Using free data mining software and clustering algorithms to find predictors from student qualifications

In this project a research both in finding predictors via clustering techniques and in reviewing the Data Mining free software is achieved. The research is based in a case of study, from where additionally to the KDD free software used by the scientific community; a new free tool for pre-processing the data is presented. The predictors are intended for the e-learning domain as the data from where these predictors have to be inferred are student qualifications from different e-learning environments. Through our case of study not only clustering algorithms are tested but also additional goals are proposed.

SwissBioisostere: a database of molecular replacements for ligand design.

The SwissBioisostere database (http://www.swissbioisostere.ch) contains information on molecular replacements and their performance in biochemical assays. It is meant to provide researchers in drug discovery projects with ideas for bioisosteric modifications of their current lead molecule, as well as to give interested scientists access to the details on particular molecular replacements. As of August 2012, the database contains 21 293 355 datapoints corresponding to 5 586 462 unique replacements that have been measured in 35 039 assays against 1948 molecular targets representing 30 target classes. The accessible data were created through detection of matched molecular pairs and mining bioactivity data in the ChEMBL database. The SwissBioisostere database is hosted by the Swiss Institute of Bioinformatics and available via a web-based interface.

Adaptive integral assessment package for the A2UN@ project

This paper presents a first approach of Evaluation Engine Architecture (EEA) as proposal to support adaptive integral assessment, in the context of a virtual learning environment. The goal of our research is design an evaluation engine tool to assist in the whole assessment process within the A2UN@ project, linking that tool with the other key elements of a learning design (learning task, learning resources and learning support). The teachers would define the relation between knowledge, competencies, activities, resources and type of assessment. Providing this relation is possible obtain more accurate estimations of student's knowledge for adaptive evaluations and future recommendations. The process is supported by usage of educational standards and specifications and for an integral user modelling

Searching for and positioning of contextualized learning objects

Learning object economies are marketplaces for the sharing and reuse of learning objects (LO). There are many motivations for stimulating the development of the LO economy. The main reason is the possibility of providing the right content, at the right time, to the right learner according to adequate quality standards in the context of a lifelong learning process; in fact, this is also the main objective of education. However, some barriers to the development of a LO economy, such as the granularity and editability of LO, must be overcome. Furthermore, some enablers, such as learning design generation and standards usage, must be promoted in order to enhance LO economy. For this article, we introduced the integration of distributed learning object repositories (DLOR) as sources of LO that could be placed in adaptive learning designs to assist teachers’ design work. Two main issues presented as a result: how to access distributed LO, and where to place the LO in the learning design. To address these issues, we introduced two processes: LORSE, a distributed LO searching process, and LOOK, a micro context-based positioning process, respectively. Using these processes, the teachers were able to reuse LO from different sources to semi-automatically generate an adaptive learning design without leaving their virtual environment. A layered evaluation yielded good results for the process of placing learning objects from controlled learning object repositories into a learning design, and permitting educators to define different open issues that must be covered when they use uncontrolled learning object repositories for this purpose. We verified the satisfaction users had with our solution

HLA Class I alleles associated with HCV polymorphisms and response to antiviral therapy in HCV genotype 1-infected patients

Aims: The adaptive immune response against hepatitis C virus (HCV) is significantly shaped by the host's composition of HLA alleles. Thus, the HLA phenotype is a critical determinant of viral evolution during adaptive immune pressure. Potential associations of HLA class I alleles with polymorphisms of HCV immune escape variants are largely unknown. Methods: Direct sequence analysis of the genes encoding the HCV proteins E2, NS3 and NS5B in a cohort of 159 patients with chronic HCV genotype 1 infection who were treated with pegylated interferon-alfa 2b and ribavirin in a prospective controlled trial for 48 weeks was exhibited. HLA class I genotyping was performed by strand-specific reverse hybridization with the INNO-LiPA line probe assays for HLA-A and HLA-B and by strand-specific PCR-SSP. We analyzed each amino acid position of HCV proteins using an extension of Fisher's exact test for associations with HLA alleles. In addition, associations of specific HLA alleles with inflammatory activity, liver fibrosis, HCV RNA viral load and virologic treatment outcome were investigated. Results: Separate analyses of HCV subtype 1a and 1b isolates revealed substantially different patterns of HLA-restricted polymorphisms between subtypes. Only one polymorphism within NS5B (V2758x) was significantly associated with HLA B*15 in HCV genotype 1b infected patients (adjusted p=0,048). However, a number of HLA class I-restricted polymorphisms within novel putative HCV CD8+ T cell epitopes (genotype 1a: HLA-A*11 GTRTIASPK1086-1094 [NS3], HLA-B*07 WPAPQGARSL1111-1120 [NS3]; genotype 1b: HLA-A*24 HYAPRPCGI488-496 [E2], HLA-B*44 GENETDVLL530-538 [E2], HLA-B*15 RVFTEAMTRY2757-2766 [NS5B]) were observed with high predicted epitope binding scores assessed by the web-based software SYFPEITHI (>21). Most of the identified putative epitopes were overlapping with already otherwise published epitopes, indicating a high immunogenicity of the accordant HCV protein region. In addition, certain HLA class I alleles were associated with inflammatory activity, stage of liver fibrosis, and sustained virologic response to antiviral therapy. Conclusions: HLA class I restricted HCV sequence polymorphisms are rare. HCV polymorphisms identified within putative HCV CD8+ T cell epitopes in the present study differ in their genomic distribution between genotype 1a and 1b isolates, implying divergent adaptation to the host's immune pressure on the HCV subtype level.

