Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms

Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html

Закономерности формирования структуры и фазового состава поверхностного слоя силумина, подвергнутого электронно-пучковой обработке

It has been shown that electron beam treatment of silumin is accompanied by the formation of multilayer submicro-and nanocrystalline structure and result in increasing the microhardness of the surface layer (towards the core) is ~ 1.5 times up to 2 GPa

Oral Administration of Levo-Tetrahydropalmatine Attenuates Reinstatement of Extinguished Cocaine Seeking by Cocaine, Stress or Drug-Associated Cues in Rats

Cocaine addiction is characterized by a persistently heightened susceptibility to drug relapse. For this reason, the identification of medications that prevent drug relapse is a critical goal of drug abuse research. Drug re-exposure, the onset of stressful life events, and exposure to cues previously associated with drug use have been identified as determinants of relapse in humans and have been found to reinstate extinguished cocaine seeking in rats. This study examined the effects of acute oral (gavage) administration of levo-tetrahydropalmatine (l-THP), a tetrahydroprotoberberine isoquinoline with a pharmacological profile that includes antagonism of D1, D2 and D3 dopamine receptors, on the reinstatement of extinguished cocaine seeking by a cocaine challenge (10 mg/kg, ip), a stressor (uncontrollable electric footshock [EFS]) or response-contingent exposure to a stimulus (tone and light complex) previously associated with drug delivery in male Sprague–Dawley rats. Extinguished drug seeking was reinstated by ip cocaine, EFS, or response-contingent presentation of drug-associated cues in vehicle-pretreated rats following extinction of iv cocaine self-adminisration. Oral administration of either 3.0 or 10.0 mg/kg l-THP 1 h prior to reinstatement testing significantly attenuated reinstatement by each of the stimuli. Food-reinforced responding and baseline post-extinction responding were significantly attenuated at the 10.0, but not the 3.0 mg/kg, l-THP dose, indicating that the effects of 3 mg/kg l-THP on reinstatement were likely independent of non-specific motor impairment. These findings further suggest that l-THP may have utility for the treatment of cocaine addiction

Nonperturbative Effects from the Resummation of Perturbation Theory

Using the general argument in Borel resummation of perturbation theory that links the divergent perturbation theory to the nonperturbative effect we argue that the nonperturbative effect associated with the perturbation theory should have a branch cut only along the positive real axis in the complex coupling plane. The component in the weak coupling expansion of the nonperturbative amplitude, which usually includes the leading term in the weak coupling expansion, that gives rise to the branch cut can be calculated in principle from the perturbation theory combined with some exactly calculable properties of the nonperturbative effect. The realization of this mechanism is demonstrated in the double well potential and the two-dimensional O(N) nonlinear sigma model. In these models the leading term in weak coupling of the nonperturbative effect can be obtained with good accuracy from the first terms of the perturbation theory. Applying this mechanism to the infrared renormalon induced nonperturbative effect in QCD, we suggest some of the QCD condensate effects can be calculated in principle from the perturbation theory.Comment: 21 Pages, 1 Figure; To appear in Phys Rev

Fluctuating selection models and Mcdonald-Kreitman type analyses

It is likely that the strength of selection acting upon a mutation varies through time due to changes in the environment. However, most population genetic theory assumes that the strength of selection remains constant. Here we investigate the consequences of fluctuating selection pressures on the quantification of adaptive evolution using McDonald-Kreitman (MK) style approaches. In agreement with previous work, we show that fluctuating selection can generate evidence of adaptive evolution even when the expected strength of selection on a mutation is zero. However, we also find that the mutations, which contribute to both polymorphism and divergence tend, on average, to be positively selected during their lifetime, under fluctuating selection models. This is because mutations that fluctuate, by chance, to positive selected values, tend to reach higher frequencies in the population than those that fluctuate towards negative values. Hence the evidence of positive adaptive evolution detected under a fluctuating selection model by MK type approaches is genuine since fixed mutations tend to be advantageous on average during their lifetime. Never-the-less we show that methods tend to underestimate the rate of adaptive evolution when selection fluctuates

Origin of the surface-orientation dependence of the reduction kinetics of ultrathin ceria

