Reverse immunology approach for the identification of CD8 T-cell-defined antigens: advantages and hurdles.

One of the challenges of tumour immunology remains the identification of strongly immunogenic tumour antigens for vaccination. Reverse immunology, that is, the procedure to predict and identify immunogenic peptides from the sequence of a gene product of interest, has been postulated to be a particularly efficient, high-throughput approach for tumour antigen discovery. Over one decade after this concept was born, we discuss the reverse immunology approach in terms of costs and efficacy: data mining with bioinformatic algorithms, molecular methods to identify tumour-specific transcripts, prediction and determination of proteasomal cleavage sites, peptide-binding prediction to HLA molecules and experimental validation, assessment of the in vitro and in vivo immunogenic potential of selected peptide antigens, isolation of specific cytolytic T lymphocyte clones and final validation in functional assays of tumour cell recognition. We conclude that the overall low sensitivity and yield of every prediction step often requires a compensatory up-scaling of the initial number of candidate sequences to be screened, rendering reverse immunology an unexpectedly complex approach.

Estudi de les possibles causes de l'abandonament d'un determinat pla d'estudis del departament d'Economia de la UOC

La UOC ha detectat que en els estudis de Diplomatura de Ciències Empresarials hi ha una quarta part dels estudiants que no continuen els estudis després del primer semestre. La UOC, com a client, ha facilitat les dades de matrícula de 20 semestres d'aquests estudis. Es demana que es cerqui quina o quines poden ser les causes d'aquest abandonament i una proposta per evitar-ho.

Estudio sobre las causas del abandono de los estudiantes de economía de la Universidad Oberta de Catalunya entre los años 1998 y 2008

Estudio de minería de datos sobre las causas del abandono de los estudiantes de una carrera de la UOC

Quantifying urban attractiveness from the distribution and density of digital footprints

In the past, sensors networks in cities have been limited to fixed sensors, embedded in particular locations, under centralised control. Today, new applications can leverage wireless devices and use them as sensors to create aggregated information. In this paper, we show that the emerging patterns unveiled through the analysis of large sets of aggregated digital footprints can provide novel insights into how people experience the city and into some of the drivers behind these emerging patterns. We particularly explore the capacity to quantify the evolution of the attractiveness of urban space with a case study of in the area of the New York City Waterfalls, a public art project of four man-made waterfalls rising from the New York Harbor. Methods to study the impact of an event of this nature are traditionally based on the collection of static information such as surveys and ticket-based people counts, which allow to generate estimates about visitors’ presence in specific areas over time. In contrast, our contribution makes use of the dynamic data that visitors generate, such as the density and distribution of aggregate phone calls and photos taken in different areas of interest and over time. Our analysis provides novel ways to quantify the impact of a public event on the distribution of visitors and on the evolution of the attractiveness of the points of interest in proximity. This information has potential uses for local authorities, researchers, as well as service providers such as mobile network operators.

The future key role of LC-high-resolution-MS analyses in clinical laboratories: a focus on quantification.

For the last decade, high-resolution (HR)-MS has been associated with qualitative analyses while triple quadrupole MS has been associated with routine quantitative analyses. However, a shift of this paradigm is taking place: quantitative and qualitative analyses will be increasingly performed by HR-MS, and it will become the common 'language' for most mass spectrometrists. Most analyses will be performed by full-scan acquisitions recording 'all' ions entering the HR-MS with subsequent construction of narrow-width extracted-ion chromatograms. Ions will be available for absolute quantification, profiling and data mining. In parallel to quantification, metabotyping will be the next step in clinical LC-MS analyses because it should help in personalized medicine. This article is aimed to help analytical chemists who perform targeted quantitative acquisitions with triple quadrupole MS make the transition to quantitative and qualitative analyses using HR-MS. Guidelines for the acceptance criteria of mass accuracy and for the determination of mass extraction windows in quantitative analyses are proposed.

Sistema de Informação de Apoio à Detecção de Perdas de Energia Eléctrica – O Caso da Electra

A realidade mundial é preocupante no que diz respeito ao aumento de ocorrências de perdas e fraudes em redes de distribuição de energia eléctrica. Em Cabo Verde, mas precisamente na Cidade da Praia a realidade é ainda mais preocupante devido ao número de ocorrências e a gravidade dos mesmos. Propõe-se um trabalho de investigação sobre perdas e fraudes de energia eléctrica baseado na análise dos dados relativos aos registos dos clientes na Base de Dados da Electra (Cabo Verde), com o intuito de nortear as tomadas de decisões de gestão estratégica no que diz respeito às políticas de controlo e prevenção de perdas e fraudes de energia eléctrica. O trabalho baseia-se na recolha e selecção de dados a organizar numa Data Warehouse para depois aplicar as tecnologias OLAP para a identificação de perdas nos Postos de Transformação e zonas geográficas da Cidade da Praia em Cabo Verde e posteriormente identificar possíveis fraudes de energia eléctrica nos clientes finais utilizando Data Mining. Os resultados principais consistiram na identificação de situações de perdas de energia eléctrica nos Postos de Transformação, a identificação de áreas críticas seleccionadas para inspecção dos seus clientes finais e a detecção de padrões de anomalias associadas ao perfil dos clientes.

