Digital Commons Network^™

Identifying Polyglutamine Protein Species In Situ That Best Predict Neurodegeneration, Jason Miller, Montserrat Arrasate, Elizabeth Brooks, Clare Peter Libeu, Justin Legleiter, Danny Hatters, Jessica Curtis, Kenneth Cheung, Preethi Krishnan, Siddhartha Mitra, Kartika Widjaja, Benjamin A. Shaby, Gregor P. Lotz, Yvonne Newhouse, Emily M. Sontag, Alex Osmand, Michelle Gray, Vanitha Thulasiramin, Frederic Saudou, Mark Segal, X William Yang, Eliezer Masliah, Leslie M. Thompson, Paul J. Muchowski, Karl H. Weisgraber, Steven Finkbeiner

Biological Sciences Faculty Research and Publications

Polyglutamine (polyQ) stretches exceeding a threshold length confer a toxic function to proteins that contain them and cause at least nine neurological disorders. The basis for this toxicity threshold is unclear. Although polyQ expansions render proteins prone to aggregate into inclusion bodies, this may be a neuronal coping response to more toxic forms of polyQ. The exact structure of these more toxic forms is unknown. Here we show that the monoclonal antibody 3B5H10 recognizes a species of polyQ protein in situ that strongly predicts neuronal death. The epitope selectively appears among some of the many low-molecular-weight conformational states assumed by …

Majority-Minority Voting Rights: Is Cumulative Voting A Valid Remedy For Violations Of The Voting Rights Act Or An Impermissible Tactic To Advance Racial Politics., Erica Lynne Mirehouse

The Scholar: St. Mary's Law Review on Race and Social Justice

Abstract Forthcoming.

Alignment-Free Methods And Its Applications, Ramez Mina

Student Work

Comparing biological sequences remains one of the most vital activities in Bioinformatics. Comparing biological sequences would address the relatedness between species, and find similar structures that might lead to similar functions.

Sequence alignment is the default method, and has been used in the domain for over four decades. It gained a lot of trust, but limitations and even failure has been reported, especially with the new generated genomes. These new generated genomes have bigger size, and to some extent suffer errors. Such errors come mainly as a result from the sequencing machine. These sequencing errors should be considered when submitting …

Tuning Model Reference Adaptive Controller For Avr Of Synchronous Generator, Abdulrahim Thiab

Iraqi Journal of Computers, Communications, Control and Systems Engineering

A Tuning Model Reference Adaptive Controller (TMRAC) for a synchronous generator is presented in this paper. The controller performs the function of terminal Voltage of the machine. The proposed controller is used to overcome the problems of nonlinearities and parametric uncertainties for Synchronous Generator (SG). The results verify improved performance of TMRAC compared to conventional Automatic Voltage Regulator (AVR) under various operating conditions.

Enrollment Extract Suite: Improved Enrollment Reporting For Dsu, Marilyn Halgerson

Masters Theses & Doctoral Dissertations

It has been custom in the South Dakota Higher Education system for the past thirty years to collect and report enrollment data at a central level using a central data repository. That process has evolved over the years but the basic information collected and reported remains consistent. Central computing staff at Regents Information Systems (RJS) utilizes this data for the South Dakota State Board of Regents in support of overall management of the South Dakota university higher education system. The extracted data is also used by Dakota State University (DSU) for institutional research, federal reporting, and other university data needs. …

Early Detection And Control Of Potential Pandemics., Shengpeng Jin

Electronic Theses and Dissertations

Early information is crucial for policy makers and public health officials responsible for protecting the public from the virulent spread of contagious diseases. Current indicators of the spread of contagious outbreaks lag behind the actual spread of the epidemic, leaving no time for a planned response. The studies of Christakis et al. in 2010 have shown that social networks can provide more timely information for prediction. Our focus, however, is on the effective control of the spread of contagious outbreaks in their early stages. We do this by defining a more effective way to chart the spread of contagious outbreaks, …

Avoiding, Pretending, And Querying : Three Combinatorial Problems., Adam S. Jobson

