Comparison of Approximation Schemes in Stochastic Simulation Methods for Stiff Chemical Systems

Interest in stochastic simulations of chemical systems is growing. One of the aspects of simulation of chemical systems that has been the prime focus over the past few years is accelerated simulation methods applicable when there is a separation of time scale. With so many new methods being developed we have decided to look at four methods that we consider to be the main foundation for this research area. The four methods that will be the focus of this thesis are: the slow scale stochastic simulation algorithm, the quasi steady state assumption applied to the stochastic simulation algorithm, the nested stochastic simulation algorithm and the implicit tau leaping method. These four methods are designed to deal with stiff chemical systems so that the computational time is decreased from that of the "gold standard" Gillespie algorithm, the stochastic simulation algorithm. These approximation methods will be tested against a variety of sti examples such as: a fast reversible dimerization, a network of isomerizations, a fast species acting as a catalyst, an oscillatory system and a bistable system. Also, these methods will be tested against examples that are marginally stiff, where the time scale separation is not that distinct. From the results of testing stiff examples, the slow scale SSA was typically the best approximation method to use. The slow scale SSA was highly accurate and extremely fast in comparison with the other methods. We also found for certain cases, where the time scale separation was not as distinct, that the nested SSA was the best approximation method to use

Identification of H19 polymorphism for an assessment of biallelic expression

Abstract only availableAnimals produced from assisted reproductive technologies suffer from developmental abnormalities and early fetal death at a higher frequency than that observed in those produced by natural breeding. These symptoms are reminiscent of imprinting disruptions, suggesting the possibility of an alteration in the expression of imprinted genes such as biallelic expression or silencing. H19 is one of the imprinted genes first identified in mice and humans, but its imprinting status has not been determined in pigs. The objective of this study was to identify an H19 polymorphism and estimate its frequency in the commercial pig population. In this study a polymorphism in the H19 gene was identified. The PCR products contained a pooled genome with over 900 specimens to support this finding. From the positive PCR products, the DNA was cloned and transformed with a TOPO TA Cloning kit (Invitrogen). Positive colonies were identified and digested with an AciI enzyme, which cut the DNA in specific fragments that were identifiable in a gel. Analysis of the gel showed evidence that a polymorphism exists on the H19 gene.F.B. Miller Undergraduate Research Program in Animal Science

Flooding Fragility Model Development Using Bayesian Regression

Traditional component pass/fail design analysis and testing protocol drives excessively conservative operating limits and setpoints as well as unnecessarily large margins of safety. Component performance testing coupled with failure probability model development can support selection of more flexible operating limits and setpoints as well as softening defense-in-depth elements. This chapter discuses the process of Bayesian regression fragility model development using Markov Chain Monte Carlo methods and model checking protocol using three types of Bayesian p-values. The chapter also discusses application of the model development and testing techniques through component flooding performance experiments associated with industrial steel doors being subjected to a rising water scenario. These component tests yield the necessary data for fragility model development while providing insight into development of testing protocol that will yield meaningful data for fragility model development. Finally, the chapter discusses development and selection of a fragility model for industrial steel door performance when subjected to a water-rising scenario

HE AMOT FAMILY OF PROTEINS BINDS AND ACTIVATES NEDD4 FAMILY LIGASES TO PROMOTE THE UBIQUITINATION OF LATS AND YAP

poster abstractAmot adaptor proteins bind and integrate signaling that controls cell po-larity and growth. All three Amot family members (Amot, AmotL1 and AmotL2) directly bind YAP; a transcriptional co-activator that controls the expression of genes involved in organ homeostasis and cell growth. Preven-tion of nuclear accumulation of YAP by either sequestration or degradation in the cytosol abolishes its transcriptional functions and is a major mechanism for growth arrest in response to cellular differentiation. This is mainly thought to be regulated by phosphorylation of YAP by the Hippo kinases LATS1/2. Recently, binding by the Amot proteins was also found to inhibit YAP by sequestering it in the cytosol through both LATS dependent and in-dependent mechanisms. This study identifies a novel mechanism whereby Amot proteins control YAP activation in a Hippo independent mechanism by coupling it to ubiquitination by Nedd4 family ligases. Amot proteins mediate the coupling of Nedd4 ligases with YAP by simultaneously binding both pro-teins via multiple PY motifs that are recognized by WW domains in both YAP and Nedd4. Binding of Nedd4 by Amot is also shown to relieve the auto-inhibition of its ligase activity. This may be a direct consequence of binding Amot or from being re-targeted in cells by Amot proteins to endosomes. Im-portantly, Amot induced ubiquitination of YAP by Nedd4 proteins is shown to enhance the residence of YAP in the nucleus and in YAP activated transcrip-tion. Taken together our data suggest that Amot couples Nedd4 family ubiq-uitin ligases with the transcriptional co-activator YAP to drive the ubiquitination and activation of YAP

