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Search Results: 1 - 10 of 1062 matches for " Jesse Newby "
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Seasonal Foraging Ecology of Non-Migratory Cougars in a System with Migrating Prey
L. Mark Elbroch, Patrick E. Lendrum, Jesse Newby, Howard Quigley, Derek Craighead
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0083375
Abstract: We tested for seasonal differences in cougar (Puma concolor) foraging behaviors in the Southern Yellowstone Ecosystem, a multi-prey system in which ungulate prey migrate, and cougars do not. We recorded 411 winter prey and 239 summer prey killed by 28 female and 10 male cougars, and an additional 37 prey items by unmarked cougars. Deer composed 42.4% of summer cougar diets but only 7.2% of winter diets. Males and females, however, selected different proportions of different prey; male cougars selected more elk (Cervus elaphus) and moose (Alces alces) than females, while females killed greater proportions of bighorn sheep (Ovis canadensis), pronghorn (Antilocapra americana), mule deer (Odocoileus hemionus) and small prey than males. Kill rates did not vary by season or between males and females. In winter, cougars were more likely to kill prey on the landscape as: 1) elevation decreased, 2) distance to edge habitat decreased, 3) distance to large bodies of water decreased, and 4) steepness increased, whereas in summer, cougars were more likely to kill in areas as: 1) elevation decreased, 2) distance to edge habitat decreased, and 3) distance from large bodies of water increased. Our work highlighted that seasonal prey selection exhibited by stationary carnivores in systems with migratory prey is not only driven by changing prey vulnerability, but also by changing prey abundances. Elk and deer migrations may also be sustaining stationary cougar populations and creating apparent competition scenarios that result in higher predation rates on migratory bighorn sheep in winter and pronghorn in summer. Nevertheless, cougar predation on rare ungulates also appeared to be influenced by individual prey selection.
Bistable switching asymptotics for the self regulating gene
Jay Newby
Physics , 2014,
Abstract: A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate. Before an mRNA is degraded, it synthesizes protein, which in turn regulates gene activity by influencing the activity of transcription factors. Protein is slowly removed from the system through degradation. Depending on how the protein regulates gene activity, the protein concentration can exhibit noise induced bistable switching. An asymptotic approximation of the mean switching rate is derived that includes the pre exponential factor, which improves upon a previously reported logarithmically accurate approximation. With the improved accuracy, a uniformly accurate approximation of the stationary probability density, describing the gene, mRNA copy number, and protein concentration is also obtained.
Spontaneous excitability in the Morris--Lecar model with ion channel noise
Jay Newby
Quantitative Biology , 2014,
Abstract: Noise induced excitability is studied in type I and II Morris-Lecar neurons subject to constant sub threshold input, where fluctuations arise from sodium and potassium ion channels. Ion channels open and close randomly, creating current fluctuations that can induce spontaneous firing of action potentials. Both noise sources are assumed to be weak so that spontaneous action potentials occur on a longer timescale than ion channel fluctuations. Asymptotic approximations of the stationary density function and most probable paths are developed to understand the role of channel noise in spontaneous excitability. Even though the deterministic dynamical behavior of type I and II action potentials differ, results show that a single mechanism explains how ion channel noise generates spontaneous action potentials.
Asymptotic and numerical methods for metastable events in stochastic gene networks
Jay Newby
Quantitative Biology , 2014,
Abstract: A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating when the proteins they produce affect the rate of switching between regulatory states. Under weak noise conditions, the deterministic forces are much stronger than fluctuations from gene switching and protein synthesis. Metastable transitions, such as bistable switching, can occur under weak noise conditions, causing dramatic shifts in the expression of a gene. A general tool used to describe metastability is the quasi stationary analysis (QSA). A large deviation principle is derived so that the QSA can explicitly account for random gene switching without using an adiabatic limit or diffusion approximation, which are unreliable and inaccurate for metastable events.This allows the existing asymptotic and numerical methods that have been developed for continuous Markov processes to be used to analyze the full model.
Isolating intrinsic noise sources in a stochastic genetic switch
Jay Newby
Quantitative Biology , 2011, DOI: 10.1088/1478-3975/9/2/026002
Abstract: The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule that binds to the promotor of the other gene. When the repressor is bound to a promotor, the corresponding gene is not transcribed and no protein is produced. Either one of the promotors can be repressed at any given time or both can be unrepressed, leaving three possible promotor states. This model is analysed in its bistable regime in which the deterministic limit exhibits two stable fixed points and an unstable saddle, and the case of small noise is considered. On small time scales, the stochastic process fluctuates near one of the stable fixed points, and on large time scales, a metastable transition can occur, where fluctuations drive the system past the unstable saddle to the other stable fixed point. To explore how different intrinsic noise sources affect these transitions, fluctuations in protein production and degradation are eliminated, leaving fluctuations in the promotor state as the only source of noise in the system. Perturbation methods are then used to compute the stability landscape and the distribution of transition times, or first exit time density. To understand how protein noise affects the system, small magnitude fluctuations are added back into the process, and the stability landscape is compared to that of the process without protein noise. It is found that significant differences in the random process emerge in the presence of protein noise.