Electronic Theses and Dissertations

A k-term quasi-progression of diameter d is a sequence {Xl,... ,xk} for which there exists a positive integer l such that l < Xi-Xi-1 < l+d, for all i = 2, ... ,k. Quasi-progressions may be thought of as arithmetic progressions with a certain amount of 'wiggle-room' allowed. Let Q(d, k) be the least positive integer such that every 2-coloring of {1, ... , Q(d, k)} contains a monochromatic k-term quasi-progression of diameter d. We prove a conjecture of Landman for certain values of k and d, provide counterexamples for some other cases, and determine that the conjecture always has the correct order of growth. Let A be the adjacency matrix of a non empty graph. Is there always a nonzero {0, 1}-vector in the row space of A that is not a row of A? Akbari, Cameron, and Khosrovshahi have shown that an affirmative answer to this question would imply bounds on many graph parameters as a function of the rank of the adjacency matrix. We demonstrate the existence of such vectors for certain families of graphs, examine techniques to find and verify the existence of such vectors, and show that if you generalize the problem to allow asymmetry in the matrices then some {0, 1 }-matrices do not have such vectors. In 1981, Andrew Yao asked "Should tables be sorted?". When the table has n cells that are filled with entries taken from a key space of m possibilities, he showed that it is possible to decide whether any member of the key space is present in the table by inspecting (querying) only one cell of the table if and only if m < 2n - 2. We make steps toward extending his result to the case where you are permitted two queries by considering several variations of the problem.

Use Of Statistical Analysis, Data Mining, Decision Analysis And Cost Effectiveness Analysis To Analyze Medical Data : Application To Comparative Effectiveness Of Lumpectomy And Mastectomy For Breast Cancer., Beatrice Ugiliweneza

Electronic Theses and Dissertations

Statistical models have been the first choice for comparative effectiveness in clinical research. Though effective, these models are limited when the data to be analyzed do not fit the assumed distributions; which is mostly the case when the study is not a clinical trial. In this project, data mining, decision analysis and cost effectiveness analysis methods were used to supplement statistical models in comparing lumpectomy to mastectomy for surgical treatment of breast cancer. Mastectomy has been the gold standard for breast cancer treatment for since the 1800s. In the 20th century, an equivalence of mastectomy and lumpectomy was established in …

Acute Myocardial Infarction Patient Data To Assess Healthcare Utilization And Treatments., Pedro Ramos

Electronic Theses and Dissertations

The goal of this study is to use a data mining framework to assess the three main treatments for acute myocardial infarction: thrombolytic therapy, percutaneous coronary intervention (percutaneous angioplasty), and coronary artery bypass surgery. The need for a data mining framework in this study arises because of the use of real world data rather than highly clean and homogenous data found in most clinical trials and epidemiological studies. The assessment is based on determining a profile of patients undergoing an episode of acute myocardial infarction, determine resource utilization by treatment, and creating a model that predicts each treatment resource utilization …

An Examination Of Teacher Instruction And Student Engagement Involving Adolescents With And Without Challenging Behavior., Regina Gilkey Hirn

Electronic Theses and Dissertations

The interactions between teachers and students provide a venue for instructional delivery and ultimately student achievement in the school setting. However, not all students experience positive interactions with teachers in the typical classroom setting, especially those students exhibiting behavioral challenges. These students are observed with greater off task behavior and increased classroom disruptions when compared with their peers. This dissertation examined teacher and student behavior observed in a typical high school classroom exemplifying these interactions. Direct observations of students and teachers were conducted to answer several research questions addressing teacher behaviors: classroom instruction, opportunities to respond, and feedback to students …

Mathematical Modeling Of Peristaltic Flow Of Chyme In Small Intestine, Daniel N. Riahi, Ranadhir Roy

Applications and Applied Mathematics: An International Journal (AAM)

Mathematical models based on axisymmetric Newtonian incompressible fluid flow are studied for the peristaltic flow of chyme in the small intestines, which is an axisymmetric cylindrical tube. The flow is modeled more realistically modeled by assuming that the peristaltic rush wave is a non-periodic mode composed of two sinusoidal waves of different wavelengths, which propagate at the same speed along the outer boundary of the tube. Both cases of flow in a tube and in an annulus that are modeled and investigated in the present paper correspond respectively to the cases of flow of chyme in the small intestine in …