Prospectus, February 8, 1978

LESS THAN 3% UNEMPLOYED: COMMUNITY COLLEGE GRADS IN FINE COMPANY; ICCB nixes state budget; Snow days used: now what?; Letters to the editor: Beating a dead cow: Kudos from the U…, Carbon monoxide…The sweet smell of death?; \u27Greening of Women\u27s Studies\u27 is topic of Midwest conference; Some good ideas? The LRC wants them; Many \u27how-to\u27 courses start of U of I \u27Y\u27; Parkland College News in brief: Candadian coins confuse machines, CHI has answers to depression, Bradley U. delegate visits Parkland today, Long Living program offers activities for the aged this month, Sign up to save now; Cold hands, warm hearts is even true of Parkland\u27s winter drivers; Mainstreaming disabled kids into regular schools; Man-made clouds may create ★&/! weather; 1977 was not your imagination; 10 tips to Keep kids from slip-sliding away; Musings on money, bee-stings & Radio City Music Hall; Spring play tryouts next week; Students aid in Dental Health Week; Bob confesses error, three win the fins; Bouncing Bob Basketball Bonanza; What\u27s all the fuss about metric?; Protein-free diet discovery: PKU child\u27s chances can grow; Woolfork, Berry, Kirby, Rucks...pow!!; Tracksters take third in Chicago meet, three Cobras post personal records; Long live the A(A)BA!; Classifieds; Lose to EIU JV\u27s in OT: Women\u27s streak stalled at seven; Cobras & Kim: mutual admiration society; This week\u27s box scoreshttps://spark.parkland.edu/prospectus_1978/1026/thumbnail.jp

Harnessing case isolation and ring vaccination to control Ebola.

As a devastating Ebola outbreak in West Africa continues, non-pharmaceutical control measures including contact tracing, quarantine, and case isolation are being implemented. In addition, public health agencies are scaling up efforts to test and deploy candidate vaccines. Given the experimental nature and limited initial supplies of vaccines, a mass vaccination campaign might not be feasible. However, ring vaccination of likely case contacts could provide an effective alternative in distributing the vaccine. To evaluate ring vaccination as a strategy for eliminating Ebola, we developed a pair approximation model of Ebola transmission, parameterized by confirmed incidence data from June 2014 to January 2015 in Liberia and Sierra Leone. Our results suggest that if a combined intervention of case isolation and ring vaccination had been initiated in the early fall of 2014, up to an additional 126 cases in Liberia and 560 cases in Sierra Leone could have been averted beyond case isolation alone. The marginal benefit of ring vaccination is predicted to be greatest in settings where there are more contacts per individual, greater clustering among individuals, when contact tracing has low efficacy or vaccination confers post-exposure protection. In such settings, ring vaccination can avert up to an additional 8% of Ebola cases. Accordingly, ring vaccination is predicted to offer a moderately beneficial supplement to ongoing non-pharmaceutical Ebola control efforts

Soil Resources Area Affects Herbivore Health

Soil productivity effects nutritive quality of food plants, growth of humans and animals, and reproductive health of domestic animals. Game-range surveys sometimes poorly explained variations in wildlife populations, but classification of survey data by major soil types improved effectiveness. Our study evaluates possible health effects of lower condition and reproductive rates for wild populations of Odocoileus virginianus Zimmerman (white-tailed deer) in some physiographic regions of Mississippi. We analyzed condition and reproductive data for 2400 female deer from the Mississippi Department of Wildlife, Fisheries, and Parks herd health evaluations from 1991–1998. We evaluated age, body mass (Mass), kidney mass, kidney fat mass, number of corpora lutea (CL) and fetuses, as well as fetal ages. Region affected kidney fat index (KFI), which is a body condition index, and numbers of fetuses of adults (P ≤ 0.001). Region affected numbers of CL of adults (P ≤ 0.002). Mass and conception date (CD) were affected (P ≤ 0.001) by region which interacted significantly with age for Mass (P ≤ 0.001) and CD (P < 0.04). Soil region appears to be a major factor influencing physical characteristics of female deer