Mathematics Commons^™

Development And Implementation Of High-Throughput Snpgenotyping In Barley, Serdar Bozdag, Timothy J. Close, Prasanna R. Bhat, Stefano Lonardi, Yonghui Wu, Nils Rostoks, Luke Ramsay, Arnis Druka, Nils Stein, Jan T. Svensson, Steve Wanamaker, Mikeal L. Roose, Matthew J. Moscou, Shiaoman Chao, Rajeev K. Varshney, Peter Szucs, Kazuhiro Sato, Patrick M. Hayes, David E. Matthews, Andris Kleinhofs, Gary J. Muehlbauer, Joseph Deyoung, David F. Marshall, Kavitha Madishetty, Raymond D. Fenton, Pascal Condamine, Andreas Graner, Robbie Waugh

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of …

Design And Implementation Of S-Marks: A Secure Middleware For Pervasive Computing Applications, Sheikh Iqbal Ahamed, Haifeng Li, Nilothpal Talukder, Mehrab Monjur, Chowdhury Sharif Hasan

Mathematics, Statistics and Computer Science Faculty Research and Publications

As portable devices have become a part of our everyday life, more people are unknowingly participating in a pervasive computing environment. People engage with not a single device for a specific purpose but many devices interacting with each other in the course of ordinary activity. With such prevalence of pervasive technology, the interaction between portable devices needs to be continuous and imperceptible to device users. Pervasive computing requires a small, scalable and robust network which relies heavily on the middleware to resolve communication and security issues. In this paper, we present the design and implementation of S-MARKS which incorporates device …

A Compartmentalized Approach To The Assembly Of Physical Maps, Serdar Bozdag, Timothy J. Close, Stefano Lonardi

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background: Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint data. Results: We propose a novel compartmentalized method for the assembly of high quality physical maps from fingerprinted clones. The knowledge of genetic markers enables us to group clones into clusters so that clones in the same cluster are more likely to overlap. For each cluster of clones, a local physical map is first …

Compartmentalized Approach To The Assembly Of Physical Maps, Serdar Bozdag, Timothy J. Close, Stefano Lonardi

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint data.

Results

We propose a novel compartmentalized method for the assembly of high quality physical maps from fingerprinted clones. The knowledge of genetic markers enables us to group clones into clusters so that clones in the same cluster are more likely to overlap. For each cluster of clones, a local physical map is first …

Development And Implementation Of High-Throughput Snp Genotyping In Barley, Timothy J. Close, Prasanna R. Bhat, Stefano Lonardi, Yonghui Wu, Nils Rostoks, Luke Ramsay, Arnis Druka, Nils Stein, Jan T. Svensson, Steve Wanamaker, Serdar Bozdag, Mikeal L. Roose, Matthew J. Moscou, Shiaoman Chao, Rajeev K. Varshney, Peter Szucs, Kazuhiro Sato, Patrick M. Hayes, David E. Matthews, Andris Kleinhofs, Gary J. Muehlbauer, Joseph Deyoung, David F. Marshall, Kavitha Madishetty, Raymond D. Fenton, Pascal Condamine, Andreas Graner, Robbie Waugh

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of …

Preferential Utilization Of Nadph As The Endogenous Electron Donor For Nad(P)H:Quinone Oxidoreductase 1 (Nqo1) In Intact Pulmonary Arterial Endothelial Cells, Robert D. Bongard, Brian J. Lindemer, Gary S. Krenz, Marilyn P. Merker

Mathematics, Statistics and Computer Science Faculty Research and Publications

The goal was to determine whether endogenous cytosolic NAD(P)H:quinone oxidoreductase 1 (NQO1) preferentially uses NADPH or NADH in intact pulmonary arterial endothelial cells in culture. The approach was to manipulate the redox status of the NADH/NAD⁺ and NADPH/NADP⁺ redox pairs in the cytosolic compartment using treatment conditions targeting glycolysis and the pentose phosphate pathway alone or with lactate, and to evaluate the impact on the intact cell NQO1 activity. Cells were treated with 2-deoxyglucose, iodoacetate, or epiandrosterone in the absence or presence of lactate, NQO1 activity was measured in intact cells using duroquinone as the electron acceptor, and …

Dendrites, Topological Graphs, And 2-Dominance, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

For each positive ordinal α, the reflexive and transitive binary relation of α-dominance between compacta was first defined in our paper [Mapping properties of co-existentially closed continua, Houston J. Math., 31 (2005), 1047-1063] using the ultracopower construction. Here we consider the important special case α =2, and show that any Peano compactum 2-dominated by a dendrite is itself a dendrite (with the same being true for topological graphs and trees). We also characterize the topological graphs that 2-dominate arcs (resp., simple closed curves) as those that have cut points of order 2 (resp., those that are not trees).

