Showing papers by "Pompeu Fabra University published in 2006"

Global variation in copy number in the human genome

Abstract: Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.

Prediction, learning, and games

Abstract: This important text and reference for researchers and students in machine learning, game theory, statistics and information theory offers a comprehensive treatment of the problem of predicting individual sequences. Unlike standard statistical approaches to forecasting, prediction of individual sequences does not impose any probabilistic assumption on the data-generating mechanism. Yet, prediction algorithms can be constructed that work well for all possible sequences, in the sense that their performance is always nearly as good as the best forecasting strategy in a given reference class. The central theme is the model of prediction using expert advice, a general framework within which many related problems can be cast and discussed. Repeated game playing, adaptive data compression, sequential investment in the stock market, sequential pattern analysis, and several other problems are viewed as instances of the experts' framework and analyzed from a common nonstochastic standpoint that often reveals new and intriguing connections.

Discourse and manipulation

Abstract: ‘Manipulation’ is one of the crucial notions of Critical Discourse Analysis that require further theoretical analysis. This article offers a triangulated approach to manipulation as a form of social power abuse, cognitive mind control and discursive interaction. Socially, manipulation is defined as illegitimate domination confirming social inequality. Cognitively, manipulation as mind control involves the interference with processes of understanding, the formation of biased mental models and social representations such as knowledge and ideologies. Discursively, manipulation generally involves the usual forms and formats of ideological discourse, such as emphasizing Our good things, and emphasizing Their bad things. At all these levels of analysis it is shown how manipulation is different from legitimate mind control, such as in persuasion and providing information, for instance by stipulating that manipulation is in the best interest of the dominated group and against the best interests of dominated group...

Ideology and discourse analysis

Abstract: Contrary to most traditional approaches, ideologies are defined here within a multidisciplinary framework that combines a social, cognitive and discursive component. As ‘systems of ideas’, ideologies are sociocognitively defined as shared representations of social groups, and more specifically as the ‘axiomatic’ principles of such representations. As the basis of a social group's self-image, ideologies organize its identity, actions, aims, norms and values, and resources as well as its relations to other social groups. Ideologies are distinct from the sociocognitive basis of broader cultural communities, within which different ideological groups share fundamental beliefs such as their cultural knowledge. Ideologies are expressed and generally reproduced in the social practices of their members, and more particularly acquired, confirmed, changed and perpetuated through discourse. Although general properties of language and discourse are not, as such, ideologically marked, systematic discourse analysis offe...

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Abstract: The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.

Causes of Sprawl: A Portrait from Space

Abstract: We study the extent to which U. S. urban development is sprawling and what determines differences in sprawl across space. Using remote-sensing data to track the evolution of land use on a grid of 8.7 billion 30 30 meter cells, we measure sprawl as the amount of undeveloped land surrounding an average urban dwelling. The extent of sprawl remained roughly unchanged between 1976 and 1992, although it varied dramatically across metropolitan areas. Ground water availability, temperate climate, rugged terrain, decentralized employment, early public transport infrastructure, uncertainty about metropolitan growth, and unincorporated land in the urban fringe all increase sprawl.

GENCODE: producing a reference annotation for ENCODE

Abstract: Background The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.

Bladder Cancer and Exposure to Water Disinfection By-Products through Ingestion, Bathing, Showering, and Swimming in Pools

Abstract: Bladder cancer has been associated with exposure to chlorination by-products in drinking water, and experimental evidence suggests that exposure also occurs through inhalation and dermal absorption. The authors examined whether bladder cancer risk was associated with exposure to trihalomethanes (THMs) through ingestion of water and through inhalation and dermal absorption during showering, bathing, and swimming in pools. Lifetime personal information on water consumption and water-related habits was collected for 1,219 cases and 1,271 controls in a 1998-2001 case-control study in Spain and was linked with THM levels in geographic study areas. Long-term THM exposure was associated with a twofold bladder cancer risk, with an odds ratio of 2.10 (95% confidence interval: 1.09, 4.02) for average household THM levels of >49 versus 35 micro g/day through ingestion had an odds ratio of 1.35 (95% confidence interval: 0.92, 1.99). The odds ratio for duration of shower or bath weighted by residential THM level was 1.83 (95% confidence interval: 1.17, 2.87) for the highest compared with the lowest quartile. Swimming in pools was associated with an odds ratio of 1.57 (95% confidence interval: 1.18, 2.09). Bladder cancer risk was associated with long-term exposure to THMs in chlorinated water at levels regularly occurring in industrialized countries.

