Comparison of Contemporary Protocols for High-speed Data Transport via 10 Gbps WAN Connections

This work is dedicated to comparison of open source as well as proprietary transport protocols for highspeed data transmission via IP networks. The contemporary common TCP needs significant improvement since it was developed as general-purpose transport protocol and firstly introduced four decades ago. In nowadays networks, TCP fits not all communication needs that society has. Caused of it another transport protocols have been developed and successfully used for e.g. Big Data movement. In scope of this research the following protocols have been investigated for its efficiency on 10Gbps links: UDT, RBUDP, MTP and RWTP. The protocols were tested under different impairments such as Round Trip Time up to 400 ms and packet losses up to 2%. Investigated parameters are the data rate under different conditions of the network, the CPU load by sender andreceiver during the experiments, size of feedback data, CPU usage per Gbps and the amount of feedback data per GiByte of effectively transmitted data. The best performance and fair resources consumption was observed by RWTP. From the opensource projects, the best behavior is showed by RBUDP.

Seasonal dynamics of a drosophilid (Diptera) assemblage and its potencial as bioindicator in open environments

Drosophila Fallen, 1823 (Diptera, Drosophilidae) is for long a well-established model organism for genetics and evolutionary research. The ecology of these flies, however, has only recently been better studied. Recent papers show that Drosophila assemblies can be used as bioindicators of forested environment degradation. In this work the bioindicator potential of drosophilids was evaluated in a naturally opened environment, a coastal strand-forest (restinga). Data from nine consecutive seasonal collections revealed strong temporal fluctuation pattern of the majority of Drosophila species groups. Drosophila willistoni group was more abundant at autumns, whereas D. cardini and D. tripunctata groups were, respectively, expressive at winters and springs, and D. repleta group at both seasons. The exotic species D. simulans Sturtevant, 1919 (from D. melanogaster group) and Zaprionus indianus Gupta, 1970 were most abundant at summers. Overall, the assemblage structure did not show the same characteristics of forested or urban environments, but was similar to the forests at winters and to cities at summers. This raises the question that this locality may already been under urbanization impact. Also, this can be interpreted as an easily invaded site for exotic species, what might lead to biotic homogenization and therefore can put in check the usage of drosophilid assemblages as bioindicators at open environments.

Learning from Shocks and the Decision to Open

Two claims pervade the literature on the political economy of market reforms: that economic crises cause reforms; and that crises matter because they bring into question the validity of the economic model held to be responsible for them. Economic crises are said to spur a process of learning that is conducive to the abandonment of failing models and to the adoption of successful models. But although these claims have become the conventional wisdom, they have been hardly tested empirically due to the lack of agreement on what constitutes a crisis and to difficulties in measuring learning from them. I propose a model of rational learning from experience and apply it to the decision to open the economy. Using data from 1964 through 1990, I show that learning from the 1982 debt crisis was relevant to the first wave of adoption of an export promotion strategy, but learning was conditional on the high variability of economic outcomes in countries that opened up to trade. Learning was also symbolic in that the sheer number of other countries that liberalized was a more important driver of others’ decisions to follow suit.

Addressing Sea Surface Salinity retrieval at different spatial resolution. Feasibility study using OCCAM data within SEPS simulator and L2 processor tools

