Mathematics Commons^™

Evaluation Of Multiple Models To Distinguish Closely Related Forms Of Disease Using Dna Microarray Data: An Application To Multiple Myeloma, Johanna S. Hardin, Michael Waddell, C. David Page, Fenghuang Zhan, Bart Barlogie, John Shaughnessy, John J. Crowley

Pomona Faculty Publications and Research

Motivation: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are caused by inherited or acquired genetic mutations that manifest themselves in altered gene expression patterns in the clonally related cancer cells. Microarray technology allows for qualitative and quantitative measurements of the expression levels of thousands of genes simultaneously, and it has now been used both to classify cancers that are morphologically indistinguishable and to predict response to therapy. It is …

Modeling Of The Inverse Heat -Conduction Problem With Application To Laser Chemical Vapor Deposition And Bioheat Transfer, Peng Zhen

Doctoral Dissertations

This dissertation consists of two parts. Part one deals with three-dimensional laser induced chemical vapor deposition (3D-LCVD), whereas part two deals with a Pennes model of a 3D skin structure. LCVD is an important technique in manufacturing complex micro-structures with high aspect ratio. In part one, a numerical model was developed for simulating kinetically-limited growth of an axisymmetric cylindrical rod by pre-specifying the surface temperature distribution required for growing the rod and then by obtaining optimized laser power that gives rise to the pre-specified temperature distribution. The temperature distribution at the surface of the rod was assumed to be at …

Sheep Updates 2003 - Wool, Richard Coole, Stephen Gherardi, Chris Oldham, K. Curtis, J. Stanton, Johan Greeff, Chris Oldham, Mike Hyder, Beth Pagamoni, Andrew Thompson, Tom Plaisted, Kazue Tanaka, Mike Ferguson, Darren Gordon, Andrew Peterson, Peter Sommerville

Sheep Updates

This session covers six papers from different authors:1.‘Pastures from space’ - an opportunity to increase the profitability of sheep production Richard Coole Farmer Kojonup W.A. Stephen Gherardi Chris Oldham Department of Agriculture Western Australia 2. K. Curtis Department of Agriculture WA J. Stanton Department of Agriculture WA and Curtin University 3. Is selection of ewe hogget replacement on measurement profitable? Johan Greeff Department of Agriculture of Western Australia 4. Optimising the nutrition/grazing management of ewe flocks Chris Oldham Mike Hyder Beth Paganoni Department of Agriculture of Western Australia Andrew Thompson Department of Primary Industries, Hamilton, Victoria Tom Plaisted Kazue Tanaka …

Taking The Sting Out Of Wasp Nests: A Dialogue On Modeling In Mathematical Biology, Jennifer C. Klein, Thomas Q. Sibley

Mathematics Faculty Publications

Wasps in hot climates build elongated nests, while in colder areas they tend to be circular. Mathematics cannot explain that, but there are questions about numbers of cells that can be answered.

Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen

Mathematics & Statistics Faculty Publications

We report our results in classifying protein matrix-assisted laser desorption/ionizationtime of flight mass spectra obtained from serum samples into diseased and healthy groups. We discuss in detail five of the steps in preprocessing the mass spectral data for biomarker discovery, as well as our criterion for choosing a small set of peaks for classifying the samples. Cross-validation studies with four selected proteins yielded misclassification rates in the 10-15% range for all the classification methods. Three of these proteins or protein fragments are down-regulated and one up-regulated in lung cancer, the disease under consideration in this data set. When cross-validation studies …

Sedimentological And Plant Taphonomic Evaluation Of The Early Middle Devonian Trout Valley Formation, Jonathan Allen

Honors Theses

The Trout Valley Formation of Emsian-Eifelian age, outcropped in Baxter State Park, Maine, consists offluvial and coastal deposits preserving early land plants. Massive, crudely bedded conglomerate represents deposits of proximal braided channels on an alluvial fan complex. Lithic sandstone bodies in channel-form geometries represent deposits of river channels draining the Acadian highlands whereas associated siltstones represent overbank deposits, intertidal flats, and tidal channels. Localized lenticular quartz arenites represent nearshore shelf bar deposits that were storm influenced. The majority of plant assemblages preserved mainly in siltstone lithologies are allochthonous and parautochthonous, with only one autochthonous assemblage identified in the sequence. Plant …

Communicator-In-Chief: Presidential Use Of Television Past, Present, And Future, Jenna Wasson

Honors Theses

This thesis seeks to determine how television has changed as a communication medium for presidents over the past half century. An evaluation of the evolving ways presidents use television to communicate with and to build support from the American people has been conducted. Presidential communication strategies have been identified by drawing primarily from primary sources written by presidents and White House staff. Television technology and the television audience have changed over the years. Presidents have taken a more pro-active, aggressive role in their efforts to harness television for their own purposes. Why have these changes occurred? What impact have these …

Environmental Factors Contributing To The Disaggregation Of A Colonial Cyanoprokaryote And Its Influence On Picoplankton Abundance Within Lake Joyce, Virginia, Lewis F. Affronti Jr., B. Thomas Duquette

Virginia Journal of Science

A colonial cyanoprokaryote, Aphanocapsa holsatica and autotrophic picoplankton abundance were monitored weekly over a two year period in Lake Joyce, Virginia. Significant differences were observed in both the cyanoprokaryote and picoplankton abundance over the study period and an inverse relationship was observed between these two plankton groups. Disaggregation of colonies was shown to contribute to picoplankton populations where water temperature and precipitation input apparently trigger colony dispersion. This relationship is suggested to occur in other aquatic habitats. Results of this work and its implications for ecosystem dynamics are discussed.

