Digital Commons Network^™

Mapk Signaling Promotes Axonal Degeneration By Speeding The Turnover Of The Axonal Maintenance Factor Nmnat2, Lauren J. Walker, Daniel W. Summers, Yo Sasaki, Ej Brace, Jeffrey Milbrandt, Aaron Diantonio

Open Access Publications

Injury-induced (Wallerian) axonal degeneration is regulated via the opposing actions of pro-degenerative factors such as SARM1 and a MAPK signal and pro-survival factors, the most important of which is the NAD

Learning Robot Control Using A Hierarchical Som-Based Encoding, Ts Dahl, G Pierris

School of Engineering, Computing and Mathematics

Hierarchical representations and modeling of sensorimotor observations is a fundamental approach for the development of scalable robot control strategies. Previously, we introduced the novel Hierarchical Self-Organizing Map-based Encoding algorithm (HSOME) that is based on a computational model of infant cognition. Each layer is a temporally augmented SOM and every node updates a decaying activation value. The bottom level encodes sensori-motor instances while their temporal associations are hierarchically built on the layers above. In the past, HSOME has shown to support hierarchical encoding of sequential sensor-actuator observations both in abstract domains and real humanoid robots. Two novel features are presented here …

Computational Analysis Of Residue Interaction Networks And Coevolutionary Relationships In The Hsp70 Chaperones: A Community- Hopping Model Of Allosteric Regulation And Communication, Gabrielle Stetz, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks …

In The News: Jan. 17, 2017, Michael Duricy

Marian Library Blog Archive

Read recent items about Mary in both Catholic and secular news. Also see International Marian Research Institute news and updates.

The Rider (2017-01-16), Jesus Sanchez

The Rider Archives

Vol.2 No.15

Persistent Amygdala Novelty Response Is Associated With Less Anterior Cingulum Integrity In Trauma-Exposed Women, Seungyeon A. Yoon, Mariann R. Weierich

Publications and Research

Objectives: We investigated the potential role of cingulum and uncinate fasciculus integrity in trauma-related neural hypervigilance, indexed by less discrimination between amygdala activation to novel and familiar affective images.

Participants: 22 women (mean age 21.7 ± 3.9 years) with a history of trauma, and 20 no-trauma controls (mean age 21.9 ± 4.8 years).

Measures: Trauma exposure and trauma-related symptoms were assessed during structured clinical interview. White matter integrity in the anterior cingulum, parahippocampal cingulum, and uncinate fasciculus was measured using diffusion weighted imaging. Amygdala response to novel and familiar affective scenes was measured with functional magnetic resonance imaging.

Results: Trauma-exposed …

Deuterateer: A Tool For Quantifying Peptide Isotope Precision And Kinetic Proteomics, Bradley C. Naylor, Michael T. Porter, Elise Wilson, Adam Herring, Spencer Lofthouse, Austin Hannemann, Stephen R. Piccolo, Alan L. Rockwood, John C. Price

Faculty Publications

Motivation

Using mass spectrometry to measure the concentration and turnover of the individual proteins in a proteome, enables the calculation of individual synthesis and degradation rates for each protein. Software to analyze concentration is readily available, but software to analyze turnover is lacking. Data analysis workflows typically don’t access the full breadth of information about instrument precision and accuracy that is present in each peptide isotopic envelope measurement. This method utilizes both isotope distribution and changes in neutromer spacing, which benefits the analysis of both concentration and turnover.

Results

We have developed a data analysis tool, DeuteRater, to measure protein …

A Computational Psychiatry Approach Identifies How Alpha-2a Noradrenergic Agonist Guanfacine Affects Feature-Based Reinforcement Learning In The Macaque, S. A. Hassani, M. Oemisch, M. Balcarras, S. Westendorff, S Ardid, M. A. Van Der Meer, P. Tiesinga, T. Womelsdorf

Dartmouth Scholarship

Noradrenaline is believed to support cognitive flexibility through the alpha 2A noradrenergic receptor (a2A-NAR) acting in prefrontal cortex. Enhanced flexibility has been inferred from improved working memory with the a2A-NA agonist Guanfacine. But it has been unclear whether Guanfacine improves specific attention and learning mechanisms beyond working memory, and whether the drug effects can be formalized computationally to allow single subject predictions. We tested and confirmed these suggestions in a case study with a healthy nonhuman primate performing a feature-based reversal learning task evaluating performance using Bayesian and Reinforcement learning models. In an initial dose-testing phase we found a Guanfacine …

