A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

Learning-induced plasticity in human audition: Objects, time, and space.

The human auditory system is comprised of specialized but interacting anatomic and functional pathways encoding object, spatial, and temporal information. We review how learning-induced plasticity manifests along these pathways and to what extent there are common mechanisms subserving such plasticity. A first series of experiments establishes a temporal hierarchy along which sounds of objects are discriminated along basic to fine-grained categorical boundaries and learned representations. A widespread network of temporal and (pre)frontal brain regions contributes to object discrimination via recursive processing. Learning-induced plasticity typically manifested as repetition suppression within a common set of brain regions. A second series considered how the temporal sequence of sound sources is represented. We show that lateralized responsiveness during the initial encoding phase of pairs of auditory spatial stimuli is critical for their accurate ordered perception. Finally, we consider how spatial representations are formed and modified through training-induced learning. A population-based model of spatial processing is supported wherein temporal and parietal structures interact in the encoding of relative and absolute spatial information over the initial ∼300ms post-stimulus onset. Collectively, these data provide insights into the functional organization of human audition and open directions for new developments in targeted diagnostic and neurorehabilitation strategies.

Nineteen additional unpredicted transcripts from human chromosome 21.

The identification of all human chromosome 21 (HC21) genes is a necessary step in understanding the molecular pathogenesis of trisomy 21 (Down syndrome). The first analysis of the sequence of 21q included 127 previously characterized genes and predicted an additional 98 novel anonymous genes. Recently we evaluated the quality of this annotation by characterizing a set of HC21 open reading frames (C21orfs) identified by mapping spliced expressed sequence tags (ESTs) and predicted genes (PREDs), identified only in silico. This study underscored the limitations of in silico-only gene prediction, as many PREDs were incorrectly predicted. To refine the HC21 annotation, we have developed a reliable algorithm to extract and stringently map sequences that contain bona fide 3' transcript ends to the genome. We then created a specific 21q graphical display allowing an integrated view of the data that incorporates new ESTs as well as features such as CpG islands, repeats, and gene predictions. Using these tools we identified 27 new putative genes. To validate these, we sequenced previously cloned cDNAs and carried out RT-PCR, 5'- and 3'-RACE procedures, and comparative mapping. These approaches substantiated 19 new transcripts, thus increasing the HC21 gene count by 9.5%. These transcripts were likely not previously identified because they are small and encode small proteins. We also identified four transcriptional units that are spliced but contain no obvious open reading frame. The HC21 data presented here further emphasize that current gene prediction algorithms miss a substantial number of transcripts that nevertheless can be identified using a combination of experimental approaches and multiple refined algorithms.

Usabilitat en entorns de telèfons mòbils

Aquí es reuneix la documentació tècnica actual per a fer-ne un anàlisi de facilitat d'ús des del punt de vista de l'usuari. Se centra en les funcionalitats, les tecnologies actuals i les interfícies. La metodologia emprada per a fer les anàlisis i arribar a les conclusions consta de tres fases: fer un recull de la tecnologia i les funcionalitats necessàries i analitzar-ne la facilitat d'ús; establir grups d'usuaris amb necessitats comunes o perfils d'usuari, i definir els paràmetres de facilitat d'ús que fem servir en els tests d'usuaris-dispositius i en els dissenys de tests.

Projecte Nova Economia

Disseny d'un model informàtic i de comunicacions basat en programari lliure que permeti l'estandardització de la instal·lació i posterior manteniment de les TIC aplicables a les delegacions territorials d'una entitat bancària.

I-SS: integrated supervision systems approach based on interactive components

Process supervision is the activity focused on monitoring the process operation in order to deduce conditions to maintain the normality including when faults are present Depending on the number/distribution/heterogeneity of variables, behaviour situations, sub-processes, etc. from processes, human operators and engineers do not easily manipulate the information. This leads to the necessity of automation of supervision activities. Nevertheless, the difficulty to deal with the information complicates the design and development of software applications. We present an approach called "integrated supervision systems". It proposes multiple supervisors coordination to supervise multiple sub-processes whose interactions permit one to supervise the global process

Eigen Faces: Detecció, Classificació/Reconeixement de cares

En aquest projecte es pretén utilitzar mètodes coneguts com ara Viola&Jones (detecció) i EigenFaces (reconeixement) per a detectar i reconèixer cares dintre d’imatges de vídeo. Per a aconseguir aquesta tasca cal partir d’un conjunt de dades d’entrenament per a cada un dels mètodes (base de dades formada per imatges i anotacions manuals). A partir d’aquí, l’aplicació, ha de ser capaç de detectar cares en noves imatges i reconèixer-les (identificar de quina cara es tracta)

Identificació de subjectes a partir de l'anàlisi de dades multimodals RGB-Depth

En aquest treball s'explora el camp de la identificació facial de subjectes utilitzant tècniques d'anàlisi multimodal. Això és utilitzant imatges RGB i imatges de profunditat (3D) amb l'objecte de validar les diverses tècniques emprades en el reconeixement facial i aprofundir en sistemes que incorporen informació tridimensional als algorismes de detecció i identificació facial.