The Necessity for Information Space Mapping for Information Retrieval on the Semantic Web
Gregory B. Newby
Information Research: an international electronic journal , 2002,
Abstract: The Semantic Web offers exciting possibilities for information retrieval (IR). In IR, we would like systems that go beyond simply matching words in documents and queries, and instead match based on topic, data type, relations among data, and many other qualities. The Semantic Web, through fuzzy matching of information spaces from different sources, will provide for much more specific information seeking than current Web-based search engines or other IR systems. In order to succeed, however, it is necessary to map between the differing schema, metadata standards, namespaces and so forth used by documents on the Semantic Web. This information space mapping may be accomplished by a simple match or table lookup when document sets come from similar or otherwise well-defined domains. When the match is less precise, sets of rules or algorithms may be employed to map between information spaces. When schema or metadata are inconsistent, though, we are left with a similar data environment as the modern Web, and must rely on the context of the documents themselves to determine the mapping between information spaces.
Efectos del idioma en el estimulo de retrievabilidad en la asociacion libre
Robert W. Newby
Revista Latinoamericana de Psicología , 1976,
Abstract: Ease of free reeal], of ltimuli following paired-assodate (PA) leaming was studied varying relatedness of the PA responses and the langue.ge in which the responses were written. In two of the PA lists the responses were grouped according to four categories; the third líst was unrelated, In each Hst one half of the responses were in Spanísh and one half were in English. Following PA Iearning the Ss recalled the stimuli under three condítíons, related eued,:related uncued, and unrelated, It was faund that the stimuli were grouped according to the language of the responses and not according to the category.
Metastable behavior in Markov processes with internal states
Jay Newby,Jon Chapman
Quantitative Biology , 2013, DOI: 10.1007/s00285-013-0723-1
Abstract: A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is bistable is considered. A general analytical approximation is derived for the stationary probability density and the mean switching time between metastable states, which includes the pre exponential factor. The results are illustrated with a model of gene expression that displays bistable switching. In this model, the external state represents the number of protein molecules produced by a hypothetical gene. Once produced, a protein is eventually degraded. The internal state represents the activated or unactivated state of the gene; in the activated state the gene produces protein more rapidly than the unactivated state. The gene is activated by a dimer of the protein it produces so that the activation rate depends on the current protein level. This is a well studied model, and several model reductions and diffusion approximation methods are available to analyze its behavior. However, it is unclear if these methods accurately approximate long-time metastable behavior (i.e., mean switching time between metastable states of the bistable system). Diffusion approximations are generally known to fail in this regard.
The interface between metallurgy and mechanics in material performance
M. N. James,M. Newby
Frattura ed Integrità Strutturale , 2010,
Abstract: This paper considers an important topic, and one that is often poorly understood or misinterpreted, but which is a determining factor in many aspects of the service performance of metals (and other materials). Engineering components and structures must, of necessity, provide a bridge between the macroscopic, homogeneous and generally continuum aspects of applied load and displacement, and the microscopic, heterogeneous and often non-continuum reality of material structure and behaviour. This bridge can take the form of a genuine interface between material and environment, e.g. at a surface, or can be a virtual one where the differing philosophies of design have to be merged. The interface has particular importance in circumstances where environmental influences have a key role in determining performance characteristics (e.g. creep, environmentally-assisted cracking, or corrosion), where performance is dominated by fatigue or fracture, where welding is used to join components, or where tribology plays a role. The paper focuses on the problems associated with cracking and uses case study examples drawn from engineering practice to illustrate the role of metallurgical factors in mechanical performance of materials.
Uniform asymptotic approximation of diffusion to a small target
Samuel A. Isaacson,Jay Newby
Physics , 2013, DOI: 10.1103/PhysRevE.88.012820
Abstract: The problem of the time required for a diffusing molecule, within a large bounded domain, to first locate a small target is prevalent in biological modeling. Here we study this problem for a small spherical target. We develop uniform in time asymptotic expansions in the target radius of the solution to the corresponding diffusion equation. Our approach is based on combining short-time expansions using pseudo-potential approximations with long-time expansions based on first eigenvalue and eigenfunction approximations. These expansions allow the calculation of corresponding expansions of the first passage time density for the diffusing molecule to find the target. We demonstrate the accuracy of our method in approximating the first passage time density and related statistics for the spherically symmetric problem where the domain is a large concentric sphere about a small target centered at the origin.
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