Estimating Methane Emissions From Biological And Fossil-Fuel Sources In The San Francisco Bay Area, Seongeun Jeong, Xinguang Cui, Donald Blake, Ben Miller, Stephen Montzka, Arlyn Andrews, Abhinav Guha, Philip Martien, Ray Bambha, Brian Lafranchi, Hope Michelsen, Craig Clements, Pierre Glaize, Marc Fischer

Faculty Publications, Meteorology and Climate Science

We present the first sector-specific analysis of methane (CH4) emissions from the San Francisco Bay Area (SFBA) using CH4 and volatile organic compound (VOC) measurements from six sites during September – December 2015. We apply a hierarchical Bayesian inversion to separate the biological from fossil-fuel (natural gas and petroleum) sources using the measurements of CH4 and selected VOCs, a source-specific 1 km CH4 emission model, and an atmospheric transport model. We estimate that SFBA CH4 emissions are 166–289 Gg CH4/yr (at 95% confidence), 1.3–2.3 times higher than a recent inventory with much of the underestimation from landfill. Including the VOCs, …

Conspecific Pollen On Insects Visiting Female Flowers Of Phoradendron Juniperinum (Viscaceae) In Western Arizona, William D. Wiesenborn

Western North American Naturalist

Phoradendron juniperinum (Viscaceae) is a dioecious, parasitic plant of juniper trees ( Juniperus [Cupressaceae]) that occurs from eastern California to New Mexico and into northern Mexico. The species produces minute, spherical flowers during early summer. Dioecious flowering requires pollinating insects to carry pollen from male to female plants. I investigated the pollination of P. juniperinum parasitizing Juniperus osteosperma trees in the Cerbat Mountains in western Arizona during June–July 2016. I examined pollen from male flowers, aspirated insects from female flowers, counted conspecific pollen grains on insects, and estimated floral constancy from proportions of conspecific pollen in pollen loads. The tricolpate …

Academic Voice In Scholarly Writing, Garry Gray

The Qualitative Report

Tensions across disciplines and methodologies over what constitutes appropriate academic voice in writing is far from arbitrary and instead is rooted in competing notions of epistemology, representation, and science. In this paper, I examine these tensions as well as address current issues affecting academic voice such as gender bias and the rise of social media. I begin by discussing reflexivity in research and then turn to the ways in which personal-reflexive voice has been hidden and revealed by academic writers. I also illustrate how the commercialization of academic science intersects with the use of distant-authoritative voice in sometimes corrupting ways. …

Relations In The Dyer-Laslof Algebra For Morava E-Theory, Louis Atsaves

Rose-Hulman Undergraduate Mathematics Journal

In this paper, we prove that a map u between two polynomial rings, each with an associated Adem relation, is injective. We prove injectivity of u, by first finding formulas for elements within each ring polynomial, and then by computing the map with our associated formulas. After having computed the mapping of u, we then use our computations to show that the kernel of $u$ only contains the zero vector, which proves that the map u is injective. Then having proved that the map u is injective, we then use it to find a basis for u*, the dual map …

The Mathematical Modeling Behind Duchenne Muscular Dystrophy, William A. Berrigan

Rose-Hulman Undergraduate Mathematics Journal

We look at a mathematical model for the role of the immune system in Duchenne Muscular Dystrophy. A linear stability analysis is used on a set of differential equations to determine stable and unstable states. These states are a basis for investigation into possible therapeutic treatments.

Using Biomechanical Optimization To Interpret Dancers' Pose Selection For A Partnered Spin, Megan E. Selbach-Allen

Rose-Hulman Undergraduate Mathematics Journal

Swing dancing is a high tempo, athletic form of dancing. In performing their physically rigorous jumps, lifts, and spins, dancers often talk about using the laws of physics. However, they do not have mathematical evidence to support these claims. Our goal was to determine whether expert swing dancers physically optimize their pose for a partnered spin. In a partnered spin, two dancers connect hands and spin around a single vertical axis. A biomechanical model built in Mathematica allowed comparisons of mathematically produced optimal poses to live dancers with the use of a motion capture system. We hypothesized that expert swing …

Orientability Of Phylogenetic Network Graphs, Ethan Cecchetti

Rose-Hulman Undergraduate Mathematics Journal

Traditionally, genetic history of species has been modeled using phylogenetic trees. Recently, scientists have begun using phyolgenetic networks to model more complex occurrences, such as hybridization, which cannot be displayed by trees. Phylogenetic networks are represented by network graphs which are trivalent, directed graphs without directed circuits. In this paper we discuss the mathematics of network graphs. Given an unoriented trivalent graph, we determine a necessary and sufficient condition for orienting the graph as a network graph.