Tecnologies de cloud computing Openstack/StackOps

El propòsit d'aquest TFC és investigar i fer una instal·lació des de zero d'un model de negoci basat en l'allotjament web fent servir tecnologies de Cloud Computing. El software open-source que es farà servir per aquesta finalitat serà Openstack el qual es basa en un model de servei com infraestructura (IaaS). La nostra finalitat és poder implementar el model IaaS basat en Openstack. Per duu a terme aquest desplegament es farà servir dos hipervisors (KVM i VMware ESXi) per tal de testejar diferents sistemes d¿hipervisors treballant conjuntament.

Association of NTRK3 and its interaction with NGF suggest an altered cross-regulation of the neurotrophin signaling pathway in eating disorders

Eating disorders (EDs) are complex psychiatric diseases that include anorexia nervosa and bulimia nervosa, and have higher than 50% heritability. Previous studies have found association of BDNF and NTRK2 to ED, while animal models suggest that other neurotrophin genes might also be involved in eating behavior. We have performed a family-based association study with 151 TagSNPs covering 10 neurotrophin signaling genes: NGFB, BDNF, NTRK1, NGFR/p75, NTF4/5, NTRK2, NTF3, NTRK3, CNTF and CNTFR in 371 ED trios of Spanish, French and German origin. Besides several nominal associations, we found a strong significant association after correcting for multiple testing (P = 1.04 × 10−4) between ED and rs7180942, located in the NTRK3 gene, which followed an overdominant model of inheritance. Interestingly, HapMap unrelated individuals carrying the rs7180942 risk genotypes for ED showed higher levels of expression of NTRK3 in lymphoblastoid cell lines. Furthermore, higher expression of the orthologous murine Ntrk3 gene was also detected in the hypothalamus of the anx/anx mouse model of anorexia. Finally, variants in NGFB gene appear to modify the risk conferred by the NTRK3 rs7180942 risk genotypes (P = 4.0 × 10−5) showing a synergistic epistatic interaction. The reported data, in addition to the previous reported findings for BDNF and NTRK2, point neurotrophin signaling genes as key regulators of eating behavior and their altered cross-regulation as susceptibility factors for EDs.

Normalisation informatique et marchés de services : le cas du XML

Extensible Markup Language (XML) is a generic computing language that provides an outstanding case study of commodification of service standards. The development of this language in the late 1990s marked a shift in computer science as its extensibility let store and share any kind of data. Many office suites software rely on it. The chapter highlights how the largest multinational firms pay special attention to gain a recognised international standard for such a major technological innovation. It argues that standardisation processes affects market structures and can lead to market capture. By examining how a strategic use of standardisation arenas can generate profits, it shows that Microsoft succeeded in making its own technical solution a recognised ISO standard in 2008, while the same arena already adopted two years earlier the open source standard set by IBM and Sun Microsystems. Yet XML standardisation also helped to establish a distinct model of information technology services at the expense of Microsoft monopoly on proprietary software

The ViRVIG Institute

In this paper we present the ViRVIG Institute, a recently created institution that joins two well-known research groups: MOVING in Barcelona, and GGG in Girona. Our main research topics are Virtual Reality devices and interaction techniques, complex data models, realistic materials and lighting, geometry processing, and medical image visualization. We briefly introduce the history of both research groups and present some representative projects. Finally, we sketch our lines for future research

Scene representation for object monitoring

In robotics, having a 3D representation of the environment where a robot is working can be very useful. In real-life scenarios, this environment is constantly changing for example by human interaction, external agents or by the robot itself. Thus, the representation needs to be constantly updated and extended to account for these dynamic scene changes. In this work we face the problem of representing the scene where a robot is acting. Moreover, we ought to improve this representation by reusing the information obtained in previous scenes. Our goal is to build a method to represent a scene and to update it while changes are produced. In order to achieve that, different aspects of computer vision such as space representation or feature tracking are discussed