Electrical neuroimaging of memory discrimination based on single-trial multisensory learning.

Multisensory experiences influence subsequent memory performance and brain responses. Studies have thus far concentrated on semantically congruent pairings, leaving unresolved the influence of stimulus pairing and memory sub-types. Here, we paired images with unique, meaningless sounds during a continuous recognition task to determine if purely episodic, single-trial multisensory experiences can incidentally impact subsequent visual object discrimination. Psychophysics and electrical neuroimaging analyses of visual evoked potentials (VEPs) compared responses to repeated images either paired or not with a meaningless sound during initial encounters. Recognition accuracy was significantly impaired for images initially presented as multisensory pairs and could not be explained in terms of differential attention or transfer of effects from encoding to retrieval. VEP modulations occurred at 100-130ms and 270-310ms and stemmed from topographic differences indicative of network configuration changes within the brain. Distributed source estimations localized the earlier effect to regions of the right posterior temporal gyrus (STG) and the later effect to regions of the middle temporal gyrus (MTG). Responses in these regions were stronger for images previously encountered as multisensory pairs. Only the later effect correlated with performance such that greater MTG activity in response to repeated visual stimuli was linked with greater performance decrements. The present findings suggest that brain networks involved in this discrimination may critically depend on whether multisensory events facilitate or impair later visual memory performance. More generally, the data support models whereby effects of multisensory interactions persist to incidentally affect subsequent behavior as well as visual processing during its initial stages.

Current approaches and challenges for the metabolite profiling of complex natural extracts.

Metabolite profiling is critical in many aspects of the life sciences, particularly natural product research. Obtaining precise information on the chemical composition of complex natural extracts (metabolomes) that are primarily obtained from plants or microorganisms is a challenging task that requires sophisticated, advanced analytical methods. In this respect, significant advances in hyphenated chromatographic techniques (LC-MS, GC-MS and LC-NMR in particular), as well as data mining and processing methods, have occurred over the last decade. Together, these tools, in combination with bioassay profiling methods, serve an important role in metabolomics for the purposes of both peak annotation and dereplication in natural product research. In this review, a survey of the techniques that are used for generic and comprehensive profiling of secondary metabolites in natural extracts is provided. The various approaches (chromatographic methods: LC-MS, GC-MS, and LC-NMR and direct spectroscopic methods: NMR and DIMS) are discussed with respect to their resolution and sensitivity for extract profiling. In addition the structural information that can be generated through these techniques or in combination, is compared in relation to the identification of metabolites in complex mixtures. Analytical strategies with applications to natural extracts and novel methods that have strong potential, regardless of how often they are used, are discussed with respect to their potential applications and future trends.

Sistema de Informação de Apoio à Detecção de Perdas de Energia Eléctrica – O Caso da Electra

A realidade mundial é preocupante no que diz respeito ao aumento de ocorrências de perdas e fraudes em redes de distribuição de energia eléctrica. Em Cabo Verde, mas precisamente na Cidade da Praia a realidade é ainda mais preocupante devido ao número de ocorrências e a gravidade dos mesmos. Propõe-se um trabalho de investigação sobre perdas e fraudes de energia eléctrica baseado na análise dos dados relativos aos registos dos clientes na Base de Dados da Electra (Cabo Verde), com o intuito de nortear as tomadas de decisões de gestão estratégica no que diz respeito às políticas de controlo e prevenção de perdas e fraudes de energia eléctrica. O trabalho baseia-se na recolha e selecção de dados a organizar numa Data Warehouse para depois aplicar as tecnologias OLAP para a identificação de perdas nos Postos de Transformação e zonas geográficas da Cidade da Praia em Cabo Verde e posteriormente identificar possíveis fraudes de energia eléctrica nos clientes finais utilizando Data Mining. Os resultados principais consistiram na identificação de situações de perdas de energia eléctrica nos Postos de Transformação, a identificação de áreas críticas seleccionadas para inspecção dos seus clientes finais e a detecção de padrões de anomalias associadas ao perfil dos clientes.

Business Intelligence Auxílio às organizações no processo da tomada de decisão

O presente trabalho destinada para o complemento de grau de licenciatura tem como objectivo principal analisar o auxílio de Business Intelligence (BI) às organizações na sua melhoria contínua no desempenho e qualidade de serviços, sobretudo no processo de tomada de decisão e estudo da sua existência na Cabo Verde Telecom. As tecnologias associadas a ele, nomeadamente, data warehouse, data mining e olap são primordiais para a tomada de decisão sobre as actividades estratégicas no mercado de negócios. Essas tecnologias permitem uma análise cuidada dos dados, transformando-os em informações pertinentes para a tomada de decisão nas empresas, garantindo com isto o seu crescimento no mercado.