A Review Of The Potts Model, Laura Beaudin

Rose-Hulman Undergraduate Mathematics Journal

This paper examines a mathematical modeling tool for complex systems with nearest neighbor interactions known as the Potts model. We begin by explaining the structure of the model and defining its Hamiltonian, probability function, and partition function. We then focus on the partition function, giving examples and showing the equivalence of two different formulations. We then introduce the Tutte polynomial a well known graph invariant. We give details of the equivalence of the Tutte polynomial and the Potts model partition function. Since the Tutte polynomial, and hence the Potts model partition function, is computationally intractable, we explore Monte Carlo simulations …

Stabilizing A Subcritical Bifurcation In A Mapping Model Of Cardiac-Membrane Dynamics, Matthew Fischer, Colin Middleton

Rose-Hulman Undergraduate Mathematics Journal

In this paper we study an iterated map that describes action potential durations (acronym: APD) in a single cardiac cell. In particular, we are interested in alternans, a term which refers to phase locked period-two APDs. Under certain parameter values, alternans are theoretically possible but are unstable and therefore not seen under normal pacing conditions. We would like to stabilize alternans under these conditions using feedback. In essence, a feedback scheme uses information about previous iterates of an iterated map function to perturb future iterates in order to force stability. This paper builds on previous work on feeback control, but …

Moments Of The Distribution Of Okazaki Fragments, Krzysztof Bartoszek, Justyna Singerska

Rose-Hulman Undergraduate Mathematics Journal

This paper is a continuation of [1] which provides formulae for the probability distributions of the number of Okazaki fragments at time t during the process of DNA replication. Given the expressions for the moments of the probability distribution of the number of Okazaki fragments at time t in the recursive form, we evaluated formulae for the third and fourth moments, using Mathematica, and obtained results in explicit form. Having done this, we calculated the distribution's skewness and kurtosis.

On Large Rational Solutions Of Cubic Thue Equations: What Thue Did To Pell, Jarrod Anthony Cunningham, Nancy Ho, Karen Lostritto, Jon Anthony Middleton, Nikia Tenille Thomas

Rose-Hulman Undergraduate Mathematics Journal

In 1659, John Pell and Johann Rahn wrote a text which explained how to find all integer solutions to the quadratic equation u2 - d v2 = 1. In 1909, Axel Thue showed that the cubic equation u3 - d v3 = 1 has finitely many integer solutions, so it remains to examine their rational solutions. We explain how to find "large" rational solutions i.e., a sequence of rational points (un, vn) which increase without bound as n increases without bound. Such cubic equations are birationally equivalent to elliptic curves of the form y2 = x3 - D. The rational …

Population Dynamics With Nonlinear Diffusion, David Perry, Jessica Schaefer, Brian Schilling, Matthew Williams

Rose-Hulman Undergraduate Mathematics Journal

We consider reaction diffusion models in population dynamics where the per capita growth rate is a logistic type or a weak Allee type. In particular, we study the effects of nonlinear diffusion (arising due to aggregative population movements) on the steady states. We obtain our results via the quadrature method.

Modeling Dna Using Knot Theory:� An Introduction, Jenny Tomkins

Rose-Hulman Undergraduate Mathematics Journal

An application of mathematics to the field of molecular biology is introduced. More specifically, how knot theory can be used to model DNA recombination is explained. DNA is a long, thin molecule found tightly packed inside the nucleus of a cell. As a result of the tight packing in such a confined space the DNA becomes tangled and knotted inside the cell. Thus, the molecules must be topologically manipulated in order for vital life processes to take place. Nature�s answer to the tangling problem is enzymes. Enzymes play an important roll in affecting the topology of DNA. One way an …

Application Of The Mathematical Model Of Tumor-Immune Interactions For Il-2 Adoptive Immunotherapy To Studies On Patients With Metastatic Melanoma Or Renal Cell Cancer, Asad Usman, Chris Cunningham

Rose-Hulman Undergraduate Mathematics Journal

Recent developments in Adoptive Immunotherapy for cancer management have lead clinicians to employ these techniques in hospital settings. Much data has been produced that indicates the effectiveness of introducing enhanced and expanded immune systems into cancer hosts. In this retrospective study we take another look at the Kirschner mathematical model for immune-tumor interactions in light of data presented by Rosenburg on patients with Metastatic Melanoma or Renal Cell Cancer.

