Life Sciences Commons^™

Traveling The Semantic Web Through Space, Theme And Time, Amit P. Sheth, Matthew Perry

Kno.e.sis Publications

In this installment of Semantics and Services, we further develop the idea of spatial, temporal, and thematic (STT) processing of semantic Web data and describe the Web infrastructure needed to support it. Starting from Ramesh Jain's vision of the EventWeb as a view of what's possible with a Web that better accommodates all three dimensions of event-related information (thematic, spatial, and temporal), we outline the architecture needed to support it and current research that aims to realize it.

Transcriptional Regulation Of Lamb3 By P53, Meghna Jani

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The p53 tumor-suppressor plays a very important role in the prevention of cancer and it is known that about 50% of all human tumors possess p53 mutations. Although mutations in p53 are most prevalent in human cancers, inactivation of wild-type p53 occurs through many different mechanisms that are independent of p53 mutation or deletion. In an effort to determine novel p53 target genes, our lab employed a microarray method in which p53 was re-activated by RNAi mediated knockdown of Hdm2 and HdmX in MCF7 human breast cancer cell line, harboring wild-type p53 and elevated levels of Hdm2 and HdmX. Gene …

Validation Of A Custom-Made Microarray To Study Human Intestinal Microflora, Harshavardhan Kenche

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Intestinal microflora refers to all the different species of bacteria that reside in the human gut and is an important organ of the human body because almost all the digestive reactions of the host occur in the intestine. The bacteria of the intestine play a key role in this process by supplementing the intestine with various enzymes and proteins that are required for the digestive process. At the same time, these bacteria were shown to be implicated in a variety of gastrointestinal disorders like Irritable Bowel Syndrome, Inflammatory Bowel Disorder and Gastrointestinal Cancer, but with the current knowledge about the …

Qtl Analysis Of Ray Pattern In Caenorhabditis Elegans Recombinant Inbred Lines, Adam Joseph Guess

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Ray pattern is the most divergent morphological character among rhabditid nematodes. The ancestral ray pattern of Elegans group nematodes is commonly referred to as a 2(1)3+3 pattern, with rays 1 and 2 located anterior of the cloaca, ray 3 positioned at the cloaca, and rays 4-6 and 7-9 grouped in two clusters posterior of the cloaca. C. elegans males primarily exhibit the 2(1)3+3 pattern; however some isolates display variant patterns at a low frequency. The Hawaiian strain CB4856 exhibits a 3/3+3 pattern at a frequency of 0.09. In this pattern, ray 3 is located anterior of the cloaca in a …

The Response Of Vascular Dermal Enodethial Cells To House Dust Mite Extracts, Aaron Mathew Newman

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House dust mites are microscopic arthropods that can trigger moderate allergic symptoms such as sneezing, watery eyes, itching, and wheezing in sensitized individuals. People with more serious allergies to house dust mites can develop allergic diseases like atopic dermatitis and asthma. The effects of house dust mites on allergy sufferers make house dust mites and the study of their effects on the human body of great medical and economic importance. A majority of the research that has been done on house dust mite's effects on humans has dealt with the lungs and relevant disease like asthma. Little work has been …

Using Geographic Information Systems To Select Sites For Wetland Restoration In West Central Ohio's Agricultural Areas, Janice M. Hartkorn

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The Mississippi River Basin, includes a major part of Ohio has encountered increasing phosphorus and nitrogen loads from agricultural fields since the 1800's when intensive agriculture moved into the Midwest. Agriculture has drained ninety percent of Ohio's native wetlands. A portion of those drained wetlands can be restored to functional wetlands to intercept excess nutrients from non-productive or low yield agricultural fields to improve overall water quality. Little is known about finding potential restoration sites, partly because of the difficulty in locating sites capable of supporting successful restoration.

This study investigated the utility of Geographic Information Systems (GIS) as a …

Immunomodulation Of Human Skin Cells By Extracts Of The Scabies Mite, Sarcoptes Scabiei, Jeremi Stevan Mullins

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Sarcoptes scabiei infests its host through burrowing into the stratum corneum layer of skin. Keratinocytes and fibroblasts responding to the burrowing mite(s) and/or mite products produce inflammatory and immune activating cytokines and chemokines. The purpose of this study was to determine if an extract of S. scabiei can modulate cytokine and chemokine expression from keratinocytes and fibroblasts in vitro. Normal human keratinocytes and fibroblasts were exposed to an extract of S. scabiei var. canis with or without various pro-inflammatory stimuli. Cytokine and chemokine expression were measured by enzyme-linked immunosorbent assay (ELISA). Scabies extract increased expression of interleukin-6 (IL-6), growth-related oncogene-α …

