Ongoing and future developments at the Universal Protein Resource.

The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.

Mining and exploiting domain-specific corpora in the PANACEA platform

The objective of the PANACEA ICT-2007.2.2 EU project is to build a platform that automates the stages involved in the acquisition,production, updating and maintenance of the large language resources required by, among others, MT systems. The development of a Corpus Acquisition Component (CAC) for extracting monolingual and bilingual data from the web is one of the most innovative building blocks of PANACEA. The CAC, which is the first stage in the PANACEA pipeline for building Language Resources, adopts an efficient and distributed methodology to crawl for web documents with rich textual content in specific languages and predefined domains. The CAC includes modules that can acquire parallel data from sites with in-domain content available in more than one language. In order to extrinsically evaluate the CAC methodology, we have conducted several experiments that used crawled parallel corpora for the identification and extraction of parallel sentences using sentence alignment. The corpora were then successfully used for domain adaptation of Machine Translation Systems.

Phenotypic heterogeneity of antigen-specific CD4 T cells under different conditions of antigen persistence and antigen load.

The factors responsible for the phenotypic heterogeneity of memory CD4 T cells are unclear. In the present study, we have identified a third population of memory CD4 T cells characterized as CD45RA(+)CCR7(-) that, based on its replication history and the homeostatic proliferative capacity, was at an advanced stage of differentiation. Three different phenotypic patterns of memory CD4 T cell responses were delineated under different conditions of antigen (Ag) persistence and load using CD45RA and CCR7 as markers of memory T cells. Mono-phenotypic CD45RA(-)CCR7(+) or CD45RA(-)CCR7(-) CD4 T cell responses were associated with conditions of Ag clearance (tetanus toxoid-specific CD4 T cell response) or Ag persistence and high load (chronic HIV-1 and primary CMV infections), respectively. Multi-phenotypic CD45RA(-)CCR7(+), CD45RA(-)CCR7(-) and CD45RA(+)CCR7(-) CD4 T cell responses were associated with protracted Ag exposure and low load (chronic CMV, EBV and HSV infections and HIV-1 infection in long-term nonprogressors). The mono-phenotypic CD45RA(-)CCR7(+) response was typical of central memory (T(CM)) IL-2-secreting CD4 T cells, the mono-phenotypic CD45RA(-)CCR7(-) response of effector memory (T(EM)) IFN-gamma-secreting CD4 T cells and the multi-phenotypic response of both IL-2- and IFN-gamma-secreting cells. The present results indicate that the heterogeneity of different Ag-specific CD4 T cell responses is regulated by Ag exposure and Ag load.

ILS-ESP An efficient, simple, and parameter-free algorithm for solving the permutation flow-shop problem

From a managerial point of view, the more effcient, simple, and parameter-free (ESP) an algorithm is, the more likely it will be used in practice for solving real-life problems. Following this principle, an ESP algorithm for solving the Permutation Flowshop Sequencing Problem (PFSP) is proposed in this article. Using an Iterated Local Search (ILS) framework, the so-called ILS-ESP algorithm is able to compete in performance with other well-known ILS-based approaches, which are considered among the most effcient algorithms for the PFSP. However, while other similar approaches still employ several parameters that can affect their performance if not properly chosen, our algorithm does not require any particular fine-tuning process since it uses basic "common sense" rules for the local search, perturbation, and acceptance criterion stages of the ILS metaheuristic. Our approach defines a new operator for the ILS perturbation process, a new acceptance criterion based on extremely simple and transparent rules, and a biased randomization process of the initial solution to randomly generate different alternative initial solutions of similar quality -which is attained by applying a biased randomization to a classical PFSP heuristic. This diversification of the initial solution aims at avoiding poorly designed starting points and, thus, allows the methodology to take advantage of current trends in parallel and distributed computing. A set of extensive tests, based on literature benchmarks, has been carried out in order to validate our algorithm and compare it against other approaches. These tests show that our parameter-free algorithm is able to compete with state-of-the-art metaheuristics for the PFSP. Also, the experiments show that, when using parallel computing, it is possible to improve the top ILS-based metaheuristic by just incorporating to it our biased randomization process with a high-quality pseudo-random number generator.

Assessing the vulnerability of women to sexually transmitted diseases STDS/ HIV: construction and validation of markers

Objective To construct and validate markers of vulnerability of women to STDs/HIV, taking into consideration the importance of STDs/HIV. Method Methodological study carried out in three stages: 1) systematic review and identification of elements of vulnerability in the scientific production; 2) selection of elements of vulnerability, and development of markers; 3) establishment of the expert group and validation of the markers (content validity). Results Five markers were validated: no openness in the relationship to discuss aspects related to prevention of STDs/HIV; no perception of vulnerability to STDs/HIV; disregard of vulnerability to STDs/ HIV; not recognizing herself as the subject of sexual and reproductive rights; actions of health professionals that limit women’s access to prevention of STDs/HIV. Each marker contains three to eleven components. Conclusion The construction of such markers constituted an instrument, presented in another publication, which can contribute to support the identification of vulnerabilities of women in relation to STDs/HIV in the context of primary health care services. The markers constitute an important tool for the operationalization of the concept of vulnerability in primary health care and to promote inter/multidisciplinary and inter/multi-sectoral work processes.


