Twelve Theses on Reactive Rules for the Web

Reactivity, the ability to detect and react to events, is an essential functionality in many information systems. In particular, Web systems such as online marketplaces, adaptive (e.g., recommender) systems, and Web services, react to events such as Web page updates or data posted to a server. This article investigates issues of relevance in designing high-level programming languages dedicated to reactivity on the Web. It presents twelve theses on features desirable for a language of reactive rules tuned to programming Web and Semantic Web applications

Reappraising elastic thickness variation at oceanic trenches

We reassess the variation of elastic thickness as a function of lithospheric plate age using a global database of bathymetric and free-air gravity profiles which are perpendicular to oceanic trenches. As in many previous studies, our starting point is the well-known floating elastic plate model. In order to remove the influence of short-wavelength features not associated with lithospheric bending, adjacent profiles from 10-Myr bins have been stacked together to construct average profiles with standard deviations. Each average profile was then inverted in a two-stage procedure. First, singular value decomposition was used to determine two unknown flexural parameters, together with a regional slope and offset, for any given elastic thickness. This procedure was repeated for a range of elastic thicknesses. Second, residual misfit was plotted as a function of elastic thickness, and the global minimum was identified. This two-stage procedure makes no prior assumptions about magnitude of the load, size of the bending moment, or whether the elastic plate is broken/continuous. We obtained excellent fits between theory and observation for both bathymetric and gravity profiles from lithosphere with an age range of 0–150 Ma. The shape of the residual misfit function indicates the degree of confidence we have in our elastic thickness estimates. The lower limit of elastic thickness is usually well determined but upper limits are often poorly constrained. Inverse modeling was carried out using a range of profile lengths (250–300, 500, and 700 km). In general, our estimates show no consistent increase of elastic thickness as a function of plate age. This surprising result is consistent with recent reassessments of elastic thickness beneath seamounts and implies either that elastic thickness is independent of plate age or that elastic thickness cannot be measured with sufficient accuracy to reveal such a relationship. Modeling of short free-air gravity profiles (250–300 km) does tentatively suggest that elastic thickness increases linearly from 5 to 10 km between 0 and 20 Ma and from 10 to 15 km between 20 and 150 Ma. This variation roughly matches the depth to the 200°C isotherm which corresponds to an homologous temperature of 0.4 for wet peridotite. Unfortunately, for longer profile lengths, there is no temporal dependence, and elastic thicknesses vary considerably for all plate ages. Bathymetric profile modeling yields similar results although uncertainties are larger

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

Regulation of surface architecture by symbiotic bacteria mediates host colonization

Microbes occupy countless ecological niches in nature. Sometimes these environments may be on or within another organism, as is the case in both microbial infections and symbiosis of mammals. Unlike pathogens that establish opportunistic infections, hundreds of human commensal bacterial species establish a lifelong cohabitation with their hosts. Although many virulence factors of infectious bacteria have been described, the molecular mechanisms used during beneficial host–symbiont colonization remain almost entirely unknown. The novel identification of multiple surface polysaccharides in the important human symbiont Bacteroides fragilis raised the critical question of how these molecules contribute to commensalism. To understand the function of the bacterial capsule during symbiotic colonization of mammals, we generated B. fragilis strains deleted in the global regulator of polysaccharide expression and isolated mutants with defects in capsule expression. Surprisingly, attempts to completely eliminate capsule production are not tolerated by the microorganism, which displays growth deficits and subsequent reversion to express capsular polysaccharides. We identify an alternative pathway by which B. fragilis is able to reestablish capsule production and modulate expression of surface structures. Most importantly, mutants expressing single, defined surface polysaccharides are defective for intestinal colonization compared with bacteria expressing a complete polysaccharide repertoire. Restoring the expression of multiple capsular polysaccharides rescues the inability of mutants to compete for commensalism. These findings suggest a model whereby display of multiple capsular polysaccharides provides essential functions for bacterial colonization during host–symbiont mutualism

The business of genomic testing: a survey of early adopters

Purpose: The practice of “genomic” (or “personalized”) medicine requires the availability of appropriate diagnostic testing. Our study objective was to identify the reasons for health systems to bring next-generation sequencing into their clinical laboratories and to understand the process by which such decisions were made. Such information may be of value to other health systems seeking to provide next-generation sequencing testing to their patient populations. Methods: A standardized open-ended interview was conducted with the laboratory medical directors and/or department of pathology chairs of 13 different academic institutions in 10 different states. Results: Genomic testing for cancer dominated the institutional decision making, with three primary reasons: more effective delivery of cancer care, the perceived need for institutional leadership in the field of genomics, and the premise that genomics will eventually be cost-effective. Barriers to implementation included implementation cost; the time and effort needed to maintain this newer testing; challenges in interpreting genetic variants; establishing the bioinformatics infrastructure; and curating data from medical, ethical, and legal standpoints. Ultimate success depended on alignment with institutional strengths and priorities and working closely with institutional clinical programs. Conclusion: These early adopters uniformly viewed genomic analysis as an imperative for developing their expertise in the implementation and practice of genomic medicine

The business of genomic testing: a survey of early adopters

Purpose: The practice of genomic (or personalized ) medicine requires the availability of appropriate diagnostic testing. Our study objective was to identify the reasons for health systems to bring next-generation Sequencing into their clinical laboratories and to understand the process by which such decisions were made. Such information may be of value to other health systems seeking to provide next-generation sequencing-testing to their patient populations. Methods: A standardized open-ended interview was conducted With the laboratory medical directors and/or department of pathology chairs of 13 different academic institutions in 10 different states. Results: Genomic testing for cancer dominated the institutional decision making, with three primary reasons: more effective delivery of cancer care, the perceived need for institutional leadership in the field of genomics, and the premise that genomics will eventually be cost-effective. Barriers to implementation included implementation cost; the time and effort needed to maintain this newer testing; challenges in interpreting genetic variants; establishing the bioinformatics infrastructure; and curating data from medical, ethical, and legal standpoints. Ultimate success depended on alignment with institutional strengths and priorities and working closely with institutional clinical programs. Conclusion: These early adopters uniformly viewed genomic analysis as an imperative for developing their expertise in the implementation and practice of genomic medicine

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