Life Sciences Commons^™

Spatial Semantics For Better Interoperability And Analysis: Challenges And Experiences In Building Semantically Rich Applications In Web 3.0, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

A Microrna Target Prediction Algorithm, Rupinder Singh

Master's Projects

MicroRNA target prediction using the experimental methods is a challenging task. To accelerate the process of miRNA target validation, many computational methods are used. Computational methods yield many potential candidates for experimental validation. This project is about developing a new computational method using dynamic programming to predict miRNA targets with more accuracy. The project discusses the currently available computational methods and develops a new algorithm using the currently available knowledge about miRNA interactions.

Appearance Based Stage Recognition Of Drosophila Embryos, Gopi Chand Nutakki

Masters Theses & Specialist Projects

Stages in Drosophila development denote the time after fertilization at which certain specific events occur in the developmental cycle. Stage information of a host embryo, as well as spatial information of a gene expression region is indispensable input for the discovery of the pattern of gene-gene interaction. Manual labeling of stages is becoming a bottleneck under the circumstance of high throughput embryo images. Automatic recognition based on the appearances of embryos is becoming a more desirable scheme. This problem, however, is very challenging due to severe variations of illumination and gene expressions. In this research thesis, we propose an appearance …

Closing The Gap Between The Industry And Higher Education Institutions- Case Examples From East African Region, Deogratias Harorimana Mr

Dr Deogratias Harorimana

Much complained about is the quality of graduates Universities put on the labour market. Less talked about however is why knowledge institutions seems to be bad knowledge managers. In this presentation I argue that DIRECT collaborative relationship between Industry,Governments and Higher Education Institutions is a per-requisite.Good relationship is key to building such a successful knowledge transfer strategies between Industries and Educational and Research Institutions. This paper explores what makes a good Knowledge Transfer Partnership Strategy and highlights some key lessons for businesses, Universities and Government bodies. This paper was a Key note presentation to the Annual International Conference on Building …

Flexible Bootstrapping-Based Ontology Alignment, Prateek Jain, Pascal Hitzler, Amit P. Sheth

Kno.e.sis Publications

BLOOMS (Jain et al, ISWC2010) is an ontology alignment system which, in its core, utilizes the Wikipedia category hierarchy for establishing alignments. In this paper, we present a Plug-and-Play extension to BLOOMS, which allows to flexibly replace or complement the use of Wikipedia by other online or offline resources, including domain-specific ontologies or taxonomies. By making use of automated translation services and of Wikipedia in languages other than English, it makes it possible to apply BLOOMS to alignment tasks where the input ontologies are written in different languages.

The Mycobacterium Tuberculosis Drugome And Its Polypharmacological Implications, Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Phillip E. Bourne

Publications and Research

We report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. The approach has been applied to the genome of Mycobacterium tuberculosis (M.tb), the causative agent of one of today’s most widely spread infectious diseases. The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’. The TB-drugome reveals that approximately one-third of the drugs examined have the potential to be repositioned to treat tuberculosis and that many currently unexploited M.tb receptors may be chemically druggable …

A Novel Totivirus And Piscine Reovirus (Prv) In Atlantic Salmon (Salmo Salar) With Cardiomyopathy Syndrome (Cms), Torstein Tengs

Dr. Torstein Tengs

BACKGROUNDCardiomyopathy syndrome (CMS) is a severe disease affecting large farmed Atlantic salmon. Mortality often appears without prior clinical signs, typically shortly prior to slaughter. We recently reported the finding and the complete genomic sequence of a novel piscine reovirus (PRV), which is associated with another cardiac disease in Atlantic salmon; heart and skeletal muscle inflammation (HSMI). In the present work we have studied whether PRV or other infectious agents may be involved in the etiology of CMS.RESULTSUsing high throughput sequencing on heart samples from natural outbreaks of CMS and from fish experimentally challenged with material from fish diagnosed with CMS …

