An Entailment Relation for Reasoning on the Web

Reasoning on the Web is receiving an increasing attention because of emerging fields such as Web adaption and Semantic Web. Indeed, the advanced functionalities striven for in these fields call for reasoning capabilities. Reasoning on the Web, however, is usually done using existing techniques rarely fitting the Web. As a consequence, additional data processing like data conversion from Web formats (e.g. XML or HTML) into some other formats (e.g. classical logic terms and formulas) is often needed and aspects of the Web (e.g. its inherent inconsistency) are neglected. This article first gives requirements for an entailment tuned to reasoning on the Web. Then, it describes how classical logic’s entailment can be modified so as to enforce these requirements. Finally, it discusses how the proposed entailment can be used in applying logic programming to reasoning on the Web

RDF Querying

Reactive Web systems, Web services, and Web-based publish/ subscribe systems communicate events as XML messages, and in many cases require composite event detection: it is not sufficient to react to single event messages, but events have to be considered in relation to other events that are received over time. Emphasizing language design and formal semantics, we describe the rule-based query language XChangeEQ for detecting composite events. XChangeEQ is designed to completely cover and integrate the four complementary querying dimensions: event data, event composition, temporal relationships, and event accumulation. Semantics are provided as model and fixpoint theories; while this is an established approach for rule languages, it has not been applied for event queries before

On Reasoning on Time and Location on the Web

Reasoning on time and location is receiving increasing attention on the Web due to emerging fields like Web adaptation, mobile computing, and the Semantic Web. Web applications in these fields often refer to rather complex temporal, calendric, and location information. Unfortunately, today’s Web languages and formalisms have merely primitive temporal and location data types and temporal and location reasoning capabilities – if any. This article reports on work in progress aiming at integrating temporal and locational reasoning into XML query and transformation operations. We analyze the problem and propose a concrete architecture. A prototype of the temporal reasoner, the WebCal system has already been realized

Four Lessons in Versatility or How Query Languages Adapt to the Web

Exposing not only human-centered information, but machine-processable data on the Web is one of the commonalities of recent Web trends. It has enabled a new kind of applications and businesses where the data is used in ways not foreseen by the data providers. Yet this exposition has fractured the Web into islands of data, each in different Web formats: Some providers choose XML, others RDF, again others JSON or OWL, for their data, even in similar domains. This fracturing stifles innovation as application builders have to cope not only with one Web stack (e.g., XML technology) but with several ones, each of considerable complexity. With Xcerpt we have developed a rule- and pattern based query language that aims to give shield application builders from much of this complexity: In a single query language XML and RDF data can be accessed, processed, combined, and re-published. Though the need for combined access to XML and RDF data has been recognized in previous work (including the W3C’s GRDDL), our approach differs in four main aspects: (1) We provide a single language (rather than two separate or embedded languages), thus minimizing the conceptual overhead of dealing with disparate data formats. (2) Both the declarative (logic-based) and the operational semantics are unified in that they apply for querying XML and RDF in the same way. (3) We show that the resulting query language can be implemented reusing traditional database technology, if desirable. Nevertheless, we also give a unified evaluation approach based on interval labelings of graphs that is at least as fast as existing approaches for tree-shaped XML data, yet provides linear time and space querying also for many RDF graphs. We believe that Web query languages are the right tool for declarative data access in Web applications and that Xcerpt is a significant step towards a more convenient, yet highly efficient data access in a “Web of Data”