HAMAP in 2015: updates to the protein family classification and annotation system.

HAMAP (High-quality Automated and Manual Annotation of Proteins-available at http://hamap.expasy.org/) is a system for the automatic classification and annotation of protein sequences. HAMAP provides annotation of the same quality and detail as UniProtKB/Swiss-Prot, using manually curated profiles for protein sequence family classification and expert curated rules for functional annotation of family members. HAMAP data and tools are made available through our website and as part of the UniRule pipeline of UniProt, providing annotation for millions of unreviewed sequences of UniProtKB/TrEMBL. Here we report on the growth of HAMAP and updates to the HAMAP system since our last report in the NAR Database Issue of 2013. We continue to augment HAMAP with new family profiles and annotation rules as new protein families are characterized and annotated in UniProtKB/Swiss-Prot; the latest version of HAMAP (as of 3 September 2014) contains 1983 family classification profiles and 1998 annotation rules (up from 1780 and 1720). We demonstrate how the complex logic of HAMAP rules allows for precise annotation of individual functional variants within large homologous protein families. We also describe improvements to our web-based tool HAMAP-Scan which simplify the classification and annotation of sequences, and the incorporation of an improved sequence-profile search algorithm.

ExPASy: SIB bioinformatics resource portal.

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

FRAX® International Task Force of the 2010 Joint International Society for Clinical Densitometry & International Osteoporosis Foundation Position Development Conference.

Osteoporosis is a serious worldwide epidemic. FRAX® is a web-based tool developed by the Sheffield WHO Collaborating Center team, that integrates clinical risk factors and femoral neck BMD and calculates the 10 year fracture probability in order to help health care professionals identify patients who need treatment. However, only 31 countries have a FRAX® calculator. In the absence of a FRAX® model for a particular country, it has been suggested to use a surrogate country for which the epidemiology of osteoporosis most closely approximates the index country. More specific recommendations for clinicians in these countries are not available. In North America, concerns have also been raised regarding the assumptions used to construct the US ethnic specific FRAX® calculators with respect to the correction factors applied to derive fracture probabilities in Blacks, Asians and Hispanics in comparison to Whites. In addition, questions were raised about calculating fracture risk in other ethnic groups e.g., Native Americans and First Canadians. The International Society for Clinical Densitometry (ISCD) in conjunction with the International Osteoporosis Foundation (IOF) assembled an international panel of experts that ultimately developed joint Official Positions of the ISCD and IOF advising clinicians regarding FRAX® usage. As part of the process, the charge of the FRAX® International Task Force was to review and synthesize data regarding geographic and race/ethnic variability in hip fractures, non-hip osteoporotic fractures, and make recommendations about the use of FRAX® in ethnic groups and countries without a FRAX® calculator. This synthesis was presented to the expert panel and constitutes the data on which the subsequent Official Positions are predicated. A summary of the International Task Force composition and charge is presented here.

BIMS: Biomedical Information Management System

This final year project presents the design principles and prototype implementation of BIMS (Biomedical Information Management System), a flexible software system which provides an infrastructure to manage all information required by biomedical research projects.The BIMS project was initiated with the motivation to solve several limitations in medical data acquisition of some research projects, in which Universitat Pompeu Fabra takes part. These limitations,based on the lack of control mechanisms to constraint information submitted by clinicians, impact on the data quality, decreasing it.BIMS can easily be adapted to manage information of a wide variety of clinical studies, not being limited to a given clinical specialty. The software can manage both, textual information, like clinical data (measurements, demographics, diagnostics, etc ...), as well as several kinds of medical images (magnetic resonance imaging, computed tomography, etc ...). Moreover, BIMS provides a web - based graphical user interface and is designed to be deployed in a distributed andmultiuser environment. It is built on top of open source software products and frameworks.Specifically, BIMS has been used to represent all clinical data being currently used within the CardioLab platform (an ongoing project managed by Universitat Pompeu Fabra), demonstratingthat it is a solid software system, which could fulfill requirements of a real production environment.

