Discovering Implicational Knowledge in Wikidata

Knowledge graphs have recently become the state-of-the-art tool for representing the diverse and complex knowledge of the world. Examples include the proprietary knowledge graphs of companies such as Google, Facebook, IBM, or Microsoft, but also freely available ones such as YAGO, DBpedia, and Wikidata. A distinguishing feature of Wikidata is that the knowledge is collaboratively edited and curated. While this greatly enhances the scope of Wikidata, it also makes it impossible for a single individual to grasp complex connections between properties or understand the global impact of edits in the graph. We apply Formal Concept Analysis to efficiently identify comprehensible implications that are implicitly present in the data. Although the complex structure of data modelling in Wikidata is not amenable to a direct approach, we overcome this limitation by extracting contextual representations of parts of Wikidata in a systematic fashion. We demonstrate the practical feasibility of our approach through several experiments and show that the results may lead to the discovery of interesting implicational knowledge. Besides providing a method for obtaining large real-world data sets for FCA, we sketch potential applications in offering semantic assistance for editing and curating Wikidata

Trichinella pseudospiralis outbreak in France.

Four persons became ill with trichinellosis after eating meat from a wild boar hunted in Camargue, France. Nonencapsulated larvae of Trichinella pseudospiralis were detected in meat and muscle biopsy specimens. The diagnoses were confirmed by molecular typing. Surveillance for the emerging T. pseudospiralis should be expanded

The marine fish food web is globally connected

The productivity of marine ecosystems and the services they provide to humans are largely dependent on complex interactions between prey and predators. These are embedded in a diverse network of trophic interactions, resulting in a cascade of events following perturbations such as species extinction. The sheer scale of oceans, however, precludes the characterization of marine feeding networks through de novo sampling. This effort ought instead to rely on a combination of extensive data and inference. Here we investigate how the distribution of trophic interactions at the global scale shapes the marine fish food web structure. We hypothesize that the heterogeneous distribution of species ranges in biogeographic regions should concentrate interactions in the warmest areas and within species groups. We find that the inferred global metaweb of marine fish—that is, all possible potential feeding links between co-occurring species—is highly connected geographically with a low degree of spatial modularity. Metrics of network structure correlate with sea surface temperature and tend to peak towards the tropics. In contrast to open-water communities, coastal food webs have greater interaction redundancy, which may confer robustness to species extinction. Our results suggest that marine ecosystems are connected yet display some resistance to perturbations because of high robustness at most locations.Using a global interaction dataset, the authors quantify the distribution of trophic interactions among marine fish, finding a high degree of geographic connectivity but low spatial modularity.C.A. was supported by a MELS-FQRNT Postdoctoral Fellowship and a Ressources Aquatique Québec (RAQ) fellowship during the conception and writing of this manuscript. T.P., D.G. and D.B.S. acknowledge financial support by the CIEE through their working group programme. M.B.A. is funded through FCT project No. PTDC/AAG-MAA/3764/2014. A.R.C. is funded by a Natural Sciences and Engineering Research Council of Canada (NSERC) PGS-D scholarship. D.G., T.P., M.-J.F., P.A. and S.J.L. are supported by NSERC Discovery Grants. T.P. also acknowledges a FRQNT New Investigator award and a Université de Montréal starting grant. D.B.S. acknowledges support from the Royal Society of New Zealand (via Marsden Fast-Start No. UOC-1101 and a Rutherford Discovery Fellowship)

Phosphine-Catalyzed Formation of Carbon-Sulfur Bonds: Catalytic Asymmetric Synthesis of gamma-Thioesters

Supporting Information Available: Experimental procedures and compound characterization data. This material is available free of charge via the Internet at http://pubs.acs.org.A method for catalytic asymmetric γ sulfenylation of carbonyl compounds has been developed. In the presence of an appropriate catalyst, thiols not only add to the γ position of allenoates, overcoming their propensity to add to the β position in the absence of a catalyst, but do so with very good enantioselectivity. Sulfur nucleophiles are now added to the three families of nucleophiles (carbon, nitrogen, and oxygen) that had earlier been shown to participate in catalyzed γ additions. The phosphine catalyst of choice, TangPhos, had previously only been employed as a chiral ligand for transition metals, not as an efficient enantioselective nucleophilic catalyst.National Institutes of Health (U.S.)National Institute of General Medical Sciences (U.S.) (R01-GM57034)Merck & Co.Novartis (Firm

A Holistic Landscape Description Reveals That Landscape Configuration Changes More over Time than Composition: Implications for Landscape Ecology Studies

International audienceBackground: Space-for-time substitution—that is, the assumption that spatial variations of a system can explain and predict the effect of temporal variations—is widely used in ecology. However, it is questionable whether it can validly be used to explain changes in biodiversity over time in response to land-cover changes.Hypothesis: ere, we hypothesize that different temporal vs spatial trajectories of landscape composition and configuration may limit space-for-time substitution in landscape ecology. Land-cover conversion changes not just the surface areas given over to particular types of land cover, but also affects isolation, patch size and heterogeneity. This means that a small change in land cover over time may have only minor repercussions on landscape composition but potentially major consequences for landscape configuration.Methods: sing land-cover maps of the Paris region for 1982 and 2003, we made a holistic description of the landscape disentangling landscape composition from configuration. After controlling for spatial variations, we analyzed and compared the amplitudes of changes in landscape composition and configuration over time.Results: For comparable spatial variations, landscape configuration varied more than twice as much as composition over time. Temporal changes in composition and configuration were not always spatially matched.Significance: The fact that landscape composition and configuration do not vary equally in space and time calls into question the use of space-for-time substitution in landscape ecology studies. The instability of landscapes over time appears to be attributable to configurational changes in the main. This may go some way to explaining why the landscape variables that account for changes over time in biodiversity are not the same ones that account for the spatial distribution of biodiversity

