Life Sciences Commons^™

P63 And Vdr Are Regulated By Vitamin D (Vd3) And Uv Signaling, Andrew J. Whitlatch

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Skin cancers, such as squamous cell carcinoma (SCC), develop from accumulated mutations as a result of excessive exposure to Ultraviolet B (UVB) radiation. Intriguingly, UVB also catalyzes the synthesis of 1alpha, 25-dihydroxy Vitamin D3 (VD3), the hormonally active form of Vitamin D. Downstream VD3 signaling has been associated with promoting the inhibition of cell cycle progression, regulating calcium homeostasis, and inducing differentiation and apoptosis. VD3 mediates these processes via genomic mechanisms through interaction with its cognate receptor, the Vitamin D Receptor, (VDR). In addition, it was recently discovered that VD3 reduces UVB-mediated phosphorylation of the SAPK/c-Jun N-terminal kinase (JNK), which …

Hyperbaric Oxygen In The Prevention Of Carbon Monoxide Induced Delayed Neurological Sequelae In Male Sprague Dawley Rats (Rattus Norvegicus), Chester P. Gut Jr.

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In Carbon Monoxide (CO) induced Delayed Neurological Sequelae (DNS) clinical signs develop 1 to 6 weeks after CO has cleared the body. The aim of this experiment was to develop a model of CO induced DNS which closely mimics "real world" conditions both in exposure and treatment. The model was challenged with hyperbaric or normobaric oxygen, or room air. Basic behaviors were measured by Open Field test on days 1, 7, 14 post exposure and treatment. No significant difference in behavior was observed between exposed and control animals or between treatment groups. Histological analyses showed no DNA or necrotic damage …

Impacts Of A Herbivorous Fish, Campostoma Anomalum (Central Stoneroller), On Nitrogen Fixation By Benthic Algae, Chad Robert Schwinnen

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Herbivorous fish negatively impact algal biomass and promote the growth of cyanobacteria. In nutrient poor conditions that sustain high levels of productivity nitrogen fixing cyanobacteria can supply up to 28% of the available nitrogen (Higgins et al. 2001) We investigated the role of grazing fish in sustaining high levels of productivity in nutrient poor conditions. We used the grazing minnow, Campostoma anomalum, and the acetylene reduction technique in a controlled environment to analyze rates of nitrogen fixation and primary production by the periphyton. Fish grazing reduced algal biomass and promoted the growth of cyanobacteria but had no impact on overall …

Tissue Specific Effects Of Adipose Stem Cells (Asc) In A Melanoma Tumor Environment, Drew Michael Nedderman

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This study determined the tissue-specific effect of adipose stem cells (ASC) within a melanoma environment for development of a cell-based melanoma therapy. Analysis included a subcutaneous B16-F1 melanoma model using thirty-one C57BL/6 wild-type mice. Melanoma xenografts were treated with cell-based therapies of CFDA-SE-labeled human fibroblasts HF20x (control), non-differentiated ndASC or hematopoietic-differentiated HdASC. No tumor regression was observed in presence of cell-based therapies, thus, the HdASC group demonstrated an increase in tumor growth accompanied with an up-regulated macrophage response, and increased angiogenesis. In addition, this group demonstrated a decrease in Melan-A tumor marker and interferon-γ expression suggesting that ASC-supported tumor angiogenesis …

Ecological Speciation In A Multi-Trophic Complex: Gall Midges, Goldenrods, And Parasitoids, Brenda L. Wells

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The importance of ecological interactions in the origin and maintenance of species diversity remains unclear. The current study assesses how ecological interactions shape the process of evolutionary diversification using a gall midge-host plant system in Ohio involving the gall midge, Asteromyia carbonifera (Diptera: Cecidomyiidae), and its goldenrod (Solidago) host-plants. A. carbonifera form four morphologically distinctive gall morphs and differ genetically. I studied phenology, host-plant specialization, and parasitism at three field sites in Southwestern Ohio. Phenology was assessed for twelve weeks while host-plant distribution and pressure from parasitoids were measured by monthly plot and rearing gall collections. Relative gall frequencies and …

Inhibition Of Cell Invasion By Targeting Pld, Terry C. Farkaly

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Phospholipase D (PLD) is a crucial signaling enzyme involved in many cellular processes. The catalytic activity of PLD is essential for the production of Phosphatidic Acid (PA), a critical second messenger in cell signaling cascades downstream. Using the highly invasive rat mammary adenocarcinoma cell line mTLn3 as a metastatic model, we investigated the proficiency of these cells to invade using matrigels that mimic the basement membrane of the extracellular matrix (ECM), their activity through PLD enzymatic assays, as well as the potency of our potential inhibitors to inhibit PLD-mediated cell invasion and lipase activity. This study reveals that PLD-mediated cell …

