Speedy Transactions in Multicore In-Memory Databases

Silo is a new in-memory database that achieves excellent performance and scalability on modern multicore machines. Silo was designed from the ground up to use system memory and caches efficiently. For instance, it avoids all centralized contention points, including that of centralized transaction ID assignment. Silo's key contribution is a commit protocol based on optimistic concurrency control that provides serializability while avoiding all shared-memory writes for records that were only read. Though this might seem to complicate the enforcement of a serial order, correct logging and recovery is provided by linking periodically-updated epochs with the commit protocol. Silo provides the same guarantees as any serializable database without unnecessary scalability bottlenecks or much additional latency. Silo achieves almost 700,000 transactions per second on a standard TPC-C workload mix on a 32-core machine, as well as near-linear scalability. Considered per core, this is several times higher than previously reported results.Engineering and Applied Science

Expressiveness of Temporal Query Languages: On the Modelling of Intervals, Interval Relationships and States

Storing and retrieving time-related information are important, or even critical, tasks on many areas of Computer Science (CS) and in particular for Artificial Intelligence (AI). The expressive power of temporal databases/query languages has been studied from different perspectives, but the kind of temporal information they are able to store and retrieve is not always conveniently addressed. Here we assess a number of temporal query languages with respect to the modelling of time intervals, interval relationships and states, which can be thought of as the building blocks to represent and reason about a large and important class of historic information. To survey the facilities and issues which are particular to certain temporal query languages not only gives an idea about how useful they can be in particular contexts, but also gives an interesting insight in how these issues are, in many cases, ultimately inherent to the database paradigm. While in the area of AI declarative languages are usually the preferred choice, other areas of CS heavily rely on the extended relational paradigm. This paper, then, will be concerned with the representation of historic information in two well known temporal query languages: it Templog in the context of temporal deductive databases, and it TSQL2 in the context of temporal relational databases. We hope the results highlighted here will increase cross-fertilisation between different communities. This article can be related to recent publications drawing the attention towards the different approaches followed by the Databases and AI communities when using time-related concepts

Parallel Evaluation of Multi-join Queries

A number of execution strategies for parallel evaluation of multi-join queries have been proposed in the literature. In this paper we give a comparative performance evaluation of four execution strategies by implementing all of them on the same parallel database system, PRISMA/DB. Experiments have been done up to 80 processors. These strategies, coming from the literature, are named: Sequential Parallel, Synchronous Execution, Segmented Right-Deep, and Full Parallel. Based on the experiments clear guidelines are given when to use which strategy. This is an extended abstract; the full paper appeared in Proc. ACM SIGMOD'94, Minneapolis, Minnesota, May 24–27, 199

Glycocalyx Restricts Adenoviral Vector Access to Apical Receptors Expressed on Respiratory Epithelium In Vitro and In Vivo: Role for Tethered Mucins as Barriers to Lumenal Infection

Inefficient adenoviral vector (AdV)-mediated gene transfer to the ciliated respiratory epithelium has hindered gene transfer strategies for the treatment of cystic fibrosis lung disease. In part, the inefficiency is due to an absence of the coxsackie B and adenovirus type 2 and 5 receptor (CAR) from the apical membranes of polarized epithelia. In this study, using an in vitro model of human ciliated airway epithelium, we show that providing a glycosylphosphatidylinositol (GPI)-linked AdV receptor (GPI-CAR) at the apical surface did not significantly improve AdV gene transfer efficiency because the lumenal surface glycocalyx limited the access of AdV to apical GPI-CAR. The highly glycosylated tethered mucins were considered to be significant glycocalyx components that restricted AdV access because proteolytic digestion and inhibitors of O-linked glycosylation enhanced AdV gene transfer. To determine whether these in vitro observations are relevant to the in vivo situation, we generated transgenic mice expressing GPI-CAR at the surface of the airway epithelium, crossbred these mice with mice that were genetically devoid of tethered mucin type 1 (Muc1), and tested the efficiency of gene transfer to murine airways expressing apical GPI-human CAR (GPI-hCAR) in the presence and absence of Muc1. We determined that AdV gene transfer to the murine airway epithelium was inefficient even in GPI-hCAR transgenic mice but that the gene transfer efficiency improved in the absence of Muc1. However, the inability to achieve a high gene transfer efficiency, even in mice with a deletion of Muc1, suggested that other glycocalyx components, possibly other tethered mucin types, also provide a significant barrier to AdV interacting with the airway lumenal surface