Projecte de recerca elaborat a partir d’una estada a la National Oceanography Centre of Southampton (NOCS), Gran Bretanya, entre maig i juliol del 2006. La possibilitat d’obtenir una estimació precissa de la salinitat marina (SSS) és important per a investigar i predir l’extensió del fenòmen del canvi climàtic. La missió Soil Moisture and Ocean Salinity (SMOS) va ser seleccionada per l’Agència Espacial Europea (ESA) per a obtenir mapes de salinitat de la superfície marina a escala global i amb un temps de revisita petit. Abans del llençament de SMOS es preveu l’anàlisi de la variabilitat horitzontal de la SSS i del potencial de les dades recuperades a partir de mesures de SMOS per a reproduir comportaments oceanogràfics coneguts. L’objectiu de tot plegat és emplenar el buit existent entre les fonts de dades d’entrada/auxiliars fiables i les eines desenvolupades per a simular i processar les dades adquirides segons la configuració de SMOS. El SMOS End-to-end Performance Simulator (SEPS) és un simulador adhoc desenvolupat per la Universitat Politècnica de Catalunya (UPC) per a generar dades segons la configuració de SMOS. Es va utilitzar dades d’entrada a SEPS procedents del projecte Ocean Circulation and Climate Advanced Modeling (OCCAM), utilitzat al NOCS, a diferents resolucions espacials. Modificant SEPS per a poder fer servir com a entrada les dades OCCAM es van obtenir dades de temperatura de brillantor simulades durant un mes amb diferents observacions ascendents que cobrien la zona seleccionada. Les tasques realitzades durant l’estada a NOCS tenien la finalitat de proporcionar una tècnica fiable per a realitzar la calibració externa i per tant cancel•lar el bias, una metodologia per a promitjar temporalment les diferents adquisicions durant les observacions ascendents, i determinar la millor configuració de la funció de cost abans d’explotar i investigar les posibiltats de les dades SEPS/OCCAM per a derivar la SSS recuperada amb patrons d’alta resolució.

Modelling of bird distribution under complex mediterranean landscape dynamics: open habitat birds and fire (MEDFIRE)

Report for the scientific sojourn at the Simon Fraser University, Canada, from July to September 2007. General context: landscape change during the last years is having significant impacts on biodiversity in many Mediterranean areas. Land abandonment, urbanisation and specially fire are profoundly transforming large areas in the Western Mediterranean basin and we know little on how these changes influence species distribution and in particular how these species will respond to further change in a context of global change including climate. General objectives: integrate landscape and population dynamics models in a platform allowing capturing species distribution responses to landscape changes and assessing impact on species distribution of different scenarios of further change. Specific objective 1: develop a landscape dynamic model capturing fire and forest succession dynamics in Catalonia and linked to a stochastic landscape occupancy (SLOM) (or spatially explicit population, SEPM) model for the Ortolan bunting, a species strongly linked to fire related habitat in the region. Predictions from the occupancy or spatially explicit population Ortolan bunting model (SEPM) should be evaluated using data from the DINDIS database. This database tracks bird colonisation of recently burnt big areas (&50 ha). Through a number of different SEPM scenarios with different values for a number of parameter, we should be able to assess different hypothesis in factors driving bird colonisation in new burnt patches. These factors to be mainly, landscape context (i.e. difficulty to reach the patch, and potential presence of coloniser sources), dispersal constraints, type of regenerating vegetation after fire, and species characteristics (niche breadth, etc).

Big data and other challenges in the quest for orthologs.

Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. AVAILABILITY AND IMPLEMENTATION: All such materials are available at http://questfororthologs.org. CONTACT: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk.

The Rio de Janeiro HIV Vaccine Site: I. Recruitment Strategies and Socio-demographic Data of a HIV Negative Homosexual and Bisexual Male Cohort in Rio de Janeiro, Brazil

The initial effort of the Brazilian Ministry of Health to be an active partner in the world effort in the preparation of future accurate human immune deficiency virus (HIV) efficacy trials was the establishment of a multi-centered cohort of homosexual and bisexual men. An open cohort was established to determine the HIV incidence and the socio-behavioral aspects involved in Rio de Janeiro. A total of 318 potential participants, originated from multiple sources (health units, public information, snowball recruitment), were screened and recruitment became effective through the direct involvement of target communities (with the support of Non Governmental Organizations) and the population. Among this group, seropositivity for sexually transmitted diseases was high with 23, 32 and 46% for HIV, syphilis and hepatitis B, respectively. The socio-demographic data from the first 200 participants of this HIV negative cohort suggests that the cohort volunteers are an appropriate sample of the general male population of the State of Rio de Janeiro