Diffusion Problems In Wound Healing And A Scattering Approach To Immune System Interactions, Julia Suzanne Arnold

Mathematics & Statistics Theses & Dissertations

A theoretical model for the existence of a Critical Size Defect (CSD) in certain animals is the focus of the majority of this dissertation. Adam [1] recently developed a one-dimensional model of this phenomenon, and chapters I–V address the exist the CSD in a two-dimensional model and a three-dimensional model. The two dimensional (or 1-d circular) model is the more appropriate for a study of CSD's. In that model we assume a circular wound of uniform depth and develop a time-independent form of the diffusion equation relevant to the study of the CSD phenomenon. It transpires that the range of …

Method For Identification Of Origins Of Replication And Genes Regulated By Dnaa In Bacteria, Olga G. Troyanskaya

Honors Theses

The study is focused on developing computer programs to identify origin of DNA replication based on analysis of total bacterial genomes, scoring regions for number of DnaA binding sites, AT content, DNA adenine methylase boxes, and integration host factors binding sites. The programs were tested on cyanobacterium Synechocystis, and several potential origins were identified. However, no one definite region could be located. Currently, software is being developed to analyze common motifs around the origins of all bacteria with known origins. Genes whose transcription could be regulated by DnaA were identified by searching for DnaA boxes preceding promoter regions.

Reaction-Diffusion Models Of Cancer Dispersion, Kim Yvette Ward

Mathematics & Statistics Theses & Dissertations

The phenomenological modeling of the spatial distribution and temporal evolution of one-dimensional models of cancer dispersion are studied. The models discussed pertain primarily to the transition of a tumor from an initial neoplasm to the dormant avascular state, i.e. just prior to the vascular state, whenever that may occur. Initiating the study is the mathematical analysis of a reaction-diffusion model describing the interaction between cancer cells, normal cells and growth inhibitor. The model leads to several predictions, some of which are supported by experimental data and clinical observations $\lbrack25\rbrack$. We will examine the effects of additional terms on these characteristics. …

Celluloid Blackness : Race, Modernity, And The Conflicted Roots Of American Cinema (1915-1939), Lincoln Farr

Honors Theses

Introduction: "The Problem of the Twentieth Century" In a full page interview in the New York Times on May 29, 1912, the Swiss psychiatrist Dr. Carl G. Jung told the American people, "It seems to me that you are about to discover yourselves. You have discovered everything else-all the land of this continent; all the resources, all the hidden things of nature."Jung used the interview to address the American people, at a moment which he somehow recognized as crucial in the development of human civilization. America, the "tragic" country which he struggled to comprehend, would soon become the harbinger of …

Genetic Algorithms: A Visual Search, Paul W. Jones

Honors Theses, 1963-2015

Genetic algorithms apply the biological principles of selection, mutation, and crossover to a population set containing individuals representing target solutions to a given problem. Using these principles genetic algorithms attempt to create a migration of the individuals in subsequent generations toward the optimal solution.

This project is an attempt to visually represent the progress of a genetic algorithm. The coordinate fitness program attempts to find the maximum or minimum value of a given function. It visually represents the progress of the algorithm by providing a plot of each individual in each generation in time. It is then possible to view …

The Role Of The Federal Aid In Sportfish Restoration Program In Promoting State Marine Artificial Reef Development Activities, Loren Clark Evans

Marine Affairs Theses and Major Papers

The passage of the Wallop-Breaux Amendments to the Federal Aid in Sportfish Restoration Program (FASRP), in 1984, significantly increased the funding available to states participating in the Program. Subsequently, the FASRP became the largest single source of funding for state marine artificial reef development activities. In recent years, there has been concern among program constituents that FASRP funds are not being utilized as intended. The principle question of the current research focused on how effective FASRP subsidies have been in providing meaningful benefits to state fisheries management programs. Specifically, the research focused on the application of FASRP monies in promoting …

Complex Dynamics And Multistability In A Damped Harmonic Oscillator With Delayed Negative Feedback, Sue Ann Campbell, Jacques Bélair, Toru Ohira, John Milton

WM Keck Science Faculty Papers

A center manifold reduction and numerical calculations are used to demonstrate the presence of limit cycles, two-tori, and multistability in the damped harmonic oscillator with delayed negative feedback. This model is the prototype of a mechanical system operating with delayed feedback. Complex dynamics are thus seen to arise in very plausible and commonly occurring mechanical and neuromechanical feedback systems.

