Mean-Payoff Optimization in Continuous-Time Markov Chains with Parametric Alarms

Continuous-time Markov chains with alarms (ACTMCs) allow for alarm events that can be non-exponentially distributed. Within parametric ACTMCs, the parameters of alarm-event distributions are not given explicitly and can be subject of parameter synthesis. An algorithm solving the $\varepsilon$-optimal parameter synthesis problem for parametric ACTMCs with long-run average optimization objectives is presented. Our approach is based on reduction of the problem to finding long-run average optimal strategies in semi-Markov decision processes (semi-MDPs) and sufficient discretization of parameter (i.e., action) space. Since the set of actions in the discretized semi-MDP can be very large, a straightforward approach based on explicit action-space construction fails to solve even simple instances of the problem. The presented algorithm uses an enhanced policy iteration on symbolic representations of the action space. The soundness of the algorithm is established for parametric ACTMCs with alarm-event distributions satisfying four mild assumptions that are shown to hold for uniform, Dirac and Weibull distributions in particular, but are satisfied for many other distributions as well. An experimental implementation shows that the symbolic technique substantially improves the efficiency of the synthesis algorithm and allows to solve instances of realistic size.Comment: This article is a full version of a paper accepted to the Conference on Quantitative Evaluation of SysTems (QEST) 201

Prevalence of Gastrointestinal Endoparasites from Confiscated Long Tailed Macaque (Macaca fascicularis) Formerly Used as Dancing Monkey, Pet and Human Wildlife Conflict in Java Areas of Indonesia

The purpose of this study is to identify the type, intensity, and prevalence of intestinal helminth infection in confiscated Long-tailed macaque (Macaca fascicularis). Thirty samples of feces from long-tailed monkeys (18 females and 12 males), with a total of 7 Dancing Monkeys, 5 Human Wildlife Conflict groups, and 18 Pet macaque groups. West Java's Cikole Animal Hospital collected samples aseptically, labeled them, and then analyzed them in its clinical laboratory. Using the floating method, samples were evaluated to determine the intensity of infection and the identification of parasites. The incidence of endoparasites in confiscated macaques is 20 %. The prevalence of endoparasites was highest in the individual group of pet macaques, at 27.78 %, and lowest in the Dancing Monkey group, at 14.29%. The prevalence of endoparasite infection was highest in the pet macaques, at 83.33 percent, compared to 16.67% among the dancing monkeys. In the human-infection conflict group, no endoparasite infections were detected. The prevalence of endoparasites in positive infected infant samples was as high as 75%, but the prevalence in sub-adult and adult age groups was 11% and 14%, respectively. From the number of positive samples, the male individual group had the highest percentage, 66.66 %, while the female individual group had the lowest proportion, 33.33 %. In general, the pattern of infection is the same, consisting of 50% double infection types and 50% single infection types. The average intensity of helminth infection in Strongyle spp. was 45.50±25.10 eggs per gram of feces, while in Trichuris spp., it was 120.00±0.00 eggs per gram of feces. Strongyle spp. infects 100% of the positive samples, while Trichuris spp. infects 50% of the samples.   Keywords: Macaca fascicularis, Confiscated macaque, Endoparasite, Prevalence

KIVP-6 Case Report: Seroprevalensi Tuberkulosis Menggunakan Uji Tuberkulin Kulit Mammalian Old Tuberculine (MOT) pada Macaca fascicularis Hasil Penyitaan Topeng Monyet

Di Indonesia, salah satu atraksi populer di masyarakat yang menggunakan monyet ekor panjang adalah atraksi Topeng Monyet. Di Pulau Jawa, topeng monyet juga disebut ledhek kethek. Menurut Cohen (2006)  pada era tahun 1980an topeng monyet digunakan mengamen di pasar, perkotaan dan perdesaan diiringi musik tradisional. Kesenian ini melibatkan pawang untuk melatih monyet meniru perilaku manusia, seperti berpakaian, menari dan berdandan. Penonton topeng monyet umumnya adalah anak-anak (Aiai 2015).Monyet yang digunakan untuk atraksi topeng monyet berpotensi untuk menularkan penyakit zoonosis pada manusia. Penelitian Schillaci et al (2002) menyatakan bahwa monyet yang digunakan untuk atraksi topeng monyet merupakan hewan reservoir  untuk virus enzootic simian yang dapat menginfeksi manusia.Salah satu penyakit lainnya yang bersifat zoonosis dan memiliki resiko ditularkan dari monyet topeng monyet adalah penyakit tuberkulosis. Tuberkulosis (TBC) adalah penyakit yang disebabkan oleh bakteri tahan asam yaitu Mycobacterium tuberculosis.Untuk mengetahui status infeksi tuberkulosis dari individu primata, salah satu metode pemeriksaan yang disetujui oleh Institute for Laboratory Animal Research (ILAR) dan Center for Disease Control (CDC) adalah metode pemeriksaan dengan menggunakan uji tuberculin kulit pada hewan dalam tahapan karantina. Uji tuberculin kulit yang dapat digunakan yaitu mamalian old tuberculin (mot), bovine purified protein derivates (bovine ppd) dan avian purified protein derivates ( avian ppd) (Lecu et al 2013)

KIVP-6 Case Report: Seroprevalensi Tuberkulosis Menggunakan Uji Tuberkulin Kulit Mammalian Old Tuberculine (MOT) pada Macaca fascicularis Hasil Penyitaan Topeng Monyet

