Vitro Toxicity Assessment Of Silver Nanoparticles In Rat Alveolar Macrophages, Cataleya Carlson Jan 2006

In Vitro Toxicity Assessment Of Silver Nanoparticles In Rat Alveolar Macrophages, Cataleya Carlson

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The present study was conducted to assess the toxicity of nanosized silver particles (Ag-15nm, 30nm and 55nm) in rat alveolar macrophages. For toxicity evaluations, cellular morphology, mitochondrial function (MTT assay), membrane leakage (LDH assay) and reactive oxygen species generation (ROS) were assessed after a 24h under control and exposed conditions. The morphological appearance of control and exposed cells were observed by an inverted, phase contrast microscope and the uptake of nanoparticles was observed using the CytoViva Ultra Resolution Imaging (URI) system. Morphological images captured at 100x magnification demonstrated that nanoparticle-exposed cells at higher doses became abnormal in size, and most …

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Susceptibility Of Primary Eosinophils To Infection With Hiv-1 Strain Htlv-Iiib, Jai Govind Marathe Jan 2006

Susceptibility Of Primary Eosinophils To Infection With Hiv-1 Strain Htlv-Iiib, Jai Govind Marathe

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Over the past two decades, much research has been done in the field of human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS). However, many of the aspects of pathogenesis of HIV infection and its persistence in the body, despite treatment, remain a mystery. Recent evidence suggests that HIV positive patients develop eosinophilia, especially in the later stages of infection and AIDS. Eosinophils are CD4 positive cells that have the potential to be infected by HIV. Studies have shown that an eosinophilic cell line, AML14.3D10, can be productively infected with a T-cell tropic, CXCR4-using (X4) strain of HIV-1. In this …

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Phenotypic Characterization Of Escherichia Coli Strains Taken From Human Intestinal And Urinary Tracts, Kruthi Murthy Jan 2006

Phenotypic Characterization Of Escherichia Coli Strains Taken From Human Intestinal And Urinary Tracts, Kruthi Murthy

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Escherichia coli (E. coli) is a gram negative bacterium commonly found as a commensal in the intestinal tract of humans and other warm blooded animals. The commensal strains of E. coli are non-pathogenic and do not cause an infection in the host. However, some strains of E. coli are pathogenic and can cause several diseases in humans that include neonatal meningitis, intestinal infections and urinary tract infections. Almost 80-85% of the uncomplicated urinary tract infections are caused by uropathogenic E. coli. Our project involved the characterization of 12 strains of E. coli, isolated from humans in health and disease. These …

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Coronary Heart Disease Risk Stratification In Full-Time Miami Valley Hospital Employees, Vicki K. Streng Jan 2006

Coronary Heart Disease Risk Stratification In Full-Time Miami Valley Hospital Employees, Vicki K. Streng

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Heart disease is the number one killer in the United States (American Heart Association, 2005). The purpose of this study was to demonstrate the results of a twelve-week exercise program on coronary heart disease risk factors in full-time hospital employees. Methods: The participants were given cardiovascular, weight training, and flexibility recommendations to follow during a twelve-week period. The main heart disease risk factors measured before and after the completion of the exercise program were blood pressure, total cholesterol, HDL-cholesterol, and body mass index. The information was put into the Framingham Heart Score to estimate the participants’ 10-year risk of developing …

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Determining The Effect Of Substitutions At Alanine 47 In Synechococcus Pcc6301 Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco), Christopher R. Salyer Jan 2006

Determining The Effect Of Substitutions At Alanine 47 In Synechococcus Pcc6301 Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco), Christopher R. Salyer

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Mutant screening and genetic selection in various organisms have shown that residues far from the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) can influence catalytic efficiency and CO2/O2 specificity. Because RubisCO catalyzes the rate-limiting step of photosynthesis, further study of these sites distant from the primary reaction center may provide the necessary information for engineering an increase in primary productivity of crop plants. In a previously described system of random mutagenesis and bioselection (Smith, 2002), the RubisCO genes from the cyanobacterium Synechococcus PCC6301, were randomly mutated and introduced into the photosynthetic bacterium Rhodobacter capsulatus. An A47T substitution resulted in a very …