Rev Interacts With Tubulin Heterodimers To Cause Cell Cycle Defects, Poornima Kotha Lakshmi Narayan

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Rev is a regulatory protein that plays an important role in the replication of HIV virus by post-transcriptionally promoting expression of viral proteins late in infection. Rev expression also slows cell growth, leads to an accumulation of cells in G2/M specifically before the spindle checkpoint, and can produce changes in ploidy. Because Rev is capable of depolymerizing microtubules (MTs) in vitro, possibly by a mechanism shared with Kinesin-13 proteins, themselves potent cellular MT depolymerases, I tested the hypothesis that these cellular defects were due to an interaction between Rev and tubulin.

To this end, Rev and select Rev mutants defective …

Constitutive And Jasmonate-Inducible Defenses In Phloem Of Two North American And Two Asian Ash Species Grown In A Common Garden, Qin Wang

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Emerald Ash Borer (EAB) is more damaging to North American ashes than Asian ashes. Variation in the resistance of ash species to feeding by larvae of EAB may be related to variation in levels of chemical defenses in the phloem. I compared constitutive and methyl jasmonate (MeJA)-inducible levels of several chemical defenses in the phloem of young Manchurian, Chinese, white, and green ashes. Manchurian ash is known to be highly resistant to attack by EAB in the field, while white and green ashes are both susceptible. The hypotheses of this experiment were that: (1) Manchurian (Fraxinus mandshurica) and Chinese ash …

The Influence Of Stored Product Mites On The Function Of Skin Microvascular Endothelial Cells, Jennifer Graff Curp

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The prevalence of allergenic diseases and sensitization to stored product mites is increasing worldwide. Stored product mites are prevalent in homes, foods, and some work environments. Stored product mites need to be further studied so we can characterize their inflammatory properties to understand their role in skin disease, and provide proper treatment to patients with mite allergies. The purpose of the study was to show the role of stored product mites in modulating the inflammatory and immune response to human dermal endothelial cells in the skin. The epidermis serves as the first line of defense between the body and the …

Genetic Studies Of Genes Involved In The Initiation Of Dna Replication In The Fission Yeast Schizosaccharomyces Pombe, Zhuo Wang

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The initiation of DNA replication is a highly conserved process in all eukaryotes. However, the underlying mechanism is not well understood. Genetic studies in the fission yeast S. pombe have contributed greatly to and will continue to provide insights to our understanding of this important biological process.

In the first chapter, we have used a complementary method to test three recently identified human replication proteins DUE-B, Ticrr/Treslin, and GEMC1 as the candidate functional homologue of Sld3 in S. pombe. Sld3 is an essential replication initiation protein discovered in yeasts. Since no apparent sequence similarity can be found, its homologue in …

Characterization Of Three Mutations In Conserved Domain Of Subunit Iii Of Cytochrome C Oxidase From Rhodobacter Sphaeroides, Rachel Omolewu

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Cytochrome c oxidase (COX) is the final electron acceptor in mitochondrial respiratory chain and in many bacterial species including Rhodobacter sphaeroides. Electron transfer is coupled with the pumping of protons across the membrane. Previous work has shown that reaction of beef COX with dicyclohexylcarbodiimide (DCCD) resulted in an inhibition of proton translocation by covalently binding to the conserved amino acid residue E90 located in a nonpolar region of subunit III (SIII). E90 is involved in a bonding pair with another conserved residue H212, possibly connected by a salt bridge or a hydrogen bond in the three dimensional structure of SIII. …

Research In Semantic Web And Information Retrieval: Trust, Sensors, And Search, Krishnaprasad Thirunarayan

Kno.e.sis Publications

No abstract provided.

Sparql Query Re-Writing For Spatial Datasets Using Partonomy Based Transformation Rules, Prateek Jain, Cory Andrew Henson, Amit P. Sheth, Peter Z. Yeh, Kunal Verma

Kno.e.sis Publications

Often the information present in a spatial knowledge base is represented at a different level of granularity and abstraction than the query constraints. For querying ontology’s containing spatial information, the precise relationships between spatial entities has to be specified in the basic graph pattern of SPARQL query which can result in long and complex queries. We present a novel approach to help users intuitively write SPARQL queries to query spatial data, rather than relying on knowledge of the ontology structure. Our framework re-writes queries, using transformation rules to exploit part-whole relations between geographical entities to address the mismatches between query …

A Local Qualitative Approach To Referral And Functional Trust, Krishnaprasad Thirunarayan, Dharan Althuru, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

Trust and confidence are becoming key issues in diverse applications such as ecommerce, social networks, semantic sensor web, semantic web information retrieval systems, etc. Both humans and machines use some form of trust to make informed and reliable decisions before acting. In this work, we briefly review existing work on trust networks, pointing out some of its drawbacks. We then propose a local framework to explore two different kinds of trust among agents called referral trust and functional trust, that are modelled using local partial orders, to enable qualitative trust personalization. The proposed approach formalizes reasoning with trust, distinguishing between …

Towards Reasoning Pragmatics, Pascal Hitzler

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 force us to question established lines of research and to rethink the underlying approaches.