Di Indonesia, salah satu atraksi populer di masyarakat yang menggunakan monyet ekor panjang adalah atraksi Topeng Monyet. Di Pulau Jawa, topeng monyet juga disebut ledhek kethek. Menurut Cohen (2006)  pada era tahun 1980an topeng monyet digunakan mengamen di pasar, perkotaan dan perdesaan diiringi musik tradisional. Kesenian ini melibatkan pawang untuk melatih monyet meniru perilaku manusia, seperti berpakaian, menari dan berdandan. Penonton topeng monyet umumnya adalah anak-anak (Aiai 2015).Monyet yang digunakan untuk atraksi topeng monyet berpotensi untuk menularkan penyakit zoonosis pada manusia. Penelitian Schillaci et al (2002) menyatakan bahwa monyet yang digunakan untuk atraksi topeng monyet merupakan hewan reservoir  untuk virus enzootic simian yang dapat menginfeksi manusia.Salah satu penyakit lainnya yang bersifat zoonosis dan memiliki resiko ditularkan dari monyet topeng monyet adalah penyakit tuberkulosis. Tuberkulosis (TBC) adalah penyakit yang disebabkan oleh bakteri tahan asam yaitu Mycobacterium tuberculosis.Untuk mengetahui status infeksi tuberkulosis dari individu primata, salah satu metode pemeriksaan yang disetujui oleh Institute for Laboratory Animal Research (ILAR) dan Center for Disease Control (CDC) adalah metode pemeriksaan dengan menggunakan uji tuberculin kulit pada hewan dalam tahapan karantina. Uji tuberculin kulit yang dapat digunakan yaitu mamalian old tuberculin (mot), bovine purified protein derivates (bovine ppd) dan avian purified protein derivates ( avian ppd) (Lecu et al 2013)

Gitana: a SQL-based Git Repository Inspector

International audienceSoftware development projects are notoriously complex and difficult to deal with. Several support tools such as issue tracking, code review and Source Control Management (SCM) systems have been introduced in the past decades to ease development activities. While such tools efficiently track the evolution of a given aspect of the project (e.g., bug reports), they provide just a partial view of the project and often lack of advanced querying mechanisms limiting themselves to command line or simple GUI support. This is particularly true for projects that rely on Git, the most popular SCM system today. In this paper, we propose a conceptual schema for Git and an approach that, given a Git repository, exports its data to a relational database in order to (1) promote data integration with other existing SCM tools and (2) enable writing queries on Git data using standard SQL syntax. To ensure efficiency, our approach comes with an incremental propagation mechanism that refreshes the database content with the latest modifications. We have implemented our approach in Gitana, an open-source tool available on GitHub

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data

Fungal iron availability during deep seated candidiasis is defined by a complex interplay involving systemic and local events

Peer reviewedPublisher PD

Serratamolide is a hemolytic factor produced by Serratia marcescens

Serratia marcescens is a common contaminant of contact lens cases and lenses. Hemolytic factors of S. marcescens contribute to the virulence of this opportunistic bacterial pathogen. We took advantage of an observed hyper-hemolytic phenotype of crp mutants to investigate mechanisms of hemolysis. A genetic screen revealed that swrW is necessary for the hyper-hemolysis phenotype of crp mutants. The swrW gene is required for biosynthesis of the biosurfactant serratamolide, previously shown to be a broad-spectrum antibiotic and to contribute to swarming motility. Multicopy expression of swrW or mutation of the hexS transcription factor gene, a known inhibitor of swrW expression, led to an increase in hemolysis. Surfactant zones and expression from an swrW-transcriptional reporter were elevated in a crp mutant compared to the wild type. Purified serratamolide was hemolytic to sheep and murine red blood cells and cytotoxic to human airway and corneal limbal epithelial cells in vitro. The swrW gene was found in the majority of contact lens isolates tested. Genetic and biochemical analysis implicate the biosurfactant serratamolide as a hemolysin. This novel hemolysin may contribute to irritation and infections associated with contact lens use. © 2012 Shanks et al

On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm

N-Acetyl-L-Glutamate Kinase (NAGK) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members. Given that the slow conformational dynamics of the NAGK (at the microseconds time scale or slower) may be rate-limiting, it is of importance to assess the mechanisms of the most cooperative modes of motion intrinsically accessible to this enzyme. Here, we present the results from normal mode analysis using an elastic network model representation, which shows that the conformational mechanisms for substrate binding by NAGK strongly correlate with the intrinsic dynamics of the enzyme in the unbound form. We further analyzed the potential mechanisms of allosteric signalling within NAGK using a Markov model for network communication. Comparative analysis of the dynamics of family members strongly suggests that the low-frequency modes of motion and the associated intramolecular couplings that establish signal transduction are highly conserved among family members, in support of the paradigm sequence→structure→dynamics→function © 2010 Marcos et al

Do We Practice What We Preach? A Review of Actual Clinical Practice with Regards to Preconception Care Guidelines

Objectives: To review what past studies have found with regard to existing clinical practices and approaches to providing preconception care. Methods: A literature review between 1966 and September 2005 was performed using Medline. Key words included preconception care, preconception counseling, preconception surveys, practice patterns, pregnancy outcomes, prepregnancy planning, and prepregnancy surveys. Results: There are no current national recommendations that fully address preconception care; as a result, there is wide variability in what is provided clinically under the rubric of preconception care. Conclusions: In 2005, the Centers for Disease Control and Prevention sponsored a national summit regarding preconception care and efforts are underway to develop a uniform set of national recommendations and guidelines for preconception care. Understanding how preconception care is presently incorporated and manifested in current medical practices should help in the development of these national guidelines. Knowing where, how, and why some specific preconception recommendations have been successfully adopted and translated into clinical practice, as well as barriers to implementation of other recommendations or guidelines, is vitally important in developing an overarching set of national guidelines. Ultimately, the success of these recommendations rests on their ability to influence and shape women's health policy