Integrated care prevents hospitalisations for exacerbations in COPD patients

Abstract: Hospital admissions due to chronic obstructive pulmonary disease (COPD) exacerbations have a major impact on the disease evolution and costs. The current authors postulated that a simple and well-standardised, low-intensity integrated care intervention can be effective to prevent such hospitalisations. Therefore, 155 exacerbated COPD patients (17% females) were recruited after hospital discharge from centres in Barcelona (Spain) and Leuven (Belgium). They were randomly assigned to either integrated care (IC; n565; age meaniSD 70i9 yrs; forced expiratory volume in one second (FEV1) 1.1i0.5 L, 43% predicted) or usual care (UC; n590; age 72i9 yrs; FEV1 1.1i0.05 L, 41% pred). The IC intervention consisted of an individually tailored care plan upon discharge shared with the primary care team, as well as accessibility to a specialised nurse case manager through a web-based call centre. After 12 months' follow-up, IC showed a lower hospitalisation rate (1.5i2.6 versus 2.1i3.1) and a higher percentage of patients without re-admissions (49 versus 31%) than UC without differences in mortality (19 versus 16%, respectively). In conclusion, this trial demonstrates that a standardised integrated care intervention, based on shared care arrangements among different levels of the system with support of information technologies, effectively prevents hospitalisations for exacerbations in chronic obstructive pulmonary disease patients.

Discourse, context and cognition

Abstract: In this article the relevance of a sociocognitive approach to discourse is shown by presenting a new theory of context, defined as subjective participants’ constructs of communicative situations, a...

EGASP: the human ENCODE Genome Annotation Assessment Project

Abstract: Background: We present the results of EGASP, a community experiment to assess the state-ofthe-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a ‘reference set’ of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. Results: The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of

Prospective Study of FGFR3 Mutations As a Prognostic Factor in Nonmuscle Invasive Urothelial Bladder Carcinomas

Abstract: Purpose To determine the frequency and the prognostic value of fibroblast growth factor receptor 3 (FGFR3) mutations in patients with nonmuscle invasive bladder tumors according to tumor stage and grade. Patients and Methods Seven hundred seventy-two patients with newly diagnosed bladder tumors were recruited. Tumors were reviewed by expert pathologists. Patients were prospectively followed-up (median, 62.6 months for disease-free patients) through review of hospital records and telephone interviews. The sequence of exons 7 and 10 of FGFR3 was analyzed by polymerase chain reaction and direct sequencing. We assessed the association of mutations with stage and grade. The predictive value of mutations for recurrence, progression, and mortality were assessed using Kaplan-Meier and Cox multivariable models. Results Mutations were more common among low malignant potential neoplasms (LMPN; 77%) and TaG1/TaG2 tumors (61%/58%) than among TaG3 tumors (34%) and T1G3 tumors (17%). The S249C, Y375C, S248C, and G372C m...

A Variational Model for P+XS Image Fusion

Abstract: We propose an algorithm to increase the resolution of multispectral satellite images knowing the panchromatic image at high resolution and the spectral channels at lower resolution. Our algorithm is based on the assumption that, to a large extent, the geometry of the spectral channels is contained in the topographic map of its panchromatic image. This assumption, together with the relation of the panchromatic image to the spectral channels, and the expression of the low-resolution pixel in terms of the high-resolution pixels given by some convolution kernel followed by subsampling, constitute the elements for constructing an energy functional (with several variants) whose minima will give the reconstructed spectral images at higher resolution. We discuss the validity of the above approach and describe our numerical procedure. Finally, some experiments on a set of multispectral satellite images are displayed.

Publication and Patent Behaviour of Academic Researchers: Conflicting, Reinforcing or Merely Co-Existing?

Abstract: Increasing entrepreneurial activity within academia has raised concerns that the amount of publications added to the scientific commons might become reduced or that academic research would become directed exclusively towards the application-oriented needs of industry. In the case of academic inventions, the potential conflict between public and private oriented considerations seems most salient. With this contribution, we examine whether the publication behaviour of academic inventors (at K.U.Leuven) differs from their colleagues (non-inventors) working within similar fields of research. Our analysis reveals that inventors publish significantly more. Moreover, no empirical evidence was found for the 'skewing problem'. These findings not only suggest the co-existence of both activities; they may actually reinforce one another.