A Contrast Pattern Based Clustering Quality Index For Categorical Data, Qingbao Liu, Guozhu Dong

Kno.e.sis Publications

Since clustering is unsupervised and highly explorative, clustering validation (i.e. assessing the quality of clustering solutions) has been an important and long standing research problem. Existing validity measures have significant shortcomings. This paper proposes a novel contrast pattern based clustering quality index (CPCQ) for categorical data, by utilizing the quality and diversity of the contrast patterns (CPs) which contrast the clusters in clusterings. High quality CPs can characterize clusters and discriminate them against each other. Experiments show that the CPCQ index (1) can recognize that expert-determined classes are the best clusters for many datasets from the UCI repository; (2) does …

Evaluating Forensic Dna Evidence, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Ontology-Driven Provenance Management In Escience: An Application In Parasite Research, Satya S. Sahoo, D. Brent Weatherly, Raghava Mutharaju, Pramod Anantharam, Amit P. Sheth, Rick L. Tarleton

Kno.e.sis Publications

Provenance, from the French word “provenir”, describes the lineage or history of a data entity. Provenance is critical information in scientific applications to verify experiment process, validate data quality and associate trust values with scientific results. Current industrial scale eScience projects require an end-to-end provenance management infrastructure. This infrastructure needs to be underpinned by formal semantics to enable analysis of large scale provenance information by software applications. Further, effective analysis of provenance information requires well-defined query mechanisms to support complex queries over large datasets. This paper introduces an ontology-driven provenance management infrastructure for biology experiment data, as part …

An Anytime Algorithm For Computing Inconsistency Measurement, Yue Ma, Guilin Qi, Guohui Xiao, Pascal Hitzler, Zuoquan Lin

Computer Science and Engineering Faculty Publications

Measuring inconsistency degrees of inconsistent knowledge bases is an important problem as it provides context information for facilitating inconsistency handling. Many methods have been proposed to solve this problem and a main class of them is based on some kind of paraconsistent semantics. In this paper, we consider the computational aspects of inconsistency degrees of propositional knowledge bases under 4-valued semantics. We first analyze its computational complexity. As it turns out that computing the exact inconsistency degree is intractable, we then propose an anytime algorithm that provides tractable approximation of the inconsistency degree from above and below. We show that …

A Survey Of The Semantic Specification Of Sensors, Michael Compton, Cory Andrew Henson, Laurent Lefort, Holger Neuhaus, Amit P. Sheth

Kno.e.sis Publications

Semantic sensor networks use declarative descriptions of sensors promote reuse and integration, and to help solve the difficulties of installing, querying and maintaining complex, heterogeneous sensor networks. This paper reviews the state of the art for the semantic specification of sensors, one of the fundamental technologies in the semantic sensor network vision. Twelve sensor ontologies are reviewed and analysed for the range and expressive power of their concepts. The reasoning and search technology developed in conjunction with these ontologies is also reviewed, as is technology for annotating OGC standards with links to ontologies. Sensor concepts that cannot be expressed accurately …

Provenir Ontology: Towards A Framework For Escience Provenance Management, Satya S. Sahoo, Amit P. Sheth

Kno.e.sis Publications

Provenance metadata describes the 'lineage' or history of an entity and necessary information to verify the quality of data, validate experiment protocols, and associate trust value with scientific results. eScience projects generate data and the associated provenance metadata in a distributed environment (such as myGrid) and on a very large scale that often precludes manual analysis. Given this scenario, provenance information should be, (a) interoperable across projects, research groups, and application domains, and (b) support analysis over large datasets using reasoning to discover implicit information. In this paper, we introduce an ontology-driven framework for eScience provenance management underpinned by an …

Suggestions For Owl 3, Pascal Hitzler

Computer Science and Engineering Faculty Publications

With OWL 2 about to be completed, it is the right time to start discussions on possible future modifications of OWL. We present here a number of suggestions in order to discuss them with the OWL user community. They encompass expressive extensions on polynomial OWL 2 profiles, a suggestion for an OWL Rules language, and expressive extensions for OWL DL.