Effect of Bacillus sphaericus Neide on Anopheles (Diptera: Culicidae) and associated insect fauna in fish ponds in the Amazon

ABSTRACTWe analyzed the effects of Bacillus sphaericus on Anopheles larvae and on the associated insect fauna in fish farming ponds. Five breeding sites in the peri-urban area of the city of Manaus, AM, Brazil, were studied. Seven samples were collected from each breeding site and B. sphaericus was applied and reapplied after 15 days. The samples were made at 24 h before application, 24 h post-application and 5 and 15 days post-application. We determined abundance, larval reduction and larval density for Anopheles, and abundance, richness, Shannon diversity index and classified according to the functional trophic groups for associated insect fauna. A total of 904 Anopheles larvae were collected and distributed into five species. Density data and larval reduction demonstrated the rapid effect of the biolarvicide 24 h after application. A total of 4874 associated aquatic insects belonging to six orders and 23 families were collected. Regression analysis of diversity and richness indicated that the application of the biolarvicide had no influence on these indices and thus no effect on the associated insect fauna for a period of 30 days. B. sphaericus was found to be highly effective against the larvae of Anopheles, eliminating the larvae in the first days after application, with no effect on the associated insect fauna present in the fish ponds analyzed.

Late Pan-African magmatism in the Himalaya: new geochronological and geochemical data from the Ordovician Tso Morari metagranites (Ladakh, NW India)

Two granitic plutons, the Tso Morari gneiss and the Rupshu metagranite, crop out in the Tso Morari area. The Polokongka La granite, classically interpreted as a young intrusion in the Tso Morari gneiss, has been recognized as the undeformed facies of the latter. Conventional isotope dilution U-Pb zircon dating on single-grain and small multi-grain fractions yielded magmatic ages of 479 +/- 2 Ma for the Tso Morari gneiss and the Polokongka La granite, and 482.5 +/- 1 Ma for the Rupshu granite. There is a great difference in zircon morphology between the Tso Morari gneiss (peraluminous type) and the Rupshu granite (alkaline type). This difference is confirmed by whole-rock chemistry. The Tso Morari gneiss is a typical deformed S-type granite, resulting from crustal anatexis. On the other hand, the Rupshu granite is an essentially metaluminous alkali-calcic intrusion derived from a different source material. Data compilation from other Himalayan Cambro-Ordovician granites reveals huge and widespread magmatic activity all along and beyond the northern Indian plate between 570 and 450 Ma, with a peak at 500-480 Ma. A major, continental-scale tectonic event is required to generate such a large magmatic belt; it has been tentatively compared to the Variscan post-orogenic extensional regime of Western Europe, as a late evolution stage of a Pan-African orogenic event.

Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure) and ammonia-oxidizing Archaea (richness and community composition) were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009) from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old), agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE) using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA) of Archaea (306 sequences), the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366), followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715), crops (H' = 1.4613; D = 0.3309) and secondary forest (H' = 0.8633; D = 0.5405). All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 %) previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils.

LiveCount Assay: concomitant measurement of cytolytic activity and phenotypic characterisation of CD8(+) T-cells by flow cytometry.

Tumour immunologists strive to develop efficient tumour vaccination and adoptive transfer therapies that enlarge the pool of tumour-specific and -reactive effector T-cells in vivo. To assess the efficiency of the various strategies, ex vivo assays are needed for the longitudinal monitoring of the patient's specific immune responses providing both quantitative and qualitative data. In particular, since tumour cell cytolysis is the end goal of tumour immunotherapy, routine immune monitoring protocols need to include a read-out for the cytolytic efficiency of Ag-specific cells. We propose to combine current immune monitoring techniques in a highly sensitive and reproducible multi-parametric flow cytometry based cytotoxicity assay that has been optimised to require low numbers of Ag-specific T-cells. The possibility of re-analysing those T-cells that have undergone lytic activity is illustrated by the concomitant detection of CD107a upregulation on the surface of degranulated T-cells. To date, the LiveCount Assay provides the only possibility of assessing the ex vivo cytolytic activity of low-frequency Ag-specific cytotoxic T-lymphocytes from patient material.

Lactate and the injured brain: friend or foe?

