Trees over Infinite Structures and Path Logics with Synchronization

We provide decidability and undecidability results on the model-checking problem for infinite tree structures. These tree structures are built from sequences of elements of infinite relational structures. More precisely, we deal with the tree iteration of a relational structure M in the sense of Shelah-Stupp. In contrast to classical results where model-checking is shown decidable for MSO-logic, we show decidability of the tree model-checking problem for logics that allow only path quantifiers and chain quantifiers (where chains are subsets of paths), as they appear in branching time logics; however, at the same time the tree is enriched by the equal-level relation (which holds between vertices u, v if they are on the same tree level). We separate cleanly the tree logic from the logic used for expressing properties of the underlying structure M. We illustrate the scope of the decidability results by showing that two slight extensions of the framework lead to undecidability. In particular, this applies to the (stronger) tree iteration in the sense of Muchnik-Walukiewicz.Comment: In Proceedings INFINITY 2011, arXiv:1111.267

Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis

Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we introduce tools from topological data analysis to characterize the frequency and scale of lateral gene transfer in bacteria, focusing on a set of pathogens of significant public health relevance. As a case study, we examine the spread of antibiotic resistance in Staphylococcus aureus. Finally, we consider the possible role of the human microbiome as a reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on Advanced Methods of Interactive Data Mining for Personalized Medicin

BandEst: Measurement-based available bandwidth estimation and flow admission control algorithm for Ad Hoc IEEE 802.15.4-based wireless multimedia networks

We highlight different important factors that must be considered for an effective available-bandwidth-based flow admission control algorithm in ad hoc wireless networks. Moreover, we present BandEst; it is a combination of a measurement-based available bandwidth estimation technique and a flow admission control algorithm for ad hoc IEEE 802.15.4-based ad hoc networks that considers the identified factors. Extensive simulations are performed to compare BandEst with the state-of-the-art available-bandwidth-based flow admission control algorithms for ad hoc wireless networks. Our simulation results demonstrate that BandEst significantly outperforms the state-of-the-art available-bandwidth-based flow admission control algorithms for ad hoc wireless networks

Operating systems for wireless sensor networks: A survey

This paper presents a survey on the current state-of-the-art in Wireless Sensor Network (WSN) Operating Systems (OSs). In recent years, WSNs have received tremendous attention in the research community, with applications in battlefields, industrial process monitoring, home automation, and environmental monitoring, to name but a few. A WSN is a highly dynamic network because nodes die due to severe environmental conditions and battery power depletion. Furthermore, a WSN is composed of miniaturized motes equipped with scarce resources e.g., limited memory and computational abilities. WSNs invariably operate in an unattended mode and in many scenarios it is impossible to replace sensor motes after deployment, therefore a fundamental objective is to optimize the sensor motes' life time. These characteristics of WSNs impose additional challenges on OS design for WSN, and consequently, OS design for WSN deviates from traditional OS design. The purpose of this survey is to highlight major concerns pertaining to OS design in WSNs and to point out strengths and weaknesses of contemporary OSs for WSNs, keeping in mind the requirements of emerging WSN applications. The state-of-the-art in operating systems for WSNs has been examined in terms of the OS Architecture, Programming Model, Scheduling, Memory Management and Protection, Communication Protocols, Resource Sharing, Support for Real-Time Applications, and additional features. These features are surveyed for both real-time and non-real-time WSN operating systems

Quantifying bladder outflow obstruction in men:A comparison of four approximation methods exploiting large data samples