A Trust-Based Secure Service Discovery (Tssd) Model For Pervasive Computing, Sheikh Iqbal Ahamed, Moushumi Sharmin

Mathematics, Statistics and Computer Science Faculty Research and Publications

To cope with the challenges posed by device capacity and capability, and also the nature of ad hoc networks, a Service discovery model is needed that can resolve security and privacy issues with simple solutions. The use of complex algorithms and powerful fixed infrastructure is infeasible due to the volatile nature of pervasive environment and tiny pervasive devices. In this paper, we present a trust-based secure Service discovery model, TSSD (trust-based secure service discovery) for a truly pervasive environment. Our model is a hybrid one that allows both secure and non-secure discovery of services. This model allows Service discovery and …

Ubi-App: A Ubiquitous Application For Universal Access From Handheld Devices, Shameem Ahmed, Moushumi Sharmin, Sheikh Iqbal Ahamed

Mathematics, Statistics and Computer Science Faculty Research and Publications

Universal access from a handheld device (such as a PDA, cell phone) at any time or anywhere is now a reality. Ubicomp Assistant (UA) (Sharmin et al. in Proceedings of the 21st annual ACM symposium on applied computing (ACM SAC 2006), Dijon, France, pp 1013–1017, 2006) is an integral service of MARKS (Sharmin et al. in Proceedings of the third international conference on information technology: new generations (ITNG 2006), Las Vegas, Nevada, USA, pp 306–313, 2006). It is a middleware developed for handheld devices, and has been designed to accommodate different types of users (e.g., education, healthcare, marketing, or business). …

Coenzyme Q1 Redox Metabolism During Passage Through The Rat Pulmonary Circulation And The Effect Of Hyperoxia, Said H. Audi, Marilyn P. Merker, Gary S. Krenz, Taniya Ahuja, David L. Roerig, Robert D. Bongard

Mathematics, Statistics and Computer Science Faculty Research and Publications

The objective was to evaluate the pulmonary disposition of the ubiquinone homolog coenzyme Q₁ (CoQ₁) on passage through lungs of normoxic (exposed to room air) and hyperoxic (exposed to 85% O₂ for 48 h) rats. CoQ₁ or its hydroquinone (CoQ₁H₂) was infused into the arterial inflow of isolated, perfused lungs, and the venous efflux rates of CoQ₁H₂ and CoQ₁ were measured. CoQ₁H₂ appeared in the venous effluent when CoQ₁ was infused, and CoQ₁ appeared when CoQ1H2 was infused. In normoxic lungs, CoQ …

A Poisson-Like Model Of Sub-Clinical Signs From The Examination Of Healthy Aging Subjects, Stephen Merrill, Barbara Myklebust, Joel B. Myklebust, Norman Reynolds, Edmund Duthie

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background and aims: Our studies of the standard neurological examination on 66 middle-aged (50–64 yrs) and elderly subjects (65–84 yrs) demonstrate that healthy elders have neurological deficits (or “signs”) that are not associated with specific known neurological disease. The purpose of the current study is to describe this loss of neurological function in healthy aging subjects as seen through accumulated subclinical neurological signs present.

Methods: Logistic regression is applied to the data on each of six signs. Parameters determined are used to describe the distribution of first occurrence times for each sign. The results are then used to construct a …

Architecture And Implementation Of A Trust Model For Pervasive Applications, Sheikh Iqbal Ahamed, Mohammad Zulkernine, Sailaja Bulusu, Mehrab Monjur

Mathematics, Statistics and Computer Science Faculty Research and Publications

Collaborative effort to share resources is a significant feature of pervasive computing environments. To achieve secure service discovery and sharing, and to distinguish between malevolent and benevolent entities, trust models must be defined. It is critical to estimate a device's initial trust value because of the transient nature of pervasive smart space; however, most of the prior research work on trust models for pervasive applications used the notion of constant initial trust assignment. In this paper, we design and implement a trust model called DIRT. We categorize services in different security levels and depending on the service requester's context information, …