Ultrastructural Analysis Of Excitatory And Inhibitory Synapses Within The Medial Nucleus Of The Trapezoid Body Of Normal Hearing And Congenitally Deaf Mice, Melissa A. Bautista

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The auditory brainstem has been the area of much focus in recent years due to its advantages in circuitry and synaptic connections. The endbulbs and calyces of Held are large, glutamatergic synapses within the AVCN and MNTB, respectively. Because of their large size and accessibility these synapses have offered the ability to study pre- and post-synaptic mechanisms of neurotransmission within the central nervous system. The calyx of Held synapse is the main excitatory input into the MNTB principal cells, containing hundreds of individual synaptic specializations, or release sites. Previous studies have identified physiological and morphological changes at the endbulb of …

Human Immunodeficiency Virus-1 Productively Infects Mature Terminally Differentiated Eosinophils In Hiv/Aids Patients, Jude N. Atem

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Eosinophils express membrane CD4 protein and can bind HIV-1 glycoprotein (gp) 120. Therefore, eosinophils could serve as host cells for HIV-1 infection in vivo, especially in the late phase of the infection. In culture, HIV-1 infects eosinophil precursors and primary eosinophils. Additionally HIV-1 proviral DNA sequences have been detected in the eosinophils of some HIV-1 positive patients. Since elevated levels of eosinophils occur during HIV-1 infection and parasitic infections, it implies that co-infection of parasites and HIV-1 could cause a much greater increase in the level of potential HIV-1 susceptible eosinophils. Therefore HIV-1 infection of eosinophils could partly explain the …

Sensitization To Trail-Induced Apoptosis In K-Ras 12 Mutant Pancreatic Cancer Cells By Bitc, Christina Ann Wicker

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Pancreatic adenocarcinoma is an aggressive cancer with a greater than 95% mortality rate and short survival after diagnosis. Chemotherapeutic resistance hinders successful treatment. This resistance is associated with mutations within codon 12 of the K-Ras gene (K-Ras 12), which is present in over 90% of all pancreatic adenocarcinomas. Codon 12 mutations maintain Ras in a constitutively active state leading to continuous cellular proliferation. Our study determined if TRAIL resistance in pancreatic adenocarcinomas with K-Ras 12 mutations could be overcome by first sensitizing the cells with Benzyl isothiocyanate (BITC). BITC is a component of cruciferous vegetable extracts and a cell cycle …

Mdm2 Amplification In Nih3t3l1 Preadipocytes Leads To Mdm2 Elevation In Terminal Adipogenesis, Vaughn Litteral

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The p53 protein is a tumor suppressor protein that is mutated or non-functional in nearly all cancers. The Mdm2 protein has the ability to functionally inactivate p53 and these two proteins have been studied extensively in the context of cellular proliferation. In this study, expression of the murine double minute 2 (mdm2) gene was examined in the mouse NIH3T3L1 cell line. Under the proper conditions, the immortalized NIH3T3L1 cells have the ability to differentiate from fibroblasts to adipocytes (Green et al., 1975). This well characterized cell line provides an excellent model to study mdm2 in differentiation. While evaluating the regulation …

The Effects Of Nutritional Supplement, Mass Fx™, On Muscular Strength, Body Composition, And Blood Chemistries In Resistance Trained Adult Males, Patrick S. Dib

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The purpose of this study was to determine the effects of a nutritional supplement, Mass FX, on muscular strength, body composition, and blood chemistries in resistance-trained adult males. Eight subjects, mean age 25 +/- 3.02 years, were randomly assigned to two groups (n=4). Each group was given either Mass FX or a Placebo in a double-blind manner to be taken orally for six weeks (4caps/day regardless of bodyweight). For the duration of the study, both groups were following the same training program and a diet customized to each subject's bodyweight in conjunction to the supplementation. Data were analyzed using Analysis …

In Search For New P53 Regulated Genes, Meldrick Daniel Mpagi

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The p53 tumor suppressor protein has the ability to transactivate its target genes whose gene products are involved in carrying out cell cycle arrest, apoptosis, DNA repair, and senescence. Here, I report that two genes may be p53 regulated. Utilizing a microarray method to search for novel p53 target genes, I was able to identify a possible transcriptional target of p53 being solute carrier family 1a1 (SLC1a1). Along with that finding I also identified an E2F-target gene, minichromosome maintenance 10 (MCM10), as being p53 regulated. Gene expression profiling of MCF7 breast cancer cells treated with RNAi targeting Hdm2 and HdmX …