AWSum-Combining Classification with Knowledge Aquisition

Many classifiers achieve high levels of accuracy but have limited applicability in real world situations because they do not lead to a greater understanding or insight into the^way features influence the classification. In areas such as health informatics a classifier that clearly identifies the influences on classification can be used to direct research and formulate interventions. This research investigates the practical applications of Automated Weighted Sum, (AWSum), a classifier that provides accuracy comparable to other techniques whilst providing insight into the data. This is achieved by calculating a weight for each feature value that represents its influence on the class value. The merits of this approach in classification and insight are evaluated on a Cystic Fibrosis and Diabetes datasets with positive results.

Mineria d'opinions a Twitter en un entorn multilingüe

L'objectiu d'aquest treball serà fer mineria d'opinions de la xarxa social de microblogging Twitter. En primer lloc, durem a terme una tasca de classificació de sentiments fent servir un lexicó simple. A continuació, emprarem la tècnica de les regles d'associació i, finalment, farem tasques de clustering.

Rpe65 microarrays, from genes to phosphorylated proteins

Purpose:To describe a novel in silico method to gather and analyze data from high-throughput heterogeneous experimental procedures, i.e. gene and protein expression arrays. Methods:Each microarray is assigned to a database which handles common data (names, symbols, antibody codes, probe IDs, etc.). Links between informations are automatically generated from knowledge obtained in freely accessible databases (NCBI, Swissprot, etc). Requests can be made from any point of entry and the displayed result is fully customizable. Results:The initial database has been loaded with two sets of data: a first set of data originating from an Affymetrix-based retinal profiling performed in an RPE65 knock-out mouse model of Leber's congenital amaurosis. A second set of data generated from a Kinexus microarray experiment done on the retinas from the same mouse model has been added. Queries display wild type versus knock out expressions at several time points for both genes and proteins. Conclusions:This freely accessible database allows for easy consultation of data and facilitates data mining by integrating experimental data and biological pathways.

Multi-well fungal co-culture for de novo metabolite-induction in time-series studies based on untargeted metabolomics.

The induction of fungal metabolites by fungal co-cultures grown on solid media was explored using multi-well co-cultures in 2 cm diameter Petri dishes. Fungi were grown in 12-well plates to easily and rapidly obtain the large number of replicates necessary for employing metabolomic approaches. Fungal culture using such a format accelerated the production of metabolites by several weeks compared with using the large-format 9 cm Petri dishes. This strategy was applied to a co-culture of a Fusarium and an Aspergillus strain. The metabolite composition of the cultures was assessed using ultra-high pressure liquid chromatography coupled to electrospray ionisation and time-of-flight mass spectrometry, followed by automated data mining. The de novo production of metabolites was dramatically increased by nutriment reduction. A time-series study of the induction of the fungal metabolites of interest over nine days revealed that they exhibited various induction patterns. The concentrations of most of the de novo induced metabolites increased over time. However, interesting patterns were observed, such as with the presence of some compounds only at certain time points. This result indicates the complexity and dynamic nature of fungal metabolism. The large-scale production of the compounds of interest was verified by co-culture in 15 cm Petri dishes; most of the induced metabolites of interest (16/18) were found to be produced as effectively as on a small scale, although not in the same time frames. Large-scale production is a practical solution for the future production, identification and biological evaluation of these metabolites.

Bioinformatics-driven identification and examination of candidate genes for non-alcoholic fatty liver disease.

ObjectiveCandidate genes for non-alcoholic fatty liver disease (NAFLD) identified by a bioinformatics approach were examined for variant associations to quantitative traits of NAFLD-related phenotypes.Research Design and MethodsBy integrating public database text mining, trans-organism protein-protein interaction transferal, and information on liver protein expression a protein-protein interaction network was constructed and from this a smaller isolated interactome was identified. Five genes from this interactome were selected for genetic analysis. Twenty-one tag single-nucleotide polymorphisms (SNPs) which captured all common variation in these genes were genotyped in 10,196 Danes, and analyzed for association with NAFLD-related quantitative traits, type 2 diabetes (T2D), central obesity, and WHO-defined metabolic syndrome (MetS).Results273 genes were included in the protein-protein interaction analysis and EHHADH, ECHS1, HADHA, HADHB, and ACADL were selected for further examination. A total of 10 nominal statistical significant associations (P<0.05) to quantitative metabolic traits were identified. Also, the case-control study showed associations between variation in the five genes and T2D, central obesity, and MetS, respectively. Bonferroni adjustments for multiple testing negated all associations.ConclusionsUsing a bioinformatics approach we identified five candidate genes for NAFLD. However, we failed to provide evidence of associations with major effects between SNPs in these five genes and NAFLD-related quantitative traits, T2D, central obesity, and MetS.