An Impregnable Lightweight Device Discovery (Ildd) Model For The Pervasive Computing Environment Of Enterprise Applications, Munirul H. Haque, Sheikh Iqbal Ahamed

Mathematics, Statistics and Computer Science Faculty Research and Publications

The worldwide use of handheld devices (personal digital assistants, cell phones, etc.) with wireless connectivity will reach 2.6 billion units this year and 4 billion by 2010. More specifically, these handheld devices have become an integral part of industrial applications. These devices form pervasive ad hoc wireless networks that aide in industry applications. However, pervasive computing is susceptible and vulnerable to malicious active and passive snoopers. This is due to the unavoidable interdevice dependency, as well as a common shared medium, very transitory connectivity, and the absence of a fixed trust infrastructure. In order to ensure security and privacy in …

Molecular Targets Of 2,3,7,8-Tetrachlorodibenzo-P-Dioxin (Tcdd) Within The Zebrafish Ovary: Insights Into Tcdd-Induced Endocrine Disruption And Reproductive Toxicity, Tisha C. King Heiden, Craig Struble, Matthew L. Rise, Martin J. Hessner, Reinhold J. Hutz, Michael J. Carvan Iii

Mathematics, Statistics and Computer Science Faculty Research and Publications

TCDD is a reproductive toxicant and endocrine disruptor, yet the mechanisms by which it causes these reproductive alterations are not fully understood. In order to provide additional insight into the molecular mechanisms that underlie TCDD's reproductive toxicity, we assessed TCDD-induced transcriptional changes in the ovary as they relate to previously described impacts on serum estradiol concentrations and altered follicular development in zebrafish. In silico computational approaches were used to correlate candidate regulatory motifs with observed changes in gene expression. Our data suggest that TCDD inhibits follicle maturation via attenuated gonadotropin responsiveness and/or depressed estradiol biosynthesis, and that interference of estrogen-regulated …

Pathos: Pervasive At Home Sleep Monitoring, Ian Obermiller, Sheikh Iqbal Ahamed

Mathematics, Statistics and Computer Science Faculty Research and Publications

Sleeping disorders affect a large percentage of the population, and many of them go undiagnosed each year because the method of diagnosis is to stay overnight at a sleep center. Because pervasive technologies have become so prevalent and affordable, sleep monitoring is no longer confined to a permanent installation, and can therefore be brought directly into the user home. We present a unique solution to the problem of home sleep monitoring that has the possibility to take the place of and expand on the data from a sleep center. PATHOS focuses not only on analyzing patterns during the night, but …

Characterization Of Digraphs With Equal Domination Graphs And Underlying Graphs, Kim A. S. Factor, Larry J. Langley

Mathematics, Statistics and Computer Science Faculty Research and Publications

A domination graph of a digraph D , dom(D)dom(D), is created using the vertex set of D and edge {u,v}∈E[dom(D)]{u,v}∈E[dom(D)] whenever (u,z)∈A(D)(u,z)∈A(D) or (v,z)∈A(D)(v,z)∈A(D) for every other vertex z∈V(D)z∈V(D). The underlying graph of a digraph DD, UG(D)UG(D), is the graph for which D is a biorientation. We completely characterize digraphs whose underlying graphs are identical to their domination graphs, UG(D)=dom(D)UG(D)=dom(D). The maximum and minimum number of single arcs in these digraphs, and their characteristics, is given.

Empirical Bayes And Hierarchical Bayes Estimation Of Skew Normal Populations, Naveen K. Bansal, Mehdi Maadooliat, Xiaowei Wang

Mathematics, Statistics and Computer Science Faculty Research and Publications

We develop empirical and hierarchical Bayesian methodologies for the skew normal populations through the EM algorithm and the Gibbs sampler. A general concept of skewness to the normal distribution is considered throughout. Motivations are given for considering the skew normal population in applications, and an example is presented to demonstrate why the skew normal distribution is more applicable than the normal distribution for certain applications.