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Kinetics And Passive Protection Efficacy Induced By Purified Ava Human Immunoglobulin G In Rabbits Against A Bacillus Anthracis Aerosol Challenge, Jennifer Lee Plahovinsak Jan 2006

Kinetics And Passive Protection Efficacy Induced By Purified Ava Human Immunoglobulin G In Rabbits Against A Bacillus Anthracis Aerosol Challenge, Jennifer Lee Plahovinsak

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The present study was conducted to determine the half-life, assess the toxicity, and passive protection efficacy of purified immunoglobulin G (IgG) from Anthrax Vaccine Adsorbed (AVA) vaccinated human donors. Half-life determinations were calculated from the reportable values obtained using the anti-PA ELISA assay and the Centers for Disease Control's (CDC) "ELISA for Windows" software. For toxicity evaluations animals were observed clinical for one hour post administration and for 14-days post-treatment. The protection efficacy was determined based upon the mortality results from a lethal Bacillus anthracis aerosol challenge. While no protection was achieved in this delayed exposure scenario, the study yielded …

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Openws-Transaction: Enabling Reliable Web Service Transactions, Ivan Vasquez, John A. Miller, Kunal Verma, Amit P. Sheth Dec 2005

Openws-Transaction: Enabling Reliable Web Service Transactions, Ivan Vasquez, John A. Miller, Kunal Verma, Amit P. Sheth

Kno.e.sis Publications

OpenWS-Transaction is an open source middleware that enables Web services to participate in a distributed transaction as prescribed by the WS-Coordination and WS-Transaction set of specifications. Central to the framework are the Coordinator and Participant entities, which can be integrated into existing services by introducing minimal changes to application code. OpenWS-Transaction allows transaction members to recover their original state in case of operational failure by leveraging techniques in logical logging and recovery at the application level. Depending on transaction style, system recovery may involve restoring key application variables and replaying uncommitted database activity. Transactions are assumed to be defined in …

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Demonstrating Dynamic Configuration And Execution Of Web Processes, Karthik Gomadam, Kunal Verma, Amit P. Sheth, John A. Miller Dec 2005

Demonstrating Dynamic Configuration And Execution Of Web Processes, Karthik Gomadam, Kunal Verma, Amit P. Sheth, John A. Miller

Kno.e.sis Publications

Web processes are next generation workflows on the web, created using Web services. In this paper we demonstrate the METEOR-S Configuration and Execution Environment (MCEE) system. It will illustrate the capabilities of the system to a) Discover partners b) Optimize partner selection using constraint analysis, c) Perform interaction protocol and data mediation. A graphical execution monitor to monitor the various phases of execution will be used to demonstrate various aspects of the system.

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Discovering Informative Connection Subgraphs In Multi-Relational Graphs, Cartic Ramakrishnan, William Milnor, Matthew Perry, Amit P. Sheth Dec 2005

Discovering Informative Connection Subgraphs In Multi-Relational Graphs, Cartic Ramakrishnan, William Milnor, Matthew Perry, Amit P. Sheth

Kno.e.sis Publications

Discovering patterns in graphs has long been an area of interest. In most approaches to such pattern discovery either quantitative anomalies, frequency of substructure or maximum flow is used to measure the interestingness of a pattern. In this paper we introduce heuristics that guide a subgraph discovery algorithm away from banal paths towards more "informative" ones. Given an RDF graph a user might pose a question of the form: "What are the most relevant ways in which entity X is related to entity Y?" the response to which is a subgraph connecting X to Y. We use our heuristics to …

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Ontoqa: Metric-Based Ontology Quality Analysis, Samir Tartir, I. Budak Arpinar, Michael Moore, Amit P. Sheth, Boanerges Aleman-Meza Nov 2005