Transitions In Masculinity And Hemingway's Developed "Code", Daniel Polk

Honors Theses

The "Hemingway Code" is much more than two words that fit nicely together for a scholar's usage; the words signify a much deeper championing of masculinity, almost a haunting presence. For Ernest Hemingway living life every day, every moment with its fullest masculine fervor, became an obsession, a never-ending quest to be at one with the attitude of never complaining, never crying out, panicking, thinking too much, or regretting. To live a manly life in a series of tactical victories, performed with steadfast ritualistic mannerisms, is to embody masculinity, and therefore the "Hemingway Code."

Approximation Methods For Singular Diffusions Arising In Genetics, Nacer E. Abrouk

Mathematical Sciences Technical Reports (MSTR)

Stochastic models in population genetics leading to diffusion equations are considered. When the drift and the square of the diffusion coefficients are polynomials, an infinite system of ordinary differential equations for the moments of the diffusion process can be derived using the Martingale property. An example is provided to show how the classical Fokker-Planck Equation approach may not be appropriate for this derivation. A Gauss-Galerkin method for approximating the laws of the diffusion, originally proposed by Dawson (1980), is examined. In the few special cases for which exact solutions are known, comparison shows that the method is accurate and the …

Mathematical Programming Applications In Agroforestry Planning, Laurence H. Reeves

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Agroforestry as a sustainable production system has been recognized as a land use system with the potential to slow encroachment of agriculture onto forested lands in developing countries. However, the acceptance of nontraditional agroforestry systems has been hampered in some areas due to the risk-averse nature of rural agriculturalists. By explicitly recognizing risk in agroforestry planning, a wider acceptance of agroforestry is possible. This thesis consists of a collection of three papers that explore the potential of modern stock portfolio theory to reduce financial risk in agroforestry planning.

The first paper presents a theoretical framework that incorporates modern stock portfolio …

Activator-Inhibitor Control Of Tissue Growth, John A. Adam

Mathematics & Statistics Faculty Publications

This note develops a simple model for the competition between activator and inhibitor control mechanisms in one-dimensional tissue growth. The pedagogic usefulness of such a model is that it is easily accessible to undergraduate applied mathematicians and is suggestive of behavior known to occur in more realistic biological systems (e.g., some types of cancer). The limitations of the model are obvious and can provide a basis for discussion of the applicability of complementary levels of description in mathematical modeling.

Rise To Power Of Senator Joseph R. Mccarthy: Reflections Of The Cold War Mccarthy Era In American Film, Scott Lainer

Honors Theses

The common bond between much of the film industry and Joseph McCarthy was insecurity and the drive for national approval. If one grasps the specific characteristics of McCarthy the man, and the methods of these politically "inspired" movies, we can to better place the period into context and acknowledge the fact that, if the citizenry is not aware, and is again caught by an ever-building wave of trickle down sentiment, the 1950s might not prove to be an isolated period in American history. Insecurity was not a fifties novelty. It still exists, and could potentially escalate anti-Communist policy and sentiment …

An Analysis Of The Massachusetts Inshore Lobster Fishery, Peter Robertson Hoar

Marine Affairs Theses and Major Papers

The purpose of this thesis was to explore the limited entry alternative of fishery management by examining the history of a particular limited entry scheme: the Massachusetts inshore commercial lobster fishery license limitation law. A review was made of existing limited entry theory, followed by a description of limited entry programs extant in U.S. fisheries. The legislative and political histories of the Massachusetts lobster fishery limited entry program was then examined. The limited entry law was then analyzed by comparing what actually occurred with what is supposed to occur according to limited entry theory. A quantitative analysis of changes in …

Sequence Alignment With Matched Sections, Jerrold R. Griggs, Philip J. Hanlon, Michael S. Waterman

Faculty Publications

In molecular biology, two finite sequences are compared by displaying one sequence written over another in an alignment. The number of alignments of two sequences is related to the Stanton-Cowan numbers. This paper gives asymptotics for the number of alignments of two sequences of length n with matching sections of size at least b.

Mathematical Programming Model Of Western Australian Dairy Farms, G R. Olney, D A. Falconer

Animal production and livestock research reports

A profit maximising mathematical programming dairy farm model has been developed which determines the most profitable management strategies for the full year. This model was initially an extension of the one used in the Western Australian Dairy Feed Management Service (DFMS) which determines the most profitable ration to feed for a specific period, the milk yield per cow and the number of cows to milk. The DFMS is useful for formulating a ration for a specific period, particularly during summer on non-irrigated farms in Western Australia when complete hand feeding is required, but it cannot be used to determine optimum …

Role And Responsibilities Of State Cooperative Extension Services For Wildlife Damage Control, James L. Byford

Wildlife Damage Management Conference

The Cooperative Extension Service was established by the Smith-Lever Act in 1914. It was designed to improve the lives of people, through education in: agriculture, natural resources, home economics and community development. Its audiences include both adult and youth. 4-H is the primary youth audience. The Cooperative Extension Service is an "extension" of the Land employees include university faculty (specialists) and professional agents in every county, in every state in the country. Extension's primary mission is to conduct an educational program, using research-based information. Research results are condensed into a form that the average person can understand. The role of …

An Iteration Formula For Finding Roots Of Equations, R. W. P. Masenge

Tanzania Journal of Science

We seek the roots of the equation f(x) = 0.