Software Transactional Memory (STM) systems have emerged as a powerful paradigm to develop concurrent applications. At current date, however, the problem of how to build distributed and replicated STMs to enhance both dependability and performance is still largely unexplored. This time by a non-blocking distributed certification scheme, which we name BFC (Bloom Filter Certification). BFC exploits a novel Bloom Filter-based encoding mechanism that permits to significantly reduce the overheads of replica coordination at the cost of a user tunable increase in the probability of transaction abort. Through an extensive experimental study based on standard STM benchmarks we show that the BFC scheme permits to achieve remarkable performance gains even for negligible (e.g. 1%) increases of the transaction abort rate.

The Cell Line Data Base (CLDB) is a well-known reference information source on human and animal cell lines including information on more than 6000 cell lines. Main biological features are coded according to controlled vocabularies derived from international lists and taxonomies. HyperCLDB (http://bioinformatics.istge.it/hypercldb/) is a hypertext version of CLDB that improves data accessibility by also allowing information retrieval through web spiders. Access to HyperCLDB is provided through indexes of biological characteristics and navigation in the hypertext is granted by many internal links. HyperCLDB also includes links to external resources. Recently, an interest was raised for a reference nomenclature for cell lines and CLDB was seen as an authoritative system. Furthermore, to overcome the cell line misidentification problem, molecular authentication methods, such as fingerprinting, single-locus short tandem repeat (STR) profile and single nucleotide polymorphisms validation, were proposed. Since this data is distributed, a reference portal on authentication of human cell lines is needed. We present here the architecture and contents of CLDB, its recent enhancements and perspectives. We also present a new related database, the Cell Line Integrated Molecular Authentication (CLIMA) database (http://bioinformatics.istge.it/clima/), that allows to link authentication data to actual cell lines.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Abstract-In this article we introduce GMU, a genuine partial replication protocol for transactional systems, which exploits an innovative, highly scalable, distributed multiversioning scheme. Unlike existing multiversion-based solutions, GMU does not rely on a global logical clock, which represents a contention point and can limit system scalability. Also, GMU never aborts read-only transactions and spares them from distributed validation schemes. This makes GMU particularly efficient in presence of read-intensive workloads, as typical of a wide range of real-world applications.GMU guarantees the Extended Update Serializability (EUS) isolation level. This consistency criterion is particularly attractive as it is sufficiently strong to ensure correctness even for very demanding applications (such as TPC-C), but is also weak enough to allow efficient and scalable implementations, such as GMU. Further, unlike several relaxed consistency models proposed in literature, EUS has simple and intuitive semantics, thus being an attractive, scalable consistency model for ordinary programmers.We integrated the GMU protocol in a popular open source in-memory transactional data grid, namely Infinispan. On the basis of a large scale experimental study performed on heterogeneous experimental platforms and using industry standard benchmarks (namely TPC-C and YCSB), we show that GMU achieves linear scalability and that it introduces negligible overheads (less than 10%), with respect to solutions ensuring non-serializable semantics, in a wide range of workloads.

Abstract. In this article we present SCORe, a scalable one-copy serializable partial replication protocol. Differently from any other literature proposal, SCORe jointly guarantees the following properties: (i) it is genuine, thus ensuring that only the replicas that maintain data accessed by a transaction are involved in its processing, and (ii) it guarantees that read operations always access consistent snapshots, thanks to a one-copy serializable multiversion scheme, which never aborts read-only transactions and spares them from any (distributed) validation phase. This makes SCORe particularly efficient in presence of read-intensive workloads, as typical of a wide range of real-world applications. We have integrated SCORe into a popular open source distributed data grid and performed a large scale experimental study with well-known benchmarks using both private and public cloud infrastructures. The experimental results demonstrate that SCORe provides stronger consistency guarantees (namely One-Copy Serializability) than existing multiversion partial replication protocols at no additional overhead.

Regional cerebral blood flow was studied by means of the U3 Xe inhalation method hi 26 untreated and 10 treated patients with essential hypertension. The untreated subjects were divided into newly and previously diagnosed groups to assess the relation between regional cerebral blood flow and the duration of hypertension. The overall flow reduction was more marked in the frontal and temporal regions hi the previously diagnosed group, and this was attributed to pathological changes in the district served by the middle cerebral artery. Regional temporal lobe impairment was also noted in the newly diagnosed and treated subjects. A significant correlation was found between regional cerebral blood flow and mean arterial blood pressure. (Stroke 1987; 18:13-20)

Over the last years Transactional Memory (TM) gained growing popularity as a simpler, attractive alternative to classic lock-based synchronization schemes. Recently, the TM landscape has been profoundly changed by the integration of Hardware TM (HTM) in Intel commodity processors, raising a number of questions on the future of TM.We seek answers to these questions by conducting the largest study on TM to date, comparing different locking techniques, hardware and software TMs, as well as different combinations of these mechanisms, from the dual perspective of performance and power consumption.Our study sheds a mix of light and shadows on currently available commodity HTM: on one hand, we identify workloads in which HTM clearly outperforms any alternative synchronization mechanism; on the other hand, we show that current HTM implementations suffer of restrictions that narrow the scope in which these can be more effective than state of the art software solutions. Thanks to the results of our study, we identify a number of compelling research problems in the areas of TM design, compilers and self-tuning.

Data integration is needed in order to cope with the huge amounts of biological information now available and to perform data mining effectively. Current data integration systems have strict limitations, mainly due to the number of resources, their size and frequency of updates, their heterogeneity and distribution on the Internet. Integration must therefore be achieved by accessing network services through flexible and extensible data integration and analysis network tools. EXtensible Markup Language (XML), Web Services and Workflow Management Systems (WMS) can support the creation and deployment of such systems. Many XML languages and Web Services for bioinformatics have already been designed and implemented and some WMS have been proposed. In this article, we review a methodology for data integration in biomedical research that is based on these technologies. We also briefly describe some of the available WMS and discuss the current limitations of this methodology and the ways in which they can be overcome.