Effects Of Forest Fragmentation And Honeysuckle Invasion On Forest Lepidoptera In Southwest Ohio, Annie Lynn Doyle

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Habitat loss and exotic species invasion is a rapidly growing threat facing forest animal communities worldwide. The goal of the current study is to assess the impact of forest fragmentation and the associated invasion of honeysuckle on immature tree-feeding Lepidoptera communities in southwestern Ohio. Caterpillar abundance, richness, and honeysuckle density were sampled along 100 meter transects conducted in ten forest fragments. Generalized linear models were developed to determine the effects of fragment area, landscape forest cover, and honeysuckle density on caterpillar abundance and richness. Caterpillar abundance and richness was positively related to landscape forest cover and fragment area. However, these …

The Role Of Phospholipase D (Pld) And Grb2 In Chemotaxis, Katie J. Knapek

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Phospholipase D (PLD) is an enzyme that hydrolyzes phosphatidylcholine yielding choline and phosphatidic acid. PLD is activated by mitogens (lead to cell division) and motogens (leading to cell migration). PLD is known to contribute to cellular proliferation and deregulated expression of PLD has been implicated in several human cancers. PLD has been found to play a role in leukocyte chemotaxis and adhesion as studied through the formation of chemokine gradients. We have established a model of cell migration comprising three cell lines: macrophages RAW 264.7 and LR-5 (for innate defense), and fibroblast COS-7 cells (for wound healing). COS-7 cells respond …

The Community Structure Of Methanogenic, Methanotrophic, And Ammonia Oxidizing Bacteria In Vertical Flow Greenhouse Wetland Mesocosms Exposed To Pce, William Evan Gruner

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Chlorinated ethenes are among the top contaminants on the EPA National Priorities List due to their abundance in contaminated sites and their recalcitrant nature. These compounds, which are used in large scale degreasing and textile processes, are known liver and kidney toxins, and suspected carcinogens. Wetland ecosystems are capable of degrading PCE and its breakdown products TCE, DCE, and VC by providing anaerobic and aerobic growth conditions for microbes that express enzymes such as dehalogenases and monooxygenases with dual affinity for chlorinated solvents. Greenhouse mesocosms at Wright State University are used to mimic field conditions at a treatment wetland at …

Regulation Of Calcium Entry Pathway In Jurkat T Cells, Petronilla A. Fruasaha

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Calcium release-activated calcium channels (CRAC) control influx of calcium in human T lymphocytes. Hour-long calcium elevations are necessary for efficient gene expression during T cell activation and proliferation. We report here that, the time course for store-operated Ca2+ entry is short-lived (3-4 min) and therefore, cannot account for the prolonged Ca2+ elevations necessary for NFAT translocation into nucleus. Previous findings strongly suggest that T cell activation is accompanied by cytosolic alkalinization. Here, we show that pH changes in Jurkat T cells following activation with mitogenic lectin, phytohemagglutinin (PHA), depends on the length of time of exposure and the concentration (potency) …

A General Boosting Method And Its Application To Learning Ranking Functions For Web Search, Zhaohui Zheng, Hongyuan Zha, Tong Zhang, Olivier Chapelle, Keke Chen, Gordon Sun

Kno.e.sis Publications

We present a general boosting method extending functional gradient boosting to optimize complex loss functions that are encountered in many machine learning problems. Our approach is based on optimization of quadratic upper bounds of the loss functions which allows us to present a rigorous convergence analysis of the algorithm. More importantly, this general framework enables us to use a standard regression base learner such as decision trees for fitting any loss function. We illustrate an application of the proposed method in learning ranking functions for Web search by combining both preference data and labeled data for training. We present experimental …

Video On The Semantic Sensor Web, Cory Andrew Henson, Amit P. Sheth, Prateek Jain, Josh Pschorr, Terry Rapoch

Kno.e.sis Publications

Millions of sensors around the globe currently collect avalanches of data about our world. The rapid development and deployment of sensor technology is intensifying the existing problem of too much data and not enough knowledge. With a view to alleviating this glut, we propose that sensor data, especially video sensor data, can be annotated with semantic metadata to provide contextual information about videos on the Web. In particular, we present an approach to annotating video sensor data with spatial, temporal, and thematic semantic metadata. This technique builds on current standardization efforts within the W3C and Open Geospatial Consortium (OGC) and …

