Polynomial Time Algorithms for Branching Markov Decision Processes and Probabilistic Min(Max) Polynomial Bellman Equations

We show that one can approximate the least fixed point solution for a multivariate system of monotone probabilistic max(min) polynomial equations, referred to as maxPPSs (and minPPSs, respectively), in time polynomial in both the encoding size of the system of equations and in log(1/epsilon), where epsilon > 0 is the desired additive error bound of the solution. (The model of computation is the standard Turing machine model.) We establish this result using a generalization of Newton's method which applies to maxPPSs and minPPSs, even though the underlying functions are only piecewise-differentiable. This generalizes our recent work which provided a P-time algorithm for purely probabilistic PPSs. These equations form the Bellman optimality equations for several important classes of infinite-state Markov Decision Processes (MDPs). Thus, as a corollary, we obtain the first polynomial time algorithms for computing to within arbitrary desired precision the optimal value vector for several classes of infinite-state MDPs which arise as extensions of classic, and heavily studied, purely stochastic processes. These include both the problem of maximizing and mininizing the termination (extinction) probability of multi-type branching MDPs, stochastic context-free MDPs, and 1-exit Recursive MDPs. Furthermore, we also show that we can compute in P-time an epsilon-optimal policy for both maximizing and minimizing branching, context-free, and 1-exit-Recursive MDPs, for any given desired epsilon > 0. This is despite the fact that actually computing optimal strategies is Sqrt-Sum-hard and PosSLP-hard in this setting. We also derive, as an easy consequence of these results, an FNP upper bound on the complexity of computing the value (within arbitrary desired precision) of branching simple stochastic games (BSSGs)

Analysis of Probabilistic Basic Parallel Processes

Basic Parallel Processes (BPPs) are a well-known subclass of Petri Nets. They are the simplest common model of concurrent programs that allows unbounded spawning of processes. In the probabilistic version of BPPs, every process generates other processes according to a probability distribution. We study the decidability and complexity of fundamental qualitative problems over probabilistic BPPs -- in particular reachability with probability 1 of different classes of target sets (e.g. upward-closed sets). Our results concern both the Markov-chain model, where processes are scheduled randomly, and the MDP model, where processes are picked by a scheduler.Comment: This is the technical report for a FoSSaCS'14 pape

Capacity Bounded Grammars and Petri Nets

A capacity bounded grammar is a grammar whose derivations are restricted by assigning a bound to the number of every nonterminal symbol in the sentential forms. In the paper the generative power and closure properties of capacity bounded grammars and their Petri net controlled counterparts are investigated

Polyunsaturated fatty acids in the pathogenesis and treatment of multiple sclerosis

Epidemiological, biochemical, animal model and clinical trial data described in this overview strongly suggest that polyunsaturated fatty acids, particularly n-6 fatty acids, have a role in the pathogenesis and treatment of multiple sclerosis (MS). Data presented provides further evidence for a disturbance in n-6 fatty acid metabolism in MS. Disturbance of n-6 fatty acid metabolism and dysregulation of cytokines are shown to be linked and a "proof of concept clinical trial" further supports such a hypothesis. In a randomised double-blind, placebo controlled trial of a high dose and low dose selected GLA (18:3n-6)-rich oil and placebo control, the high dose had a marked clinical effect in relapsing-remitting MS, significantly decreasing the relapse rate and the progression of disease. Laboratory findings paralleled clinical changes in the placebo group in that production of mononuclear cell pro-inflammatory cytokines (TNF-alpha, IL-1 beta) was increased and anti-inflammatory TGF-beta markedly decreased with loss of membrane n-6 fatty acids linoleic (18:2n-6) and arachidonic acids (20:4n-6). In contrast there were no such changes in the high dose group. The improvement in disability (Expanded Disability Status Scale) in the high dose suggests there maybe a beneficial effect on neuronal lipids and neural function in MS. Thus disturbed n-6 fatty acid metabolism in MS gives rise to loss of membrane long chain n-6 fatty acids and loss of the anti-inflammatory regulatory cytokine TGF-beta, particularly during the relapse phase, as well as loss of these important neural fatty acids for CNS structure and function and consequent long term neurological deficit in MS

Exact Gap Computation for Code Coverage Metrics in ISO-C

Test generation and test data selection are difficult tasks for model based testing. Tests for a program can be meld to a test suite. A lot of research is done to quantify the quality and improve a test suite. Code coverage metrics estimate the quality of a test suite. This quality is fine, if the code coverage value is high or 100%. Unfortunately it might be impossible to achieve 100% code coverage because of dead code for example. There is a gap between the feasible and theoretical maximal possible code coverage value. Our review of the research indicates, none of current research is concerned with exact gap computation. This paper presents a framework to compute such gaps exactly in an ISO-C compatible semantic and similar languages. We describe an efficient approximation of the gap in all the other cases. Thus, a tester can decide if more tests might be able or necessary to achieve better coverage.Comment: In Proceedings MBT 2012, arXiv:1202.582

Declining HIV-1 Prevalence and Incidence among Police Officers - A potential Cohort for HIV Vaccine Trials, in Dar es Salaam, Tanzania.

A safe effective and affordable HIV vaccine is the most cost effective way to prevent HIV infection worldwide. Current studies of HIV prevalence and incidence are needed to determine potentially suitable cohorts for vaccine studies. The prevalence and incidence of HIV-1 infection among the police in Dar es Salaam in 1996 were 13.8% and 19.6/1000 PYAR respectively. This study aimed at determining the current prevalence and incidence of HIV in a police cohort 10 years after a similar study was conducted. Police officers in Dar es Salaam, Tanzania were prospectively enrolled into the study from 2005 and followed-up in an incidence study three years later. HIV infection was determined by two sequential enzyme linked immunosorbent assays (ELISAs) in the prevalence study and discordant results between two ELISAs were resolved by a Western blot assay. Rapid HIV assays (SD Bioline and Determine) were used for the incidence study. A total of 1,240 police participated in the HIV prevalence study from August 2005 to November 2008. Of these, 1101 joined the study from August 2005-September 2007 and an additional 139 were recruited between October 2007 to November 2008 while conducting the incidence study. A total of 726 (70%) out of the 1043 eligible police participated in the incidence study.The overall HIV-1 prevalence was 65/1240 (5.2%). Females had a non-statistically significant higher prevalence of HIV infection compared to males 19/253, (7.5%) vs. 46/987 (4.7%) respectively (p = 0.07). The overall incidence of HIV-1 was 8.4 per 1000 PYAR (95% CI 4.68-14.03), and by gender was 8.8 and 6.9 per 1000 PYAR, among males and females respectively, (p = 0.82). The HIV prevalence and incidence among the studied police has declined over the past 10 years, and therefore this cohort is better suited for phase I/II HIV vaccine studies than for efficacy trials

L’ADAPTATION POSITIVE DES FAMILLES LATINOS AVEC UN ENFANT AYANT UNE DÉFICIENCE INTELLECTUELLE: UNE PREMIÈRE VUE DE LA THÉORIE DE L’ADAPTATION POSITIVE