WindS@UP: the e-science platform for windscanner.eu

The WindScanner e-Science platform architecture and the underlying premises are discussed. It is a collaborative platform that will provide a repository for experimental data and metadata. Additional data processing capabilities will be incorporated thus enabling in-situ data processing. Every resource in the platform is identified by a Uniform Resource Identifier (URI), enabling an unequivocally identification of the field(s) campaign(s) data sets and metadata associated with the data set or experience. This feature will allow the validation of field experiment results and conclusions as all managed resources will be linked. A centralised node (Hub) will aggregate the contributions of 6 to 8 local nodes from EC countries and will manage the access of 3 types of users: data-curator, data provider and researcher. This architecture was designed to ensure consistent and efficient research data access and preservation, and exploitation of new research opportunities provided by having this “Collaborative Data Infrastructure”. The prototype platform—WindS@UP—enables the usage of the platform by humans via a Web interface or by machines using an internal API (Application Programming Interface). Future work will improve the vocabulary (“application profile”) used to describe the resources managed by the platform.The WindScanner.eu|The European WindScanner Facility|is an ESFRI project (N: 312372) under the FP7-Infrastructures-2012-1. The authors are grateful to all colleagues in WP5 for the fruitful discussions, namely Dimitri Foussekis (CRES), Doron Callies (IWES Fraunhofer), Hans Verhoef (ECN), Harald Svendsen (Sintef), Jan Willem Wagenaar (ECN), Javier Sanz Rodrigo (CENER), Martin Bitter (Forwind), Mikael Sj oholm (DTU), Steen Arne S rensen (DTU) and Teresa Sim~oes (LNEG)

Genetic Modifiers of Cystic Fibrosis-Related Diabetes

Diabetes is a common age-dependent complication of cystic fibrosis (CF) that is strongly influenced by modifier genes. We conducted a genome-wide association study in 3,059 individuals with CF (644 with CF-related diabetes [CFRD]) and identified single nucleotide polymorphisms (SNPs) within and 5′ to the SLC26A9 gene that associated with CFRD (hazard ratio [HR] 1.38; P = 3.6 × 10−8). Replication was demonstrated in 694 individuals (124 with CFRD) (HR, 1.47; P = 0.007), with combined analysis significant at P = 9.8 × 10−10. SLC26A9 is an epithelial chloride/bicarbonate channel that can interact with the CF transmembrane regulator (CFTR), the protein mutated in CF. We also hypothesized that common SNPs associated with type 2 diabetes also might affect risk for CFRD. A previous association of CFRD with SNPs in TCF7L2 was replicated in this study (P = 0.004; combined analysis P = 3.8 × 10−6), and type 2 diabetes SNPs at or near CDKAL1, CDKN2A/B, and IGF2BP2 were associated with CFRD (P < 0.004). These five loci accounted for 8.3% of the phenotypic variance in CFRD onset and had a combined population-attributable risk of 68%. Diabetes is a highly prevalent complication of CF, for which susceptibility is determined in part by variants at SLC26A9 (which mediates processes proximate to the CF disease-causing gene) and at four susceptibility loci for type 2 diabetes in the general population

Data science

Even though it has only entered public perception relatively recently, the term "data science" already means many things to many people. This chapter explores both top-down and bottom-up views on the field, on the basis of which we define data science as "a unique blend of principles and methods from analytics, engineering, entrepreneurship and communication that aim at generating value from the data itself". The chapter then discusses the disciplines that contribute to this "blend", briefly outlining their contributions and giving pointers for readers interested in exploring their backgrounds further