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles

Background: The healthy microbiome protects against the development of Clostridium difficile infection (CDI), which typically develops following antibiotics. The microbiome metabolises primary to secondary bile acids, a process if disrupted by antibiotics, may be critical for the initiation of CDI. Aim: To assess the levels of primary and secondary bile acids associated with CDI and associated microbial changes. Methods: Stool and serum were collected from patients with (i) first CDI (fCDI), (ii) recurrent CDI (rCDI) and (iii) healthy controls. 16S rRNA sequencing and bile salt metabolomics were performed. Random forest regression models were constructed to predict disease status. PICRUSt analyses were used to test for associations between predicted bacterial bile salt hydrolase (BSH) gene abundances and bile acid levels. Results: Sixty patients (20 fCDI, 19 rCDI and 21 controls) were enrolled. Secondary bile acids in stool were significantly elevated in controls compared to rCDI and fCDI (P < 0.0001 and P = 0.0007 respectively). Primary bile acids in stool were significantly elevated in rCDI compared to controls (P < 0.0001) and in rCDI compared to fCDI (P = 0.02). Using random forest regression, we distinguished rCDI and fCDI patients 84.2% of the time using bile acid ratios. Stool deoxycholate to glycoursodeoxycholate ratio was the single best predictor. PICRUSt analyses found significant differences in predicted abundances of bacterial BSH genes in stool samples across the groups. Conclusions: Primary and secondary bile acid composition in stool was different in those with rCDI, fCDI and controls. The ratio of stool deoxycholate to glycoursodeoxycholate was the single best predictor of disease state and may be a potential biomarker for recurrence.American College of Gastroenterology (Clinical Research Award ACGJR-017-2015

Sampling-based Algorithms for Optimal Motion Planning

During the last decade, sampling-based path planning algorithms, such as Probabilistic RoadMaps (PRM) and Rapidly-exploring Random Trees (RRT), have been shown to work well in practice and possess theoretical guarantees such as probabilistic completeness. However, little effort has been devoted to the formal analysis of the quality of the solution returned by such algorithms, e.g., as a function of the number of samples. The purpose of this paper is to fill this gap, by rigorously analyzing the asymptotic behavior of the cost of the solution returned by stochastic sampling-based algorithms as the number of samples increases. A number of negative results are provided, characterizing existing algorithms, e.g., showing that, under mild technical conditions, the cost of the solution returned by broadly used sampling-based algorithms converges almost surely to a non-optimal value. The main contribution of the paper is the introduction of new algorithms, namely, PRM* and RRT*, which are provably asymptotically optimal, i.e., such that the cost of the returned solution converges almost surely to the optimum. Moreover, it is shown that the computational complexity of the new algorithms is within a constant factor of that of their probabilistically complete (but not asymptotically optimal) counterparts. The analysis in this paper hinges on novel connections between stochastic sampling-based path planning algorithms and the theory of random geometric graphs.Comment: 76 pages, 26 figures, to appear in International Journal of Robotics Researc

Behavioural syndrome in a solitary predator is independent of body size and growth rate.

Models explaining behavioural syndromes often focus on state-dependency, linking behavioural variation to individual differences in other phenotypic features. Empirical studies are, however, rare. Here, we tested for a size and growth-dependent stable behavioural syndrome in the juvenile-stages of a solitary apex predator (pike, Esox lucius), shown as repeatable foraging behaviour across risk. Pike swimming activity, latency to prey attack, number of successful and unsuccessful prey attacks was measured during the presence/absence of visual contact with a competitor or predator. Foraging behaviour across risks was considered an appropriate indicator of boldness in this solitary predator where a trade-off between foraging behaviour and threat avoidance has been reported. Support was found for a behavioural syndrome, where the rank order differences in the foraging behaviour between individuals were maintained across time and risk situation. However, individual behaviour was independent of body size and growth in conditions of high food availability, showing no evidence to support the state-dependent personality hypothesis. The importance of a combination of spatial and temporal environmental variation for generating growth differences is highlighted

College of American Pathologists\u27 Laboratory Standards for Next-Generation Sequencing Clinical Tests