Identifying Human Capital Externalities. Theory with Applications

Abstract: The identification of aggregate human capital externalities is still not fully understood. The existing (Mincerian) approach confounds positive externalities with wage changes due to a downward sloping demand curve for human capital. As a result, it yields positive externalities even when wages equal marginal social products. We propose an approach that identifies human capital externalities whether or not aggregate demand for human capital slopes downward. Another advantage of our approach is that it does not require estimates of the individual return to human capital. Applications to US cities and states between 1970 and 1990 yield no evidence of significant average -schooling

Topological patterns in street networks of self-organized urban settlements

Abstract: Many urban settlements result from a spatially distributed, decentralized building process. Here we analyze the topological patterns of organization of a large collection of such settlements using the approach of complex networks. The global efficiency (based on the inverse of shortest-path lengths), robustness to disconnections and cost (in terms of length) of these graphs is studied and their possible origins analyzed. A wide range of patterns is found, from tree-like settlements (highly vulnerable to random failures) to meshed urban patterns. The latter are shown to be more robust and efficient.

Politics, Ideology, and Discourse

Abstract: In this article, an ideology is first defined, namely the foundation of the socially shared mental representations of a social group, and hence also the basic social cognitive basis for the identity of a group. Ideologies are articulated by fundamental categories about a group's identifying characteristics, actions, aims, norms and values, relations to reference groups, and resources. Ideologies control the other social representations of groups, such as their knowledge and attitudes, and indirectly the mental models group members form when engaging in concrete social practices, as well as discourse. Political ideologies are defined as the ideologies shared by political groups, such as political parties, social movements, and so on. Ideologies are expressed in discourse by way of the ideologically based mental models people form of specific events, as well as the ideological representations they form of the very communicative event itself (context). As is suggested by the underlying polarized structures of ideologies and the attitudes and models based on them, discourses also show this ideological polarization, namely as an emphasis on Our (ingroup's) good things and Their (outgroup's) bad things (and a correlated lack of emphasis on Our bad things and Their good things). This overall strategy can be observed at the level of topic choice, the local semantics of description (precise vs. vague, general vs. specific, explicit vs. implicit, assertion vs. presupposition, etc.), metaphor, rhetoric (hyperbole vs. euphemism), and surface structure expressions (shouting or big headlines vs. whispering or small headlines, etc.). Examples are chosen from different political discourses, such as parliamentary debates, party programs, and political campaign discourse.

Human cytomegalovirus infection is associated with increased proportions of NK cells that express the CD94/NKG2C receptor in aviremic HIV-1-positive patients.

Abstract: In healthy blood donors, serological positivity for human cytomegalovirus (HCMV) is associated with an increased proportion of NK cells bearing the CD94/NKG2C NK cell receptor (NKR). The expression of the activating CD94/NKG2C NKR and of the inhibitory CD94/NKG2A NKR was studied in a cohort of 45 aviremic human immunodeficiency virus type 1 (HIV-1)-positive patients receiving highly active antiretroviral therapy. The proportions of NKG2C+ NK cells were significantly increased in HIV-1-positive patients (mean +/- SD, 25.9% +/- 23.0%), compared with those in 31 healthy individuals (mean +/- SD, 16.1% +/- 20.7%). Yet, the association vanished when HCMV serological status was considered in a multivariate regression model. These results support the conclusion that changes in the NKR repertoire in HIV1-positive patients are related to a concomitant HCMV infection.

Positive Cueing: Promoting Sustainable Consumer Behavior By Cueing Common Environmental Behaviors as Environmental

Abstract: People frequently fail to see themselves as environmentally-conscious consumers; one reason for this is that they are oftentimes prone to dismissing their more common ecological behaviors (e.g., avoid littering) as non-diagnostic for that particular self-image. The cueing of commonly performed ecological behaviors as environmentally-friendly (what we call positive cueing) renders both cued and non-cued common ecological behaviors more diagnostic for the inference of pro-environmental attitudes (Study 1). As a result, positive cueing increases the likelihood that people will see themselves as consumers who are concerned with the degree to which their behavior is environmentally responsible (Study 2). The cueing of common ecological behaviors leads participants to choose environmentally-friendly products with greater frequency, and even to use scrap paper more efficiently (Study 3). We discuss the implications for effective social marketing campaigns.