Ontoqa: Metric-Based Ontology Quality Analysis, Samir Tartir, I. Budak Arpinar, Michael Moore, Amit P. Sheth, Boanerges Aleman-Meza

Kno.e.sis Publications

As the Semantic Web gains importance for sharing knowledge on the Internet this has lead to the development and publishing of many ontologies in different domains. When trying to reuse existing ontologies into their applications, users are faced with the problem of determining if an ontology is suitable for their needs. In this paper, we introduce OntoQA, an approach that analyzes ontology schemas and their populations (i.e. knowledgebases) and describes them through a well defined set of metrics. These metrics can highlight key characteristics of an ontology schema as well as its population and enable users to make an informed …

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Semantics For Scientific Experiments And The Web: The Implicit, The Formal And The Powerful, Amit P. Sheth Nov 2005

Semantics For Scientific Experiments And The Web: The Implicit, The Formal And The Powerful, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

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Optimal Adaptation In Autonomic Web Processes With Inter-Service Dependencies, Kunal Verma, Prashant Doshi, Karthik Gomadam, John A. Miller, Amit P. Sheth Nov 2005

Optimal Adaptation In Autonomic Web Processes With Inter-Service Dependencies, Kunal Verma, Prashant Doshi, Karthik Gomadam, John A. Miller, Amit P. Sheth

Kno.e.sis Publications

We present methods for optimally adapting Web processes to exogenous events while preserving inter-service dependencies. For example, in a supply chain process, orders placed by the manufacturer may get delayed in arriving. In response to this event, the manufacturer has the choice of either waiting out the delay or changing the supplier.

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Dlp Isn't So Bad After All, Peter Haase, Markus Krotzsch, York Sure, Rudi Studer, Pascal Hitzler Nov 2005

Dlp Isn't So Bad After All, Peter Haase, Markus Krotzsch, York Sure, Rudi Studer, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We discuss some of the recent controversies concerning the DLP fragment of OWL. We argue that it is a meaningful fragment and can serve as a basic interoperability layer between OWL and logic programming-based ontology languages.

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Modeling Fuzzy Rules With Description Logics, Sudhir Agarwal, Pascal Hitzler Nov 2005

Modeling Fuzzy Rules With Description Logics, Sudhir Agarwal, Pascal Hitzler

Computer Science and Engineering Faculty Publications

In real application scenarios, input data and knowledge is often vague. Likewise, it is often the case that exact reasoning over data is impossible due to complex dependencies between input data and target outputs. For practical applications, however, good approximations often suffice, and efficient calculation of an approximate answer is often preferable over complex processing which may take a long time to come up with an exact answer. Fuzzy logic supports both features by providing fuzzy membership functions and fuzzy IF-THEN rule bases. In this paper, we show how fuzzy membership functions and fuzzy rules can be modeled by means …

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Computing For Human Experience And Wellness, Amit P. Sheth Oct 2005

Computing For Human Experience And Wellness, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

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Work In Progress: The Wsu Model For Engineering Mathematics Education, Nathan W. Klingbeil, Richard Mercer, Kuldip S. Rattan, Michael L. Raymer, David B. Reynolds Oct 2005

Work In Progress: The Wsu Model For Engineering Mathematics Education, Nathan W. Klingbeil, Richard Mercer, Kuldip S. Rattan, Michael L. Raymer, David B. Reynolds

Kno.e.sis Publications

This paper summarizes progress to date on the WSU model for engineering mathematics education, an NSF funded curriculum reform initiative at Wright State University. The WSU model seeks to increase student retention, motivation and success in engineering through application-driven, just-in-time engineering math instruction. The WSU approach involves the development of a novel freshman-level engineering mathematics course EGR 101, as well as a large-scale restructuring of the engineering curriculum. By removing traditional math prerequisites and moving core engineering courses earlier in the program, the WSU model shifts the traditional emphasis on math prerequisite requirements to an emphasis on engineering motivation for …