Context.-The higher throughput and lower per-base cost of next-generation sequencing (NGS) as compared to Sanger sequencing has led to its rapid adoption in clinical testing. The number of laboratories offering NGS-based tests has also grown considerably in the past few years, despite the fact that specific Clinical Laboratory Improvement Amendments of 1988/College of American Pathologists (CAP) laboratory standards had not yet been developed to regulate this technology. Objective.-To develop a checklist for clinical testing using NGS technology that sets standards for the analytic wet bench process and for bioinformatics or \u27\u27 dry bench\u27\u27 analyses. As NGS-based clinical tests are new to diagnostic testing and are of much greater complexity than traditional Sanger sequencing-based tests, there is an urgent need to develop new regulatory standards for laboratories offering these tests. Design.-To develop the necessary regulatory framework for NGS and to facilitate appropriate adoption of this technology for clinical testing, CAP formed a committee in 2011, the NGS Work Group, to deliberate upon the contents to be included in the checklist. Results.-A total of 18 laboratory accreditation checklist requirements for the analytic wet bench process and bioinformatics analysis processes have been included within CAP\u27s molecular pathology checklist (MOL). Conclusions.-This report describes the important issues considered by the CAP committee during the development of the new checklist requirements, which address documentation, validation, quality assurance, confirmatory testing, exception logs, monitoring of upgrades, variant interpretation and reporting, incidental findings, data storage, version traceability, and data transfer confidentiality

Effect of initial pH of medium with potato wastewater and glycerol on protein, lipid and carotenoid biosynthesis by Rhodotorula glutinis

Background: Rhodotorula glutinis is capable of synthesizing numerous valuable metabolites with extensive potential industrial usage. This paper reports the effect of initial culture medium pH on growth and protein, lipid, and carotenoid biosynthesis by R. glutinis. Results: The highest biomass yield was obtained in media with pH 4.0\u20137.0, and the value after 72 h was 17.2\u201319.4 gd.w./L. An initial pH of the medium in the range of 4.0\u20137.0 has no significant effect on the protein (38.5\u201341.3 g/100 gd.w.), lipid (10.2\u201312.7 g/100 gd.w.), or carotenoid (191.7\u2013202.9 \u3bcg/gd.w.) content in the biomass or on the profile of synthesized fatty acids and carotenoids. The whole pool of fatty acids was dominated by oleic (48.1\u201353.4%), linoleic (21.4\u201325.1%), and palmitic acids (13.0\u201315.8%). In these conditions, the yeast mainly synthesized torulene (43.5\u201347.7%) and \u3b2-carotene (34.7\u201338.6%), whereas the contribution of torularhodin was only 12.1\u201316.8%. Cultivation in medium with initial pH 3.0 resulted in a reduction in growth (13.0 gd.w./L) and total carotenoid (115.8 \u3bcg/gd.w.), linoleic acid (11.5%), and torularhodin (4.5%) biosynthesis. Conclusion: The different values of initial pH of the culture medium with glycerol and deproteinized potato wastewater had a significant effect on the growth and protein, lipid, and carotenoid biosynthesis by R. glutinis

Estimation, planning, and mapping for autonomous flight using an RGB-D camera in GPS-denied environments

RGB-D cameras provide both color images and per-pixel depth estimates. The richness of this data and the recent development of low-cost sensors have combined to present an attractive opportunity for mobile robotics research. In this paper, we describe a system for visual odometry and mapping using an RGB-D camera, and its application to autonomous flight. By leveraging results from recent state-of-the-art algorithms and hardware, our system enables 3D flight in cluttered environments using only onboard sensor data. All computation and sensing required for local position control are performed onboard the vehicle, reducing the dependence on an unreliable wireless link to a ground station. However, even with accurate 3D sensing and position estimation, some parts of the environment have more perceptual structure than others, leading to state estimates that vary in accuracy across the environment. If the vehicle plans a path without regard to how well it can localize itself along that path, it runs the risk of becoming lost or worse. We show how the belief roadmap algorithm prentice2009belief, a belief space extension of the probabilistic roadmap algorithm, can be used to plan vehicle trajectories that incorporate the sensing model of the RGB-D camera. We evaluate the effectiveness of our system for controlling a quadrotor micro air vehicle, demonstrate its use for constructing detailed 3D maps of an indoor environment, and discuss its limitations.United States. Office of Naval Research (Grant MURI N00014-07-1-0749)United States. Office of Naval Research (Science of Autonomy Program N00014-09-1-0641)United States. Army Research Office (MAST CTA)United States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant N00014-09-1-1052)National Science Foundation (U.S.) (Contract IIS-0812671)United States. Army Research Office (Robotics Consortium Agreement W911NF-10-2-0016)National Science Foundation (U.S.). Division of Information, Robotics, and Intelligent Systems (Grant 0546467