A Modified Lotka-Volterra Competition Model With A Non-Linear Relationship Between Species, Austin Taylor, Amy Crizer

Rose-Hulman Undergraduate Mathematics Journal

In this article, we consider a modified Lotka-Volterra competition model, which incorporates a non-linear relationship representing the interaction between species. We study the qualitative properties of this new system and compare them to the qualitative properties of the classical Lotka-Volterra equations and obtain results suggesting that the modified model is a better representation of some biological situations.

The Effect Of A `Smart' Predator In A One Predator, Two Prey System, Elizabeth Green

Rose-Hulman Undergraduate Mathematics Journal

This paper analyzes a food web with a predator and two non-competing preys where the predation follows the density gradient of the prey. The long-term dynamics of the food web and short-term population crashes and outbreaks are analyzed using singular perturbation analysis.

A Procedure For Determining The Exact Solution To A 2x2 First Order Homogeneous Nonautonomous System, Alexander K. Shveyd

Rose-Hulman Undergraduate Mathematics Journal

First order linear nonautonomous homogenous systems of differential equations are characterized by a matrix differential equation where the matrix is a function of the independent variable. These nonautonomous systems are used extensively in the study of Floquet and Lyapunov theories, and the applications of such systems reaches into fields such as physics, biology, and engineering. The following paper develops a technique for finding the closed form solution to a 2×2 nonautonomous system. The paper shows that the solution to such a system is directly related to the solution of a Riccati differential equation constructed from the coefficients of the system's …

Neonatal Jaundice-Its Mathematical Model And Treatments, Tram Hoang, Sazia Khan, Lorena Ortiz

Rose-Hulman Undergraduate Mathematics Journal

Neonatal jaundice (icterus neonatorium) is caused by the excessive accumulation of bilirubin, a byproduct of the red blood cells decomposition. Shortly after birth, newborn babies carry a very high level of red blood cells and thus a high concentration of bilirubin. If a baby�s liver is premature, it cannot process the bilirubin as quickly as its body produces. The excessive bilirubin then flows out of the bloodstream and permeates to the body surface causing yellow-colored skin and sclera of the eye and inside lining of the mouth. If jaundice is left untreated, the infant can develop Kernicterus, a form of …

Long Term Dynamics For Two Three-Species Food Webs, Brian Bockelman, Elizabeth Green, Leslie Lippitt, Jason Sherman

Rose-Hulman Undergraduate Mathematics Journal

In this paper, we analyze two possible scenarios for food webs with two prey and one predator (a food web is similar to a food chain except that in a web we have more than one species at some levels). In neither scenario do the prey compete, rather the scenarios differ in the selection method used by the predator. We determine how the dynamics depend on various parameter values. For some parameter values, one or more species dies out. For other parameter values, all species co-exist at equilibrium. For still other parameter values, the populations behave cyclically. We have even …

A Predator Prey Model With Disease Dynamics, Chris Flake, Tram Hoang, Elizabeth Perrigo

Rose-Hulman Undergraduate Mathematics Journal

We propose a model to describe the interaction between a diseased fish population and their predators. Analysis of the system is performed to determine the stability of equilibrium points for a large range of parameter values. The existence and uniqueness of solutions is established and solutions are shown to be uniformly bounded for all nonnegative initial conditions. The model predicts that a deadly disease and a predator population cannot co-exist. Numerical simulations illustrate a variety of dynamical behaviors that can be obtained by varying the problem data.

Mathematical Methods For Modelling Price Fluctuations Of Financial Time Series, Sabyasachi Guharay

Rose-Hulman Undergraduate Mathematics Journal

Statistical analysis of financial time series is studied. We use wavelet analysis to study signal to noise ratios along with auto-correlation function to study correlation length for time series data of daily stock prices for specific sectors of the market. We study the "high beta" stocks versus the "low beta" stocks. We sample ten companies from both of these sectors. We find that the signal to noise ratio is not uniformly high for the "high beta" classified stocks nor is the correlation length large for the "high beta" classified stocks. We explain reasons for this and possible further applications.

An Analysis Of The Belousov-Zhabotinskii Reaction, Casey Gray

Rose-Hulman Undergraduate Mathematics Journal

In this survey paper, we begin with a brief history of the celebrated Belousov-Zhabotinskii (BZ) reaction. In particular, we consider the BZ reaction in a continuously stirred, closed vessel in the presence of a ferroin indicator. We examine the underlying chemical kinetics of the most significant reactions involved. This leads to the Oregonator model and an associated 3 x 3 system of nonlinear ordinary differential equations. We nondimensionalize this system and further reduce it to a 2 x 2 stiff system. Relaxation oscillations are expected and an analysis of the phase plane confirms this. Finally, we solve the system numerically …