Introduction: A pressure flow study (PFS), part of the International Continence Society standard urodynamic test, is regarded gold standard for the classification and quantification of the urethral resistance (UR), expressed in the bladder outflow obstruction (BOO). For men with benign prostatic hyperplasia, the minimum urethral opening pressure (pmuo), found at the end of the passive urethral resistance relation is considered the relevant parameter describing BOO. However, in clinical practice, direct measurements of pmuo are easily confounded by terminal dribbling. For that reason, alternative methods were developed to derive pmuo, and thereby assess BOO using the maximum urine flow rate (Qmax) and the corresponding pressure (pdetQmax) instead. These methods were never directly compared against a large data set. With the increasing variety of treatments becoming available more precise grading of UR may become of relevance. The current study compares four well-known methods to approximate pmuo and examines the relation between pmuo and pdetQmax. Methods: In total, 1717 high-quality PFS of men referred with lower urinary tract symptoms between 2003 and 2020 without earlier lower urinary tract surgery were included. From these recordings, pmuo was calculated according to three one-parameter methods. In addition, a three-parameter method (3PM) was used, based on a fit through the lowest pressure flank of the pressure-flow plot. The estimated pmuo's were compared with a precisely assessed pmuo. A difference of &lt;10 cmH2O between an estimate and the actual pmuo was considered accurate. A comparison between the four approximation methods and the actual pmuo was visualized using a Bland–Altman plot. The differences between the actual and the estimated slope were assessed and dependency on pmuo was analyzed. Results: A total of 1717 studies were analyzed. In 55 (3.2%) PFS, 3PM analysis was impossible because all pressures after Qmax were higher than pdetQmax. The 3PM model was superior in predicting pmuo, with 75.9% of the approximations within a range of +10 or −10 cmH2O of the actual pmuo. Moreover, pmuo according to urethral resistance A (URA) and linearized passive urethral resistance relation (linPURR) appear equally reliable. Bladder outflow obstruction index (BOOI) was significantly less accurate when compared to all others. Bland–Altman analysis showed a tendency of BOOI to overestimate pmuo in men with higher grades of UR, while URA tended to underestimate pmuo in those cases. The slope between pmuo and pdetQmax-Qmax increased with larger pmuo, as opposed to the constant relation proposed within BOOI. Although significant differences were found, the clinical relevance of those differences is not known. Conclusion: Of the four methods to estimate pmuo and quantify BOO, 3PM was found the most accurate and BOOI the least accurate. As 3PM is not generally available and performance in lower quality PFS is unknown, linPURR is (for now) the most physiologically accurate.</p

Biological Resolution of Virulence Genes of Salmonella Species from different Microbiomes

The pathogenic promiscuity of virulence associated macromolecules in Salmonella infection is a key driver to their wide epidemiology and curtailing&nbsp; such distribution is contingent upon proper clarification of these virulence genes. This study was therefore aimed at determining the virulence&nbsp; genes of Salmonella species from different microbiomes. To achieve this, a total of three hundred (300) biological specimens were aseptically&nbsp; collected and processed for Salmonella presence using the BAM USFDA technique prior to their genotypic characterization while virulence gene&nbsp; detection was carried out in a primer specific polymerase chain reaction. Results obtained depict the distribution of the following Salmonella species&nbsp; viz; Salmonella gallinarum 19(26.39%), Salmonella heidelberg 19(26.39%), Salmonella enteritidis 18(25%) and Salmonella typhimurium&nbsp; 16(22.22%) while the occurrence of the virulence genes (InvA, SopE, AgfA and SpvC) were Salmonella enteritidis ( 7(38.8), 6(33.3), 9(50), 3(16.7),&nbsp; Salmonella typhimurium ( 5(26.3), 3(15.8), 2(10.5), 7(36.8)), Salmonella heidelberg (0(0), 8(50), 4(25), 4(25), and Salmonella gallinarum (12(63.2),&nbsp; 6(31.6), 2(10.5), 7(36.8)) respectively. It was however found that the different microbiomes analyzed were ubiquitously rich in virulence genes&nbsp; associated Salmonella species. &nbsp; La promiscuité pathogène des macromolécules associées à la virulence dans l’infection à Salmonella est un facteur clé de leur large épidémiologie&nbsp; et la réduction de cette distribution dépend de la clarification appropriée de ces gènes de virulence. Cette étude visait donc à déterminer les gènes&nbsp; de virulence des espèces de Salmonella de différents microbiomes. Pour ce faire, un total de trois cents (300) échantillons biologiques ont été&nbsp; collectés et traités de manière aseptique pour la présence de Salmonella à l’aide de la technique BAM USFDA avant leur caractérisation génotypique&nbsp; tandis que la détection du gène de virulence a été effectuée dans une réaction en chaîne par polymérase spécifique à l’amorce. Les résultats&nbsp; obtenus décrivent la distribution des espèces de Salmonella suivantes, à savoir ; Salmonella gallinarum 19(26,39%), Salmonella heidelberg&nbsp; 19(26,39%), Salmonella enteritidis 18(25%) et Salmonella typhimurium 16(22,22%) alors que la présence des gènes de virulence (InvA, SopE, AgfA et&nbsp; SpvC) était Salmonella enteritidis ( 7(38,8), 6(33,3), 9(50), 3(16,7), Salmonella typhimurium ( 5(26,3), 3(15,8), 2(10,5), 7(36,8)), Salmonella heidelberg (0(&nbsp; 0), 8(50), 4(25), 4(25) et Salmonella gallinarum (12(63.2), 6(31.6), 2(10.5), 7(36.8)) respectivement. différents microbiomes analysés étaient&nbsp; ubiquitairement riches en gènes de virulence associés aux espèces de Salmonella&nbsp;&nbsp;&nbsp

External validation of the fatty liver index and lipid accumulation product indices, using H-1-magnetic resonance spectroscopy, to identify hepatic steatosis in healthy controls and obese, insulin-resistant individuals