Institute of Public Health in Ireland's (IPH) Open Access Statement

This document states the Institute of Public Health in Ireland’s (IPH) commitment to an Open Access policy and outlines how it implements that policy. "Open Access is the immediate, online, free availability of research outputs without restrictions on use commonly imposed by publisher copyright agreements. Open Access includes the outputs that scholars normally give away for free for publication; it includes peer-reviewed journal articles, conference papers and data of various kinds."1 The Open Access (OA) movement aims to: Provide access to scientific outputs in publications that are freely available Foster the adoption of open access publication models

Selecting control genes for RT-QPCR using public microarray data.

Background: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e. g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones. Results: We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at http://www.isrec.isb-sib.ch/similar to vpopovic/research/ Conclusion: We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable.

Arrested kinetic Li isotope fractionation at the margin of the llimaussaq complex, South Greenland: Evidence for open-system processes during final cooling of peralkaline igneous rocks

Li contents [Li] and isotopic composition (delta Li-7) of mafic minerals (mainly amphibole and clinopyroxene) from the alkaline to peralkaline Ilimaussaq plutonic complex, South Greenland, track the behavior of Li and its isotopes during magmatic differentiation and final cooling of an alkaline igneous system. [Li] in amphibole increase from < 10 ppm in Caamphiboles of the least differentiated unit to >3000 ppm in Na-amphiboles of the highly evolved units. In contrast, [Li] in clinopyroxene are comparatively low (<85 ppm) and do not vary systematically with differentiation. The distribution of Li between amphibole and pyroxene is controlled by the major element composition of the minerals (Ca-rich and Na-rich, respectively) and changes in oxygen fugacity (due to Li incorporation via coupled substitution with ferric iron) during magmatic differentiation. delta(7) Li values of all minerals span a wide range from + 17 to - 8 parts per thousand, with the different intrusive units of the complex having distinct Li isotopic systematics. Amphiboles, which dominate the Li budget of whole-rocks from the inner part of the complex, have constant delta Li-7 of + 1.8 +/- 2.2 parts per thousand (2 sigma, n = 15). This value reflects a homogeneous melt reservoir and is consistent with their mantle derivation, in agreement with published O and Nd isotopic data. Clinopyroxenes of these samples are consistently lighter, with Delta Li-7(amph-cpx). as large as 8 parts per thousand and are thus not in Li isotope equilibrium. These low values probably reflect late-stage diffusion of Li into clinopyroxene during final cooling of the rocks, thus enriching the clinopyroxene in 6 Li. At the margin of the complex delta(7) Li in the syenites increases systematically, from +2 to high values of + 14 parts per thousand. This, coupled with the observed Li isotope systematics of the granitic country rocks, reflects post-magmatic open-system processes occurring during final cooling of the intrusion. Although the shape and magnitude of the Li isotope and elemental profiles through syenite and country rock are suggestive of diffusion-driven isotope fractionation, they cannot be modeled by one-dimensional diffusive transport and point to circulation of a fluid having a high 67 Li value (possibly seawater) along the chilled contact. In all, this study demonstrates that Li isotopes can be used to identify complex fluid- and diffusion-governed processes taking place during the final cooling of such rocks. (c) 2007 Elsevier B.V All rights reserved.

A prospective, randomized, open label, phase iii clinical trial of novottf-100a vs best standard of care chemotherapy in patients with recurrent glioblastoma