Ontology Alignment For Linked Open Data, Prateek Jain, Pascal Hitzler, Amit P. Sheth, Kunal Verma, Peter Z. Yeh

Kno.e.sis Publications

The Web of Data currently coming into existence through the Linked Open Data (LOD) effort is a major milestone in realizing the Semantic Web vision. However, the development of applications based on LOD faces difficulties due to the fact that the different LOD datasets are rather loosely connected pieces of information. In particular, links between LOD datasets are almost exclusively on the level of instances, and schema-level information is being ignored. In this paper, we therefore present a system for finding schema-level links between LOD datasets in the sense of ontology alignment. Our system, called BLOOMS, is based on the …

(1e,3e)-1,4-Bis(4-Methoxyphenyl)Buta1,3-Diene, Gopinathan Narayan, Nigam Rath, Suresh Das

Chemistry & Biochemistry Faculty Works

The title compound, C18H18O2, which exhibits blue emission in the solid state, is an inter­mediate in the preparation of liquid crystals and polymers. The mol­ecule is located on an inversion centre. In the crystal, mol­ecules are arranged in a herringbone motif.

(1e,3e)-1,4-Bis(4-Methoxyphenyl)Buta1,3-Diene, Gopinathan Narayan, Nigam P. Rath, Suresh Das

Nigam Rath

Impact Of Interdisciplinary Undergraduate Research In Mathematics And Biology On The Development Of A New Course Integrating Five Stem Disciplines, Lester Caudill, April L. Hill, Kathy Hoke, Ovidiu Z. Lipan

Biology Faculty Publications

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a …

Impact Of Interdisciplinary Undergraduate Research In Mathematics And Biology On The Development Of A New Course Integrating Five Stem Disciplines, Lester Caudill, April L. Hill, Kathy Hoke, Ovidiu Z. Lipan

Department of Math & Statistics Faculty Publications

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a …

Drug Off-Target Effects Predicted Using Structural Analysis In The Context Of A Metabolic Network Model, Roger L. Chang, Lei Xie, Philip E. Bourne, Bernhard O. Palsson

Publications and Research

Recent advances in structural bioinformatics have enabled the prediction of protein-drug off-targets based on their ligand binding sites. Concurrent developments in systems biology allow for prediction of the functional effects of system perturbations using large-scale network models. Integration of these two capabilities provides a framework for evaluating metabolic drug response phenotypes in silico. This combined approach was applied to investigate the hypertensive side effect of the cholesteryl ester transfer protein inhibitor torcetrapib in the context of human renal function. A metabolic kidney model was generated in which to simulate drug treatment. Causal drug off-targets were predicted that have previously been …

2,2′,5,5′-Tetra­Chloro­Benzidine, Onome Ugono, Marcel Douglas, Nigam Rath, Alicia Beatty

Chemistry & Biochemistry Faculty Works

In the crystal structure of the title compound, C12H8Cl4N2, mol­ecules lie on crystallographic twofold axes at the centre of the C-C bonds linking the benzene rings, such that the asymmetric unit consists of a half-mol­ecule. The individual mol­ecules participate in inter­molecular N-H...N, N-H...Cl, C-H...Cl and Cl...Cl [3.4503 (3) Å] inter­actions.

2,2′,5,5′-Tetra­Chloro­Benzidine, Onome Ugono, Marcel Douglas, Nigam P. Rath, Alicia M. Beatty

Nigam Rath

2,2′,5,5′-Tetra­Chloro­Benzidine, Onome Ugono, Marcel Douglas, Nigam P. Rath, Alicia M. Beatty

Alicia Beatty

Bioinformatics Across The Sciences, Nigel Yarlett

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

A Taxonomy-Based Model For Expertise Extrapolation, Delroy H. Cameron, Boanerges Aleman-Meza, Ismailcem Budak Arpinar, Sheron L. Decker, Amit P. Sheth