Histopathological differences of myotonic dystrophy type 1 (DM1) and PROMM/DM2

Muscle biopsy findings in DM2 have been reported to be similar to those in DM1. The authors used myosin heavy chain immunohistochemistry and enzyme histochemistry for fiber type differentiation on muscle biopsies. Their results show that DM2 patients display a subpopulation of type 2 nuclear clump and other very small fibers and, hence, preferential type 2 fiber atrophy in contrast to type 1 fiber atrophy in DM1 patients

Do Stacked Species Distribution Models Reflect Altitudinal Diversity Patterns?

The objective of this study was to evaluate the performance of stacked species distribution models in predicting the alpha and gamma species diversity patterns of two important plant clades along elevation in the Andes. We modelled the distribution of the species in the Anthurium genus (53 species) and the Bromeliaceae family (89 species) using six modelling techniques. We combined all of the predictions for the same species in ensemble models based on two different criteria: the average of the rescaled predictions by all techniques and the average of the best techniques. The rescaled predictions were then reclassified into binary predictions (presence/absence). By stacking either the original predictions or binary predictions for both ensemble procedures, we obtained four different species richness models per taxa. The gamma and alpha diversity per elevation band (500 m) was also computed. To evaluate the prediction abilities for the four predictions of species richness and gamma diversity, the models were compared with the real data along an elevation gradient that was independently compiled by specialists. Finally, we also tested whether our richness models performed better than a null model of altitudinal changes of diversity based on the literature. Stacking of the ensemble prediction of the individual species models generated richness models that proved to be well correlated with the observed alpha diversity richness patterns along elevation and with the gamma diversity derived from the literature. Overall, these models tend to overpredict species richness. The use of the ensemble predictions from the species models built with different techniques seems very promising for modelling of species assemblages. Stacking of the binary models reduced the over-prediction, although more research is needed. The randomisation test proved to be a promising method for testing the performance of the stacked models, but other implementations may still be developed

GFAP-Driven GFP Expression in Activated Mouse Muller Glial Cells Aligning Retinal Blood Vessels Following Intravitreal Injection of AAV2/6 Vectors

Background: Muller cell gliosis occurs in various retinal pathologies regardless of the underlying cellular defect. Because activated Muller glial cells span the entire retina and align areas of injury, they are ideal targets for therapeutic strategies, including gene therapy.Methodology/Principal Findings: We used adeno-associated viral AAV2/6 vectors to transduce mouse retinas. The transduction pattern of AAV2/6 was investigated by studying expression of the green fluorescent protein (GFP) transgene using scanning-laser ophthalmoscopy and immuno-histochemistry. AAV2/6 vectors transduced mouse Muller glial cells aligning the retinal blood vessels. However, the transduction capacity was hindered by the inner limiting membrane (ILM) and besides Muller glial cells, several other inner retinal cell types were transduced. To obtain Muller glial cell-specific transgene expression, the cytomegalovirus (CMV) promoter was replaced by the glial fibrillary acidic protein (GFAP) promoter. Specificity and activation of the GFAP promoter was tested in a mouse model for retinal gliosis. Mice deficient for Crumbs homologue 1 (CRB1) develop gliosis after light exposure. Light exposure of Crb1(-/-) retinas transduced with AAV2/6-GFAP-GFP induced GFP expression restricted to activated Muller glial cells aligning retinal blood vessels.Conclusions/Significance: Our experiments indicate that AAV2 vectors carrying the GFAP promoter are a promising tool for specific expression of transgenes in activated glial cells

Non-parametric class completeness estimators for collaborative knowledge graphs — the case of wikidata

Collaborative Knowledge Graph platforms allow humans and automated scripts to collaborate in creating, updating and interlinking entities and facts. To ensure both the completeness of the data as well as a uniform coverage of the different topics, it is crucial to identify underrepresented classes in the Knowledge Graph. In this paper, we tackle this problem by developing statistical techniques for class cardinality estimation in collaborative Knowledge Graph platforms. Our method is able to estimate the completeness of a class—as defined by a schema or ontology—hence can be used to answer questions such as “Does the knowledge base have a complete list of all {Beer Brands—Volcanos—Video Game Consoles}?” As a use-case, we focus on Wikidata, which poses unique challenges in terms of the size of its ontology, the number of users actively populating its graph, and its extremely dynamic nature. Our techniques are derived from species estimation and data-management methodologies, and are applied to the case of graphs and collaborative editing. In our empirical evaluation, we observe that i) the number and frequency of unique class instances drastically influence the performance of an estimator, ii) bursts of inserts cause some estimators to overestimate the true size of the class if they are not properly handled, and iii) one can effectively measure the convergence of a class towards its true size by considering the stability of an estimator against the number of available instances