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Ga-Facilitated Knn Classifier Optimization With Varying Similarity Measures, Michael R. Peterson, Travis E. Doom, Michael L. Raymer Sep 2005

Ga-Facilitated Knn Classifier Optimization With Varying Similarity Measures, Michael R. Peterson, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

Genetic algorithms are powerful tools for k-nearest neighbors classifier optimization. While traditional knn classification techniques typically employ Euclidian distance to assess pattern similarity, other measures may also be utilized. Previous research demonstrates that GAs can improve predictive accuracy by searching for optimal feature weights and offsets for a cosine similarity-based knn classifier. GA-selected weights determine the classification relevance of each feature, while offsets provide alternative points of reference when assessing angular similarity. Such optimized classifiers perform competitively with other contemporary classification techniques. This paper explores the effectiveness of GA weight and offset optimization for knowledge discovery using knn classifiers with …

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Enterprise Applications Of Semantic Web: The Sweet Spot Of Risk And Compliance, Amit P. Sheth Aug 2005

Enterprise Applications Of Semantic Web: The Sweet Spot Of Risk And Compliance, Amit P. Sheth

Kno.e.sis Publications

Semantic Web is in the transition from vision and research to reality. In this early state, it is important to study the technical capabilities in the context of real-world applications, and how applications built using the Semantic Web technology meet the real market needs. Beyond push from research, it is the market pull and the ability of the technology to meet real business needs that is a key to ultimate success of any technology. In this paper, we discuss the market of Risk and Compliance which presents unique market opportunity combined with challenging technical requirements. We discuss how the Semantic …

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Ontology Learning As A Use-Case For Neural-Symbolic Integration, Pascal Hitzler, Sebastian Bader, Artur Garcez Aug 2005

Ontology Learning As A Use-Case For Neural-Symbolic Integration, Pascal Hitzler, Sebastian Bader, Artur Garcez

Computer Science and Engineering Faculty Publications

We argue that the field of neural-symbolic integration is in need of identifying application scenarios for guiding further research. We furthermore argue that ontology learning - as occurring in the context of semantic technologies - provides such an application scenario with potential for success and high impact on neural-symbolic integration.

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Implications Of Spatial Autocorrelation And Dispersal For The Modeling Of Species Distributions, Volker Bahn Aug 2005

Implications Of Spatial Autocorrelation And Dispersal For The Modeling Of Species Distributions, Volker Bahn

Biological Sciences Faculty Publications

Modeling the geographical distributions of wildlife species is important for ecology and conservation biology. Spatial autocorrelation in species distributions poses a problem for distribution modeling because it invalidates the assumption of independence among sample locations. I explored the prevalence and causes of spatial autocorrelation in data from the Breeding Bird Survey, covering the conterminous United States, using Regression Trees, Conditional Autoregressive Regressions (CAR), and the partitioning of variance. I also constructed a simulation model to investigate dispersal as a process contributing to spatial autocorrelation, and attempted to verify the connection between dispersal and spatial autocorrelation in species’ distributions in empirical …

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Integrating First-Order Logic Programs And Connectionist Systems - A Constructive Approach, Sebastian Bader, Andreas Witzel, Pascal Hitzler Aug 2005

Integrating First-Order Logic Programs And Connectionist Systems - A Constructive Approach, Sebastian Bader, Andreas Witzel, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Significant advances have recently been made concerning the integration of symbolic knowledge representation with artificial neural networks (also called connectionist systems). However, while the integration with propositional paradigms has resulted in applicable systems, the case of first-order knowledge representation has so far hardly proceeded beyond theoretical studies which prove the existence of connectionist systems for approximating first-order logic programs up to any chosen precision. Advances were hindered severely by the lack of concrete algorithms for obtaining the approximating networks which were known to exist: the corresponding proofs are not constructive in that they do not yield concrete methods for building …

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