Unit Rectangle Visibility Graphs, Alice M. Dean, Joanna A. Ellis-Monaghan, Sarah J. Hamilton, Greta Pangborn

Mathematics, Statistics and Computer Science Faculty Research and Publications

Over the past twenty years, rectangle visibility graphs have generated consider- able interest, in part due to their applicability to VLSI chip design. Here we study unit rectangle visibility graphs, with fixed dimension restrictions more closely modeling the constrained dimensions of gates and other circuit components in computer chip applications. A graph G is a unit rectangle visibility graph (URVG) if its vertices can be represented by closed unit squares in the plane with sides parallel to the axes and pairwise disjoint interiors, in such a way that two vertices are adjacent if and only if there is a non-degenerate …

A Software-Based Trust Framework For Distributed Industrial Management Systems, Sheikh Iqbal Ahamed, Mohammad Zulkernine, Steve Wolfe

Mathematics, Statistics and Computer Science Faculty Research and Publications

One of the major problems in industrial security management is that most organizations or enterprises do not provide adequate guidelines or well-defined policy with respect to trust management, and trust is still an afterthought in most security engineering projects. With the increase of handheld devices, managers of business organizations tend to use handheld devices to access the information systems. However, the connection or access to an information system requires appropriate level of trust. In this paper, we present a flexible, manageable, and configurable software-based trust framework for the handheld devices of mangers to access distributed information systems. The presented framework …

Ets (Efficient, Transparent, And Secured) Self-Healing Service For Pervasive Computing Applications, Shameem Ahmed, Moushumi Sharmin, Sheikh Iqbal Ahamed

Mathematics, Statistics and Computer Science Faculty Research and Publications

To ensure smooth functioning of numerous handheld devices anywhere anytime, the importance of self-healing mechanism cannot be overlooked. Incorporation of efficient fault detection and recovery in device itself is the quest for long but there is no existing self-healing scheme for devices running in pervasive computing environments that can be claimed as the ultimate solution. Moreover, the highest degree of transparency, security and privacy attainability should also be maintained. ETS Self-healing service, an integral part of our developing middleware named MARKS (Middleware Adaptability for Resource discovery, Knowledge usability, and Self-healing), holds promise for offering all of those functionalities.

Security In Pervasive Computing: Current Status And Open Issues, Munirul Haque, Sheikh Iqbal Ahamed

Mathematics, Statistics and Computer Science Faculty Research and Publications

Million of wireless device users are ever on the move, becoming more dependent on their PDAs, smart phones, and other handheld devices. With the advancement of pervasive computing, new and unique capabilities are available to aid mobile societies. The wireless nature of these devices has fostered a new era of mobility. Thousands of pervasive devices are able to arbitrarily join and leave a network, creating a nomadic environment known as a pervasive ad hoc network. However, mobile devices have vulnerabilities, and some are proving to be challenging. Security in pervasive computing is the most critical challenge. Security is needed to …

Chainability And Hemmingsen's Theorem, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

On the surface, the definitions of chainability and Lebesgue covering dimension ⩽1 are quite similar as covering properties. Using the ultracoproduct construction for compact Hausdorff spaces, we explore the assertion that the similarity is only skin deep. In the case of dimension, there is a theorem of E. Hemmingsen that gives us a first-order lattice-theoretic characterization. We show that no such characterization is possible for chainability, by proving that if κ is any infinite cardinal and AA is a lattice base for a nondegenerate continuum, then AA is elementarily equivalent to a lattice base for a continuum Y …

Specific Antibodies To Recombinant Allergens Of Aspergillus Fumigatus In Cystic Fibrosis Patients With Abpa, Viswanath P. Kurup, Alan P. Knutsen, Richard B. Moss, Naveen K. Bansal

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

Aspergillus fumigatus, a widely distributed fungus, has been implicated in causing life threatening infections as well as severe asthma and allergic diseases in man. Allergic affliction like allergic bronchopulmonary aspergillosis (ABPA) is a disabling lung disease frequently seen in patients with asthma and cystic fibrosis. Immunodiagnosis of the former is comparatively easier due to the availability of purified antigens and sensitive methods. However, this is not true with cystic fibrosis patients where the prevalence of ABPA is fairly high and the morbidity and mortality are significant.

Methods

In the present study, we have evaluated purified recombinant allergens from …

The Chang-Los-Suszko Theorem In A Topological Setting, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

The Chang-Łoś-Suszko theorem of first-order model theory characterizes universal-existential classes of models as just those elementary classes that are closed under unions of chains. This theorem can then be used to equate two model-theoretic closure conditions for elementary classes; namely unions of chains and existential substructures. In the present paper we prove a topological analogue and indicate some applications.