Kno.e.sis Publications

While many ExpertFinder applications succeed in finding experts, their techniques are not always designed to capture the various levels at which expertise can be expressed. Indeed, expertise can be inferred from relationships between topics and subtopics in a taxonomy. The conventional wisdom is that expertise in subtopics is also indicative of expertise in higher level topics as well. The enrichment of Expertise Profiles for finding experts can therefore be facilitated by taking domain hierarchies into account. We present a novel semantics-based model for finding experts, expertise levels and collaboration levels in a peer review context, such as composing a Program …

Ranking Documents Semantically Using Ontological Relationships, Boanerges Aleman-Meza, I. Budak Arpinar, Mustafa V. Nural, Amit P. Sheth

Kno.e.sis Publications

Although arguable success of today’s keyword based search engines in certain information retrieval tasks, ranking search results in a meaningful way remains an open problem. In this work, the goal is to use of semantic relationships for ranking documents without relying on the existence of any specific structure in a document or links between documents. Instead, real-world entities are identified and the relevance of documents is determined using relationships that are known to exist between the entities in a populated ontology. We introduce a measure of relevance that is based on traversal and the semantics of relationships that link entities …

The Maximum Clique Problem: Algorithms, Applications, And Implementations, John David Eblen

Doctoral Dissertations

Computationally hard problems are routinely encountered during the course of solving practical problems. This is commonly dealt with by settling for less than optimal solutions, through the use of heuristics or approximation algorithms. This dissertation examines the alternate possibility of solving such problems exactly, through a detailed study of one particular problem, the maximum clique problem. It discusses algorithms, implementations, and the application of maximum clique results to real-world problems. First, the theoretical roots of the algorithmic method employed are discussed. Then a practical approach is described, which separates out important algorithmic decisions so that the algorithm can be easily …

Cross-Market Model Adaptation With Pairwise Preference Data For Web Search Ranking, Jing Bai, Fernando Diaz, Yi Chang, Zhaohui Zheng, Keke Chen

Kno.e.sis Publications

Machine-learned ranking techniques automatically learn a complex document ranking function given training data. These techniques have demonstrated the effectiveness and flexibility required of a commercial web search. However, manually labeled training data (with multiple absolute grades) has become the bottleneck for training a quality ranking function, particularly for a new domain. In this paper, we explore the adaptation of machine-learned ranking models across a set of geographically diverse markets with the market-specific pairwise preference data, which can be easily obtained from clickthrough logs. We propose a novel adaptation algorithm, Pairwise-Trada, which is able to adapt ranking models that are trained …

Pattern Space Maintenance For Data Updates And Interactive Mining, Mengling Feng, Guozhu Dong, Jinyan Li, Yap-Peng Tan, Limsoon Wong

Kno.e.sis Publications

This article addresses the incremental and decremental maintenance of the frequent pattern space. We conduct an in-depth investigation on how the frequent pattern space evolves under both incremental and decremental updates. Based on the evolution analysis, a new data structure, Generator-Enumeration Tree (GE-tree), is developed to facilitate the maintenance of the frequent pattern space. With the concept of GE-tree, we propose two novel algorithms, Pattern Space Maintainer+ (PSM+) and Pattern Space Maintainer− (PSM−), for the incremental and decremental maintenance of frequent patterns. Experimental results demonstrate that the proposed algorithms, on average, outperform the representative state-of-the-art …

2,4,6-Triphenyl­Aniline, Onome Ugono, Stephanie Cowin, Alicia Beatty

Chemistry & Biochemistry Faculty Works

Individual mol­ecules of the title compound, C24H19N, do not participate in hydrogen-bonding inter­actions due to the steric bulk of the phenyl rings ortho to the amine. The dihedral angles between the central ring and the pendant rings are 68.26 (10), 55.28 (10) and 30.61 (11)°.