PURPOSE OF REVIEW: Energy metabolism is increasingly recognized as a key factor in the pathogenesis of acute brain injury (ABI). We review the role of cerebral lactate metabolism and summarize evidence showing that lactate may act as supplemental fuel after ABI. RECENT FINDINGS: The role of cerebral lactate has shifted from a waste product to a potentially preferential fuel and signaling molecule. According to the astrocyte-neuron lactate shuttle model, glycolytic lactate might act as glucose-sparing substrate. Lactate also is emerging as a key signal to regulate cerebral blood flow (CBF) and a neuroprotective agent after experimental ABI. Clinical investigation using cerebral microdialysis shows the existence of two main lactate patterns, ischemic - from anaerobic metabolism - and nonischemic, from activated glycolysis, whereby lactate can be used as supplemental energy fuel. Preliminary clinical data suggests hypertonic lactate solutions improve cerebral energy metabolism and are an effective treatment for elevated intracranial pressure (ICP) after ABI. SUMMARY: Lactate can be a supplemental fuel for the injured brain and is important to regulate glucose metabolism and CBF. Exogenous lactate supplementation may be neuroprotective after experimental ABI. Recent clinical data from ABI patients suggest hypertonic lactate solutions may be a valid therapeutic option for secondary energy dysfunction and elevated ICP.

Width and serialization of classical planning problems

We introduce a width parameter that bounds the complexity of classical planning problems and domains, along with a simple but effective blind-search procedure that runs in time that is exponential in the problem width. We show that many benchmark domains have a bounded and small width provided thatgoals are restricted to single atoms, and hence that such problems are provably solvable in low polynomial time. We then focus on the practical value of these ideas over the existing benchmarks which feature conjunctive goals. We show that the blind-search procedure can be used for both serializing the goal into subgoals and for solving the resulting problems, resulting in a ‘blind’ planner that competes well with a best-first search planner guided by state-of-the-art heuristics. In addition, ideas like helpful actions and landmarks can be integrated as well, producing a planner with state-of-the-art performance.

Multi-Purpose ESS/ITS Data Collection Sites, SPR72-00-0003-042, 2014

This document presents the results of a state-of-practice survey of transportation agencies that are installing intelligent transportation sensors (ITS) and other devices along with their environmental sensing stations (ESS) also referred to as roadway weather information system (RWIS) assets.

Workforce Training and Economic Development Fund Annual Progress Report, 2014 December 9, 2014

The Department of Education, Division of Community Colleges, will annually provide the State Board of Education with the Workforce Training and Economic Development Fund Annual Progress Report. Administration and oversight responsibility for the fund was transferred from the Iowa Economic Development Authority to the Iowa Department of Education effective July 1, 2013 (FY 2014). This report is the first annual progress report produced and distributed by the Iowa Department of Education. The full report outlines the programs, projects, and initiatives that the community colleges have implemented during the past fiscal year.

Optimointijärjestelmän kehittäminen sähköä ja lämpöä tuottavaan voimalaitokseen

Työn tavoitteena oli kehittää automaattinen optimointijärjestelmä energiayhtiön omistamaan pieneen sähkön- ja lämmöntuotantolaitokseen (CHP-laitos). Optimointitarve perustuu energiayhtiön sähkön hankintaan sähköpörssistä, kaasun hankintahintaan, kohteen paikallisiin sähkö- ja lämpökuormituksiin ja muihin laitoksen talouteen vaikuttaviin tekijöihin. Kehitettävällä optimointijärjestelmällä ontarkoitus tulevaisuudessa hallita useita hajautetun energiantuotannon yksiköitäkeskitetysti. Työssä kehitettiin algoritmi, joka optimoi voimalaitoksen taloutta sähkötehoa säätävillä ajomalleilla ja suoralla sähköteho-ohjeella. Työssä kehitetyn algoritmin tuottamia hyötyjä selvitettiin Harjun oppimiskeskuksen CHP-laitoksen mittaushistoriatiedoilla. CHP-laitosten käytön optimointiin luotiin keskitettyyn laskentaan ja hajautettuun ohjaukseen perustuva järjestelmä. Se ohjaa CHP-laitoksia reaaliaikaisesti ja ennustaa historiatietoihin perustuvalla aikasarjamallilla laitoksen tulevaa käyttöä. Optimointijärjestelmän toimivuus ja saatu hyöty selvitettiin Harjun oppimiskeskuksen CHP-laitoksella vertaamalla mittauksista laskettua toteutunutta hyötyä optimointijärjestelmän laskemaan ennustettuun hyötyyn.

Sistema de presa de decisions distribuït

DDM is a framework that combines intelligent agents and artificial intelligence traditional algorithms such as classifiers. The central idea of this project is to create a multi-agent system that allows to compare different views into a single one.