Historically, research on disability and family dynamics drew from Psychology and Medicine. Consequently, eugenics models, grief theory, and other largely decontextualized frameworks of stress and coping were used to explain families of children with disabilities. This is a report of an initial test of a set of ideas the Singer research team has combined in order to explore the cognitive and problem-solving approaches of families of children with disabilities. Our purpose is to propose a contextualized theory for explaining how cultural diversity has an impact on positive adaptation to a child’s disability. This theory addresses the following: 1) attachment; 2) internal and external cultural resistance to stigmas about disability; and 3) perceived informal (family/friends) and formal (professionals) sources of support for positive views about disability and parenting. Sampling Latino families demonstrated how cultural contexts demonstrate a different flavour from majority culture interpretations of these cognitive terms of our proposed theory. Transcripts of the interviews were coded using grounded theory analysis, specifically, the constant comparative method. We discuss the goodness of fit for themes emerging from the coding process with the proposed theory terms. Results confirm attachment, social supports, and cultural resistance as terms for future development of this proposed theory. Keywords: Disability and parenting, positive adaptation, Latinos and disability, culture and disabilityÀ travers l’histoire, la recherche sur les handicapés et les relations intrafamiliales utilisait comme sources la psychologie et la médicine. Par conséquent, les modèles de l’eugénisme, les théories sur le deuil, et d’autres cadres analytiques sur le stress et les stratégies d’adaptation, plutôt décontextualisés, étaient utilisés afin d’expliquer aux autres comment fonctionnaient les familles avec un enfant handicapé. Ceci est un reportage sur un test initial d’un ensemble d’idées qu’a combiné l’équipe de recherche Singer afin d’aborder les approches cognitives et méthodes actives des familles des enfants handicapés. Nous proposons une théorie contextualisée afin d’expliquer comment la diversité culturelle aurait un effet sur l’adaptation positive de la famille face à l’handicap de leur enfant. Cette théorie aborde les idées suivantes : 1) l’attachement; 2) les résistances culturelles internes et externes aux stigmates sur l’handicap; et 3) les sources d’information sur l’handicap et le parentage liées à l’adaptation positive perçues comme informelles (famille/amis) et formelles (les professionnels). En utilisant un échantillon de familles Latinos, nous démontrons comment les contextes culturels démontrent des interprétations différentes des termes cognitifs de notre théorie, et non l’interprétation de la culture majoritaire. Les transcriptions des interviews étaient codées selon la théorie ancrée, plus spécifiquement la méthode de la comparaison constante. Nous discutons la concordance des thèmes venus via le processus d’encodage avec les termes clés de la nouvelle théorie proposée. Les résultats de cette recherche confirment que l’attachement, le soutien social, et la résistance culturelle seront des termes clés dans le développement de cette théorie proposée. Mots clés : Handicap et parentage, Adaptation positive, Latinos et handicap, culture et handica

Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, Carbon fixation in A. ferrooxidans

<p>Abstract</p> <p>Background</p> <p><it>Acidithiobacillus ferrooxidans </it>is chemolithoautotrophic γ-proteobacterium that thrives at extremely low pH (pH 1-2). Although a substantial amount of information is available regarding CO₂uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study.</p> <p>Results</p> <p>Four gene clusters (termed <it>cbb1-4</it>) in the <it>A. ferrooxidans </it>genome are predicted to encode enzymes and structural proteins involved in carbon assimilation via the Calvin-Benson-Bassham (CBB) cycle including form I of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO, EC 4.1.1.39) and the CO₂-concentrating carboxysomes. RT-PCR experiments demonstrated that each gene cluster is a single transcriptional unit and thus is an operon. Operon <it>cbb1 </it>is divergently transcribed from a gene, <it>cbbR</it>, encoding the LysR-type transcriptional regulator CbbR that has been shown in many organisms to regulate the expression of RubisCO genes. Sigma⁷⁰-like -10 and -35 promoter boxes and potential CbbR-binding sites (T-N₁₁-A/TNA-N₇TNA) were predicted in the upstream regions of the four operons. Electrophoretic mobility shift assays (EMSAs) confirmed that purified CbbR is able to bind to the upstream regions of the <it>cbb1</it>, <it>cbb2 </it>and <it>cbb3 </it>operons, demonstrating that the predicted CbbR-binding sites are functional <it>in vitro</it>. However, CbbR failed to bind the upstream region of the <it>cbb4 </it>operon that contains <it>cbbP</it>, encoding phosphoribulokinase (EC 2.7.1.19). Thus, other factors not present in the assay may be required for binding or the region lacks a functional CbbR-binding site. The <it>cbb3 </it>operon contains genes predicted to encode anthranilate synthase components I and II, catalyzing the formation of anthranilate and pyruvate from chorismate. This suggests a novel regulatory connection between CO₂fixation and tryptophan biosynthesis. The presence of a form II RubisCO could promote the ability of <it>A. ferrooxidans </it>to fix CO₂at different concentrations of CO₂.</p> <p>Conclusions</p> <p><it>A. ferrooxidans </it>has features of <it>cbb </it>gene organization for CO₂-assimilating functions that are characteristic of obligate chemolithoautotrophs and distinguish this group from facultative autotrophs. The most conspicuous difference is a separate operon for the <it>cbbP </it>gene. It is hypothesized that this organization may provide greater flexibility in the regulation of expression of genes involved in inorganic carbon assimilation.</p