BACKGROUND: Glioblastoma, the most common adult primary malignant brain tumor, confers poor prognosis (median survival of 15 months) notwithstanding aggressive treatment. Combination chemotherapy including carmustine (BCNU) or temozolomide (TMZ) with the MGMT inhibitor O6-benzylguanine (O6BG) has been used, but has been associated with dose-limiting hematopoietic toxicity. OBJECTIVE: To assess safety and efficacy of a retroviral vector encoding the O6BG-resistant MGMTP140K gene for transduction and autologous transplantation of hematopoietic stem cells (HSCs) in MGMT unmethylated, newly diagnosed glioblastoma patients in an attempt to chemoprotect bone marrowduring combination O6BG/TMZ therapy. METHODS: Three patients have been enrolled in the first cohort. Patients underwent standard radiation therapy without TMZ followed by G-CSF mobilization, apheresis, and conditioning with 600 mg/m2 BCNU prior to infusion of gene-modified cells. Posttransplant, patients were treated with 28-day cycles of single doseTMZ (472 mg/m2) with 48-hour intravenous O6BG (120 mg/m2 bolus, then 30 mg/m2/d). RESULTS: The BCNU dose was nonmyeloablative with ANC ,500/mL for ≤3 d and nadir thrombocytopenia of 28,000/mL. Gene marking in pre-infusion colony forming units (CFUs) was 70.6%, 79.0%, and 74.0% in Patients 1, 2, and 3, respectively, by CFU-PCR. Following engraftment, gene marking in white blood cells and sorted granulocytes ranged between 0.37-0.84 and 0.33-0.83 provirus copies, respectively, by real-time PCR. Posttransplant gene marking in CFUs from CD34-selected cells ranged from 28.5% to 47.4%. Patients have received 4, 3, and 2 cycles of O6BG/TMZ, respectively, with evidence for selection of gene-modified cells. One patient has received a single dose-escalated cycle at 590 mg/m2 TMZ. No additional extra-hematopoietic toxicity has been observed thus far and all three patients exhibit stable disease at 7-8 months since diagnosis CONCLUSIONS: We believe that these data demonstrate the feasibility of achieving significant engraftment of MGMTP140K-modified cells with a well-tolerated dose of BCNU. Further follow-up will determine whether this approach will allow for further dose escalation of TMZ and improved survival.

Health Inequalities Intervention Tool for Spearheads 2009 (Click SAVE NOT OPEN when prompted)

The Spearhead Intervention Tool has been commissioned by the Department of Health through the Association of Public Health Observatories (APHO). This version of the tool has been updated with latest data for 2005-07. The tool is designed to assist commissioners in Spearhead Primary Care Trusts (PCTs) with their Local Delivery Planning (LDP) and commissioning and to assist Spearhead Local Authorities (LAs) with the delivery of Local Area Agreements (LAAs). It highlights key issues for Spearhead PCTs and LAs to consider in order to achieve the life expectancy element of the Government̢?Ts Public Service Agreement (PSA) on health inequalities by 2010.

Gestió de projectes informàtics

Aquesta aplicació es l¿evolució d¿un programa existent, realitzat amb una base de dades d¿escriptori amb capacitats de programació i creació d¿interfícies d¿usuari, que per executar-la cal una llicencia i que ha de funcionar sobre un sistema operatiu privatiu (també amb llicencia). Evoluciona cap a un entorn realitzat sobre programari lliure, que funciona sobre qualsevol sistema operatiu i no es necessari pagar cap llicencia per a fer-lo servir, ni en la part servidora ni en la part client.

BCN­Routing : càlcul web de rutes amb pgRouting, OpenStreetMap i OpenLayers

En aquest projecte s'ha desenvolupat una interfície web per calcular rutes a la ciutat de Barcelona. Les rutes calculades són a peu, entre un punt d'origen qualsevol i un punt d'interès turístic de la ciutat com a destí. Per això s'han extret les dades dels carrers de Barcelona d'OpenStreetMap i s'han insertat a una base de dades postgreSQL/postGIS, juntament amb una capa vectorial de punts d'interès turístic que s'ha creat amb el SIG d'escriptori qGIS. El càlcul de les rutes amb les dades de la base de dades s'ha realitzat amb l'extensió pgRouting, i la interfície web per seleccionar els punts d'origen i destí, mostrar els mapes, i mostrar les rutes resultat, s'ha desenvolupat utilitzant la llibreria OpenLayers.