Query Optimization Techniques For Scaling Up To Data Variety

Even though Data Lakes are efficient in terms of data storage, they increase the complexity of query processing; this can lead to expensive query execution. Hence, novel techniques for generating query execution plans are demanded. Those techniques have to be able to exploit the main characteristics of Data Lakes. Ontario is a federated query engine capable of processing queries over heterogeneous data sources. Ontario uses source descriptions based on RDF Molecule Templates, i.e., an abstract description of the properties belonging to the entities in the unified schema of the data in the Data Lake. This thesis proposes new heuristics tailored to the problem of query processing over heterogeneous data sources including heuristics specifically designed for certain data models. The proposed heuristics are integrated into the Ontario query optimizer. Ontario is compared to state-of-the-art RDF query engines in order to study the overhead introduced by considering heterogeneity during query processing. The results of the empirical evaluation suggest that there is no significant overhead when considering heterogeneity. Furthermore, the baseline version of Ontario is compared to two different sets of additional heuristics, i.e., heuristics specifically designed for certain data models and heuristics that do not consider the data model. The analysis of the obtained experimental results shows that source-specific heuristics are able to improve query performance. Ontario optimization techniques are able to generate effective and efficient query plans that can be executed over heterogeneous data sources in a Data Lake

A quantum information processor with trapped ions

Quantum computers hold the promise to solve certain problems exponentially faster than their classical counterparts. Trapped atomic ions are among the physical systems in which building such a computing device seems viable. In this work we present a small-scale quantum information processor based on a string of [superscript 40]Ca[superscript +] ions confined in a macroscopic linear Paul trap. We review our set of operations which includes non-coherent operations allowing us to realize arbitrary Markovian processes. In order to build a larger quantum information processor it is mandatory to reduce the error rate of the available operations which is only possible if the physics of the noise processes is well understood. We identify the dominant noise sources in our system and discuss their effects on different algorithms. Finally we demonstrate how our entire set of operations can be used to facilitate the implementation of algorithms by examples of the quantum Fourier transform and the quantum order finding algorithm.United States. Office of the Director of National Intelligence (United States. Army Research Office Grant W911NF-10-1-0284

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

SDM-TIB/SDM-RDFizer: v4.7.2

An Efficient RML-Compliant Engine for Knowledge Graph Constructio

SDM-TIB/SDM-RDFizer: v4.7.2.1

An Efficient RML-Compliant Engine for Knowledge Graph Constructio

Aquatische Optische Technologien in Deutschland

Optische Technologien und Verfahren sind sowohl in der limnischen als auch marinen Forschung Deutschlands über alle Bereiche und Skalen etabliert und entwickeln sich rasant weiter. Die Arbeitsgruppe „Aquatische Optische Technologien“ (AOT) will Forschern und Anwendern eine Plattform bieten, die Wissenstransfer fördert, der nationalen Entwicklergemeinschaft ein synergistisches Umfeld eröffnet und die internationale Sichtbarkeit der deutschen Aktivitäten in diesem Forschungsfeld erhöht. Diese Zusammenfassung dokumentiert erstmalig die AOT-Verfahren und -Technologien, die von nationalen Forschungsinstitutionen eingesetzt werden. Wir erwarten, dass die Dokumentation einen Trend in Richtung institutsübergreifender Harmonisierung initiiert. Dies wird die Etablierung offener Standards, eine Verbesserung im Zugang zu Dokumentationen und gegenseitige technischer Hilfestellung bei (System-) Integrationen ermöglichen. Effizienz und Leistungsfähigkeit der AOT-Entwicklung und Anwendung auf nationaler Ebene werden von diesen Bestrebungen profitieren. Weitere Arbeitsgruppen und Entwickler werden ausdrücklich ermutigt, Kontakt aufzunehmen, um in einer späteren Auflage berücksichtigt zu werden

Increasing numbers and complexity of Staphylococcus aureus bloodstream infection - 14 years of prospective evaluation at a German tertiary care center with multi-center validation of findings

Objectives: Staphylococcus aureus bloodstream infection (SAB) is a common and severe infection. This study aims to describe temporal trends in numbers, epidemiological characteristics, clinical manifestations, and outcomes of SAB. Methods: We performed a post-hoc analysis of three prospective SAB cohorts at the University Medical Center Freiburg between 2006 and 2019. We validated our findings in a large German multi-center cohort of five tertiary care centers (R-Net consortium, 2017-2019). Time-dependent trends were estimated using Poisson or beta regression models. Results: We included 1,797 patients in the mono-centric and 2,336 patients in the multi-centric analysis. Overall, we observed an increasing number of SAB cases over 14 years (+6.4%/year and 1,000 patient days, 95%-CI: +5.1%-7.7%), paralleled by an increase in the proportion of community-acquired SAB (+4.9%/year (95%-CI: +2.1-7.8%), CA-SAB) and a decrease in the rate of methicillin-resistant-SAB (-8.5%/year (95%-CI: -11.2-(-5.6%)), MRSA-SAB). All of these findings were confirmed in the multi-center validation cohort (+6.2% cases per 1000 patient cases/year (95%-CI: -0.6-+12.6%), CA-SAB +8.7% (95%-CI: -1.2-+19.6%), MRSA-SAB -18.6% (95%-CI: -30.6-(-5.8%))). Moreover, we found an increasing proportion of patients with multiple risk factors for complicated/difficult-to-treat SAB (+8.5%/year, 95%-CI: +3.6-13.5%, p<0.001), alongside an overall higher level of comorbidities (Charlson comorbidity score +0.23 points/year, 95%-CI: +0.09-0.37, p=0.005). At the same time, the rate of deep-seated foci like osteomyelitis or deep-seated abscesses significantly increased (+6.7%, 95%-CI: +3.9-9.6%, p<0.001). A reduction of in-hospital mortality by 0.6% per year (95%-CI: 0.08-1%) was observed in the subgroup of patients with infectious diseases (ID) consultations. Conclusions: We found an increasing number of SAB combined with a significant increase in comorbidities and complicating factors in tertiary care centers. The resulting challenges in securing adequate SAB management in the face of high patient turnover will become an important task for physicians

Overview of the MOSAiC expedition: Snow and sea ice

Year-round observations of the physical snow and ice properties and processes that govern the ice pack evolution and its interaction with the atmosphere and the ocean were conducted during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition of the research vessel Polarstern in the Arctic Ocean from October 2019 to September 2020. This work was embedded into the interdisciplinary design of the 5 MOSAiC teams, studying the atmosphere, the sea ice, the ocean, the ecosystem, and biogeochemical processes.The overall aim of the snow and sea ice observations during MOSAiC was to characterize the physical properties of the snow and ice cover comprehensively in the central Arctic over an entire annual cycle. This objective was achieved by detailed observations of physical properties and of energy and mass balance of snow and ice. By studying snow and sea ice dynamics over nested spatial scales from centimeters to tens of kilometers, the variability across scales can be considered. On-ice observations of in situ and remote sensing properties of the different surface types over all seasons will help to improve numerical process and climate models and to establish and validate novel satellite remote sensing methods; the linkages to accompanying airborne measurements, satellite observations, and results of numerical models are discussed. We found large spatial variabilities of snow metamorphism and thermal regimes impacting sea ice growth. We conclude that the highly variable snow cover needs to be considered in more detail (in observations, remote sensing, and models) to better understand snow-related feedback processes.The ice pack revealed rapid transformations and motions along the drift in all seasons. The number of coupled ice–ocean interface processes observed in detail are expected to guide upcoming research with respect to the changing Arctic sea ice

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat