Self-organizing Structured RDF in MonetDB

The semantic web uses RDF as its data model, providing ultimate flexibility for users to represent and evolve data without need of a schema. Yet, this flexibility poses challenges in implementing efficient RDF stores, leading from plans with very many self-joins to a triple table, difficulties to optimize these, and a lack of data locality since without a notion of multi-attribute data structure, clustered indexing opportunities are lost. Apart from performance issues, users of huge RDF graphs often have problems formulating queries as they lack any system-supported notion of the structure in the data. In this research, we exploit the observation that real RDF data, while not as regularly structured as relational data, still has the great majority of triples conforming to regular patterns. We conjecture that a system that would recognize this structure automatically would both allow RDF stores to become more efficient and also easier to use. Concretely, we propose to derive self-organizing RDF that stores data in PSO format in such a way that the regular parts of the data physically correspond to relational columnar storage; and propose RDFscan/RDFjoin algorithms that compute star-patterns over these without wasting effort in self-joins. These regular parts, i.e. tables, are identified on ingestion by a schema discovery algorithm -- as such users will gain an SQL view of the regular part of the RDF data. This research aims to produce a state-of-the-art SPARQL frontend for MonetDB as a by-product, and we already present some preliminary results on this platform

Exploiting emergent schemas to make RDF systems more efficient

We build on our earlier finding that more than 95 % of the triples in actual RDF triple graphs have a remarkably tabular structure, whose schema does not necessarily follow from explicit metadata such as ontologies, but for which an RDF store can automatically derive by looking at the data using so-called “emergent schema” detection techniques. In this paper we investigate how computers and in particular RDF stores can take advantage from this emergent schema to more compactly store RDF data and more efficiently optimize and execute SPARQL queries. To this end, we contribute techniques for efficient emergent schema aware RDF storage and new query operator algorithms for emergent schema aware scans and joins. In all, these techniques allow RDF schema processors fully catch up with relational database techniques in terms of rich physical database design options and efficiency, without requiring a rigid upfront schema structure definition

S3G2: a Scalable Structure-correlated Social Graph Generator

Benchmarking graph-oriented database workloads and graph-oriented database systems are increasingly becoming relevant in analytical Big Data tasks, such as social network analysis. In graph data, structure is not mainly found inside the nodes, but especially in the way nodes happen to be connected, i.e. structural correlations. Because such structural correlations determine join fan-outs experienced by graph analysis algorithms and graph query executors, they are an essential, yet typically neglected, ingredient of synthetic graph generators. To address this, we present S3G2: a Scalable Structure-correlated Social Graph Generator. This graph generator creates a synthetic social graph, containing non-uniform value distributions and structural correlations, and is intended as a testbed for scalable graph analysis algorithms and graph database systems. We generalize the problem to decompose correlated graph generation in multiple passes that each focus on one so-called "correlation dimension"; each of which can be mapped to a MapReduce task. We show that using S3G2 can generate social graphs that (i) share well-known graph connectivity characteristics typically found in real social graphs (ii) contain certain plausible structural correlations that influence the performance of graph analysis algorithms and queries, and (iii) can be quickly generated at huge sizes on common cluster hardware

Benchmarking RDF Storage Engines

In this deliverable, we present version V1.0 of SRBench, the first benchmark for Streaming RDF engines, designed in the context of Task 1.4 of PlanetData, completely based on real-world datasets. With the increasing problem of too much streaming data but not enough knowledge, researchers have set out for solutions in which Semantic Web technologies are adapted and extended for the publishing, sharing, analysing and understanding of such data. Various approaches are emerging. To help researchers and users to compare streaming RDF engines in a standardised application scenario, we propose SRBench, with which one can assess the abilities of a streaming RDF engine to cope with a broad range of use cases typically encountered in real-world scenarios. We offer a set of queries that cover the major aspects of streaming RDF engines, ranging from simple pattern matching queries to queries with complex reasoning tasks. To give a first baseline and illustrate the state of the art, we show results obtained from implementing SRBench using the SPARQLStream query-processing engine developed by UPM

An evaluation of purified Salmonella Typhi protein antigens for the serological diagnosis of acute typhoid fever.

OBJECTIVES: The diagnosis of typhoid fever is a challenge. Aiming to develop a typhoid diagnostic we measured antibody responses against Salmonella Typhi (S. Typhi) protein antigens and the Vi polysaccharide in a cohort of Bangladeshi febrile patients. METHODS: IgM against 12 purified antigens and the Vi polysaccharide was measured by ELISA in plasma from patients with confirmed typhoid fever (n = 32), other confirmed infections (n = 17), and healthy controls (n = 40). ELISAs with the most specific antigens were performed on plasma from 243 patients with undiagnosed febrile disease. RESULTS: IgM against the S. Typhi protein antigens correlated with each other (rho > 0.8), but not against Vi (rho 0.85, respectively. Applying a dynamic cut-off to patients with undiagnosed febrile disease suggested that 34-58% had an IgM response indicative of typhoid. CONCLUSIONS: We evaluated the diagnostic potential of several S. Typhi antigens; our assays give good sensitivity and specificity, but require further assessment in differing patient populations

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population

Socializing One Health: an innovative strategy to investigate social and behavioral risks of emerging viral threats

In an effort to strengthen global capacity to prevent, detect, and control infectious diseases in animals and people, the United States Agency for International Development’s (USAID) Emerging Pandemic Threats (EPT) PREDICT project funded development of regional, national, and local One Health capacities for early disease detection, rapid response, disease control, and risk reduction. From the outset, the EPT approach was inclusive of social science research methods designed to understand the contexts and behaviors of communities living and working at human-animal-environment interfaces considered high-risk for virus emergence. Using qualitative and quantitative approaches, PREDICT behavioral research aimed to identify and assess a range of socio-cultural behaviors that could be influential in zoonotic disease emergence, amplification, and transmission. This broad approach to behavioral risk characterization enabled us to identify and characterize human activities that could be linked to the transmission dynamics of new and emerging viruses. This paper provides a discussion of implementation of a social science approach within a zoonotic surveillance framework. We conducted in-depth ethnographic interviews and focus groups to better understand the individual- and community-level knowledge, attitudes, and practices that potentially put participants at risk for zoonotic disease transmission from the animals they live and work with, across 6 interface domains. When we asked highly-exposed individuals (ie. bushmeat hunters, wildlife or guano farmers) about the risk they perceived in their occupational activities, most did not perceive it to be risky, whether because it was normalized by years (or generations) of doing such an activity, or due to lack of information about potential risks. Integrating the social sciences allows investigations of the specific human activities that are hypothesized to drive disease emergence, amplification, and transmission, in order to better substantiate behavioral disease drivers, along with the social dimensions of infection and transmission dynamics. Understanding these dynamics is critical to achieving health security--the protection from threats to health-- which requires investments in both collective and individual health security. Involving behavioral sciences into zoonotic disease surveillance allowed us to push toward fuller community integration and engagement and toward dialogue and implementation of recommendations for disease prevention and improved health security