Expression of Snail protein in tumor-stroma interface.

Abstract: The product of Snail gene is a repressor of E-cadherin transcription and an inductor of the epithelial-to-mesenchymal transition in several epithelial tumor cell lines. In order to examine Snail expression in animal and human tissues, we have raised a monoclonal antibody (MAb) that reacts with the regulatory domain of this protein. Analysis of murine embryos shows that Snail is expressed in extraembryonic tissues and embryonic mesoderm, in mesenchymal cells of lungs and dermis as well as in cartilage. Little reactivity was detected in adult tissues as Snail was not constitutively expressed in most mesenchymal cells. However, Snail expression was observed in activated fibroblasts involved in wound healing in mice skin. Moreover, Snail was detected in pathological conditions causing hyperstimulation of fibroblasts, such as fibromatosis. Analysis of Snail expression in tumors revealed that it was highly expressed in sarcomas and fibrosarcomas. In epithelial tumors, it presented a more limited distribution, restricted to stromal cells placed in the vicinity of the tumor and to tumoral cells in the same areas. These results demonstrate that Snail is present in activated mesenchymal cells, indicate its relevance in the communication between tumor and stroma and suggest that it can promote the conversion of carcinoma cells to stromal cells.

Associations between temporary employment and occupational injury: what are the mechanisms?

Abstract: Objective: To determine whether observed higher risks of occupational injury among temporary workers are due to exposure to hazardous working conditions and/or to lack of job experience level. Methods: Data systematically recorded for 2000 and 2001 by the Spanish Ministry of Labour and Social Affairs on fatal and non-fatal traumatic occupational injuries were examined by type of employment and type of accident, while adjusting for gender, age, occupation, and length of employment in the company. In the study period there were 1500 fatal and 1 806 532 non-fatal traumatic occupational injuries that occurred at the workplace. Incidence rates and rate ratios (RR) were estimated using Poisson regression models. Results: Temporary workers showed a rate ratio of 2.94 for non-fatal occupational injuries (95% CI 2.40 to 3.61) and 2.54 for fatal occupational injuries (95% CI 1.88 to 3.42). When these associations were adjusted by gender, age, occupation, and especially length of employment, they loose statistic significance: 1.05 (95% CI 0.97 to 1.12) for non-fatal and 1.07 (95% CI 0.91 to 1.26) for fatal. Conclusions: Lower job experience and knowledge of workplace hazards, measured by length of employment, is a possible mechanism to explain the consistent association between temporary workers and occupational injury. The role of working conditions associated with temporary jobs should be assessed more specifically.

A degradation-sensitive anionic trypsinogen ( PRSS2 ) variant protects against chronic pancreatitis

Abstract: Chronic pancreatitis is a common inflammatory disease of the pancreas. Mutations in the genes encoding cationic trypsinogen (PRSS1) and the pancreatic secretory trypsin inhibitor (SPINK1) are associated with chronic pancreatitis. Because increased proteolytic activity owing to mutated PRSS1 enhances the risk for chronic pancreatitis, mutations in the gene encoding anionic trypsinogen (PRSS2) may also predispose to disease. Here we analyzed PRSS2 in individuals with chronic pancreatitis and controls and found, to our surprise, that a variant of codon 191 (G191R) is overrepresented in control subjects: G191R was present in 220/6,459 (3.4%) controls but in only 32/2,466 (1.3%) affected individuals (odds ratio 0.37; P = 1.1 x 10(-8)). Upon activation by enterokinase or trypsin, purified recombinant G191R protein showed a complete loss of trypsin activity owing to the introduction of a new tryptic cleavage site that renders the enzyme hypersensitive to autocatalytic proteolysis. In conclusion, the G191R variant of PRSS2 mitigates intrapancreatic trypsin activity and thereby protects against chronic pancreatitis.

Minor Components of Olive Oil: Evidence to Date of Health Benefits in Humans

Abstract: Olive oil is a functional food, which in addition to a high level of monounsaturated fatty acids also contains multiple minor components with biological properties. A large number of studies, mainly experimental, have been carried out on some of these components. However, the precepts of evidence-based medicine require adequate scientific evidence (level I or II) to be provided before nutritional recommendations for the general public can be formulated. In this review, we summarize the state of the art of the body of knowledge and discuss the extent to which there exists evidence for the health benefits of the minor components of olive oil.

Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations

Abstract: The human mitochondrial 12S ribosomal RNA (rRNA) A1555G mutation has been associated with aminoglycoside-induced and nonsyndromic deafness in many families worldwide. Our previous investigation revealed that the A1555G mutation is a primary factor underlying the development of deafness but is not sufficient to produce a deafness phenotype. However, it has been proposed that nuclear-modifier genes modulate the phenotypic manifestation of the A1555G mutation. Here, we identified the nuclear-modifier gene TRMU, which encodes a highly conserved mitochondrial protein related to transfer RNA (tRNA) modification. Genotyping analysis of TRMU in 613 subjects from 1 Arab-Israeli kindred, 210 European (Italian pedigrees and Spanish pedigrees) families, and 31 Chinese pedigrees carrying the A1555G or the C1494T mutation revealed a missense mutation (G28T) altering an invariant amino acid residue (A10S) in the evolutionarily conserved N-terminal region of the TRMU protein. Interestingly, all 18 Arab-Israeli/Italian-Spanish matrilineal relatives carrying both the TRMU A10S and 12S rRNA A1555G mutations exhibited prelingual profound deafness. Functional analysis showed that this mutation did not affect importation of TRMU precursors into mitochondria. However, the homozygous A10S mutation leads to a marked failure in mitochondrial tRNA metabolisms, specifically reducing the steady-state levels of mitochondrial tRNA. As a consequence, these defects contribute to the impairment of mitochondrial-protein synthesis. Resultant biochemical defects aggravate the mitochondrial dysfunction associated with the A1555G mutation, exceeding the threshold for expressing the deafness phenotype. These findings indicate that the mutated TRMU, acting as a modifier factor, modulates the phenotypic manifestation of the deafness-associated 12S rRNA mutations.

A Price is a Social Thing: Towards a Material Sociology of Arbitrage

Abstract: Arbitrage is a form of trading crucial both to the modern theory of finance and to market practice, yet it has seldom been the focus of study outside of economics. This article draws upon four initially separate ethnographic and interview-based studies to sketch a ‘material sociology’ of arbitrage. (The article follows financial market usage in viewing ‘arbitrage’ as trading that exploits discrepancies in relative prices, trading which is seldom the entirely riskless arbitrage posited by finance theory.) Prices are physical entities, and the extent and speed of the mobility of these entities are crucial to arbitrage. Traders' bodies sometimes need to be trained to conduct arbitrage, and the relative placement of different bodies can be crucial. Arbitrage generally involves a theory of the similarity of different assets, and material representations of relative value are often required in order to check the theory's plausibility. Arbitrageurs need to convince themselves and others such as investment-bank m...

An experimental comparison of audio tempo induction algorithms

Abstract: We report on the tempo induction contest organized during the International Conference on Music Information Retrieval (ISMIR 2004) held at the University Pompeu Fabra in Barcelona, Spain, in October 2004. The goal of this contest was to evaluate some state-of-the-art algorithms in the task of inducing the basic tempo (as a scalar, in beats per minute) from musical audio signals. To our knowledge, this is the first published large scale cross-validation of audio tempo induction algorithms. Participants were invited to submit algorithms to the contest organizer, in one of several allowed formats. No training data was provided. A total of 12 entries (representing the work of seven research teams) were evaluated, 11 of which are reported in this document. Results on the test set of 3199 instances were returned to the participants before they were made public. Anssi Klapuri's algorithm won the contest. This evaluation shows that tempo induction algorithms can reach over 80% accuracy for music with a constant tempo, if we do not insist on finding a specific metrical level. After the competition, the algorithms and results were analyzed in order to discover general lessons for the future development of tempo induction systems. One conclusion is that robust tempo induction entails the processing of frame features rather than that of onset lists. Further, we propose a new "redundant" approach to tempo induction, inspired by knowledge of human perceptual mechanisms, which combines multiple simpler methods using a voting mechanism. Machine emulation of human tempo induction is still an open issue. Many avenues for future work in audio tempo tracking are highlighted, as for instance the definition of the best rhythmic features and the most appropriate periodicity detection method. In order to stimulate further research, the contest results, annotations, evaluation software and part of the data are available at http://ismir2004.ismir.net/ISMIR_Contest.html