Background and Aims. Simple clinical algorithms including the Fatty Liver Index (FLI) and Lipid Accumulation Product (LAP) have been developed as a surrogate marker for Non-Alcoholic Fatty Liver Disease (NAFLD). These algorithms have been constructed using ultrasonography, a semi-quantitative method. This study aimed to validate FLI and LAP as measures of hepatic steatosis, as measured quantitatively by proton magnetic resonance spectroscopy (1H-MRS). Methods. Data were collected from 168 patients with NAFLD and 168 controls who had undergone clinical, biochemical and anthropometric assessment in the course of research studies. Values of FLI and LAP were determined, and assessed both as predictors of the presence of hepatic steatosis (liver fat >5.5 %) and of actual liver fat content, as measured by 1H MRS. The discriminative ability of FLI and LAP was estimated using the area under the Receiver Operator Characteristic curve (AUROC). Since FLI can also be interpreted as a predictive probability of hepatic steatosis, we assessed how well calibrated it was in our cohort. Linear regression with prediction intervals was used to assess the ability of FLI and LAP to predict liver fat content. Results. FLI and LAP discriminated between patients with and without hepatic steatosis with an AUROC of 0.79 (IQR= 0.74, 0.84) and 0.78 (IQR= 0.72, 0.83), although quantitative prediction of liver fat content was unsuccessful. Additionally, the algorithms accurately matched the observed percentages of patients with hepatic steatosis in our cohort. Conclusions. FLI and LAP may be used clinically, and for metabolic and epidemiological research, to identify patients with hepatic steatosis, but not as surrogates for liver fat content

Higher-order mutual coherence of optical and matter waves

We use an operational approach to discuss ways to measure the higher-order cross-correlations between optical and matter-wave fields. We pay particular attention to the fact that atomic fields actually consist of composite particles that can easily be separated into their basic constituents by a detection process such as photoionization. In the case of bosonic fields, that we specifically consider here, this leads to the appearance in the detection signal of exchange contributions due to both the composite bosonic field and its individual fermionic constituents. We also show how time-gated counting schemes allow to isolate specific contributions to the signal, in particular involving different orderings of the Schr\"odinger and Maxwell fields.Comment: 11 pages, 2 figure

LEAP2 changes with body mass and food intake in humans and mice

Acyl-ghrelin administration increases food intake, body weight, and blood glucose. In contrast, mice lacking ghrelin or ghrelin receptors (GHSRs) exhibit life-threatening hypoglycemia during starvation-like conditions but do not consistently exhibit overt metabolic phenotypes when given ad libitum food access. These results, and findings of ghrelin resistance in obese states, imply nutritional state-dependence of ghrelin’s metabolic actions. Here, we hypothesized that LEAP2 (liver enriched antimicrobial peptide-2), a recently-characterized endogenous GHSR antagonist, blunts ghrelin action during obese states and post-prandially. To test this hypothesis, we determined changes in plasma LEAP2 and acyl-ghrelin due to fasting, eating, obesity, Roux-en-Y gastric bypass (RYGB), vertical sleeve gastrectomy (VSG), oral glucose administration, and type 1 diabetes mellitus (T1DM) using humans and/or mice. Our results suggest that plasma LEAP2 is regulated by metabolic status: its levels increase with body mass and blood glucose, and decrease with fasting, RYGB, and in post-prandial states following VSG. These changes were mostly opposite to those of acyl-ghrelin. Furthermore, using electrophysiology, we showed that LEAP2 both hyperpolarizes and prevents acyl-ghrelin from activating arcuate NPY neurons. We predict that the plasma LEAP2:acyl-ghrelin molar ratio may be a key determinant modulating acyl-ghrelin activity in response to body mass, feeding status, and blood glucose

Exploiting the Temporal Logic Hierarchy and the Non-Confluence Property for Efficient LTL Synthesis

The classic approaches to synthesize a reactive system from a linear temporal logic (LTL) specification first translate the given LTL formula to an equivalent omega-automaton and then compute a winning strategy for the corresponding omega-regular game. To this end, the obtained omega-automata have to be (pseudo)-determinized where typically a variant of Safra's determinization procedure is used. In this paper, we show that this determinization step can be significantly improved for tool implementations by replacing Safra's determinization by simpler determinization procedures. In particular, we exploit (1) the temporal logic hierarchy that corresponds to the well-known automata hierarchy consisting of safety, liveness, Buechi, and co-Buechi automata as well as their boolean closures, (2) the non-confluence property of omega-automata that result from certain translations of LTL formulas, and (3) symbolic implementations of determinization procedures for the Rabin-Scott and the Miyano-Hayashi breakpoint construction. In particular, we present convincing experimental results that demonstrate the practical applicability of our new synthesis procedure