The Singular Perturbation In The Analysis Of Mode I Fracture Based Upon A New Multiscale Theory, Kai-Bin Fu

Applications and Applied Mathematics: An International Journal (AAM)

A theory of fracture is presented that is based upon an extension of continuum mechanics to the nanoscale fracture through the incorporation of long-range intermolecular forces which correct bulk material descriptions near interfaces. To be consistent with the literature, constant surface energies are assigned to interfaces. In the analysis of mode I fracture for quasi-brittle material, it is observed that the incorporation of these long-range intermolecular forces predicts sharp fracture tip rather than blunt and avoids stress singularity. The details of the singular perturbation employed in this analysis are also presented.

The Power Series Solution Of Fingering Phenomenon Arising In Fluid Flow Through Homogeneous Porous Media, Kinjal Patel, M. N. Mehta, Twinkle R. Patel

Applications and Applied Mathematics: An International Journal (AAM)

The present paper deals with the approximate solution of the fingering phenomenon occurring when water is pushed into oil in homogeneous porous media with capillary mean pressure. The phenomenon is formulated mathematically as a water-oil double phase flow problem. The solution of the nonlinear partial differential equation of fingering phenomenon has been discussed in terms of the power series using appropriate boundary conditions for any timeT>0 . The solution is in ascending power series which represents saturation of injected fluid in fingering phenomenon & its graphical and numerical presentation is given in MATLAB coding.

The Dynamics Of Stage Structured Prey-Predator Model Involving Parasitic Infectious Disease, Raid K. Naji, Dina S. Al-Jaf

Applications and Applied Mathematics: An International Journal (AAM)

In this paper a prey-predator model involving parasitic infectious disease is proposed and analyzed. It is assumed that the life cycle of predator species is divided into two stages immature and mature. The analysis of local and global stability of all possible subsystems is carried out. The dynamical behaviors of the model system around biologically feasible equilibria are studied. The global dynamics of the model are investigated with the help of Suitable Lyapunov functions. Conditions for which the model persists are established. Finally, to nationalize our analytical results, numerical simulations are worked out for a hypothetical set of parameter values.

Pattern Avoiding Partitions, Sequence A054391 And The Kernel Method, Toufik Mansour, Mark Shattuck

Applications and Applied Mathematics: An International Journal (AAM)

Sequence A054391 in OEIS, which we will denote by a_n , counts a certain two-pattern avoidance class of the permutations of size n . In this paper, we provide additional combinatorial interpretations for these numbers in terms of finite set partitions. In particular, we identify six classes of the partitions of size n , all of which have cardinality a_n and each avoiding two classical patterns. We use both algebraic and combinatorial methods to establish our results. In one apparently more difficult case, to show the result, we make use of the kernel method in solving a system …

Reflection Of Waves In Transversely Isotropic Thermoelastic Solid, Raj R. Gupta

Applications and Applied Mathematics: An International Journal (AAM)

The main objective of the present paper is to study the propagation of waves in the transversely isotropic medium in the context of thermoelasticity with GN theory of type-II and III. By imposing the boundary conditions on the components of displacement, stresses and temperature distribution, wave equation have been solved. Numerically simulated results have been plotted graphically with respect to frequency to evince the effect of anisotropy. Keywords: Thermoelasticity, transversely isotropic, reflection, plane wave AMS 2010 No.: 74JXX, 74F, 74B, 80A. 1. Introduction In last three decades, non-classical theories involving finite speed of heat transportation in elastic solids have been …

Stability Of Stratified Couple-Stress Dusty Fluid In The Presence Of Magnetic Field Through Porous Medium, Vivek Kumar

Applications and Applied Mathematics: An International Journal (AAM)

The combined effect of magnetic field and dust particles on the stability of a stratified couplestress fluid through a porous medium is considered. For stable stratification, the system is found to be stable for disturbances of all wave numbers. The magnetic field succeeds in stabilizing the potentially unstable stratifications for a certain wave-number range which were unstable in the absence of the magnetic field. Discussions of oscillatory and non-oscillatory modes are also made.