The Stochastic Dance Of Early Hiv Infection, Stephen J. Merrill

Mathematics, Statistics and Computer Science Faculty Research and Publications

The stochastic nature of early HIV infection is described in a series of models, each of which captures aspects of the dance of HIV during the early stages of infection. It is to this highly variable target that the immune response must respond. The adaptability of the various components of the immune response is an important aspect of the system's operation, as the nature of the pathogens that the response will be required to respond to and the order in which those responses must be made cannot be known beforehand. As HIV infection has direct influence over cells responsible for …

Specific Ige Response To Purified And Recombinant Allergens In Latex Allergy, Viswanath P. Kurup, Gordon L. Sussman, Hoong Y. Yeang, Nancy Elms, Heimo Breiteneder, Siti Am Arif, Kevin J. Kelly, Naveen K. Bansal, Jordan N. Fink

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

In recent years, allergy to natural rubber latex has emerged as a major allergy among certain occupational groups and patients with underlying diseases. The sensitization and development of latex allergy has been attributed to exposure to products containing residual latex proteins. Although improved manufacturing procedures resulted in a considerable reduction of new cases, the potential risk for some patient groups is still great. In addition the prevalent cross-reactivity of latex proteins with other food allergens poses a major concern. A number of purified allergens and a few commercial kits are currently available, but no concerted effort was undertaken to …

Mapping Properties Of Co-Existentially Closed Continua, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

A continuous surjection between compacta is called co-existential if it is the second of two maps whose composition is a standard ultracopower projection. A continuum is called co-existentially closed if it is only a co-existential image of other continua. This notion is not only an exact dual of Abraham Robinson's existentially closed structures in model theory, it also parallels the definition of other classes of continua defined by what kinds of continuous images they can be. In this paper we continue our study of co-existentially closed continua, especially how they (and related continua) behave in certain mapping situations.

Modulation Of Airway Inflammation By Immunostimulatory Cpg Oligodeoxynucleotides In A Murine Model Of Allergic Aspergillosis, Banani Banerjee, Kevin J. Kelly, Jordan N. Fink, James D. Henderson Jr., Naveen K. Bansal, Viswanath P. Kurup

Mathematics, Statistics and Computer Science Faculty Research and Publications

Allergic aspergillosis is a Th2 T-lymphocyte-mediated pulmonary complication in patients with atopic asthma and cystic fibrosis. Therefore, any therapeutic strategy that selectively inhibits Th2 T-cell activation may be useful in downregulating allergic lung inflammation in asthma. In the present study, we developed a CpG oligodeoxynucleotide (ODN)-based immune intervention of allergic inflammation in a mouse model of allergic aspergillosis. Four different groups of mice were used in a short-term immunization protocol. Three experimental groups of animals (groups 1 to 3) were sensitized with Aspergillus fumigatus antigens. Animals in group 1 were immunized with A. fumigatus antigen alone, while those in group …

Deadline Analysis Of Interrupt-Driven Software, Dennis Brylow, Jens Palsberg

Mathematics, Statistics and Computer Science Faculty Research and Publications

Real-time, reactive, and embedded systems are increasingly used throughout society (e.g., flight control, railway signaling, vehicle management, medical devices, and many others). For real-time, interrupt-driven software, timely interrupt handling is part of correctness. It is vital for software verification in such systems to check that all specified deadlines for interrupt handling are met. Such verification is a daunting task because of the large number of different possible interrupt arrival scenarios. For example, for a Z86-based microcontroller, there can be up to six interrupt sources and each interrupt can arrive during any clock cycle. Verification of such systems has traditionally relied …

Gamma-Set Domination Graphs. I: Complete Biorientations Of Q-Extended Stars And Wounded Spider Graphs, Kim A. S. Factor

Mathematics, Statistics and Computer Science Faculty Research and Publications

The domination number of a graph G, γ(G), and the domination graph of a digraph D, dom(D) are integrated in this paper. The γ-set domination graph of the complete biorientation of a graph G, dom_γ(G) is created. All γ-sets of specific trees T are found, and dom-_γ(T) is characterized for those classes.