Optable : The operation table serious game

Aquest treball consisteix en la realització d'un estudi al voltant dels anomenats serious games, jocs destinats a l'aprenentatge. Concretament, el projecte es centra en els serious games d'àmbit sanitari. A més d'un estudi de l'art, el treball consta del desenvolupament d'un serious game anomenat Optable per a la pràctica de la preparació del material quirúrgic d'una taula d'operacions. Aquesta aplicació ha estat desenvolupada sota llicència GNU GPL.

Organização e Publicação dos Termos do Website da ANACOM sob uma Perspetiva Linked Open Data

O propósito da Web Semântica é conseguir uma Web de dados totalmente ligada, isto é, numa perspetiva Linked Open Data. A Web Semântica deve garantir (estabelecendo padrões tecnológicos, vocabulários, linguagens lógicas, etc.) que os conteúdos publicados na Websejam inteligíveis quer por agentes humanos, quer por agentes máquina. Esta dissertação tem como objetivo responder à um problema delimitado, propondo uma solução no quadro da Web Semântica e suas tecnologias. Partindo-se de uma lista de termos em linguagem natural utilizados no Website da ANACOM (Autoridade Nacional de Comunicações), propomos uma organização de acordo com metodologias de construção de ontologias e vocabulários. Inspirámo-nos em duas metodologias, o Ontology Development 101 e o Process and Methodology for Core Vocabularies. O vocabulário controlado resultante, tem como base tecnológica o modelo de organização de conhecimento, recomendado pelo W3C (World Wide Web Consortium), o SKOS (Simple Knowledge Organization System). Trata-sede uma tecnologia standard da W3C desde 2009, utilizada na criação de tesauros,esquemas de classificação, taxonomias, glossários e outros tipos de vocabulários controlados. Como resultado da nossa intervenção, conseguimos organizar e codificar em SKOS, cerca de cinco centenas de termos identificados no Website da ANACOM. Para além da proposta do vocabulário controlado, passámos em revista às tecnologias e teorias que sustentam a temática da Web Semântica.

Programari J2EE : Projecte Hera

El treball es basa en desenvolupar una aplicació web per a un client.

Official Positions for FRAX® clinical regarding international differences from Joint Official Positions Development Conference of the International Society for Clinical Densitometry and International Osteoporosis Foundation on FRAX®.

Osteoporosis is a serious worldwide epidemic. Increased risk of fractures is the hallmark of the disease and is associated with increased morbidity, mortality and economic burden. FRAX® is a web-based tool developed by the Sheffield WHO Collaborating Center team, that integrates clinical risk factors, femoral neck BMD, country specific mortality and fracture data and calculates the 10 year fracture probability in order to help health care professionals identify patients who need treatment. However, only 31 countries have a FRAX® calculator at the time paper was accepted for publication. In the absence of a FRAX® model for a particular country, it has been suggested to use a surrogate country for which the epidemiology of osteoporosis most closely approximates the index country. More specific recommendations for clinicians in these countries are not available. In North America, concerns have also been raised regarding the assumptions used to construct the US ethnic specific FRAX® calculators with respect to the correction factors applied to derive fracture probabilities in Blacks, Asians and Hispanics in comparison to Whites. In addition, questions were raised about calculating fracture risk in other ethnic groups e.g., Native Americans and First Canadians. In order to provide additional guidance to clinicians, a FRAX® International Task Force was formed to address specific questions raised by physicians in countries without FRAX® calculators and seeking to integrate FRAX® into their clinical practice. The main questions that the task force tried to answer were the following: The Task Force members conducted appropriate literature reviews and developed preliminary statements that were discussed and graded by a panel of experts at the ISCD-IOF joint conference. The statements approved by the panel of experts are discussed in the current paper.

Iowa Influenza Surveillance Network Final Report 2007-2008

The Iowa Influenza Surveillance Network (IISN) was formally established in 2004, though surveillance has been conducted at the Iowa Department of Public Health (IDPH) for more than ten years. The IISN is comprised of four primary surveillance systems- sentinel health care providers, hospital-based, laboratory-based, and school-based. Sentinel health care providers are part of the U.S. Influenza Sentinel Provider Surveillance System. All systems, except certain sentinel sites, report October-March. Schools and long-term care facilities report data weekly into a Web-based reporting system. Schools report the number of students absent due to illness and the total enrolled. Long-term care facilities report cases of influenza and vaccination status of each case. Both passively report outbreaks of illness, including influenza, to IDPH.

Proyecto de implementación de una webapp para una agencia de viajes

Elaboración de un proyecto en el que se ha creado la documentación completa de una aplicación web para una agencia de viajes ficticia para la consulta y reserva de los productos que desea ofrecer a sus clientes.