2,4,6-Triphenyl­Aniline, Onome Ugono, Stephanie Cowin, Alicia M. Beatty

Alicia Beatty

Heart And Skeletal Muscle Inflammation Of Farmed Salmon Is Associated With Infection With A Novel Reovirus, Torstein Tengs

Dr. Torstein Tengs

Atlantic salmon (Salmo salar L.) mariculture has been associated with epidemics of infectious diseases that threaten not only local production, but also wild fish coming into close proximity to marine pens and fish escaping from them. Heart and skeletal muscle inflammation (HSMI) is a frequently fatal disease of farmed Atlantic salmon. First recognized in one farm in Norway in 1999, HSMI was subsequently implicated in outbreaks in other farms in Norway and the United Kingdom. Although pathology and disease transmission studies indicated an infectious basis, efforts to identify an agent were unsuccessful. Here we provide evidence that HSMI is associated …

Computational Modeling Of Biological Neural Networks On Gpus: Strategies And Performance, Byron Galbraith

Master's Theses (2009 -)

Simulating biological neural networks is an important task for computational neuroscientists attempting to model and analyze brain activity and function. As these networks become larger and more complex, the computational power required grows significantly, often requiring the use of supercomputers or compute clusters. An emerging low-cost, highly accessible alternative to many of these resources is the Graphics Processing Unit (GPU) - specialized massively-parallel graphics hardware that has seen increasing use as a general purpose computational accelerator thanks largely due to NVIDIA's CUDA programming interface. We evaluated the relative benefits and limitations of GPU-based tools for large-scale neural network simulation and …

10302 Summary - Learning Paradigms In Dynamic Environments, Barbara Hammer, Pascal Hitzler

Computer Science and Engineering Faculty Publications

The seminar centered around problems which arise in the context of machine learning in dynamic environments. Particular emphasis was put on a couple of specific questions in this context: how to represent and abstract knowledge appropriately to shape the problem of learning in a partially unknown and complex environment and how to combine statistical inference and abstract symbolic representations; how to infer from few data and how to deal with non i.i.d. data, model revision and life-long learning; how to come up with efficient strategies to control realistic environments for which exploration is costly, the dimensionality is high and data …

Biomedical Ontologies For Parasite Research, Vinh Nguyen, Satya S. Sahoo, Priti Parikh, Todd Minning, Brent Weatherly, Flora Logan, Amit P. Sheth, Rick Tarleton

Kno.e.sis Publications

Trypanosoma cruzi is a protozoan parasite that causes Chagas disease or American trypanosomiasis, which is the leading cause of death in Latin America. The primary objective of this study is to create an ontology-driven information infrastructure to support parasite researchers in identifying gene knockout, vaccination, or drug targets for T. cruzi. This involves querying across multiple datasets from diverse sources, such as proteome, pathway, internal lab data, etc. that are often represented in heterogeneous formats. To address this, a multi-ontology parasite knowledge repository (PKR) is being created with an intuitive graphical query interface called Cuebee. The PKR is underpinned by …

Cloud Based Scientific Workflow For Nmr Data Analysis, Ashwin Manjunatha, Paul E. Anderson, Satya S. Sahoo, Ajith Harshana Ranabahu, Michael L. Raymer, Amit P. Sheth

Kno.e.sis Publications

This work presents a service oriented scientific workflow approach to NMR-based metabolomics data analysis. We demonstrate the effectiveness of this approach by implementing several common spectral processing techniques in the cloud using a parallel map-reduce framework, Hadoop.

Trust Model For Semantic Sensor And Social Networks: A Preliminary Report, Pramod Anantharam, Cory Andrew Henson, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

Trust is an amorphous concept that is becoming Increasingly important in many domains, such as P2P networks, E-commerce, social networks, and sensor networks. While we all have an intuitive notion of trust, the literature is scattered with a wide assortment of differing definitions and descriptions; often these descriptions are highly dependent on a single domain or application of interest. In addition, they often discuss orthogonal aspects of trust while continuing to use the general term “trust”. In order to make sense of the situation, we have developed an ontology of trust that integrates and relates its various aspects into a …