Robust 𝒍𝟏 And 𝒍∞ Solutions Of Linear Inequalities, Maziar Salahi

Applications and Applied Mathematics: An International Journal (AAM)

Infeasible linear inequalities appear in many disciplines. In this paper we investigate the 𝑙₁ and 𝑙_∞ solutions of such systems in the presence of uncertainties in the problem data. We give equivalent linear programming formulations for the robust problems. Finally, several illustrative numerical examples using the cvx software package are solved showing the importance of the robust model in the presence of uncertainties in the problem data.

A New Algorithm For Solving Shortest Path Problem On A Network With Imprecise Edge Weight, Amit Kumar, Manjot Kumar

Applications and Applied Mathematics: An International Journal (AAM)

Nayeem and Pal (Shortest path problem on a network with imprecise edge weight, Fuzzy Optimization and Decision Making 4, 293-312, 2005) proposed a new algorithm for solving shortest path problem on a network with imprecise edge weight. In this paper the shortcomings of the existing algorithm, (Nayeem and Pal, 2005) are pointed out and to overcome these shortcomings a new algorithm is proposed. To show the advantages of the proposed algorithm over existing algorithm the numerical examples presented in (Nayeem and Pal, 2005) are solved using the proposed algorithm and obtained results are discussed.

Age, Stratigraphy And Depositional Environment Of The Pliocene Copper Canyon Formation, Death Valley, California, Torrey Nyborg

Loma Linda University Electronic Theses, Dissertations & Projects

The Copper Canyon Formation, a fluvial-lacustrine deposit exposed within the Black Mountains of Death Valley National Park, has only previously been broadly included in regional tectonic and depositional analyses. The formation is significant because it preserves numerous shoreline-playa features including highly abundant and diverse mammal and bird tracks. The formation represents a basin fill sequence consisting of approximately 1800 m of conglomerates, basalt flows, and lacustrine deposits. A measured type section along with x-ray diffraction, isotopic analysis, and thin section petrography shows an evolution of the ancient Copper Canyon lake from an hypersaline evaporative lake to a perennial saline lake …

Quantitative Comparison Of Late Effects Following Photon Versus Proton External-Beam Radiation Therapies: To Ward An Evidence-Based Approach To Selecting A Treatment Modality, Rui Zhang

Dissertations and Theses (Open Access)

Radiation therapy has been used as an effective treatment for malignancies in pediatric patients. However, in many cases, the side effects of radiation diminish these patients’ quality of life. In order to develop strategies to minimize radiogenic complications, one must first quantitatively estimate pediatric patients’ relative risk for radiogenic late effects, which has not become feasible till recently because of the calculational complexity. The goals of this work were to calculate the dose delivered to tissues and organs in pediatric patients during contemporary photon and proton radiotherapies; to estimate the corresponding risk of radiogenic second cancer and cardiac toxicity based …

In Search Of Shell Space: A Look At A Unique Sea Turtle Nesting Behavior, Mia Dawson

The Synapse: Intercollegiate science magazine

No abstract provided.

Issue 0

The Synapse: Intercollegiate science magazine

No abstract provided.

To The Brink Of Understanding, Isaac H. Mcceery

The Synapse: Intercollegiate science magazine

No abstract provided.

So That They May Model, Isaac H. Mcceery

The Synapse: Intercollegiate science magazine

No abstract provided.

Artificial Intelligence In Digital Music: Musicians Using Techology To Streamline The Creative Process, Sam Fisher

The Synapse: Intercollegiate science magazine

No abstract provided.

Kinship Between The Kingdoms: Horizontal Gene Transfer, Darrin Schultz, Ben Garfinkel

The Synapse: Intercollegiate science magazine

No abstract provided.

Its About (Geological) Time, Paris Achenbach

The Synapse: Intercollegiate science magazine

No abstract provided.

Cruzin' With Yolanda: The Life And Research Of The Biology 100 Icon

The Synapse: Intercollegiate science magazine

No abstract provided.

The Short-Term Effects Of Cortisol

The Synapse: Intercollegiate science magazine

No abstract provided.