Performance of catalytic redox reactions depends crucially on the oxygen storage and release capability of the catalyst and with that the catalyst’s defect chemistry. Here, we show that the surface defect chemistry of cerium oxide, a prototypical reducible oxide, differs markedly between two surface terminations. The results are in good agreement with density functional theory calculations and provide important guiding factors for rational design of industrially relevant catalysts. The study is conducted by preparing (100) and (111) terminated nanoislands of cerium oxide next to each other on Cu(111). Leveraging the benefits of full-field imaging capability of photoemission electron microscopy (PEEM), we follow the structural and chemical properties of the nanoislands under reducing hydrogen atmosphere simultaneously and in situ. The results, summarized in Figure 1, directly reveal different overall reducibility that can be traced to equilibrium oxygen vacancy concentrations via a kinetic model. The density functional theory calculations provide further details regarding the equilibrium co-ordination of oxygen vacancies for both surface planes. Conjoining the two, the unique simultaneous nature of the PEEM-facilitated structure–activity relationship study allows us to separate the thermodynamics of reduction from the kinetics of oxygen exchange, revealing the fact that the difference in reducibility of the two surfaces of ceria is not determined by the kinetic rate constants of the reduction reaction, but rather by the equilibrium concentration of oxygen vacancies, an information that has not been provided by the isolated model system approach to date. Surprisingly, the reason for the different reducibilities is a purely geometric one: the creation of nearest neighbor oxygen vacancies. Please click Additional Files below to see the full abstract

Departure from solid solution behavior in double perovskites

Mixed ionic electronic conducting oxides (MIEC) serve a plethora of electrochemical applications such as cathodes for solid oxide electrochemical cells and oxygen evolution reaction catalysts for water splitting. These applications rely to a large extent on the MIEC’s ability for electron and/or ion transfer across the solid/gas or solid/liquid interface. The efficacy of these reactions being governed by the surface defect chemistry and electronic structure, rational design of the (surface) chemistry presents itself as an auspicious path to tune these properties towards optimal device performance. Please click Additional Files below to see the full abstract

NK-Like T Cells and Plasma Cytokines, but Not Anti-Viral Serology, Define Immune Fingerprints of Resilience and Mild Disability in Exceptional Aging

Exceptional aging has been defined as maintenance of physical and cognitive function beyond the median lifespan despite a history of diseases and/or concurrent subclinical conditions. Since immunity is vital to individual fitness, we examined immunologic fingerprint(s) of highly functional elders. Therefore, survivors of the Cardiovascular Health Study in Pittsburgh, Pennsylvania, USA were recruited (n = 140; mean age = 86 years) and underwent performance testing. Blood samples were collected and examined blindly for humoral factors and T cell phenotypes. Based on results of physical and cognitive performance testing, elders were classified as “impaired” or “unimpaired”, accuracy of group assignment was verified by discriminant function analysis. The two groups showed distinct immune profiles as determined by factor analysis. The dominant immune signature of impaired elders consisted of interferon (IFN)-γ, interleukin (IL)-6, tumor necrosis factor-α, and T cells expressing inhibitory natural killer-related receptors (NKR) CD158a, CD158e, and NKG2A. In contrast, the dominant signature of unimpaired elders consisted of IL-5, IL-12p70, and IL-13 with co-expression of IFN-γ, IL-4, and IL-17, and T cells expressing stimulatory NKRs CD56, CD16, and NKG2D. In logistic regression models, unimpaired phenotype was predicted independently by IL-5 and by CD4+CD28nullCD56+CD57+ T cells. All elders had high antibody titers to common viruses including cytomegalovirus. In cellular bioassays, T cell receptor (TCR)-independent ligation of either CD56 or NKG2D elicited activation of T cells. Collectively, these data demonstrate the importance of immunological parameters in distinguishing between health phenotypes of older adults. NKR+ T cells and cytokine upregulation indicate a unique physiologic environment in old age. Correlation of particular NKR+ T cell subsets and IL-5 with unimpaired performance, and NKR-driven TCR-independent activation of T cells suggest novel immunopathway(s) that could be exploited to improve immunity in old age