Ibm Altocumulus: A Cross-Cloud Middleware And Platform, E. Michael Maximilien, Ajith Harshana Ranabahu, Roy Engehausen, Laura Anderson

Kno.e.sis Publications

Cloud computing has become the new face of computing and promises to offer virtually unlimited, cheap, readily available, "utility type" computing resources. Many vendors have entered this market with different offerings ranging from infrastructure-as-a-service such as Amazon, to fully functional platform services such as Google App Engine. However, as a result of this heterogeneity, deploying applications to a cloud and managing them needs to be done using vendor specific methods. This "lock in" is seen as a major hurdle in adopting cloud technologies to the enterprise. IBM Altocumulus, the cloud middleware platform from IBM Almaden Services Research, aims to solve …

Paraconsistent Reasoning For Owl 2, Yue Ma, Pascal Hitzler

Computer Science and Engineering Faculty Publications

A four-valued description logic has been proposed to reason with description logic based inconsistent knowledge bases. This approach has a distinct advantage that it can be implemented by invoking classical reasoners to keep the same complexity as under the classical semantics. However, this approach has so far only been studied for the basid description logic ALC. In this paper, we further study how to extend the four-valued semantics to the more expressive description logic SROIQ which underlies the forthcoming revision of the Web Ontology Language, OWL 2, and also investigate how it fares when adapated to tractable description logics including …

A Preferential Tableaux Calculus For Circumscriptive Alco, Stephan Grimm, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Nonmonotonic extensions of description logics (DLs) allow for default and local closed-world reasoning and are an acknowledged desired feature for applications, e.g. in the Semantic Web. A recent approach to such an extension is based on McCarthy's circumscription, which rests on the principle of minimising the extension of selected predicates to close off dedicated parts of a domain model. While decidability and complexity results have been established in the literature, no practical algorithmisation for circumscriptive DLs has been proposed so far. In this paper, we present a tableaux calculus that can be used as a decision procedure for concept satisfiability …

A Best Practice Model For Cloud Middleware Systems, Ajith Harshana Ranabahu, E. Michael Maximilien

Kno.e.sis Publications

Cloud computing is the latest trend in computing where the intention is to facilitate cheap, utility type computing resources in a service-oriented manner. However, the cloud landscape is still maturing and there are heterogeneities between the clouds, ranging from the application development paradigms to their service interfaces,and scaling approaches. These differences hinder the adoption of cloud by major enterprises. We believe that a cloud middleware can solve most of these issues to allow cross-cloud inter-operation. Our proposed system is Altocumulus, a cloud middleware that homogenizes the clouds. In order to provide the best use of the cloud resources and make …

Context And Domain Knowledge Enhanced Entity Spotting In Informal Text, Daniel Gruhl, Meena Nagarajan, Jan Pieper, Christine Robson, Amit P. Sheth

Kno.e.sis Publications

This paper explores the application of restricted relationship graphs (RDF) and statistical NLP techniques to improve named entity annotation in challenging Informal English domains. We validate our approach using on-line forums discussing popular music. Named entity annotation is particularly difficult in this domain because it is characterized by a large number of ambiguous entities, such as the Madonna album “Music” or Lilly Allen’s pop hit “Smile”.

We evaluate improvements in annotation accuracy that can be obtained by restricting the set of possible entities using real-world constraints. We find that constrained domain entity extraction raises the annotation accuracy significantly, making an …

Context Is Highly Contextual!, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

“Best K”: Critical Clustering Structures In Categorical Datasets, Keke Chen, Ling Liu

Kno.e.sis Publications

The demand on cluster analysis for categorical data continues to grow over the last decade. A well-known problem in categorical clustering is to determine the best K number of clusters. Although several categorical clustering algorithms have been developed, surprisingly, none has satisfactorily addressed the problem of best K for categorical clustering. Since categorical data does not have an inherent distance function as the similarity measure, traditional cluster validation techniques based on geometric shapes and density distributions are not appropriate for categorical data. In this paper, we study the entropy property between the clustering results of categorical data with different K …

Tableau Algorithm For Concept Satisfiability In Description Logic Alch, Satya S. Sahoo, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The provenir ontology is an upper-level ontology to facilitate interoperability of provenance information in scientific applications. The description logic (DL) expressivity of provenir ontology is ALCH, that is, it models role hierarchies (H) (without transitive roles and inverse roles). Even though the complexity results for concept satisfiability for numerous variants of DL such as ALC with transitively closed roles (ALC_R+ also called S), inverse roles SI, and role hierarchy SHI have been well-established, similar results for ALCH has been surprisingly missing from the literature. Here, we show that the complexity of the concept satisfiability problem for the ALCH variant …