Towards Tractable Local Closed World Reasoning For The Semantic Web, Matthias Knorr, Jose Julio Alferes, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Recently, the logics of minimal knowledge and negation as failure MKNF [12] was used to introduce hybrid MKNF knowledge bases [14], a powerful formalism for combining open and closed world reasoning for the Semantic Web. We present an extension based on a new three-valued framework including an alternating fixpoint, the well-founded MKNF model. This approach, the well-founded MKNF semantics, derives its name from the very close relation to the corresponding semantics known from logic programming. We show that the well-founded MKNF model is the least model among all (three-valued) MKNF models, thus soundly approximating also the two-valued MKNF models from …

Semantic Web For Health Care And Biomedical Informatics, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Leveraging Semantic Web Techniques To Gain Situational Awareness, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Conjunctive Queries For A Tractable Fragment Of Owl 1.1, Markus Krotzsch, Sebastian Rudolph, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Despite the success of the Web Ontology Language OWL, the development of expressive means for querying OWL knowledge bases is still an open issue. In this paper, we investigate how a very natural and desirable form of queries-namely conjunctive ones-can be used in conjunction with OWL such that one of the major design criteria of the latter-namely decidability-can be retained. More precisely, we show that querying the tractable fragment EL++ of OWL 1.1 is decidable. We also provide a complexity analysis and show that querying unrestricted EL++ is undecidable.

Can Semantic Web Techniques Empower Comprehension And Projection In Cyber Situational Awareness?, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Semantic Convergence Of Wikipedia Articles, Christopher J. Thomas, Amit P. Sheth

Kno.e.sis Publications

Social networking, distributed problem solving and human computation have gained high visibility. Wikipedia is a well established service that incorporates aspects of these three fields of research. For this reason it is a good object of study for determining quality of solutions in a social setting that is open, completely distributed, bottom up and not peer reviewed by certified experts. In particular, this paper aims at identifying semantic convergence of Wikipedia articles; the notion that the content of an article stays stable regardless of continuing edits. This could lead to an automatic recommendation of good article tags but also add …

Supporting Complex Thematic, Spatial And Temporal Queries Over Semantic Web Data, Matthew Perry, Amit P. Sheth, Farshad Hakimpour, Prateek Jain

Kno.e.sis Publications

Spatial and temporal data are critical components in many applications. This is especially true in analytical domains such as national security and criminal investigation. Often, the analytical process requires uncovering and analyzing complex thematic relationships between disparate people, places and events. Fundamentally new query operators based on the graph structure of Semantic Web data models, such as semantic associations, are proving useful for this purpose. However, these analysis mechanisms are primarily intended for thematic relationships. In this paper, we describe a framework built around the RDF metadata model for analysis of thematic, spatial and temporal relationships between named entities. We …

Evaluating Forensic Dna Evidence - A Day-Long Workshop, Dan E. Krane, William C. Thompson

Biological Sciences Faculty Publications

No abstract provided.

A Multi-Objective Genetic Algorithm That Employs A Hybrid Approach For Isolating Codon Usage Bias Indicative Of Translational Efficiency, Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

Isolation of translational efficiency bias can have important applications in gene expression prediction and heterologous protein production. In some genomes the presence of a high GC(AT)-content bias can confound the isolation of translational efficiency bias. In other organisms translational efficiency bias is weak making it difficult to isolate. Described here is a multi-objective genetic algorithm that improves the isolation of translational efficiency bias in Streptomyces coelicolor A3(2) and Pseudomonas aeruginosa PAO1, two organisms shown to have high GC-content and weak translational efficiency bias.

Swashup: Situational Web Applications Mashups, E. Michael Maximilien, Ajith Harshana Ranabahu, Stefan Tai

Kno.e.sis Publications

Distributed programming has shifted from private networks to the Internet using heterogeneous Web APIs. This enables the creation of situational applications of composed services exposing user interfaces, i.e., mashups. However, this programmable Web lacks unified models that can facilitate mashup creation, reuse, and deployments. This poster demonstrates a platform to facilitate Web 2.0 mashups.

A Proposed Statistical Protocol For The Analysis Of Metabolic Toxicological Data Derived From Nmr Spectroscopy, Benjamin J. Kelly, Paul E. Anderson, Nicholas V. Reo, Nicholas J. Delraso, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

Nuclear magnetic resonance (NMR) spectroscopy is a non-invasive method of acquiring a metabolic profile from biofluids. This metabolic information may provide keys to the early detection of exposure to a toxin. A typical NMR toxicology data set has low sample size and high dimensionality. Thus, traditional pattern recognition techniques are not always feasible. In this paper, we evaluate several common alternatives for isolating these biomarkers. The fold test, unpaired t-test, and paired t-test were performed on an NMR-derived toxicological data set and results were compared. The paired t-test method was preferred, due to its ability to attribute statistical significance, to …